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How the Lewis Base F– Catalyzes the 1,3-Dipolar Cycloaddition between Carbon Dioxide and Nitrilimines

  • Dennis Svatunek
    Dennis Svatunek
    Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMSS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
    Institute of Applied Synthetic Chemistry, TU Wien (Vienna University of Technology), A-1060, Vienna, Austria
    Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, Los Angeles, United States
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  • , 
  • Thomas Hansen
    Thomas Hansen
    Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMSS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
    Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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    Orcidhttp://orcid.org/0000-0002-6291-1569
  • , 
  • Kendall N. Houk
    Kendall N. Houk
    Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, Los Angeles, United States
    More by Kendall N. Houk
    Orcidhttp://orcid.org/0000-0002-8387-5261
  • , and 
  • Trevor A. Hamlin*
    Trevor A. Hamlin
    Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMSS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
    *E-mail: [email protected]
    More by Trevor A. Hamlin
    Orcidhttp://orcid.org/0000-0002-5128-1004
Cite this: J. Org. Chem. 2021, 86, 5, 4320–4325
Publication Date (Web):February 12, 2021
https://doi.org/10.1021/acs.joc.0c02963

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Abstract

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The mechanism of the Lewis base F– catalyzed 1,3-dipolar cycloaddition between CO2 and nitrilimines is interrogated using DFT calculations. F– activates the nitrilimine, not CO2 as proposed in the literature, and imparts a significant rate enhancement for the cycloaddition. The origin of this catalysis is in the strength of the primary orbital interactions between the reactants. The Lewis base activated nitrilimine–F– has high-lying filled FMOs. The smaller FMO-LUMO gap promotes a rapid nucleophilic attack and overall cycloaddition with CO2.

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The general use of small, highly abundant organic molecules, such as carbon dioxide (CO2), as building blocks in organic synthesis by activation and selective transformation to useful chemicals is highly attractive from both an economic and societal point of view. (1) Carbon dioxide is a desired feedstock for more complex hydrocarbon derivatives, since it is an abundant green-house gas that is cheap. (2) Chemists have engaged in significant efforts toward crafting methods to activate these otherwise unreactive molecules; however, it is in many cases a trial-and-error process, as the factors that play a role in the bond activation are not entirely understood.
In 2017, Lu and co-workers developed a convenient methodology to efficiently activate CO2 by F– (used as CsF/18-crown-6) and subsequently trap it with nitrilimines via a 1,3-dipolar cycloaddition to access 1,3,4-oxadiazole-2(3H)-ones (Scheme 1). (3) In this reaction, F– first acts as a base to produce the nitrilimine intermediate (i.e., a 1,3-dipole) from hydrazonyl chloride. The nitrilimine then undergoes a cycloaddition reaction with CO2 (i.e., dipolarophile) to form the oxadiazolone. It was found that the presence of a base (e.g., amines or carbonates) alone does not facilitate efficient conversion to the product, but instead generates a large amount of the (undesired) dimerized dipole product.

Scheme 1

Scheme 1. Proposed Mechanism of the Fluoride-Catalyzed 1,3-Dipolar Cycloaddition between CO2 and Nitrilimines by Lu and Co-workers, in Which the Lewis Base F– Together with CO2 Forms the Activated Dipolarophile (i.e., CO2F–); (3) R1 and R2 = Aryl or Alkyl
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The authors proposed the formation of the known and stable fluorocarbonate (CO2F–), (4) formed from CO2 and F–. Fluorocarbonate has been suggested to enhance the reactivity of CO2 in some reactions (Scheme 1). (5) The use of simple Lewis bases (e.g., F–) as catalysts for the activation of small molecules, which allows for efficient transformations under mild conditions, is of high interest. (6) Merino and co-workers previously investigated this reaction computationally and provided evidence for an operative mechanism based on the analysis of a number of possibly competing potential energy surfaces; however, they did not comment on the origin of the catalytic effect of the F– Lewis base. (7) Lu and co-workers experimentally showed that a base alone does not efficiently facilitate the cycloaddition reaction, so that F– is playing another role, presumably as a catalyst. (3) In contrast to the work of Merino et al., this indicates that F– does not solely act as a base. It is widely accepted that these 1,3-dipoles are readily formed from the hydrazonyl chloride, even in the presence of weak bases. (8) We have revisited the mechanism of this formal 1,3-dipolar cycloaddition between CO2 and nitrilimine to identify the catalytic role of the F– in this transformation.
Three possible reaction pathways (Scheme 2) have been investigated, using state-of-the-art DFT calculations, to unravel the physical mechanism behind the Lewis base F– activation in 1,3-dipolar cycloaddition reactions: (i) the uncatalyzed cycloaddition, (ii) the activation of the dipolarophile, by the generation of CO2F– by F–, followed by the cycloaddition, and (iii) the activation of the dipole by the addition of F– to nitrilimine 1 forming activated nitrilimine–F–2, followed by the cycloaddition. In order to pinpoint the actual role of F– in lowering the reaction barrier, we selected the model system depicted in Scheme 2. We found that the inclusion of Cs+ and 18-crown-6, as Merino and co-workers did, slightly raises the reaction barrier due to the fact that F– is less Lewis basic because of the interaction with the Cs+ (Supporting Information Figure S1), while the overall mechanism remained unchanged.

Scheme 2

Scheme 2. Possible Reaction Pathways for the 1,3-Dipolar Cycloaddition between Carbon Dioxide and Nitrilimine 1 in the Presence of the Lewis Base F–
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To identify the origin of the catalytic effect of the Lewis base, we employed the distortion/interaction–activation strain model (9) in combination with Kohn–Sham molecular orbital (KS-MO) (10) theory and energy decomposition analysis (EDA). (11) This methodological approach facilitates the analysis of the potential energy surface and, more importantly, the activation barrier, by decomposing the total energy of the system into chemically meaningful and easily interpretable terms and has been used by us to study other related 1,3-dipolar cycloadditions. (12)
The reaction profiles of the three reaction pathways of the studied 1,3-dipolar cycloaddition between carbon dioxide and nitrilimine 1 in the presence of the Lewis base F–, as well as their key transition state structures, are shown in Figure 1. The uncatalyzed pathway (i.e., pathway I; black) follows a concerted cycloaddition reaction with a barrier of ΔG‡ = 22.7 kcal mol–1 leading to product 3 (Figure 1a). The transition state, I-TS, is highly asynchronous, but is still concerted, with a C···N distance of 1.57 Å and a C···O distance of 2.33 Å (Figure 1b). This relatively high computed reaction barrier is consistent with the experimentally observed dimerization of nitrilimine 1 in the absence of F–, a process that goes with a more favorable barrier of ΔG⧧ = 20.1 kcal mol–1 (see SI Figure S2). (3)

Figure 1

Figure 1. (a) Reaction profiles (ΔGtoluene in kcal mol–1) for the three reaction pathways of the studied 1,3-dipolar cycloaddition between carbon dioxide and nitrilimine 1, including (i) uncatalyzed cycloaddition (black), (ii) formation of CO2F– followed by stepwise cycloaddition (blue), and (iii) formation of 2 followed by stepwise cycloaddition (red), computed at SMD(toluene)-M06-2X-D3/def2-TZVP; TS = transition state and INT = intermediate. (b) Key transition state structures with key bond lengths (in Å) for the three reaction pathways.

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Pathway II (blue) begins with the exergonic (ΔGrxn = −18.9 kcal mol–1) formation of CO2F– from CO2 and F–. Coodination of F– to CO2 is driven by stabilizing covalent and electrostatic interactions and induces a buildup of electron density on the oxygens of CO2F– compared to CO2 (see SI Table S1 and Figure S3). This leads, in contrast to pathway I, to a stepwise mechanism, whereby addition of the oxygen of the CO2F– to the electrophilic imine carbon center in II-TS occurs first and leads to II-INT (Figure 1b). This is the rate-limiting step of pathway II and goes with a reaction barrier of ΔG⧧ = 16.2 kcal mol–1, which is 6.5 kcal mol–1 lower than the uncatalyzed cycloaddition. Next, II-INT undergoes ring closure via a near barrierless pathway through II-TS2 (ΔG‡ = 1.2 kcal mol–1). Formation of product 3 and F– from II-INT2 is endergonic; however, the F– transfer, either to a second molecule of CO2 leading to 3 and CO2F– or to a second nitrilimine leading to 3 and 2, is exergonic. Lastly, pathway III (red), which like pathway II proceeds via a stepwise process, first begins with the barrierless formation of a Lewis base (or nucleophilic catalyst) activated nitrilimine–F– (i.e., 2) by the coordination of F– on the electrophilic nitrile carbon of nitrilimine 1 (see SI Figure S6). Formation of 2 is highly exergonic (ΔGrxn = −34.2 kcal mol–1) and is more than twice as favorable compared to the formation of CO2F– due to even more stabilizing covalent and electrostatic interactions (pathway II; blue, ΔΔGrxn = −15.3 kcal mol–1; see Table S1). The imine nitrogen of nitrilimine–F–2 exhibits an increased electron density, compared to dipole 1 (see SI Figure S3), and can engage in an efficient addition to CO2. Activated nitrilimine–F–2 can then proceed through transition state III-TS with a very low barrier of only 6.6 kcal mol–1, resulting in III-INT. This intermediate then undergoes intramolecular ring formation, through III-TS2 with a barrier of 14.3 kcal mol–1, to then form product 3 and regain the Lewis base F–. We have also computed pathway III with the corresponding Cl– adduct of 1, which is a similar intermediate to that proposed by Merino and co-workers, (7) and we found that F– adduct 2 follows a lower energy pathway in the reaction with CO2 (see Supporting Information, Schemes S1–S3 and Figure S1).
In order to gain quantitative insight into the physical factors why Lewis base catalyzed (i.e., nucleophilic-catalyzed) reaction pathway III is highly favored over the uncatalyzed pathway I, we turned to the distortion/interaction–activation strain model (D/I-ASM). (9) The D/I-ASM decomposes the electronic energy (ΔE) into two distinct energy terms, namely, the strain energy (ΔEstrain) and the interaction energy (ΔEint). The strain energy results from the deformation of the individual reactants and the interaction energy accounts for all chemical interactions between the deformed reactants along the reaction coordinate, defined, in this case, as the forming N···C bond. (12) As previously discussed, pathway I goes with a reaction barrier of 22.7 kcal mol–1, while the first step of pathway III proceeds with a barrier of only 6.6 kcal mol–1. Figure 2a shows the D-I/ASM analysis of pathway I (black) and pathway III (red). The origin of the lower barrier, in terms of electronic energy (trends are consistent for ΔE‡ and ΔG‡) for Lewis base catalyzed pathway III, can be traced exclusively to a more stabilizing interaction energy, while having a comparable strain energy.

Figure 2

Figure 2. (a) Distortion/interaction–activation strain model analysis; and (b) energy decomposition analysis of the cycloaddition reaction of 1 (black) and 2 (red) with CO2 (transition states indicated with a dot). (13) (c) Frontier molecular orbital diagram of the most important FMO-LUMOCO2 orbital interaction with the calculated energy gaps, orbital overlaps, and the S2/Δε terms, at consistent geometries with a N···C bond length of 2.14 Å. Computed at SMD(toluene)-M06-2X-D3/def2-TZVP using autoDIAS (14) for (a) and M06-2X-D3/TZ2P//SMD(toluene)-M06-2X-D3/def2-TZVP using PyFrag (15) for (b,c).

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The interaction energy between the deformed reactants can be further analyzed in terms of quantitative Kohn–Sham molecular orbital theory (KS-MO) (10) together with a canonical energy decomposition analysis (EDA). (11) The EDA decomposes the ΔEint into the following four physically meaningful energy terms: electrostatic interactions (ΔVelstat), (steric) Pauli repulsion (ΔEPauli), orbital interactions (ΔEoi), and disperision interactions (ΔEdisp). The EDA (Figure 2b) shows that the more stabilizing ΔEint for the Lewis base catalyzed pathway III originates from a significantly more stabilizing ΔEoi. The ΔVelstat is slightly more stabilizing and the ΔEPauli remains almost unchanged. The origin of the more stabilizing of the Lewis base catalyzed pathway can be analyzed and explained by means of a Kohn–Sham molecular orbital analysis (KS-MO). We have quantified the key occupied–unoccupied orbital interaction between the FMO of 1 and 2 and the antibonding unoccupied orbital of CO2 at consistent geometries with a N···C bond length of 2.14 Å (Figure 2c). The stronger orbital interaction of the Lewis base catalyzed pathway could be traced back to the smaller FMO energy gap for the normal electron demand (NED) orbital interactions with the LUMOCO2. This originates from the much higher energy of the filled FMOs of 2 (i.e., nitrilimine–F–), compared to 1 (i.e., uncatalyzed pathway). The HOMO of 2 also shows a similar trend, but the overlap is much lower since the orientation of this orbital is nearly orthogonal to the LUMOCO2 (see SI Figure S4). In all, the presence of the negatively charged Lewis base F– in 2 causes a significant negative external potential that destabilizes the FMOs (see SI Figure S5). Additionally, the FMOs, especially the HOMO–12, are further destabilized as a result of (steric) Pauli repulsion with the filled FMOs of F– (see SI Figure S5).
In conclusion, we have investigated the Lewis base, nucleophile, F– catalyzed 1,3-dipolar cycloaddition between CO2 and nitrilimine. In contrast to the previous proposed mechanism, (3) we find that the reaction actually proceeds via the addition of the Lewis base F– to the dipole (i.e., nitrilimine), thereby activating the dipole, which rapidly engages in nucleophilic attack and overall cycloaddition with CO2 (Scheme 3). Our distortion/interaction–activation strain analysis revealed that the mechanism behind the Lewis base catalysis was driven by the more stabilizing interaction energy between the reactants. This could be traced back to the stronger normal electron demand (NED) orbital interactions, as a result of the higher-lying donor orbitals of 2 (i.e., nitrilimine–F– species). This leads to smaller NED energy gaps and, thus, more stabilizing orbital interactions with the LUMO of CO2. F– destabilizes all FMOs of 2 by (i) the presence of a negative potential of the anion and (ii) the Pauli repulsion between the filled FMOs of the nitrilimine and F–. In all, this showcases the potential of Lewis base catalyzed small molecule activation, in which one can tune the reactivity of the reactants by the Lewis base.

