**Cite This:**

*J. Chem. Theory Comput.*2021, 17, 9, 5849-5862

# Chemically Accurate Vibrational Free Energies of Adsorption from Density Functional Theory Molecular Dynamics: Alkanes in Zeolites

- Daria Ruth Galimberti
*****Daria Ruth GalimbertiInstitut für Chemie, Humboldt-Universität, Unter den Linden 6, 10117 Berlin, GermanyInstitute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands*****Email: [email protected]More by Daria Ruth Galimberti - and
- Joachim SauerJoachim SauerInstitut für Chemie, Humboldt-Universität, Unter den Linden 6, 10117 Berlin, GermanyMore by Joachim Sauer

## Abstract

We present a methodology to compute, at reduced computational cost, Gibbs free energies, enthalpies, and entropies of adsorption from molecular dynamics. We calculate vibrational partition functions from vibrational energies, which we obtain from the vibrational density of states by projection on the normal modes. The use of a set of well-chosen reference structures along the trajectories accounts for the anharmonicities of the modes. For the adsorption of methane, ethane, and propane in the H-CHA zeolite, we limit our treatment to a set of vibrational modes localized at the adsorption site (zeolitic OH group) and the alkane molecule interacting with it. Only two short trajectories (1–20 ps) are required to reach convergence (<1 kJ/mol) for the thermodynamic functions. The mean absolute deviations from the experimentally measured values are 2.6, 2.8, and 4.7 kJ/mol for the Gibbs free energy, the enthalpy, and the entropy term (−*T*ΔS), respectively. In particular, the entropy terms show a major improvement compared to the harmonic approximation and almost reach the accuracy of the previous use of anharmonic frequencies obtained with curvilinear distortions of individual modes. The thermodynamic functions so obtained follow the trend of the experimental values for methane, ethane, and propane, and the Gibbs free energy of adsorption at experimental conditions is correctly predicted to change from positive for methane (5.9 kJ/mol) to negative for ethane (−4.8 kJ/mol) and propane (−7.1 kJ/mol).

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### License Summary*

You are free to share (copy and redistribute) this article in any medium or format within the parameters below:

Creative Commons (CC): This is a Creative Commons license.

Attribution (BY): Credit must be given to the creator.

Non-Commercial (NC): Only non-commercial uses of the work are permitted.

No Derivatives (ND): Derivative works may be created for non-commercial purposes, but sharing is prohibited.

*Disclaimer

This summary highlights only some of the key features and terms of the actual license. It is not a license and has no legal value. Carefully review the actual license before using these materials.

### License Summary*

You are free to share (copy and redistribute) this article in any medium or format within the parameters below:

Creative Commons (CC): This is a Creative Commons license.

Attribution (BY): Credit must be given to the creator.

Non-Commercial (NC): Only non-commercial uses of the work are permitted.

No Derivatives (ND): Derivative works may be created for non-commercial purposes, but sharing is prohibited.

*Disclaimer

This summary highlights only some of the key features and terms of the actual license. It is not a license and has no legal value. Carefully review the actual license before using these materials.

### License Summary*

Creative Commons (CC): This is a Creative Commons license.

Attribution (BY): Credit must be given to the creator.

Non-Commercial (NC): Only non-commercial uses of the work are permitted.

*Disclaimer

### License Summary*

Creative Commons (CC): This is a Creative Commons license.

Attribution (BY): Credit must be given to the creator.

Non-Commercial (NC): Only non-commercial uses of the work are permitted.

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## 1. Introduction

*ab initio*with the desired accuracy and affordable computational cost, (4,5) the prediction of free energies and their variations is still challenging. Substantial progress has been made (3) since early approaches which used the harmonic approximation (6,7) and were often limited to the six rigid body coordinates of the adsorbed molecules relative to the surface. (1,2)

*ab initio*molecular dynamics (MD), for example, umbrella sampling and thermodynamic integration, or Monte Carlo (MC) simulations requires many steps, for example, long dynamic runs from 50 ps to even 1 ns, (8−15) with millions of energy and force calculations. (9,16−18) This is computationally extremely challenging even if density functional theory (DFT) with the more affordable but less accurate GGA-type functionals (GGA—generalized gradient approximation) is applied in

*ab initio*MD (AIMD) or MC (AIMC) simulations. Metadynamics (19,20) allows one to force the sampling of rare events. However, even for optimal cases simulation times of 50–100 ps are still required for an accurate sampling of a single barrier. (8) Moreover, the computed quantity is the variation of the free energy. It is not straightforward and is extremely expensive to obtain, following this path, absolute free energies or to separate the enthalpic component from the entropic one. As a consequence, AIMD or AIMC simulations for surface problems have been completed only in exceptional cases. (10,18,21−26) While for molecular enthalpies, MD schemes have been proposed to approach chemical accuracy at reasonable computational cost, (27) the entropic contributions are more challenging because they require extensive sampling of the complete phase space with all degrees of freedom.

*.*(36) have made use of a hybrid scheme that combines MD simulations and harmonic phonon calculations. However, the underlying implicit assumption that the anharmonic modes only slightly differ from the harmonic ones is not valid anymore when large amplitude vibrations are involved, for example, when floppy organic molecules or non-rigid solids such as zeolite frameworks are tackled.

_{4}tetrahedra. The acidity of zeolites is due to bridging Si–O(H)–Al hydroxyl groups obtained by the isoelectronic substitution of Al for Si (Si/Al ratio of 11/1) and addition of a proton for charge compensation. The small dimensions of its unit cell make H-CHA suitable as a benchmark for computational methods, (10,18,28−30,40−42) before more extended systems of similar nature and industrial relevance, (43) such as H-MFI, H-ZSM-22, or H-FAU zeolites, will be studied.

_{2})

_{2}(SiO

_{2})

_{22}. The proton (one for each unit cell) is attached to the oxygen in position O2 which is shared by two eight-membered rings and one four-membered ring. (30) Together with the bare surface, Figure 1 also shows the adsorption complex formed with methane (1B), ethane (1C), and propane via the primary carbon (1D). The Si–O(H)–Al hydroxyl group points toward the nearest carbon of the adsorbed alkane. In the harmonic VDOS (Figure 1E), the O–H stretching bands of the “free” bridging OH group (3675 cm

^{–1}) and of the bridging OH group interacting with ethane (3473 cm

^{–1}) are well separated from each other, and also from the CH stretching vibrations of the alkane molecule that are positioned around 3000 cm

^{–1}. As expected, the region between 1800 and 2900 cm

^{–1}shows no harmonic vibrations, while the region below 1200 cm

^{–1}is quite crowded. Here, we can find contributions belonging both to the alkane molecules (bending, torsions...), the Si–O(H)–Al bridges (bending, out-of-plane bending, torsion...), and the full set of the Si–O–Si framework vibrations.

## 2. Methods

### 2.1. Quasi-Harmonic Approximation

*G*

^{a}, of a system at temperature

*T*can be calculated as

*H*

^{a}and Δ

*S*

^{a}are the enthalpy and entropy of adsorption. For the vibrational contributions of the gas phase molecule, molec, the bare surface, surf, and the adsorbed molecule on the surface, molec@surf,

*G*

^{vib}is computed directly from the vibrational partition function

*Z*

^{vib}of the system; for the rotational and translational contributions of the gas phase molecules see the Supporting Information. In the harmonic approximation,

*Z*

^{vib}is the product of the vibrational partition functions of a set {

*i*} of independent vibrational states for which the summation can be performed analytically (44)

*k*

_{b}is the Boltzmann constant,

*T*is the temperature, ω

_{i}is the vibrational frequency of the

*i*-th mode, and ℏ =

*h*/2π with the Planck constant

*h*.

*S*

^{vib}, and enthalpies,

*H*

^{vib}, are obtained from

_{i}becomes the anharmonic fundamental frequency of the vibrational mode. Differently from Piccini et al

*.*(30) who solved one-dimensional Schrödinger equations for each vibrational mode, here we obtain the anharmonic frequencies from the VDOS computed by MD simulations. (21,35,36,45−48)

### 2.2. VDOS—without and with Projection

**v**

_{α}(

*t*) is the velocity of atom α at time

*t*in mass-weighted coordinates and

*E*

_{k}is the average kinetic energy of the system. We will call this method in the following density of state integration (DOS-I).

*D*(ω), computed according to eq 6 from MD cartesian velocities, by construction includes also overtones and combination bands. The latter arise from the mechanical anharmonicities that are naturally included in the MD trajectories.

^{–1}obtained from the cartesian velocity autocorrelation function of a trajectory of gas phase ethane at 300 K: a band can be clearly spotted at 2870 cm

^{–1}. At this frequency, no fundamental bands are expected and most probably this contribution arises from a combination band between the CH stretching and the CH

_{3}torsion.

### 2.3. VDOS—Projection Method

*D*(ω) is equal to the sum of the vibrational densities of states

*d*

_{i}(ω) of each independent vibration

*i*

*N*-mode = 3

*N*– 6 for a gas phase molecule and

*N*-mode = 3

*N*– 3 for the surface.

*N*is the number of atoms of the system.

*d*

_{i}(ω) can be obtained in turn by the FT of the autocorrelation function of the velocities of the vibrational mode

**q**

_{i}

_{k}

^{i}is the average contribution to the kinetic energy of the

*i*-th mode. Notice that at equipartition ε

_{k}

^{i}=

*k*

_{b}

*T*/2 for each vibrational mode.

**q̇**

_{i}(

*t*)} from the fully anharmonic “coupled” trajectories, one possibility is to project the cartesian velocities of the atoms onto the normal modes. (35,36,48) If we call

**L**the eigenvector matrix solution of the harmonic problem

**v**

_{α}(

*t*) is the velocity of atom α at time t in mass-weighted coordinates,

**v**

_{α}

^{i}(

*t*) is the projection of the velocity of α on the normal mode

*i*, and

**L**

_{i}is the eigenvector of the normal mode

*i*. In this case

*i*-th vibrational mode is a single-well potential,

*d*

_{i}(ω) will show a single peak function centered on the anharmonic frequency of the fundamental for the

*i*-th mode. In this case, the anharmonic frequencies can be extracted by fitting

*d*

_{i}(ω) with, for example, a Lorentzian function. (36) The

*H*

^{vib},

*S*

^{vib}, and

*G*

^{vib}values can then be computed by entering these anharmonic frequencies in eqs 2–4. If, however, multiple quasi-degenerate minima are present on the potential energy curve as it is the case, for example, for hindered rotations and translations, the VDOS spectra will show broad bands and possibly multiple maxima. Moreover, even in the case of a single-well, the inhomogeneous broadening of the bands can play a role in determining

*G*

^{vib}. To take these effects into account, one possibility is to evaluate the contribution of each vibrational band by eqs 2a–5a, integrating this time over the individual VDOS

*d*

_{i}(ω) instead of the total

*D*(ω)

*E*

_{0}

^{vib}can be computed separately. For each mode, one can therefore freely choose either to follow the “fitting strategy” to extract the anharmonic frequency for use with eq 2 or to perform the integration on

*d*

_{i}(ω). As we will discuss in more detail in Section 2.9, this choice can be made depending on the shape of the band and on the accuracy of its prediction.

*d*

_{i}(ω) in eqs 2b–5b for

*G*

^{vib},

*S*

^{vib}, and

*H*

^{vib}must contain vibrational fundamental bands only. By construction, the FT of the velocity autocorrelation function from MD trajectories, even after the projection, includes contributions coming from overtones and combination bands. Because combination bands and overtones are most of the time much less intense than the fundamental ones in our classical trajectories, they do not constitute a problem if one decides to extract anharmonic frequencies by fitting

*d*

_{i}(ω),

*cf.*eq 2. However, they will artificially modify the values of

*S*

^{vib}and

*H*

^{vib}if one instead directly integrates

*d*

_{i}(ω) or

*D*(ω).

**L**, does not exactly correspond to the real anharmonic one, especially when cartesian coordinates are used to define the vibrations and large amplitude motions are involved. This can create noise in the projected spectra.

*d*

_{i}(ω) of each mode. The width of the window is usually chosen in a way to be four times the guessed width for the band (estimated by fitting

*d*

_{i}(ω) with a Lorentzian function). This way, we are able to both clean

*d*

_{i}(ω) from the spurious contributions and to preserve the shape of the fundamental bands, that is, to still take the possible inhomogeneous broadening into account.

^{–1}spectral region of the bare H-CHA surface. The contribution of the SiO stretching band of the Si–O(H)–Al bridge to the total VDOS computed following the above strategy, that is, projection and filter (red line), is compared to the one coming from the projected velocities but without applying any filter (blue line). While the fundamental band of the Si–O stretching, ω

_{0}, is clearly recognizable in both cases, a set of additional peaks rise when the Lorentzian window filter is not applied. These additional contributions are due to the couplings of this Si–O stretching with other vibrational modes of the framework, in particular with other Si–O vibrations. For this mode, the difference in the integrated VDOS is around 25%.

### 2.4. Initial Conditions for the Trajectories

*H*

^{vib}and

*S*

^{vib}from the MD simulations, next we should clarify at which conditions we run the trajectories. A set of initial positions and velocities for the atom of the system must be chosen. The strategy commonly adopted (21,35,36,45−48) is to prepare the system to be at equipartition at a target temperature and to sample the system at these conditions. This we will do here as well.

**v**

_{α}(0) is the velocity of atom α at time 0 in mass-weighted cartesian coordinates, ω

_{i}

^{H}is the harmonic frequency of the

*i*-th vibrational mode, and ϕ

_{i}∈ {0,π} is a random phase assigned to the mode. Therefore,

**v**

_{α}(0) includes contributions from the excitation of all modes to which it contributes.

_{i}}, an ensemble of replicas for the system is created: each replica will have the same initial positions, the same total energy, but different velocities of the atoms. After running the MD simulations, the atomic velocities

**v**

_{α}(

*t*) are projected on the vibrational modes (eq 9) to compute the vibrational mode velocities

**q̇**

_{i}(

*t*). Then, for each replica, the velocity autocorrelation function, δ

**q̇**

_{i}(

*t*)δ

**q̇**

_{i}(0) of each mode

*i*, is computed separately. Finally, the

*i*-th velocity autocorrelation function to be used in eq 8 is obtained as the average of the velocity autocorrelation functions computed for each replica.

_{k}

^{i}is no longer equal to

*k*

_{b}

*T*/2 in eqs 8 and 10. One possibility is to estimate ε

_{k}

^{i}from the vibrational temperature of the harmonic mode. Another possible choice is to select ε

_{k}

^{i}to ensure that ∫

_{0}

^{∞}dω

*d*

_{i}(ω) = 1 and, thus, each mode contribute with exactly 1 to the total VDOS, as it should be. This latter strategy allows one to compensate for small errors in the preparation of the system, for example, that the system is excited to the harmonic ZPE and not to the exact anharmonic ZPE.

*H*

^{vib}and

*S*

^{vib}computed with DOS-P according to the two protocols: equipartition at a target temperature (superscript

*T*:

^{T}DOS-P) or preparation in the harmonic ZPE state (superscript ZPE:

^{ZPE}DOS-P).

### 2.5. Vibrational Relaxation Time Scale

*H*

^{vib}and

*S*

^{vib}values is the right simulation length/time scale for sampling the PES. The usual perception is that the longer the simulations the higher the accuracy and that the simulation length should be limited only as a compromise between the accuracy and computational cost. Whereas this is still true for our trajectories prepared at equipartition (we have used two simulations of 20 ps each), the ZPE initial condition case is special. The replicas of the system are prepared in a way in which each mode is at its ZPE. Unfortunately, for MD with classical nuclei such as the ones used here, the ZPE is a non-equilibrium condition. The system will spontaneously relax and redistribute the energy between the modes to reach equipartition.

_{i}of the

*i*-th vibrational mode is, the longer are the trajectories used to compute the

*d*

_{i}(ω). For example, for a mode vibrating at 40 cm

^{–1}, we would use a 3 ps trajectory, while for one vibrating at 3000 cm

^{–1}the trajectory is reduced to 100 fs (see Supporting Information for more details, Table S1).

### 2.6. Rotations

**ξ**(

*t*), the (3

*N*) vector that collects the Cartesian coordinates of the

*N*atoms of the molecule in the center of the mass reference, a rotation-free trajectory can be obtained by

**R**(

*t*) is the rotational matrix that guarantees the best overlap between

**ξ**(

*t*) and the initial geometry

**ξ**(0).

**R**(

*t*) can be obtained by a quaternion fit that minimizes the sum of the squared distances between the mass weight coordinates of corresponding atoms. (52) Such a rotation satisfies the Eckart conditions for small displacements (53) and can still be used for the large ones. (38) Once

**ξ**

^{vib}(

*t*) is obtained, the velocities can be computed by numerical differentiation. We use a five-point central difference formula (see Section S4 of Supporting Information for details) to guarantee a negligible numerical error on the kinetic energy.

### 2.7. From a Constant **L** to **L** Evolving in Time

*.*(36) and Zhang et al

*.*(35) assume that the eigenvector matrix

**L**(eq 9) which projects the cartesian coordinates on the vibrational space is constant in time. This can be considered a valid approximation for crystalline solids, such as the ones they were studying, for example, crystalline silicon, (36) MgSiO

_{3}perovskite, (35) and CaSiO

_{3}perovskite. (48) In contrast, we are dealing here with systems that show large amplitude motions and can explore multiple minima on the PES. Therefore,

**L**is not constant in time and a way to compute its changes is needed.

**L**by diagonalizing the hessian matrix at each time step is not a viable route. Because for most of the simulation time, the system is out of a minimum of the PES, the solution of the harmonic problem would generate a huge number of negative eigenvalues that one must deal with. Moreover, the computational cost would be enormous.

**L**(

*t*), while not constant in time, at instant

*t*can still be properly described by a linear combination of the eigenvector matrices

**L**

^{ref}(solution of the harmonic vibrational problem) for a set of appropriate reference structures

*P*

^{j}(

*t*) is the probability that at time

*t*the system is vibrating around the

*j*-th reference structure. The relevant structures can be set up by an educated guess (knowing the structure of the systems) and/or by a preliminary MD run to explore the phase space.

*P*

^{j}(

*t*), we assumed a Gaussian distribution around the reference structures (38,54)

*m*

_{j}is a properly defined metric measuring the “distance” between the geometry of the system at instant

*t*and the reference structure

*j*and σ

_{c}is the width of the Gaussian. The metric

*m*

_{j}must be chosen in a way that it is easy and cheap to be evaluated on-the-fly but that it can still capture the fundamental differences between the reference structures. It has been shown (38,54) that the following definition has the required characteristics

_{k}} can be a set of coordinates of the same type, for example, all interatomic distances, bond angles, torsional angles, or coordination numbers. Notice that in the case of the coordination number, the following continuous definition has been adopted (55)

*r*(

*t*) is the distance between the two atoms at time

*t*and

*R*

_{0}is a cutoff distance for the interactions.

**m**

_{j}= {

*m*

_{j}

^{x}} and

*P*

^{j}can be generalized to

*x*} is a subset of coordinates of the same type.

_{3}torsions, avoiding the introduction of a huge number of reference structures, a multifragment strategy can be applied. (38) The system is divided in a set of relevant fragments and for each fragment the

**L**

_{α∈frag}matrix is rotated in a way to guarantee the consistency of the reference system at each time step.

**R**

^{α∈frag}can be obtained by minimizing the sum of the squared distances between the mass weight coordinates of the corresponding atoms.

### 2.8. Divide-and-Conquer Approach for the **L** Matrix

**L**in a block matrix in which each block is localized on a particular set of atoms of the system. In all cases, the alkane molecules, both gas-phase and adsorbed, have been modeled with a single block of atoms. The zeolite has been modeled with two separated blocks: the O–H group of the Si–O(H)–Al bridge that interacts with the adsorbed molecule (

**L**

^{OH}) and the rest of the silicate framework (

**L**

^{frame}). The H-CHA zeolite presents a huge number of quasi-degenerate harmonic modes below 1000 cm

^{–1}, as shown in Figure 1. The correct description of

**L**

^{frame}(

*t*) requires the introduction of multiple blocks and fragments which would increase the computational cost. Because the major contributions to the adsorption free energies are expected to come mainly from the Si–O(H)–Al site onto which the alkane is adsorbed, we decide to choose a simpler path and neglect any direct contribution to the VDOS from the vibrational modes localized on the zeolite but the O–H of the Si–O(H)–Al ones, imposing

**L**

^{frame}= 0.

_{4}), 30 for ethane@H-CHA, and 39 for propane@H-CHA. Only this subset of modes is used to compute

*D*(ω) and the vibrational partition function according to eqs 2–4 or 2b–4b, while we neglect the contributions from the modes localized at the rest of the silicate framework.

### 2.9. Summary and Additional Choices

*H*

^{vib}and

*S*

^{vib}from the projected

*d*

_{i}(ω) as follows: anharmonic frequencies were extracted by fitting

*d*

_{i}(ω) and using eqs 2–4, or direct integration of

*d*

_{i}(ω) (eq 5b). The integration of

*d*

_{i}(ω) accounts for the inhomogeneous broadening of the bands. However, for the high-frequency modes, the 0.4 fs time step combined with the short length of the trajectories imposes a width of the FT of ∼50 cm

^{–1}, artificially inducing a Gaussian shape to

*d*

_{i}(ω). Therefore, the integration of

*d*

_{i}(ω) is not meaningful for these cases and it is better to extract the anharmonic fundamental frequencies needed for eqs 2–5 by fitting. In contrast, for the lower frequency modes, the longer trajectories allow one to reasonably predict the shape of the bands and it is worth to use the full integral of

*d*

_{i}(ω) in eqs 2b–4b to get

*H*

^{vib}and

*S*

^{vib}. In this way, the complex shape of the PES, which is due, among other features, to the quasi-degenerate minima of the hindered rotations and translations, can be taken into account.

_{i}

^{H}of a mode

*i*is below 450 cm

^{–1}, eqs 2b–4b are used, whereas if ω

_{i}

^{H}is above 450 cm

^{–1}, eqs 2–4 are applied with frequencies extracted by the Lorentzian fitting.

^{–1}), we prefer to calculate the ZPE contributions employing eq 5 with the frequencies extracted by the Lorentzian fitting:

*G*

_{i}

^{vib}is the contribution to the vibrational free energy of the

*i*-th mode and ω

_{i}

^{anh}is the anharmonic frequency obtained by fitting.

### 2.10. DOS-Projection Method

1. | Structure optimization and calculation of the harmonic normal modes for the minimum energy structures | ||||||||||||||||

2. | Generation of a set of replicas of the system by vertical excitation of the full set of harmonic modes for the system
| ||||||||||||||||

3. | Running the trajectories | ||||||||||||||||

4. | Decision about use of the full vibrational space for the projection or of a subspace only (see Section 2.8). In the case of the sub-space, | ||||||||||||||||

5. | Prediction of the evolution of the eigenvector matrix along the trajectories by a weighted sum of the | ||||||||||||||||

6. | |||||||||||||||||

7. | Calculation of the FT of the velocity autocorrelation function of the vibrational modes (eq 8)
| ||||||||||||||||

8. | For all modes, use of a Lorentzian to fit | ||||||||||||||||

9. | With these anharmonic frequencies for all the vibrational modes the ZPE was computed according to eq 5. | ||||||||||||||||

10. | For modes with an original harmonic frequency
| ||||||||||||||||

11. | Calculation of the thermodynamic functions |

## 3. Computational Details

### 3.1. Systems, Electronic Energies, and MD Simulations

*a*= 18.90 Å,

*b*= 9.44 Å,

*c*= 9.29 Å, α = 94.0051, β = 94.8903, and γ = 95.3793°. (30) The optimized structures for the adsorption complexes correspond to half coverage (θ = 0.5). This ensures that the lateral interactions between the adsorbed molecules are negligible. For gas phase molecules, a 15 Å × 15 Å × 15 Å cell has been adopted.

_{3}group) or the secondary carbon atom (CH

_{2}group). Bučko et al

*.*(10) have shown that at 300 K, the probability for adsorption via the primary carbon is around 7 times higher than via the secondary carbon atom. Piccini et al

*.*(30) found that adsorption via the primary carbon is entropically favored by

*T*Δ

*S*= 12 kJ/mol at 313 K. Therefore, in the following, we will consider only the adsorption of propane via primary carbon (shown in Figure 1D), while adsorption via the secondary carbon is further discussed in Section S6 of Supporting Information.

^{–8}eV/cell has been applied.

*E*

_{el}used in this paper are the ones already published in ref (30), obtained with the hybrid MP2:PDE + D2 approach. They are reported in Supporting Information, Table S3, together with the rotational and translational entropy terms for the gas phase (Table S4).

^{–6}eV/cell. The classical Newton equations of motion for the nuclei have been integrated through the Verlet algorithm with a time step of 0.4 fs.

*k*

_{b}

*T*, where

*T*is equal to 303 K for methane and 313 K for ethane and propane. Two trajectories of 20 ps each have been run for each system. Notice that in this way also the “quasi-free” state in which the molecule is not directly interacting with the surface but still in the pore is sampled.

*a posteriori*by imposing ε

_{k}

^{i}in a way to ensure ∫

_{0}

^{∞}dω

*d*

_{i}(ω) = 1.

### 3.2. Reference Structures

_{3}group.

*vs*−17.1°), that is, the angle between the (Si)–O–H bond and the Si–O(H)–Al plane. Due to the low energy barrier, during the dynamics sometimes the system jumps between the two minima along the path of the H·Si·Al·O out-of-plane bending. (61)

## 4. Results and Discussion

### 4.1. Vertical Excitation at the Target Temperature *Versus* Harmonic ZPE

^{T}DOS-P) or all the modes excited at their own harmonic ZPE (

^{ZPE}DOS-P).

^{T}DOS-P), most of the modes are well below their ZPE, and therefore only a small portion of the phase space is accessible. In particular, the PES near the ZPE level that can show for some modes a strong anharmonic shape is not sampled, shifting the computed frequencies of the fundamental bands. As a consequence,

*E*

_{0}

^{vib}can be up to 10 kJ/mol higher than in the case of the system initially at the harmonic ZPE level (

^{ZPE}DOS-P).

adsorbate | ^{ZPE}DOS-P | ^{T}DOS-P | Δ | |
---|---|---|---|---|

methane | E_{0}^{vib} | 150.1 | 155.8 | –5.7 |

H^{vib} | 15.6 | 15.8 | 0.2 | |

–TS^{vib} | –37.0 | –40.2 | 3.2 | |

G^{vib} | 128.7 | 131.4 | –2.7 | |

ethane | E_{0}^{vib} | 222.6 | 229.2 | –6.6 |

H^{vib} | 19.5 | 19.1 | 0.4 | |

–TS_{vib} | –49.8 | –51.7 | 1.9 | |

G^{vib} | 192.3 | 196.6 | –4.3 | |

propane | E_{0}^{vib} | 293.3 | 302.8 | –9.5 |

H^{vib} | 23.1 | 23.0 | 0.1 | |

–TS^{vib} | –58.3 | –59.3 | 1.0 | |

G^{vib} | 258.1 | 266.5 | –8.4 |

^{a}

In the last column, we report the difference Δ between the two. All in kJ/mol.

