Pair your accounts.

Export articles to Mendeley

Get article recommendations from ACS based on references in your Mendeley library.

Pair your accounts.

Export articles to Mendeley

Get article recommendations from ACS based on references in your Mendeley library.

You’ve supercharged your research process with ACS and Mendeley!

STEP 1:
Click to create an ACS ID

Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

MENDELEY PAIRING EXPIRED
Your Mendeley pairing has expired. Please reconnect
ACS Publications. Most Trusted. Most Cited. Most Read
Low-Barrier Hydrogen Bond in Fujikurin A–D: A Computational Study
More

OR SEARCH CITATIONS

My Activity
Publications

Figure 1Loading Img
Download Hi-Res ImageDownload to MS-PowerPointCite This:ACS Omega 2022, 7, 16, 14244-14251
  • Open Access
Article

Low-Barrier Hydrogen Bond in Fujikurin A–D: A Computational Study
Click to copy article linkArticle link copied!

  • Hikaru Tanaka
    Hikaru Tanaka
    Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
    More by Hikaru Tanaka
  • Kazuaki Kuwahata
    Kazuaki Kuwahata
    Graduate School of NanobioScience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027, Japan
    More by Kazuaki Kuwahata
  • Masanori Tachikawa*
    Masanori Tachikawa
    Graduate School of NanobioScience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027, Japan
    *Email: [email protected]
    More by Masanori Tachikawa
    Orcidhttps://orcid.org/0000-0002-5489-5714
  • Taro Udagawa*
    Taro Udagawa
    Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
    *Email: [email protected]. Phone: +81-58-293-2575. Fax: +81-58-293-2794.
    More by Taro Udagawa
    Orcidhttps://orcid.org/0000-0002-4072-253X
Open PDF

ACS Omega

Cite this: ACS Omega 2022, 7, 16, 14244–14251
Click to copy citationCitation copied!
https://doi.org/10.1021/acsomega.2c00857
Published April 15, 2022

Copyright © 2022 The Authors. Published by American Chemical Society. This publication is licensed under

CC-BY-NC-ND 4.0 .

Abstract

Click to copy section linkSection link copied!
High Resolution Image
Download MS PowerPoint Slide

The compounds Fujikurin A, B, and D, recently isolated from Fusarium fujikuroi, possess intramolecular low-barrier hydrogen bonds (LBHBs), which are hydrogen bonds with a very low-energy barrier for proton transfer. The isolated compounds have a hydrogen-bonded proton that appears to rapidly switch between two equilibrium states via a transition state (TS). To understand the characteristics of these intramolecular LBHBs in detail, we performed path integral molecular dynamics (PIMD) simulations, which can consider nuclear quantum effects (NQEs) under a finite temperature. The PIMD simulations predicted that the NQE completely washed out the energy barrier for the proton transfer reaction. Consequently, a single-well shape emerged in the results, along with the effective free-energy potential surface for the hydrogen-bonded proton distribution. Thus, we conclude that the hydrogen-bonded proton in Fujikurin does not in fact transfer between two equilibrium structures but widely delocalizes around the global minimum structure involving the TS region.

This publication is licensed under

CC-BY-NC-ND 4.0 .
  • cc licence
  • by licence
  • nc licence
  • nd licence
Copyright © 2022 The Authors. Published by American Chemical Society

Subjects

what are subjects

Introduction

Click to copy section linkSection link copied!
Fungi of the genus Fusarium, including Fusarium fujikuroi, produce harmful substances that include mycotoxins. They also induce crop damage with gibberellins that cause the rice disease bakanae. Fusarium fujikuroi is known to produce various secondary metabolites in addition to gibberellins. (1,2) These metabolites have been studied extensively over time. (1−8) Three new compounds, Fujikurin A, B, and D (Figure 1), were recently identified by Bargen et al. These compounds are a secondary metabolite produced by polyketide synthases (PKSs). (6)

Figure 1

Figure 1. Chemical structures of Fujikurin A–D.

High Resolution Image
Download MS PowerPoint Slide
Bargen et al. focused on the main product, Fujikurin D, analyzing its structure experimentally (mass spectrometry and NMR) and theoretically (density functional theory, DFT), and determined that it had an intramolecular hydrogen bond. Furthermore, they proposed that the hydrogen-bonded proton may rapidly shift back and forth between two equilibrium structures, EQ(1) and EQ(2) (Figure 2). Moreover, Fujikurin A and B were also found to have intramolecular hydrogen bonds that have the same characteristics as those of Fujikurin D.

Figure 2

Figure 2. Equilibrium and TS structures of Fujikurin D.

High Resolution Image
Download MS PowerPoint Slide
However, most of the widely used theoretical calculation methods based on the Born–Oppenheimer approximation do not consider nuclear motion (nuclear quantum effects (NQEs)). The fixed nuclear approach based on the Born–Oppenheimer approximation works well in most situations due to the fact that nuclei are considerably heavier than electrons. However, to analyze systems containing strong hydrogen bonds, including low-barrier hydrogen bonds (LBHBs), where the energy barrier for proton transfer is very low, NQEs are highly useful, enabling the qualitative reproduction of structures. (9−12) Strongly hydrogen-bonded systems have been studied with many helpful methods, including those that involve NQEs. For example, Litman et al. studied porphycene, which has strong intramolecular hydrogen bonds, and reported the temperature dependence of the double hydrogen transfer dynamics, which can be well-understood only if NQEs are taken into account. (13) Ogata et al. investigated asymmetric LBHBs in protonated lysine (LysH+), analyzing the NQEs using the path integral molecular dynamics (PIMD) method. (11) They determined that the hydrogen-bonded proton is not localized on the proton donor or acceptor heavy atoms but is instead delocalized between the heavy atoms from the PIMD simulation.
Thus, the consideration of NQEs is important to correctly understand LBHBs. However, Fujikurin D was analyzed via conventional DFT methods in Bargen’s work, which means that NQEs were not included. Many theoretical methods have been proposed to include NQEs. For example, we have developed multicomponent molecular orbital (MC_MO) methods (9,10,14−16) that go beyond the Born–Oppenheimer approximation to extend the concept of molecular orbitals for electrons to light nuclei. We used MC_MO methods to successfully evaluate the effects of NQEs and H/D isotopes in different hydrogen-bonded systems and proton transfer reactions. PIMD can also consider NQEs statistically within the Born–Oppenheimer approximation framework. (11−13,17−24) The PIMD approach considers NQEs as well as thermal effects. Many PIMD studies have been used to understand NQEs in the context of hydrogen-bonded systems, including LBHBs. In this study, we concentrated on the distribution of hydrogen-bonded protons within Fujikurin A–D. Hence, we carried out PIMD simulations on Fujikurin A–D. We also incorporated typical DFT calculations and conventional MD simulations to elucidate the NQEs and thermal effects in Fujikurin A–D.

Computational Methods

Click to copy section linkSection link copied!
Nuclei are treated as quantum particles in PIMD simulations. In this study, each nucleus was expanded using 16 beads. PIMD simulations were then performed for 90 000 steps, after a thermal equilibration of 10 000 steps using a time step size of 0.1 fs. Furthermore, classical MD (CLMD) simulations, in which each nucleus was represented by one bead, were carried out for 900 000 steps following a thermal equilibration of 100 000 steps using the same time step size for comparison. We performed both CLMD and PIMD simulations in the canonical ensemble (NVT) using a Nosé–Hoover chain (31) at 300 K.
The position of the hydrogen-bonded proton was clarified by defining the proton transfer coordinate (δOH) as
where RO1H and RHO2 are the O1–H covalent bond length and H···O2 hydrogen bond distance, respectively. The notation is illustrated in Figure 3. The value of δOH = 0 implies that the proton is at the center of the oxygen atoms, while a positive or negative δOH value means that the proton is located at a position closer to one of the oxygen atoms.

Figure 3

Figure 3. Hydrogen bond structure of Fujikurin D and definition of atomic labels and coordinates.

High Resolution Image
Download MS PowerPoint Slide
The relative effective free energy (ΔF) was calculated from the obtained distributions using the following equation:
where kB, T, and P(δOH) are the Boltzmann constant, temperature, and probability distribution, respectively, as a function of δOH. P(δOHmax)) is the largest distribution of P(δOH) in the histogram, and the free energy in this region is set to 0.0 kcal/mol.

Results and Discussion

Click to copy section linkSection link copied!

Level of Electronic Structure Calculation

The level of electronic structure calculations for the PIMD simulations was based on the relative energy of each stationary point structure of the main product, Fujikurin D. Table 1 shows the relative energies obtained by DFT (CAM-B3LYP), (25) MP2, and semiempirical PM series methods. (26−30)
Table 1. Relative Energies (kcal/mol) of Stationary Point Structures of Intramolecular Proton Transfer Reaction in Fujikurin D Obtained by Several Methods
methodEQ(1)TSEQ(2)
CAM-B3LYP/6-311+G**0.01.81.1
MP2/aug-cc-pVDZ//CAM-B3LYP/6-311+G**0.01.90.9
PM60.0  
PM6-DH20.0  
PM6-DH+0.03.22.0
PM6-D3H40.03.01.9
PM70.02.72.5
The MP2/aug-cc-pVDZ//CAM-B3LYP/6-311+G** energy was considered to be a highly accurate reference. The CAM-B3LYP/6-311+G** energies were similar to the MP2/6-311+G** energies. Hence, the CAM-B3LYP/6-311+G** method describes the potential energy surface (PES) for the proton-transfer reaction in Fujikurin D accurately. It was also determined that EQ(1) has a lower energy than that of EQ(2). Therefore, EQ(1) is the global minimum structure, and EQ(2) is the metastable equilibrium structure. PIMD simulations require very large numbers of atomic force calculations; therefore, selecting a method that can reproduce highly accurate results with a low computational cost is very important. We focused on a semiempirical PM series method. In Table 1, only the equilibrium state EQ(1) exists on the PM6 and PM6-DH2 PESs, while the proton-transfer equilibrium state EQ(2) and the TS exist on the PM6-DH+, PM6-D3H4, and PM7 PESs. In particular, the PM6-D3H4 method reproduced the relative energies obtained by the MP2/aug-cc-pVDZ//CAM-B3LYP/6-311+G** method.
Next, we confirmed the validity of the PM6-D3H4 method for Fujikurins A and B. The relative energies of Fujikurin A and B are listed in Table 2.
Table 2. Relative Energies (kcal/mol) of Stationary Point Structures of Intramolecular Proton-Transfer Reaction in Fujikurin A and B Obtained by Several Methods
 Fujikurin AFujikurin B
methodEQ(1)TSEQ(2)EQ(1)TSEQ(2)
CAM-B3LYP/6-311+G**0.01.40.20.02.31.7
MP2/aug-cc-pVDZ//CAM-B3LYP/6-311+G**0.01.4–0.20.02.21.4
PM6-D3H40.02.81.70.03.72.9
Similar to the case of Fujikurin D, the CAM-B3LYP/6-311+G** relative energies are like those calculated by MP2/aug-cc-pVDZ//CAM-B3LYP/6-311+G**, indicating that the CAM-B3LYP-optimized geometries were adequate for Fujikurin A and B. The MP2/aug-cc-pVDZ//CAM-B3LYP/6-311+G** activation barriers of Fujikurin A and Fujikurin B were 0.5 kcal/mol lower and 0.3 kcal/mol higher than that of Fujikurin D, respectively. Moreover, the PM6-D3H4 method estimated the activation barriers of Fujikurin A and Fujikurin B as 0.2 kcal/mol lower and 0.7 kcal/mol higher than those of Fujikurin D, respectively. This implies that the PM6-D3H4 method is also adequate for analyzing the intramolecular proton-transfer reaction in Fujikurin A and B. Finally, we used the PM6-D3H4 method to calculate atomic forces.

Structural Features of Fujikurin D

For Fujikurin D, Figure 4 shows the one-dimensional distributions of RO1H, RHO2, and RO1O2, while Table 3 has the average values of RO1H, RHO2, and RO1O2 obtained by CLMD and PIMD simulations. The values shown in parentheses are the statistical errors of the average bond lengths calculated using the block average method. (32)Table 3 lists the optimized RO1H, RHO2, and RO1O2 values in the equilibrium structure.

Figure 4

Figure 4. One-dimensional distributions of (a) RO1H, (b) RHO2, and (c) RO1O2 obtained by CLMD and PIMD simulations. The dashed lines represent the values of two equilibrium structures.

High Resolution Image
Download MS PowerPoint Slide
Table 3. Average Values of RO1H (Å), RHO2 (Å), and RO1O2 (Å) Obtained by CLMD and PIMD Simulations and the Interatomic Distances in Equilibrium Structures EQ(1) and EQ(2)
 RO1HRHO2RO1O2
CLMD1.103(7)1.607(8)2.525(2)
PIMD1.112(4)1.601(10)2.512(6)
EQ(1)1.0911.5822.504
EQ(2)1.4201.1742.440
In a comparison of the CLMD and PIMD results for the one-dimensional distributions of RO1H and RHO2 (Figure 4a,b), the distributions generated by PIMD simulations are much wider than those produced by CLMD simulations owing to quantum fluctuations. The results of the CLMD simulations showed two peaks. Because EQ(1) is more stable than EQ(2), the peak around EQ(1) is much larger. However, the distributions for the CLMD and PIMD simulations for RO1O2 are similar. Thus, the impact of the NQEs on RO1O2 was smaller than that on RO1H.
We focused on the covalent RO1H average bond lengths in Table 3 and found that the relationship of the RO1H values is as follows:
The average value obtained in the CLMD simulation was greater than the ROH in EQ(1). The CLMD simulation includes thermal effects only; therefore, the elongation of the covalent RO1H bond length is due to thermal motion. The PIMD simulation, which includes both thermal effects and NQEs, provided a greater RO1H average bond length than that of the CLMD simulation. Thus, the NQEs stretch the covalent bond length. These results are often observed in other hydrogen-bonded systems. (11,12)
However, the average values of RHO2 and RO1O2 in Table 3 show the following relationship, which is different from that for the covalent ROH lengths:
The bond lengths obtained from the CLMD and PIMD simulations were greater than those in EQ(1) because of the thermal effect, as in the case of RO1H. To explain why the RHO2 and RO1O2 values obtained in the PIMD simulations were smaller than those obtained in the CLMD simulation, we focused on the Mulliken charges of oxygen and hydrogen atoms (Figure 5).

Figure 5

Figure 5. Mulliken charges of the oxygen and the hydrogen atoms obtained in (a) CLMD and (b) PIMD simulations.

High Resolution Image
Download MS PowerPoint Slide
The Mulliken charge of H was found to be +0.426 in the CLMD result, whereas it was +0.430 from PIMD, which means that the hydrogen-bonded proton in the PIMD simulation was more positively charged than that in the CLMD simulation. The finite spread of the nuclei in the PIMD simulation induced the NQEs, which affected the surrounding electron distributions. We can find that the proton acceptor, O2, is more negative than O1. In addition, O2 in the PIMD simulation is less negative than that in the CLMD one, unlike O1. Since the proton donor and acceptor atoms swap their roles by the proton transfer, O1 and O2 become more and less negative around the TS region. The hydrogen-bonded proton can access the TS region more easily in the PIMD simulation rather than in the CLMD one, as described below. Thus, O2 seems to be less negative in the PIMD simulation than in the CLMD one. We should focus on the sum of the negative charges of O1 and O2 for the strength of the interaction. The greater negative charge is found in the PIMD simulation than in the CLMD. The more positively charged hydrogen-bonded proton interacts more strongly with the negatively charged oxygen atoms in the hydrogen bond moiety. Thus, the distance between the oxygen atoms in the PIMD result was smaller than that in the CLMD result owing to the strong hydrogen bond interaction.

Relative Free-Energy Potential Surface for Proton-Transfer Coordinate

To understand the hydrogen-bonded proton distribution, we focused on the one-dimensional relative free-energy potential surface for the proton-transfer coordinate δOH. Figure 6 shows the one-dimensional relative effective free-energy potential surfaces from the CLMD and PIMD simulations.

Figure 6

Figure 6. One-dimensional relative effective free-energy landscapes of δOH obtained by CLMD and PIMD simulations. The dashed lines represent two equilibrium structures.