Scheme 3

Scheme 3. Novel Mechanism Emerging from Our Study for the Lewis Base F– Catalyzed 1,3-Dipolar Cycloaddition of CO2 to Nitrilimines, Where F– Activates the Dipole, Instead of the Dipolarophile
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Methods

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Computational Details

Conformer searches were performed using Grimme’s CREST 2.7.1 (16) using default settings and toluene as solvent. DFT calculations were performed using Gaussian 09 Rev. D.01 (17) employing the M06-2X density functional (18) in combination with the def2-TZVP (19) basis set. Solvent effects were included by using the SMD model (20) as implemented in Gaussian with toluene as a solvent. Empirical dispersion was included using Grimme’s D3 model (21) without additional dampening as proposed by Grimme and co-workers. Quasi-harmonic correction (22) was applied to all frequencies by raising all vibrations below 100 cm–1 to 100 cm–1. All computed stationary points have been verified by performing a vibrational analysis calculation, to be energy minima (no imaginary frequencies) or transition states (only one imaginary frequency). The character of the normal mode associated with the imaginary frequency of the transition state has been inspected to ensure that it is associated with the reaction of interest. The potential energy surfaces of the studied cycloaddition reactions were obtained by performing intrinsic reaction coordinate (IRC) calculations. The distortion/interaction–activation strain model (D/I-ASM) (9) was performed by the use of autoDIAS, (14) followed by an energy decomposition analysis (EDA) (11) in the gas phase, based on the solution PES, using PyFrag (15) and the Amsterdam Density Functional (ADF2018.106) software package at M06-2X-D3/TZ2P. (23) The optimized structures were illustrated using CYLview. (24)

Distortion/Interaction–Activation Strain and Energy Decomposition Analysis

The distortion/interaction–activation strain model (9) is a fragment-based approach in which the potential energy surface (PES) can be described with respect to, and understood in terms of the characteristics of, the reactants. It considers the rigidity of the reactants and to which extent they need to deform during the reaction plus their capability to interact with each other as the reaction proceeds. With the help of this model, we decompose the total energy, ΔE, into the strain and interaction energy, ΔEstrain and ΔEint, respectively [eq 1].
(1)
In this equation, the strain energy, ΔEstrain, is the energy required in order to deform the reactants from their equilibrium to the geometry they adopt over the course of the reaction. On the other hand, the interaction energy, ΔEint, accounts for all the chemical interactions that occur between these two deformed reactants along the reaction coordinate.
The interaction energy between the deformed reactants can be further analyzed in terms of quantitative Kohn–Sham molecular orbital (KS-MO) (10) theory together with a canonical energy decomposition analysis (EDA). (11) The EDA decomposes the ΔEint into the following three energy terms [eq 2]:
(2)
Herein, ΔVelstat is the classical electrostatic interaction between the unperturbed charge distributions of the (deformed) reactants and is usually attractive. The Pauli repulsion, ΔEPauli, includes the destabilizing interaction between the fully occupied orbitals of both fragments due to the Pauli principle. The orbital interaction energy, ΔEoi, accounts for, among others, charge transfer between the fragments, such as HOMO–LUMO interactions. Finally, the ΔEdisp term accounts for the interactions coming from disperion forces. In the herein presented distortion/interaction–activation strain and accompanied energy decomposition diagrams, the energy terms are projected onto the forming bond (N···C) distance. This critical reaction coordinate undergoes a well-defined change during the reaction from the reactant complex via the transition state to the product. (12)

Voronoi Deformation Density

The atomic charge distribution was analyzed by using the Voronoi Deformation Density (VDD) method. (25) The VDD method partitions the space into so-called Voronoi cells, which are nonoverlapping regions of space that are closer to nucleus A than to any other nucleus. The charge distribution is determined by taking a fictitious promolecule as reference point, in which the electron density is simply the superposition of the atomic densities. The change in density in the Voronoi cell when going from this promolecule to the final molecular density of the interacting system is associated with the VDD atomic charge Q. The VDD atomic charge QA of atom A is calculated according to eq 3.
(3)
So, instead of computing the amount of charge contained in an atomic volume, we compute the flow of charge from one atom to the other upon formation of the molecule. The physical interpretation is therefore straightforward. A positive atomic charge QA corresponds to the loss of electrons, whereas a negative atomic charge QA is associated with the gain of electrons in the Voronoi cell of atom A.

Supporting Information

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The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.joc.0c02963.

  • Additional computational results; and Cartesian coordinates, energies, and number of imaginary frequencies of all stationary points (PDF)

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Author Information

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  • Corresponding Author
    • Trevor A. Hamlin - Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMSS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands;  Orcidhttp://orcid.org/0000-0002-5128-1004;  Email: [email protected]
  • Authors
    • Dennis Svatunek - Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMSS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands;  Institute of Applied Synthetic Chemistry, TU Wien (Vienna University of Technology), A-1060, Vienna, Austria;  Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, Los Angeles, United States
    • Thomas Hansen - Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMSS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands;  Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands;  Orcidhttp://orcid.org/0000-0002-6291-1569
    • Kendall N. Houk - Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, Los Angeles, United States;  Orcidhttp://orcid.org/0000-0002-8387-5261
  • Notes
    The authors declare no competing financial interest.

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D.S. is grateful to the Christiana Hörbiger Award (TU Wien) and the “Hochschuljubiläumsstiftung der Stadt Wien” (H-331849/2018) for financial support. K.N.H. is grateful to the National Science Foundation of the US for financial support of this research (CHE-1764328). Quantum chemical calculations were performed on the Vienna Scientific Cluster (Austria), the Hoffman2 Cluster (UCLA Institute for Digital Research and Education), and the Cartesius supercomputer (SURFsara, Amsterdam). The authors also acknowledge Pascal Vermeeren of the Vrije Universiteit Amsterdam for fruitful discussions.