*TS*

^{vib}) is lower for

^{T}DOS-P, with a maximum difference of 3.2 kJ/mol for methane. The

*H*

^{vib}values predicted by the two approaches agree within 0.5 kJ/mol. This different sensitivities with respect to the initial conditions of

*E*

_{0}

^{vib},

*H*

^{vib}, and −

*TS*

^{vib}are related to the fact that the lower frequency modes that dominate

*S*

^{vib}and

*H*

^{vib}at 300 K are also in our classical dynamics not so far from their real quantum vibrational ground state levels, whereas the high-frequency ones that carry the major contributions to

*E*

_{0}

^{vib}are well below this.

*S*

^{vib}is more sensitive than

*H*

^{vib}because it is influenced also by the tail of the vibrational partition function.

^{ZPE}DOS-P) than for

*T*excitation (

^{T}DOS-P). The ZPE, enthalpy, and entropy terms add up to Gibbs free energies that, therefore, are more positive for

^{ZPE}DOS-P than for

^{T}DOS-P.

^{ZPE}DOS-P | ^{T}DOS-P | Δ | ||
---|---|---|---|---|

methane@H-CHA | ΔE_{el}^{a} | –25.3 | –25.3 | |

ΔE_{0-vib}^{a} | 2.8 | 1.8 | 1.0 | |

ΔH^{a} | –20.4 | –21.8 | 1.4 | |

–TΔS^{a} | 25.3 | 23.8 | 1.5 | |

ΔG^{a} | 4.9 | 2.0 | 2.9 | |

ethane@H-CHA | ΔE_{el}^{a} | –36.2 | –36.2 | |

ΔE_{0-vib}^{a} | 2.5 | 0.1 | 2.4 | |

ΔH^{a} | –31.1 | –34.3 | 3.2 | |

–TΔS^{a} | 29.9 | 27.2 | 2.7 | |

ΔG^{a} | –1.1 | –7.1 | 6.0 | |

propane@H-CHA | ΔE_{el}^{a} | –46.7 | –46.7 | |

ΔE_{0-vib}^{a} | 3.5 | 1.6 | 1.9 | |

ΔH^{a} | –40.5 | –43.1 | 2.6 | |

–TΔS^{a} | 34.9 | 33.5 | 1.4 | |

ΔG^{a} | –5.8 | –9.7 | 3.9 |

^{a}

In the last column, we report the difference between the two.

*T*excitation explores less energetic parts of the PES, producing lower Δ

*H*

^{a}values. At the same time, the longer trajectories (20 ps) allow the exploration also of the “quasi-free” gas phase state in which the molecule is in the pore but not close to the surface. The contributions of this state, only in a small part explored by ZPE excitation, diminish the entropy loss on adsorption.

### 4.2. Comparison with Experiments

^{ZPE}DOS-P,

^{T}DOS-P, and DOS-I simulations from experimental values. (30) As reference, we also include the results of Piccini et al. obtained from harmonic (HARM) and anharmonic (curvilinear distortions, ANH) vibrational partition functions. (30)

*G*

^{a}predictions of

^{ZPE}DOS-P and

^{T}DOS-P both agree within chemical accuracy limits (±4 kJ/mol, red dotted line in Figure 4) with the experimental values and apparently indicate a similarly good, for

^{T}DOS-P even slightly better, performance than the anharmonic reference calculations. However, the larger deviations for Δ

*H*

^{a}and

*T*Δ

*S*

^{a}show that this is in part due to an error compensation. For

*T*Δ

*S*

^{a}, the mean absolute deviations (MAD) of 6.5 and 4.7 kJ/mol for ZPE and

*T*excitations, respectively, are a significant improvement compared to the harmonic approach, but outside the chemical accuracy range and much larger than that of the anharmonic calculations.

*H*

^{a}, DOS-P with ZPE excitation yields an improvement with respect to the harmonic approach but

*T*excitation does not. The origin is not in the thermal part but in the ZPE contribution to Δ

*H*

^{a}(Figure 5).

*E*

_{0-vib}

^{a}reference values (30) decrease from methane to ethane and further to propane. The DOS-P and harmonic results reproduce this trend for methane to ethane but not for ethane to propane for which all three show an increase. The DOS-P results with ZPE excitation agree with the anharmonic results for ethane but show large deviations for methane (−2.7 kJ/mol) and propane (1.6 kJ/mol), whereas the DOS-P with

*T*excitation closely agrees with the anharmonic result for propane but show large deviations for methane (−3.7 kJ/mol) and ethane (−2.7 kJ/mol).

^{ZPE}DOS-P and

^{T}DOS-P methods (1.5 and 2.1 kJ/mol, respectively), we considered also substituting Δ

*E*

_{0-vib}

^{a}in the DOS-P adsorption enthalpies with the harmonic ones. The results are shown in the right panel of Figure 4 labeled “harmonic ZPE”.

*H*

^{a}values: the MAD decrease to 2.1 and 2.8 kJ/mol for ZPE and T excitations, respectively. Because this also diminishes the favorable cancellation of error between Δ

*H*

^{a}and

*T*Δ

*S*

^{a}, the MAD for Δ

*G*

^{a}slightly increases to 4.5 and 2.6 kJ/mol for

^{ZPE}DOS-P and

^{T}DOS-P, respectively.

^{T}DOS-P method with harmonic ZPE as the method of choice. However,

^{ZPE}DOS-P has other advantages, see Section 4.4.

^{ZPE}DOS-P and the

^{T}DOS-P excitation and harmonic Δ

*E*

_{0-vib}

^{a}. The results of gravimetric/calorimetric sorption experiments (30) are shown as black dots with vertical bars, indicating the chemical accuracy range (±4 kJ/mol). For comparison, the predictions from harmonic and anharmonic frequencies (curvilinear distortions) of Piccini et al. (30) are also shown (see Sections S11 and table S10 of Supporting Information for the data).

*T*Δ

*S*

^{a}, Δ

*H*

^{a}, and Δ

*G*

^{a}. The adsorption enthalpy decreases in this series, whereas the entropy loss (−

*T*Δ

*S*

^{a}) increases. As a result, for the experimental conditions, Δ

*G*

^{a}changes from positive for methane, to slightly negative for ethane, and to strongly negative for propane. Hence, ethane and propane are correctly predicted to form stable adsorbates at 313 K, contrary to the prediction based on the harmonic approximation.

*H*

^{a}results are within chemical accuracy limits of the experimental values but systematically too negative, whereas the −

*T*Δ

*S*

^{a}term is systematically predicted too positive, on average 6.5 and 4.7 kJ/mol for ZPE and

*T*excitation, respectively.

*G*

^{a}, the remaining deviations from the ANH results are smaller for the

*T*excitation (3.0 kJ/mol on average) than for the ZPE excitation (5.6 kJ/mol on average).

*T*and ZPE excitation, respectively. Part of the missing contributions come from the Si–O–Si soft modes of the zeolite framework, which we are not including in the calculation of the thermodynamic functions (see Section 2.8). The better performance of

^{T}DOS-P can be due to the larger contributions of the “quasi-free” state of the alkane molecule to the partition function that compensates the missing ones from the zeolite framework.

### 4.3. Effect of the Projection on the Computed Thermodynamic Functions

*E*

_{0}

^{vib}can only be computed via eq 5a. Therefore, also in this case, we calculate Δ

*E*

_{0-vib}

^{a}from harmonic frequencies as we do for our DOS-P projection methods in Section 4.2. Third, compared to DOS-P, additional MD trajectories are needed to reduce statistical fluctuations.

^{T}DOS-P plus a third one which was needed to reduce the statistical fluctuations for −

*T*Δ

*S*

^{a}below 10 kJ/mol (see Figure S7 of Supporting Information).

^{T}DOS-P and

^{T}DOS-I, projection on normal modes (

^{T}DOS-P) strongly reduces the statistical uncertainty (gray shadows in the figure) compared to the direct VDOS integration (

^{T}DOS-I) of the same trajectories. For example, for

*T*Δ

*S*

^{a}(Figure 4, gray shaded), the statistical uncertainty goes from 10 kJ/mol with

^{T}DOS-I to 1 kJ/mol with

^{T}DOS-P and to 0.5 kJ/mol with

^{ZPE}DOS-P (see Supporting Information, Sections S8 and S9, for more details). Similarly, the statistical uncertainty of Δ

*H*

^{a}(when the harmonic ZPE is used) decreases from 5 kJ/mol without projection to less than 0.5 kJ/mol with projection.

^{T}DOS-P,

^{T}DOS-I is not reproducing the experimental trend with the alkane chain length (see Supporting Information, Section S10, for the full set of data). For example, −

*T*Δ

*S*

^{a}is predicted to be lower for propane (23.9 kJ/mol) than for ethane (32.3 kJ/mol), whereas the experimental entropy contribution is 27.5 kJ/mol for propane and 23.8 kJ/mol for ethane. (30) One of the consequences is that

^{T}DOS-I predicts a positive Δ

*G*

^{a}value for ethane (2.5 kJ/mol), while experimentally it is slightly negative (−3.7 kJ/mol). Instead, both

^{T}DOS-P and

^{ZPE}DOS-P predict the correct sign for Δ

*G*

^{a}for all cases considered.

### 4.4. Comments on Sampling Statistics

^{T}DOS-I), for the same length and number of trajectories, that is, for the same computational cost.

^{T}DOS-P seems to perform slightly better than

^{ZPE}DOS-P in terms of accuracy (see Section 4.2), the latter, with its short trajectories, allows a better control of the sampled phase space and seems to further reduce the statistical uncertainty, for example, below 0.2 kJ/mol in the case of Δ

*H*

^{a}. The

^{ZPE}DOS-P is particularly suitable for large systems, because it is based on the use of a set of really short simulations (no longer than 3 ps) which can easily run in parallel, reducing the required wall time.

^{T}DOS-P and

^{ZPE}DOS-P, respectively, for each system, distributed on multiple short trajectories of maximum 20 ps for the former and 3 ps for the latter. This is much below the usual time scale of 50 ps to 1 ns, (8−14) needed for thermodynamic function calculations (Δ

*H*

^{a},–

*T*Δ

*S*

^{a}, Δ

*G*

^{a}), especially for the entropic contributions, with our statistical precision.

*.*(27) report Δ

*H*

^{a}= −25.5 ± 0.75 kJ/mol for CH

_{4}in the H-CHA at 300 K (PBE + D2, 400 eV plane wave cutoff) using simulations of 100 ps, whereas with

^{ZPE}DOS-P, using a set of trajectories of maximum 3 ps, we predict Δ

*H*

^{a}= −26.9 ± 0.2 kJ/mol. To get a directly comparable Δ

*H*

^{a}value, we replaced our hybrid MP2/PBE + D2 electronic energy (−25.3 kJ/mol, Table 2) (30) with the corresponding PBE + D2 value (−34.7 kJ/mol). (30) Our

^{ZPE}DOS-P results agree within 1.4 ± 0.95 kJ/mol with that of Rocca et al

*.*(27)

## 5. Conclusions

*.*, (30) which solves one-dimensional Schrödinger equations for each mode separately using curvilinear distortions.

^{T}DOS-P) is required to reach convergence within 1 kJ/mol: 1–20 ps are sufficient not only for the enthalpy but also for the entropy and free energy instead of the 50 ps to 1 ns usually required by MD.

^{T}DOS-P method yields Gibbs free energies of adsorption in close agreement with the experiment (MAD 2.6 kJ/mol), whereas the harmonic approximation including all vibrations yields a MAD of 12.2 kJ/mol.

^{T}DOS-P is almost as accurate as the use of anharmonic frequencies obtained with the curvilinear distortion of (all) individual modes (MAD 2.4 kJ/mol). Reaching or approaching chemical accuracy also for adsorption enthalpies and the entropies, our

^{T}DOS-P method is a good compromise between accuracy and computational cost.

## Supporting Information

The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jctc.1c00519.

Additional equations for the calculation of the free energies, decoupling of the vibrations due to the anharmonicity, additional computational details, data on adsorption of propane via secondary carbon, discussion on the vibrational active space, convergence check, and summary of the computed thermodynamic values (PDF)

## Terms & Conditions

Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system: http://pubs.acs.org/page/copyright/permissions.html.

## Acknowledgments

This work has been supported by the Alexander von Humboldt Foundation with a fellowship to DG and by German Research Foundation (DFG) with a Reinhart Koselleck grant, as well as by the “Fonds der Chemischen Industrie”. The authors gratefully acknowledge the Gauss Center for Supercomputing e.V. (www.gauss-centre.eu) for providing computing time on the GCS Supercomputer SuperMUC-NG at Leibniz Supercomputing Center (www.lrz.de), Project ID pn68qu. Discussions with Dr Marcin Rybicki and Fabian Berger are gratefully acknowledged.