High Resolution Image
Download MS PowerPoint Slide
First, we focused on the CLMD results. The relative effective free-energy potential obtained by the CLMD simulation is a double-well potential with two minima. The positions of the minima are in good agreement with the δOH values of the equilibrium structures shown by the black dashed lines in Figure 6. Thus, it is difficult to overcome the activation energy barrier using thermal effects alone. The barrier height of the free-energy potential in the CLMD result was estimated as 3.6 kcal/mol, which is slightly larger than that from the static electronic structure calculation, 3.0 kcal/mol (Table 1). This trend has also been reported for other LBHB systems. (11,17) However, the energy barrier completely disappeared in the PIMD results, and the shape of the free-energy potential was a single well. The PIMD simulation took the thermal effect and NQEs into account; thus, the energy barrier of the proton transfer was washed out by the NQEs. Similar NQE influences on the proton distribution around the TS structure were reported for LBHB in LysH+ by Ogata et al. (11) In particular, the NQEs on proton transfer might be the primary factor because the NQEs of light nuclei were more prominent than those of heavier nuclei. It should be noted here that, in a symmetrical hydrogen-bonded system such as a maleate anion, (12) the potential minimum should be at δOH = 0 Å. However, in Fujikurin D, the minimum potential is located at approximately δOH = −0.5 Å, which corresponds to the global minimum structure EQ(1), because Fujikurin D has an asymmetric PES in the proton-transfer coordinate.
The two-dimensional free-energy landscapes of δOH and ROO are shown in Figure 7 to aid a better understanding of the proton distribution. There are two minima located around the equilibrium structures in the free-energy landscape simulated using the CLMD method (Figure 7a). Thus, the equilibrium structure analogues, in the which transferring proton is localized to either oxygen atom, are frequently observed as expected from the one-dimensional free-energy landscape (Figure 6). In addition, the energy maximum exists near the TS structure. Therefore, the distribution near the TS region is sparse compared to those around the equilibrium structures. Moreover, the low-energy regions are distributed along the IRC pathways. Thus, the hydrogen-bonded proton is mainly distributed around the equilibrium structures, and proton transfer may occur between the two equilibrium structures. Thus, the predictions of the CLMD are consistent with those by Bargen.

Figure 7

Figure 7. Two-dimensional free-energy landscapes of δOH and ROO obtained with (a) CLMD and (b) PIMD. Triangles and circles represent the equilibrium and the TS structures, respectively, and dashed lines are IRC pathways. Free energy is in units of kcal/mol.

High Resolution Image
Download MS PowerPoint Slide
In contrast, the PIMD simulation results are qualitatively different from the CLMD results. As seen in Figure 7b, the energy barrier for the proton transfer was completely overcome by the NQEs. The PIMD results show a broad single-well potential centered at the global minimum (δOH = −0.5 Å) and the corresponding one-dimensional free-energy potential (Figure 6). The regions around the TS and metastable structures are also included in this broad single-well potential. Unlike in the CLMD predictions, the proton distribution extends to regions far from the IRC. This corner-cutting phenomenon is induced by the NQEs and is seen in several systems, such as N2H7+. (18) Our PIMD simulation shows a broad single-well potential centered on the global minimum structure for Fujikurin D. In other words, in the PIMD predictions, the proton overcomes the proton-transfer barrier freely and is not localized around either oxygen atoms, in contrast to Bargen’s prediction of fast transfer between the two equilibrium structures.

Proton Coordinate

We defined a coordinate system to analyze how the hydrogen-bonded protons are distributed, as shown in Figure 8. The origin is the center of mass of two oxygen atoms, and the xy-plane is defined to be in the O1–O2–C plane. Proton-distribution landscapes were obtained in three dimensions from both CLMD (Figure 8a) and PIMD (Figure 8b). Simulations in this coordinate system are shown in Figure 8.

Figure 8

Figure 8. Three-dimensional distribution of hydrogen-bonded proton in Fujikurin D. The origin is defined as the center of mass of the O atoms and the xy-plane as the O1–O2–C plane.

High Resolution Image
Download MS PowerPoint Slide
The CLMD results are shown in Figure 8a. Many structures are located around the two equilibrium structures, which were indicated by two peaks exhibited by the proton distribution in the xy- and xz-planes. In contrast, the PIMD result (Figure 8b) shows single broad distributions in every direction, depicting the activation barrier wash out caused by the NQEs, as mentioned above. While there are pronounced differences in the x- and y-directions when PIMD is compared to CLMD, the changes in the z-axis direction are not significant. To illustrate the changes more clearly, we show the difference distribution landscapes, which are the differences between the proton distributions obtained in the CLMD and PIMD simulations, in Figure 9.

Figure 9

Figure 9. Difference distribution landscapes of proton distributions obtained from CLMD and PIMD simulations of Fujikurin D. Red (blue) indicates regions where the distribution in the PIMD (CLMD) simulated results is denser than that in the CLMD (PIMD) simulated results.

High Resolution Image
Download MS PowerPoint Slide
In Figure 9, red indicates regions where the distributions in the PIMD results are denser than those in the CLMD results. This red area is spread in the xy-plane. Thus, distributions in the x- and y-directions increase because of the NQEs. However, in the yz- and zx-planes, the distribution in the z-direction did not increase much compared to the x- and y-directions. This means the NQEs did not considerably affect the protonic motion along the z-axis direction. The presence of the intramolecular hydrogen bond is considered to be a reason for the directional behavior of the NQE. The NQEs influence the electronic distribution, and as a result, the hydrogen bond interaction was enhanced in the PIMD simulations. Proton donor and acceptor atoms are always in the xy-plane in this environment. Hence, the hydrogen-bonded proton was attracted more strongly from the x- and y-directions than from the z-direction. This explains why the NQEs are pronounced in only the x- and y-directions.

Proton Distribution in Fujikurin A and B

Figure 10a,b shows the two-dimensional free-energy values, δOH and ROO, for Fujikurin A and B, respectively, to demonstrate how the distribution of the transferring proton is affected by the height of the activation barrier.

Figure 10

Figure 10. Two-dimensional free-energy landscapes δOH and ROO of Fujikurin A and B for (a) CLMD and (b) PIMD. Triangles and circles represent equilibrium and the TS structures, respectively, and dashed lines represent IRC pathways. Free energy is expressed in units of kcal/mol.

High Resolution Image
Download MS PowerPoint Slide
The CLMD results exhibit two minima, while the PIMD results show one minimum. This means the NQEs washed out the activation barrier in all Fujikurin compounds. Among the Fujikurin A–D compounds, Fujikurin A has the lowest activation barrier and largest low-energy region (represented by orange and yellow) in the two-dimensional free-energy results obtained by PIMD. NQEs extend the low-energy region around the TS, as well as near the metastable equilibrium structure.
It is worth noting that the PM6-D3H4 calculations overestimate the activation barrier slightly, when compared to those of the MP2/aug-cc-pVDZ//CAM-B3LYP/6-311+G** method. Hence, the distributions near the TS and metastable equilibrium structure may be denser on the more precise potential energy hypersurface.

Conclusion

Click to copy section linkSection link copied!
In this study, we investigated the NQE and thermal effects on Fujikurin A–D intramolecular hydrogen bonds via PIMD simulation, which takes the thermal effect and the NQE into account.
For Fujikurin D, the CLMD simulations demonstrate that the hydrogen-bonded proton is rapidly switching between two equilibrium states, as predicted in a previous study by Bargen et al. In contrast, the PIMD simulation results are qualitatively different because NQEs are taken into consideration. The results imply a delocalized distribution on the single-well potential as a result of the wash out of the proton-transfer energy barrier. Furthermore, the NQE in Fujikurin D was found to be direction-dependent. The PIMD simulations demonstrated that the change in the PES of the proton-transfer reaction in Fujikurin D after considering NQEs could be observed even qualitatively.
Among Fujikurin A, B, and D, the widest proton distribution was found in Fujikurin A, which has the lowest activation barrier for proton transfer. In Fujikurin A, protons are distributed around the TS, as well as in the metastable equilibrium structure. Because the activation barriers were overestimated slightly by the PM6-D3H4 level of calculation, the proton distribution near the TS should actually be denser than calculated in this study. Our results can help elucidate the structures and properties of new secondary metabolites of Fujikurins.

Author Information

Click to copy section linkSection link copied!
  • Corresponding Authors
  • Authors
    • Hikaru Tanaka - Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
    • Kazuaki Kuwahata - Graduate School of NanobioScience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027, Japan
  • Notes
    The authors declare no competing financial interest.

Acknowledgments

Click to copy section linkSection link copied!

This work was supported by JSPS KAKENHI Grants 21J00806 (to K.K.); 18H01945, 19H05063, and 21H00026 (to M.T.); and 20H05739 and 21K04991 (to T.U.). The generous allotment of computational resources from the Research Center for Computational Science, National Institute of Natural Science, Japan, is also gratefully acknowledged.

References

Click to copy section linkSection link copied!

This article references 32 other publications.