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    Carbon dioxide is a desired feedstock for platform molecules, such as carbon monoxide or higher hydrocarbons, from which we will be able to make many different useful, value-added chemicals. Its catalytic hydrogenation over abundant metals requires the amalgamation of theoretical knowledge with materials design. Here we leverage a theoretical understanding of structure sensitivity, along with a library of different supports, to tune the selectivity of methanation in the Power-to-Gas concept over nickel. For example, we show that carbon dioxide hydrogenation over nickel can and does form propane, and that activity and selectivity can be tuned by supporting different nickel particle sizes on various oxides. This theoretical and experimental toolbox is not only useful for the highly selective production of methane, but also provides new insights for carbon dioxide activation and subsequent carbon-carbon coupling towards value-added products thereby reducing the deleterious effects of this environmentally harmful molecule.
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    Transition Metal-Free Synthesis of Carbamates Using CO2 as the Carbon Source
    Schilling, Waldemar; Das, Shoubhik
    ChemSusChem (2020), 13 (23), 6246-6258CODEN: CHEMIZ; ISSN:1864-5631. (Wiley-VCH Verlag GmbH & Co. KGaA)
    A review. Utilization of carbon dioxide as a C1 synthon is highly attractive for the synthesis of valuable chems. However, activation of CO2 is highly challenging, owing to its thermodn. stability and kinetic inertness. With this in mind, several strategies have been developed for the generation of carbon-heteroatom bonds. Among these, formation of C-N bonds is highly attractive, esp., when carbamates can be synthesized directly from CO2. This Minireview focuses on transition metal-free approaches for the fixation of CO2 to generate carbamates for the prodn. of fine chems. and pharmaceuticals. Within the past decade, transition metal-free approaches have gained increasing attention, but traditional reviews have rarely focused on these approaches. Direct comparisons between such methods have been even more scarce. This Minireview seeks to address this discrepancy.
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  3. 3
    Guo, C.-X.; Zhang, W.-Z.; Zhang, N.; Lu, X.-B. 1,3-Dipolar Cycloaddition of Nitrile Imine with Carbon Dioxide: Access to 1,3,4-Oxadiazole-2(3H)-ones. J. Org. Chem. 2017, 82, 7637,  DOI: 10.1021/acs.joc.7b00963
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    1,3-Dipolar Cycloaddition of Nitrile Imine with Carbon Dioxide: Access to 1,3,4-Oxadiazole-2(3H)-ones
    Guo, Chun-Xiao; Zhang, Wen-Zhen; Zhang, Ning; Lu, Xiao-Bing
    Journal of Organic Chemistry (2017), 82 (14), 7637-7642CODEN: JOCEAH; ISSN:0022-3263. (American Chemical Society)
    Efficient synthesis of 1,3,4-oxadiazole-2(3H)-one was achieved by CsF/18-crown-6 mediated 1,3-dipolar cycloaddn. of nitrile imine and 2.0 MPa of CO2. CsF/18-crown-6 played a key role in enhancing the reactivity of CO2 as a 1,3-dipolarophile. The practical utility of this transition-metal-free approach to 1,3,4-oxadiazole-2(3H)-one is highlighted by the convenient synthesis of a com. herbicide Oxadiazon and a MAO B inhibitor.
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    (a) Zhang, X.; Gross, U.; Seppelt, K. Fluorocarbonate, [FCO2]−: Preparation and Structure. Angew. Chem., Int. Ed. Engl. 1995, 34, 1858– 1860,  DOI: 10.1002/anie.199518581
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    Zhang, Xiongzhi; Gross, Udo; Seppelt, Konrad
    Angewandte Chemie, International Edition in English (1995), 34 (17), 1858-60CODEN: ACIEAY; ISSN:0570-0833. (VCH)
    CO2 reacts with F- salts of Me4N+ or Me3(Me3CCH2)N+ or 1,1,3,3,5,5-hexamethylpiperidinium (pip+) to give [FCO2]- salts. Elemental anal. of pip+[FCO2] and NMR of Me4N[FCO2] confirm the identity of the anion. For the latter, multinuclear NMR, IR and Raman data are given. Ab initio calcns. for enthalpy of reaction of F- with CO, N2O, or H2C:C:CH2 indicate the fluoride affinity of CO2 may be the approx. lower limit for a reaction.
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    (b) Arnold, D. W.; Bradforth, S. E.; Kim, E. H.; Neumark, D. M. Study of halogen-carbon dioxide clusters and the fluoroformyloxyl radical by photodetachment of X–(CO2) (X= I, Cl, Br) and FCO2–. J. Chem. Phys. 1995, 102, 3493,  DOI: 10.1063/1.468575
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    Study of halogen-carbon dioxide clusters and the fluoroformyloxyl radical by photodetachment of X-(CO2) (X = I,Cl,Br) and FCO-2
    Arnold, Don W.; Bradforth, Stephen E.; Kim, Eun H.; Neumark, Daniel M.
    Journal of Chemical Physics (1995), 102 (9), 3493-509CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
    Photoelectron spectra have been measured for the anions X-(CO2), with X = I, Br, Cl, and F. The vibrationally resolved spectra show that I-(CO2), Br-(CO2), and Cl-(CO2) are primarily electrostatically bound clusters, although the charge-quadrupole interaction is strong enough to distort the CO2 mol. by as much as 10° [in Cl-(CO2)]. Ab initio calcns. and electrostatic models are used to describe the geometry and bonding of these clusters. The photoelectron spectrum of FCO2- is qual. different and shows transitions to both the ~X 2B2 ground and the ~A2A2 first excited electronic states of the covalently bound FCO2 radical. The previously unobserved ~A 2A2 state is measured to lie 0.579 eV above the ground state. Vibrational frequencies are assigned with the assistance of ab initio calcns. The FCO2 heat of formation is detd. to be ΔfH0298(FCO2)= -85.2±2.8 kcal/mol. While both FCO2- and FCO2 are more strongly bound than the other halide-CO2 clusters, the C-F bonds are very weak relative to C-F bounds found in other halocarbon compds.
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    (a) Ukai, K.; Aoki, M.; Takaya, J.; Iwasawa, N. Rhodium(I)-Catalyzed Carboxylation of Aryl- and Alkenylboronic Esters with CO2. J. Am. Chem. Soc. 2006, 128, 8706,  DOI: 10.1021/ja061232m
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    Rhodium(I)-Catalyzed Carboxylation of Aryl- and Alkenylboronic Esters with CO2
    Ukai, Kazutoshi; Aoki, Masao; Takaya, Jun; Iwasawa, Nobuharu
    Journal of the American Chemical Society (2006), 128 (27), 8706-8707CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    When the esters of arylboronic acids with 2,2-dimethyl-1,3-propanol were treated with a catalytic amt. of [Rh(OH)(cod)]2 in the presence of 1,3-bis(diphenylphosphino)propane and CsF in dioxane at 60 °C under carbon dioxide atm., the benzoic acid derivs. were obtained in good yields. Reactions of alkenylboronic esters also proceeded under similar conditions to give α,β-unsatd. carboxylic acids. As these boronic esters are now easily available through coupling or direct borylation reactions, this method would be a useful method for the prepn. of various functionalized aryl- and alkenyl carboxylic acids. For example, the rhodium-catalyzed reaction of a boronic acid ester, i.e., 5,5-dimethyl-2-phenyl-1,3,2-dioxaborinane, with carbon dioxide gave benzoic acid.
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    (b) Li, S.; Ma, S. Quadri-Synergetic Effect for Highly Effective Carbon Dioxide Fixation and Its Application to Indoloquinolinone. Adv. Synth. Catal. 2012, 354, 2387– 2394,  DOI: 10.1002/adsc.201200469
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    Quadri-Synergetic Effect for Highly Effective Carbon Dioxide Fixation and Its Application to Indoloquinolinone
    Li, Suhua; Ma, Shengming
    Advanced Synthesis & Catalysis (2012), 354 (13), 2387-2394, S2387/1-S2387/65CODEN: ASCAF7; ISSN:1615-4150. (Wiley-VCH Verlag GmbH & Co. KGaA)
    The first copper-catalyzed cyclic anti-nucleometallation-carboxylation of 2-alkynylanilines with carbon dioxide in the presence of dimethylzinc (ZnMe2) and cesium fluoride (CsF) for the effective synthesis of indolyl-3-carboxylic acids and indolodihydropyran-2-one is described. Through a mechanistic study, it is unveiled that the metal ions Cu2+, Zn2+, Cs+ and F- are working together for this CO2-based highly efficient carboxylation.
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    (c) Takaya, J.; Tadami, S.; Ukai, K.; Iwasawa, N. Copper (I)-catalyzed carboxylation of aryl-and alkenylboronic esters. Org. Lett. 2008, 10, 2697– 2700,  DOI: 10.1021/ol800829q
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    5c
    Copper(I)-Catalyzed Carboxylation of Aryl- and Alkenylboronic Esters
    Takaya, Jun; Tadami, Satoshi; Ukai, Kazutoshi; Iwasawa, Nobuharu
    Organic Letters (2008), 10 (13), 2697-2700CODEN: ORLEF7; ISSN:1523-7060. (American Chemical Society)
    The copper(I)-catalyzed carboxylation reaction of aryl- and alkenylboronic esters proceeded smoothly under CO2 to give the corresponding carboxylic acids in good yield. This reaction showed wide generality with higher functional group tolerance compared to the corresponding Rh(I)-catalyzed reaction.
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    Denmark, S. E.; Beutner, G. L. Lewis Base Catalysis in Organic Synthesis. Angew. Chem., Int. Ed. 2008, 47, 1560– 1638,  DOI: 10.1002/anie.200604943
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    Lewis base catalysis in organic synthesis
    Denmark, Scott E.; Beutner, Gregory L.
    Angewandte Chemie, International Edition (2008), 47 (9), 1560-1638CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
    A review. The legacy of Gilbert Newton Lewis (1875-1946) pervades the lexicon of chem. bonding and reactivity; the power of his concept of donor-acceptor bonding is evident in the eponymous foundations of electron-pair acceptors (Lewis acids) and donors (Lewis bases). His discovery ushered in the use of Lewis acids as reagents and catalysts for org. reactions. However, in recent years, the recognition that Lewis bases can also serve in this capacity has grown enormously. Most importantly, it has become increasingly apparent that the behavior of Lewis bases as agents for promoting chem. reactions is not merely as an electronic complement of the cognate Lewis acids: in fact Lewis bases are capable of enhancing both the electrophilic and nucleophilic character of mols. to which they are bound. This diversity of behavior leads to a remarkable versatility for the catalysis of reactions by Lewis bases.
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    Murillo, F.; Barroso, J.; de los Santos, M. G.; Ávila, G.; Pan, S.; Fernández-Herrera, M. A.; Merino, G. Revisiting the Formation Mechanism of 1,3,4-Oxadiazole-2(3H)-ones from Hydrazonyl Chloride and Carbon Dioxide. J. Org. Chem. 2018, 83, 13045– 13050,  DOI: 10.1021/acs.joc.8b01676
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    7
    Revisiting the Formation Mechanism of 1,3,4-Oxadiazole-2(3H)-ones from Hydrazonyl Chloride and Carbon Dioxide
    Murillo, Fernando; Barroso, Jorge; de los Santos, Maria G.; Avila, Gustavo; Pan, Sudip; Fernandez-Herrera, Maria A.; Merino, Gabriel
    Journal of Organic Chemistry (2018), 83 (21), 13045-13050CODEN: JOCEAH; ISSN:0022-3263. (American Chemical Society)
    The reaction mechanism for the synthesis of 1,3,4-oxadiazole-2(3H)-ones from hydrazonyl chloride and CO2 in the presence of CsF/18-crown-6 and toluene, is revisited via d. functional theory computations. Although this reaction was earlier classified as a 1,3-dipolar cycloaddn., we found some competing pathways involved therein. The mechanisms including the (F-CO2)- anion and the nitrile imine intermediate are some options. The dimerization of nitrile imine is another competing mechanism in this reaction. Our results show that the most favorable mechanism proceeds via a stepwise pathway without involving any nitrile imine intermediate or the (F-CO2)- anion. The F- anion, resulting from the formation of a complex between 18-crown-6 and Cs+ cation, deprotonates the nitrile imine precursor easily, which acts then as a nucleophilic anion, enhancing the reactivity of CO2 toward it. The mechanism for the reaction with COS, an isoelectronic analog of CO2, is also explored.
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  8. 8
    (a) Wang, X. S.; Lee, Y. J.; Liu, W. R. The nitrilimine-alkene cycloaddition is an ultra rapid click reaction. Chem. Commun. 2014, 50, 3176– 3179,  DOI: 10.1039/C3CC48682F
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    8a
    The nitrilimine-alkene cycloaddition is an ultra rapid click reaction
    Wang, Xiaoshan Shayna; Lee, Yan-Jiun; Liu, Wenshe R.
    Chemical Communications (Cambridge, United Kingdom) (2014), 50 (24), 3176-3179CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)
    The transient formation of nitrilimine in aq. conditions is greatly influenced by pH and chloride. In basic conditions (pH 10) with no chloride, a diarylnitrilimine precursor readily ionizes to form diarylnitrilimine that reacts almost instantly with an acrylamide-contg. protein and fluorescently labels it.
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    (b) Molteni, G.; Ponti, A. The Nitrilimine-Alkene Cycloaddition Regioselectivity Rationalized by Density Functional Theory Reactivity Indices. Molecules 2017, 22, 202,  DOI: 10.3390/molecules22020202
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    The nitrilimine-alkene cycloaddition regioselectivity rationalized by density functional theory reactivity indices
    Molteni, Giorgio; Ponti, Alessandro
    Molecules (2017), 22 (2), 202/1-202/12CODEN: MOLEFW; ISSN:1420-3049. (MDPI AG)
    Conventional frontier MO theory is not able to satisfactorily explain the regioselectivity outcome of the nitrilimine-alkene cycloaddn. We considered that conceptual d. functional theory (DFT) could be an effective theor. framework to rationalize the regioselectivity of the title reaction. Several nitrilimine-alkene cycloaddns. were analyzed, for which we could find regioselectivity data in the literature. We computed DFT reactivity indexes at the B3LYP/6-311G(2d,p)//B3LYP/6-31G(d,p) and employed the grand potential stabilization criterion to calc. the preferred regioisomer. Exptl. and calcd. regioselectivity agree in the vast majority of cases. It was concluded that predominance of a single regioisomer can be obtained by maximizing (i) the chem. p.d. between nitrilimine and alkene and (ii) the local softness difference between the reactive at. sites within each reactant. Such maximization can be achieved by carefully selecting the substituents on both reactants.