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In agreement with IR expts., we predict transformation of water-rich structures, [SO42-,2H+,3H2O], into pyrosulfate structures, [S2O72-,2H+,H2O], during calcination. Further increase of the temp. yields adsorbed SO3 before the clean surface is reached. Water adsorbed on the t-ZrO2(101) surface leaves in three steps upon heating from 250 to 730 K at 0.01 bar pressure: physisorbed water below room temp., the first chemisorbed water at about 440 K and the last water at about 730 K.**8**Laio, A.; Rodriguez-Fortea, A.; Gervasio, F. L.; Ceccarelli, M.; Parrinello, M. Assessing the Accuracy of Metadynamics.*J. Phys. Chem. B*2005,*109*, 6714– 6721, DOI: 10.1021/jp045424kGoogle Scholar8https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXht1ygurs%253D&md5=f0946da733889a7e05d4f97f6608468bAssessing the Accuracy of MetadynamicsLaio, Alessandro; Rodriguez-Fortea, Antonio; Gervasio, Francesco Luigi; Ceccarelli, Matteo; Parrinello, MicheleJournal of Physical Chemistry B (2005), 109 (14), 6714-6721CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)Metadynamics is a powerful technique that has been successfully exploited to explore the multidimensional free energy surface of complex polyat. systems and predict transition mechanisms in very different fields, ranging from chem. and solid-state physics to biophysics. We here derive an explicit expression for the accuracy of the methodol. and provide a way to choose the parameters of the method in order to optimize its performance.**9**Trzesniak, D.; Kunz, A.-P. E.; van Gunsteren, W. F. A Comparison of Methods to Compute the Potential of Mean Force.*ChemPhysChem*2007,*8*, 162– 169, DOI: 10.1002/cphc.200600527Google Scholar9https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXpsFSktA%253D%253D&md5=efaa9fcddd87b53f819e2d1b6530cad0A comparison of methods to compute the potential of mean forceTrzesniak, Daniel; Kunz, Anna-Pitschna E.; van Gunsteren, Wilfred F.ChemPhysChem (2007), 8 (1), 162-169CODEN: CPCHFT; ISSN:1439-4235. (Wiley-VCH Verlag GmbH & Co. KGaA)Most processes occurring in a system are detd. by the relative free energy between two or more states because the free energy is a measure of the probability of finding the system in a given state. When the two states of interest are connected by a pathway, usually called reaction coordinate, along which the free-energy profile is detd., this profile or potential of mean force (PMF) will also yield the relative free energy of the two states. Twelve different methods to compute a PMF are reviewed and compared, with regard to their precision, for a system consisting of a pair of methane mols. in aq. soln. We analyze all combinations of the type of sampling (unbiased, umbrella-biased or constraint-biased), how to compute free energies (from d. of states or force averaging) and the type of coordinate system (internal or Cartesian) used for the PMF degree of freedom. The method of choice is constraint-bias simulation combined with force averaging for either an internal or a Cartesian PMF degree of freedom.**10**Bučko, T.; Benco, L.; Hafner, J.; Ángyán, J. Proton exchange of small hydrocarbons over acidic chabazite: Ab initio study of entropic effects.*J. Catal.*2007,*250*, 171– 183, DOI: 10.1016/j.jcat.2007.05.025Google Scholar10https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXotl2qsLw%253D&md5=31281f03ab09e4b1c154bed254d6845fProton exchange of small hydrocarbons over acidic chabazite: Ab initio study of entropic effectsBucko, Tomas; Benco, Lubomir; Hafner, Juergen; Angyan, Janos G.Journal of Catalysis (2007), 250 (1), 171-183CODEN: JCTLA5; ISSN:0021-9517. (Elsevier Ltd.)The proton-exchange reaction of a series of short hydrocarbons over an acidic zeolite (chabazite) was studied using periodic d. functional theory (DFT) calcns. It was found that the chain length of hydrocarbons does not have a significant effect on the height of the potential-energy barrier. The exptl. obsd. regioselectivity between Me and methylene groups in propane and between Me and methine groups in isobutane was shown to be an entropic effect. In addn. to the direct H-exchange, a mechanism mediated by a methylpropene mol. recently suggested by experimentalists was explored. It was found that entropy plays a very important role in driving the reaction.**11**Rey, J.; Gomez, A.; Raybaud, P.; Chizallet, C.; Bučko, T. On the origin of the difference between type A and type B skeletal isomerization of alkenes catalyzed by zeolites: The crucial input of ab initio molecular dynamics.*J. Catal.*2019,*373*, 361– 373, DOI: 10.1016/j.jcat.2019.04.014Google Scholar11https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXot12jt78%253D&md5=eaa14cd9b2f4915b494fb248f67375d6On the origin of the difference between type A and type B skeletal isomerization of alkenes catalyzed by zeolites: The crucial input of ab initio molecular dynamicsRey, Jerome; Gomez, Axel; Raybaud, Pascal; Chizallet, Celine; Bucko, TomasJournal of Catalysis (2019), 373 (), 361-373CODEN: JCTLA5; ISSN:0021-9517. (Elsevier Inc.)Alkene skeletal isomerization elementary steps catalyzed by acid zeolites are key reactions in refining, petrochem. and biomass conversion. We unravel the at.-scale origin of the higher rate const. of type A isomerization (involving a direct alkyl transfer, without any change in the branching degree) than the one of type B isomerization (involving non-classical carbonium ions such as protonated cyclopropane (PCP), inducing a change in the branching degree) of C7 carbenium ions in chabazite. Accurate free energy barriers are calcd. at 300 and 500 K for both reactions by means of mol. dynamics in combination with blue moon ensemble approach, whereas the static approach is shown to fail to describe these reactions. The slow transformation between individual rotational isomers, causing non-ergodic sampling of reactant state, largely overlooked in literature, is carefully addressed in the present work. At 500 K (representative of exptl. conditions), free energy barriers of 83.4 kJ/mol and 15.0 kJ/mol are detd. for type B and type A isomerization resp. The much lower barrier for type A is thus recovered, and assigned to a loose transition state, with free rotation of the migrating alkyl group, while the transition state of type B isomerization is tighter, with such a rotation blocked, due to the simultaneous hydride shift taking place on the edge of the PCP.**12**Barducci, A.; Bussi, G.; Parrinello, M. Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method.*Phys. Rev. Lett.*2008,*100*, 020603, DOI: 10.1103/PhysRevLett.100.020603Google Scholar12https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXovFensQ%253D%253D&md5=701ccfeee476c2e9a5d1e5a6b0e82197Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy MethodBarducci, Alessandro; Bussi, Giovanni; Parrinello, MichelePhysical Review Letters (2008), 100 (2), 020603/1-020603/4CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)We present a method for detg. the free-energy dependence on a selected no. of collective variables using an adaptive bias. The formalism provides a unified description which has metadynamics and canonical sampling as limiting cases. Convergence and errors can be rigorously and easily controlled. The parameters of the simulation can be tuned so as to focus the computational effort only on the phys. relevant regions of the order parameter space. The algorithm is tested on the reconstruction of an alanine dipeptide free-energy landscape.**13**Muñoz-Santiburcio, D.; Marx, D. Chemistry in nanoconfined water.*Chem. Sci.*2017,*8*, 3444– 3452, DOI: 10.1039/c6sc04989cGoogle Scholar13https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXksVyjtbo%253D&md5=95a211a58f29adb2812b4ecc7dfb2711Chemistry in nanoconfined waterMunoz-Santiburcio, Daniel; Marx, DominikChemical Science (2017), 8 (5), 3444-3452CODEN: CSHCCN; ISSN:2041-6520. (Royal Society of Chemistry)Nanoconfined liqs. have extremely different properties from the bulk, which profoundly affects chem. reactions taking place in nanosolvation. Here, we present extensive ab initio simulations of a vast set of chem. reactions within a water lamella that is nanoconfined by mineral surfaces, which might be relevant to prebiotic peptide formation in aq. environments. Our results disclose a rich interplay of distinct effects, from steric factors typical of reactions occurring in small spaces to a charge-stabilization effect in nanoconfined water at extreme conditions similar to that obsd. in bulk water when changing from extreme to ambient conditions. These effects are found to modify significantly not only the energetics but also the mechanisms of reactions happening in nanoconfined water in comparison to the corresponding bulk regime.**14**Steinmann, C.; Olsson, M. A.; Ryde, U. Relative Ligand-Binding Free Energies Calculated from Multiple Short QM/MM MD Simulations.*J. Chem. Theory Comput.*2018,*14*, 3228– 3237, DOI: 10.1021/acs.jctc.8b00081Google Scholar14https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXpslaisbs%253D&md5=0756c0de92c581bc323f6122019b0479Relative Ligand-Binding Free Energies Calculated from Multiple Short QM/MM MD SimulationsSteinmann, Casper; Olsson, Martin A.; Ryde, UlfJournal of Chemical Theory and Computation (2018), 14 (6), 3228-3237CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)We have devised a new efficient approach to compute combined quantum mech. (QM) and mol. mech. (MM, i.e. QM/MM) ligand-binding relative free energies. Our method employs the ref.-potential approach with free-energy perturbation both at the MM level (between the two ligands) and from MM to QM/MM (for each ligand). To ensure that converged results are obtained for the MM → QM/MM perturbations, explicit QM/MM mol. dynamics (MD) simulations are performed with two intermediate mixed states. To speed up the calcns., we utilize the fact that the phase space can be extensively sampled at the MM level. Therefore, we run many short QM/MM MD simulations started from snapshots of the MM simulations, instead of a single long simulation. As a test case, we study the binding of nine cyclic carboxylate ligands to the octa-acid deep cavitand. Only the ligand is in the QM system, treated with the semiempirical PM6-DH + method. We show that for eight of the ligands, we obtain well converged results with short MD simulations (1-15 ps). However, in one case, the convergence is slower (∼50 ps) owing to a mismatch between the conformational preferences of the MM and QM/MM potentials. We test the effect of initial minimization, the need of equilibration, and how many independent simulations are needed to reach a certain precision. The results show that the present approach is about four times faster than using std. MM → QM/MM free-energy perturbations with the same accuracy and precision.**15**Amsler, J.; Plessow, P. N.; Studt, F.; Bučko, T. Anharmonic Correction to Adsorption Free Energy from DFT-Based MD Using Thermodynamic Integration.*J. Chem. Theory Comput.*2021,*17*, 1155– 1169, DOI: 10.1021/acs.jctc.0c01022Google Scholar15https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXhvVWks7s%253D&md5=d46cca0400079914a19d7a4ebe8f0cb5Anharmonic Correction to Adsorption Free Energy from DFT-Based MD Using Thermodynamic IntegrationAmsler, Jonas; Plessow, Philipp N.; Studt, Felix; Bucko, TomasJournal of Chemical Theory and Computation (2021), 17 (2), 1155-1169CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)Adsorption processes are often governed by weak interactions for which the estn. of entropy contributions by the harmonic approxn. is prone to be inaccurate. Thermodn. integration (TI) from the harmonic to the fully interacting system (λ-path integration) can be used to compute anharmonic corrections. Here, the authors combine TI with (curvilinear) internal coordinates in periodic systems to make the formalism available in computational studies. Implementation of ab initio mol. dynamics in VASP is independent of the reaction path and can be thus applied to study adsorption processes relative to the gas phase and does hence provide a useful tool for computational catalysis. The application of the approach on 3 model systems for which exact semianal. solns. exist and illustrate and quantify the importance of anharmonic vibrations, hindered rotations, and hindered translations (dissocn.) are discussed. Eventually, the authors apply the method to study the adsorption of small adsorbates in a zeolite (H-SSZ-13).**16**Rod, T. H.; Ryde, U. Accurate QM/MM Free Energy Calculations of Enzyme Reactions: Methylation by Catechol O-Methyltransferase.*J. Chem. Theory Comput.*2005,*1*, 1240– 1251, DOI: 10.1021/ct0501102Google Scholar16https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXpt1CntrY%253D&md5=28b8c0949050ce98c001f67afb90c6f2Accurate QM/MM Free Energy Calculations of Enzyme Reactions: Methylation by Catechol O-MethyltransferaseRod, Thomas H.; Ryde, UlfJournal of Chemical Theory and Computation (2005), 1 (6), 1240-1251CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)We recently described a method to compute accurate quantum mech. free energies [Rod, T. H.; Ryde, U. Phys. Rev. Lett. 2005, 94, 138302]. The method, which we term quantum mech. thermodn. cycle perturbation (QTCP), employs a mol. mechanics force field to sample phase space and, subsequently, a thermodn. cycle to est. QM/MM free energy changes. Here, we discuss the methodol. in detail and test an approach based on a different thermodn. cycle. We also show that a new way of treating hydrogen link atoms makes the free energy changes converge faster and that extrapolation to higher accuracy can be performed. We finally discuss the quantum mech. free energy (QM/MM-FE) method in the framework of the QTCP method. All methods considered are applied to the methylation of catecholate catalyzed by catechol O-methyltransferase. We compute the free energy barrier for the reaction by computing free energy changes in steps between fixed QM regions along a predetd. reaction pathway. Using the QTCP approach, an extrapolated activation free energy of 69 kJ/mol for the forward reaction and 90 kJ/mol for the reverse reaction are obtained at the level of the B3LYP functional and the 6-311++G(2d,2p) basis set. The value for the forward reaction is in excellent agreement with the exptl. value of 75 kJ/mol. Results based on the QM/MM-FE method differ by less than 10 kJ/mol from those values, indicating that QM/MM-FE may be a fairly accurate and cheap alternative to calc. QM/MM free energy changes. Moreover, the results are compared to barriers obtained with a fixed mol. mechanics environment as well as with structures optimized in a vacuum. All the computed free energy barriers are well converged. A major approxn. in the current implementation of the QTCP method is that the QM region is fixed. The approxn. leads to well-converged free energy barriers, which has been a problem in similar studies.**17**Smit, B.; Maesen, T. L. M. Molecular Simulations of Zeolites: Adsorption, Diffusion, and Shape Selectivity.*Chem. Rev.*2008,*108*, 4125– 4184, DOI: 10.1021/cr8002642Google Scholar17https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXhtFKlurrL&md5=7a607f8f328c57fb1c88a004d4cf04daMolecular Simulations of Zeolites: Adsorption, Diffusion, and Shape SelectivitySmit, Berend; Maesen, Theo L. M.Chemical Reviews (Washington, DC, United States) (2008), 108 (10), 4125-4184CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)A review. Details of simulation studies for adsorption, diffusion, and shape selectivity on zeolites have been reviewed.**18**Bučko, T.; Benco, L.; Hafner, J.; Ángyán, J. G. Monomolecular cracking of propane over acidic chabazite: An ab initio molecular dynamics and transition path sampling study.*J. Catal.*2011,*279*, 220– 228Google Scholar18https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXjsFWmtb8%253D&md5=583b9bd4dbadfbfd464d7380fd0e51a0Monomolecular cracking of propane over acidic chabazite: An ab initio molecular dynamics and transition path sampling studyBucko, Tomas; Benco, Lubomir; Hafner, Juergen; Angyan, Janos G.Journal of Catalysis (2011), 279 (1), 220-228CODEN: JCTLA5; ISSN:0021-9517. (Elsevier Inc.)The monomol. Haag-Dessau mechanism for propane cracking over acidic chabazite has been studied using dispersion-cor. periodic DFT calcns. in combination with ab initio mol. dynamics (AIMD) simulations, transition path sampling (TPS), and free-energy integrations. The AIMD simulations show that due to the weak specific interaction of the satd. mol. with Bronsted acid sites, the adsorption energy is considerably reduced at elevated temp. and that only a fraction of the mols. adsorbed within the zeolite is sufficiently close to the acid site to form a reactant complex for protonation. TPS shows that the preferred reaction mechanism is the protonation of a terminal Me group. The direct proton attack on the C-C bond between the Me and methylene groups is not excluded but occurs with lower probability. The intrinsic reaction parameters such as free energy and entropy of activation are detd. using thermodn. integration based on constrained mol. dynamics simulations.**19**Laio, A.; Parrinello, M. Escaping free-energy minima.*Proc. Natl. Acad. Sci. U.S.A.*2002,*99*, 12562– 12566, DOI: 10.1073/pnas.202427399Google Scholar19https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38XnvFGiurc%253D&md5=48d5bc7436f3ef9d78369671e70fa608Escaping free-energy minimaLaio, Alessandro; Parrinello, MicheleProceedings of the National Academy of Sciences of the United States of America (2002), 99 (20), 12562-12566CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)We introduce a powerful method for exploring the properties of the multidimensional free energy surfaces (FESs) of complex many-body systems by means of coarse-grained non-Markovian dynamics in the space defined by a few collective coordinates. A characteristic feature of these dynamics is the presence of a history-dependent potential term that, in time, fills the min. in the FES, allowing the efficient exploration and accurate detn. of the FES as a function of the collective coordinates. We demonstrate the usefulness of this approach in the case of the dissocn. of a NaCl mol. in water and in the study of the conformational changes of a dialanine in soln.**20**Pietrucci, F.; Saitta, A. M. Formamide reaction network in gas phase and solution via a unified theoretical approach: Toward a reconciliation of different prebiotic scenarios.*Proc. Natl. Acad. Sci. U.S.A.*2015,*112*, 15030– 15035, DOI: 10.1073/pnas.1512486112Google Scholar20https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhvFWqs7%252FF&md5=c97eca22e01430d5ceeca39542740feaFormamide reaction network in gas phase and solution via a unified theoretical approach: Toward a reconciliation of different prebiotic scenariosPietrucci, Fabio; Saitta, Antonino MarcoProceedings of the National Academy of Sciences of the United States of America (2015), 112 (49), 15030-15035CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)Increasing exptl. and theor. evidence points to formamide as a possible hub in the complex network of prebiotic chem. reactions leading from simple precursors like H2, H2O, N2, NH3, CO, and CO2 to key biol. mols. like proteins, nucleic acids, and sugars. We present an in-depth computational study of the formation and decompn. reaction channels of formamide by means of ab initio mol. dynamics. To this aim we introduce a new theor. method combining the metadynamics sampling scheme with a general purpose topol. formulation of collective variables able to track a wide range of different reaction mechanisms. Our approach is flexible enough to discover multiple pathways and intermediates starting from minimal insight on the systems, and it allows passing in a seamless way from reactions in gas phase to reactions in liq. phase, with the solvent active role fully taken into account. We obtain crucial new insight into the interplay of the different formamide reaction channels and into environment effects on pathways and barriers. In particular, our results indicate a similar stability of formamide and hydrogen cyanide in soln. as well as their relatively facile interconversion, thus reconciling expts. and theory and, possibly, two different and competing prebiotic scenarios. Moreover, although not explicitly sought, formic acid/ammonium formate is produced as an important formamide decompn. byproduct in soln.**21**Alexopoulos, K.; Lee, M.-S.; Liu, Y.; Zhi, Y.; Liu, Y.; Reyniers, M.-F.; Marin, G. B.; Glezakou, V.-A.; Rousseau, R.; Lercher, J. A. Anharmonicity and Confinement in Zeolites: Structure, Spectroscopy, and Adsorption Free Energy of Ethanol in H-ZSM-5.*J. Phys. Chem. C*2016,*120*, 7172– 7182, DOI: 10.1021/acs.jpcc.6b00923Google Scholar21https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xks1eitbc%253D&md5=f5b61bae1a3edc2e03e7fe11be723ee8Anharmonicity and Confinement in Zeolites: Structure, Spectroscopy, and Adsorption Free Energy of Ethanol in H-ZSM-5Alexopoulos, Konstantinos; Lee, Mal-Soon; Liu, Yue; Zhi, Yuchun; Liu, Yuanshuai; Reyniers, Marie-Francoise; Marin, Guy B.; Glezakou, Vassiliki-Alexandra; Rousseau, Roger; Lercher, Johannes A.Journal of Physical Chemistry C (2016), 120 (13), 7172-7182CODEN: JPCCCK; ISSN:1932-7447. (American Chemical Society)To account for thermal and entropic effects caused by the dynamics of the motion of the reaction intermediates, ethanol adsorption on the Bronsted acid site of the H-ZSM-5 catalyst has been studied at different temps. and ethanol loadings using ab initio mol. dynamics (AIMD) simulations, IR (IR) spectroscopy, and calorimetric measurements. At low temps. (T ≤ 400 K) and ethanol loading, a single ethanol mol. adsorbed in H-ZSM-5 forms a Zundel-like structure where the proton is equally shared between the oxygen of the zeolite and the oxygen of the alc. At higher ethanol loading, a second ethanol mol. helps to stabilize the protonated ethanol at all temps. by acting as a solvating agent. The vibrational d. of states (VDOS), as calcd. from the AIMD simulations, are in excellent agreement with measured IR spectra for C2H5OH, C2H5OD, and C2D5OH isotopomers and support the existence of both monomers and dimers. A quasi-harmonic approxn. (QHA), applied to the VDOS obtained from the AIMD simulations, provides ests. of adsorption free energy within ∼10 kJ/mol of the exptl. detd. quantities, whereas the traditional approach, employing harmonic frequencies from a single ground state min., strongly overestimates the adsorption free energy by at least 20∼50 kJ/mol. This discrepancy is traced back to the inability of the harmonic approxn. to represent the contributions to the vibrational motions of the ethanol mol. upon confinement in the zeolite.**22**Cnudde, P.; De Wispelaere, K.; Vanduyfhuys, L.; Demuynck, R.; Van der Mynsbrugge, J.; Waroquier, M.; Van Speybroeck, V. How Chain Length and Branching Influence the Alkene Cracking Reactivity on H-ZSM-5.*ACS Catal.*2018,*8*, 9579– 9595, DOI: 10.1021/acscatal.8b01779Google Scholar22https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhs1GmsbzO&md5=dbd3738ed1b6b05923ae9b97cfecad16How Chain Length and Branching Influence the Alkene Cracking Reactivity on H-ZSM-5Cnudde, Pieter; De Wispelaere, Kristof; Vanduyfhuys, Louis; Demuynck, Ruben; Van der Mynsbrugge, Jeroen; Waroquier, Michel; Van Speybroeck, VeroniqueACS Catalysis (2018), 8 (10), 9579-9595CODEN: ACCACS; ISSN:2155-5435. (American Chemical Society)Catalytic alkene cracking on H-ZSM-5 involves a complex reaction network with many possible reaction routes and often elusive intermediates. Herein, advanced mol. dynamics simulations at 773 K, a typical cracking temp., are performed to clarify the nature of the intermediates and to elucidate dominant cracking pathways at operating conditions. A series of C4-C8 alkene intermediates are investigated to evaluate the influence of chain length and degree of branching on their stability. Our simulations reveal that linear, secondary carbenium ions are relatively unstable, although their lifetime increases with carbon no. Tertiary carbenium ions, on the other hand, are shown to be very stable, irresp. of the chain length. Highly branched carbenium ions, though, tend to rapidly rearrange into more stable cationic species, either via cracking or isomerization reactions. Dominant cracking pathways were detd. by combining these insights on carbenium ion stability with intrinsic free energy barriers for various octene β-scission reactions, detd. via umbrella sampling simulations at operating temp. (773 K). Cracking modes A (3° → 3°) and B2 (3° → 2°) are expected to be dominant at operating conditions, whereas modes B1 (2° → 3°), C (2° → 2°), D2 (2° → 1°), and E2 (3° → 1°) are expected to be less important. All β-scission modes in which a transition state with primary carbocation character is involved have high intrinsic free energy barriers. Reactions starting from secondary carbenium ions will contribute less as these intermediates are short living at the high cracking temp. Our results show the importance of simulations at operating conditions to properly evaluate the carbenium ion stability for β-scission reactions and to assess the mobility of all species in the pores of the zeolite.**23**Cnudde, P.; De Wispelaere, K.; Van der Mynsbrugge, J.; Waroquier, M.; Van Speybroeck, V. Effect of temperature and branching on the nature and stability of alkene cracking intermediates in H-ZSM-5.*J. Catal.*2017,*345*, 53– 69, DOI: 10.1016/j.jcat.2016.11.010Google Scholar23https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhvFGrur%252FL&md5=3f1f86fe905e17804f167ebc784dff01Effect of temperature and branching on the nature and stability of alkene cracking intermediates in H-ZSM-5Cnudde, P.; De Wispelaere, K.; Van der Mynsbrugge, J.; Waroquier, M.; Van Speybroeck, V.Journal of Catalysis (2017), 345 (), 53-69CODEN: JCTLA5; ISSN:0021-9517. (Elsevier Inc.)Catalytic cracking of alkenes takes place at elevated temps. in the order of 773-833 K. In this work, the nature of the reactive intermediates at typical reaction conditions is studied in H-ZSM-5 using a complementary set of modeling tools. Ab initio static and mol. dynamics simulations are performed on different C4-C5 alkene cracking intermediates to identify the reactive species in terms of temp. At 323 K, the prevalent intermediates are linear alkoxides, alkene π-complexes and tertiary carbenium ions. At a typical cracking temp. of 773 K, however, both secondary and tertiary alkoxides are unlikely to exist in the zeolite channels. Instead, more stable carbenium ion intermediates are found. Branched tertiary carbenium ions are very stable, while linear carbenium ions are predicted to be metastable at high temp. Our findings confirm that carbenium ions, rather than alkoxides, are reactive intermediates in catalytic alkene cracking at 773 K.**24**Janda, A.; Vlaisavljevich, B.; Lin, L.-C.; Mallikarjun Sharada, S.; Smit, B.; Head-Gordon, M.; Bell, A. T. Adsorption Thermodynamics and Intrinsic Activation Parameters for Monomolecular Cracking of n-Alkanes on Brønsted Acid Sites in Zeolites.*J. Phys. Chem. C*2015,*119*, 10427– 10438, DOI: 10.1021/acs.jpcc.5b01715Google Scholar24https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXms1Ohsr0%253D&md5=b45a34de6cf0ea727ee57554f6486edfAdsorption Thermodynamics and Intrinsic Activation Parameters for Monomolecular Cracking of n-Alkanes on Bronsted Acid Sites in ZeolitesJanda, Amber; Vlaisavljevich, Bess; Lin, Li-Chiang; Mallikarjun Sharada, Shaama; Smit, Berend; Head-Gordon, Martin; Bell, Alexis T.Journal of Physical Chemistry C (2015), 119 (19), 10427-10438CODEN: JPCCCK; ISSN:1932-7447. (American Chemical Society)Exptl. measurements of the rate coeff. (kapp) and apparent enthalpies and entropies of activation (ΔHapp and ΔSapp) for alkane cracking catalyzed by acidic zeolites can be used to characterize the effects of zeolite structure and alkane size on the intrinsic enthalpy and entropy of activation, ΔH⧺int and ΔS⧺int. To det. ΔH⧺int and ΔS⧺int, enthalpies and entropies of adsorption, ΔHads-H+ and ΔSads-H+, must be detd. for alkane mols. moving from the gas phase to Bronsted acid sites at reaction temps. (>673 K). Exptl. values of ΔHapp and ΔSapp must also be properly defined in terms of ΔHads-H+ and ΔSads-H+. We report here a method for detg. ΔHads-H+ and ΔSads-H+ in which the adsorption site is represented by a fixed vol. that includes the proton. Values of ΔHads-H+ and ΔSads-H+ obtained from Monte Carlo simulations are in good agreement with values obtained from exptl. data measured at 300-400 K. An important feature of the simulations, however, is their ability to account for the redistribution of alkane adsorbed at protons in different locations with increasing temp. Values of ΔH⧺int and ΔS⧺int for the cracking of propane through n-hexane, detd. from measured values of kapp and ΔHapp and simulated values of ΔHads-H+ and ΔSads-H+, agree well with values obtained independently from quantum mechanics/mol. mechanics calcns. Application of our method of anal. reveals that the obsd. increase in kapp with increasing n-alkane size is due primarily to a decrease in ΔH⧺int with increasing chain length and that ΔS⧺int is independent of chain length.