  1. 1
    Yabuta, T.; Kambe, K.; Hayashi, T. Biochemistry of the ″bakanae″ fungus. I. Fusarinic acid, a new product of the “bakanae” fungus. Nippon Nogei Kagaku Kaishi 1934, 10, 1059– 1068
    Google Scholar
    1
    Biochemistry of the "bakanae" fungus. I. Fusarinic acid, a new product of the "bakanae" fungus
    Yabuta, Teijiro; Kambe, Katsuji; Hayashi, Takeshi
    Nippon Nogei Kagaku Kaishi (1934), 10 (), 1059-68CODEN: NNKKAA; ISSN:0002-1407.
    The "bakanae" fungus, Fusarium heterosporium Nees, excretes a growth-promoting substance for rice seedlings. It also excretes a growth-restraining substance according to the condition of the culture. The growth-restraining substance was isolated by extn. of the culture soln. with benzine or petr. ether. The fungus was cultured in a soln. contg. (NH4)2SO4 4.8 g., Na2HPO4 2.8 g., KCl 1.8 g., CaCl2 0.32 g., MgCl2 0.6 g., 0.5 N HCl 6 cc., glucose 100 g. and H2O 2 l. at 27-8° for 40-50 days. The product was filtered and the filtrate was evapd. to a sirup. Succinic acid was isolated by extn. of the sirup with ether. The residue was then extd. with benzine, petr. ether or ligroin. From the ext. there crystd. in colorless plates, m. 108-9°, fusarinic acid, C10H13NO2, in a yield of 0.5-1.0 g. from 10 l. of the culture soln. It forms a Cu salt, light-violet plates (C10H12NO2)2Cu. Distn. of fusarinic acid with CaO gave fusarin, picrate, m. 142°. Fusarinic acid is oxidized to isocinchomeronic acid and propionic acid by KMnO4. Oxidation of fusarin with KMnO4 gives nicotinic acid. Fusarinic acid may be 5-butyl- or 5-sec-butyl-picolinic acid.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaA2MXoslek&md5=8774dfda4bb93f33eece72f3b2c7d3c3
  2. 2
    Graebe, J. E. Gibberellin Biosynthesis and Control. Annu. Rev. Plant. Physiol. 1987, 38, 419,  DOI: 10.1146/annurev.pp.38.060187.002223
    Google Scholar
    2
    Gibberellin biosynthesis and control
    Graebe, Jan E.
    Annual Review of Plant Physiology (1987), 38 (), 419-65CODEN: ARPPA3; ISSN:0066-4294.
    A review with 206 refs. Gibberellin biosynthesis in higher plants is discussed in three phases: (1) the biosynthesis of ent-kaurene, (2) the biosynthesis of GA12-aldehyde, and (3) the pathways after GA12-aldehyde. The biochem. and physiol. control of gibberellin biosynthesis is also discussed.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL2sXksFGlu7s%253D&md5=14334df1f0b6101e653c7f776ab4ac69
  3. 3
    Brady, S. F.; Clardy, J. CR377, a New Pentaketide Antifungal Agent Isolated from an Endophytic Fungus. J. Nat. Prod. 2000, 63, 1447– 1448,  DOI: 10.1021/np990568p
    Google Scholar
    3
    CR377, a new pentaketide antifungal agent isolated from an endophytic fungus
    Brady, Sean F.; Clardy, Jon
    Journal of Natural Products (2000), 63 (10), 1447-1448CODEN: JNPRDF; ISSN:0163-3864. (American Chemical Society)
    Cultures of endophytic fungi collected in the Guanacaste Conservation Area of Costa Rica were screened for antifungal activity. CR377 (I), a new pentaketide antifungal agent, was isolated from the culture broth of a fungus, CR377 (Fusarium sp.), that showed potent activity against Candida albicans in this assay. The structure of I was established using 1- and 2-D NMR and HRFABMS.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3cXmtVGqtbY%253D&md5=ce2ba46075f1ad98345ad6e0298eaf2f
  4. 4
    Niehaus, E. M.; Kleigrewe, K.; Wiemann, P.; Studt, L.; Sieber, C. M. K.; Connolly, L. R.; Freitag, M.; Güldener, U.; Tudzynski, B.; Humpf, H. U. Genetic Manipulation of the Fusarium Fujikuroi Fusarin Gene Cluster Yields Insight into the Complex Regulation and Fusarin Biosynthetic Pathway. Chem. Biol. 2013, 20, 1055– 1066,  DOI: 10.1016/j.chembiol.2013.07.004
    Google Scholar
    4
    Genetic Manipulation of the Fusarium fujikuroi Fusarin Gene Cluster Yields Insight into the Complex Regulation and Fusarin Biosynthetic Pathway
    Niehaus, Eva-Maria; Kleigrewe, Karin; Wiemann, Philipp; Studt, Lena; Sieber, Christian M. K.; Connolly, Lanelle R.; Freitag, Michael; Gueldener, Ulrich; Tudzynski, Bettina; Humpf, Hans-Ulrich
    Chemistry & Biology (Oxford, United Kingdom) (2013), 20 (8), 1055-1066CODEN: CBOLE2; ISSN:1074-5521. (Elsevier Ltd.)
    The biosynthesis and regulation of the polyketide synthase/nonribosomal peptide synthetase (PKS/NRPS)-derived mutagenic mycotoxin fusarin C was studied in the fungus Fusarium fujikuroi. The fusarin gene cluster consists of nine genes (fus1-fus9) that are coexpressed under high-nitrogen and acidic pH conditions. Chromatin immunopptn. revealed a correlation between high expression and enrichment of activating H3K9-acetylation marks under inducing conditions. The authors provide evidence that only four genes are sufficient for the biosynthesis. The combination of genetic engineering with NMR and mass-spectrometry-based structure elucidation allowed the discovery of the putative fusarin biosynthetic pathway. Surprisingly, PKS/NRPS releases its product with an open ring structure, probably as an alc. The authors' data indicate that 2-pyrrolidone ring closure, oxidn. at C-20, and, finally, methylation at C-20 are catalyzed by Fus2, Fus8, and Fus9, resp.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXht1Gmur7M&md5=919d67a5ebb0d933687786fc191c23f4
  5. 5
    Niehaus, E. M.; von Bargen, K. W.; Espino, J. J.; Pfannmüller, A.; Humpf, H. U.; Tudzynski, B. Characterization of the Fusaric Acid Gene Cluster in Fusarium Fujikuroi. Appl. Microbiol. Biotechnol. 2014, 98, 1749– 1762,  DOI: 10.1007/s00253-013-5453-1
    Google Scholar
    5
    Characterization of the fusaric acid gene cluster in Fusarium fujikuroi
    Niehaus, Eva-Maria; von Bargen, Katharina W.; Espino, Jose J.; Pfannmueller, Andreas; Humpf, Hans-Ulrich; Tudzynski, Bettina
    Applied Microbiology and Biotechnology (2014), 98 (4), 1749-1762CODEN: AMBIDG; ISSN:0175-7598. (Springer)
    The "bakanae" fungus Fusarium fujikuroi is a common pathogen of rice and produces a variety of mycotoxins, pigments, and phytohormones. Fusaric acid is one of the oldest known secondary metabolites produced by F. fujikuroi and some other Fusarium species. Study of its biosynthesis and regulation is of great interest due to its occurrence in cereal-based food and feed. This study describes the identification and characterization of the fusaric acid gene cluster in F. fujikuroi consisting of the PKS-encoding core gene and four co-regulated genes, FUB1-FUB5. Besides fusaric acid, F. fujikuroi produces two fusaric acid-like derivs.: fusarinolic acid and 9,10-dehydrofusaric acid. The authors provide evidence that these derivs. are not intermediates of the fusaric acid biosynthetic pathway, and that their formation is catalyzed by genes outside of the fusaric acid gene cluster. Target gene deletions of all five cluster genes revealed that not all of them are involved in fusaric acid biosynthesis. The authors suggest that only two genes, FUB1 and FUB4, are necessary for the biosynthesis. Expression of the FUB genes and prodn. of fusaric acid and the two derivs. are favored under high nitrogen. Nitrogen-dependent expression of fusaric acid genes is pos. regulated by the nitrogen-responsive GATA transcription factor AreB, and pH-dependent regulation is mediated by the transcription factor PacC. In addn., fusaric acid prodn. is regulated by two members of the fungal-specific velvet complex: Vel1 and Lae1. In planta expression studies show a higher expression in the favorite host plant rice compared to maize.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXis1aktg%253D%253D&md5=d5a4c47a409656139f239ec5b85bb329
  6. 6
    von Bargen, K. W.; Niehaus, E. M.; Krug, I.; Bergander, K.; Würthwein, E. U.; Tudzynski, B.; Humpf, H. U. Isolation and Structure Elucidation of Fujikurins A-D: Products of the PKS19 Gene Cluster in Fusarium Fujikuroi. J. Nat. Prod. 2015, 78, 1809– 1815,  DOI: 10.1021/np5008137
    Google Scholar
    6
    Isolation and Structure Elucidation of Fujikurins A-D: Products of the PKS19 Gene Cluster in Fusarium fujikuroi
    von Bargen, Katharina Walburga; Niehaus, Eva-Maria; Krug, Isabel; Bergander, Klaus; Wuerthwein, Ernst-Ulrich; Tudzynski, Bettina; Humpf, Hans-Ulrich
    Journal of Natural Products (2015), 78 (8), 1809-1815CODEN: JNPRDF; ISSN:0163-3864. (American Chemical Society-American Society of Pharmacognosy)
    Fusarium fujikuroi is a member of the Gibberella fujikuroi species complex and well known for the prodn. of gibberellins and mycotoxins including fusarins and fusaric acid. A recent genome sequencing study revealed that the fungus has the genetic potential to produce many more secondary metabolites than have been reported. This paper describes the structure elucidation of the products of the cryptic and silent PKS19 gene cluster that were recently identified (fujikurins A-D). We present the complete NMR data for the structure elucidation of the main compd. fujikurin D, which shows tautomeric 1,3-diketo elements. The different tautomeric structures could be confirmed using quantum chem. calcns. Addnl., the structures of the minor compds. fujikurins A-C were elucidated by high-resoln. mass spectrometric fragmentation expts. It emerged that fujikurin A was identical to the bioactive compd. CR377 of the taxonomically unclassified Fusarium strain CR377, while fujikurins B-D have not been reported from other fungi.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhtF2ltrvN&md5=97fb1c8a577face4ce27d11f2eaff8f3
  7. 7
    Niehaus, E. M.; Kim, H. K.; Münsterkötter, M.; Janevska, S.; Arndt, B.; Kalinina, S. A.; Houterman, P. M.; Ahn, I. P.; Alberti, I.; Tonti, S.; Kim, D. W.; Sieber, C. M. K.; Humpf, H. U.; Yun, S. H.; Güldener, U.; Tudzynski, B. Comparative Genomics of Geographically Distant Fusarium Fujikuroi Isolates Revealed Two Distinct Pathotypes Correlating with Secondary Metabolite Profiles. PLoS Pathogens 2017, 13, e1006670  DOI: 10.1371/journal.ppat.1006670
    Google Scholar
    7
    Comparative genomics of geographically distant Fusarium fujikuroi isolates revealed two distinct pathotypes correlating with secondary metabolite profiles
    Niehaus, Eva-Maria; Kim, Hee-Kyoung; Muensterkoetter, Martin; Janevska, Slavica; Arndt, Birgit; Kalinina, Svetlana A.; Houterman, Petra M.; Ahn, Il-Pyung; Alberti, Ilaria; Tonti, Stefano; Kim, Da-Woon; Sieber, Christian M. K.; Humpf, Hans-Ulrich; Yun, Sung-Hwan; Gueldener, Ulrich; Tudzynski, Bettina
    PLoS Pathogens (2017), 13 (10), e1006670/1-e1006670/38CODEN: PPLACN; ISSN:1553-7374. (Public Library of Science)
    Fusarium fujikuroi causes bakanae ("foolish seedling") disease of rice which is characterized by hyper-elongation of seedlings resulting from prodn. of gibberellic acids (GAs) by the fungus. This plant pathogen is also known for prodn. of harmful mycotoxins, such as fusarins, fusaric acid, apicidin F and beauvericin. Recently, we generated the first de novo genome sequence of F. fujikuroi strain IMI 58289 combined with extensive transcriptional, epigenetic, proteomic and chem. product analyses. GA prodn. was shown to provide a selective advantage during infection of the preferred host plant rice. Here, we provide genome sequences of eight addnl. F. fujikuroi isolates from distant geog. regions. The isolates differ in the size of chromosomes, most likely due to variability of subtelomeric regions, the type of asexual spores (microconidia and/or macroconidia), and the no. and expression of secondary metabolite gene clusters. While most of the isolates caused the typical bakanae symptoms, one isolate, B14, caused stunting and early withering of infected seedlings. In contrast to the other isolates, B14 produced no GAs but high amts. of fumonisins during infection on rice. Furthermore, it differed from the other isolates by the presence of three addnl. polyketide synthase (PKS) genes (PKS40, PKS43, PKS51) and the absence of the F. fujikuroi-specific apicidin F (NRPS31) gene cluster. Anal. of addnl. field isolates confirmed the strong correlation between the pathotype (bakanae or stunting/withering), and the ability to produce either GAs or fumonisins. Deletion of the fumonisin and fusaric acid-specific PKS genes in B14 reduced the stunting/withering symptoms, whereas deletion of the PKS51 gene resulted in elevated symptom development. Phylogenetic analyses revealed two subclades of F. fujikuroi strains according to their pathotype and secondary metabolite profiles.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXht1WjtrvP&md5=50146de72cb0a7aa2f20aaceff8b6820
  8. 8
    Wang, W. G.; Wang, H.; Du, L. Q.; Li, M.; Chen, L.; Yu, J.; Cheng, G. G.; Zhan, M. T.; Hu, Q. F.; Zhang, L.; Yao, M.; Matsuda, Y. Molecular Basis for the Biosynthesis of an Unusual Chain-Fused Polyketide, Gregatin A. J. Am. Chem. Soc. 2020, 142, 8464– 8472,  DOI: 10.1021/jacs.0c02337
    Google Scholar
    8
    Molecular Basis for the Biosynthesis of an Unusual Chain-Fused Polyketide, Gregatin A
    Wang, Wei-Guang; Wang, Hang; Du, Lian-Qiong; Li, Min; Chen, Lin; Yu, Jian; Cheng, Gui-Guang; Zhan, Meng-Tao; Hu, Qiu-Fen; Zhang, Lihan; Yao, Min; Matsuda, Yudai
    Journal of the American Chemical Society (2020), 142 (18), 8464-8472CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    Gregatin A (1) is a fungal polyketide featuring an alkylated furanone core, but the biosynthetic mechanism to furnish the intriguing mol. skeleton has yet to be elucidated. Herein, we have identified the biosynthetic gene cluster of gregatin A (1) in Penicillium sp. sh18 and investigated the mechanism that produces the intriguing structure of 1 by in vivo and in vitro reconstitution of its biosynthesis. Our study established the biosynthetic route leading to 1 and illuminated that 1 is generated by the fusion of two different polyketide chains, which are, amazingly, synthesized by a single polyketide synthase GrgA with the aid of a trans-acting enoylreductase GrgB. Chain fusion, as well as chain hydrolysis, is catalyzed by an α/β hydrolase, GrgF, hybridizing the C11 and C4 carbon chains by Claisen condensation. Finally, structural anal. and mutational expts. using GrgF provided insight into how the enzyme facilitates the unusual chain-fusing reaction. In unraveling a new biosynthetic strategy involving a bifunctional PKS and a polyketide fusing enzyme, our study expands our knowledge concerning fungal polyketide biosynthesis.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXmvFSitLc%253D&md5=1d4db4f3134b41a0fb923cfa61b8c7c7
  9. 9
    Moreno, D. v.; González, S. A.; Reyes, A. Turning Symmetric an Asymmetric Hydrogen Bond with the Inclusion of NQEs: The Case of the [CN···H···NC]− Complex. J. Chem. Phys. 2011, 134, 024115,  DOI: 10.1063/1.3521272
    Google Scholar
    9
    Turning symmetric an asymmetric hydrogen bond with the inclusion of nuclear quantum effects: The case of the [CN···H···NC]- complex
    Moreno, Diego V.; Gonzalez, Sergio A.; Reyes, Andres
    Journal of Chemical Physics (2011), 134 (2), 024115/1-024115/7CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
    Nuclear quantum effects (NQE) on the geometry, energy, and electronic structure of the [CN·L·NC]- complex (L = H, D, T) are investigated with the recently developed APMO/MP2 code. This code implements the nuclear MO approach (NMO) at the Hartree-Fock (HF) and MP2 levels of theory for electrons and quantum nuclei. In a first study, we examd. the H/D/T isotope effects on the geometry and electronic structure of the CNH mol. at NMO/HF and NMO/MP2 levels of theory. We found that when increasing the hydrogen nuclear mass there is a redn. of the RN-H bond distance and an increase of the electronic population on the hydrogen atom. Our calcd. bond distances are in good agreement with exptl. and other theor. results. In a second investigation, we explored the hydrogen NQE on the geometry of CNHNC- complex at the NMO/HF and NMO/MP2 levels of theory. We discovered that while a NMO/HF calcn. presented an asym. hydrogen bond, the NMO/MP2 calcn. revealed a sym. H-bond. We also examd. the H/D/T isotope effects on the geometry and stabilization energy of the CNHNC- complex. We noted that gradual increases in hydrogen mass led to redns. of the RNN distance and destabilization of the hydrogen bond (H-bond). A discussion of these results is given in terms of the hydrogen nuclear delocalization effects on the electronic structure and energy components. To the best of our knowledge, this is the first ab initio NMO study that reveals the importance of including nuclear quantum effects in conventional electronic structure calcns. for an enhanced description of strong-low-barrier H-bonded systems. (c) 2011 American Institute of Physics.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXltlymug%253D%253D&md5=b66ddf19358ce000d41b70a512a6fced
  10. 10
    Kanematsu, Y.; Tachikawa, M. Theoretical Analysis of Geometry and NMR Isotope Shift in Hydrogen-Bonding Center of Photoactive Yellow Protein by Combination of Multicomponent Quantum Mechanics and ONIOM Scheme. J. Chem. Phys. 2014, 141, 185101,  DOI: 10.1063/1.4900987
    Google Scholar
    10
    Theoretical analysis of geometry and NMR isotope shift in hydrogen-bonding center of photoactive yellow protein by combination of multicomponent quantum mechanics and ONIOM scheme
    Kanematsu, Yusuke; Tachikawa, Masanori
    Journal of Chemical Physics (2014), 141 (18), 185101/1-185101/8CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