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    (c) Shawali, A. S. Chemoselectivity in 1,3-dipolar cycloaddition reactions of nitrilimines with multifunctionalized dipolarophiles. Curr. Org. Chem. 2014, 18, 598– 614,  DOI: 10.2174/1385272819666140201002900
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    Chemoselectivity in 1,3-Dipolar Cycloaddition Reactions of Nitrilimines with Multifunctionalized Dipolarophiles
    Shawali, Ahmad S.
    Current Organic Chemistry (2014), 18 (5), 598-614CODEN: CORCFE; ISSN:1385-2728. (Bentham Science Publishers Ltd.)
    A review. This review presents a survey of literature reports dealing with both site and peri-selectivities in cycloaddn. reactions of nitrilimines with multifunctionalized dipolarophiles. The literature results covered in this review, during the period from 1970 to mid 2013, demonstrated that chemo-selectivity plays an important role in synthetic design.
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    (a) Bickelhaupt, F. M.; Houk, K. N. Analyzing Reaction Rates with the Distortion/Interaction-Activation Strain Model. Angew. Chem., Int. Ed. 2017, 56, 10070– 10086,  DOI: 10.1002/anie.201701486
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    Analyzing Reaction Rates with the Distortion/Interaction-Activation Strain Model
    Bickelhaupt, F. Matthias; Houk, Kendall N.
    Angewandte Chemie, International Edition (2017), 56 (34), 10070-10086CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
    The activation strain or distortion/interaction model is a tool to analyze activation barriers that det. reaction rates. For bimol. reactions, the activation energies are the sum of the energies to distort the reactants into geometries they have in transition states plus the interaction energies between the two distorted mols. The energy required to distort the mols. is called the activation strain or distortion energy. This energy is the principal contributor to the activation barrier. The transition state occurs when this activation strain is overcome by the stabilizing interaction energy. Following the changes in these energies along the reaction coordinate gives insights into the factors controlling reactivity. This model has been applied to reactions of all types in both org. and inorg. chem., including substitutions and eliminations, cycloaddns., and several types of organometallic reactions.
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    Bickelhaupt, F. M.; Houk, K. N. Angew. Chem. 2017, 129, 10204– 10221,  DOI: 10.1002/ange.201701486
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    (b) Vermeeren, P.; van der Lubbe, S. C. C.; Fonseca Guerra, C.; Bickelhaupt, F. M.; Hamlin, T. A. Understanding Chemical Reactivity Using the Activation Strain Model. Nat. Protoc. 2020, 15, 649– 667,  DOI: 10.1038/s41596-019-0265-0
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    9b
    Understanding chemical reactivity using the activation strain model
    Vermeeren, Pascal; van der Lubbe, Stephanie C. C.; Fonseca Guerra, Celia; Bickelhaupt, F. Matthias; Hamlin, Trevor A.
    Nature Protocols (2020), 15 (2), 649-667CODEN: NPARDW; ISSN:1750-2799. (Nature Research)
    Understanding chem. reactivity through the use of state-of-the-art computational techniques enables chemists to both predict reactivity and rationally design novel reactions. This protocol aims to provide chemists with the tools to implement a powerful and robust method for analyzing and understanding any chem. reaction using PyFrag 2019. The approach is based on the so-called activation strain model (ASM) of reactivity, which relates the relative energy of a mol. system to the sum of the energies required to distort the reactants into the geometries required to react plus the strength of their mutual interactions. Other available methods analyze only a stationary point on the potential energy surface, but our methodol. analyzes the change in energy along a reaction coordinate. The use of this methodol. has been proven to be crit. to the understanding of reactions, spanning the realms of the inorg. and org., as well as the supramol. and biochem., fields. This protocol provides step-by-step instructions-starting from the optimization of the stationary points and extending through calcn. of the potential energy surface and anal. of the trend-decisive energy terms-that can serve as a guide for carrying out the anal. of any given reaction of interest within hours to days, depending on the size of the mol. system.
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    The activation strain model and molecular orbital theory: understanding and designing chemical reactions
    Fernandez, Israel; Bickelhaupt, F. Matthias
    Chemical Society Reviews (2014), 43 (14), 4953-4967CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)
    A review. In this Tutorial Review, we make the point that a true understanding of trends in reactivity (as opposed to measuring or simply computing them) requires a causal reactivity model. To this end, we present and discuss the Activation Strain Model (ASM). The ASM establishes the desired causal relationship between reaction barriers, on one hand, and the properties of reactants and characteristics of reaction mechanisms, on the other hand. In the ASM, the potential energy surface ΔE(ζ) along the reaction coordinate ζ is decompd. into the strain ΔEstrain(ζ) of the reactants that become increasingly deformed as the reaction proceeds, plus the interaction ΔEint(ζ) between these deformed reactants, i.e., ΔE(ζ) = ΔEstrain(ζ) + ΔEint(ζ). The ASM can be used in conjunction with any quantum chem. program. An anal. of the method and its application to problems in org. and organometallic chem. illustrate the power of the ASM as a unifying concept and a tool for rational design of reactants and catalysts.
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    Bickelhaupt, F. M.; Baerends, E. J. Kohn-Sham Density Functional Theory: Predicting and Understanding Chemistry. In Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B., Eds.; Wiley-VCH: New York, 2000; Vol. 15, pp 1– 86.
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    (a) van Meer, R.; Gritsenko, O. V.; Baerends, E. J. Physical Meaning of Virtual Kohn-Sham Orbitals and Orbital Energies: An Ideal Basis for the Description of Molecular Excitations. J. Chem. Theory Comput. 2014, 10, 4432– 4441,  DOI: 10.1021/ct500727c
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    Physical Meaning of Virtual Kohn-Sham Orbitals and Orbital Energies: An Ideal Basis for the Description of Molecular Excitations
    van Meer, R.; Gritsenko, O. V.; Baerends, E. J.
    Journal of Chemical Theory and Computation (2014), 10 (10), 4432-4441CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
    In recent years, several benchmark studies on the performance of large sets of functionals in time-dependent d. functional theory (TDDFT) calcns. of excitation energies have been performed. The tested functionals do not approx. exact Kohn-Sham orbitals and orbital energies closely. We highlight the advantages of (close to) exact Kohn-Sham orbitals and orbital energies for a simple description, very often as just a single orbital-to-orbital transition, of mol. excitations. Benchmark calcns. are performed for the statistical av. of orbital potentials (SAOP) functional for the potential [J. Chem. Phys. 2000, 112, 1344; 2001, 114, 652], which approximates the true Kohn-Sham potential much better than LDA, GGA, mGGA, and hybrid potentials do. An accurate Kohn-Sham potential not only performs satisfactorily for calcd. vertical excitation energies of both valence and Rydberg transitions, but also exhibits appealing properties of the KS orbitals including occupied orbital energies close to ionization energies, virtual-occupied orbital energy gaps very close to excitation energies, realistic shapes of virtual orbitals, leading to straightforward interpretation of most excitations as single orbital transitions. We stress that such advantages are completely lost in time-dependent Hartree-Fock and partly in hybrid approaches. Many excitations and excitation energies calcd. with local d., generalized gradient, and hybrid functionals are spurious. There is, with an accurate KS, or even the LDA or GGA potentials, nothing problematic about the "band gap" in mols.: the HOMO-LUMO gap is close to the first excitation energy (the optical gap).
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  12. 12
    (a) Yu, S.; Vermeeren, P.; van Dommelen, K.; Bickelhaupt, F. M.; Hamlin, T. A. Understanding the 1,3-Dipolar Cycloadditions of Allenes. Chem. - Eur. J. 2020, 26, 11529– 11539,  DOI: 10.1002/chem.202000857
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    12a
    Understanding the 1,3-Dipolar Cycloadditions of Allenes
    Yu, Song; Vermeeren, Pascal; van Dommelen, Kevin; Bickelhaupt, F. Matthias; Hamlin, Trevor A.
    Chemistry - A European Journal (2020), 26 (50), 11529-11539CODEN: CEUJED; ISSN:0947-6539. (Wiley-VCH Verlag GmbH & Co. KGaA)
    We have quantum chem. studied the reactivity, site-, and regioselectivity of the 1,3-dipolar cycloaddn. between Me azide and various allenes, including the archetypal allene propadiene, heteroallenes, and cyclic allenes, by using d. functional theory (DFT). The 1,3-dipolar cycloaddn. reactivity of linear (hetero)allenes decreases as the no. of heteroatoms in the allene increases, and formation of the 1,5-adduct is, in all cases, favored over the 1,4-adduct. Both effects find their origin in the strength of the primary orbital interactions. The cycloaddn. reactivity of cyclic allenes was also investigated, and the increased predistortion of allenes, that results upon cyclization, leads to systematically lower activation barriers not due to the expected variations in the strain energy, but instead from the differences in the interaction energy. The geometric predistortion of cyclic allenes enhances the reactivity compared to linear allenes through a unique mechanism that involves a smaller HOMO-LUMO gap, which manifests as more stabilizing orbital interactions.
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    .
    (b) Hamlin, T. A.; Levandowski, B. J.; Narsaria, A. K.; Houk, K. N.; Bickelhaupt, F. M. Bickelhaupt. Structural Distortion of Cycloalkynes Influences Cycloaddition Rates by both Strain and Interaction Energies. Chem. - Eur. J. 2019, 25, 6342– 6348,  DOI: 10.1002/chem.201900295
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    12b
    Structural Distortion of Cycloalkynes Influences Cycloaddition Rates both by Strain and Interaction Energies
    Hamlin, Trevor A.; Levandowski, Brian J.; Narsaria, Ayush K.; Houk, Kendall N.; Bickelhaupt, F. Matthias
    Chemistry - A European Journal (2019), 25 (25), 6342-6348CODEN: CEUJED; ISSN:0947-6539. (Wiley-VCH Verlag GmbH & Co. KGaA)
    The reactivities of 2-butyne, cycloheptyne, cyclooctyne, and cyclononyne in the 1,3-dipolar cycloaddn. reaction with Me azide were evaluated through DFT calcns. at the M06-2X/6-311++G(d)//M06-2X/6-31+G(d) level of theory. Computed activation free energies for the cycloaddns. of cycloalkynes are 16.5-22.0 kcal mol-1 lower in energy than that of the acyclic 2-butyne. The strained or predistorted nature of cycloalkynes is often solely used to rationalize this significant rate enhancement. Our distortion/interaction-activation strain anal. has been revealed that the degree of geometrical predistortion of the cycloalkyne ground-state geometries acts to enhance reactivity compared with that of acyclic alkynes through three distinct mechanisms, not only due to (i) a reduced strain or distortion energy, but also to (ii) a smaller HOMO-LUMO gap, and (iii) an enhanced orbital overlap, which both contribute to more stabilizing orbital interactions.
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    .
    (c) Hamlin, T. A.; Svatunek, D.; Yu, S.; Ridder, L.; Infante, I.; Visscher, L.; Bickelhaupt, F. M. Elucidating the Trends in Reactivity of Aza-1,3-Dipolar Cycloadditions. Eur. J. Org. Chem. 2019, 2019, 378– 386,  DOI: 10.1002/ejoc.201800572
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    12c
    Elucidating the Trends in Reactivity of Aza-1,3-Dipolar Cycloadditions
    Hamlin, Trevor A.; Svatunek, Dennis; Yu, Song; Ridder, Lars; Infante, Ivan; Visscher, Lucas; Bickelhaupt, F. Matthias
    European Journal of Organic Chemistry (2019), 2019 (2-3), 378-386CODEN: EJOCFK; ISSN:1099-0690. (Wiley-VCH Verlag GmbH & Co. KGaA)
    This report describes a d. functional theory investigation into the reactivities of a series of aza-1,3-dipoles with ethylene at the BP86/TZ2P level. A benchmark study was carried out using QMflows, a newly developed program for automated workflows of quantum chem. calcns. In total, 24 1,3-dipolar cycloaddn. (1,3-DCA) reactions were benchmarked using the highly accurate G3B3 method as a ref. We screened a no. of exchange and correlation functionals, including PBE, OLYP, BP86, BLYP, both with and without explicit dispersion corrections, to assess their accuracies and to det. which of these computationally efficient functionals performed the best for calcg. the energetics for cycloaddn. reactions. The BP86/TZ2P method produced the smallest errors for the activation and reaction enthalpies. Then, to understand the factors controlling the reactivity in these reactions, seven archetypal aza-1,3-dipolar cycloaddns. were investigated using the activation strain model and energy decompn. anal. Our investigations highlight the fact that differences in activation barrier for these 1,3-DCA reactions do not arise from differences in strain energy of the dipole, as previously proposed. Instead, relative reactivities originate from differences in interaction energy. Anal. of the 1,3-dipole-dipolarophile interactions reveals the reactivity trends primarily result from differences in the extent of the primary orbital interactions.
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  13. 13