**25**Janda, A.; Vlaisavljevich, B.; Smit, B.; Lin, L.-C.; Bell, A. T. Effects of Pore and Cage Topology on the Thermodynamics of n-Alkane Adsorption at Brønsted Protons in Zeolites at High Temperature.*J. Phys. Chem. C*2017,*121*, 1618– 1638, DOI: 10.1021/acs.jpcc.6b09703Google Scholar25https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XitFWgt7jJ&md5=f6ff94ee25a0aa6edd5ee11218e554afEffects of Pore and Cage Topology on the Thermodynamics of n-Alkane Adsorption at Bronsted Protons in Zeolites at High TemperatureJanda, Amber; Vlaisavljevich, Bess; Smit, Berend; Lin, Li-Chiang; Bell, Alexis T.Journal of Physical Chemistry C (2017), 121 (3), 1618-1638CODEN: JPCCCK; ISSN:1932-7447. (American Chemical Society)Monte Carlo simulations are used to systematically investigate the effects of structural topol. on the thermodn. of n-alkanes adsorbed at Bronsted protons in zeolites having one-dimensional channel systems. In zeolites without cages, the enthalpy and entropy of adsorption (ΔHads H + and ΔSads H + ) at fixed pore-limiting diam. (PLD) generally increase (become less neg.) as the ratio of the min. to max. channel diam. decreases, and are lowest when this ratio equals 1 (corresponding to approx. circular cross-sections). The effect of a change in diam. ratio on the free energy of adsorption (ΔAads-H + ) is weak because the changes in ΔHads H + and TΔSads H + largely cancel. The addn. of cages having a largest-cavity diam. (LCD) greater than the PLD increases both ΔHads H + and ΔSads H +. Replacing channels with cages of the same diam. does not change ΔSads H + significantly when the PLD is similar to the alkane length, but decreases both ΔHads H + and ΔAads-H + because of the greater surface area of cages relative to channels. The selectivity to adsorption via a central C C bond vs. a terminal bond when cages are absent is smallest for PLDs near the alkane length, and when cages are present, is even lower when the LCD exceeds the alkane length. This effect is attributed to more rotation of the alkane in cages vs. channels. The results show that ΔAads H + at 773 K can be tuned by manipulating a characteristic dimension (LCD, PLD) and topol. (e.g., adding cages) simultaneously, in order to circumvent the compensating changes in TΔSads H + and ΔHads H + that occur upon changing only one structural parameter.**26**Fetisov, E. O.; Shah, M. S.; Long, J. R.; Tsapatsis, M.; Siepmann, J. I. First principles Monte Carlo simulations of unary and binary adsorption: CO2, N2, and H2O in Mg-MOF-74.*Chem. Commun.*2018,*54*, 10816– 10819, DOI: 10.1039/c8cc06178eGoogle Scholar26https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhsFCktr7F&md5=185a5a8b6c834353a462758e0a031fc8First principles Monte Carlo simulations of unary and binary adsorption: CO2, N2, and H2O in Mg-MOF-74Fetisov, Evgenii O.; Shah, Mansi S.; Long, Jeffrey R.; Tsapatsis, Michael; Siepmann, J. IljaChemical Communications (Cambridge, United Kingdom) (2018), 54 (77), 10816-10819CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)Dative bonding of adsorbate mols. onto coordinatively-unsatd. metal sites in metal-org. frameworks can lead to unique adsorption selectivities. However, the distortion of the electron d. during dative bonding poses a challenge for force-field-based simulations. Here, we report first principles Monte Carlo simulations with the PBE-D3 functional for the adsorption of CO2, N2, and H2O in Mg-MOF-74, and obtain accurate predictions of the unary isotherms without any of the adjustments or fitting often required for systems with strong adsorption sites. Simulations of binary CO2/N2 and H2O/CO2 mixts. yield selectivities of 200 and 160, resp., and indicate that predictions from ideal adsorbed soln. theory need to be viewed with caution.**27**Rocca, D.; Dixit, A.; Badawi, M.; Lebègue, S.; Gould, T.; Bučko, T. Bridging molecular dynamics and correlated wave-function methods for accurate finite-temperature properties.*Phys. Rev. Mater.*2019,*3*, 040801, DOI: 10.1103/physrevmaterials.3.040801Google Scholar27https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXpsFynt7o%253D&md5=0649207eb5db2b32538aaafec5d12e6cBridging molecular dynamics and correlated wave-function methods for accurate finite-temperature propertiesRocca, Dario; Dixit, Anant; Badawi, Michael; Lebegue, Sebastien; Gould, Tim; Bucko, TomasPhysical Review Materials (2019), 3 (4), 040801CODEN: PRMHBS; ISSN:2475-9953. (American Physical Society)A review. We introduce the "selPT" perturbative approach, based on ab initio mol. dynamics (AIMD), for computing accurate finite-temp. properties by efficiently using correlated wave-function methods. We demonstrate the power of the method by computing prototypical mol. enthalpies of adsorption in zeolite (CH4 and CO2 on protonated chabazite at 300 K) using the RPA. Results are in excellent agreement with expt. The improved accuracy provided by selPT represents a crucial step towards the goal of truly quant. AIMD predictions of exptl. observables at finite temp.**28**Piccini, G.; Sauer, J. Quantum Chemical Free Energies: Structure Optimization and Vibrational Frequencies in Normal Modes.*J. Chem. Theory Comput.*2013,*9*, 5038– 5045, DOI: 10.1021/ct4005504Google Scholar28https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhs1Cgtr3P&md5=ff7eebe2da0bdc213c5ee7a3050952fdQuantum Chemical Free Energies: Structure Optimization and Vibrational Frequencies in Normal ModesPiccini, GiovanniMaria; Sauer, JoachimJournal of Chemical Theory and Computation (2013), 9 (11), 5038-5045CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)A computational protocol is presented that uses normal mode coordinates for structure optimization and for obtaining harmonic frequencies by numerical differentiation. It reduces numerical accuracy problems encountered when d. functional theory with plane wave basis sets is applied to systems with flat potential energy surfaces. The approach is applied to calc. Gibbs free energies for adsorption of methane, ethane, and propane on the Bronsted acidic sites of zeolite H-CHA. The values obtained (273.15 K, 0.1 MPa,), -0.25, -5.95, and -16.76 kJ/mol, resp., follow the trend of the exptl. values, which is not the case for results obtained with the std. approach (Cartesian optimization, frequencies from Cartesian distortions). Anharmonicity effects have been approx. taken into account by solving one-dimensional Schrodinger equations along each normal mode. This leads to a systematic increase of the Gibbs free energy of adsorption of 4.5, 5.0, and 3.1 kJ/mol for methane, ethane, and propane, resp., making adsorption at a given pressure and temp. less likely. This is due to an increase of low vibrational frequencies assocd. with hindered translations and rotations of the adsorbed mols. and the floppy modes of the zeolite framework.**29**Piccini, G.; Sauer, J. Effect of Anharmonicity on Adsorption Thermodynamics.*J. Chem. Theory Comput.*2014,*10*, 2479– 2487, DOI: 10.1021/ct500291xGoogle Scholar29https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXosVamt70%253D&md5=305a84e64520643091c677c0d0d46a00Effect of Anharmonicity on Adsorption ThermodynamicsPiccini, GiovanniMaria; Sauer, JoachimJournal of Chemical Theory and Computation (2014), 10 (6), 2479-2487CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)The effect of anharmonic corrections to the vibrational energies of extended systems is explored. Particular attention is paid to the thermodn. of adsorption of small mols. on catalytically relevant systems typically affected by anharmonicity. The implemented scheme obtains one-dimensional anharmonic model potentials by distorting the equil. structure along the normal modes using both rectilinear (Cartesian) or curvilinear (internal) representations. Only in the latter case, the modes are decoupled also at higher order of the potential and the thermodn. functions change in the expected directions. The method is applied to calc. ab initio enthalpies, entropies, and Gibbs free energies for the adsorption of methane in acidic chabazite (H-CHA) and on MgO(001) surface. The values obtained for the adsorption of methane in H-CHA (273.15 K, 0.1 MPa, θ = 0.5) are ΔH = -19.3, -TΔS = 11.9, and ΔG = -7.5 kJ/mol. For methane on the MgO(001) (47 K, 1.3 × 10-14 MPa, θ = 1) ΔH = -14.4, -TΔS = 16.6, and ΔG = 2.1 kJ/mol are obtained. The calcd. desorption temp. is 44 K, and the desorption prefactor is 4.26 × 1012 s-1. All calcd. results agree within chem. accuracy limits with exptl. data.**30**Piccini, G.; Alessio, M.; Sauer, J.; Zhi, Y.; Liu, Y.; Kolvenbach, R.; Jentys, A.; Lercher, J. A. Accurate Adsorption Thermodynamics of Small Alkanes in Zeolites. Ab initio Theory and Experiment for H-Chabazite.*J. Phys. Chem. C*2015,*119*, 6128– 6137, DOI: 10.1021/acs.jpcc.5b01739Google Scholar30https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXkt1Oisbw%253D&md5=d617f794d481a436cb5cbb1c86fa2f2aAccurate Adsorption Thermodynamics of Small Alkanes in Zeolites. Ab initio Theory and Experiment for H-ChabazitePiccini, GiovanniMaria; Alessio, Maristella; Sauer, Joachim; Zhi, Yuchun; Liu, Yuanshuai; Kolvenbach, Robin; Jentys, Andreas; Lercher, Johannes A.Journal of Physical Chemistry C (2015), 119 (11), 6128-6137CODEN: JPCCCK; ISSN:1932-7447. (American Chemical Society)Heats of adsorption of methane, ethane, and propane in H-chabazite (Si/Al = 14.4) have been measured and entropies have been derived from adsorption isotherms. For these systems quantum chem. ab initio calcns. of Gibbs free energies have been performed. The deviations from the exptl. values for methane, ethane, and propane are below 3 kJ/mol for the enthalpy, and the Gibbs free energy. A hybrid high-level (MP2/CBS): low-level (DFT+dispersion) method is used to det. adsorption structures and energies. Vibrational entropies and thermal enthalpy contributions are obtained from vibrational partition functions for the DFT+dispersion potential energy surface. Anharmonic corrections have been evaluated for each normal mode sep. One-dimensional Schrodinger equations are solved for potentials obtained by (curvilinear) distortions of the normal modes using a representation in internal coordinates.**31**Njegic, B.; Gordon, M. S. Exploring the effect of anharmonicity of molecular vibrations on thermodynamic properties.*J. Chem. Phys.*2006,*125*, 224102, DOI: 10.1063/1.2395940Google Scholar31https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXht1Onug%253D%253D&md5=1cfa7641c6df19c423f1a106a12e339eExploring the effect of anharmonicity of molecular vibrations on thermodynamic propertiesNjegic, Bosiljka; Gordon, Mark S.Journal of Chemical Physics (2006), 125 (22), 224102/1-224102/12CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)Thermodn. properties of selected small and medium size mols. were calcd. using harmonic and anharmonic vibrational frequencies. Harmonic vibrational frequencies were obtained by normal mode anal., whereas anharmonic ones were calcd. using the vibrational SCF (VSCF) method. The calcd. and available exptl. thermodn. data for zero point energy, enthalpy, entropy, and heat capacity are compared. The anharmonicity and coupling of mol. vibrations can play a significant role in predicting accurate thermodn. quantities. Limitations of the current VSCF method for low frequency modes have been partially removed by following normal mode displacements in internal, rather than Cartesian, coordinates.**32**Kundu, A.; Piccini, G.; Sillar, K.; Sauer, J. Ab Initio Prediction of Adsorption Isotherms for Small Molecules in Metal–Organic Frameworks.*J. Am. Chem. Soc.*2016,*138*, 14047– 14056, DOI: 10.1021/jacs.6b08646Google Scholar32https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xhs1KqsLbK&md5=960cbf4fe313b6aa11a574258fcbb666Ab Initio Prediction of Adsorption Isotherms for Small Molecules in Metal-Organic FrameworksKundu, Arpan; Piccini, GiovanniMaria; Sillar, Kaido; Sauer, JoachimJournal of the American Chemical Society (2016), 138 (42), 14047-14056CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)For CO and N2 on Mg2+ sites of the metal-org. framework CPO-27-Mg (Mg-MOF-74), ab initio calcns. of Gibbs free energies of adsorption have been performed. Combined with the Bragg-Williams/Langmuir model and taking into account the exptl. site availability (76.5%), we obtained adsorption isotherms in close agreement with those in expt. The remaining deviations in the Gibbs free energy (about 1 kJ/mol) are significantly smaller than the "chem. accuracy" limit of about 4 kJ/mol. The presented approach uses (i) a DFT dispersion method (PBE + D2) to optimize the structure and to calc. anharmonic frequencies for vibrational partition functions and (ii) a "hybrid MP2:(PBE + D2) + ΔCCSD(T)" method to det. electronic energies. With the achieved accuracy (estd. uncertainty ±1.4 kJ/mol), the ab initio energies become useful benchmarks for assessing different DFT + dispersion methods (PBE + D2, B3LYP + D*, and vdW-D2), whereas the ab initio heats, entropies, and Gibbs free energies of adsorption are used to assess the reliability of exptl. values derived from fitting isotherms or from variable-temp. IR studies.**33**Piccini, G.; Alessio, M.; Sauer, J. Ab Initio Calculation of Rate Constants for Molecule–Surface Reactions with Chemical Accuracy.*Angew. Chem., Int. Ed.*2016,*55*, 5235– 5237, DOI: 10.1002/anie.201601534Google Scholar33https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XkvVChsb0%253D&md5=178fc9825c3a63a8359e1c525c3fcb1dAb initio Calculation of Rate Constants for Molecule-Surface Reactions with Chemical AccuracyPiccini, Giovanni Maria; Alessio, Maristella; Sauer, JoachimAngewandte Chemie, International Edition (2016), 55 (17), 5235-5237CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)The ab initio prediction of reaction rate consts. for systems with hundreds of atoms with an accuracy that is comparable to expt. is a challenge for computational quantum chem. We present a divide-and-conquer strategy that departs from the potential energy surfaces obtained by std. d. functional theory with inclusion of dispersion. The energies of the reactant and transition structures are refined by wavefunction-type calcns. for the reaction site. Thermal effects and entropies are calcd. from vibrational partition functions, and the anharmonic frequencies are calcd. sep. for each vibrational mode. This method is applied to a key reaction of an industrially relevant catalytic process, the methylation of small alkenes over zeolites. The calcd. reaction rate consts. (free energies), pre-exponential factors (entropies), and enthalpy barriers show that our computational strategy yields results that agree with expt. within chem. accuracy limits (less than one order of magnitude).**34**Bučko, T.; Hafner, J.; Ángyán, J. G. Geometry optimization of periodic systems using internal coordinates.*J. Chem. Phys.*2005,*122*, 124508Google Scholar34https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXjtFKqs7g%253D&md5=4067f672f62fc3686d023646d6320bf1Geometry optimization of periodic systems using internal coordinatesBucko, Tomas; Hafner, Jurgen; Angyan, Janos G.Journal of Chemical Physics (2005), 122 (12), 124508/1-124508/10CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)An algorithm is proposed for the structural optimization of periodic systems in internal (chem.) coordinates. Internal coordinates may include in addn. to the usual bond lengths, bond angles, out-of-plane and dihedral angles, various "lattice internal coordinates" such as cell edge lengths, cell angles, cell vol., etc. The coordinate transformations between Cartesian (or fractional) and internal coordinates are performed by a generalized Wilson B-matrix, which in contrast to the previous formulation by Kudin et al. [J. Chem. Phys. 114, 2919 (2001)] includes the explicit dependence of the lattice parameters on the positions of all unit cell atoms. The performance of the method, including constrained optimizations, is demonstrated on several examples, such as layered and microporous materials (gibbsite and chabazite) as well as the urea mol. crystal. The calcns. used energies and forces from the ab initio d. functional theory plane wave method in the projector-augmented wave formalism.**35**Zhang, D.-B.; Sun, T.; Wentzcovitch, R. M. Phonon Quasiparticles and Anharmonic Free Energy in Complex Systems.*Phys. Rev. Lett.*2014,*112*, 058501, DOI: 10.1103/PhysRevLett.112.058501Google Scholar35https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXjtlSmurk%253D&md5=e04dec8780c4fea55e37580230761a21Phonon quasiparticles and anharmonic free energy in complex systemsZhang, Dong-Bo; Sun, Tao; Wentzcovitch, Renata M.Physical Review Letters (2014), 112 (5), 058501/1-058501/5CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)We use a hybrid strategy to obtain anharmonic frequency shifts and lifetimes of phonon quasiparticles from first principles mol. dynamics simulations in modest size supercells. This approach is effective irresp. of crystal structure complexity and facilitates calcn. of full anharmonic phonon dispersions, as long as phonon quasiparticles are well defined. We validate this approach to obtain anharmonic effects with calcns. in MgSiO3 perovskite, the major Earth forming mineral phase. First, we reproduce irregular thermal frequency shifts of well characterized Raman modes. Second, we combine the phonon gas model (PGM) with quasiparticle frequencies and reproduce free energies obtained using thermodn. integration. Combining thoroughly sampled quasiparticle dispersions with the PGM we then obtain first-principles anharmonic free energy in the thermodn. limit (N → ∞).**36**Carreras, A.; Togo, A.; Tanaka, I. DynaPhoPy: A code for extracting phonon quasiparticles from molecular dynamics simulations.*Comput. Phys. Commun.*2017,*221*, 221– 234, DOI: 10.1016/j.cpc.2017.08.017Google Scholar36https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhsVWhurfO&md5=179605903557cb9f1d5c9479163c6db3DynaPhoPy: A code for extracting phonon quasiparticles from molecular dynamics simulationsCarreras, Abel; Togo, Atsushi; Tanaka, IsaoComputer Physics Communications (2017), 221 (), 221-234CODEN: CPHCBZ; ISSN:0010-4655. (Elsevier B.V.)A review. We have developed a computational code, DYNAPHOPY, that allows us to ext. the microscopic anharmonic phonon properties from mol. dynamics (MD) simulations using the normal-mode-decompn. technique as presented by Sun et al. (2014). Using this code we calcd. the quasiparticle phonon frequencies and linewidths of cryst. silicon at different temps. using both of first-principles and the Tersoff empirical potential approaches. In this work we show the dependence of these properties on the temp. using both approaches and compare them with reported exptl. data obtained by Raman spectroscopy (Balkanski et al., 1983; Tsu and Hernandez, 1982).Manuscript Title: DynaPhoPy: A code for extg. phonon quasiparticles from mol. dynamics simulationsAuthors: Abel Carreras, Atsushi Togo and Isao TanakaProgram Title: DynaPhoPyJournal Ref.:Catalog identifier:Licensing provisions: MIT LicenseProgramming language: Python and CComputer: PC and cluster computersOperating system: UNIX/OSXRAM: Depends strongly on no. of input data (several Gb)No. of processors used: 1-16Supplementary material:Keywords: anharmonicity, phonon, linewidth, frequency shift, mol. dynamicsClassification: 7.8 Structure and Lattice DynamicsExternal routines/libraries: phonopy, numpy, matplotlib, scipy and h5py python modules. Optional: FFTW and CudaSubprograms used:Catalog identifier of previous version: *Journal ref. of previous version: *Does the new version supersede the previous version: *Nature of problem:Increasing temp., a crystal potential starts to deviate from the harmonic regime and anharmonicity is getting to be evident [1]. To treat anharmonicity, perturbation approach often describes successfully phenomena such as phonon lifetime and lattice thermal cond. However it fails when the system contains large at. displacements.Soln. method:Extg. the phonon quasiparticles from mol. dynamics (MD) simulations using the normal-mode-decompn. technique.Reasons for the new version: *Summary of revisions: *Restrictions:Quantum effects of lattice dynamics are not considered.Unusual features:Addnl. comments:Running time:It is highly dependent on the type of calcn. requested. It depends mainly on the no. of atoms in the primitive cell, the no. of time steps of the MD simulation and the method employed to calc. the power spectra. Currently two methods are implemented in DyaPhoPy: The Fourier transform and the max. entropy methods. The Fourier transform method scales to O [N2] and the max. entropy method scales to O [N × M] where N is the no. of time steps and M is the no. of coeffs.**37**Peters, L. D. M.; Dietschreit, J. C. B.; Kussmann, J.; Ochsenfeld, C. Calculating free energies from the vibrational density of states function: Validation and critical assessment.*J. Chem. Phys.*2019,*150*, 194111, DOI: 10.1063/1.5079643Google Scholar37https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXpvFOlsLk%253D&md5=bdccb228a8ddc5282d129c9b1e3ca8b2Calculating free energies from the vibrational density of states function: Validation and critical assessmentPeters, Laurens D. M.; Dietschreit, Johannes C. B.; Kussmann, Joerg; Ochsenfeld, ChristianJournal of Chemical Physics (2019), 150 (19), 194111/1-194111/11CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)We explore and show the usefulness of the d. of states function for computing vibrational free energies and free energy differences between small systems. Therefore, we compare this d. of states integration method (DSI) to more established schemes such as Bennett's Acceptance Ratio method (BAR), the Normal Mode Anal. (NMA), and the Quasiharmonic Anal. (QHA). The strengths and shortcomings of all methods are highlighted with three numerical examples. Furthermore, the free energy of the ionization of ammonia and the mutation from serine to cysteine are computed using extensive ab initio mol. dynamics simulations. We conclude that DSI improves upon the other frequency-based methods (NMA and QHA) regarding the treatment of anharmonicity and yielding results comparable to BAR in all cases without the need for alchem. transformations. Low-frequency modes lead to larger errors indicating that long simulation times might be required for larger systems. In addn., we introduce the use of DSI for the localization of the vibrational free energy to specific atoms or residues, leading to insights into the underlying process, a unique feature that is only offered by this method. (c) 2019 American Institute of Physics.**38**Galimberti, D. R.; Milani, A.; Tommasini, M.; Castiglioni, C.; Gaigeot, M.-P. Combining Static and Dynamical Approaches for Infrared Spectra Calculations of Gas Phase Molecules and Clusters.*J. Chem. Theory Comput.*2017,*13*, 3802– 3813, DOI: 10.1021/acs.jctc.7b00471Google Scholar38https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhtVOnsbjJ&md5=bb5a07ba8b029c9455ce829d0b4c0453Combining Static and Dynamical Approaches for Infrared Spectra Calculations of Gas Phase Molecules and ClustersGalimberti, Daria R.; Milani, Alberto; Tommasini, Matteo; Castiglioni, Chiara; Gaigeot, Marie-PierreJournal of Chemical Theory and Computation (2017), 13 (8), 3802-3813CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)Four models for the calcn. of the IR spectrum of gas phase mols. and clusters from mol. dynamics simulations are presented with the aim to reduce the computational cost of the usual Fourier transform (FT) of the time correlation function of the dipole moment. These models are based on the VDOS, FT of time correlation function of velocities, and at. polar tensors (APT). The models differ from each other by the no. of APTs inserted into the velocities correlation function. Excellent accuracy is achieved by the model adopting a weighted linear combination of a few selected APTs adapted for the rotation of the mol. (model D). The achieved accuracy relates to band positions, band shapes, and band intensities. Depending on the degree of actual dynamics of the mol., rotational motion, conformational isomerization, and large amplitude motions that can be seen during the finite temp. trajectory, 1 could also apply 1 of the other models (models A, B, or C), but with caution. Model D is therefore found simple and accurate, with appealing computational cost and should be systematically applied. Its generalization to condensed phase systems should be straightforward.**39**Brehm, M.; Kirchner, B. TRAVIS - A Free Analyzer and Visualizer for Monte Carlo and Molecular Dynamics Trajectories.*J. Chem. Inf. Model.*2011,*51*, 2007– 2023, DOI: 10.1021/ci200217wGoogle Scholar39https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXptleqs7s%253D&md5=68eac025b6aaefd7961cba05b68e7ca3TRAVIS - A Free Analyzer and Visualizer for Monte Carlo and Molecular Dynamics TrajectoriesBrehm, Martin; Kirchner, BarbaraJournal of Chemical Information and Modeling (2011), 51 (8), 2007-2023CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)We present TRAVIS ("TRajectory Analyzer and VISualizer"), a free program package for analyzing and visualizing Monte Carlo and mol. dynamics trajectories. The aim of TRAVIS is to collect as many analyses as possible in one program, creating a powerful tool and making it unnecessary to use many different programs for evaluating simulations. This should greatly rationalize and simplify the work-flow of analyzing trajectories. TRAVIS is written in C++, open-source free-ware and licensed under the terms of the GNU General Public License (GPLv3). It is easy to install (platform independent, no external libraries) and easy to use. In this article, we present some of the algorithms that are implemented in TRAVIS - many of them widely known for a long time, but some of them also to appear in literature for the first time. All shown analyses only require a std. MD trajectory as input data.**40**Nielsen, M.; Brogaard, R. Y.; Falsig, H.; Beato, P.; Swang, O.; Svelle, S. Kinetics of Zeolite Dealumination: Insights from H-SSZ-13.*ACS Catal.*2015,*5*, 7131– 7139, DOI: 10.1021/acscatal.5b01496Google Scholar40https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhs1Glu73P&md5=76e82f86dfa5901188a8e91892ca4045Kinetics of Zeolite Dealumination: Insights from H-SSZ-13Nielsen, Malte; Brogaard, Rasmus Yding; Falsig, Hanne; Beato, Pablo; Swang, Ole; Svelle, StianACS Catalysis (2015), 5 (12), 7131-7139CODEN: ACCACS; ISSN:2155-5435. (American Chemical Society)When zeolite catalysts are subjected to steam at high temps., a permanent loss of activity happens, because of the loss of aluminum from the framework. This dealumination is a complex process involving the hydrolysis of four Al-O bonds. This work addresses the dealumination from a theor. point of view, modeling the kinetics in zeolite H-SSZ-13 to gain insights that can extend to other zeolites. We employ periodic d. functional theory (DFT) to obtain free-energy profiles, and we solve a microkinetic model to derive the rates of dealumination. We argue that such modeling should consider water that has been physisorbed in the zeolite as the ref. state and propose a scheme for deriving the free energy of this state. The results strongly suggest that the first of the four hydrolysis steps is insignificant for the kinetics of zeolite dealumination. Furthermore, the results indicate that, in H-SSZ-13, it is sufficient to include only the fourth hydrolysis step when estg. the rate of dealumination at temps. above 700 K. These are key aspects to investigate in further work on the process, particularly when comparing different zeolite frameworks.