    Multicomponent quantum mech. (MC_QM) calcn. has been extended with ONIOM (our own N-layered integrated MO + mol. mechanics) scheme [ONIOM(MC_QM:MM)] to take account of both the nuclear quantum effect and the surrounding environment effect. The authors have demonstrated the first implementation and application of ONIOM(MC_QM:MM) method for the anal. of the geometry and the isotope shift in hydrogen-bonding center of photoactive yellow protein. ONIOM(MC_QM:MM) calcn. for a model with deprotonated Arg52 reproduced the elongation of O-H bond of Glu46 obsd. by neutron diffraction crystallog. Among the unique isotope shifts in different conditions, the model with protonated Arg52 with solvent effect reasonably provided the best agreement with the corresponding exptl. values from liq. NMR measurement. Our results implied the availability of ONIOM(MC_QM:MM) to distinguish the local environment around hydrogen bonds in a biomol. (c) 2014 American Institute of Physics.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhvV2mtb3K&md5=17de481a00beec43b35e9154880c3722
  11. 11
    Ogata, Y.; Daido, M.; Kawashima, Y.; Tachikawa, M. NQEs on Protonated Lysine with an Asymmetric Low Barrier Hydrogen Bond: An Ab Initio Path Integral Molecular Dynamics Study. RSC Adv. 2013, 3, 25252– 25257,  DOI: 10.1039/c3ra44077j
    Google Scholar
    11
    Nuclear quantum effects on protonated lysine with an asymmetric low barrier hydrogen bond: an ab initio path integral molecular dynamics study
    Ogata, Yudai; Daido, Masashi; Kawashima, Yukio; Tachikawa, Masanori
    RSC Advances (2013), 3 (47), 25252-25257CODEN: RSCACL; ISSN:2046-2069. (Royal Society of Chemistry)
    The nuclear quantum effect on the short and asym. hydrogen bond of protonated lysine (LysH+) at room temp. is explored by ab initio path integral mol. dynamics (PIMD) simulation. From static electronic structure calcns., the barrier height of proton transfer in LysH+ is 1.1 kcal mol-1, which is much lower than that of typical hydrogen bonds. The hydrogen-bonded proton is delocalized in between two nitrogen atoms in the PIMD simulation including both thermal and nuclear quantum effects, while the proton is localized on a nitrogen atom in a conventional ab initio mol. dynamics simulation including thermal effects alone. We found that the proton transfer barrier found in the static calcn. and conventional ab initio simulation is completely washed out in the PIMD simulation. Meanwhile, the proton distribution at the Nζ atom was larger than that at the N atom, as found in the static calcn. and conventional ab initio mol. dynamics simulation. We clarified from our PIMD simulation that an asym. low barrier hydrogen bond exists in LysH+ at room temp.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhslCrsL7P&md5=f730d96032e11ef4065b665dd8126222
  12. 12
    Kawashima, Y.; Tachikawa, M. Ab Initio Path Integral Molecular Dynamics Study of the NQE on Out-of-Plane Ring Deformation of Hydrogen Maleate Anion. J. Chem. Theory Comput. 2014, 10, 153– 163,  DOI: 10.1021/ct4007986
    Google Scholar
    12
    Ab Initio Path Integral Molecular Dynamics Study of the Nuclear Quantum Effect on Out-of-Plane Ring Deformation of Hydrogen Maleate Anion
    Kawashima, Yukio; Tachikawa, Masanori
    Journal of Chemical Theory and Computation (2014), 10 (1), 153-163CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
    Ab initio path integral mol. dynamics (PIMD) simulation was performed to understand the nuclear quantum effect on the out-of-plane ring deformation of hydrogen maleate anion and investigate the existence of a stable structure with ring deformation, which was suggested in exptl. observation. The isotope effect and the temp. effect are studied as well. We first investigated the nuclear quantum effect on the proton transfer. In static calcn. and classical ab initio mol. dynamics simulations, the proton in the hydrogen bond is localized to either oxygen atom. On the other hand, the proton is located at the center of two oxygen atoms in quantum ab initio PIMD simulations. The nuclear quantum effect washes out the barrier of proton transfer. We next examd. the nuclear quantum effect on the motion of hydrogen maleate anion. Principal component anal. revealed that the out-of-plane ring bending modes have dominant contribution to the entire mol. motion. In quantum ab initio PIMD simulations, structures with ring deformation were the global min. for the deuterated isotope at 300 K. We analyzed the out-of-plane ring bending mode further and found that there are three min. along a ring distortion mode. We successfully found a stable structure with ring deformation of hydrogen maleate for the first time, to our knowledge, using theor. calcn. The structures with ring deformation found in quantum simulation of the deuterated isotope allowed the proton transfer to occur more frequently than the planar structure. Static ab initio electronic structure calcn. found that the structures with ring deformation have very small proton transfer barrier compared to the planar structure. We suggest that the "proton transfer driven" mechanism is the origin of stabilization for the structure with out-of-plane ring deformation.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhvFSqtrfK&md5=f9a8636c40caaec0e7cf0c047765eee8
  13. 13
    Litman, Y.; Richardson, J. O.; Kumagai, T.; Rossi, M. Elucidating the Nuclear Quantum Dynamics of Intramolecular Double Hydrogen Transfer in Porphycene. J. Am. Chem. Soc. 2019, 141, 2526– 2534,  DOI: 10.1021/jacs.8b12471
    Google Scholar
    13
    Elucidating the Nuclear Quantum Dynamics of Intramolecular Double Hydrogen Transfer in Porphycene
    Litman, Yair; Richardson, Jeremy O.; Kumagai, Takashi; Rossi, Mariana
    Journal of the American Chemical Society (2019), 141 (6), 2526-2534CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    We address the double hydrogen transfer (DHT) dynamics of the porphycene mol.: a complex paradigmatic system where the making and breaking of H-bonds in a highly anharmonic potential energy surface requires a quantum mech. treatment not only of the electrons, but also of the nuclei. We combine d.-functional theory calcns., employing hybrid functionals and van der Waals corrections, with recently proposed and optimized path-integral ring-polymer methods for the approxn. of quantum vibrational spectra and reaction rates. Our full-dimensional ring-polymer instanton simulations show that below 100 K the concerted DHT tunneling pathway dominates, but between 100 K and 300 K there is a competition between concerted and stepwise pathways when nuclear quantum effects are included. We obtain ground-state reaction rates of 2.19 x 1011 s-1 at 150 K and 0.63 x 1011 s-1 at 100 K, in good agreement with expt. We also reproduce the puzzling N-H stretching band of porphycene with very good accuracy from thermostatted ring-polymer mol. dynamics simulations. The position and lineshape of this peak, centered at around 2600 cm-1 and spanning 750 cm-1, stems from a combination of very strong H-bonds, the coupling to low-frequency modes, and the access to cis-like isomeric conformations, which cannot be appropriately captured with classical-nuclei dynamics. These results verify the appropriateness of our general theor. approach and provide a framework for a deeper phys. understanding of hydrogen transfer dynamics in complex systems.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXht1anu7w%253D&md5=b670255601ae46db67b484288e3e0b87
  14. 14
    Udagawa, T.; Tachikawa, M. H/D Isotope Effect on Porphine and Porphycene Molecules with Multicomponent Hybrid Density Functional Theory. J. Chem. Phys. 2006, 125, 244105,  DOI: 10.1063/1.2403857
    Google Scholar
    14
    H/D isotope effect on porphine and porphycene molecules with multicomponent hybrid density functional theory
    Udagawa, Taro; Tachikawa, Masanori
    Journal of Chemical Physics (2006), 125 (24), 244105/1-244105/9CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
    To analyze the H/D isotope effect on porphine and porphycene mols. including the protonic/deuteronic quantum nature and electron correlation efficiently, the authors have developed the new scheme of the multicomponent hybrid d. functional theory [MC_(HF+DFT)]. The optimized geometries of porphine, porphycene, and these deuterated isotopomers by our MC-(HF+DFT) method are in good agreement with the exptl. "high-sym." structures, contrary to the "low-sym." geometries optimized by pure multicomponent Hartree-Fock method. The optimized geometries for HD-porphine and HD-porphycene mols., in which an inner hydrogen is replaced to a deuterium, are found to be low sym. Such drastic geometrical change induces the electronic polarization, and gives rise to the slight dipole moment values in these HD species. Their results clearly indicate that the difference of the nuclear quantum nature between inner proton and inner deuteron directly influences the mol. geometry and electronic structure.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXosVChtw%253D%253D&md5=91d0dd5803355e9bb890e8b3d7fa71f0
  15. 15
    Funahashi, H.; Tachikawa, M.; Udagawa, T. Determining If Reaction Selectivity Can Be Controlled by the H/D Isotope Effect in CH···O Interactions. Org. Lett. 2020, 22, 9439– 9443,  DOI: 10.1021/acs.orglett.0c03351
    Google Scholar
    15
    Determining if Reaction Selectivity Can Be Controlled by the H/D Isotope Effect in CH···O Interactions
    Funahashi, Haruki; Tachikawa, Masanori; Udagawa, Taro
    Organic Letters (2020), 22 (24), 9439-9443CODEN: ORLEF7; ISSN:1523-7052. (American Chemical Society)
    The H/D isotope effect in the CH···O interactions of several systems is systematically analyzed to det. whether it exerts control over reaction selectivity. Our theor. study demonstrates that deuterium substitution has a negligible effect on CH···O interactions; thus, reaction selectivity likely cannot be controlled by the H/D isotope effect in these CH···O interactions.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXit1OrsL%252FE&md5=102df76861bfba4561abb4d9f403f1bf
  16. 16
    Udagawa, T.; Murphy, R. B.; Darwish, T. A.; Tachikawa, M.; Mori, S. H/D Isotope Effects in Keto-Enol Tautomerism of β-Dicarbonyl Compounds ─Importance of NQEs of Hydrogen Nuclei─. Bull. Chem. Soc. Jpn. 2021, 94, 1954– 1962,  DOI: 10.1246/bcsj.20210083
    Google Scholar
    16
    H/D Isotope Effects in Keto-Enol Tautomerism of β-Dicarbonyl Compounds -Importance of Nuclear Quantum Effects of Hydrogen Nuclei-
    Udagawa, Taro; Murphy, Rhys B.; Darwish, Tamim A.; Tachikawa, Masanori; Mori, Seiji
    Bulletin of the Chemical Society of Japan (2021), 94 (7), 1954-1962CODEN: BCSJA8; ISSN:0009-2673. (Chemical Society of Japan)
    Deuterium isotope effects in the keto-enol tautomerism of β-dicarbonyl compds. (malonaldehyde, acetylacetone, dibenzoylmethane, and avobenzone) have been studied using a B3LYP+D functional level of multi-component d. functional theory (MC_DFT), which can directly take nuclear quantum effects (NQEs) of the hydrogen nuclei into account. We clearly show that the keto-enol energy difference becomes smaller by deuterium substitution, which is in reasonable agreement with the corresponding exptl. evidence. Our MC_DFT study also reveals the hydrogen/deuterium (H/D) isotope effect in geometries and shows that the deuterium substitution weakens the intramol. hydrogen-bonded interaction in the enol form. Direct treatment of NQEs of hydrogen nuclei via the MC_DFT method is essential for analyzing the H/D isotope effect in keto-enol tautomerism of β-dicarbonyl compds. Such isotope effects cannot be reproduced in the conventional DFT scheme with harmonic zero-point vibrational corrections.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXhvVansrjK&md5=32ab97a747bdd6c5ffec001a2325523d
  17. 17
    Tuckerman, M. E.; Marx, D.; Klein, M. L.; Parrinello, M. On the Quantum Nature of the Shared Proton in Hydrogen Bonds. Science 1997, 275, 817– 820,  DOI: 10.1126/science.275.5301.817
    Google Scholar
    17
    On the quantum nature of the shared proton in hydrogen bonds
    Tuckerman, Mark E.; Marx, Dominik; Klein, Michael L.; Parrinello, Michele
    Science (Washington, D. C.) (1997), 275 (5301), 817-820CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
    The relative influence of thermal and quantum fluctuations on the proton transfer properties of the charged water complexes H5O2+ and H3O2- was investigated with the use of ab initio techniques. These small systems can be considered as prototypical representatives of strong and intermediate-strength hydrogen bonds. The shared proton in the strongly hydrogen bonded H5O2+ behaved in an essentially classical manner, whereas in the H3O2- low-barrier hydrogen bond, quantum zero-point motion played a crucial role even at room temp. This behavior can be traced back to a small difference in the oxygen-oxygen sepn. and hence of the strength of the hydrogen.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2sXhtFahsrg%253D&md5=8776bd58df40e8a5199818331b53ac04
  18. 18
    Ishibashi, H.; Hayashi, A.; Shiga, M.; Tachikawa, M. Geometric Isotope Effect on the N2H7+ Cation and N2H5– Anion by Ab Initio Path Integral Molecular Dynamics Simulation. ChemPhysChem 2008, 9, 383– 387,  DOI: 10.1002/cphc.200700570
    Google Scholar
    18
    Geometric isotope effect on the N2H7+ cation and N2H5- anion by ab initio path integral molecular dynamics simulation
    Ishibashi, Hiroaki; Hayashi, Aiko; Shiga, Motoyuki; Tachikawa, Masanori
    ChemPhysChem (2008), 9 (3), 383-387CODEN: CPCHFT; ISSN:1439-4235. (Wiley-VCH Verlag GmbH & Co. KGaA)
    The geometric isotope effect (GIE) for the hydrogen bonds in pos. and neg. charged ammonia dimers is studied by ab initio path integral MD simulation. The hydrogen-bonded H atom in the N2H7+ cation is located around the center of two N atoms, while the hydrogen-bonded D atom in the N2D7+ cation is closer to one of the N atoms.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXltVKqs78%253D&md5=306a1fbcd01fc10f47ab870f3b917ac7
  19. 19
    Durlak, P.; Latajka, Z. Car-Parrinello and Path Integral Molecular Dynamics Study of the Intramolecular Hydrogen Bonds in the Crystals of Benzoylacetone and dideuterobenzoylacetone. Phys. Chem. Chem. Phys. 2014, 16, 23026– 23037,  DOI: 10.1039/C4CP02569E
    Google Scholar
    19
    Car-Parrinello and path integral molecular dynamics study of the intramolecular hydrogen bonds in the crystals of benzoylacetone and dideuterobenzoylacetone
    Durlak, Piotr; Latajka, Zdzislaw
    Physical Chemistry Chemical Physics (2014), 16 (42), 23026-23037CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)
    The dynamics of the intramol. short hydrogen bond in the mol. crystal of benzoylacetone and its deuterated analog are investigated using ab initio mol. dynamics simulations. A study on intramol. hydrogen bonding in 1-phenyl-1,3-butadione (I) and 1-deuteroxy-2-deutero-1-phenylbut-1-en-3-one (II) crystals has been carried out at 160 K and 300 K on the CPMD method level and at 300 K on the PIMD method level. The anal. of the two-dimensional free-energy landscape of reaction coordinate δ-parameter and RO···O distances shows that the hydrogen (deuter) between the two oxygen atoms adopts a slightly asym. position in the single potential well. When the nuclear quantum effects are taken into account, very large delocalization of the bridging proton is obsd. These studies indicate that hydrogen bonds in the crystal of benzoylacetone have characteristic properties for the type of bonding model resonance-assisted hydrogen bonds (RAHB) without existing the equil. of the two tautomers. The IR spectrum has been calcd., and a comparative vibrational anal. has been performed. The CPMD vibrational results appear to qual. agree with the exptl. ones.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhsVGjurrF&md5=f95e3825e60e31be544aba13d9f1596f
  20. 20
    Etinski, M.; Ensing, B. Puzzle of the Intramolecular Hydrogen Bond of Dibenzoylmethane Resolved by Molecular Dynamics Simulations. J. Phys. Chem. A 2018, 122, 5945– 5954,  DOI: 10.1021/acs.jpca.8b01930
    Google Scholar
    20
    Puzzle of the Intramolecular Hydrogen Bond of Dibenzoylmethane Resolved by Molecular Dynamics Simulations
    Etinski, Mihajlo; Ensing, Bernd
    Journal of Physical Chemistry A (2018), 122 (28), 5945-5954CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
    The enol form of dibenzoylmethane has been the subject of many exptl. and theor. studies, yet the symmetry and the spectral response of the OHO intramol. hydrogen bond remains mysterious due to conflicting assignments. In order to qual. understand the complex proton dynamics, it is necessary to probe the neighborhood of stationary points on the potential energy landscape. Here, we employ d. functional theory-based mol. dynamics (DFT-MD) simulations to sample the coupling between the intermol. proton transfer and all other mol. modes. To account for the quantum nature of the proton motion, we employ the path integral formalism within the DFT-MD simulations. Our results reveal that the hydrogen-bonded proton is delocalized between two oxygen atoms with sightly higher probability to be obsd. in the asym. than the sym. position. The simulated IR spectrum is found to be in a reasonably good agreement with the exptl. spectrum. The computed νOH band is remarkably broad and centered around 2640 cm-1. The origin of the discrepancy between the simulated and exptl. intensities of the νOH band is discussed.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXht1eksb3E&md5=482b9baba2e1a2ac97100a80b12ecdb4