    Differences in the dispersion curves were neglectable and were omitted for clarity.

    There is no corresponding record for this reference.
  14. 14
    Svatunek, D.; Houk, K. N. autoDIAS: a python tool for an automated distortion/interaction activation strain analysis. J. Comput. Chem. 2019, 40, 2509,  DOI: 10.1002/jcc.26023
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    14
    autoDIAS: a python tool for an automated distortion/interaction activation strain analysis
    Svatunek, Dennis; Houk, Kendall N.
    Journal of Computational Chemistry (2019), 40 (28), 2509-2515CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)
    The distortion/interaction activation strain (DIAS) anal. is a powerful tool for the investigation of energy barriers. However, setup and data anal. of such a calcn. can be cumbersome and requires lengthy intervention of the user. We present autoDIAS, a python tool for the automated setup, performance, and data extn. of the DIAS anal., including automated detection of fragments and relevant geometric parameters. © 2019 Wiley Periodicals, Inc.
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  15. 15
    Sun, X.; Soini, T. M.; Poater, J.; Hamlin, T. A.; Bickelhaupt, F. M. PyFrag 2019—Automating the exploration and analysis of reaction mechanisms. J. Comput. Chem. 2019, 40, 2227,  DOI: 10.1002/jcc.25871
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    15
    PyFrag 2019-Automating the exploration and analysis of reaction mechanisms
    Sun, Xiaobo; Soini, Thomas M.; Poater, Jordi; Hamlin, Trevor A.; Bickelhaupt, F. Matthias
    Journal of Computational Chemistry (2019), 40 (25), 2227-2233CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)
    We present a substantial update to the PyFrag 2008 program, which was originally designed to perform a fragment-based activation strain anal. along a provided potential energy surface. The original PyFrag 2008 workflow facilitated the characterization of reaction mechanisms in terms of the intrinsic properties, such as strain and interaction, of the reactants. The new PyFrag 2019 program has automated and reduced the time-consuming and laborious task of setting up, running, analyzing, and visualizing computational data from reaction mechanism studies to a single job. PyFrag 2019 resolves three main challenges assocd. with the automated computational exploration of reaction mechanisms: it (1) computes the reaction path by carrying out multiple parallel calcns. using initial coordinates provided by the user; (2) monitors the entire workflow process; and (3) tabulates and visualizes the final data in a clear way. The activation strain and canonical energy decompn. results that are generated relate the characteristics of the reaction profile in terms of intrinsic properties (strain, interaction, orbital overlaps, orbital energies, populations) of the reactant species.
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  16. 16
    (a) Pracht, P.; Bohle, F.; Grimme, S. Automated exploration of the low-energy chemical space with fast quantum chemical methods. Phys. Chem. Chem. Phys. 2020, 22, 7169– 7192,  DOI: 10.1039/C9CP06869D
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    16a
    Automated exploration of the low-energy chemical space with fast quantum chemical methods
    Pracht, Philipp; Bohle, Fabian; Grimme, Stefan
    Physical Chemistry Chemical Physics (2020), 22 (14), 7169-7192CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)
    We propose and discuss an efficient scheme for the in silico sampling for parts of the mol. chem. space by semiempirical tight-binding methods combined with a meta-dynamics driven search algorithm. The focus of this work is set on the generation of proper thermodn. ensembles at a quantum chem. level for conformers, but similar procedures for protonation states, tautomerism and non-covalent complex geometries are also discussed. The conformational ensembles consisting of all significantly populated min. energy structures normally form the basis of further, mostly DFT computational work, such as the calcn. of spectra or macroscopic properties. By using basic quantum chem. methods, electronic effects or possible bond breaking/formation are accounted for and a very reasonable initial energetic ranking of the candidate structures is obtained. Due to the huge computational speedup gained by the fast low-cost quantum chem. methods, overall short computation times even for systems with hundreds of atoms (typically drug-sized mols.) are achieved. Furthermore, specialized applications, such as sampling with implicit solvation models or constrained conformational sampling for transition-states, metal-, surface-, or noncovalently bound complexes are discussed, opening many possible applications in modern computational chem. and drug discovery. The procedures have been implemented in a freely available computer code called CREST, that makes use of the fast and reliable GFNn-xTB methods.
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    .
    (b) Grimme, S.; Bannwarth, C.; Dohm, S.; Hansen, A.; Pisarek, J.; Pracht, P.; Neese, F. Fully Automated Quantum-Chemistry-Based Computation of Spin-Spin-Coupled Nuclear Magnetic Resonance Spectra. Angew. Chem., Int. Ed. 2017, 56, 14763– 14769,  DOI: 10.1002/anie.201708266
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    16b
    Fully Automated Quantum-Chemistry-Based Computation of Spin-Spin-Coupled Nuclear Magnetic Resonance Spectra
    Grimme, Stefan; Bannwarth, Christoph; Dohm, Sebastian; Hansen, Andreas; Pisarek, Jana; Pracht, Philipp; Seibert, Jakob; Neese, Frank
    Angewandte Chemie, International Edition (2017), 56 (46), 14763-14769CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
    The authors present a composite procedure for the quantum-chem. computation of spin-spin-coupled 1H NMR spectra for general, flexible mols. in soln. that is based on four main steps, namely conformer/rotamer ensemble (CRE) generation by the fast tight-binding method GFN-xTB and a newly developed search algorithm, computation of the relative free energies and NMR parameters, and solving the spin Hamiltonian. In this way the NMR-specific nuclear permutation problem is solved, and the correct spin symmetries were obtained. Energies, shielding consts., and spin-spin couplings are computed at state-of-the-art DFT levels with continuum solvation. A few (in)org. and transition-metal complexes are presented, and very good, unprecedented agreement between the theor. and exptl. spectra was achieved. The approach is routinely applicable to systems with up to 100-150 atoms and may open new avenues for the detailed (conformational) structure elucidation of, for example, natural products or drug mols.
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    Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Nakatsuji, H.; Caricato, M.; Li, X.; Hratchian, H. P.; Izmaylov, A. F.; Bloino, J.; Zheng, G.; Sonnenberg, J. L.; Hada, M.; Ehara, M. Gaussian 09, rev. D.01; Gaussian Inc.: Wallingford, CT, 2009.
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  18. 18
    Zhao, Y.; Truhlar, D. G. The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals. Theor. Chem. Acc. 2008, 120, 215,  DOI: 10.1007/s00214-007-0310-x
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    18
    The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals
    Zhao, Yan; Truhlar, Donald G.
    Theoretical Chemistry Accounts (2008), 120 (1-3), 215-241CODEN: TCACFW; ISSN:1432-881X. (Springer GmbH)
    We present two new hybrid meta exchange-correlation functionals, called M06 and M06-2X. The M06 functional is parametrized including both transition metals and nonmetals, whereas the M06-2X functional is a high-nonlocality functional with double the amt. of nonlocal exchange (2X), and it is parametrized only for nonmetals. The functionals, along with the previously published M06-L local functional and the M06-HF full-Hartree-Fock functionals, constitute the M06 suite of complementary functionals. We assess these four functionals by comparing their performance to that of 12 other functionals and Hartree-Fock theory for 403 energetic data in 29 diverse databases, including ten databases for thermochem., four databases for kinetics, eight databases for noncovalent interactions, three databases for transition metal bonding, one database for metal atom excitation energies, and three databases for mol. excitation energies. We also illustrate the performance of these 17 methods for three databases contg. 40 bond lengths and for databases contg. 38 vibrational frequencies and 15 vibrational zero point energies. We recommend the M06-2X functional for applications involving main-group thermochem., kinetics, noncovalent interactions, and electronic excitation energies to valence and Rydberg states. We recommend the M06 functional for application in organometallic and inorganometallic chem. and for noncovalent interactions.
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    Weigend, F.; Ahlrichs, R. Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy. Phys. Chem. Chem. Phys. 2005, 7, 3297– 3305,  DOI: 10.1039/b508541a
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    Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy
    Weigend, Florian; Ahlrichs, Reinhart
    Physical Chemistry Chemical Physics (2005), 7 (18), 3297-3305CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)
    Gaussian basis sets of quadruple zeta valence quality for Rb-Rn are presented, as well as bases of split valence and triple zeta valence quality for H-Rn. The latter were obtained by (partly) modifying bases developed previously. A large set of more than 300 mols. representing (nearly) all elements-except lanthanides-in their common oxidn. states was used to assess the quality of the bases all across the periodic table. Quantities investigated were atomization energies, dipole moments and structure parameters for Hartree-Fock, d. functional theory and correlated methods, for which we had chosen Moller-Plesset perturbation theory as an example. Finally recommendations are given which type of basis set is used best for a certain level of theory and a desired quality of results.
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    Marenich, A. V.; Cramer, C. J.; Truhlar, D. G. Generalized born solvation model SM12. J. Phys. Chem. B 2009, 113, 6378,  DOI: 10.1021/jp810292n
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    20
    Universal Solvation Model Based on Solute Electron Density and on a Continuum Model of the Solvent Defined by the Bulk Dielectric Constant and Atomic Surface Tensions
    Marenich, Aleksandr V.; Cramer, Christopher J.; Truhlar, Donald G.
    Journal of Physical Chemistry B (2009), 113 (18), 6378-6396CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)
    We present a new continuum solvation model based on the quantum mech. charge d. of a solute mol. interacting with a continuum description of the solvent. The model is called SMD, where the "D" stands for "d." to denote that the full solute electron d. is used without defining partial at. charges. "Continuum" denotes that the solvent is not represented explicitly but rather as a dielec. medium with surface tension at the solute-solvent boundary. SMD is a universal solvation model, where "universal" denotes its applicability to any charged or uncharged solute in any solvent or liq. medium for which a few key descriptors are known (in particular, dielec. const., refractive index, bulk surface tension, and acidity and basicity parameters). The model separates the observable solvation free energy into two main components. The first component is the bulk electrostatic contribution arising from a self-consistent reaction field treatment that involves the soln. of the nonhomogeneous Poisson equation for electrostatics in terms of the integral-equation-formalism polarizable continuum model (IEF-PCM). The cavities for the bulk electrostatic calcn. are defined by superpositions of nuclear-centered spheres. The second component is called the cavity-dispersion-solvent-structure term and is the contribution arising from short-range interactions between the solute and solvent mols. in the first solvation shell. This contribution is a sum of terms that are proportional (with geometry-dependent proportionality consts. called at. surface tensions) to the solvent-accessible surface areas of the individual atoms of the solute. The SMD model has been parametrized with a training set of 2821 solvation data including 112 aq. ionic solvation free energies, 220 solvation free energies for 166 ions in acetonitrile, methanol, and DMSO, 2346 solvation free energies for 318 neutral solutes in 91 solvents (90 nonaq. org. solvents and water), and 143 transfer free energies for 93 neutral solutes between water and 15 org. solvents. The elements present in the solutes are H, C, N, O, F, Si, P, S, Cl, and Br. The SMD model employs a single set of parameters (intrinsic at. Coulomb radii and at. surface tension coeffs.) optimized over six electronic structure methods: M05-2X/MIDI!6D, M05-2X/6-31G*, M05-2X/6-31+G**, M05-2X/cc-pVTZ, B3LYP/6-31G*, and HF/6-31G*. Although the SMD model has been parametrized using the IEF-PCM protocol for bulk electrostatics, it may also be employed with other algorithms for solving the nonhomogeneous Poisson equation for continuum solvation calcns. in which the solute is represented by its electron d. in real space. This includes, for example, the conductor-like screening algorithm. With the 6-31G* basis set, the SMD model achieves mean unsigned errors of 0.6-1.0 kcal/mol in the solvation free energies of tested neutrals and mean unsigned errors of 4 kcal/mol on av. for ions with either Gaussian03 or GAMESS.
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  21. 21
    Goerigk, L.; Hansen, A.; Bauer, C.; Ehrlich, S.; Najibi, A.; Grimme, S. A look at the density functional theory zoo with the advanced GMTKN55 database for general main group thermochemistry, kinetics and noncovalent interactions. Phys. Chem. Chem. Phys. 2017, 19, 32184,  DOI: 10.1039/C7CP04913G
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    21
    A look at the density functional theory zoo with the advanced GMTKN55 database for general main group thermochemistry, kinetics and noncovalent interactions
    Goerigk, Lars; Hansen, Andreas; Bauer, Christoph; Ehrlich, Stephan; Najibi, Asim; Grimme, Stefan
    Physical Chemistry Chemical Physics (2017), 19 (48), 32184-32215CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)
    We present the GMTKN55 benchmark database for general main group thermochem., kinetics and noncovalent interactions. Compared to its popular predecessor GMTKN30, it allows assessment across a larger variety of chem. problems - with 13 new benchmark sets being presented for the first time - and it also provides ref. values of significantly higher quality for most sets. GMTKN55 comprises 1505 relative energies based on 2462 single-point calcns. and it is accessible to the user community via a dedicated website. Herein, we demonstrate the importance of better ref. values, and we re-emphasize the need for London-dispersion corrections in d. functional theory (DFT) treatments of thermochem. problems, including Minnesota methods. We assessed 217 variations of dispersion-cor. and -uncorrected d. functional approxns., and carried out a detailed anal. of 83 of them to identify robust and reliable approaches. Double-hybrid functionals are the most reliable approaches for thermochem. and noncovalent interactions, and they should be used whenever tech. feasible. These are, in particular, DSD-BLYP-D3(BJ), DSD-PBEP86-D3(BJ), and B2GPPLYP-D3(BJ). The best hybrids are ωB97X-V, M052X-D3(0), and ωB97X-D3, but we also recommend PW6B95-D3(BJ) as the best conventional global hybrid. At the meta-generalized-gradient (meta-GGA) level, the SCAN-D3(BJ) method can be recommended. Other meta-GGAs are outperformed by the GGA functionals revPBE-D3(BJ), B97-D3(BJ), and OLYP-D3(BJ). We note that many popular methods, such as B3LYP, are not part of our recommendations. In fact, with our results we hope to inspire a change in the user community's perception of common DFT methods. We also encourage method developers to use GMTKN55 for cross-validation studies of new methodologies.
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    Ribeiro, R. F.; Marenich, A. V.; Cramer, C. J.; Truhlar, D. G. Use of solution-phase vibrational frequencies in continuum models for the free energy of solvation. J. Phys. Chem. B 2011, 115, 14556,  DOI: 10.1021/jp205508z
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    22
    Use of Solution-Phase Vibrational Frequencies in Continuum Models for the Free Energy of Solvation
    Ribeiro, Raphael F.; Marenich, Aleksandr V.; Cramer, Christopher J.; Truhlar, Donald G.
    Journal of Physical Chemistry B (2011), 115 (49), 14556-14562CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
    We find that vibrational contributions to a solute's free energy are in general insensitive to whether the solute vibrational frequencies are computed in the gas phase or in soln. In most cases, the difference is smaller than the intrinsic error in solvation free energies assocd. with the continuum approxn. to solvation modeling, although care must be taken to avoid spurious results assocd. with limitations in the quantum-mech. harmonic-oscillator approxn. for very low-frequency mol. vibrations. We compute solute vibrational partition functions in aq. and carbon tetrachloride soln. and compare them to gas-phase mol. partition functions computed with the same level of theory and the same quasiharmonic approxn. for the diverse and extensive set of mols. and ions included in the training set of the SMD continuum solvation model, and we find mean unsigned differences in vibrational contributions to the solute free energy of only about 0.2 kcal/mol. On the basis of these results and a review of the theory, we conclude, in contrast to previous work, that using partition functions computed for mols. optimized in soln. is a correct and useful approach for averaging over solute degrees of freedom when computing free energies of solutes in soln., and it is moreover recommended for cases where liq. and gas-phase solute structures differ appreciably or when stationary points present in liq. soln. do not exist in the gas phase, for which we provide some examples. When gas-phase and soln.-phase geometries and frequencies are similar, the use of gas-phase geometries and frequencies is a useful approxn.
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  23. 23
    te Velde, G.; Bickelhaupt, F. M.; Baerends, E. J.; Fonseca Guerra, C.; van Gisbergen, S. J. A.; Snijders, J. G.; Ziegler, T. Chemistry with ADF. J. Comput. Chem. 2001, 22, 931,  DOI: 10.1002/jcc.1056
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    Chemistry with ADF
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  • Abstract

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    Scheme 1

    Scheme 1. Proposed Mechanism of the Fluoride-Catalyzed 1,3-Dipolar Cycloaddition between CO2 and Nitrilimines by Lu and Co-workers, in Which the Lewis Base F– Together with CO2 Forms the Activated Dipolarophile (i.e., CO2F–); (3) R1 and R2 = Aryl or Alkyl
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    Scheme 2

    Scheme 2. Possible Reaction Pathways for the 1,3-Dipolar Cycloaddition between Carbon Dioxide and Nitrilimine 1 in the Presence of the Lewis Base F–
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    Figure 1

    Figure 1. (a) Reaction profiles (ΔGtoluene in kcal mol–1) for the three reaction pathways of the studied 1,3-dipolar cycloaddition between carbon dioxide and nitrilimine 1, including (i) uncatalyzed cycloaddition (black), (ii) formation of CO2F– followed by stepwise cycloaddition (blue), and (iii) formation of 2 followed by stepwise cycloaddition (red), computed at SMD(toluene)-M06-2X-D3/def2-TZVP; TS = transition state and INT = intermediate. (b) Key transition state structures with key bond lengths (in Å) for the three reaction pathways.

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    Figure 2

    Figure 2. (a) Distortion/interaction–activation strain model analysis; and (b) energy decomposition analysis of the cycloaddition reaction of 1 (black) and 2 (red) with CO2 (transition states indicated with a dot). (13) (c) Frontier molecular orbital diagram of the most important FMO-LUMOCO2 orbital interaction with the calculated energy gaps, orbital overlaps, and the S2/Δε terms, at consistent geometries with a N···C bond length of 2.14 Å. Computed at SMD(toluene)-M06-2X-D3/def2-TZVP using autoDIAS (14) for (a) and M06-2X-D3/TZ2P//SMD(toluene)-M06-2X-D3/def2-TZVP using PyFrag (15) for (b,c).