**41**Shi, L.; Yang, J.; Shen, G.; Zhao, Y.; Chen, R.; Shen, M.; Wen, Y.; Shan, B. The influence of adjacent Al atoms on the hydrothermal stability of H-SSZ-13: a first-principles study.*Phys. Chem. Chem. Phys.*2020,*22*, 2930– 2937, DOI: 10.1039/c9cp05141dGoogle Scholar41https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXisVyqsrbP&md5=0806ae3cec63974b332daa0b680a999eThe influence of adjacent Al atoms on the hydrothermal stability of H-SSZ-13: a first-principles studyShi, Lu; Yang, Jiaqiang; Shen, Gurong; Zhao, Yunkun; Chen, Rong; Shen, Meiqing; Wen, Yanwei; Shan, BinPhysical Chemistry Chemical Physics (2020), 22 (5), 2930-2937CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)The Al concn. and distribution have a great influence on the hydrothermal stability of the H-SSZ-13 zeolites in expts. First-principles calcns. are performed to clarify the decompn. mechanism of an H-SSZ-13 framework with adjacent Al atom pair distribution under hydrothermal conditions. The adjacent Al atoms have a tendency to occupy the para-sites of the 4-membered rings (4MRs) in the framework. H2O mols. are chemisorbed onto the Al atom 1 by 1, and the hydroxylation of the neighboring O atoms induces the breaking of the Al-O bonds, which causes the 1st dealumination in 4MRs. The other Al atom in the para-site can be easily removed from the framework once the 1st 1 is lost. The feasible subsequent dealumination of adjacent Al atoms would break the linker of 6MRs in the framework, which is responsible for the degraded hydrothermal stability. Also, the partial substitution of metal ions (such as Na+ and Cu+) for the protons in the framework will greatly stabilize the Al-O bonds and enlarge the energy barrier of para-site Al dealumination, which leads to the improved hydrothermal stability of H-SSZ-13.**42**Plessow, P. N.; Studt, F. Olefin methylation and cracking reactions in H-SSZ-13 investigated with ab initio and DFT calculations.*Catal. Sci. Technol.*2018,*8*, 4420– 4429, DOI: 10.1039/c8cy01194jGoogle Scholar42https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhsV2isbnL&md5=6797d0831ded189c0fa510f10ccbcc23Olefin methylation and cracking reactions in H-SSZ-13 investigated with ab initio and DFT calculationsPlessow, Philipp N.; Studt, FelixCatalysis Science & Technology (2018), 8 (17), 4420-4429CODEN: CSTAGD; ISSN:2044-4753. (Royal Society of Chemistry)The olefin cycle of the methanol-to-olefins process is investigated for the zeolite H-SSZ-13 using periodic, van-der-Waals cor. DFT calcns., together with MP2 corrections derived from cluster models, which are essential for accurate barriers. The two main reactions, olefin methylation and cracking are systematically investigated for different olefin isomers up to C9. The barrier for cracking depends sensitively on the involved cationic intermediates. The most favorable cracking reactions involve tertiary cations, in particular the t-Bu cation that leads to the formation of isobutene along with another olefin. The transition state for olefin methylation is mainly influenced by van-der-Waals interactions and is therefore stabilized for larger olefins.**43**Sarazen, M. L.; Doskocil, E.; Iglesia, E. Effects of Void Environment and Acid Strength on Alkene Oligomerization Selectivity.*ACS Catal.*2016,*6*, 7059– 7070, DOI: 10.1021/acscatal.6b02128Google Scholar43https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhsFals7nE&md5=3d2261c16a6f0a1677b5d1cc38f84d8eEffects of Void Environment and Acid Strength on Alkene Oligomerization SelectivitySarazen, Michele L.; Doskocil, Eric; Iglesia, EnriqueACS Catalysis (2016), 6 (10), 7059-7070CODEN: ACCACS; ISSN:2155-5435. (American Chemical Society)The effects of channel connectivity, void environment, and acid strength on the relative rates of oligomerization, β-scission, and isomerization reactions during light alkene conversion (ethene, propene, isobutene; 2-400 kPa alkene; 473-533 K) were examd. on microporous (TON, MFI, MOR, BEA, FAU) and mesoporous (amorphous silica-alumina (SiAl), MCM-41, Keggin POM) Bronsted acids with a broad range of confining voids and acid strength. Skeletal and regioisomers equilibrate under all conditions of pressure and conversion and on all catalysts, irresp. of their acid strength, void size, or framework connectivity, consistent with rapid hydride and Me shifts of alkoxides intermediates and with their fast adsorption-desorption steps. Such equilibration is evident from detailed chem. speciation of the products and also from intramol. isotopic scrambling in all oligomers formed from 2-13C-propene on TON, MFI, SiAl, and POM clusters. Previous claims of kinetic control of skeletal isomers in oligomerization catalysis through shape-selective effects conferred by void environments may have used inaccurate tabulated thermodn., as we show in this study. The void environment, however, influences the size distribution of the chains formed in these acid-catalyzed alkene reactions. One-dimensional microporous aluminosilicates predominantly form true oligomers, those expected from dimerization and subsequent oligomerization events for a given reactant alkene; such chains are preserved because they cannot grow to sizes that would inhibit their diffusion through essentially cylindrical channels in these frameworks. Amorphous SiAl and colloidal silica-supported POM clusters contain acid sites of very different strength; both exhibit size variations across the void space, but at length scales much larger than mol. diams., thus preserving true oligomers by allowing them to egress the void before β-scission events. Mesoporous acids of very different strength (POM, SiAl) give similar true isomer selectivities, as also obsd. on MFI structures with different heteroatoms (X-MFI, where X = Al, Ga, Fe, B), which also differ in acid strength; this insensitivity reflects oligomerization and β-scission reactions that involve similar ion-pair transition states and therefore depend similarly on the stability of the conjugate anion. Three-dimensional microporous frameworks contain voids larger than their interconnecting paths, an inherent consequence of intersecting channels and cage-window structures. As a result, oligomers can reach sizes that restrict their diffusion through the interconnections, until β-scission events form smaller and faster diffusing chains. These undulations are of mol. dimensions and their magnitude, which is defined here as the ratio of the largest scale to the smallest scale along intracrystal diffusion paths, dets. the extent to which oligomerization-scission cycles contribute to the size distribution of products. These contributions are evident in the extent to which chain size and the no. of 13C atoms in each mol. formed from 2-13C-propene approach their binomial distributions, as they do on microporous acids with significant undulations. The general nature of these conclusions is evident from the similar effects of void shape and connectivity and of acid strength on selectivity for ethene, propene, and isobutene reactants.**44**McQuarrie, D. A.*Statistical Thermodynamics*; Harper & Row, 1973.Google ScholarThere is no corresponding record for this reference.**45**Balog, E.; Becker, T.; Oettl, M.; Lechner, R.; Daniel, R.; Finney, J.; Smith, J. C. Direct Determination of Vibrational Density of States Change on Ligand Binding to a Protein.*Phys. Rev. Lett.*2004,*93*, 028103, DOI: 10.1103/PhysRevLett.93.028103Google Scholar45https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXls1Whtr0%253D&md5=5efebe3e961811528a196aa831aa4c40Direct Determination of Vibrational Density of States Change on Ligand Binding to a ProteinBalog, Erika; Becker, Torsten; Oettl, Martin; Lechner, Ruep; Daniel, Roy; Finney, John; Smith, Jeremy C.Physical Review Letters (2004), 93 (2), 028103/1-028103/4CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)The change in the vibrational d. of states of a protein (dihydrofolate reductase) on binding a ligand (methotrexate) is detd. using inelastic neutron scattering. The vibrations of the complex soften significantly relative to the unbound protein. The resulting free-energy change, which is directly detd. by the d. of states change, is found to contribute significantly to the binding equil.**46**Lin, S.-T.; Maiti, P. K.; Goddard, W. A. Dynamics and Thermodynamics of Water in PAMAM Dendrimers at Subnanosecond Time Scales.*J. Phys. Chem. B*2005,*109*, 8663– 8672, DOI: 10.1021/jp0471958Google Scholar46https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXjtFSisrg%253D&md5=5b04f64c580eae653f778eaab4da2f13Dynamics and Thermodynamics of Water in PAMAM Dendrimers at Subnanosecond Time ScalesLin, Shiang-Tai; Maiti, Prabal K.; Goddard, William A., IIIJournal of Physical Chemistry B (2005), 109 (18), 8663-8672CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)Atomistic mol. dynamics simulations are used to study generation 5 polyamidoamine (PAMAM) dendrimers immersed in a bath of water. We interpret the results in terms of three classes of water: buried water well inside of the dendrimer surface, surface water assocd. with the dendrimer-water interface, and bulk water well outside of the dendrimer. We studied the dynamic and thermodn. properties of the water at three pH values: high pH with none of the primary or tertiary amines protonated, intermediate pH with only the primary amines protonated, and low pH with all amines protonated. For all pH values we find that both buried and surface water exhibit two relaxation times: a fast relaxation (∼1 ps) corresponding to the libration motion of the water and a slow (∼20 ps) diffusional component related to the escaping of water from one domain to another. In contrast for bulk water the fast relaxation is ∼0.4 ps while the slow relaxation is ∼14 ps. These results are similar to those found in biol. systems, where the fast relaxation is ∼1 ps while the slow relaxation ranges from 20 to 1000 ps. We used the 2PT MD method to ext. the vibrational (power) spectrum and found substantial differences for the three classes of water. The translational diffusion coeff. for buried water is 11-33% (depending on pH) of the bulk value while the surface water is about 80%. The change in rotational diffusion is quite similar: 21-45% of the bulk value for buried water and 80% for surface water. This shows that translational and rotational dynamics of water are affected by the PAMAM-water interactions and due to the confinement in the interior of the dendrimer. We find that the redn. of translational or rotational diffusion is accompanied by a blue shift of the corresponding libration motions (∼10 cm-1 for translation, ∼35 cm-1 for rotation), indicating higher local force consts. for these motions. These effects are most pronounced for the lowest pH, probably because of the increased rigidity caused by the internal charges. From the vibrational d. of states we also calc. the enthalpies and entropies of the various waters. We find that water mols. are enthalpically favored near the PAMAM dendrimer: energy for surface water is ∼0.1 kcal/mol lower to that in the bulk, and ∼0.5-0.9 kcal/mol lower for buried water. In contrast, we find that both the buried and surface water are entropically unfavored: buried water is 0.9-2.2 kcal/mol lower than the bulk while the surface water is 0.1-0.2 kcal/mol lower. The net result is a thermodynamically unfavored state of the water surrounding the PAMAM dendrimer: 0.4-1.3 kcal/mol higher for buried water and 0.1-0.2 kcal/mol for surface water. This excess free energy of the surface and buried waters is released when the PAMAM dendrimer binds to DNA or metal ions, providing an extra driving force.**47**Sousa, R. L. d.; Alves, H. W. L. Ab initio calculation of the dynamical properties of PPP and PPV.*Braz. J. Phys.*2006,*36*, 501– 504, DOI: 10.1590/s0103-97332006000300072Google ScholarThere is no corresponding record for this reference.**48**Sun, T.; Zhang, D.-B.; Wentzcovitch, R. M. Dynamic stabilization of cubic CaSiO3 perovskite at high temperatures and pressures from ab initio molecular dynamics.*Phys. Rev. B: Condens. Matter Mater. Phys.*2014,*89*, 094109, DOI: 10.1103/physrevb.89.094109Google Scholar48https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXns1Gqs7w%253D&md5=7abaa088ccfd0295fcd70949e71e7546Dynamic stabilization of cubic CaSiO3 perovskite at high temperatures and pressures from ab initio molecular dynamicsSun, Tao; Zhang, Dong-Bo; Wentzcovitch, Renata M.Physical Review B: Condensed Matter and Materials Physics (2014), 89 (9), 094109/1-094109/9CODEN: PRBMDO; ISSN:1098-0121. (American Physical Society)The stability of cubic CaSiO3 perovskite (CaPv) at high temps. and pressures is investigated by vibrational normal-mode anal. We compute power spectra of mode autocorrelation functions using a recently developed hybrid approach combining ab initio mol. dynamics with lattice dynamics. These power spectra, together with the probability distributions of at. displacements, indicate that cubic CaPv is stabilized at T ∼ 600 K and P ∼ 26 GPa. We then utilize the concept of phonon quasiparticles to characterize the vibrational properties of cubic CaPv at high temp. and obtain anharmonic phonon dispersions through the whole Brillouin zone. Such temp.-dependent phonon dispersions pave the way for more accurate calcns. of free-energy, thermodn., and thermoelastic properties of cubic CaPv at Earth's lower mantle conditions.**49**Landau, L. D.; Lifshitz, E. M.*Statistical Physics*; Elsevier, 2013; Vol. 5.Google ScholarThere is no corresponding record for this reference.**50**Jones, W.; March, N. H.*Theoretical Solid State Physics*; Courier Corporation, 1985; Vol. 35.Google ScholarThere is no corresponding record for this reference.**51**Berens, P. H.; Mackay, D. H. J.; White, G. M.; Wilson, K. R. Thermodynamics and quantum corrections from molecular dynamics for liquid water.*J. Chem. Phys.*1983,*79*, 2375– 2389, DOI: 10.1063/1.446044Google Scholar51https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL3sXlsVOjtbY%253D&md5=c832fda28699084a387496f89a817df2Thermodynamics and quantum corrections from molecular dynamics for liquid waterBerens, Peter H.; Mackay, Donald H. J.; White, Gary M.; Wilson, Kent R.Journal of Chemical Physics (1983), 79 (5), 2375-89CODEN: JCPSA6; ISSN:0021-9606.It is discussed how to quantum correct the classical mech. thermodn. values available from mol. dynamics, Monte Carlo, perturbation, or integral methods in order to compare with exptl. quantum reality.**52**Kearsley, S. K. On the orthogonal transformation used for structural comparisons.*Acta Crystallogr., Sect. A: Cryst. Phys., Diffr., Theor. Gen. Crystallogr.*1989,*45*, 208– 210, DOI: 10.1107/s0108767388010128Google ScholarThere is no corresponding record for this reference.**53**Kudin, K. N.; Dymarsky, A. Y. Eckart axis conditions and the minimization of the root-mean-square deviation: Two closely related problems.*J. Chem. Phys.*2005,*122*, 224105, DOI: 10.1063/1.1929739Google Scholar53https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXlsFGls7k%253D&md5=aea31385c90766ae2e81d9eafbce7940Eckart axis conditions and the minimization of the root-mean-square deviation: Two closely related problemsKudin, Konstantin N.; Dymarsky, Anatoly Y.Journal of Chemical Physics (2005), 122 (22), 224105/1-224105/2CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)We highlight the fact that the rotation matrix minimizing the root-mean-square deviation between two mol. conformations [W. Kabsch, Acta Cryst. A32, 922 (1976)] also satisfies the Eckart axis conditions [C. Eckart, Phys. Rev. 47, 552 (1935)].**54**Mathias, G.; Ivanov, S. D.; Witt, A.; Baer, M. D.; Marx, D. Infrared Spectroscopy of Fluxional Molecules from (ab Initio) Molecular Dynamics: Resolving Large-Amplitude Motion, Multiple Conformations, and Permutational Symmetries.*J. Chem. Theory Comput.*2012,*8*, 224– 234, DOI: 10.1021/ct2006665Google Scholar54https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhsFCisLvM&md5=c2de7ef791e8977d596756deb175e86eInfrared Spectroscopy of Fluxional Molecules from (ab Initio) Molecular Dynamics: Resolving Large-Amplitude Motion, Multiple Conformations, and Permutational SymmetriesMathias, Gerald; Ivanov, Sergei D.; Witt, Alexander; Baer, Marcel D.; Marx, DominikJournal of Chemical Theory and Computation (2012), 8 (1), 224-234CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)The computation of vibrational spectra of complex mols. from time correlation functions generated by ab initio mol. dynamics simulations has made lively progress in recent years. However, the anal. of such spectra, i.e., the assignment of vibrational bands to at. motions, is by no means straightforward. In a recent article, Mathias and Baer presented a corresponding anal. method that derives generalized normal coordinates (GNCs) from mol. dynamics trajectories, which furnish band positions, band shapes, and IR intensities of the sepd. vibrational modes. This vibrational anal. technique relies on the usual quasi-rigidity assumption; i.e., at. motions are described by small oscillations around a single ref. structure. This assumption, however, breaks down if the mol. undergoes large-amplitude motion and visits different conformations along the trajectory or if the same conformation can be adopted by a different ordering of the atoms, i.e., if permutational symmetries have to be considered. Here, the authors present an extension of the GNC method that handles such cases by considering multiple ref. structures, both for different conformations and for permutational symmetries. By introducing a projection technique and computing probabilities that assign the time frames of the trajectories to these ref. structures, the vibrational spectra are split into conformational contributions via a consistent time correlation formalism. For each conformation, the permutational symmetries are resolved, which permits one to det. conformation-local GNCs for the band assignment. The working principle and the virtues of this generalization are demonstrated for the simple case of a Me group rotation. This is followed by an application to a more intricate case: Upon replacing one proton by a deuteron in protonated methane, CH5+, significant changes of its IR spectrum were obsd. since the CH4D+ isotopologue features five different isotopomers. Here, a total of 120 conformational and permutational refs. are required in the projection scheme to capture the frequent and versatile structural transitions of this small but utmost floppy mol. and to assign its IR spectrum. The extended GNC method is general. Thus, it can be applied readily to systems that require more than one ref. structure, and it can be transferred to other theor. spectroscopies that are formulated in terms of time correlation functions.**55**Iannuzzi, M.; Laio, A.; Parrinello, M. Efficient Exploration of Reactive Potential Energy Surfaces Using Car-Parrinello Molecular Dynamics.*Phys. Rev. Lett.*2003,*90*, 238302, DOI: 10.1103/physrevlett.90.238302Google Scholar55https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXksFyqsb4%253D&md5=529eba2c53f92cd9cfae4708e50303b0Efficient Exploration of Reactive Potential Energy Surfaces Using Car-Parrinello Molecular DynamicsIannuzzi, Marcella; Laio, Alessandro; Parrinello, MichelePhysical Review Letters (2003), 90 (23), 238302/1-238302/4CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)The possibility of observing chem. reactions in ab initio mol. dynamics runs is severely hindered by the short simulation time accessible. We propose a new method for accelerating the reaction process, based on the ideas of the extended Lagrangian and coarse-grained non-Markovian metadynamics. We demonstrate that by this method it is possible to simulate reactions involving complex at. rearrangements and very large energy barriers in runs of a few picoseconds.**56**Cazzaniga, M.; Micciarelli, M.; Moriggi, F.; Mahmoud, A.; Gabas, F.; Ceotto, M. Anharmonic calculations of vibrational spectra for molecular adsorbates: A divide-and-conquer semiclassical molecular dynamics approach.*J. Chem. Phys.*2020,*152*, 104104, DOI: 10.1063/1.5142682Google Scholar56https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXkvFyrs7o%253D&md5=50d14431c40293dbe4f0b386f21627b1Anharmonic calculations of vibrational spectra for molecular adsorbates: A divide-and-conquer semiclassical molecular dynamics approachCazzaniga, Marco; Micciarelli, Marco; Moriggi, Francesco; Mahmoud, Agnes; Gabas, Fabio; Ceotto, MicheleJournal of Chemical Physics (2020), 152 (10), 104104CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)A semiclassical mol. dynamics method able to reproduce the vibrational energy levels of systems composed by mols. adsorbed on solid surfaces is presented. The divide-and-conquer semiclassical method for power spectra calcns. was extended to gas-surface systems and interfaced with plane-wave electronic structure codes. The Born-Oppenheimer classical dynamics underlying the semiclassical calcn. is full dimensional, and the method includes not only the motion of the adsorbate but also those of the surface and the bulk. The vibrational spectroscopic peaks related to the adsorbate are accounted together with the most coupled phonon modes to obtain spectra amenable to phys. interpretations. The method was applied to the adsorption of CO, NO, and H2O on the anatase-TiO2 (101) surface. The semiclassical results were compared with the single-point harmonic ests. and the classical power spectra obtained from the same trajectory employed in the semiclassical calcn. CO and NO anharmonic effects of fundamental vibrations are similarly reproduced by the classical and semiclassical dynamics and H2O adsorption is fully and properly described in its overtone and combination band relevant components only by the semiclassical approach. (c) 2020 American Institute of Physics.**57**Bates, S. P.; Van Well, W. J. M.; Van Santen, R. A.; Smit, B. Configurational-Bias Monte Carlo (CB-MC) Calculations of n-Alkane Sorption in Zeolites Rho and Fer.*Mol. Simul.*1997,*19*, 301– 318, DOI: 10.1080/08927029708024159Google Scholar57https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2sXnvFWiu7s%253D&md5=067f0531d58a0f03680c270cca02cf97Configurational-bias Monte Carlo (CB-MC) calculations of n-alkane sorption in zeolites rho and ferBates, Simon P.; Van Well, Willy J. M.; Van Santen, Rutger A.; Smit, BerendMolecular Simulation (1997), 19 (5-6), 301-318CODEN: MOSIEA; ISSN:0892-7022. (Gordon & Breach Science Publishers)A newly-developed Monte Carlo method is used to simulate the energetics, location and conformation of n-alkanes from butane to decane inside all-silica polymorphs of zeolites rho and ferrierite. Sorption in ferrierite yields far larger heats of adsorption than in rho. In rho, the alkanes adopt highly coiled conformations within the α-cages of the structure, whereas in ferrierite they are confined to all-trans conformations within the 10-ring channel. Only butane is distributed over both the 8-ring and 10-ring channels of ferrierite in the approx. ratio of 1:2. An increase in temp. to 498 K has little effect on the heats of adsorption, locations or conformations of the alkanes.**58**Kresse, G.; Furthmüller, J. Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set.*Phys. Rev. B: Condens. Matter Mater. Phys.*1996,*54*, 11169– 11186, DOI: 10.1103/physrevb.54.11169Google Scholar58https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK28Xms1Whu7Y%253D&md5=9c8f6f298fe5ffe37c2589d3f970a697Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis setKresse, G.; Furthmueller, J.Physical Review B: Condensed Matter (1996), 54 (16), 11169-11186CODEN: PRBMDO; ISSN:0163-1829. (American Physical Society)The authors present an efficient scheme for calcg. the Kohn-Sham ground state of metallic systems using pseudopotentials and a plane-wave basis set. In the first part the application of Pulay's DIIS method (direct inversion in the iterative subspace) to the iterative diagonalization of large matrixes will be discussed. This approach is stable, reliable, and minimizes the no. of order Natoms3 operations. In the second part, we will discuss an efficient mixing scheme also based on Pulay's scheme. A special "metric" and a special "preconditioning" optimized for a plane-wave basis set will be introduced. Scaling of the method will be discussed in detail for non-self-consistent and self-consistent calcns. It will be shown that the no. of iterations required to obtain a specific precision is almost independent of the system size. Altogether an order Natoms2 scaling is found for systems contg. up to 1000 electrons. If we take into account that the no. of k points can be decreased linearly with the system size, the overall scaling can approach Natoms. They have implemented these algorithms within a powerful package called VASP (Vienna ab initio simulation package). The program and the techniques have been used successfully for a large no. of different systems (liq. and amorphous semiconductors, liq. simple and transition metals, metallic and semiconducting surfaces, phonons in simple metals, transition metals, and semiconductors) and turned out to be very reliable.**59**Perdew, J. P.; Burke, K.; Ernzerhof, M. Generalized Gradient Approximation Made Simple [Phys. Rev. Lett. 77, 3865 (1996)].*Phys. Rev. Lett.*1997,*78*, 1396, DOI: 10.1103/physrevlett.78.1396Google Scholar59https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2sXht1Gns7o%253D&md5=ecdb6e129b112a3a10e08cba26a083aeGeneralized gradient approximation made simple. [Erratum to document cited in CA126:51093]Perdew, John P.; Burke, Kieron; Ernzerhof, MatthiasPhysical Review Letters (1997), 78 (7), 1396CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)The errors were not reflected in the abstr. or the index entries.**60**Grimme, S. Semiempirical GGA-type density functional constructed with a long-range dispersion correction.*J. Comput. Chem.*2006,*27*, 1787– 1799, DOI: 10.1002/jcc.20495Google Scholar60https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XhtFenu7bO&md5=0b4aa16bebc3a0a2ec175d4b161ab0e4Semiempirical GGA-type density functional constructed with a long-range dispersion correctionGrimme, StefanJournal of Computational Chemistry (2006), 27 (15), 1787-1799CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)A new d. functional (DF) of the generalized gradient approxn. (GGA) type for general chem. applications termed B97-D is proposed. It is based on Becke's power-series ansatz from 1997 and is explicitly parameterized by including damped atom-pairwise dispersion corrections of the form C6·R-6. A general computational scheme for the parameters used in this correction has been established and parameters for elements up to xenon and a scaling factor for the dispersion part for several common d. functionals (BLYP, PBE, TPSS, B3LYP) are reported. The new functional is tested in comparison with other GGAs and the B3LYP hybrid functional on std. thermochem. benchmark sets, for 40 noncovalently bound complexes, including large stacked arom. mols. and group II element clusters, and for the computation of mol. geometries. Further cross-validation tests were performed for organometallic reactions and other difficult problems for std. functionals. In summary, it is found that B97-D belongs to one of the most accurate general purpose GGAs, reaching, for example for the G97/2 set of heat of formations, a mean abs. deviation of only 3.8 kcal mol-1. The performance for noncovalently bound systems including many pure van der Waals complexes is exceptionally good, reaching on the av. CCSD(T) accuracy. The basic strategy in the development to restrict the d. functional description to shorter electron correlation lengths scales and to describe situations with medium to large interat. distances by damped C6·R-6 terms seems to be very successful, as demonstrated for some notoriously difficult reactions. As an example, for the isomerization of larger branched to linear alkanes, B97-D is the only DF available that yields the right sign for the energy difference. From a practical point of view, the new functional seems to be quite robust and it is thus suggested as an efficient and accurate quantum chem. method for large systems where dispersion forces are of general importance.**61**Wilson, E. B.; Decius, J. C.; Cross, P. C.*Molecular Vibrations: The Theory of Infrared and Raman Vibrational Spectra*; Courier Corporation, 1980.Google ScholarThere is no corresponding record for this reference.