  21. 21
    Durlak, P.; Latajka, Z. Investigations of the Hydrogen Bond in the Crystals of Tropolone and Thiotropolone via Car-Parrinello and Path Integral Molecular Dynamics. J. Comput. Chem. 2018, 40, 671– 687,  DOI: 10.1002/jcc.25753
    Google Scholar
    There is no corresponding record for this reference.
  22. 22
    Sauceda, H. E.; Vassilev-Galindo, V.; Chmiela, S.; Müller, K. R.; Tkatchenko, A. Dynamical Strengthening of Covalent and Non-Covalent Molecular Interactions by NQEs at Finite Temperature. Nat. Commun. 2021, 12 (1), 442,  DOI: 10.1038/s41467-020-20212-1
    Google Scholar
    22
    Dynamical strengthening of covalent and non-covalent molecular interactions by nuclear quantum effects at finite temperature
    Sauceda, Huziel E.; Vassilev-Galindo, Valentin; Chmiela, Stefan; Muller, Klaus-Robert; Tkatchenko, Alexandre
    Nature Communications (2021), 12 (1), 442CODEN: NCAOBW; ISSN:2041-1723. (Nature Research)
    Nuclear quantum effects (NQE) tend to generate delocalized mol. dynamics due to the inclusion of the zero point energy and its coupling with the anharmonicities in interat. interactions. Here, we present evidence that NQE often enhance electronic interactions and, in turn, can result in dynamical mol. stabilization at finite temp. The underlying phys. mechanism promoted by NQE depends on the particular interaction under consideration. First, the effective redn. of interat. distances between functional groups within a mol. can enhance the n → π* interaction by increasing the overlap between MOs or by strengthening electrostatic interactions between neighboring charge densities. Second, NQE can localize Me rotors by temporarily changing mol. bond orders and leading to the emergence of localized transient rotor states. Third, for noncovalent van der Waals interactions the strengthening comes from the increase of the polarizability given the expanded av. interat. distances induced by NQE. The implications of these boosted interactions include counterintuitive hydroxyl-hydroxyl bonding, hindered Me rotor dynamics, and mol. stiffening which generates smoother free-energy surfaces. Our findings yield new insights into the versatile role of nuclear quantum fluctuations in mols. and materials.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXhvFeqtr4%253D&md5=e5b48c98270d1b4993a58b5ddb87e547
  23. 23
    Kuwahata, K.; Tachikawa, M. Path Integral Molecular Dynamics Study on NH 4+(H2O). Few-Body Sys. 2021, 62, 96,  DOI: 10.1007/s00601-021-01689-y
    Google Scholar
    23
    Path Integral Molecular Dynamics Study on NH4+(H2O)
    Kuwahata, Kazuaki; Tachikawa, Masanori
    Few-Body Systems (2021), 62 (4), 96CODEN: FBSYEQ; ISSN:0177-7963. (Springer-Verlag GmbH)
    Among the hydrogen bonds, which are crit. to sustaining life, the interaction between ammonium ions (NH4+) and water is considered a model interaction in biol. systems. Although this interaction has been examd. in earlier studies on mol. dynamics, the nuclear quantum effect was not considered in those studies. In this study, we investigate the nuclear quantum effect of a singly-hydrated ammonium ion cluster, NH4+(H2O), using an ab initio on-the-fly path integral mol. dynamics (PIMD) simulation with a BHandHLYP/6-31++G(d,p) level of calcns. We find that the nuclear quantum effect shortens the N-O bond and increases the angle of the O-N-Hb bond. The results indicate that the nuclear quantum effect has two competing contributions. The first contribution involves strengthening the intermol. interaction, which reduces the intermol. distance, and the other contribution involves weakening the interaction, and it facilitates the rotation of NH4+.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXitVyrsb3M&md5=3e55a23d7f6237494760b6cb432e5b56
  24. 24
    Udagawa, T.; Kuwahata, K.; Tachikawa, M. Competitive NQE and H/D Isotope Effect on Torsional Motion of H2O2: An Ab Initio Path Integral Molecular Dynamics Study. Comput. Theor. Chem. 2022, 1208, 113542,  DOI: 10.1016/j.comptc.2021.113542
    Google Scholar
    24
    Competitive nuclear quantum effect and H/D isotope effect on torsional motion of H2O2: An ab initio path integral molecular dynamics study
    Udagawa, Taro; Kuwahata, Kazuaki; Tachikawa, Masanori
    Computational & Theoretical Chemistry (2022), 1208 (), 113542CODEN: CTCOA5; ISSN:2210-271X. (Elsevier B.V.)
    Ab initio path integral mol. dynamics (PIMD) simulations were performed to understand the nuclear quantum effect and thermal effect on the torsional motion of H2O2 (D2O2). A broad distribution of geometrical parameters (OH and OO bond lengths [ROH and ROO] and HOO bond angle [∠HOO]) was obtained in quantum ab initio PIMD simulations, rather than in classical MD simulations. However, a modest distribution around the trans-configuration TS (∠HOOH = 180°) was found in the quantum ab initio PIMD simulations of H2O2 at low temps. Thus, the nuclear quantum effect slightly enhanced the HOOH torsional motion at low temps. A series of simulations also revealed that the thermal effect enhanced the HOOH torsional motion. However, it was restrained by the primary nuclear quantum effect on the ROH in quantum simulations at high temps. Therefore, an interesting competitive nuclear quantum effect on the torsional motion of H2O2 was obsd.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXislelsLnI&md5=15ba55b73a772ded68c1b276bdaa9d2b
  25. 25
    Yanai, T.; Tew, D. P.; Handy, N. C. A New Hybrid Exchange-Correlation Functional Using the Coulomb-Attenuating Method (CAM-B3LYP). Chem. Phys. Lett. 2004, 393, 51– 57,  DOI: 10.1016/j.cplett.2004.06.011
    Google Scholar
    25
    A new hybrid exchange-correlation functional using the Coulomb-attenuating method (CAM-B3LYP)
    Yanai, Takeshi; Tew, David P.; Handy, Nicholas C.
    Chemical Physics Letters (2004), 393 (1-3), 51-57CODEN: CHPLBC; ISSN:0009-2614. (Elsevier Science B.V.)
    A new hybrid exchange-correlation functional named CAM-B3LYP is proposed. It combines the hybrid qualities of B3LYP and the long-range correction presented by Tawada et al. [J. Chem. Phys., in press]. We demonstrate that CAM-B3LYP yields atomization energies of similar quality to those from B3LYP, while also performing well for charge transfer excitations in a dipeptide model, which B3LYP underestimates enormously. The CAM-B3LYP functional comprises of 0.19 Hartree-Fock (HF) plus 0.81 Becke 1988 (B88) exchange interaction at short-range, and 0.65 HF plus 0.35 B88 at long-range. The intermediate region is smoothly described through the std. error function with parameter 0.33.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXlsFKgtbs%253D&md5=75f311240ff8ebedb174757f3eedbf3e
  26. 26
    Stewart, J. J. P. Optimization of Parameters for Semiempirical Methods V: Modification of NDDO Approximations and Application to 70 Elements. J. Mol. Model. 2007, 13, 1173– 1213,  DOI: 10.1007/s00894-007-0233-4
    Google Scholar
    26
    Optimization of parameters for semiempirical methods V: modification of NDDO approximations and application to 70 elements
    Stewart, James J. P.
    Journal of Molecular Modeling (2007), 13 (12), 1173-1213CODEN: JMMOFK; ISSN:0948-5023. (Springer GmbH)
    Several modifications that have been made to the NDDO core-core interaction term and to the method of parameter optimization are described. These changes have resulted in a more complete parameter optimization, called PM6, which has, in turn, allowed 70 elements to be parameterized. The av. unsigned error (AUE) between calcd. and ref. heats of formation for 4,492 species was 8.0 kcal mol-1. For the subset of 1,373 compds. involving only the elements H, C, N, O, F, P, S, Cl, and Br, the PM6 AUE was 4.4 kcal mol-1. The equivalent AUE for other methods were: RM1: 5.0, B3LYP 6-31G*: 5.2, PM5: 5.7, PM3: 6.3, HF 6-31G*: 7.4, and AM1: 10.0 kcal mol-1. Several long-standing faults in AM1 and PM3 have been cor. and significant improvements have been made in the prediction of geometries.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXhtlequr7N&md5=7d22928c8e3423f3ca8f2e7c77e6e6c9
  27. 27
    Korth, M.; Pitoňák, M.; Řezáč, J.; Hobza, P. A Transferable H-Bonding Correction for Semiempirical Quantum-Chemical Methods. J. Chem. Theory Comput. 2010, 6, 344– 352,  DOI: 10.1021/ct900541n
    Google Scholar
    27
    A Transferable H-Bonding Correction for Semiempirical Quantum-Chemical Methods
    Korth, Martin; Pitonak, Michal; Rezac, Jan; Hobza, Pavel
    Journal of Chemical Theory and Computation (2010), 6 (1), 344-352CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
    Semiempirical methods could offer a feasible compromise between ab initio and empirical approaches for the calcn. of large mols. with biol. relevance. A key problem for attempts in this direction is the rather bad performance of current semiempirical methods for noncovalent interactions, esp. hydrogen-bonding. On the basis of the recently introduced PM6-DH method, which includes empirical corrections for dispersion (D) and hydrogen-bond (H) interactions, we have developed an improved and transferable H-bonding correction for semiempirical quantum chem. methods. The performance of the improved correction is evaluated for PM6, AM1, OM3, and SCC-DFTB (enhanced by std. empirical dispersion corrections) with several test sets for noncovalent interactions and is shown to reach the quality of current DFT-D approaches for these types of problems.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhsFektr%252FK&md5=6b8845ee0e334284ca8b3b5e60ad612f
  28. 28
    Korth, M. Third-Generation Hydrogen-Bonding Corrections for Semiempirical QM Methods and Force Fields. J. Chem. Theroy Comput. 2010, 6, 3808– 3816,  DOI: 10.1021/ct100408b
    Google Scholar
    28
    Third-Generation Hydrogen-Bonding Corrections for Semiempirical QM Methods and Force Fields
    Korth, Martin
    Journal of Chemical Theory and Computation (2010), 6 (12), 3808-3816CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
    Computational modeling of biol. systems is a rapidly evolving field that calls for methods that are able to allow for extensive sampling with systems consisting of thousands of atoms. Semiempirical quantum chem. (SE) methods are a promising tool to aid with this, but the rather bad performance of std. SE methods for noncovalent interactions is clearly a limiting factor. Enhancing SE methods with empirical corrections for dispersion and hydrogen-bonding interactions was found to be a big improvement, but for the hydrogen-bonding corrections the drawback of breaking down in the case of substantial changes to the hydrogen bond, e.g., proton transfer, posed a serious limitation for its general applicability. This work presents a further improved hydrogen-bonding correction that can be generally included in parameter fitting procedures, as it does not suffer from the conceptual flaws of previous approaches: hydrogen bonds are now treated as an interaction term between electroneg. acceptor and donor atoms, "weighted" by a function of the position of H atoms between them, and multiplied with a damping function to correct the short- and long-range behavior. The performance of the new approach is evaluated for PM6, AM1, OM3, and SCC-DFTB as well as several force-field (FF) methods for a no. of std. benchmark sets with hydrogen-bonded systems. The new approach is found to reach the same accuracy as the second-generation hydrogen-bonding correction with less parameters, while it avoids among other issues the conceptual problem with electronic structure changes. SE methods augmented this way reach the accuracy of DFT-D approaches for a large no. of cases investigated, while still being about 3 orders of magnitude faster. Moreover, the new correction scheme is transferable also to FF methods that were shown to have serious problems with hydrogen-bonding interactions.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXhtlKjs7%252FF&md5=c02f35bdeb307c2bd52fc5e069bddb4c
  29. 29
    Řezáč, J.; Hobza, P. Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods. J. Chem. Theory Comput. 2012, 8, 141– 151,  DOI: 10.1021/ct200751e
    Google Scholar
    29
    Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods
    Rezac, Jan; Hobza, Pavel
    Journal of Chemical Theory and Computation (2012), 8 (1), 141-151CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
    Semiempirical quantum mech. methods with corrections for noncovalent interactions, namely dispersion and hydrogen bonds, reach an accuracy comparable to much more expensive methods while being applicable to very large systems (up to 10 000 atoms). These corrections have been successfully applied in computer-assisted drug design, where they significantly improve the correlation with the exptl. data. Despite these successes, there are still several unresolved issues that limit the applicability of these methods. We introduce a new generation of both hydrogen-bonding and dispersion corrections that address these problems, make the method more robust, and improve its accuracy. The hydrogen-bonding correction has been completely redesigned and for the first time can be used for geometry optimization and mol.-dynamics simulations without any limitations, as it and its derivs. have a smooth potential energy surface. The form of this correction is simpler than its predecessors, while the accuracy has been improved. For the dispersion correction, we adopt the latest developments in DFT-D, using the D3 formalism by Grimme. The new corrections have been parametrized on a large set of benchmark data including nonequil. geometries, the S66x8 data set. As a result, the newly developed D3H4 correction can accurately describe a wider range of interactions. We have parametrized this correction for the PM6, RM1, OM3, PM3, AM1, and SCC-DFTB methods.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhs1Gls77L&md5=1c15239efc1338484dcd0b9d6e70518d
  30. 30
    Stewart, J. J. P. Optimization of Parameters for Semiempirical Methods VI: More Modifications to the NDDO Approximations and Re-Optimization of Parameters. J. Mol. Model. 2013, 19, 1– 32,  DOI: 10.1007/s00894-012-1667-x
    Google Scholar
    30
    Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters
    Stewart, James J. P.
    Journal of Molecular Modeling (2013), 19 (1), 1-32CODEN: JMMOFK; ISSN:0948-5023. (Springer)
    Modern semiempirical methods are of sufficient accuracy when used in the modeling of mols. of the same type as used as ref. data in the parameterization. Outside that subset, however, there is an abundance of evidence that these methods are of very limited utility. In an attempt to expand the range of applicability, a new method called PM7 has been developed. PM7 was parameterized using exptl. and high-level ab initio ref. data, augmented by a new type of ref. data intended to better define the structure of parameter space. The resulting method was tested by modeling crystal structures and heats of formation of solids. Two changes were made to the set of approxns.: a modification was made to improve the description of noncovalent interactions, and two minor errors in the NDDO formalism were rectified. Av. unsigned errors (AUEs) in geometry and ΔH f for PM7 were reduced relative to PM6; for simple gas-phase org. systems, the AUE in bond lengths decreased by about 5 % and the AUE in ΔH f decreased by about 10 %; for org. solids, the AUE in ΔH f dropped by 60 % and the redn. was 33.3 % for geometries. A two-step process (PM7-TS) for calcg. the heights of activation barriers has been developed. Using PM7-TS, the AUE in the barrier heights for simple org. reactions was decreased from values of 12.6 kcal/mol-1 in PM6 and 10.8 kcal/mol-1 in PM7 to 3.8 kcal/mol-1. The origins of the errors in NDDO methods have been examd., and were found to be attributable to inadequate and inaccurate ref. data. This conclusion provides insight into how these methods can be improved.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXjtVegtA%253D%253D&md5=7177311730da8242d5e05f7f4e045e57
  31. 31
    Martyna, G. J.; Klein, M. L.; Tuckerman, M. Nosé-Hoover Chains: The Canonical Ensemble via Continuous Dynamics. J. Chem. Phys. 1992, 97, 2635– 2643,  DOI: 10.1063/1.463940
    Google Scholar
    There is no corresponding record for this reference.
  32. 32
    Flyvbjerg, H.; Petersen, H. G. Error Estimates on Averages of Correlated Data. J. Chem. Phys. 1989, 91, 461– 466,  DOI: 10.1063/1.457480
    Google Scholar
    32
    Error estimates on averages of correlated data
    Flyvbjerg, H.; Petersen, H. G.
    Journal of Chemical Physics (1989), 91 (1), 461-6CODEN: JCPSA6; ISSN:0021-9606.
    A description is given on how the true statistical error on an av. of correlated data can be obtained with ease and efficiency by a renormalization group method. The method is illustrated with numerical and anal. examples, having finite as well as infinite range correlations.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL1MXkslOis7s%253D&md5=a424bd42502aa2989d102aa4c87b8eca