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    Scheme 3

    Scheme 3. Novel Mechanism Emerging from Our Study for the Lewis Base F– Catalyzed 1,3-Dipolar Cycloaddition of CO2 to Nitrilimines, Where F– Activates the Dipole, Instead of the Dipolarophile
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  • References

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      The first copper-catalyzed cyclic anti-nucleometallation-carboxylation of 2-alkynylanilines with carbon dioxide in the presence of dimethylzinc (ZnMe2) and cesium fluoride (CsF) for the effective synthesis of indolyl-3-carboxylic acids and indolodihydropyran-2-one is described. Through a mechanistic study, it is unveiled that the metal ions Cu2+, Zn2+, Cs+ and F- are working together for this CO2-based highly efficient carboxylation.
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      Copper(I)-Catalyzed Carboxylation of Aryl- and Alkenylboronic Esters
      Takaya, Jun; Tadami, Satoshi; Ukai, Kazutoshi; Iwasawa, Nobuharu
      Organic Letters (2008), 10 (13), 2697-2700CODEN: ORLEF7; ISSN:1523-7060. (American Chemical Society)
      The copper(I)-catalyzed carboxylation reaction of aryl- and alkenylboronic esters proceeded smoothly under CO2 to give the corresponding carboxylic acids in good yield. This reaction showed wide generality with higher functional group tolerance compared to the corresponding Rh(I)-catalyzed reaction.
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      Denmark, S. E.; Beutner, G. L. Lewis Base Catalysis in Organic Synthesis. Angew. Chem., Int. Ed. 2008, 47, 1560– 1638,  DOI: 10.1002/anie.200604943
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      Lewis base catalysis in organic synthesis
      Denmark, Scott E.; Beutner, Gregory L.
      Angewandte Chemie, International Edition (2008), 47 (9), 1560-1638CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
      A review. The legacy of Gilbert Newton Lewis (1875-1946) pervades the lexicon of chem. bonding and reactivity; the power of his concept of donor-acceptor bonding is evident in the eponymous foundations of electron-pair acceptors (Lewis acids) and donors (Lewis bases). His discovery ushered in the use of Lewis acids as reagents and catalysts for org. reactions. However, in recent years, the recognition that Lewis bases can also serve in this capacity has grown enormously. Most importantly, it has become increasingly apparent that the behavior of Lewis bases as agents for promoting chem. reactions is not merely as an electronic complement of the cognate Lewis acids: in fact Lewis bases are capable of enhancing both the electrophilic and nucleophilic character of mols. to which they are bound. This diversity of behavior leads to a remarkable versatility for the catalysis of reactions by Lewis bases.
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      Murillo, F.; Barroso, J.; de los Santos, M. G.; Ávila, G.; Pan, S.; Fernández-Herrera, M. A.; Merino, G. Revisiting the Formation Mechanism of 1,3,4-Oxadiazole-2(3H)-ones from Hydrazonyl Chloride and Carbon Dioxide. J. Org. Chem. 2018, 83, 13045– 13050,  DOI: 10.1021/acs.joc.8b01676
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      Revisiting the Formation Mechanism of 1,3,4-Oxadiazole-2(3H)-ones from Hydrazonyl Chloride and Carbon Dioxide
      Murillo, Fernando; Barroso, Jorge; de los Santos, Maria G.; Avila, Gustavo; Pan, Sudip; Fernandez-Herrera, Maria A.; Merino, Gabriel
      Journal of Organic Chemistry (2018), 83 (21), 13045-13050CODEN: JOCEAH; ISSN:0022-3263. (American Chemical Society)
      The reaction mechanism for the synthesis of 1,3,4-oxadiazole-2(3H)-ones from hydrazonyl chloride and CO2 in the presence of CsF/18-crown-6 and toluene, is revisited via d. functional theory computations. Although this reaction was earlier classified as a 1,3-dipolar cycloaddn., we found some competing pathways involved therein. The mechanisms including the (F-CO2)- anion and the nitrile imine intermediate are some options. The dimerization of nitrile imine is another competing mechanism in this reaction. Our results show that the most favorable mechanism proceeds via a stepwise pathway without involving any nitrile imine intermediate or the (F-CO2)- anion. The F- anion, resulting from the formation of a complex between 18-crown-6 and Cs+ cation, deprotonates the nitrile imine precursor easily, which acts then as a nucleophilic anion, enhancing the reactivity of CO2 toward it. The mechanism for the reaction with COS, an isoelectronic analog of CO2, is also explored.
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    8. 8
      (a) Wang, X. S.; Lee, Y. J.; Liu, W. R. The nitrilimine-alkene cycloaddition is an ultra rapid click reaction. Chem. Commun. 2014, 50, 3176– 3179,  DOI: 10.1039/C3CC48682F
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      The nitrilimine-alkene cycloaddition is an ultra rapid click reaction
      Wang, Xiaoshan Shayna; Lee, Yan-Jiun; Liu, Wenshe R.
      Chemical Communications (Cambridge, United Kingdom) (2014), 50 (24), 3176-3179CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)
      The transient formation of nitrilimine in aq. conditions is greatly influenced by pH and chloride. In basic conditions (pH 10) with no chloride, a diarylnitrilimine precursor readily ionizes to form diarylnitrilimine that reacts almost instantly with an acrylamide-contg. protein and fluorescently labels it.
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      (b) Molteni, G.; Ponti, A. The Nitrilimine-Alkene Cycloaddition Regioselectivity Rationalized by Density Functional Theory Reactivity Indices. Molecules 2017, 22, 202,  DOI: 10.3390/molecules22020202
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      The nitrilimine-alkene cycloaddition regioselectivity rationalized by density functional theory reactivity indices
      Molteni, Giorgio; Ponti, Alessandro
      Molecules (2017), 22 (2), 202/1-202/12CODEN: MOLEFW; ISSN:1420-3049. (MDPI AG)
      Conventional frontier MO theory is not able to satisfactorily explain the regioselectivity outcome of the nitrilimine-alkene cycloaddn. We considered that conceptual d. functional theory (DFT) could be an effective theor. framework to rationalize the regioselectivity of the title reaction. Several nitrilimine-alkene cycloaddns. were analyzed, for which we could find regioselectivity data in the literature. We computed DFT reactivity indexes at the B3LYP/6-311G(2d,p)//B3LYP/6-31G(d,p) and employed the grand potential stabilization criterion to calc. the preferred regioisomer. Exptl. and calcd. regioselectivity agree in the vast majority of cases. It was concluded that predominance of a single regioisomer can be obtained by maximizing (i) the chem. p.d. between nitrilimine and alkene and (ii) the local softness difference between the reactive at. sites within each reactant. Such maximization can be achieved by carefully selecting the substituents on both reactants.
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      (c) Shawali, A. S. Chemoselectivity in 1,3-dipolar cycloaddition reactions of nitrilimines with multifunctionalized dipolarophiles. Curr. Org. Chem. 2014, 18, 598– 614,  DOI: 10.2174/1385272819666140201002900
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      Chemoselectivity in 1,3-Dipolar Cycloaddition Reactions of Nitrilimines with Multifunctionalized Dipolarophiles
      Shawali, Ahmad S.
      Current Organic Chemistry (2014), 18 (5), 598-614CODEN: CORCFE; ISSN:1385-2728. (Bentham Science Publishers Ltd.)
      A review. This review presents a survey of literature reports dealing with both site and peri-selectivities in cycloaddn. reactions of nitrilimines with multifunctionalized dipolarophiles. The literature results covered in this review, during the period from 1970 to mid 2013, demonstrated that chemo-selectivity plays an important role in synthetic design.
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      (a) Bickelhaupt, F. M.; Houk, K. N. Analyzing Reaction Rates with the Distortion/Interaction-Activation Strain Model. Angew. Chem., Int. Ed. 2017, 56, 10070– 10086,  DOI: 10.1002/anie.201701486
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      9a
      Analyzing Reaction Rates with the Distortion/Interaction-Activation Strain Model
      Bickelhaupt, F. Matthias; Houk, Kendall N.
      Angewandte Chemie, International Edition (2017), 56 (34), 10070-10086CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
      The activation strain or distortion/interaction model is a tool to analyze activation barriers that det. reaction rates. For bimol. reactions, the activation energies are the sum of the energies to distort the reactants into geometries they have in transition states plus the interaction energies between the two distorted mols. The energy required to distort the mols. is called the activation strain or distortion energy. This energy is the principal contributor to the activation barrier. The transition state occurs when this activation strain is overcome by the stabilizing interaction energy. Following the changes in these energies along the reaction coordinate gives insights into the factors controlling reactivity. This model has been applied to reactions of all types in both org. and inorg. chem., including substitutions and eliminations, cycloaddns., and several types of organometallic reactions.
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      Bickelhaupt, F. M.; Houk, K. N. Angew. Chem. 2017, 129, 10204– 10221,  DOI: 10.1002/ange.201701486
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      (b) Vermeeren, P.; van der Lubbe, S. C. C.; Fonseca Guerra, C.; Bickelhaupt, F. M.; Hamlin, T. A. Understanding Chemical Reactivity Using the Activation Strain Model. Nat. Protoc. 2020, 15, 649– 667,  DOI: 10.1038/s41596-019-0265-0
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      9b
      Understanding chemical reactivity using the activation strain model
      Vermeeren, Pascal; van der Lubbe, Stephanie C. C.; Fonseca Guerra, Celia; Bickelhaupt, F. Matthias; Hamlin, Trevor A.
      Nature Protocols (2020), 15 (2), 649-667CODEN: NPARDW; ISSN:1750-2799. (Nature Research)