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**1**Hobza, P.; Sauer, J.; Morgeneyer, C.; Hurych, J.; Zahradnik, R. Bonding ability of surface sites on silica and their effect on hydrogen bonds. A quantum-chemical and statistical thermodynamic treatment.*J. Phys. Chem.*1981,*85*, 4061– 4067, DOI: 10.1021/j150626a0221https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL3MXmt1Kit7o%253D&md5=b9e8bcfcd2157b2b553fab62bc720255Bonding ability of surface sites on silica and their effect on hydrogen bonds. A quantum-chemical and statistical thermodynamic treatmentHobza, Pavel; Sauer, Joachim; Morgeneyer, Christoph; Hurych, Josef; Zahradnik, RudolfJournal of Physical Chemistry (1981), 85 (26), 4061-7CODEN: JPCHAX; ISSN:0022-3654.Disiloxane and silicic acid were used as mol. models (M) for -Si-O-Si- and Si-OH surface sites. The formation of hydrogen-bonded complexes between them and water was studied by combined quantum-chem. and statistical thermodn. approaches. In all of the complexes only intermol. coordinates were optimized; the resp. stabilization energy was obtained by the SCF method using a 4-31G basis set and cor. for the basis-set superposition error. A semiempirical est. of the dispersion energy was added. Vibrational frequencies for the complexes investigated were either detd. by Wilson FG anal. or estd. Thermodn. treatment was performed within the rigid rotor-harmonic oscillator-ideal gas approxn. Comparison with the formation of water dimers permits discussion of the action of silica sites (-Si-O-Si- and -SiOH acting as either proton donor or acceptor) on the hydrogen bond in water and similar media; i.e., the equil. M + (H2O)2 M...H2O + H2O were considered. It turns out that silanol groups acting as proton donors are the preferred adsorption sites and are able to perturb the hydrogen bonds in water dimers. The relatively low ability of -Si-O-Si- sites to form hydrogen bonds with water is due to both interaction energy and interaction entropy. This accounts for the hydrophobicity of microporous silica modifications. In order to understand the strong adsorption of water on surfaces with a high d. of -Si-OH groups, we consider formation of surface complexes involving two hydrogen bonds. The ability of the silanol group, acting as a proton donor, to perturb the hydrogen bond in the water dimer (modeling the hydrogen bond in the biomols.) is compared with the action of anesthetic mols. studied previously. Several reasons accounting for the different biol. response of silica and anesthetic compds. are discussed briefly.**2**Sauer, J.; Zahradník, R. Quantum Chemical Studies on Zeolites and Silica.*Int. J. Quantum Chem.*1984,*26*, 793– 822, DOI: 10.1002/qua.5602605192https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL2cXmtlGqtbk%253D&md5=d04e37bc3cbf11ac0102fd1cf9b72aaeQuantum chemical studies on zeolites and silicaSauer, Joachim; Zahradnik, RudolfInternational Journal of Quantum Chemistry (1984), 26 (5), 793-822CODEN: IJQCB2; ISSN:0020-7608.A review with 75 refs.**3**Collinge, G.; Yuk, S. F.; Nguyen, M.-T.; Lee, M.-S.; Glezakou, V.-A.; Rousseau, R. Effect of Collective Dynamics and Anharmonicity on Entropy in Heterogenous Catalysis: Building the Case for Advanced Molecular Simulations.*ACS Catal.*2020,*10*, 9236– 9260, DOI: 10.1021/acscatal.0c015013https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhsVWiu7bE&md5=ab4ac2a2ef896f38551b9591435091bdEffect of Collective Dynamics and Anharmonicity on Entropy in Heterogeneous Catalysis: Building the Case for Advanced Molecular SimulationsCollinge, Greg; Yuk, Simuck F.; Nguyen, Manh-Thuong; Lee, Mal-Soon; Glezakou, Vassiliki-Alexandra; Rousseau, RogerACS Catalysis (2020), 10 (16), 9236-9260CODEN: ACCACS; ISSN:2155-5435. (American Chemical Society)A review. A perspective is presented on the computational detn. of entropy and its effects and consequences on heterogeneous catalysis. Special attention is paid to the role of anharmonicity (a result of collective phenomena) and the deviations from the std. harmonic oscillator approxns., which can fail to provide a reliable assessment of entropy. To address these challenges, advanced methodologies are needed that can explicitly account for these thermodn. drivers through the appropriate statistical sampling of reactive free-energy surfaces. Where anharmonicity should be expected, where it was obsd. from a theor. perspective, and the methods currently employed to address it are discussed. The authors conc. on 3 types of systems where the authors obsd. major, nonnegligible anharmonic effects: (1) supported nanoparticles, where the migration of metal atoms, complexes, and entire clusters exhibit anharmonic behavior in their dynamic motion; (2) porous solids, where confinement effects distort potential energy surfaces and hinder mol. motions, resulting in large entropic terms; and (3) solid/liq. interfaces, where interactions between solvent mols. and adsorbed species can result in large solvent organization free energy and unique reactivity.**4**Sauer, J. Ab Initio Calculations for Molecule–Surface Interactions with Chemical Accuracy.*Acc. Chem. Res.*2019,*52*, 3502– 3510, DOI: 10.1021/acs.accounts.9b005064https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXit1SqsbvF&md5=9834bbb8a5046f1c60f2f40965fe7e6eAb Initio Calculations for Molecule-Surface Interactions with Chemical AccuracySauer, JoachimAccounts of Chemical Research (2019), 52 (12), 3502-3510CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)Conspectus: Atomistic understanding of complex surface phenomena such as heterogeneous catalysis or storage and sepn. of energy-relevant gases in nanoporous materials (zeolites; metal-org. frameworks, MOFs) requires knowledge about reaction energies and energy barriers for elementary steps. This is difficult to obtain from expt. since the no. of possible chem., adsorption/desorption, and diffusion steps coupled to complex reaction networks is large, and so is the no. of possible surface sites. Here is an important role of quantum chem. which can provide rate and equil. consts. for elementary steps ab initio. To be useful, the predictions have to reach chem. accuracy (4 kJ/mol) which is difficult to achieve because realistic models of the surface systems may comprise of the order of a thousand atoms. While d. functional theory (DFT) as a rule cannot be trusted to yield results within chem. accuracy limits, methods that are accurate enough (Coupled Cluster with Single, Double, and perturbative Triple Substitution, CCSD(T)) cannot be applied because of their exponential scaling with system size. This Account presents a hybrid high-level-low-level quantum method that combines DFT with dispersion for the full periodic system with 2nd order Moller-Plesset perturbation theory (MP2) for the reaction site within a mech. embedding scheme. To check if MP2 is accurate enough, the authors calc. Coupled Cluster (CC) corrections with Single, Double, and perturbatively treated Triple substitutions (CCSD(T)) for sufficiently small models of the reaction site. This multilevel hybrid MP2:DFT-D+ΔCC method yields chem. accuracy for a set of 12 mol.-surface interaction systems for which reliable exptl. data are available. For CO/MgO(001), the history of the expt.-theory comparison illustrates 2 problems: (i) Do expt. and theory look at the same surface site (ii) Does theory calc. the same quantity as derived from expt.. The hybrid MP2:DFT-D+ΔCC data set generated includes the MgO(001) surface, the Mg2(dobdc) metal-org. framework, and the proton forms of the CHA and MFI zeolites interacting with the mols. It serves 2 purposes. First, it will be useful for testing d. functionals with respect to their performance for mol.-surface interactions. Second, it establishes the hybrid MP2:DFT-D+ΔCC method as a reliable and powerful tool for ab initio predictions of adsorption and reaction energies as well as energy barriers when testing reaction mechanisms. For adsorption of small mols. in MOFs, isotherm predictions have reached a level of accuracy that deviations between theor. predictions and expts. indicate sample imperfections. For elementary steps of the industrially important MeOH-to-olefin process, hybrid MP2:PBE+D+ΔCC calcns. yield rate consts. in agreement with expt. within chem. accuracy limits, finally achieving for mol.-surface reactions which was possible so hitherto only for gas phase reactions involving ≤10 atoms.**5**Brandenburg, J. G.; Zen, A.; Fitzner, M.; Ramberger, B.; Kresse, G.; Tsatsoulis, T.; Grüneis, A.; Michaelides, A.; Alfè, D. Physisorption of Water on Graphene: Subchemical Accuracy from Many-Body Electronic Structure Methods.*J. Phys. Chem. Lett.*2019,*10*, 358– 368, DOI: 10.1021/acs.jpclett.8b036795https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXkslOgtQ%253D%253D&md5=c70fd9fa814880b69e3d97977083079bPhysisorption of Water on Graphene: Subchemical Accuracy from Many-Body Electronic Structure MethodsBrandenburg, Jan Gerit; Zen, Andrea; Fitzner, Martin; Ramberger, Benjamin; Kresse, Georg; Tsatsoulis, Theodoros; Gruneis, Andreas; Michaelides, Angelos; Alfe, DarioJournal of Physical Chemistry Letters (2019), 10 (3), 358-368CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)Wet carbon interfaces are ubiquitous in the natural world and exhibit anomalous properties, which could be exploited by emerging technologies. However, progress is limited by lack of understanding at the mol. level. Remarkably, even for the most fundamental system (a single water mol. interacting with graphene), there is no consensus on the nature of the interaction. We tackle this by performing an extensive set of complementary state-of-the-art computer simulations on some of the world's largest supercomputers. From this effort a consensus on the water-graphene interaction strength has been obtained. Our results have significant impact for the phys. understanding, as they indicate that the interaction is weaker than predicted previously. They also pave the way for more accurate and reliable studies of liq. water at carbon interfaces.**6**Sauer, J.; Ugliengo, P.; Garrone, E.; Saunders, V. R. Theoretical Study of van der Waals Complexes at Surface Sites in Comparison with the Experiment.*Chem. Rev.*1994,*94*, 2095– 2160, DOI: 10.1021/cr00031a0146https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2cXmtlyqt7o%253D&md5=a97d036b8bf8fb3313a6d596e8b29bb7Theoretical Study of van der Waals Complexes at Surface Sites in Comparison with the ExperimentSauer, J.; Ugliengo, P.; Garrone, E.; Saunders, V. R.Chemical Reviews (Washington, DC, United States) (1994), 94 (7), 2095-160CODEN: CHREAY; ISSN:0009-2665.A review with 444 refs. classifying the adsorption of van der Waals (vdW) mols. on different types of surfaces in terms of the nature of the interaction instead of the magnitude of the interaction energy. The correspondence between vdW gas-phase mols. and vdW interactions with surfaces is discussed. Exptl. techniques include calorimetry, adsorption isotherm measurement, IR spectroscopy (esp. using probe mols. (CO, NH3, H2O, MeOH, NO, etc.)), and NMR. Theor. methods for calcg. intermol. interaction energies, adsorption energies, and thermodn. functions of clusters are described in detail. Ionic materials (e.g., oxides) providing the surface sites include MgO and zeolites. The role of surface hydroxyl groups in vdW interactions (which the authors define as including H bond interactions) is emphasized.**7**Hofmann, A.; Sauer, J. The surface structure of hydroxylated and sulphated zirconia. A periodic density-functional study.*J. Phys. Chem. B*2004,*108*, 14652– 14662, DOI: 10.1021/jp049220f7https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXksVGqtL0%253D&md5=b5f954a39ef0177a2c1a491616c568c7Surface Structure of Hydroxylated and Sulfated Zirconia. A Periodic Density-Functional StudyHofmann, Alexander; Sauer, JoachimJournal of Physical Chemistry B (2004), 108 (38), 14652-14662CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)The surface structure of sulfated zirconia (SZ) is examd. by d.-functional theory (DFT) with periodic boundary conditions. Adsorption of H2O and SO3 (or H2SO4) on the (101) surface of tetragonal zirconia is studied for different loadings up to H2SO4·3H2O and 2H2SO4·2H2O per two surface unit cells (four Zr surface sites). The considered surface species include H2O, [H+,OH-], SO3, [H+,HSO4-], [2H+,SO42-], [H+,HS2O7-], and [2H+,S2O72-]. Statistical thermodn. is used to evaluate the relative stability of different surface structures for different temps. and pressures of H2O and SO3 (or H2SO4). The simulated surface phase diagrams show a strong dependency on the considered sulfur species (H2SO4 or SO3) as well as on pressure and temp. Monosulfates and pyrosulfates may occur, but higher condensated sulfates are not obsd. In agreement with IR expts., we predict transformation of water-rich structures, [SO42-,2H+,3H2O], into pyrosulfate structures, [S2O72-,2H+,H2O], during calcination. Further increase of the temp. yields adsorbed SO3 before the clean surface is reached. Water adsorbed on the t-ZrO2(101) surface leaves in three steps upon heating from 250 to 730 K at 0.01 bar pressure: physisorbed water below room temp., the first chemisorbed water at about 440 K and the last water at about 730 K.**8**Laio, A.; Rodriguez-Fortea, A.; Gervasio, F. L.; Ceccarelli, M.; Parrinello, M. Assessing the Accuracy of Metadynamics.*J. Phys. Chem. B*2005,*109*, 6714– 6721, DOI: 10.1021/jp045424k8https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXht1ygurs%253D&md5=f0946da733889a7e05d4f97f6608468bAssessing the Accuracy of MetadynamicsLaio, Alessandro; Rodriguez-Fortea, Antonio; Gervasio, Francesco Luigi; Ceccarelli, Matteo; Parrinello, MicheleJournal of Physical Chemistry B (2005), 109 (14), 6714-6721CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)Metadynamics is a powerful technique that has been successfully exploited to explore the multidimensional free energy surface of complex polyat. systems and predict transition mechanisms in very different fields, ranging from chem. and solid-state physics to biophysics. We here derive an explicit expression for the accuracy of the methodol. and provide a way to choose the parameters of the method in order to optimize its performance.**9**Trzesniak, D.; Kunz, A.-P. E.; van Gunsteren, W. F. A Comparison of Methods to Compute the Potential of Mean Force.*ChemPhysChem*2007,*8*, 162– 169, DOI: 10.1002/cphc.2006005279https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXpsFSktA%253D%253D&md5=efaa9fcddd87b53f819e2d1b6530cad0A comparison of methods to compute the potential of mean forceTrzesniak, Daniel; Kunz, Anna-Pitschna E.; van Gunsteren, Wilfred F.ChemPhysChem (2007), 8 (1), 162-169CODEN: CPCHFT; ISSN:1439-4235. (Wiley-VCH Verlag GmbH & Co. KGaA)Most processes occurring in a system are detd. by the relative free energy between two or more states because the free energy is a measure of the probability of finding the system in a given state. When the two states of interest are connected by a pathway, usually called reaction coordinate, along which the free-energy profile is detd., this profile or potential of mean force (PMF) will also yield the relative free energy of the two states. Twelve different methods to compute a PMF are reviewed and compared, with regard to their precision, for a system consisting of a pair of methane mols. in aq. soln. We analyze all combinations of the type of sampling (unbiased, umbrella-biased or constraint-biased), how to compute free energies (from d. of states or force averaging) and the type of coordinate system (internal or Cartesian) used for the PMF degree of freedom. The method of choice is constraint-bias simulation combined with force averaging for either an internal or a Cartesian PMF degree of freedom.**10**Bučko, T.; Benco, L.; Hafner, J.; Ángyán, J. Proton exchange of small hydrocarbons over acidic chabazite: Ab initio study of entropic effects.*J. Catal.*2007,*250*, 171– 183, DOI: 10.1016/j.jcat.2007.05.02510https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXotl2qsLw%253D&md5=31281f03ab09e4b1c154bed254d6845fProton exchange of small hydrocarbons over acidic chabazite: Ab initio study of entropic effectsBucko, Tomas; Benco, Lubomir; Hafner, Juergen; Angyan, Janos G.Journal of Catalysis (2007), 250 (1), 171-183CODEN: JCTLA5; ISSN:0021-9517. (Elsevier Ltd.)The proton-exchange reaction of a series of short hydrocarbons over an acidic zeolite (chabazite) was studied using periodic d. functional theory (DFT) calcns. It was found that the chain length of hydrocarbons does not have a significant effect on the height of the potential-energy barrier. The exptl. obsd. regioselectivity between Me and methylene groups in propane and between Me and methine groups in isobutane was shown to be an entropic effect. In addn. to the direct H-exchange, a mechanism mediated by a methylpropene mol. recently suggested by experimentalists was explored. It was found that entropy plays a very important role in driving the reaction.**11**Rey, J.; Gomez, A.; Raybaud, P.; Chizallet, C.; Bučko, T. On the origin of the difference between type A and type B skeletal isomerization of alkenes catalyzed by zeolites: The crucial input of ab initio molecular dynamics.*J. Catal.*2019,*373*, 361– 373, DOI: 10.1016/j.jcat.2019.04.01411https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXot12jt78%253D&md5=eaa14cd9b2f4915b494fb248f67375d6On the origin of the difference between type A and type B skeletal isomerization of alkenes catalyzed by zeolites: The crucial input of ab initio molecular dynamicsRey, Jerome; Gomez, Axel; Raybaud, Pascal; Chizallet, Celine; Bucko, TomasJournal of Catalysis (2019), 373 (), 361-373CODEN: JCTLA5; ISSN:0021-9517. (Elsevier Inc.)Alkene skeletal isomerization elementary steps catalyzed by acid zeolites are key reactions in refining, petrochem. and biomass conversion. We unravel the at.-scale origin of the higher rate const. of type A isomerization (involving a direct alkyl transfer, without any change in the branching degree) than the one of type B isomerization (involving non-classical carbonium ions such as protonated cyclopropane (PCP), inducing a change in the branching degree) of C7 carbenium ions in chabazite. Accurate free energy barriers are calcd. at 300 and 500 K for both reactions by means of mol. dynamics in combination with blue moon ensemble approach, whereas the static approach is shown to fail to describe these reactions. The slow transformation between individual rotational isomers, causing non-ergodic sampling of reactant state, largely overlooked in literature, is carefully addressed in the present work. At 500 K (representative of exptl. conditions), free energy barriers of 83.4 kJ/mol and 15.0 kJ/mol are detd. for type B and type A isomerization resp. The much lower barrier for type A is thus recovered, and assigned to a loose transition state, with free rotation of the migrating alkyl group, while the transition state of type B isomerization is tighter, with such a rotation blocked, due to the simultaneous hydride shift taking place on the edge of the PCP.**12**Barducci, A.; Bussi, G.; Parrinello, M. Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method.*Phys. Rev. Lett.*2008,*100*, 020603, DOI: 10.1103/PhysRevLett.100.02060312https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXovFensQ%253D%253D&md5=701ccfeee476c2e9a5d1e5a6b0e82197Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy MethodBarducci, Alessandro; Bussi, Giovanni; Parrinello, MichelePhysical Review Letters (2008), 100 (2), 020603/1-020603/4CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)We present a method for detg. the free-energy dependence on a selected no. of collective variables using an adaptive bias. The formalism provides a unified description which has metadynamics and canonical sampling as limiting cases. Convergence and errors can be rigorously and easily controlled. The parameters of the simulation can be tuned so as to focus the computational effort only on the phys. relevant regions of the order parameter space. The algorithm is tested on the reconstruction of an alanine dipeptide free-energy landscape.**13**Muñoz-Santiburcio, D.; Marx, D. Chemistry in nanoconfined water.*Chem. Sci.*2017,*8*, 3444– 3452, DOI: 10.1039/c6sc04989c13https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXksVyjtbo%253D&md5=95a211a58f29adb2812b4ecc7dfb2711Chemistry in nanoconfined waterMunoz-Santiburcio, Daniel; Marx, DominikChemical Science (2017), 8 (5), 3444-3452CODEN: CSHCCN; ISSN:2041-6520. (Royal Society of Chemistry)Nanoconfined liqs. have extremely different properties from the bulk, which profoundly affects chem. reactions taking place in nanosolvation. Here, we present extensive ab initio simulations of a vast set of chem. reactions within a water lamella that is nanoconfined by mineral surfaces, which might be relevant to prebiotic peptide formation in aq. environments. Our results disclose a rich interplay of distinct effects, from steric factors typical of reactions occurring in small spaces to a charge-stabilization effect in nanoconfined water at extreme conditions similar to that obsd. in bulk water when changing from extreme to ambient conditions. These effects are found to modify significantly not only the energetics but also the mechanisms of reactions happening in nanoconfined water in comparison to the corresponding bulk regime.**14**Steinmann, C.; Olsson, M. A.; Ryde, U. Relative Ligand-Binding Free Energies Calculated from Multiple Short QM/MM MD Simulations.*J. Chem. Theory Comput.*2018,*14*, 3228– 3237, DOI: 10.1021/acs.jctc.8b0008114https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXpslaisbs%253D&md5=0756c0de92c581bc323f6122019b0479Relative Ligand-Binding Free Energies Calculated from Multiple Short QM/MM MD SimulationsSteinmann, Casper; Olsson, Martin A.; Ryde, UlfJournal of Chemical Theory and Computation (2018), 14 (6), 3228-3237CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)We have devised a new efficient approach to compute combined quantum mech. (QM) and mol. mech. (MM, i.e. QM/MM) ligand-binding relative free energies. Our method employs the ref.-potential approach with free-energy perturbation both at the MM level (between the two ligands) and from MM to QM/MM (for each ligand). To ensure that converged results are obtained for the MM → QM/MM perturbations, explicit QM/MM mol. dynamics (MD) simulations are performed with two intermediate mixed states. To speed up the calcns., we utilize the fact that the phase space can be extensively sampled at the MM level. Therefore, we run many short QM/MM MD simulations started from snapshots of the MM simulations, instead of a single long simulation. As a test case, we study the binding of nine cyclic carboxylate ligands to the octa-acid deep cavitand. Only the ligand is in the QM system, treated with the semiempirical PM6-DH + method. We show that for eight of the ligands, we obtain well converged results with short MD simulations (1-15 ps). However, in one case, the convergence is slower (∼50 ps) owing to a mismatch between the conformational preferences of the MM and QM/MM potentials. We test the effect of initial minimization, the need of equilibration, and how many independent simulations are needed to reach a certain precision. The results show that the present approach is about four times faster than using std. MM → QM/MM free-energy perturbations with the same accuracy and precision.**15**Amsler, J.; Plessow, P. N.; Studt, F.; Bučko, T. Anharmonic Correction to Adsorption Free Energy from DFT-Based MD Using Thermodynamic Integration.*J. Chem. Theory Comput.*2021,*17*, 1155– 1169, DOI: 10.1021/acs.jctc.0c0102215https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXhvVWks7s%253D&md5=d46cca0400079914a19d7a4ebe8f0cb5Anharmonic Correction to Adsorption Free Energy from DFT-Based MD Using Thermodynamic IntegrationAmsler, Jonas; Plessow, Philipp N.; Studt, Felix; Bucko, TomasJournal of Chemical Theory and Computation (2021), 17 (2), 1155-1169CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)Adsorption processes are often governed by weak interactions for which the estn. of entropy contributions by the harmonic approxn. is prone to be inaccurate. Thermodn. integration (TI) from the harmonic to the fully interacting system (λ-path integration) can be used to compute anharmonic corrections. Here, the authors combine TI with (curvilinear) internal coordinates in periodic systems to make the formalism available in computational studies. Implementation of ab initio mol. dynamics in VASP is independent of the reaction path and can be thus applied to study adsorption processes relative to the gas phase and does hence provide a useful tool for computational catalysis. The application of the approach on 3 model systems for which exact semianal. solns. exist and illustrate and quantify the importance of anharmonic vibrations, hindered rotations, and hindered translations (dissocn.) are discussed. Eventually, the authors apply the method to study the adsorption of small adsorbates in a zeolite (H-SSZ-13).**16**Rod, T. H.; Ryde, U. Accurate QM/MM Free Energy Calculations of Enzyme Reactions: Methylation by Catechol O-Methyltransferase.*J. Chem. Theory Comput.*2005,*1*, 1240– 1251, DOI: 10.1021/ct050110216https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXpt1CntrY%253D&md5=28b8c0949050ce98c001f67afb90c6f2Accurate QM/MM Free Energy Calculations of Enzyme Reactions: Methylation by Catechol O-MethyltransferaseRod, Thomas H.; Ryde, UlfJournal of Chemical Theory and Computation (2005), 1 (6), 1240-1251CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)We recently described a method to compute accurate quantum mech. free energies [Rod, T. H.; Ryde, U. Phys. Rev. Lett. 2005, 94, 138302]. The method, which we term quantum mech. thermodn. cycle perturbation (QTCP), employs a mol. mechanics force field to sample phase space and, subsequently, a thermodn. cycle to est. QM/MM free energy changes. Here, we discuss the methodol. in detail and test an approach based on a different thermodn. cycle. We also show that a new way of treating hydrogen link atoms makes the free energy changes converge faster and that extrapolation to higher accuracy can be performed. We finally discuss the quantum mech. free energy (QM/MM-FE) method in the framework of the QTCP method. All methods considered are applied to the methylation of catecholate catalyzed by catechol O-methyltransferase. We compute the free energy barrier for the reaction by computing free energy changes in steps between fixed QM regions along a predetd. reaction pathway. Using the QTCP approach, an extrapolated activation free energy of 69 kJ/mol for the forward reaction and 90 kJ/mol for the reverse reaction are obtained at the level of the B3LYP functional and the 6-311++G(2d,2p) basis set. The value for the forward reaction is in excellent agreement with the exptl. value of 75 kJ/mol. Results based on the QM/MM-FE method differ by less than 10 kJ/mol from those values, indicating that QM/MM-FE may be a fairly accurate and cheap alternative to calc. QM/MM free energy changes. Moreover, the results are compared to barriers obtained with a fixed mol. mechanics environment as well as with structures optimized in a vacuum. All the computed free energy barriers are well converged. A major approxn. in the current implementation of the QTCP method is that the QM region is fixed. The approxn. leads to well-converged free energy barriers, which has been a problem in similar studies.**17**Smit, B.; Maesen, T. L. M. Molecular Simulations of Zeolites: Adsorption, Diffusion, and Shape Selectivity.*Chem. Rev.*2008,*108*, 4125– 4184, DOI: 10.1021/cr800264217https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXhtFKlurrL&md5=7a607f8f328c57fb1c88a004d4cf04daMolecular Simulations of Zeolites: Adsorption, Diffusion, and Shape SelectivitySmit, Berend; Maesen, Theo L. M.Chemical Reviews (Washington, DC, United States) (2008), 108 (10), 4125-4184CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)A review. Details of simulation studies for adsorption, diffusion, and shape selectivity on zeolites have been reviewed.**18**Bučko, T.; Benco, L.; Hafner, J.; Ángyán, J. G. Monomolecular cracking of propane over acidic chabazite: An ab initio molecular dynamics and transition path sampling study.*J. Catal.*2011,*279*, 220– 22818https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXjsFWmtb8%253D&md5=583b9bd4dbadfbfd464d7380fd0e51a0Monomolecular cracking of propane over acidic chabazite: An ab initio molecular dynamics and transition path sampling studyBucko, Tomas; Benco, Lubomir; Hafner, Juergen; Angyan, Janos G.Journal of Catalysis (2011), 279 (1), 220-228CODEN: JCTLA5; ISSN:0021-9517. (Elsevier Inc.)The monomol. Haag-Dessau mechanism for propane cracking over acidic chabazite has been studied using dispersion-cor. periodic DFT calcns. in combination with ab initio mol. dynamics (AIMD) simulations, transition path sampling (TPS), and free-energy integrations. The AIMD simulations show that due to the weak specific interaction of the satd. mol. with Bronsted acid sites, the adsorption energy is considerably reduced at elevated temp. and that only a fraction of the mols. adsorbed within the zeolite is sufficiently close to the acid site to form a reactant complex for protonation. TPS shows that the preferred reaction mechanism is the protonation of a terminal Me group. The direct proton attack on the C-C bond between the Me and methylene groups is not excluded but occurs with lower probability. The intrinsic reaction parameters such as free energy and entropy of activation are detd. using thermodn. integration based on constrained mol. dynamics simulations.**19**Laio, A.; Parrinello, M. Escaping free-energy minima.*Proc. Natl. Acad. Sci. U.S.A.*2002,*99*, 12562– 12566, DOI: 10.1073/pnas.20242739919https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38XnvFGiurc%253D&md5=48d5bc7436f3ef9d78369671e70fa608Escaping free-energy minimaLaio, Alessandro; Parrinello, MicheleProceedings of the National Academy of Sciences of the United States of America (2002), 99 (20), 12562-12566CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)We introduce a powerful method for exploring the properties of the multidimensional free energy surfaces (FESs) of complex many-body systems by means of coarse-grained non-Markovian dynamics in the space defined by a few collective coordinates. A characteristic feature of these dynamics is the presence of a history-dependent potential term that, in time, fills the min. in the FES, allowing the efficient exploration and accurate detn. of the FES as a function of the collective coordinates. We demonstrate the usefulness of this approach in the case of the dissocn. of a NaCl mol. in water and in the study of the conformational changes of a dialanine in soln.**20**Pietrucci, F.; Saitta, A. M. Formamide reaction network in gas phase and solution via a unified theoretical approach: Toward a reconciliation of different prebiotic scenarios.*Proc. Natl. Acad. Sci. U.S.A.*2015,*112*, 15030– 15035, DOI: 10.1073/pnas.151248611220https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhvFWqs7%252FF&md5=c97eca22e01430d5ceeca39542740feaFormamide reaction network in gas phase and solution via a unified theoretical approach: Toward a reconciliation of different prebiotic scenariosPietrucci, Fabio; Saitta, Antonino MarcoProceedings of the National Academy of Sciences of the United States of America (2015), 112 (49), 15030-15035CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)Increasing exptl. and theor. evidence points to formamide as a possible hub in the complex network of prebiotic chem. reactions leading from simple precursors like H2, H2O, N2, NH3, CO, and CO2 to key biol. mols. like proteins, nucleic acids, and sugars. We present an in-depth computational study of the formation and decompn. reaction channels of formamide by means of ab initio mol. dynamics. To this aim we introduce a new theor. method combining the metadynamics sampling scheme with a general purpose topol. formulation of collective variables able to track a wide range of different reaction mechanisms. Our approach is flexible enough to discover multiple pathways and intermediates starting from minimal insight on the systems, and it allows passing in a seamless way from reactions in gas phase to reactions in liq. phase, with the solvent active role fully taken into account. We obtain crucial new insight into the interplay of the different formamide reaction channels and into environment effects on pathways and barriers. In particular, our results indicate a similar stability of formamide and hydrogen cyanide in soln. as well as their relatively facile interconversion, thus reconciling expts. and theory and, possibly, two different and competing prebiotic scenarios. Moreover, although not explicitly sought, formic acid/ammonium formate is produced as an important formamide decompn. byproduct in soln.