Cited By

Click to copy section linkSection link copied!

This article is cited by 1 publications.

  1. Taro Udagawa, Hikaru Tanaka, Kazuaki Kuwahata, Masanori Tachikawa. Location of the Shared Proton in Proton-Bound Dimer Compound of Hydrogen Sulfate and Formate: Path Integral Molecular Dynamics Study. The Journal of Physical Chemistry A 2024, 128 (11) , 2103-2110. https://doi.org/10.1021/acs.jpca.4c00239
Download PDF
Open PDF
Go to ACS Omega
Get e-Alerts
Get e-Alerts

ACS Omega

Cite this: ACS Omega 2022, 7, 16, 14244–14251
Click to copy citationCitation copied!
https://doi.org/10.1021/acsomega.2c00857
Published April 15, 2022

Copyright © 2022 The Authors. Published by American Chemical Society. This publication is licensed under

CC-BY-NC-ND 4.0 .

Article Views

821

Altmetric

-

Citations

1
Learn about these metrics

Article Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.

Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.

The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated.

  • Abstract

    High Resolution Image
    Download MS PowerPoint Slide

    Figure 1

    Figure 1. Chemical structures of Fujikurin A–D.

    High Resolution Image
    Download MS PowerPoint Slide

    Figure 2

    Figure 2. Equilibrium and TS structures of Fujikurin D.

    High Resolution Image
    Download MS PowerPoint Slide

    Figure 3

    Figure 3. Hydrogen bond structure of Fujikurin D and definition of atomic labels and coordinates.

    High Resolution Image
    Download MS PowerPoint Slide

    Figure 4

    Figure 4. One-dimensional distributions of (a) RO1H, (b) RHO2, and (c) RO1O2 obtained by CLMD and PIMD simulations. The dashed lines represent the values of two equilibrium structures.

    High Resolution Image
    Download MS PowerPoint Slide

    Figure 5

    Figure 5. Mulliken charges of the oxygen and the hydrogen atoms obtained in (a) CLMD and (b) PIMD simulations.

    High Resolution Image
    Download MS PowerPoint Slide

    Figure 6

    Figure 6. One-dimensional relative effective free-energy landscapes of δOH obtained by CLMD and PIMD simulations. The dashed lines represent two equilibrium structures.

    High Resolution Image
    Download MS PowerPoint Slide

    Figure 7

    Figure 7. Two-dimensional free-energy landscapes of δOH and ROO obtained with (a) CLMD and (b) PIMD. Triangles and circles represent the equilibrium and the TS structures, respectively, and dashed lines are IRC pathways. Free energy is in units of kcal/mol.

    High Resolution Image
    Download MS PowerPoint Slide

    Figure 8

    Figure 8. Three-dimensional distribution of hydrogen-bonded proton in Fujikurin D. The origin is defined as the center of mass of the O atoms and the xy-plane as the O1–O2–C plane.

    High Resolution Image
    Download MS PowerPoint Slide

    Figure 9

    Figure 9. Difference distribution landscapes of proton distributions obtained from CLMD and PIMD simulations of Fujikurin D. Red (blue) indicates regions where the distribution in the PIMD (CLMD) simulated results is denser than that in the CLMD (PIMD) simulated results.

    High Resolution Image
    Download MS PowerPoint Slide

    Figure 10

    Figure 10. Two-dimensional free-energy landscapes δOH and ROO of Fujikurin A and B for (a) CLMD and (b) PIMD. Triangles and circles represent equilibrium and the TS structures, respectively, and dashed lines represent IRC pathways. Free energy is expressed in units of kcal/mol.

    High Resolution Image
    Download MS PowerPoint Slide

  • References

    This article references 32 other publications.