      Understanding chem. reactivity through the use of state-of-the-art computational techniques enables chemists to both predict reactivity and rationally design novel reactions. This protocol aims to provide chemists with the tools to implement a powerful and robust method for analyzing and understanding any chem. reaction using PyFrag 2019. The approach is based on the so-called activation strain model (ASM) of reactivity, which relates the relative energy of a mol. system to the sum of the energies required to distort the reactants into the geometries required to react plus the strength of their mutual interactions. Other available methods analyze only a stationary point on the potential energy surface, but our methodol. analyzes the change in energy along a reaction coordinate. The use of this methodol. has been proven to be crit. to the understanding of reactions, spanning the realms of the inorg. and org., as well as the supramol. and biochem., fields. This protocol provides step-by-step instructions-starting from the optimization of the stationary points and extending through calcn. of the potential energy surface and anal. of the trend-decisive energy terms-that can serve as a guide for carrying out the anal. of any given reaction of interest within hours to days, depending on the size of the mol. system.
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      (c) Fernández, I.; Bickelhaupt, F. M. The activation strain model and molecular orbital theory: understanding and designing chemical reactions. Chem. Soc. Rev. 2014, 43, 4953– 4967,  DOI: 10.1039/C4CS00055B
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      9c
      The activation strain model and molecular orbital theory: understanding and designing chemical reactions
      Fernandez, Israel; Bickelhaupt, F. Matthias
      Chemical Society Reviews (2014), 43 (14), 4953-4967CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)
      A review. In this Tutorial Review, we make the point that a true understanding of trends in reactivity (as opposed to measuring or simply computing them) requires a causal reactivity model. To this end, we present and discuss the Activation Strain Model (ASM). The ASM establishes the desired causal relationship between reaction barriers, on one hand, and the properties of reactants and characteristics of reaction mechanisms, on the other hand. In the ASM, the potential energy surface ΔE(ζ) along the reaction coordinate ζ is decompd. into the strain ΔEstrain(ζ) of the reactants that become increasingly deformed as the reaction proceeds, plus the interaction ΔEint(ζ) between these deformed reactants, i.e., ΔE(ζ) = ΔEstrain(ζ) + ΔEint(ζ). The ASM can be used in conjunction with any quantum chem. program. An anal. of the method and its application to problems in org. and organometallic chem. illustrate the power of the ASM as a unifying concept and a tool for rational design of reactants and catalysts.
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    10. 10
      Bickelhaupt, F. M.; Baerends, E. J. Kohn-Sham Density Functional Theory: Predicting and Understanding Chemistry. In Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B., Eds.; Wiley-VCH: New York, 2000; Vol. 15, pp 1– 86.
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    11. 11
      (a) van Meer, R.; Gritsenko, O. V.; Baerends, E. J. Physical Meaning of Virtual Kohn-Sham Orbitals and Orbital Energies: An Ideal Basis for the Description of Molecular Excitations. J. Chem. Theory Comput. 2014, 10, 4432– 4441,  DOI: 10.1021/ct500727c
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      11a
      Physical Meaning of Virtual Kohn-Sham Orbitals and Orbital Energies: An Ideal Basis for the Description of Molecular Excitations
      van Meer, R.; Gritsenko, O. V.; Baerends, E. J.
      Journal of Chemical Theory and Computation (2014), 10 (10), 4432-4441CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
      In recent years, several benchmark studies on the performance of large sets of functionals in time-dependent d. functional theory (TDDFT) calcns. of excitation energies have been performed. The tested functionals do not approx. exact Kohn-Sham orbitals and orbital energies closely. We highlight the advantages of (close to) exact Kohn-Sham orbitals and orbital energies for a simple description, very often as just a single orbital-to-orbital transition, of mol. excitations. Benchmark calcns. are performed for the statistical av. of orbital potentials (SAOP) functional for the potential [J. Chem. Phys. 2000, 112, 1344; 2001, 114, 652], which approximates the true Kohn-Sham potential much better than LDA, GGA, mGGA, and hybrid potentials do. An accurate Kohn-Sham potential not only performs satisfactorily for calcd. vertical excitation energies of both valence and Rydberg transitions, but also exhibits appealing properties of the KS orbitals including occupied orbital energies close to ionization energies, virtual-occupied orbital energy gaps very close to excitation energies, realistic shapes of virtual orbitals, leading to straightforward interpretation of most excitations as single orbital transitions. We stress that such advantages are completely lost in time-dependent Hartree-Fock and partly in hybrid approaches. Many excitations and excitation energies calcd. with local d., generalized gradient, and hybrid functionals are spurious. There is, with an accurate KS, or even the LDA or GGA potentials, nothing problematic about the "band gap" in mols.: the HOMO-LUMO gap is close to the first excitation energy (the optical gap).
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    12. 12
      (a) Yu, S.; Vermeeren, P.; van Dommelen, K.; Bickelhaupt, F. M.; Hamlin, T. A. Understanding the 1,3-Dipolar Cycloadditions of Allenes. Chem. - Eur. J. 2020, 26, 11529– 11539,  DOI: 10.1002/chem.202000857
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      12a
      Understanding the 1,3-Dipolar Cycloadditions of Allenes
      Yu, Song; Vermeeren, Pascal; van Dommelen, Kevin; Bickelhaupt, F. Matthias; Hamlin, Trevor A.
      Chemistry - A European Journal (2020), 26 (50), 11529-11539CODEN: CEUJED; ISSN:0947-6539. (Wiley-VCH Verlag GmbH & Co. KGaA)
      We have quantum chem. studied the reactivity, site-, and regioselectivity of the 1,3-dipolar cycloaddn. between Me azide and various allenes, including the archetypal allene propadiene, heteroallenes, and cyclic allenes, by using d. functional theory (DFT). The 1,3-dipolar cycloaddn. reactivity of linear (hetero)allenes decreases as the no. of heteroatoms in the allene increases, and formation of the 1,5-adduct is, in all cases, favored over the 1,4-adduct. Both effects find their origin in the strength of the primary orbital interactions. The cycloaddn. reactivity of cyclic allenes was also investigated, and the increased predistortion of allenes, that results upon cyclization, leads to systematically lower activation barriers not due to the expected variations in the strain energy, but instead from the differences in the interaction energy. The geometric predistortion of cyclic allenes enhances the reactivity compared to linear allenes through a unique mechanism that involves a smaller HOMO-LUMO gap, which manifests as more stabilizing orbital interactions.
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      (b) Hamlin, T. A.; Levandowski, B. J.; Narsaria, A. K.; Houk, K. N.; Bickelhaupt, F. M. Bickelhaupt. Structural Distortion of Cycloalkynes Influences Cycloaddition Rates by both Strain and Interaction Energies. Chem. - Eur. J. 2019, 25, 6342– 6348,  DOI: 10.1002/chem.201900295
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      12b
      Structural Distortion of Cycloalkynes Influences Cycloaddition Rates both by Strain and Interaction Energies
      Hamlin, Trevor A.; Levandowski, Brian J.; Narsaria, Ayush K.; Houk, Kendall N.; Bickelhaupt, F. Matthias
      Chemistry - A European Journal (2019), 25 (25), 6342-6348CODEN: CEUJED; ISSN:0947-6539. (Wiley-VCH Verlag GmbH & Co. KGaA)
      The reactivities of 2-butyne, cycloheptyne, cyclooctyne, and cyclononyne in the 1,3-dipolar cycloaddn. reaction with Me azide were evaluated through DFT calcns. at the M06-2X/6-311++G(d)//M06-2X/6-31+G(d) level of theory. Computed activation free energies for the cycloaddns. of cycloalkynes are 16.5-22.0 kcal mol-1 lower in energy than that of the acyclic 2-butyne. The strained or predistorted nature of cycloalkynes is often solely used to rationalize this significant rate enhancement. Our distortion/interaction-activation strain anal. has been revealed that the degree of geometrical predistortion of the cycloalkyne ground-state geometries acts to enhance reactivity compared with that of acyclic alkynes through three distinct mechanisms, not only due to (i) a reduced strain or distortion energy, but also to (ii) a smaller HOMO-LUMO gap, and (iii) an enhanced orbital overlap, which both contribute to more stabilizing orbital interactions.
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      .
      (c) Hamlin, T. A.; Svatunek, D.; Yu, S.; Ridder, L.; Infante, I.; Visscher, L.; Bickelhaupt, F. M. Elucidating the Trends in Reactivity of Aza-1,3-Dipolar Cycloadditions. Eur. J. Org. Chem. 2019, 2019, 378– 386,  DOI: 10.1002/ejoc.201800572
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      12c
      Elucidating the Trends in Reactivity of Aza-1,3-Dipolar Cycloadditions
      Hamlin, Trevor A.; Svatunek, Dennis; Yu, Song; Ridder, Lars; Infante, Ivan; Visscher, Lucas; Bickelhaupt, F. Matthias
      European Journal of Organic Chemistry (2019), 2019 (2-3), 378-386CODEN: EJOCFK; ISSN:1099-0690. (Wiley-VCH Verlag GmbH & Co. KGaA)
      This report describes a d. functional theory investigation into the reactivities of a series of aza-1,3-dipoles with ethylene at the BP86/TZ2P level. A benchmark study was carried out using QMflows, a newly developed program for automated workflows of quantum chem. calcns. In total, 24 1,3-dipolar cycloaddn. (1,3-DCA) reactions were benchmarked using the highly accurate G3B3 method as a ref. We screened a no. of exchange and correlation functionals, including PBE, OLYP, BP86, BLYP, both with and without explicit dispersion corrections, to assess their accuracies and to det. which of these computationally efficient functionals performed the best for calcg. the energetics for cycloaddn. reactions. The BP86/TZ2P method produced the smallest errors for the activation and reaction enthalpies. Then, to understand the factors controlling the reactivity in these reactions, seven archetypal aza-1,3-dipolar cycloaddns. were investigated using the activation strain model and energy decompn. anal. Our investigations highlight the fact that differences in activation barrier for these 1,3-DCA reactions do not arise from differences in strain energy of the dipole, as previously proposed. Instead, relative reactivities originate from differences in interaction energy. Anal. of the 1,3-dipole-dipolarophile interactions reveals the reactivity trends primarily result from differences in the extent of the primary orbital interactions.
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    13. 13