**21**Alexopoulos, K.; Lee, M.-S.; Liu, Y.; Zhi, Y.; Liu, Y.; Reyniers, M.-F.; Marin, G. B.; Glezakou, V.-A.; Rousseau, R.; Lercher, J. A. Anharmonicity and Confinement in Zeolites: Structure, Spectroscopy, and Adsorption Free Energy of Ethanol in H-ZSM-5.*J. Phys. Chem. C*2016,*120*, 7172– 7182, DOI: 10.1021/acs.jpcc.6b0092321https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xks1eitbc%253D&md5=f5b61bae1a3edc2e03e7fe11be723ee8Anharmonicity and Confinement in Zeolites: Structure, Spectroscopy, and Adsorption Free Energy of Ethanol in H-ZSM-5Alexopoulos, Konstantinos; Lee, Mal-Soon; Liu, Yue; Zhi, Yuchun; Liu, Yuanshuai; Reyniers, Marie-Francoise; Marin, Guy B.; Glezakou, Vassiliki-Alexandra; Rousseau, Roger; Lercher, Johannes A.Journal of Physical Chemistry C (2016), 120 (13), 7172-7182CODEN: JPCCCK; ISSN:1932-7447. (American Chemical Society)To account for thermal and entropic effects caused by the dynamics of the motion of the reaction intermediates, ethanol adsorption on the Bronsted acid site of the H-ZSM-5 catalyst has been studied at different temps. and ethanol loadings using ab initio mol. dynamics (AIMD) simulations, IR (IR) spectroscopy, and calorimetric measurements. At low temps. (T ≤ 400 K) and ethanol loading, a single ethanol mol. adsorbed in H-ZSM-5 forms a Zundel-like structure where the proton is equally shared between the oxygen of the zeolite and the oxygen of the alc. At higher ethanol loading, a second ethanol mol. helps to stabilize the protonated ethanol at all temps. by acting as a solvating agent. The vibrational d. of states (VDOS), as calcd. from the AIMD simulations, are in excellent agreement with measured IR spectra for C2H5OH, C2H5OD, and C2D5OH isotopomers and support the existence of both monomers and dimers. A quasi-harmonic approxn. (QHA), applied to the VDOS obtained from the AIMD simulations, provides ests. of adsorption free energy within ∼10 kJ/mol of the exptl. detd. quantities, whereas the traditional approach, employing harmonic frequencies from a single ground state min., strongly overestimates the adsorption free energy by at least 20∼50 kJ/mol. This discrepancy is traced back to the inability of the harmonic approxn. to represent the contributions to the vibrational motions of the ethanol mol. upon confinement in the zeolite.**22**Cnudde, P.; De Wispelaere, K.; Vanduyfhuys, L.; Demuynck, R.; Van der Mynsbrugge, J.; Waroquier, M.; Van Speybroeck, V. How Chain Length and Branching Influence the Alkene Cracking Reactivity on H-ZSM-5.*ACS Catal.*2018,*8*, 9579– 9595, DOI: 10.1021/acscatal.8b0177922https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhs1GmsbzO&md5=dbd3738ed1b6b05923ae9b97cfecad16How Chain Length and Branching Influence the Alkene Cracking Reactivity on H-ZSM-5Cnudde, Pieter; De Wispelaere, Kristof; Vanduyfhuys, Louis; Demuynck, Ruben; Van der Mynsbrugge, Jeroen; Waroquier, Michel; Van Speybroeck, VeroniqueACS Catalysis (2018), 8 (10), 9579-9595CODEN: ACCACS; ISSN:2155-5435. (American Chemical Society)Catalytic alkene cracking on H-ZSM-5 involves a complex reaction network with many possible reaction routes and often elusive intermediates. Herein, advanced mol. dynamics simulations at 773 K, a typical cracking temp., are performed to clarify the nature of the intermediates and to elucidate dominant cracking pathways at operating conditions. A series of C4-C8 alkene intermediates are investigated to evaluate the influence of chain length and degree of branching on their stability. Our simulations reveal that linear, secondary carbenium ions are relatively unstable, although their lifetime increases with carbon no. Tertiary carbenium ions, on the other hand, are shown to be very stable, irresp. of the chain length. Highly branched carbenium ions, though, tend to rapidly rearrange into more stable cationic species, either via cracking or isomerization reactions. Dominant cracking pathways were detd. by combining these insights on carbenium ion stability with intrinsic free energy barriers for various octene β-scission reactions, detd. via umbrella sampling simulations at operating temp. (773 K). Cracking modes A (3° → 3°) and B2 (3° → 2°) are expected to be dominant at operating conditions, whereas modes B1 (2° → 3°), C (2° → 2°), D2 (2° → 1°), and E2 (3° → 1°) are expected to be less important. All β-scission modes in which a transition state with primary carbocation character is involved have high intrinsic free energy barriers. Reactions starting from secondary carbenium ions will contribute less as these intermediates are short living at the high cracking temp. Our results show the importance of simulations at operating conditions to properly evaluate the carbenium ion stability for β-scission reactions and to assess the mobility of all species in the pores of the zeolite.**23**Cnudde, P.; De Wispelaere, K.; Van der Mynsbrugge, J.; Waroquier, M.; Van Speybroeck, V. Effect of temperature and branching on the nature and stability of alkene cracking intermediates in H-ZSM-5.*J. Catal.*2017,*345*, 53– 69, DOI: 10.1016/j.jcat.2016.11.01023https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhvFGrur%252FL&md5=3f1f86fe905e17804f167ebc784dff01Effect of temperature and branching on the nature and stability of alkene cracking intermediates in H-ZSM-5Cnudde, P.; De Wispelaere, K.; Van der Mynsbrugge, J.; Waroquier, M.; Van Speybroeck, V.Journal of Catalysis (2017), 345 (), 53-69CODEN: JCTLA5; ISSN:0021-9517. (Elsevier Inc.)Catalytic cracking of alkenes takes place at elevated temps. in the order of 773-833 K. In this work, the nature of the reactive intermediates at typical reaction conditions is studied in H-ZSM-5 using a complementary set of modeling tools. Ab initio static and mol. dynamics simulations are performed on different C4-C5 alkene cracking intermediates to identify the reactive species in terms of temp. At 323 K, the prevalent intermediates are linear alkoxides, alkene π-complexes and tertiary carbenium ions. At a typical cracking temp. of 773 K, however, both secondary and tertiary alkoxides are unlikely to exist in the zeolite channels. Instead, more stable carbenium ion intermediates are found. Branched tertiary carbenium ions are very stable, while linear carbenium ions are predicted to be metastable at high temp. Our findings confirm that carbenium ions, rather than alkoxides, are reactive intermediates in catalytic alkene cracking at 773 K.**24**Janda, A.; Vlaisavljevich, B.; Lin, L.-C.; Mallikarjun Sharada, S.; Smit, B.; Head-Gordon, M.; Bell, A. T. Adsorption Thermodynamics and Intrinsic Activation Parameters for Monomolecular Cracking of n-Alkanes on Brønsted Acid Sites in Zeolites.*J. Phys. Chem. C*2015,*119*, 10427– 10438, DOI: 10.1021/acs.jpcc.5b0171524https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXms1Ohsr0%253D&md5=b45a34de6cf0ea727ee57554f6486edfAdsorption Thermodynamics and Intrinsic Activation Parameters for Monomolecular Cracking of n-Alkanes on Bronsted Acid Sites in ZeolitesJanda, Amber; Vlaisavljevich, Bess; Lin, Li-Chiang; Mallikarjun Sharada, Shaama; Smit, Berend; Head-Gordon, Martin; Bell, Alexis T.Journal of Physical Chemistry C (2015), 119 (19), 10427-10438CODEN: JPCCCK; ISSN:1932-7447. (American Chemical Society)Exptl. measurements of the rate coeff. (kapp) and apparent enthalpies and entropies of activation (ΔHapp and ΔSapp) for alkane cracking catalyzed by acidic zeolites can be used to characterize the effects of zeolite structure and alkane size on the intrinsic enthalpy and entropy of activation, ΔH⧺int and ΔS⧺int. To det. ΔH⧺int and ΔS⧺int, enthalpies and entropies of adsorption, ΔHads-H+ and ΔSads-H+, must be detd. for alkane mols. moving from the gas phase to Bronsted acid sites at reaction temps. (>673 K). Exptl. values of ΔHapp and ΔSapp must also be properly defined in terms of ΔHads-H+ and ΔSads-H+. We report here a method for detg. ΔHads-H+ and ΔSads-H+ in which the adsorption site is represented by a fixed vol. that includes the proton. Values of ΔHads-H+ and ΔSads-H+ obtained from Monte Carlo simulations are in good agreement with values obtained from exptl. data measured at 300-400 K. An important feature of the simulations, however, is their ability to account for the redistribution of alkane adsorbed at protons in different locations with increasing temp. Values of ΔH⧺int and ΔS⧺int for the cracking of propane through n-hexane, detd. from measured values of kapp and ΔHapp and simulated values of ΔHads-H+ and ΔSads-H+, agree well with values obtained independently from quantum mechanics/mol. mechanics calcns. Application of our method of anal. reveals that the obsd. increase in kapp with increasing n-alkane size is due primarily to a decrease in ΔH⧺int with increasing chain length and that ΔS⧺int is independent of chain length.**25**Janda, A.; Vlaisavljevich, B.; Smit, B.; Lin, L.-C.; Bell, A. T. Effects of Pore and Cage Topology on the Thermodynamics of n-Alkane Adsorption at Brønsted Protons in Zeolites at High Temperature.*J. Phys. Chem. C*2017,*121*, 1618– 1638, DOI: 10.1021/acs.jpcc.6b0970325https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XitFWgt7jJ&md5=f6ff94ee25a0aa6edd5ee11218e554afEffects of Pore and Cage Topology on the Thermodynamics of n-Alkane Adsorption at Bronsted Protons in Zeolites at High TemperatureJanda, Amber; Vlaisavljevich, Bess; Smit, Berend; Lin, Li-Chiang; Bell, Alexis T.Journal of Physical Chemistry C (2017), 121 (3), 1618-1638CODEN: JPCCCK; ISSN:1932-7447. (American Chemical Society)Monte Carlo simulations are used to systematically investigate the effects of structural topol. on the thermodn. of n-alkanes adsorbed at Bronsted protons in zeolites having one-dimensional channel systems. In zeolites without cages, the enthalpy and entropy of adsorption (ΔHads H + and ΔSads H + ) at fixed pore-limiting diam. (PLD) generally increase (become less neg.) as the ratio of the min. to max. channel diam. decreases, and are lowest when this ratio equals 1 (corresponding to approx. circular cross-sections). The effect of a change in diam. ratio on the free energy of adsorption (ΔAads-H + ) is weak because the changes in ΔHads H + and TΔSads H + largely cancel. The addn. of cages having a largest-cavity diam. (LCD) greater than the PLD increases both ΔHads H + and ΔSads H +. Replacing channels with cages of the same diam. does not change ΔSads H + significantly when the PLD is similar to the alkane length, but decreases both ΔHads H + and ΔAads-H + because of the greater surface area of cages relative to channels. The selectivity to adsorption via a central C C bond vs. a terminal bond when cages are absent is smallest for PLDs near the alkane length, and when cages are present, is even lower when the LCD exceeds the alkane length. This effect is attributed to more rotation of the alkane in cages vs. channels. The results show that ΔAads H + at 773 K can be tuned by manipulating a characteristic dimension (LCD, PLD) and topol. (e.g., adding cages) simultaneously, in order to circumvent the compensating changes in TΔSads H + and ΔHads H + that occur upon changing only one structural parameter.**26**Fetisov, E. O.; Shah, M. S.; Long, J. R.; Tsapatsis, M.; Siepmann, J. I. First principles Monte Carlo simulations of unary and binary adsorption: CO2, N2, and H2O in Mg-MOF-74.*Chem. Commun.*2018,*54*, 10816– 10819, DOI: 10.1039/c8cc06178e26https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhsFCktr7F&md5=185a5a8b6c834353a462758e0a031fc8First principles Monte Carlo simulations of unary and binary adsorption: CO2, N2, and H2O in Mg-MOF-74Fetisov, Evgenii O.; Shah, Mansi S.; Long, Jeffrey R.; Tsapatsis, Michael; Siepmann, J. IljaChemical Communications (Cambridge, United Kingdom) (2018), 54 (77), 10816-10819CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)Dative bonding of adsorbate mols. onto coordinatively-unsatd. metal sites in metal-org. frameworks can lead to unique adsorption selectivities. However, the distortion of the electron d. during dative bonding poses a challenge for force-field-based simulations. Here, we report first principles Monte Carlo simulations with the PBE-D3 functional for the adsorption of CO2, N2, and H2O in Mg-MOF-74, and obtain accurate predictions of the unary isotherms without any of the adjustments or fitting often required for systems with strong adsorption sites. Simulations of binary CO2/N2 and H2O/CO2 mixts. yield selectivities of 200 and 160, resp., and indicate that predictions from ideal adsorbed soln. theory need to be viewed with caution.**27**Rocca, D.; Dixit, A.; Badawi, M.; Lebègue, S.; Gould, T.; Bučko, T. Bridging molecular dynamics and correlated wave-function methods for accurate finite-temperature properties.*Phys. Rev. Mater.*2019,*3*, 040801, DOI: 10.1103/physrevmaterials.3.04080127https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXpsFynt7o%253D&md5=0649207eb5db2b32538aaafec5d12e6cBridging molecular dynamics and correlated wave-function methods for accurate finite-temperature propertiesRocca, Dario; Dixit, Anant; Badawi, Michael; Lebegue, Sebastien; Gould, Tim; Bucko, TomasPhysical Review Materials (2019), 3 (4), 040801CODEN: PRMHBS; ISSN:2475-9953. (American Physical Society)A review. We introduce the "selPT" perturbative approach, based on ab initio mol. dynamics (AIMD), for computing accurate finite-temp. properties by efficiently using correlated wave-function methods. We demonstrate the power of the method by computing prototypical mol. enthalpies of adsorption in zeolite (CH4 and CO2 on protonated chabazite at 300 K) using the RPA. Results are in excellent agreement with expt. The improved accuracy provided by selPT represents a crucial step towards the goal of truly quant. AIMD predictions of exptl. observables at finite temp.**28**Piccini, G.; Sauer, J. Quantum Chemical Free Energies: Structure Optimization and Vibrational Frequencies in Normal Modes.*J. Chem. Theory Comput.*2013,*9*, 5038– 5045, DOI: 10.1021/ct400550428https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhs1Cgtr3P&md5=ff7eebe2da0bdc213c5ee7a3050952fdQuantum Chemical Free Energies: Structure Optimization and Vibrational Frequencies in Normal ModesPiccini, GiovanniMaria; Sauer, JoachimJournal of Chemical Theory and Computation (2013), 9 (11), 5038-5045CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)A computational protocol is presented that uses normal mode coordinates for structure optimization and for obtaining harmonic frequencies by numerical differentiation. It reduces numerical accuracy problems encountered when d. functional theory with plane wave basis sets is applied to systems with flat potential energy surfaces. The approach is applied to calc. Gibbs free energies for adsorption of methane, ethane, and propane on the Bronsted acidic sites of zeolite H-CHA. The values obtained (273.15 K, 0.1 MPa,), -0.25, -5.95, and -16.76 kJ/mol, resp., follow the trend of the exptl. values, which is not the case for results obtained with the std. approach (Cartesian optimization, frequencies from Cartesian distortions). Anharmonicity effects have been approx. taken into account by solving one-dimensional Schrodinger equations along each normal mode. This leads to a systematic increase of the Gibbs free energy of adsorption of 4.5, 5.0, and 3.1 kJ/mol for methane, ethane, and propane, resp., making adsorption at a given pressure and temp. less likely. This is due to an increase of low vibrational frequencies assocd. with hindered translations and rotations of the adsorbed mols. and the floppy modes of the zeolite framework.**29**Piccini, G.; Sauer, J. Effect of Anharmonicity on Adsorption Thermodynamics.*J. Chem. Theory Comput.*2014,*10*, 2479– 2487, DOI: 10.1021/ct500291x29https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXosVamt70%253D&md5=305a84e64520643091c677c0d0d46a00Effect of Anharmonicity on Adsorption ThermodynamicsPiccini, GiovanniMaria; Sauer, JoachimJournal of Chemical Theory and Computation (2014), 10 (6), 2479-2487CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)The effect of anharmonic corrections to the vibrational energies of extended systems is explored. Particular attention is paid to the thermodn. of adsorption of small mols. on catalytically relevant systems typically affected by anharmonicity. The implemented scheme obtains one-dimensional anharmonic model potentials by distorting the equil. structure along the normal modes using both rectilinear (Cartesian) or curvilinear (internal) representations. Only in the latter case, the modes are decoupled also at higher order of the potential and the thermodn. functions change in the expected directions. The method is applied to calc. ab initio enthalpies, entropies, and Gibbs free energies for the adsorption of methane in acidic chabazite (H-CHA) and on MgO(001) surface. The values obtained for the adsorption of methane in H-CHA (273.15 K, 0.1 MPa, θ = 0.5) are ΔH = -19.3, -TΔS = 11.9, and ΔG = -7.5 kJ/mol. For methane on the MgO(001) (47 K, 1.3 × 10-14 MPa, θ = 1) ΔH = -14.4, -TΔS = 16.6, and ΔG = 2.1 kJ/mol are obtained. The calcd. desorption temp. is 44 K, and the desorption prefactor is 4.26 × 1012 s-1. All calcd. results agree within chem. accuracy limits with exptl. data.**30**Piccini, G.; Alessio, M.; Sauer, J.; Zhi, Y.; Liu, Y.; Kolvenbach, R.; Jentys, A.; Lercher, J. A. Accurate Adsorption Thermodynamics of Small Alkanes in Zeolites. Ab initio Theory and Experiment for H-Chabazite.*J. Phys. Chem. C*2015,*119*, 6128– 6137, DOI: 10.1021/acs.jpcc.5b0173930https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXkt1Oisbw%253D&md5=d617f794d481a436cb5cbb1c86fa2f2aAccurate Adsorption Thermodynamics of Small Alkanes in Zeolites. Ab initio Theory and Experiment for H-ChabazitePiccini, GiovanniMaria; Alessio, Maristella; Sauer, Joachim; Zhi, Yuchun; Liu, Yuanshuai; Kolvenbach, Robin; Jentys, Andreas; Lercher, Johannes A.Journal of Physical Chemistry C (2015), 119 (11), 6128-6137CODEN: JPCCCK; ISSN:1932-7447. (American Chemical Society)Heats of adsorption of methane, ethane, and propane in H-chabazite (Si/Al = 14.4) have been measured and entropies have been derived from adsorption isotherms. For these systems quantum chem. ab initio calcns. of Gibbs free energies have been performed. The deviations from the exptl. values for methane, ethane, and propane are below 3 kJ/mol for the enthalpy, and the Gibbs free energy. A hybrid high-level (MP2/CBS): low-level (DFT+dispersion) method is used to det. adsorption structures and energies. Vibrational entropies and thermal enthalpy contributions are obtained from vibrational partition functions for the DFT+dispersion potential energy surface. Anharmonic corrections have been evaluated for each normal mode sep. One-dimensional Schrodinger equations are solved for potentials obtained by (curvilinear) distortions of the normal modes using a representation in internal coordinates.**31**Njegic, B.; Gordon, M. S. Exploring the effect of anharmonicity of molecular vibrations on thermodynamic properties.*J. Chem. Phys.*2006,*125*, 224102, DOI: 10.1063/1.239594031https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXht1Onug%253D%253D&md5=1cfa7641c6df19c423f1a106a12e339eExploring the effect of anharmonicity of molecular vibrations on thermodynamic propertiesNjegic, Bosiljka; Gordon, Mark S.Journal of Chemical Physics (2006), 125 (22), 224102/1-224102/12CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)Thermodn. properties of selected small and medium size mols. were calcd. using harmonic and anharmonic vibrational frequencies. Harmonic vibrational frequencies were obtained by normal mode anal., whereas anharmonic ones were calcd. using the vibrational SCF (VSCF) method. The calcd. and available exptl. thermodn. data for zero point energy, enthalpy, entropy, and heat capacity are compared. The anharmonicity and coupling of mol. vibrations can play a significant role in predicting accurate thermodn. quantities. Limitations of the current VSCF method for low frequency modes have been partially removed by following normal mode displacements in internal, rather than Cartesian, coordinates.**32**Kundu, A.; Piccini, G.; Sillar, K.; Sauer, J. Ab Initio Prediction of Adsorption Isotherms for Small Molecules in Metal–Organic Frameworks.*J. Am. Chem. Soc.*2016,*138*, 14047– 14056, DOI: 10.1021/jacs.6b0864632https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xhs1KqsLbK&md5=960cbf4fe313b6aa11a574258fcbb666Ab Initio Prediction of Adsorption Isotherms for Small Molecules in Metal-Organic FrameworksKundu, Arpan; Piccini, GiovanniMaria; Sillar, Kaido; Sauer, JoachimJournal of the American Chemical Society (2016), 138 (42), 14047-14056CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)For CO and N2 on Mg2+ sites of the metal-org. framework CPO-27-Mg (Mg-MOF-74), ab initio calcns. of Gibbs free energies of adsorption have been performed. Combined with the Bragg-Williams/Langmuir model and taking into account the exptl. site availability (76.5%), we obtained adsorption isotherms in close agreement with those in expt. The remaining deviations in the Gibbs free energy (about 1 kJ/mol) are significantly smaller than the "chem. accuracy" limit of about 4 kJ/mol. The presented approach uses (i) a DFT dispersion method (PBE + D2) to optimize the structure and to calc. anharmonic frequencies for vibrational partition functions and (ii) a "hybrid MP2:(PBE + D2) + ΔCCSD(T)" method to det. electronic energies. With the achieved accuracy (estd. uncertainty ±1.4 kJ/mol), the ab initio energies become useful benchmarks for assessing different DFT + dispersion methods (PBE + D2, B3LYP + D*, and vdW-D2), whereas the ab initio heats, entropies, and Gibbs free energies of adsorption are used to assess the reliability of exptl. values derived from fitting isotherms or from variable-temp. IR studies.**33**Piccini, G.; Alessio, M.; Sauer, J. Ab Initio Calculation of Rate Constants for Molecule–Surface Reactions with Chemical Accuracy.*Angew. Chem., Int. Ed.*2016,*55*, 5235– 5237, DOI: 10.1002/anie.20160153433https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XkvVChsb0%253D&md5=178fc9825c3a63a8359e1c525c3fcb1dAb initio Calculation of Rate Constants for Molecule-Surface Reactions with Chemical AccuracyPiccini, Giovanni Maria; Alessio, Maristella; Sauer, JoachimAngewandte Chemie, International Edition (2016), 55 (17), 5235-5237CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)The ab initio prediction of reaction rate consts. for systems with hundreds of atoms with an accuracy that is comparable to expt. is a challenge for computational quantum chem. We present a divide-and-conquer strategy that departs from the potential energy surfaces obtained by std. d. functional theory with inclusion of dispersion. The energies of the reactant and transition structures are refined by wavefunction-type calcns. for the reaction site. Thermal effects and entropies are calcd. from vibrational partition functions, and the anharmonic frequencies are calcd. sep. for each vibrational mode. This method is applied to a key reaction of an industrially relevant catalytic process, the methylation of small alkenes over zeolites. The calcd. reaction rate consts. (free energies), pre-exponential factors (entropies), and enthalpy barriers show that our computational strategy yields results that agree with expt. within chem. accuracy limits (less than one order of magnitude).**34**Bučko, T.; Hafner, J.; Ángyán, J. G. Geometry optimization of periodic systems using internal coordinates.*J. Chem. Phys.*2005,*122*, 12450834https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXjtFKqs7g%253D&md5=4067f672f62fc3686d023646d6320bf1Geometry optimization of periodic systems using internal coordinatesBucko, Tomas; Hafner, Jurgen; Angyan, Janos G.Journal of Chemical Physics (2005), 122 (12), 124508/1-124508/10CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)An algorithm is proposed for the structural optimization of periodic systems in internal (chem.) coordinates. Internal coordinates may include in addn. to the usual bond lengths, bond angles, out-of-plane and dihedral angles, various "lattice internal coordinates" such as cell edge lengths, cell angles, cell vol., etc. The coordinate transformations between Cartesian (or fractional) and internal coordinates are performed by a generalized Wilson B-matrix, which in contrast to the previous formulation by Kudin et al. [J. Chem. Phys. 114, 2919 (2001)] includes the explicit dependence of the lattice parameters on the positions of all unit cell atoms. The performance of the method, including constrained optimizations, is demonstrated on several examples, such as layered and microporous materials (gibbsite and chabazite) as well as the urea mol. crystal. The calcns. used energies and forces from the ab initio d. functional theory plane wave method in the projector-augmented wave formalism.**35**Zhang, D.-B.; Sun, T.; Wentzcovitch, R. M. Phonon Quasiparticles and Anharmonic Free Energy in Complex Systems.*Phys. Rev. Lett.*2014,*112*, 058501, DOI: 10.1103/PhysRevLett.112.05850135https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXjtlSmurk%253D&md5=e04dec8780c4fea55e37580230761a21Phonon quasiparticles and anharmonic free energy in complex systemsZhang, Dong-Bo; Sun, Tao; Wentzcovitch, Renata M.Physical Review Letters (2014), 112 (5), 058501/1-058501/5CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)We use a hybrid strategy to obtain anharmonic frequency shifts and lifetimes of phonon quasiparticles from first principles mol. dynamics simulations in modest size supercells. This approach is effective irresp. of crystal structure complexity and facilitates calcn. of full anharmonic phonon dispersions, as long as phonon quasiparticles are well defined. We validate this approach to obtain anharmonic effects with calcns. in MgSiO3 perovskite, the major Earth forming mineral phase. First, we reproduce irregular thermal frequency shifts of well characterized Raman modes. Second, we combine the phonon gas model (PGM) with quasiparticle frequencies and reproduce free energies obtained using thermodn. integration. Combining thoroughly sampled quasiparticle dispersions with the PGM we then obtain first-principles anharmonic free energy in the thermodn. limit (N → ∞).**36**Carreras, A.; Togo, A.; Tanaka, I. DynaPhoPy: A code for extracting phonon quasiparticles from molecular dynamics simulations.*Comput. Phys. Commun.*2017,*221*, 221– 234, DOI: 10.1016/j.cpc.2017.08.01736https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhsVWhurfO&md5=179605903557cb9f1d5c9479163c6db3DynaPhoPy: A code for extracting phonon quasiparticles from molecular dynamics simulationsCarreras, Abel; Togo, Atsushi; Tanaka, IsaoComputer Physics Communications (2017), 221 (), 221-234CODEN: CPHCBZ; ISSN:0010-4655. (Elsevier B.V.)A review. We have developed a computational code, DYNAPHOPY, that allows us to ext. the microscopic anharmonic phonon properties from mol. dynamics (MD) simulations using the normal-mode-decompn. technique as presented by Sun et al. (2014). Using this code we calcd. the quasiparticle phonon frequencies and linewidths of cryst. silicon at different temps. using both of first-principles and the Tersoff empirical potential approaches. In this work we show the dependence of these properties on the temp. using both approaches and compare them with reported exptl. data obtained by Raman spectroscopy (Balkanski et al., 1983; Tsu and Hernandez, 1982).Manuscript Title: DynaPhoPy: A code for extg. phonon quasiparticles from mol. dynamics simulationsAuthors: Abel Carreras, Atsushi Togo and Isao TanakaProgram Title: DynaPhoPyJournal Ref.:Catalog identifier:Licensing provisions: MIT LicenseProgramming language: Python and CComputer: PC and cluster computersOperating system: UNIX/OSXRAM: Depends strongly on no. of input data (several Gb)No. of processors used: 1-16Supplementary material:Keywords: anharmonicity, phonon, linewidth, frequency shift, mol. dynamicsClassification: 7.8 Structure and Lattice DynamicsExternal routines/libraries: phonopy, numpy, matplotlib, scipy and h5py python modules. Optional: FFTW and CudaSubprograms used:Catalog identifier of previous version: *Journal ref. of previous version: *Does the new version supersede the previous version: *Nature of problem:Increasing temp., a crystal potential starts to deviate from the harmonic regime and anharmonicity is getting to be evident [1]. To treat anharmonicity, perturbation approach often describes successfully phenomena such as phonon lifetime and lattice thermal cond. However it fails when the system contains large at. displacements.Soln. method:Extg. the phonon quasiparticles from mol. dynamics (MD) simulations using the normal-mode-decompn. technique.Reasons for the new version: *Summary of revisions: *Restrictions:Quantum effects of lattice dynamics are not considered.Unusual features:Addnl. comments:Running time:It is highly dependent on the type of calcn. requested. It depends mainly on the no. of atoms in the primitive cell, the no. of time steps of the MD simulation and the method employed to calc. the power spectra. Currently two methods are implemented in DyaPhoPy: The Fourier transform and the max. entropy methods. The Fourier transform method scales to O [N2] and the max. entropy method scales to O [N × M] where N is the no. of time steps and M is the no. of coeffs.**37**Peters, L. D. M.; Dietschreit, J. C. B.; Kussmann, J.; Ochsenfeld, C. Calculating free energies from the vibrational density of states function: Validation and critical assessment.*J. Chem. Phys.*2019,*150*, 194111, DOI: 10.1063/1.507964337https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXpvFOlsLk%253D&md5=bdccb228a8ddc5282d129c9b1e3ca8b2Calculating free energies from the vibrational density of states function: Validation and critical assessmentPeters, Laurens D. M.; Dietschreit, Johannes C. B.; Kussmann, Joerg; Ochsenfeld, ChristianJournal of Chemical Physics (2019), 150 (19), 194111/1-194111/11CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)We explore and show the usefulness of the d. of states function for computing vibrational free energies and free energy differences between small systems. Therefore, we compare this d. of states integration method (DSI) to more established schemes such as Bennett's Acceptance Ratio method (BAR), the Normal Mode Anal. (NMA), and the Quasiharmonic Anal. (QHA). The strengths and shortcomings of all methods are highlighted with three numerical examples. Furthermore, the free energy of the ionization of ammonia and the mutation from serine to cysteine are computed using extensive ab initio mol. dynamics simulations. We conclude that DSI improves upon the other frequency-based methods (NMA and QHA) regarding the treatment of anharmonicity and yielding results comparable to BAR in all cases without the need for alchem. transformations. Low-frequency modes lead to larger errors indicating that long simulation times might be required for larger systems. In addn., we introduce the use of DSI for the localization of the vibrational free energy to specific atoms or residues, leading to insights into the underlying process, a unique feature that is only offered by this method. (c) 2019 American Institute of Physics.**38**Galimberti, D. R.; Milani, A.; Tommasini, M.; Castiglioni, C.; Gaigeot, M.-P. Combining Static and Dynamical Approaches for Infrared Spectra Calculations of Gas Phase Molecules and Clusters.*J. Chem. Theory Comput.*2017,*13*, 3802– 3813, DOI: 10.1021/acs.jctc.7b0047138https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhtVOnsbjJ&md5=bb5a07ba8b029c9455ce829d0b4c0453Combining Static and Dynamical Approaches for Infrared Spectra Calculations of Gas Phase Molecules and ClustersGalimberti, Daria R.; Milani, Alberto; Tommasini, Matteo; Castiglioni, Chiara; Gaigeot, Marie-PierreJournal of Chemical Theory and Computation (2017), 13 (8), 3802-3813CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)Four models for the calcn. of the IR spectrum of gas phase mols. and clusters from mol. dynamics simulations are presented with the aim to reduce the computational cost of the usual Fourier transform (FT) of the time correlation function of the dipole moment. These models are based on the VDOS, FT of time correlation function of velocities, and at. polar tensors (APT). The models differ from each other by the no. of APTs inserted into the velocities correlation function. Excellent accuracy is achieved by the model adopting a weighted linear combination of a few selected APTs adapted for the rotation of the mol. (model D). The achieved accuracy relates to band positions, band shapes, and band intensities. Depending on the degree of actual dynamics of the mol., rotational motion, conformational isomerization, and large amplitude motions that can be seen during the finite temp. trajectory, 1 could also apply 1 of the other models (models A, B, or C), but with caution. Model D is therefore found simple and accurate, with appealing computational cost and should be systematically applied. Its generalization to condensed phase systems should be straightforward.