    1. 1
      Yabuta, T.; Kambe, K.; Hayashi, T. Biochemistry of the ″bakanae″ fungus. I. Fusarinic acid, a new product of the “bakanae” fungus. Nippon Nogei Kagaku Kaishi 1934, 10, 1059– 1068
      1
      Biochemistry of the "bakanae" fungus. I. Fusarinic acid, a new product of the "bakanae" fungus
      Yabuta, Teijiro; Kambe, Katsuji; Hayashi, Takeshi
      Nippon Nogei Kagaku Kaishi (1934), 10 (), 1059-68CODEN: NNKKAA; ISSN:0002-1407.
      The "bakanae" fungus, Fusarium heterosporium Nees, excretes a growth-promoting substance for rice seedlings. It also excretes a growth-restraining substance according to the condition of the culture. The growth-restraining substance was isolated by extn. of the culture soln. with benzine or petr. ether. The fungus was cultured in a soln. contg. (NH4)2SO4 4.8 g., Na2HPO4 2.8 g., KCl 1.8 g., CaCl2 0.32 g., MgCl2 0.6 g., 0.5 N HCl 6 cc., glucose 100 g. and H2O 2 l. at 27-8° for 40-50 days. The product was filtered and the filtrate was evapd. to a sirup. Succinic acid was isolated by extn. of the sirup with ether. The residue was then extd. with benzine, petr. ether or ligroin. From the ext. there crystd. in colorless plates, m. 108-9°, fusarinic acid, C10H13NO2, in a yield of 0.5-1.0 g. from 10 l. of the culture soln. It forms a Cu salt, light-violet plates (C10H12NO2)2Cu. Distn. of fusarinic acid with CaO gave fusarin, picrate, m. 142°. Fusarinic acid is oxidized to isocinchomeronic acid and propionic acid by KMnO4. Oxidation of fusarin with KMnO4 gives nicotinic acid. Fusarinic acid may be 5-butyl- or 5-sec-butyl-picolinic acid.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaA2MXoslek&md5=8774dfda4bb93f33eece72f3b2c7d3c3
    2. 2
      Graebe, J. E. Gibberellin Biosynthesis and Control. Annu. Rev. Plant. Physiol. 1987, 38, 419,  DOI: 10.1146/annurev.pp.38.060187.002223
      2
      Gibberellin biosynthesis and control
      Graebe, Jan E.
      Annual Review of Plant Physiology (1987), 38 (), 419-65CODEN: ARPPA3; ISSN:0066-4294.
      A review with 206 refs. Gibberellin biosynthesis in higher plants is discussed in three phases: (1) the biosynthesis of ent-kaurene, (2) the biosynthesis of GA12-aldehyde, and (3) the pathways after GA12-aldehyde. The biochem. and physiol. control of gibberellin biosynthesis is also discussed.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL2sXksFGlu7s%253D&md5=14334df1f0b6101e653c7f776ab4ac69
    3. 3
      Brady, S. F.; Clardy, J. CR377, a New Pentaketide Antifungal Agent Isolated from an Endophytic Fungus. J. Nat. Prod. 2000, 63, 1447– 1448,  DOI: 10.1021/np990568p
      3
      CR377, a new pentaketide antifungal agent isolated from an endophytic fungus
      Brady, Sean F.; Clardy, Jon
      Journal of Natural Products (2000), 63 (10), 1447-1448CODEN: JNPRDF; ISSN:0163-3864. (American Chemical Society)
      Cultures of endophytic fungi collected in the Guanacaste Conservation Area of Costa Rica were screened for antifungal activity. CR377 (I), a new pentaketide antifungal agent, was isolated from the culture broth of a fungus, CR377 (Fusarium sp.), that showed potent activity against Candida albicans in this assay. The structure of I was established using 1- and 2-D NMR and HRFABMS.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3cXmtVGqtbY%253D&md5=ce2ba46075f1ad98345ad6e0298eaf2f
    4. 4
      Niehaus, E. M.; Kleigrewe, K.; Wiemann, P.; Studt, L.; Sieber, C. M. K.; Connolly, L. R.; Freitag, M.; Güldener, U.; Tudzynski, B.; Humpf, H. U. Genetic Manipulation of the Fusarium Fujikuroi Fusarin Gene Cluster Yields Insight into the Complex Regulation and Fusarin Biosynthetic Pathway. Chem. Biol. 2013, 20, 1055– 1066,  DOI: 10.1016/j.chembiol.2013.07.004
      4
      Genetic Manipulation of the Fusarium fujikuroi Fusarin Gene Cluster Yields Insight into the Complex Regulation and Fusarin Biosynthetic Pathway
      Niehaus, Eva-Maria; Kleigrewe, Karin; Wiemann, Philipp; Studt, Lena; Sieber, Christian M. K.; Connolly, Lanelle R.; Freitag, Michael; Gueldener, Ulrich; Tudzynski, Bettina; Humpf, Hans-Ulrich
      Chemistry & Biology (Oxford, United Kingdom) (2013), 20 (8), 1055-1066CODEN: CBOLE2; ISSN:1074-5521. (Elsevier Ltd.)
      The biosynthesis and regulation of the polyketide synthase/nonribosomal peptide synthetase (PKS/NRPS)-derived mutagenic mycotoxin fusarin C was studied in the fungus Fusarium fujikuroi. The fusarin gene cluster consists of nine genes (fus1-fus9) that are coexpressed under high-nitrogen and acidic pH conditions. Chromatin immunopptn. revealed a correlation between high expression and enrichment of activating H3K9-acetylation marks under inducing conditions. The authors provide evidence that only four genes are sufficient for the biosynthesis. The combination of genetic engineering with NMR and mass-spectrometry-based structure elucidation allowed the discovery of the putative fusarin biosynthetic pathway. Surprisingly, PKS/NRPS releases its product with an open ring structure, probably as an alc. The authors' data indicate that 2-pyrrolidone ring closure, oxidn. at C-20, and, finally, methylation at C-20 are catalyzed by Fus2, Fus8, and Fus9, resp.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXht1Gmur7M&md5=919d67a5ebb0d933687786fc191c23f4
    5. 5
      Niehaus, E. M.; von Bargen, K. W.; Espino, J. J.; Pfannmüller, A.; Humpf, H. U.; Tudzynski, B. Characterization of the Fusaric Acid Gene Cluster in Fusarium Fujikuroi. Appl. Microbiol. Biotechnol. 2014, 98, 1749– 1762,  DOI: 10.1007/s00253-013-5453-1
      5
      Characterization of the fusaric acid gene cluster in Fusarium fujikuroi
      Niehaus, Eva-Maria; von Bargen, Katharina W.; Espino, Jose J.; Pfannmueller, Andreas; Humpf, Hans-Ulrich; Tudzynski, Bettina
      Applied Microbiology and Biotechnology (2014), 98 (4), 1749-1762CODEN: AMBIDG; ISSN:0175-7598. (Springer)
      The "bakanae" fungus Fusarium fujikuroi is a common pathogen of rice and produces a variety of mycotoxins, pigments, and phytohormones. Fusaric acid is one of the oldest known secondary metabolites produced by F. fujikuroi and some other Fusarium species. Study of its biosynthesis and regulation is of great interest due to its occurrence in cereal-based food and feed. This study describes the identification and characterization of the fusaric acid gene cluster in F. fujikuroi consisting of the PKS-encoding core gene and four co-regulated genes, FUB1-FUB5. Besides fusaric acid, F. fujikuroi produces two fusaric acid-like derivs.: fusarinolic acid and 9,10-dehydrofusaric acid. The authors provide evidence that these derivs. are not intermediates of the fusaric acid biosynthetic pathway, and that their formation is catalyzed by genes outside of the fusaric acid gene cluster. Target gene deletions of all five cluster genes revealed that not all of them are involved in fusaric acid biosynthesis. The authors suggest that only two genes, FUB1 and FUB4, are necessary for the biosynthesis. Expression of the FUB genes and prodn. of fusaric acid and the two derivs. are favored under high nitrogen. Nitrogen-dependent expression of fusaric acid genes is pos. regulated by the nitrogen-responsive GATA transcription factor AreB, and pH-dependent regulation is mediated by the transcription factor PacC. In addn., fusaric acid prodn. is regulated by two members of the fungal-specific velvet complex: Vel1 and Lae1. In planta expression studies show a higher expression in the favorite host plant rice compared to maize.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXis1aktg%253D%253D&md5=d5a4c47a409656139f239ec5b85bb329
    6. 6
      von Bargen, K. W.; Niehaus, E. M.; Krug, I.; Bergander, K.; Würthwein, E. U.; Tudzynski, B.; Humpf, H. U. Isolation and Structure Elucidation of Fujikurins A-D: Products of the PKS19 Gene Cluster in Fusarium Fujikuroi. J. Nat. Prod. 2015, 78, 1809– 1815,  DOI: 10.1021/np5008137
      6
      Isolation and Structure Elucidation of Fujikurins A-D: Products of the PKS19 Gene Cluster in Fusarium fujikuroi
      von Bargen, Katharina Walburga; Niehaus, Eva-Maria; Krug, Isabel; Bergander, Klaus; Wuerthwein, Ernst-Ulrich; Tudzynski, Bettina; Humpf, Hans-Ulrich
      Journal of Natural Products (2015), 78 (8), 1809-1815CODEN: JNPRDF; ISSN:0163-3864. (American Chemical Society-American Society of Pharmacognosy)
      Fusarium fujikuroi is a member of the Gibberella fujikuroi species complex and well known for the prodn. of gibberellins and mycotoxins including fusarins and fusaric acid. A recent genome sequencing study revealed that the fungus has the genetic potential to produce many more secondary metabolites than have been reported. This paper describes the structure elucidation of the products of the cryptic and silent PKS19 gene cluster that were recently identified (fujikurins A-D). We present the complete NMR data for the structure elucidation of the main compd. fujikurin D, which shows tautomeric 1,3-diketo elements. The different tautomeric structures could be confirmed using quantum chem. calcns. Addnl., the structures of the minor compds. fujikurins A-C were elucidated by high-resoln. mass spectrometric fragmentation expts. It emerged that fujikurin A was identical to the bioactive compd. CR377 of the taxonomically unclassified Fusarium strain CR377, while fujikurins B-D have not been reported from other fungi.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhtF2ltrvN&md5=97fb1c8a577face4ce27d11f2eaff8f3
    7. 7
      Niehaus, E. M.; Kim, H. K.; Münsterkötter, M.; Janevska, S.; Arndt, B.; Kalinina, S. A.; Houterman, P. M.; Ahn, I. P.; Alberti, I.; Tonti, S.; Kim, D. W.; Sieber, C. M. K.; Humpf, H. U.; Yun, S. H.; Güldener, U.; Tudzynski, B. Comparative Genomics of Geographically Distant Fusarium Fujikuroi Isolates Revealed Two Distinct Pathotypes Correlating with Secondary Metabolite Profiles. PLoS Pathogens 2017, 13, e1006670  DOI: 10.1371/journal.ppat.1006670
      7
      Comparative genomics of geographically distant Fusarium fujikuroi isolates revealed two distinct pathotypes correlating with secondary metabolite profiles
      Niehaus, Eva-Maria; Kim, Hee-Kyoung; Muensterkoetter, Martin; Janevska, Slavica; Arndt, Birgit; Kalinina, Svetlana A.; Houterman, Petra M.; Ahn, Il-Pyung; Alberti, Ilaria; Tonti, Stefano; Kim, Da-Woon; Sieber, Christian M. K.; Humpf, Hans-Ulrich; Yun, Sung-Hwan; Gueldener, Ulrich; Tudzynski, Bettina
      PLoS Pathogens (2017), 13 (10), e1006670/1-e1006670/38CODEN: PPLACN; ISSN:1553-7374. (Public Library of Science)
      Fusarium fujikuroi causes bakanae ("foolish seedling") disease of rice which is characterized by hyper-elongation of seedlings resulting from prodn. of gibberellic acids (GAs) by the fungus. This plant pathogen is also known for prodn. of harmful mycotoxins, such as fusarins, fusaric acid, apicidin F and beauvericin. Recently, we generated the first de novo genome sequence of F. fujikuroi strain IMI 58289 combined with extensive transcriptional, epigenetic, proteomic and chem. product analyses. GA prodn. was shown to provide a selective advantage during infection of the preferred host plant rice. Here, we provide genome sequences of eight addnl. F. fujikuroi isolates from distant geog. regions. The isolates differ in the size of chromosomes, most likely due to variability of subtelomeric regions, the type of asexual spores (microconidia and/or macroconidia), and the no. and expression of secondary metabolite gene clusters. While most of the isolates caused the typical bakanae symptoms, one isolate, B14, caused stunting and early withering of infected seedlings. In contrast to the other isolates, B14 produced no GAs but high amts. of fumonisins during infection on rice. Furthermore, it differed from the other isolates by the presence of three addnl. polyketide synthase (PKS) genes (PKS40, PKS43, PKS51) and the absence of the F. fujikuroi-specific apicidin F (NRPS31) gene cluster. Anal. of addnl. field isolates confirmed the strong correlation between the pathotype (bakanae or stunting/withering), and the ability to produce either GAs or fumonisins. Deletion of the fumonisin and fusaric acid-specific PKS genes in B14 reduced the stunting/withering symptoms, whereas deletion of the PKS51 gene resulted in elevated symptom development. Phylogenetic analyses revealed two subclades of F. fujikuroi strains according to their pathotype and secondary metabolite profiles.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXht1WjtrvP&md5=50146de72cb0a7aa2f20aaceff8b6820
    8. 8
      Wang, W. G.; Wang, H.; Du, L. Q.; Li, M.; Chen, L.; Yu, J.; Cheng, G. G.; Zhan, M. T.; Hu, Q. F.; Zhang, L.; Yao, M.; Matsuda, Y. Molecular Basis for the Biosynthesis of an Unusual Chain-Fused Polyketide, Gregatin A. J. Am. Chem. Soc. 2020, 142, 8464– 8472,  DOI: 10.1021/jacs.0c02337
      8
      Molecular Basis for the Biosynthesis of an Unusual Chain-Fused Polyketide, Gregatin A
      Wang, Wei-Guang; Wang, Hang; Du, Lian-Qiong; Li, Min; Chen, Lin; Yu, Jian; Cheng, Gui-Guang; Zhan, Meng-Tao; Hu, Qiu-Fen; Zhang, Lihan; Yao, Min; Matsuda, Yudai
      Journal of the American Chemical Society (2020), 142 (18), 8464-8472CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      Gregatin A (1) is a fungal polyketide featuring an alkylated furanone core, but the biosynthetic mechanism to furnish the intriguing mol. skeleton has yet to be elucidated. Herein, we have identified the biosynthetic gene cluster of gregatin A (1) in Penicillium sp. sh18 and investigated the mechanism that produces the intriguing structure of 1 by in vivo and in vitro reconstitution of its biosynthesis. Our study established the biosynthetic route leading to 1 and illuminated that 1 is generated by the fusion of two different polyketide chains, which are, amazingly, synthesized by a single polyketide synthase GrgA with the aid of a trans-acting enoylreductase GrgB. Chain fusion, as well as chain hydrolysis, is catalyzed by an α/β hydrolase, GrgF, hybridizing the C11 and C4 carbon chains by Claisen condensation. Finally, structural anal. and mutational expts. using GrgF provided insight into how the enzyme facilitates the unusual chain-fusing reaction. In unraveling a new biosynthetic strategy involving a bifunctional PKS and a polyketide fusing enzyme, our study expands our knowledge concerning fungal polyketide biosynthesis.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXmvFSitLc%253D&md5=1d4db4f3134b41a0fb923cfa61b8c7c7
    9. 9
      Moreno, D. v.; González, S. A.; Reyes, A. Turning Symmetric an Asymmetric Hydrogen Bond with the Inclusion of NQEs: The Case of the [CN···H···NC]− Complex. J. Chem. Phys. 2011, 134, 024115,  DOI: 10.1063/1.3521272
      9
      Turning symmetric an asymmetric hydrogen bond with the inclusion of nuclear quantum effects: The case of the [CN···H···NC]- complex
      Moreno, Diego V.; Gonzalez, Sergio A.; Reyes, Andres
      Journal of Chemical Physics (2011), 134 (2), 024115/1-024115/7CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
      Nuclear quantum effects (NQE) on the geometry, energy, and electronic structure of the [CN·L·NC]- complex (L = H, D, T) are investigated with the recently developed APMO/MP2 code. This code implements the nuclear MO approach (NMO) at the Hartree-Fock (HF) and MP2 levels of theory for electrons and quantum nuclei. In a first study, we examd. the H/D/T isotope effects on the geometry and electronic structure of the CNH mol. at NMO/HF and NMO/MP2 levels of theory. We found that when increasing the hydrogen nuclear mass there is a redn. of the RN-H bond distance and an increase of the electronic population on the hydrogen atom. Our calcd. bond distances are in good agreement with exptl. and other theor. results. In a second investigation, we explored the hydrogen NQE on the geometry of CNHNC- complex at the NMO/HF and NMO/MP2 levels of theory. We discovered that while a NMO/HF calcn. presented an asym. hydrogen bond, the NMO/MP2 calcn. revealed a sym. H-bond. We also examd. the H/D/T isotope effects on the geometry and stabilization energy of the CNHNC- complex. We noted that gradual increases in hydrogen mass led to redns. of the RNN distance and destabilization of the hydrogen bond (H-bond). A discussion of these results is given in terms of the hydrogen nuclear delocalization effects on the electronic structure and energy components. To the best of our knowledge, this is the first ab initio NMO study that reveals the importance of including nuclear quantum effects in conventional electronic structure calcns. for an enhanced description of strong-low-barrier H-bonded systems. (c) 2011 American Institute of Physics.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXltlymug%253D%253D&md5=b66ddf19358ce000d41b70a512a6fced
    10. 10
      Kanematsu, Y.; Tachikawa, M. Theoretical Analysis of Geometry and NMR Isotope Shift in Hydrogen-Bonding Center of Photoactive Yellow Protein by Combination of Multicomponent Quantum Mechanics and ONIOM Scheme. J. Chem. Phys. 2014, 141, 185101,  DOI: 10.1063/1.4900987
      10
      Theoretical analysis of geometry and NMR isotope shift in hydrogen-bonding center of photoactive yellow protein by combination of multicomponent quantum mechanics and ONIOM scheme
      Kanematsu, Yusuke; Tachikawa, Masanori
      Journal of Chemical Physics (2014), 141 (18), 185101/1-185101/8CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
      Multicomponent quantum mech. (MC_QM) calcn. has been extended with ONIOM (our own N-layered integrated MO + mol. mechanics) scheme [ONIOM(MC_QM:MM)] to take account of both the nuclear quantum effect and the surrounding environment effect. The authors have demonstrated the first implementation and application of ONIOM(MC_QM:MM) method for the anal. of the geometry and the isotope shift in hydrogen-bonding center of photoactive yellow protein. ONIOM(MC_QM:MM) calcn. for a model with deprotonated Arg52 reproduced the elongation of O-H bond of Glu46 obsd. by neutron diffraction crystallog. Among the unique isotope shifts in different conditions, the model with protonated Arg52 with solvent effect reasonably provided the best agreement with the corresponding exptl. values from liq. NMR measurement. Our results implied the availability of ONIOM(MC_QM:MM) to distinguish the local environment around hydrogen bonds in a biomol. (c) 2014 American Institute of Physics.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhvV2mtb3K&md5=17de481a00beec43b35e9154880c3722
    11. 11
      Ogata, Y.; Daido, M.; Kawashima, Y.; Tachikawa, M. NQEs on Protonated Lysine with an Asymmetric Low Barrier Hydrogen Bond: An Ab Initio Path Integral Molecular Dynamics Study. RSC Adv. 2013, 3, 25252– 25257,  DOI: 10.1039/c3ra44077j
      11
      Nuclear quantum effects on protonated lysine with an asymmetric low barrier hydrogen bond: an ab initio path integral molecular dynamics study
      Ogata, Yudai; Daido, Masashi; Kawashima, Yukio; Tachikawa, Masanori
      RSC Advances (2013), 3 (47), 25252-25257CODEN: RSCACL; ISSN:2046-2069. (Royal Society of Chemistry)
      The nuclear quantum effect on the short and asym. hydrogen bond of protonated lysine (LysH+) at room temp. is explored by ab initio path integral mol. dynamics (PIMD) simulation. From static electronic structure calcns., the barrier height of proton transfer in LysH+ is 1.1 kcal mol-1, which is much lower than that of typical hydrogen bonds. The hydrogen-bonded proton is delocalized in between two nitrogen atoms in the PIMD simulation including both thermal and nuclear quantum effects, while the proton is localized on a nitrogen atom in a conventional ab initio mol. dynamics simulation including thermal effects alone. We found that the proton transfer barrier found in the static calcn. and conventional ab initio simulation is completely washed out in the PIMD simulation. Meanwhile, the proton distribution at the Nζ atom was larger than that at the N atom, as found in the static calcn. and conventional ab initio mol. dynamics simulation. We clarified from our PIMD simulation that an asym. low barrier hydrogen bond exists in LysH+ at room temp.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhslCrsL7P&md5=f730d96032e11ef4065b665dd8126222
    12. 12
      Kawashima, Y.; Tachikawa, M. Ab Initio Path Integral Molecular Dynamics Study of the NQE on Out-of-Plane Ring Deformation of Hydrogen Maleate Anion. J. Chem. Theory Comput. 2014, 10, 153– 163,  DOI: 10.1021/ct4007986
      12
      Ab Initio Path Integral Molecular Dynamics Study of the Nuclear Quantum Effect on Out-of-Plane Ring Deformation of Hydrogen Maleate Anion
      Kawashima, Yukio; Tachikawa, Masanori
      Journal of Chemical Theory and Computation (2014), 10 (1), 153-163CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
      Ab initio path integral mol. dynamics (PIMD) simulation was performed to understand the nuclear quantum effect on the out-of-plane ring deformation of hydrogen maleate anion and investigate the existence of a stable structure with ring deformation, which was suggested in exptl. observation. The isotope effect and the temp. effect are studied as well. We first investigated the nuclear quantum effect on the proton transfer. In static calcn. and classical ab initio mol. dynamics simulations, the proton in the hydrogen bond is localized to either oxygen atom. On the other hand, the proton is located at the center of two oxygen atoms in quantum ab initio PIMD simulations. The nuclear quantum effect washes out the barrier of proton transfer. We next examd. the nuclear quantum effect on the motion of hydrogen maleate anion. Principal component anal. revealed that the out-of-plane ring bending modes have dominant contribution to the entire mol. motion. In quantum ab initio PIMD simulations, structures with ring deformation were the global min. for the deuterated isotope at 300 K. We analyzed the out-of-plane ring bending mode further and found that there are three min. along a ring distortion mode. We successfully found a stable structure with ring deformation of hydrogen maleate for the first time, to our knowledge, using theor. calcn. The structures with ring deformation found in quantum simulation of the deuterated isotope allowed the proton transfer to occur more frequently than the planar structure. Static ab initio electronic structure calcn. found that the structures with ring deformation have very small proton transfer barrier compared to the planar structure. We suggest that the "proton transfer driven" mechanism is the origin of stabilization for the structure with out-of-plane ring deformation.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhvFSqtrfK&md5=f9a8636c40caaec0e7cf0c047765eee8
    13. 13
      Litman, Y.; Richardson, J. O.; Kumagai, T.; Rossi, M. Elucidating the Nuclear Quantum Dynamics of Intramolecular Double Hydrogen Transfer in Porphycene. J. Am. Chem. Soc. 2019, 141, 2526– 2534,  DOI: 10.1021/jacs.8b12471
      13
      Elucidating the Nuclear Quantum Dynamics of Intramolecular Double Hydrogen Transfer in Porphycene
      Litman, Yair; Richardson, Jeremy O.; Kumagai, Takashi; Rossi, Mariana
      Journal of the American Chemical Society (2019), 141 (6), 2526-2534CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      We address the double hydrogen transfer (DHT) dynamics of the porphycene mol.: a complex paradigmatic system where the making and breaking of H-bonds in a highly anharmonic potential energy surface requires a quantum mech. treatment not only of the electrons, but also of the nuclei. We combine d.-functional theory calcns., employing hybrid functionals and van der Waals corrections, with recently proposed and optimized path-integral ring-polymer methods for the approxn. of quantum vibrational spectra and reaction rates. Our full-dimensional ring-polymer instanton simulations show that below 100 K the concerted DHT tunneling pathway dominates, but between 100 K and 300 K there is a competition between concerted and stepwise pathways when nuclear quantum effects are included. We obtain ground-state reaction rates of 2.19 x 1011 s-1 at 150 K and 0.63 x 1011 s-1 at 100 K, in good agreement with expt. We also reproduce the puzzling N-H stretching band of porphycene with very good accuracy from thermostatted ring-polymer mol. dynamics simulations. The position and lineshape of this peak, centered at around 2600 cm-1 and spanning 750 cm-1, stems from a combination of very strong H-bonds, the coupling to low-frequency modes, and the access to cis-like isomeric conformations, which cannot be appropriately captured with classical-nuclei dynamics. These results verify the appropriateness of our general theor. approach and provide a framework for a deeper phys. understanding of hydrogen transfer dynamics in complex systems.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXht1anu7w%253D&md5=b670255601ae46db67b484288e3e0b87
    14. 14
      Udagawa, T.; Tachikawa, M. H/D Isotope Effect on Porphine and Porphycene Molecules with Multicomponent Hybrid Density Functional Theory. J. Chem. Phys. 2006, 125, 244105,  DOI: 10.1063/1.2403857
      14
      H/D isotope effect on porphine and porphycene molecules with multicomponent hybrid density functional theory
      Udagawa, Taro; Tachikawa, Masanori
      Journal of Chemical Physics (2006), 125 (24), 244105/1-244105/9CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
      To analyze the H/D isotope effect on porphine and porphycene mols. including the protonic/deuteronic quantum nature and electron correlation efficiently, the authors have developed the new scheme of the multicomponent hybrid d. functional theory [MC_(HF+DFT)]. The optimized geometries of porphine, porphycene, and these deuterated isotopomers by our MC-(HF+DFT) method are in good agreement with the exptl. "high-sym." structures, contrary to the "low-sym." geometries optimized by pure multicomponent Hartree-Fock method. The optimized geometries for HD-porphine and HD-porphycene mols., in which an inner hydrogen is replaced to a deuterium, are found to be low sym. Such drastic geometrical change induces the electronic polarization, and gives rise to the slight dipole moment values in these HD species. Their results clearly indicate that the difference of the nuclear quantum nature between inner proton and inner deuteron directly influences the mol. geometry and electronic structure.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXosVChtw%253D%253D&md5=91d0dd5803355e9bb890e8b3d7fa71f0