      Differences in the dispersion curves were neglectable and were omitted for clarity.

      There is no corresponding record for this reference.
    14. 14
      Svatunek, D.; Houk, K. N. autoDIAS: a python tool for an automated distortion/interaction activation strain analysis. J. Comput. Chem. 2019, 40, 2509,  DOI: 10.1002/jcc.26023
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      14
      autoDIAS: a python tool for an automated distortion/interaction activation strain analysis
      Svatunek, Dennis; Houk, Kendall N.
      Journal of Computational Chemistry (2019), 40 (28), 2509-2515CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)
      The distortion/interaction activation strain (DIAS) anal. is a powerful tool for the investigation of energy barriers. However, setup and data anal. of such a calcn. can be cumbersome and requires lengthy intervention of the user. We present autoDIAS, a python tool for the automated setup, performance, and data extn. of the DIAS anal., including automated detection of fragments and relevant geometric parameters. © 2019 Wiley Periodicals, Inc.
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    15. 15
      Sun, X.; Soini, T. M.; Poater, J.; Hamlin, T. A.; Bickelhaupt, F. M. PyFrag 2019—Automating the exploration and analysis of reaction mechanisms. J. Comput. Chem. 2019, 40, 2227,  DOI: 10.1002/jcc.25871
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      15
      PyFrag 2019-Automating the exploration and analysis of reaction mechanisms
      Sun, Xiaobo; Soini, Thomas M.; Poater, Jordi; Hamlin, Trevor A.; Bickelhaupt, F. Matthias
      Journal of Computational Chemistry (2019), 40 (25), 2227-2233CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)
      We present a substantial update to the PyFrag 2008 program, which was originally designed to perform a fragment-based activation strain anal. along a provided potential energy surface. The original PyFrag 2008 workflow facilitated the characterization of reaction mechanisms in terms of the intrinsic properties, such as strain and interaction, of the reactants. The new PyFrag 2019 program has automated and reduced the time-consuming and laborious task of setting up, running, analyzing, and visualizing computational data from reaction mechanism studies to a single job. PyFrag 2019 resolves three main challenges assocd. with the automated computational exploration of reaction mechanisms: it (1) computes the reaction path by carrying out multiple parallel calcns. using initial coordinates provided by the user; (2) monitors the entire workflow process; and (3) tabulates and visualizes the final data in a clear way. The activation strain and canonical energy decompn. results that are generated relate the characteristics of the reaction profile in terms of intrinsic properties (strain, interaction, orbital overlaps, orbital energies, populations) of the reactant species.
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      (a) Pracht, P.; Bohle, F.; Grimme, S. Automated exploration of the low-energy chemical space with fast quantum chemical methods. Phys. Chem. Chem. Phys. 2020, 22, 7169– 7192,  DOI: 10.1039/C9CP06869D
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      16a
      Automated exploration of the low-energy chemical space with fast quantum chemical methods
      Pracht, Philipp; Bohle, Fabian; Grimme, Stefan
      Physical Chemistry Chemical Physics (2020), 22 (14), 7169-7192CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)
      We propose and discuss an efficient scheme for the in silico sampling for parts of the mol. chem. space by semiempirical tight-binding methods combined with a meta-dynamics driven search algorithm. The focus of this work is set on the generation of proper thermodn. ensembles at a quantum chem. level for conformers, but similar procedures for protonation states, tautomerism and non-covalent complex geometries are also discussed. The conformational ensembles consisting of all significantly populated min. energy structures normally form the basis of further, mostly DFT computational work, such as the calcn. of spectra or macroscopic properties. By using basic quantum chem. methods, electronic effects or possible bond breaking/formation are accounted for and a very reasonable initial energetic ranking of the candidate structures is obtained. Due to the huge computational speedup gained by the fast low-cost quantum chem. methods, overall short computation times even for systems with hundreds of atoms (typically drug-sized mols.) are achieved. Furthermore, specialized applications, such as sampling with implicit solvation models or constrained conformational sampling for transition-states, metal-, surface-, or noncovalently bound complexes are discussed, opening many possible applications in modern computational chem. and drug discovery. The procedures have been implemented in a freely available computer code called CREST, that makes use of the fast and reliable GFNn-xTB methods.
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      .
      (b) Grimme, S.; Bannwarth, C.; Dohm, S.; Hansen, A.; Pisarek, J.; Pracht, P.; Neese, F. Fully Automated Quantum-Chemistry-Based Computation of Spin-Spin-Coupled Nuclear Magnetic Resonance Spectra. Angew. Chem., Int. Ed. 2017, 56, 14763– 14769,  DOI: 10.1002/anie.201708266
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      Fully Automated Quantum-Chemistry-Based Computation of Spin-Spin-Coupled Nuclear Magnetic Resonance Spectra
      Grimme, Stefan; Bannwarth, Christoph; Dohm, Sebastian; Hansen, Andreas; Pisarek, Jana; Pracht, Philipp; Seibert, Jakob; Neese, Frank
      Angewandte Chemie, International Edition (2017), 56 (46), 14763-14769CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
      The authors present a composite procedure for the quantum-chem. computation of spin-spin-coupled 1H NMR spectra for general, flexible mols. in soln. that is based on four main steps, namely conformer/rotamer ensemble (CRE) generation by the fast tight-binding method GFN-xTB and a newly developed search algorithm, computation of the relative free energies and NMR parameters, and solving the spin Hamiltonian. In this way the NMR-specific nuclear permutation problem is solved, and the correct spin symmetries were obtained. Energies, shielding consts., and spin-spin couplings are computed at state-of-the-art DFT levels with continuum solvation. A few (in)org. and transition-metal complexes are presented, and very good, unprecedented agreement between the theor. and exptl. spectra was achieved. The approach is routinely applicable to systems with up to 100-150 atoms and may open new avenues for the detailed (conformational) structure elucidation of, for example, natural products or drug mols.
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    17. 17
      Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Nakatsuji, H.; Caricato, M.; Li, X.; Hratchian, H. P.; Izmaylov, A. F.; Bloino, J.; Zheng, G.; Sonnenberg, J. L.; Hada, M.; Ehara, M. Gaussian 09, rev. D.01; Gaussian Inc.: Wallingford, CT, 2009.
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      Zhao, Y.; Truhlar, D. G. The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals. Theor. Chem. Acc. 2008, 120, 215,  DOI: 10.1007/s00214-007-0310-x
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      The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals
      Zhao, Yan; Truhlar, Donald G.
      Theoretical Chemistry Accounts (2008), 120 (1-3), 215-241CODEN: TCACFW; ISSN:1432-881X. (Springer GmbH)
      We present two new hybrid meta exchange-correlation functionals, called M06 and M06-2X. The M06 functional is parametrized including both transition metals and nonmetals, whereas the M06-2X functional is a high-nonlocality functional with double the amt. of nonlocal exchange (2X), and it is parametrized only for nonmetals. The functionals, along with the previously published M06-L local functional and the M06-HF full-Hartree-Fock functionals, constitute the M06 suite of complementary functionals. We assess these four functionals by comparing their performance to that of 12 other functionals and Hartree-Fock theory for 403 energetic data in 29 diverse databases, including ten databases for thermochem., four databases for kinetics, eight databases for noncovalent interactions, three databases for transition metal bonding, one database for metal atom excitation energies, and three databases for mol. excitation energies. We also illustrate the performance of these 17 methods for three databases contg. 40 bond lengths and for databases contg. 38 vibrational frequencies and 15 vibrational zero point energies. We recommend the M06-2X functional for applications involving main-group thermochem., kinetics, noncovalent interactions, and electronic excitation energies to valence and Rydberg states. We recommend the M06 functional for application in organometallic and inorganometallic chem. and for noncovalent interactions.
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    19. 19
      Weigend, F.; Ahlrichs, R. Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy. Phys. Chem. Chem. Phys. 2005, 7, 3297– 3305,  DOI: 10.1039/b508541a
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      Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy
      Weigend, Florian; Ahlrichs, Reinhart
      Physical Chemistry Chemical Physics (2005), 7 (18), 3297-3305CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)
      Gaussian basis sets of quadruple zeta valence quality for Rb-Rn are presented, as well as bases of split valence and triple zeta valence quality for H-Rn. The latter were obtained by (partly) modifying bases developed previously. A large set of more than 300 mols. representing (nearly) all elements-except lanthanides-in their common oxidn. states was used to assess the quality of the bases all across the periodic table. Quantities investigated were atomization energies, dipole moments and structure parameters for Hartree-Fock, d. functional theory and correlated methods, for which we had chosen Moller-Plesset perturbation theory as an example. Finally recommendations are given which type of basis set is used best for a certain level of theory and a desired quality of results.
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      Marenich, A. V.; Cramer, C. J.; Truhlar, D. G. Generalized born solvation model SM12. J. Phys. Chem. B 2009, 113, 6378,  DOI: 10.1021/jp810292n
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      Universal Solvation Model Based on Solute Electron Density and on a Continuum Model of the Solvent Defined by the Bulk Dielectric Constant and Atomic Surface Tensions
      Marenich, Aleksandr V.; Cramer, Christopher J.; Truhlar, Donald G.
      Journal of Physical Chemistry B (2009), 113 (18), 6378-6396CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)
      We present a new continuum solvation model based on the quantum mech. charge d. of a solute mol. interacting with a continuum description of the solvent. The model is called SMD, where the "D" stands for "d." to denote that the full solute electron d. is used without defining partial at. charges. "Continuum" denotes that the solvent is not represented explicitly but rather as a dielec. medium with surface tension at the solute-solvent boundary. SMD is a universal solvation model, where "universal" denotes its applicability to any charged or uncharged solute in any solvent or liq. medium for which a few key descriptors are known (in particular, dielec. const., refractive index, bulk surface tension, and acidity and basicity parameters). The model separates the observable solvation free energy into two main components. The first component is the bulk electrostatic contribution arising from a self-consistent reaction field treatment that involves the soln. of the nonhomogeneous Poisson equation for electrostatics in terms of the integral-equation-formalism polarizable continuum model (IEF-PCM). The cavities for the bulk electrostatic calcn. are defined by superpositions of nuclear-centered spheres. The second component is called the cavity-dispersion-solvent-structure term and is the contribution arising from short-range interactions between the solute and solvent mols. in the first solvation shell. This contribution is a sum of terms that are proportional (with geometry-dependent proportionality consts. called at. surface tensions) to the solvent-accessible surface areas of the individual atoms of the solute. The SMD model has been parametrized with a training set of 2821 solvation data including 112 aq. ionic solvation free energies, 220 solvation free energies for 166 ions in acetonitrile, methanol, and DMSO, 2346 solvation free energies for 318 neutral solutes in 91 solvents (90 nonaq. org. solvents and water), and 143 transfer free energies for 93 neutral solutes between water and 15 org. solvents. The elements present in the solutes are H, C, N, O, F, Si, P, S, Cl, and Br. The SMD model employs a single set of parameters (intrinsic at. Coulomb radii and at. surface tension coeffs.) optimized over six electronic structure methods: M05-2X/MIDI!6D, M05-2X/6-31G*, M05-2X/6-31+G**, M05-2X/cc-pVTZ, B3LYP/6-31G*, and HF/6-31G*. Although the SMD model has been parametrized using the IEF-PCM protocol for bulk electrostatics, it may also be employed with other algorithms for solving the nonhomogeneous Poisson equation for continuum solvation calcns. in which the solute is represented by its electron d. in real space. This includes, for example, the conductor-like screening algorithm. With the 6-31G* basis set, the SMD model achieves mean unsigned errors of 0.6-1.0 kcal/mol in the solvation free energies of tested neutrals and mean unsigned errors of 4 kcal/mol on av. for ions with either Gaussian03 or GAMESS.
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      Goerigk, L.; Hansen, A.; Bauer, C.; Ehrlich, S.; Najibi, A.; Grimme, S. A look at the density functional theory zoo with the advanced GMTKN55 database for general main group thermochemistry, kinetics and noncovalent interactions. Phys. Chem. Chem. Phys. 2017, 19, 32184,  DOI: 10.1039/C7CP04913G
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      21
      A look at the density functional theory zoo with the advanced GMTKN55 database for general main group thermochemistry, kinetics and noncovalent interactions
      Goerigk, Lars; Hansen, Andreas; Bauer, Christoph; Ehrlich, Stephan; Najibi, Asim; Grimme, Stefan
      Physical Chemistry Chemical Physics (2017), 19 (48), 32184-32215CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)
      We present the GMTKN55 benchmark database for general main group thermochem., kinetics and noncovalent interactions. Compared to its popular predecessor GMTKN30, it allows assessment across a larger variety of chem. problems - with 13 new benchmark sets being presented for the first time - and it also provides ref. values of significantly higher quality for most sets. GMTKN55 comprises 1505 relative energies based on 2462 single-point calcns. and it is accessible to the user community via a dedicated website. Herein, we demonstrate the importance of better ref. values, and we re-emphasize the need for London-dispersion corrections in d. functional theory (DFT) treatments of thermochem. problems, including Minnesota methods. We assessed 217 variations of dispersion-cor. and -uncorrected d. functional approxns., and carried out a detailed anal. of 83 of them to identify robust and reliable approaches. Double-hybrid functionals are the most reliable approaches for thermochem. and noncovalent interactions, and they should be used whenever tech. feasible. These are, in particular, DSD-BLYP-D3(BJ), DSD-PBEP86-D3(BJ), and B2GPPLYP-D3(BJ). The best hybrids are ωB97X-V, M052X-D3(0), and ωB97X-D3, but we also recommend PW6B95-D3(BJ) as the best conventional global hybrid. At the meta-generalized-gradient (meta-GGA) level, the SCAN-D3(BJ) method can be recommended. Other meta-GGAs are outperformed by the GGA functionals revPBE-D3(BJ), B97-D3(BJ), and OLYP-D3(BJ). We note that many popular methods, such as B3LYP, are not part of our recommendations. In fact, with our results we hope to inspire a change in the user community's perception of common DFT methods. We also encourage method developers to use GMTKN55 for cross-validation studies of new methodologies.
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    22. 22
      Ribeiro, R. F.; Marenich, A. V.; Cramer, C. J.; Truhlar, D. G. Use of solution-phase vibrational frequencies in continuum models for the free energy of solvation. J. Phys. Chem. B 2011, 115, 14556,  DOI: 10.1021/jp205508z
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      Use of Solution-Phase Vibrational Frequencies in Continuum Models for the Free Energy of Solvation
      Ribeiro, Raphael F.; Marenich, Aleksandr V.; Cramer, Christopher J.; Truhlar, Donald G.
      Journal of Physical Chemistry B (2011), 115 (49), 14556-14562CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
      We find that vibrational contributions to a solute's free energy are in general insensitive to whether the solute vibrational frequencies are computed in the gas phase or in soln. In most cases, the difference is smaller than the intrinsic error in solvation free energies assocd. with the continuum approxn. to solvation modeling, although care must be taken to avoid spurious results assocd. with limitations in the quantum-mech. harmonic-oscillator approxn. for very low-frequency mol. vibrations. We compute solute vibrational partition functions in aq. and carbon tetrachloride soln. and compare them to gas-phase mol. partition functions computed with the same level of theory and the same quasiharmonic approxn. for the diverse and extensive set of mols. and ions included in the training set of the SMD continuum solvation model, and we find mean unsigned differences in vibrational contributions to the solute free energy of only about 0.2 kcal/mol. On the basis of these results and a review of the theory, we conclude, in contrast to previous work, that using partition functions computed for mols. optimized in soln. is a correct and useful approach for averaging over solute degrees of freedom when computing free energies of solutes in soln., and it is moreover recommended for cases where liq. and gas-phase solute structures differ appreciably or when stationary points present in liq. soln. do not exist in the gas phase, for which we provide some examples. When gas-phase and soln.-phase geometries and frequencies are similar, the use of gas-phase geometries and frequencies is a useful approxn.
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    23. 23
      te Velde, G.; Bickelhaupt, F. M.; Baerends, E. J.; Fonseca Guerra, C.; van Gisbergen, S. J. A.; Snijders, J. G.; Ziegler, T. Chemistry with ADF. J. Comput. Chem. 2001, 22, 931,  DOI: 10.1002/jcc.1056
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      Chemistry with ADF
      Te Velde, G.; Bickelhaupt, F. M.; Baerends, E. J.; Fonseca Guerra, C.; Van Gisbergen, S. J. A.; Snijders, J. G.; Ziegler, T.
      Journal of Computational Chemistry (2001), 22 (9), 931-967CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)
      A review with 241 refs. We present the theor. and tech. foundations of the Amsterdam D. Functional (ADF) program with a survey of the characteristics of the code (numerical integration, d. fitting for the Coulomb potential, and STO basis functions). Recent developments enhance the efficiency of ADF (e.g., parallelization, near order-N scaling, QM/MM) and its functionality (e.g., NMR chem. shifts, COSMO solvent effects, ZORA relativistic method, excitation energies, frequency-dependent (hyper)polarizabilities, at. VDD charges). In the Applications section we discuss the phys. model of the electronic structure and the chem. bond, i.e., the Kohn-Sham MO (MO) theory, and illustrate the power of the Kohn-Sham MO model in conjunction with the ADF-typical fragment approach to quant. understand and predict chem. phenomena. We review the "Activation-strain TS interaction" (ATS) model of chem. reactivity as a conceptual framework for understanding how activation barriers of various types of (competing) reaction mechanisms arise and how they may be controlled, for example, in org. chem. or homogeneous catalysis. Finally, we include a brief discussion of exemplary applications in the field of biochem. (structure and bonding of DNA) and of time-dependent d. functional theory (TDDFT) to indicate how this development further reinforces the ADF tools for the anal. of chem. phenomena.
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      Fonseca Guerra, C.; Handgraaf, J. W.; Baerends, E. J.; Bickelhaupt, F. M. Voronoi deformation density (VDD) charges: Assessment of the Mulliken, Bader, Hirshfeld, Weinhold, and VDD methods for charge analysis?. J. Comput. Chem. 2004, 25, 189– 210,  DOI: 10.1002/jcc.10351
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      Voronoi deformation density (VDD) charges: Assessment of the Mulliken, Bader, Hirshfeld, Weinhold, and VDD methods for charge analysis
      Fonseca Guerra Celia; Handgraaf Jan-Willem; Baerends Evert Jan; Bickelhaupt F Matthias
      Journal of computational chemistry (2004), 25 (2), 189-210 ISSN:0192-8651.
      We present the Voronoi Deformation Density (VDD) method for computing atomic charges. The VDD method does not explicitly use the basis functions but calculates the amount of electronic density that flows to or from a certain atom due to bond formation by spatial integration of the deformation density over the atomic Voronoi cell. We compare our method to the well-known Mulliken, Hirshfeld, Bader, and Weinhold [Natural Population Analysis (NPA)] charges for a variety of biological, organic, and inorganic molecules. The Mulliken charges are (again) shown to be useless due to heavy basis set dependency, and the Bader charges (and often also the NPA charges) are not realistic, yielding too extreme values that suggest much ionic character even in the case of covalent bonds. The Hirshfeld and VDD charges, which prove to be numerically very similar, are to be recommended because they yield chemically meaningful charges. We stress the need to use spatial integration over an atomic domain to get rid of basis set dependency, and the need to integrate the deformation density in order to obtain a realistic picture of the charge rearrangement upon bonding. An asset of the VDD charges is the transparency of the approach owing to the simple geometric partitioning of space. The deformation density based charges prove to conform to chemical experience.
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