**39**Brehm, M.; Kirchner, B. TRAVIS - A Free Analyzer and Visualizer for Monte Carlo and Molecular Dynamics Trajectories.*J. Chem. Inf. Model.*2011,*51*, 2007– 2023, DOI: 10.1021/ci200217w39https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXptleqs7s%253D&md5=68eac025b6aaefd7961cba05b68e7ca3TRAVIS - A Free Analyzer and Visualizer for Monte Carlo and Molecular Dynamics TrajectoriesBrehm, Martin; Kirchner, BarbaraJournal of Chemical Information and Modeling (2011), 51 (8), 2007-2023CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)We present TRAVIS ("TRajectory Analyzer and VISualizer"), a free program package for analyzing and visualizing Monte Carlo and mol. dynamics trajectories. The aim of TRAVIS is to collect as many analyses as possible in one program, creating a powerful tool and making it unnecessary to use many different programs for evaluating simulations. This should greatly rationalize and simplify the work-flow of analyzing trajectories. TRAVIS is written in C++, open-source free-ware and licensed under the terms of the GNU General Public License (GPLv3). It is easy to install (platform independent, no external libraries) and easy to use. In this article, we present some of the algorithms that are implemented in TRAVIS - many of them widely known for a long time, but some of them also to appear in literature for the first time. All shown analyses only require a std. MD trajectory as input data.**40**Nielsen, M.; Brogaard, R. Y.; Falsig, H.; Beato, P.; Swang, O.; Svelle, S. Kinetics of Zeolite Dealumination: Insights from H-SSZ-13.*ACS Catal.*2015,*5*, 7131– 7139, DOI: 10.1021/acscatal.5b0149640https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhs1Glu73P&md5=76e82f86dfa5901188a8e91892ca4045Kinetics of Zeolite Dealumination: Insights from H-SSZ-13Nielsen, Malte; Brogaard, Rasmus Yding; Falsig, Hanne; Beato, Pablo; Swang, Ole; Svelle, StianACS Catalysis (2015), 5 (12), 7131-7139CODEN: ACCACS; ISSN:2155-5435. (American Chemical Society)When zeolite catalysts are subjected to steam at high temps., a permanent loss of activity happens, because of the loss of aluminum from the framework. This dealumination is a complex process involving the hydrolysis of four Al-O bonds. This work addresses the dealumination from a theor. point of view, modeling the kinetics in zeolite H-SSZ-13 to gain insights that can extend to other zeolites. We employ periodic d. functional theory (DFT) to obtain free-energy profiles, and we solve a microkinetic model to derive the rates of dealumination. We argue that such modeling should consider water that has been physisorbed in the zeolite as the ref. state and propose a scheme for deriving the free energy of this state. The results strongly suggest that the first of the four hydrolysis steps is insignificant for the kinetics of zeolite dealumination. Furthermore, the results indicate that, in H-SSZ-13, it is sufficient to include only the fourth hydrolysis step when estg. the rate of dealumination at temps. above 700 K. These are key aspects to investigate in further work on the process, particularly when comparing different zeolite frameworks.**41**Shi, L.; Yang, J.; Shen, G.; Zhao, Y.; Chen, R.; Shen, M.; Wen, Y.; Shan, B. The influence of adjacent Al atoms on the hydrothermal stability of H-SSZ-13: a first-principles study.*Phys. Chem. Chem. Phys.*2020,*22*, 2930– 2937, DOI: 10.1039/c9cp05141d41https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXisVyqsrbP&md5=0806ae3cec63974b332daa0b680a999eThe influence of adjacent Al atoms on the hydrothermal stability of H-SSZ-13: a first-principles studyShi, Lu; Yang, Jiaqiang; Shen, Gurong; Zhao, Yunkun; Chen, Rong; Shen, Meiqing; Wen, Yanwei; Shan, BinPhysical Chemistry Chemical Physics (2020), 22 (5), 2930-2937CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)The Al concn. and distribution have a great influence on the hydrothermal stability of the H-SSZ-13 zeolites in expts. First-principles calcns. are performed to clarify the decompn. mechanism of an H-SSZ-13 framework with adjacent Al atom pair distribution under hydrothermal conditions. The adjacent Al atoms have a tendency to occupy the para-sites of the 4-membered rings (4MRs) in the framework. H2O mols. are chemisorbed onto the Al atom 1 by 1, and the hydroxylation of the neighboring O atoms induces the breaking of the Al-O bonds, which causes the 1st dealumination in 4MRs. The other Al atom in the para-site can be easily removed from the framework once the 1st 1 is lost. The feasible subsequent dealumination of adjacent Al atoms would break the linker of 6MRs in the framework, which is responsible for the degraded hydrothermal stability. Also, the partial substitution of metal ions (such as Na+ and Cu+) for the protons in the framework will greatly stabilize the Al-O bonds and enlarge the energy barrier of para-site Al dealumination, which leads to the improved hydrothermal stability of H-SSZ-13.**42**Plessow, P. N.; Studt, F. Olefin methylation and cracking reactions in H-SSZ-13 investigated with ab initio and DFT calculations.*Catal. Sci. Technol.*2018,*8*, 4420– 4429, DOI: 10.1039/c8cy01194j42https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhsV2isbnL&md5=6797d0831ded189c0fa510f10ccbcc23Olefin methylation and cracking reactions in H-SSZ-13 investigated with ab initio and DFT calculationsPlessow, Philipp N.; Studt, FelixCatalysis Science & Technology (2018), 8 (17), 4420-4429CODEN: CSTAGD; ISSN:2044-4753. (Royal Society of Chemistry)The olefin cycle of the methanol-to-olefins process is investigated for the zeolite H-SSZ-13 using periodic, van-der-Waals cor. DFT calcns., together with MP2 corrections derived from cluster models, which are essential for accurate barriers. The two main reactions, olefin methylation and cracking are systematically investigated for different olefin isomers up to C9. The barrier for cracking depends sensitively on the involved cationic intermediates. The most favorable cracking reactions involve tertiary cations, in particular the t-Bu cation that leads to the formation of isobutene along with another olefin. The transition state for olefin methylation is mainly influenced by van-der-Waals interactions and is therefore stabilized for larger olefins.**43**Sarazen, M. L.; Doskocil, E.; Iglesia, E. Effects of Void Environment and Acid Strength on Alkene Oligomerization Selectivity.*ACS Catal.*2016,*6*, 7059– 7070, DOI: 10.1021/acscatal.6b0212843https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhsFals7nE&md5=3d2261c16a6f0a1677b5d1cc38f84d8eEffects of Void Environment and Acid Strength on Alkene Oligomerization SelectivitySarazen, Michele L.; Doskocil, Eric; Iglesia, EnriqueACS Catalysis (2016), 6 (10), 7059-7070CODEN: ACCACS; ISSN:2155-5435. (American Chemical Society)The effects of channel connectivity, void environment, and acid strength on the relative rates of oligomerization, β-scission, and isomerization reactions during light alkene conversion (ethene, propene, isobutene; 2-400 kPa alkene; 473-533 K) were examd. on microporous (TON, MFI, MOR, BEA, FAU) and mesoporous (amorphous silica-alumina (SiAl), MCM-41, Keggin POM) Bronsted acids with a broad range of confining voids and acid strength. Skeletal and regioisomers equilibrate under all conditions of pressure and conversion and on all catalysts, irresp. of their acid strength, void size, or framework connectivity, consistent with rapid hydride and Me shifts of alkoxides intermediates and with their fast adsorption-desorption steps. Such equilibration is evident from detailed chem. speciation of the products and also from intramol. isotopic scrambling in all oligomers formed from 2-13C-propene on TON, MFI, SiAl, and POM clusters. Previous claims of kinetic control of skeletal isomers in oligomerization catalysis through shape-selective effects conferred by void environments may have used inaccurate tabulated thermodn., as we show in this study. The void environment, however, influences the size distribution of the chains formed in these acid-catalyzed alkene reactions. One-dimensional microporous aluminosilicates predominantly form true oligomers, those expected from dimerization and subsequent oligomerization events for a given reactant alkene; such chains are preserved because they cannot grow to sizes that would inhibit their diffusion through essentially cylindrical channels in these frameworks. Amorphous SiAl and colloidal silica-supported POM clusters contain acid sites of very different strength; both exhibit size variations across the void space, but at length scales much larger than mol. diams., thus preserving true oligomers by allowing them to egress the void before β-scission events. Mesoporous acids of very different strength (POM, SiAl) give similar true isomer selectivities, as also obsd. on MFI structures with different heteroatoms (X-MFI, where X = Al, Ga, Fe, B), which also differ in acid strength; this insensitivity reflects oligomerization and β-scission reactions that involve similar ion-pair transition states and therefore depend similarly on the stability of the conjugate anion. Three-dimensional microporous frameworks contain voids larger than their interconnecting paths, an inherent consequence of intersecting channels and cage-window structures. As a result, oligomers can reach sizes that restrict their diffusion through the interconnections, until β-scission events form smaller and faster diffusing chains. These undulations are of mol. dimensions and their magnitude, which is defined here as the ratio of the largest scale to the smallest scale along intracrystal diffusion paths, dets. the extent to which oligomerization-scission cycles contribute to the size distribution of products. These contributions are evident in the extent to which chain size and the no. of 13C atoms in each mol. formed from 2-13C-propene approach their binomial distributions, as they do on microporous acids with significant undulations. The general nature of these conclusions is evident from the similar effects of void shape and connectivity and of acid strength on selectivity for ethene, propene, and isobutene reactants.**44**McQuarrie, D. A.*Statistical Thermodynamics*; Harper & Row, 1973.There is no corresponding record for this reference.**45**Balog, E.; Becker, T.; Oettl, M.; Lechner, R.; Daniel, R.; Finney, J.; Smith, J. C. Direct Determination of Vibrational Density of States Change on Ligand Binding to a Protein.*Phys. Rev. Lett.*2004,*93*, 028103, DOI: 10.1103/PhysRevLett.93.02810345https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXls1Whtr0%253D&md5=5efebe3e961811528a196aa831aa4c40Direct Determination of Vibrational Density of States Change on Ligand Binding to a ProteinBalog, Erika; Becker, Torsten; Oettl, Martin; Lechner, Ruep; Daniel, Roy; Finney, John; Smith, Jeremy C.Physical Review Letters (2004), 93 (2), 028103/1-028103/4CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)The change in the vibrational d. of states of a protein (dihydrofolate reductase) on binding a ligand (methotrexate) is detd. using inelastic neutron scattering. The vibrations of the complex soften significantly relative to the unbound protein. The resulting free-energy change, which is directly detd. by the d. of states change, is found to contribute significantly to the binding equil.**46**Lin, S.-T.; Maiti, P. K.; Goddard, W. A. Dynamics and Thermodynamics of Water in PAMAM Dendrimers at Subnanosecond Time Scales.*J. Phys. Chem. B*2005,*109*, 8663– 8672, DOI: 10.1021/jp047195846https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXjtFSisrg%253D&md5=5b04f64c580eae653f778eaab4da2f13Dynamics and Thermodynamics of Water in PAMAM Dendrimers at Subnanosecond Time ScalesLin, Shiang-Tai; Maiti, Prabal K.; Goddard, William A., IIIJournal of Physical Chemistry B (2005), 109 (18), 8663-8672CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)Atomistic mol. dynamics simulations are used to study generation 5 polyamidoamine (PAMAM) dendrimers immersed in a bath of water. We interpret the results in terms of three classes of water: buried water well inside of the dendrimer surface, surface water assocd. with the dendrimer-water interface, and bulk water well outside of the dendrimer. We studied the dynamic and thermodn. properties of the water at three pH values: high pH with none of the primary or tertiary amines protonated, intermediate pH with only the primary amines protonated, and low pH with all amines protonated. For all pH values we find that both buried and surface water exhibit two relaxation times: a fast relaxation (∼1 ps) corresponding to the libration motion of the water and a slow (∼20 ps) diffusional component related to the escaping of water from one domain to another. In contrast for bulk water the fast relaxation is ∼0.4 ps while the slow relaxation is ∼14 ps. These results are similar to those found in biol. systems, where the fast relaxation is ∼1 ps while the slow relaxation ranges from 20 to 1000 ps. We used the 2PT MD method to ext. the vibrational (power) spectrum and found substantial differences for the three classes of water. The translational diffusion coeff. for buried water is 11-33% (depending on pH) of the bulk value while the surface water is about 80%. The change in rotational diffusion is quite similar: 21-45% of the bulk value for buried water and 80% for surface water. This shows that translational and rotational dynamics of water are affected by the PAMAM-water interactions and due to the confinement in the interior of the dendrimer. We find that the redn. of translational or rotational diffusion is accompanied by a blue shift of the corresponding libration motions (∼10 cm-1 for translation, ∼35 cm-1 for rotation), indicating higher local force consts. for these motions. These effects are most pronounced for the lowest pH, probably because of the increased rigidity caused by the internal charges. From the vibrational d. of states we also calc. the enthalpies and entropies of the various waters. We find that water mols. are enthalpically favored near the PAMAM dendrimer: energy for surface water is ∼0.1 kcal/mol lower to that in the bulk, and ∼0.5-0.9 kcal/mol lower for buried water. In contrast, we find that both the buried and surface water are entropically unfavored: buried water is 0.9-2.2 kcal/mol lower than the bulk while the surface water is 0.1-0.2 kcal/mol lower. The net result is a thermodynamically unfavored state of the water surrounding the PAMAM dendrimer: 0.4-1.3 kcal/mol higher for buried water and 0.1-0.2 kcal/mol for surface water. This excess free energy of the surface and buried waters is released when the PAMAM dendrimer binds to DNA or metal ions, providing an extra driving force.**47**Sousa, R. L. d.; Alves, H. W. L. Ab initio calculation of the dynamical properties of PPP and PPV.*Braz. J. Phys.*2006,*36*, 501– 504, DOI: 10.1590/s0103-97332006000300072There is no corresponding record for this reference.**48**Sun, T.; Zhang, D.-B.; Wentzcovitch, R. M. Dynamic stabilization of cubic CaSiO3 perovskite at high temperatures and pressures from ab initio molecular dynamics.*Phys. Rev. B: Condens. Matter Mater. Phys.*2014,*89*, 094109, DOI: 10.1103/physrevb.89.09410948https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXns1Gqs7w%253D&md5=7abaa088ccfd0295fcd70949e71e7546Dynamic stabilization of cubic CaSiO3 perovskite at high temperatures and pressures from ab initio molecular dynamicsSun, Tao; Zhang, Dong-Bo; Wentzcovitch, Renata M.Physical Review B: Condensed Matter and Materials Physics (2014), 89 (9), 094109/1-094109/9CODEN: PRBMDO; ISSN:1098-0121. (American Physical Society)The stability of cubic CaSiO3 perovskite (CaPv) at high temps. and pressures is investigated by vibrational normal-mode anal. We compute power spectra of mode autocorrelation functions using a recently developed hybrid approach combining ab initio mol. dynamics with lattice dynamics. These power spectra, together with the probability distributions of at. displacements, indicate that cubic CaPv is stabilized at T ∼ 600 K and P ∼ 26 GPa. We then utilize the concept of phonon quasiparticles to characterize the vibrational properties of cubic CaPv at high temp. and obtain anharmonic phonon dispersions through the whole Brillouin zone. Such temp.-dependent phonon dispersions pave the way for more accurate calcns. of free-energy, thermodn., and thermoelastic properties of cubic CaPv at Earth's lower mantle conditions.**49**Landau, L. D.; Lifshitz, E. M.*Statistical Physics*; Elsevier, 2013; Vol. 5.There is no corresponding record for this reference.**50**Jones, W.; March, N. H.*Theoretical Solid State Physics*; Courier Corporation, 1985; Vol. 35.There is no corresponding record for this reference.**51**Berens, P. H.; Mackay, D. H. J.; White, G. M.; Wilson, K. R. Thermodynamics and quantum corrections from molecular dynamics for liquid water.*J. Chem. Phys.*1983,*79*, 2375– 2389, DOI: 10.1063/1.44604451https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL3sXlsVOjtbY%253D&md5=c832fda28699084a387496f89a817df2Thermodynamics and quantum corrections from molecular dynamics for liquid waterBerens, Peter H.; Mackay, Donald H. J.; White, Gary M.; Wilson, Kent R.Journal of Chemical Physics (1983), 79 (5), 2375-89CODEN: JCPSA6; ISSN:0021-9606.It is discussed how to quantum correct the classical mech. thermodn. values available from mol. dynamics, Monte Carlo, perturbation, or integral methods in order to compare with exptl. quantum reality.**52**Kearsley, S. K. On the orthogonal transformation used for structural comparisons.*Acta Crystallogr., Sect. A: Cryst. Phys., Diffr., Theor. Gen. Crystallogr.*1989,*45*, 208– 210, DOI: 10.1107/s0108767388010128There is no corresponding record for this reference.**53**Kudin, K. N.; Dymarsky, A. Y. Eckart axis conditions and the minimization of the root-mean-square deviation: Two closely related problems.*J. Chem. Phys.*2005,*122*, 224105, DOI: 10.1063/1.192973953https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXlsFGls7k%253D&md5=aea31385c90766ae2e81d9eafbce7940Eckart axis conditions and the minimization of the root-mean-square deviation: Two closely related problemsKudin, Konstantin N.; Dymarsky, Anatoly Y.Journal of Chemical Physics (2005), 122 (22), 224105/1-224105/2CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)We highlight the fact that the rotation matrix minimizing the root-mean-square deviation between two mol. conformations [W. Kabsch, Acta Cryst. A32, 922 (1976)] also satisfies the Eckart axis conditions [C. Eckart, Phys. Rev. 47, 552 (1935)].**54**Mathias, G.; Ivanov, S. D.; Witt, A.; Baer, M. D.; Marx, D. Infrared Spectroscopy of Fluxional Molecules from (ab Initio) Molecular Dynamics: Resolving Large-Amplitude Motion, Multiple Conformations, and Permutational Symmetries.*J. Chem. Theory Comput.*2012,*8*, 224– 234, DOI: 10.1021/ct200666554https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhsFCisLvM&md5=c2de7ef791e8977d596756deb175e86eInfrared Spectroscopy of Fluxional Molecules from (ab Initio) Molecular Dynamics: Resolving Large-Amplitude Motion, Multiple Conformations, and Permutational SymmetriesMathias, Gerald; Ivanov, Sergei D.; Witt, Alexander; Baer, Marcel D.; Marx, DominikJournal of Chemical Theory and Computation (2012), 8 (1), 224-234CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)The computation of vibrational spectra of complex mols. from time correlation functions generated by ab initio mol. dynamics simulations has made lively progress in recent years. However, the anal. of such spectra, i.e., the assignment of vibrational bands to at. motions, is by no means straightforward. In a recent article, Mathias and Baer presented a corresponding anal. method that derives generalized normal coordinates (GNCs) from mol. dynamics trajectories, which furnish band positions, band shapes, and IR intensities of the sepd. vibrational modes. This vibrational anal. technique relies on the usual quasi-rigidity assumption; i.e., at. motions are described by small oscillations around a single ref. structure. This assumption, however, breaks down if the mol. undergoes large-amplitude motion and visits different conformations along the trajectory or if the same conformation can be adopted by a different ordering of the atoms, i.e., if permutational symmetries have to be considered. Here, the authors present an extension of the GNC method that handles such cases by considering multiple ref. structures, both for different conformations and for permutational symmetries. By introducing a projection technique and computing probabilities that assign the time frames of the trajectories to these ref. structures, the vibrational spectra are split into conformational contributions via a consistent time correlation formalism. For each conformation, the permutational symmetries are resolved, which permits one to det. conformation-local GNCs for the band assignment. The working principle and the virtues of this generalization are demonstrated for the simple case of a Me group rotation. This is followed by an application to a more intricate case: Upon replacing one proton by a deuteron in protonated methane, CH5+, significant changes of its IR spectrum were obsd. since the CH4D+ isotopologue features five different isotopomers. Here, a total of 120 conformational and permutational refs. are required in the projection scheme to capture the frequent and versatile structural transitions of this small but utmost floppy mol. and to assign its IR spectrum. The extended GNC method is general. Thus, it can be applied readily to systems that require more than one ref. structure, and it can be transferred to other theor. spectroscopies that are formulated in terms of time correlation functions.**55**Iannuzzi, M.; Laio, A.; Parrinello, M. Efficient Exploration of Reactive Potential Energy Surfaces Using Car-Parrinello Molecular Dynamics.*Phys. Rev. Lett.*2003,*90*, 238302, DOI: 10.1103/physrevlett.90.23830255https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXksFyqsb4%253D&md5=529eba2c53f92cd9cfae4708e50303b0Efficient Exploration of Reactive Potential Energy Surfaces Using Car-Parrinello Molecular DynamicsIannuzzi, Marcella; Laio, Alessandro; Parrinello, MichelePhysical Review Letters (2003), 90 (23), 238302/1-238302/4CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)The possibility of observing chem. reactions in ab initio mol. dynamics runs is severely hindered by the short simulation time accessible. We propose a new method for accelerating the reaction process, based on the ideas of the extended Lagrangian and coarse-grained non-Markovian metadynamics. We demonstrate that by this method it is possible to simulate reactions involving complex at. rearrangements and very large energy barriers in runs of a few picoseconds.**56**Cazzaniga, M.; Micciarelli, M.; Moriggi, F.; Mahmoud, A.; Gabas, F.; Ceotto, M. Anharmonic calculations of vibrational spectra for molecular adsorbates: A divide-and-conquer semiclassical molecular dynamics approach.*J. Chem. Phys.*2020,*152*, 104104, DOI: 10.1063/1.514268256https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXkvFyrs7o%253D&md5=50d14431c40293dbe4f0b386f21627b1Anharmonic calculations of vibrational spectra for molecular adsorbates: A divide-and-conquer semiclassical molecular dynamics approachCazzaniga, Marco; Micciarelli, Marco; Moriggi, Francesco; Mahmoud, Agnes; Gabas, Fabio; Ceotto, MicheleJournal of Chemical Physics (2020), 152 (10), 104104CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)A semiclassical mol. dynamics method able to reproduce the vibrational energy levels of systems composed by mols. adsorbed on solid surfaces is presented. The divide-and-conquer semiclassical method for power spectra calcns. was extended to gas-surface systems and interfaced with plane-wave electronic structure codes. The Born-Oppenheimer classical dynamics underlying the semiclassical calcn. is full dimensional, and the method includes not only the motion of the adsorbate but also those of the surface and the bulk. The vibrational spectroscopic peaks related to the adsorbate are accounted together with the most coupled phonon modes to obtain spectra amenable to phys. interpretations. The method was applied to the adsorption of CO, NO, and H2O on the anatase-TiO2 (101) surface. The semiclassical results were compared with the single-point harmonic ests. and the classical power spectra obtained from the same trajectory employed in the semiclassical calcn. CO and NO anharmonic effects of fundamental vibrations are similarly reproduced by the classical and semiclassical dynamics and H2O adsorption is fully and properly described in its overtone and combination band relevant components only by the semiclassical approach. (c) 2020 American Institute of Physics.**57**Bates, S. P.; Van Well, W. J. M.; Van Santen, R. A.; Smit, B. Configurational-Bias Monte Carlo (CB-MC) Calculations of n-Alkane Sorption in Zeolites Rho and Fer.*Mol. Simul.*1997,*19*, 301– 318, DOI: 10.1080/0892702970802415957https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2sXnvFWiu7s%253D&md5=067f0531d58a0f03680c270cca02cf97Configurational-bias Monte Carlo (CB-MC) calculations of n-alkane sorption in zeolites rho and ferBates, Simon P.; Van Well, Willy J. M.; Van Santen, Rutger A.; Smit, BerendMolecular Simulation (1997), 19 (5-6), 301-318CODEN: MOSIEA; ISSN:0892-7022. (Gordon & Breach Science Publishers)A newly-developed Monte Carlo method is used to simulate the energetics, location and conformation of n-alkanes from butane to decane inside all-silica polymorphs of zeolites rho and ferrierite. Sorption in ferrierite yields far larger heats of adsorption than in rho. In rho, the alkanes adopt highly coiled conformations within the α-cages of the structure, whereas in ferrierite they are confined to all-trans conformations within the 10-ring channel. Only butane is distributed over both the 8-ring and 10-ring channels of ferrierite in the approx. ratio of 1:2. An increase in temp. to 498 K has little effect on the heats of adsorption, locations or conformations of the alkanes.**58**Kresse, G.; Furthmüller, J. Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set.*Phys. Rev. B: Condens. Matter Mater. Phys.*1996,*54*, 11169– 11186, DOI: 10.1103/physrevb.54.1116958https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK28Xms1Whu7Y%253D&md5=9c8f6f298fe5ffe37c2589d3f970a697Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis setKresse, G.; Furthmueller, J.Physical Review B: Condensed Matter (1996), 54 (16), 11169-11186CODEN: PRBMDO; ISSN:0163-1829. (American Physical Society)The authors present an efficient scheme for calcg. the Kohn-Sham ground state of metallic systems using pseudopotentials and a plane-wave basis set. In the first part the application of Pulay's DIIS method (direct inversion in the iterative subspace) to the iterative diagonalization of large matrixes will be discussed. This approach is stable, reliable, and minimizes the no. of order Natoms3 operations. In the second part, we will discuss an efficient mixing scheme also based on Pulay's scheme. A special "metric" and a special "preconditioning" optimized for a plane-wave basis set will be introduced. Scaling of the method will be discussed in detail for non-self-consistent and self-consistent calcns. It will be shown that the no. of iterations required to obtain a specific precision is almost independent of the system size. Altogether an order Natoms2 scaling is found for systems contg. up to 1000 electrons. If we take into account that the no. of k points can be decreased linearly with the system size, the overall scaling can approach Natoms. They have implemented these algorithms within a powerful package called VASP (Vienna ab initio simulation package). The program and the techniques have been used successfully for a large no. of different systems (liq. and amorphous semiconductors, liq. simple and transition metals, metallic and semiconducting surfaces, phonons in simple metals, transition metals, and semiconductors) and turned out to be very reliable.**59**Perdew, J. P.; Burke, K.; Ernzerhof, M. Generalized Gradient Approximation Made Simple [Phys. Rev. Lett. 77, 3865 (1996)].*Phys. Rev. Lett.*1997,*78*, 1396, DOI: 10.1103/physrevlett.78.139659https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2sXht1Gns7o%253D&md5=ecdb6e129b112a3a10e08cba26a083aeGeneralized gradient approximation made simple. [Erratum to document cited in CA126:51093]Perdew, John P.; Burke, Kieron; Ernzerhof, MatthiasPhysical Review Letters (1997), 78 (7), 1396CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)The errors were not reflected in the abstr. or the index entries.**60**Grimme, S. Semiempirical GGA-type density functional constructed with a long-range dispersion correction.*J. Comput. Chem.*2006,*27*, 1787– 1799, DOI: 10.1002/jcc.2049560https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XhtFenu7bO&md5=0b4aa16bebc3a0a2ec175d4b161ab0e4Semiempirical GGA-type density functional constructed with a long-range dispersion correctionGrimme, StefanJournal of Computational Chemistry (2006), 27 (15), 1787-1799CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)A new d. functional (DF) of the generalized gradient approxn. (GGA) type for general chem. applications termed B97-D is proposed. It is based on Becke's power-series ansatz from 1997 and is explicitly parameterized by including damped atom-pairwise dispersion corrections of the form C6·R-6. A general computational scheme for the parameters used in this correction has been established and parameters for elements up to xenon and a scaling factor for the dispersion part for several common d. functionals (BLYP, PBE, TPSS, B3LYP) are reported. The new functional is tested in comparison with other GGAs and the B3LYP hybrid functional on std. thermochem. benchmark sets, for 40 noncovalently bound complexes, including large stacked arom. mols. and group II element clusters, and for the computation of mol. geometries. Further cross-validation tests were performed for organometallic reactions and other difficult problems for std. functionals. In summary, it is found that B97-D belongs to one of the most accurate general purpose GGAs, reaching, for example for the G97/2 set of heat of formations, a mean abs. deviation of only 3.8 kcal mol-1. The performance for noncovalently bound systems including many pure van der Waals complexes is exceptionally good, reaching on the av. CCSD(T) accuracy. The basic strategy in the development to restrict the d. functional description to shorter electron correlation lengths scales and to describe situations with medium to large interat. distances by damped C6·R-6 terms seems to be very successful, as demonstrated for some notoriously difficult reactions. As an example, for the isomerization of larger branched to linear alkanes, B97-D is the only DF available that yields the right sign for the energy difference. From a practical point of view, the new functional seems to be quite robust and it is thus suggested as an efficient and accurate quantum chem. method for large systems where dispersion forces are of general importance.**61**Wilson, E. B.; Decius, J. C.; Cross, P. C.*Molecular Vibrations: The Theory of Infrared and Raman Vibrational Spectra*; Courier Corporation, 1980.There is no corresponding record for this reference.

## Supporting Information

## Supporting Information

ARTICLE SECTIONSThe Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jctc.1c00519.

Additional equations for the calculation of the free energies, decoupling of the vibrations due to the anharmonicity, additional computational details, data on adsorption of propane via secondary carbon, discussion on the vibrational active space, convergence check, and summary of the computed thermodynamic values (PDF)

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