    15. 15
      Funahashi, H.; Tachikawa, M.; Udagawa, T. Determining If Reaction Selectivity Can Be Controlled by the H/D Isotope Effect in CH···O Interactions. Org. Lett. 2020, 22, 9439– 9443,  DOI: 10.1021/acs.orglett.0c03351
      15
      Determining if Reaction Selectivity Can Be Controlled by the H/D Isotope Effect in CH···O Interactions
      Funahashi, Haruki; Tachikawa, Masanori; Udagawa, Taro
      Organic Letters (2020), 22 (24), 9439-9443CODEN: ORLEF7; ISSN:1523-7052. (American Chemical Society)
      The H/D isotope effect in the CH···O interactions of several systems is systematically analyzed to det. whether it exerts control over reaction selectivity. Our theor. study demonstrates that deuterium substitution has a negligible effect on CH···O interactions; thus, reaction selectivity likely cannot be controlled by the H/D isotope effect in these CH···O interactions.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXit1OrsL%252FE&md5=102df76861bfba4561abb4d9f403f1bf
    16. 16
      Udagawa, T.; Murphy, R. B.; Darwish, T. A.; Tachikawa, M.; Mori, S. H/D Isotope Effects in Keto-Enol Tautomerism of β-Dicarbonyl Compounds ─Importance of NQEs of Hydrogen Nuclei─. Bull. Chem. Soc. Jpn. 2021, 94, 1954– 1962,  DOI: 10.1246/bcsj.20210083
      16
      H/D Isotope Effects in Keto-Enol Tautomerism of β-Dicarbonyl Compounds -Importance of Nuclear Quantum Effects of Hydrogen Nuclei-
      Udagawa, Taro; Murphy, Rhys B.; Darwish, Tamim A.; Tachikawa, Masanori; Mori, Seiji
      Bulletin of the Chemical Society of Japan (2021), 94 (7), 1954-1962CODEN: BCSJA8; ISSN:0009-2673. (Chemical Society of Japan)
      Deuterium isotope effects in the keto-enol tautomerism of β-dicarbonyl compds. (malonaldehyde, acetylacetone, dibenzoylmethane, and avobenzone) have been studied using a B3LYP+D functional level of multi-component d. functional theory (MC_DFT), which can directly take nuclear quantum effects (NQEs) of the hydrogen nuclei into account. We clearly show that the keto-enol energy difference becomes smaller by deuterium substitution, which is in reasonable agreement with the corresponding exptl. evidence. Our MC_DFT study also reveals the hydrogen/deuterium (H/D) isotope effect in geometries and shows that the deuterium substitution weakens the intramol. hydrogen-bonded interaction in the enol form. Direct treatment of NQEs of hydrogen nuclei via the MC_DFT method is essential for analyzing the H/D isotope effect in keto-enol tautomerism of β-dicarbonyl compds. Such isotope effects cannot be reproduced in the conventional DFT scheme with harmonic zero-point vibrational corrections.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXhvVansrjK&md5=32ab97a747bdd6c5ffec001a2325523d
    17. 17
      Tuckerman, M. E.; Marx, D.; Klein, M. L.; Parrinello, M. On the Quantum Nature of the Shared Proton in Hydrogen Bonds. Science 1997, 275, 817– 820,  DOI: 10.1126/science.275.5301.817
      17
      On the quantum nature of the shared proton in hydrogen bonds
      Tuckerman, Mark E.; Marx, Dominik; Klein, Michael L.; Parrinello, Michele
      Science (Washington, D. C.) (1997), 275 (5301), 817-820CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
      The relative influence of thermal and quantum fluctuations on the proton transfer properties of the charged water complexes H5O2+ and H3O2- was investigated with the use of ab initio techniques. These small systems can be considered as prototypical representatives of strong and intermediate-strength hydrogen bonds. The shared proton in the strongly hydrogen bonded H5O2+ behaved in an essentially classical manner, whereas in the H3O2- low-barrier hydrogen bond, quantum zero-point motion played a crucial role even at room temp. This behavior can be traced back to a small difference in the oxygen-oxygen sepn. and hence of the strength of the hydrogen.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2sXhtFahsrg%253D&md5=8776bd58df40e8a5199818331b53ac04
    18. 18
      Ishibashi, H.; Hayashi, A.; Shiga, M.; Tachikawa, M. Geometric Isotope Effect on the N2H7+ Cation and N2H5– Anion by Ab Initio Path Integral Molecular Dynamics Simulation. ChemPhysChem 2008, 9, 383– 387,  DOI: 10.1002/cphc.200700570
      18
      Geometric isotope effect on the N2H7+ cation and N2H5- anion by ab initio path integral molecular dynamics simulation
      Ishibashi, Hiroaki; Hayashi, Aiko; Shiga, Motoyuki; Tachikawa, Masanori
      ChemPhysChem (2008), 9 (3), 383-387CODEN: CPCHFT; ISSN:1439-4235. (Wiley-VCH Verlag GmbH & Co. KGaA)
      The geometric isotope effect (GIE) for the hydrogen bonds in pos. and neg. charged ammonia dimers is studied by ab initio path integral MD simulation. The hydrogen-bonded H atom in the N2H7+ cation is located around the center of two N atoms, while the hydrogen-bonded D atom in the N2D7+ cation is closer to one of the N atoms.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXltVKqs78%253D&md5=306a1fbcd01fc10f47ab870f3b917ac7
    19. 19
      Durlak, P.; Latajka, Z. Car-Parrinello and Path Integral Molecular Dynamics Study of the Intramolecular Hydrogen Bonds in the Crystals of Benzoylacetone and dideuterobenzoylacetone. Phys. Chem. Chem. Phys. 2014, 16, 23026– 23037,  DOI: 10.1039/C4CP02569E
      19
      Car-Parrinello and path integral molecular dynamics study of the intramolecular hydrogen bonds in the crystals of benzoylacetone and dideuterobenzoylacetone
      Durlak, Piotr; Latajka, Zdzislaw
      Physical Chemistry Chemical Physics (2014), 16 (42), 23026-23037CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)
      The dynamics of the intramol. short hydrogen bond in the mol. crystal of benzoylacetone and its deuterated analog are investigated using ab initio mol. dynamics simulations. A study on intramol. hydrogen bonding in 1-phenyl-1,3-butadione (I) and 1-deuteroxy-2-deutero-1-phenylbut-1-en-3-one (II) crystals has been carried out at 160 K and 300 K on the CPMD method level and at 300 K on the PIMD method level. The anal. of the two-dimensional free-energy landscape of reaction coordinate δ-parameter and RO···O distances shows that the hydrogen (deuter) between the two oxygen atoms adopts a slightly asym. position in the single potential well. When the nuclear quantum effects are taken into account, very large delocalization of the bridging proton is obsd. These studies indicate that hydrogen bonds in the crystal of benzoylacetone have characteristic properties for the type of bonding model resonance-assisted hydrogen bonds (RAHB) without existing the equil. of the two tautomers. The IR spectrum has been calcd., and a comparative vibrational anal. has been performed. The CPMD vibrational results appear to qual. agree with the exptl. ones.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhsVGjurrF&md5=f95e3825e60e31be544aba13d9f1596f
    20. 20
      Etinski, M.; Ensing, B. Puzzle of the Intramolecular Hydrogen Bond of Dibenzoylmethane Resolved by Molecular Dynamics Simulations. J. Phys. Chem. A 2018, 122, 5945– 5954,  DOI: 10.1021/acs.jpca.8b01930
      20
      Puzzle of the Intramolecular Hydrogen Bond of Dibenzoylmethane Resolved by Molecular Dynamics Simulations
      Etinski, Mihajlo; Ensing, Bernd
      Journal of Physical Chemistry A (2018), 122 (28), 5945-5954CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
      The enol form of dibenzoylmethane has been the subject of many exptl. and theor. studies, yet the symmetry and the spectral response of the OHO intramol. hydrogen bond remains mysterious due to conflicting assignments. In order to qual. understand the complex proton dynamics, it is necessary to probe the neighborhood of stationary points on the potential energy landscape. Here, we employ d. functional theory-based mol. dynamics (DFT-MD) simulations to sample the coupling between the intermol. proton transfer and all other mol. modes. To account for the quantum nature of the proton motion, we employ the path integral formalism within the DFT-MD simulations. Our results reveal that the hydrogen-bonded proton is delocalized between two oxygen atoms with sightly higher probability to be obsd. in the asym. than the sym. position. The simulated IR spectrum is found to be in a reasonably good agreement with the exptl. spectrum. The computed νOH band is remarkably broad and centered around 2640 cm-1. The origin of the discrepancy between the simulated and exptl. intensities of the νOH band is discussed.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXht1eksb3E&md5=482b9baba2e1a2ac97100a80b12ecdb4
    21. 21
      Durlak, P.; Latajka, Z. Investigations of the Hydrogen Bond in the Crystals of Tropolone and Thiotropolone via Car-Parrinello and Path Integral Molecular Dynamics. J. Comput. Chem. 2018, 40, 671– 687,  DOI: 10.1002/jcc.25753
      There is no corresponding record for this reference.
    22. 22
      Sauceda, H. E.; Vassilev-Galindo, V.; Chmiela, S.; Müller, K. R.; Tkatchenko, A. Dynamical Strengthening of Covalent and Non-Covalent Molecular Interactions by NQEs at Finite Temperature. Nat. Commun. 2021, 12 (1), 442,  DOI: 10.1038/s41467-020-20212-1
      22
      Dynamical strengthening of covalent and non-covalent molecular interactions by nuclear quantum effects at finite temperature
      Sauceda, Huziel E.; Vassilev-Galindo, Valentin; Chmiela, Stefan; Muller, Klaus-Robert; Tkatchenko, Alexandre
      Nature Communications (2021), 12 (1), 442CODEN: NCAOBW; ISSN:2041-1723. (Nature Research)
      Nuclear quantum effects (NQE) tend to generate delocalized mol. dynamics due to the inclusion of the zero point energy and its coupling with the anharmonicities in interat. interactions. Here, we present evidence that NQE often enhance electronic interactions and, in turn, can result in dynamical mol. stabilization at finite temp. The underlying phys. mechanism promoted by NQE depends on the particular interaction under consideration. First, the effective redn. of interat. distances between functional groups within a mol. can enhance the n → π* interaction by increasing the overlap between MOs or by strengthening electrostatic interactions between neighboring charge densities. Second, NQE can localize Me rotors by temporarily changing mol. bond orders and leading to the emergence of localized transient rotor states. Third, for noncovalent van der Waals interactions the strengthening comes from the increase of the polarizability given the expanded av. interat. distances induced by NQE. The implications of these boosted interactions include counterintuitive hydroxyl-hydroxyl bonding, hindered Me rotor dynamics, and mol. stiffening which generates smoother free-energy surfaces. Our findings yield new insights into the versatile role of nuclear quantum fluctuations in mols. and materials.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXhvFeqtr4%253D&md5=e5b48c98270d1b4993a58b5ddb87e547
    23. 23
      Kuwahata, K.; Tachikawa, M. Path Integral Molecular Dynamics Study on NH 4+(H2O). Few-Body Sys. 2021, 62, 96,  DOI: 10.1007/s00601-021-01689-y
      23
      Path Integral Molecular Dynamics Study on NH4+(H2O)
      Kuwahata, Kazuaki; Tachikawa, Masanori
      Few-Body Systems (2021), 62 (4), 96CODEN: FBSYEQ; ISSN:0177-7963. (Springer-Verlag GmbH)
      Among the hydrogen bonds, which are crit. to sustaining life, the interaction between ammonium ions (NH4+) and water is considered a model interaction in biol. systems. Although this interaction has been examd. in earlier studies on mol. dynamics, the nuclear quantum effect was not considered in those studies. In this study, we investigate the nuclear quantum effect of a singly-hydrated ammonium ion cluster, NH4+(H2O), using an ab initio on-the-fly path integral mol. dynamics (PIMD) simulation with a BHandHLYP/6-31++G(d,p) level of calcns. We find that the nuclear quantum effect shortens the N-O bond and increases the angle of the O-N-Hb bond. The results indicate that the nuclear quantum effect has two competing contributions. The first contribution involves strengthening the intermol. interaction, which reduces the intermol. distance, and the other contribution involves weakening the interaction, and it facilitates the rotation of NH4+.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXitVyrsb3M&md5=3e55a23d7f6237494760b6cb432e5b56
    24. 24
      Udagawa, T.; Kuwahata, K.; Tachikawa, M. Competitive NQE and H/D Isotope Effect on Torsional Motion of H2O2: An Ab Initio Path Integral Molecular Dynamics Study. Comput. Theor. Chem. 2022, 1208, 113542,  DOI: 10.1016/j.comptc.2021.113542
      24
      Competitive nuclear quantum effect and H/D isotope effect on torsional motion of H2O2: An ab initio path integral molecular dynamics study
      Udagawa, Taro; Kuwahata, Kazuaki; Tachikawa, Masanori
      Computational & Theoretical Chemistry (2022), 1208 (), 113542CODEN: CTCOA5; ISSN:2210-271X. (Elsevier B.V.)
      Ab initio path integral mol. dynamics (PIMD) simulations were performed to understand the nuclear quantum effect and thermal effect on the torsional motion of H2O2 (D2O2). A broad distribution of geometrical parameters (OH and OO bond lengths [ROH and ROO] and HOO bond angle [∠HOO]) was obtained in quantum ab initio PIMD simulations, rather than in classical MD simulations. However, a modest distribution around the trans-configuration TS (∠HOOH = 180°) was found in the quantum ab initio PIMD simulations of H2O2 at low temps. Thus, the nuclear quantum effect slightly enhanced the HOOH torsional motion at low temps. A series of simulations also revealed that the thermal effect enhanced the HOOH torsional motion. However, it was restrained by the primary nuclear quantum effect on the ROH in quantum simulations at high temps. Therefore, an interesting competitive nuclear quantum effect on the torsional motion of H2O2 was obsd.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXislelsLnI&md5=15ba55b73a772ded68c1b276bdaa9d2b
    25. 25
      Yanai, T.; Tew, D. P.; Handy, N. C. A New Hybrid Exchange-Correlation Functional Using the Coulomb-Attenuating Method (CAM-B3LYP). Chem. Phys. Lett. 2004, 393, 51– 57,  DOI: 10.1016/j.cplett.2004.06.011
      25
      A new hybrid exchange-correlation functional using the Coulomb-attenuating method (CAM-B3LYP)
      Yanai, Takeshi; Tew, David P.; Handy, Nicholas C.
      Chemical Physics Letters (2004), 393 (1-3), 51-57CODEN: CHPLBC; ISSN:0009-2614. (Elsevier Science B.V.)
      A new hybrid exchange-correlation functional named CAM-B3LYP is proposed. It combines the hybrid qualities of B3LYP and the long-range correction presented by Tawada et al. [J. Chem. Phys., in press]. We demonstrate that CAM-B3LYP yields atomization energies of similar quality to those from B3LYP, while also performing well for charge transfer excitations in a dipeptide model, which B3LYP underestimates enormously. The CAM-B3LYP functional comprises of 0.19 Hartree-Fock (HF) plus 0.81 Becke 1988 (B88) exchange interaction at short-range, and 0.65 HF plus 0.35 B88 at long-range. The intermediate region is smoothly described through the std. error function with parameter 0.33.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXlsFKgtbs%253D&md5=75f311240ff8ebedb174757f3eedbf3e
    26. 26
      Stewart, J. J. P. Optimization of Parameters for Semiempirical Methods V: Modification of NDDO Approximations and Application to 70 Elements. J. Mol. Model. 2007, 13, 1173– 1213,  DOI: 10.1007/s00894-007-0233-4
      26
      Optimization of parameters for semiempirical methods V: modification of NDDO approximations and application to 70 elements
      Stewart, James J. P.
      Journal of Molecular Modeling (2007), 13 (12), 1173-1213CODEN: JMMOFK; ISSN:0948-5023. (Springer GmbH)
      Several modifications that have been made to the NDDO core-core interaction term and to the method of parameter optimization are described. These changes have resulted in a more complete parameter optimization, called PM6, which has, in turn, allowed 70 elements to be parameterized. The av. unsigned error (AUE) between calcd. and ref. heats of formation for 4,492 species was 8.0 kcal mol-1. For the subset of 1,373 compds. involving only the elements H, C, N, O, F, P, S, Cl, and Br, the PM6 AUE was 4.4 kcal mol-1. The equivalent AUE for other methods were: RM1: 5.0, B3LYP 6-31G*: 5.2, PM5: 5.7, PM3: 6.3, HF 6-31G*: 7.4, and AM1: 10.0 kcal mol-1. Several long-standing faults in AM1 and PM3 have been cor. and significant improvements have been made in the prediction of geometries.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXhtlequr7N&md5=7d22928c8e3423f3ca8f2e7c77e6e6c9
    27. 27
      Korth, M.; Pitoňák, M.; Řezáč, J.; Hobza, P. A Transferable H-Bonding Correction for Semiempirical Quantum-Chemical Methods. J. Chem. Theory Comput. 2010, 6, 344– 352,  DOI: 10.1021/ct900541n
      27
      A Transferable H-Bonding Correction for Semiempirical Quantum-Chemical Methods
      Korth, Martin; Pitonak, Michal; Rezac, Jan; Hobza, Pavel
      Journal of Chemical Theory and Computation (2010), 6 (1), 344-352CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
      Semiempirical methods could offer a feasible compromise between ab initio and empirical approaches for the calcn. of large mols. with biol. relevance. A key problem for attempts in this direction is the rather bad performance of current semiempirical methods for noncovalent interactions, esp. hydrogen-bonding. On the basis of the recently introduced PM6-DH method, which includes empirical corrections for dispersion (D) and hydrogen-bond (H) interactions, we have developed an improved and transferable H-bonding correction for semiempirical quantum chem. methods. The performance of the improved correction is evaluated for PM6, AM1, OM3, and SCC-DFTB (enhanced by std. empirical dispersion corrections) with several test sets for noncovalent interactions and is shown to reach the quality of current DFT-D approaches for these types of problems.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhsFektr%252FK&md5=6b8845ee0e334284ca8b3b5e60ad612f
    28. 28
      Korth, M. Third-Generation Hydrogen-Bonding Corrections for Semiempirical QM Methods and Force Fields. J. Chem. Theroy Comput. 2010, 6, 3808– 3816,  DOI: 10.1021/ct100408b
      28
      Third-Generation Hydrogen-Bonding Corrections for Semiempirical QM Methods and Force Fields
      Korth, Martin
      Journal of Chemical Theory and Computation (2010), 6 (12), 3808-3816CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
      Computational modeling of biol. systems is a rapidly evolving field that calls for methods that are able to allow for extensive sampling with systems consisting of thousands of atoms. Semiempirical quantum chem. (SE) methods are a promising tool to aid with this, but the rather bad performance of std. SE methods for noncovalent interactions is clearly a limiting factor. Enhancing SE methods with empirical corrections for dispersion and hydrogen-bonding interactions was found to be a big improvement, but for the hydrogen-bonding corrections the drawback of breaking down in the case of substantial changes to the hydrogen bond, e.g., proton transfer, posed a serious limitation for its general applicability. This work presents a further improved hydrogen-bonding correction that can be generally included in parameter fitting procedures, as it does not suffer from the conceptual flaws of previous approaches: hydrogen bonds are now treated as an interaction term between electroneg. acceptor and donor atoms, "weighted" by a function of the position of H atoms between them, and multiplied with a damping function to correct the short- and long-range behavior. The performance of the new approach is evaluated for PM6, AM1, OM3, and SCC-DFTB as well as several force-field (FF) methods for a no. of std. benchmark sets with hydrogen-bonded systems. The new approach is found to reach the same accuracy as the second-generation hydrogen-bonding correction with less parameters, while it avoids among other issues the conceptual problem with electronic structure changes. SE methods augmented this way reach the accuracy of DFT-D approaches for a large no. of cases investigated, while still being about 3 orders of magnitude faster. Moreover, the new correction scheme is transferable also to FF methods that were shown to have serious problems with hydrogen-bonding interactions.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXhtlKjs7%252FF&md5=c02f35bdeb307c2bd52fc5e069bddb4c
    29. 29
      Řezáč, J.; Hobza, P. Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods. J. Chem. Theory Comput. 2012, 8, 141– 151,  DOI: 10.1021/ct200751e
      29
      Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods
      Rezac, Jan; Hobza, Pavel
      Journal of Chemical Theory and Computation (2012), 8 (1), 141-151CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
      Semiempirical quantum mech. methods with corrections for noncovalent interactions, namely dispersion and hydrogen bonds, reach an accuracy comparable to much more expensive methods while being applicable to very large systems (up to 10 000 atoms). These corrections have been successfully applied in computer-assisted drug design, where they significantly improve the correlation with the exptl. data. Despite these successes, there are still several unresolved issues that limit the applicability of these methods. We introduce a new generation of both hydrogen-bonding and dispersion corrections that address these problems, make the method more robust, and improve its accuracy. The hydrogen-bonding correction has been completely redesigned and for the first time can be used for geometry optimization and mol.-dynamics simulations without any limitations, as it and its derivs. have a smooth potential energy surface. The form of this correction is simpler than its predecessors, while the accuracy has been improved. For the dispersion correction, we adopt the latest developments in DFT-D, using the D3 formalism by Grimme. The new corrections have been parametrized on a large set of benchmark data including nonequil. geometries, the S66x8 data set. As a result, the newly developed D3H4 correction can accurately describe a wider range of interactions. We have parametrized this correction for the PM6, RM1, OM3, PM3, AM1, and SCC-DFTB methods.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhs1Gls77L&md5=1c15239efc1338484dcd0b9d6e70518d
    30. 30
      Stewart, J. J. P. Optimization of Parameters for Semiempirical Methods VI: More Modifications to the NDDO Approximations and Re-Optimization of Parameters. J. Mol. Model. 2013, 19, 1– 32,  DOI: 10.1007/s00894-012-1667-x
      30
      Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters
      Stewart, James J. P.
      Journal of Molecular Modeling (2013), 19 (1), 1-32CODEN: JMMOFK; ISSN:0948-5023. (Springer)
      Modern semiempirical methods are of sufficient accuracy when used in the modeling of mols. of the same type as used as ref. data in the parameterization. Outside that subset, however, there is an abundance of evidence that these methods are of very limited utility. In an attempt to expand the range of applicability, a new method called PM7 has been developed. PM7 was parameterized using exptl. and high-level ab initio ref. data, augmented by a new type of ref. data intended to better define the structure of parameter space. The resulting method was tested by modeling crystal structures and heats of formation of solids. Two changes were made to the set of approxns.: a modification was made to improve the description of noncovalent interactions, and two minor errors in the NDDO formalism were rectified. Av. unsigned errors (AUEs) in geometry and ΔH f for PM7 were reduced relative to PM6; for simple gas-phase org. systems, the AUE in bond lengths decreased by about 5 % and the AUE in ΔH f decreased by about 10 %; for org. solids, the AUE in ΔH f dropped by 60 % and the redn. was 33.3 % for geometries. A two-step process (PM7-TS) for calcg. the heights of activation barriers has been developed. Using PM7-TS, the AUE in the barrier heights for simple org. reactions was decreased from values of 12.6 kcal/mol-1 in PM6 and 10.8 kcal/mol-1 in PM7 to 3.8 kcal/mol-1. The origins of the errors in NDDO methods have been examd., and were found to be attributable to inadequate and inaccurate ref. data. This conclusion provides insight into how these methods can be improved.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXjtVegtA%253D%253D&md5=7177311730da8242d5e05f7f4e045e57
    31. 31
      Martyna, G. J.; Klein, M. L.; Tuckerman, M. Nosé-Hoover Chains: The Canonical Ensemble via Continuous Dynamics. J. Chem. Phys. 1992, 97, 2635– 2643,  DOI: 10.1063/1.463940
      There is no corresponding record for this reference.
    32. 32
      Flyvbjerg, H.; Petersen, H. G. Error Estimates on Averages of Correlated Data. J. Chem. Phys. 1989, 91, 461– 466,  DOI: 10.1063/1.457480
      32
      Error estimates on averages of correlated data
      Flyvbjerg, H.; Petersen, H. G.
      Journal of Chemical Physics (1989), 91 (1), 461-6CODEN: JCPSA6; ISSN:0021-9606.
      A description is given on how the true statistical error on an av. of correlated data can be obtained with ease and efficiency by a renormalization group method. The method is illustrated with numerical and anal. examples, having finite as well as infinite range correlations.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL1MXkslOis7s%253D&md5=a424bd42502aa2989d102aa4c87b8eca