Multidimensional conformational analysis of allyl methyl disulfide: a key component of garlic

2000 ◽  
Vol 78 (3) ◽  
pp. 362-382 ◽  
Author(s):  
Alvin C Lin ◽  
Salvatore J Salpietro ◽  
Eugen Deretey ◽  
Imre G Csizmadia
Keyword(s):  
Potential Energy ◽  
Conformational Analysis ◽  
Ab Initio ◽  
Lipid Lowering ◽  
Torsional Angle ◽  
Organosulfur Compounds ◽  
Cholesterol Lowering ◽  
Torsional Angles ◽  
Activity Mechanism ◽  
Molecular Computations

Organosulfur compounds in garlic, like allyl methyl disulfide, have been found to be involved in antimutagenic, anticarcinogenic, antithrombotic, and lipid-lowering activities, and it has also been found to act as an antioxidant. Ab initio molecular computations were performed on dihydrogen disulfide (1) with respect to torsional angle τ1 = τ(H·S-S·H), hydrogen methyl disulfide (2) with respect to torsional angle τ1 = τ(H·S-S·CH3), and allyl methyl disulfide (3) with respect to torsional angles τ1 = τ(H3C2·CH2·S-S·CH3), τ2 = τ(H3C2·CH2-S·S·CH3), and τ3 = τ(H3C2-CH2·S·S·CH3). Potential energy curves (PEC) were obtained from 1 and 2, i.e., E = E(τ1), from which optimized structures were obtained at the HF/6-31G* level of theory. These optimized structures were used to investigate the potential energy hypersurface surface (PEHS) of 3, i.e., E = E(τ1,τ2,τ3). One-dimensional scans along τ2 and τ3 (where τ1 = ±90°; τ1 = 180°) were performed at the HF/3-21G* level of theory. From these scans, six lower energy pairs of enantiomeric minima (i.e., [g+g+g+| g-g-g-], [g+ag- | g-ag+], [g+g-g+ | g-g+g-], [g+g+g-| g-g-g+], [g+ag- | g-ag+], and [g+g-g-| g-g+g+]) as well as 3 higher energy minima (i.e., [g+g+s | g-g-s], [g+as | g-as], and [g+g-s | g-g+s]) were optimized at τ1 = ±90° at the HF/6-31G* and B3LYP/6-31G* levels of theory. The global minimum was determined to be the [g+g-g+ | g-g+g-] enantiomeric pair of conformers, and the fully symmetrical anti-anti-anti [a a a] structure was determined to be a second-order saddle point on the PEHS of 3. Although there are no stereocentres in 3, there is chirality in the conformational twist with respect to the [a a a] conformation through τ1 = τ2 = τ3 = 180°. Based on the energies and MO diagrams of the HUMO and LUMO +1 of 3, the anticarcinogenic and cholesterol lowering activity mechanism of 3 is presented.Key words: ab initio MO computations, allyl methyl disulfide, multidimensional conformational analysis (MDCA), anticarcinogenic, cholesterol lowering.

On Comparing Experimental and Calculated Structural Parameters

1998 ◽  
Author(s):  
Lothar Schäfer ◽  
John D. Ewbank
Keyword(s):  
Electron Diffraction ◽  
Potential Energy ◽  
Ab Initio ◽  
Structural Parameters ◽  
Molecular Structures ◽  
Gas Electron Diffraction ◽  
Torsional Angle ◽  
Internuclear Distances ◽  
Molecular Potential Energy ◽  
The One

The tacit assumption underlying all science is that, of two competing theories, the one in closer agreement with experiment is the better one. In structural chemistry the same principle applies but, when calculated and experimental structures are compared, closer is not necessarily better. Structures from ab initio calculations, specifically, must not be the same as the experimental counterparts the way they are observed. This is so because ab initio geometries refer to nonexistent, vibrationless states at the minimum of potential energy, whereas structural observables represent specifically defined averages over distributions of vibrational states. In general, if one wants to make meaningful comparisons between calculated and experimental molecular structures, one must take recourse of statistical formalisms to describe the effects of vibration on the observed parameters. Among the parameters of interest to structural chemists, internuclear distances are especially important because other variables, such as bond angles, dihedral angles, and even crystal spacings, can be readily derived from them. However, how a rigid torsional angle derived from an ab initio calculation compares with the corresponding experimental value in a molecule subject to vibrational anharmonicity, is not so easy to determine. The same holds for the lattice parameters of a molecule in a dynamical crystal, and their temperature dependence as a function of the molecular potential energy surface. In contrast, vibrational effects are readily defined and best described for internuclear distances, bonded and non-bonded ones. In general, all observed internuclear distances are vibrationally averaged parameters. Due to anharmonicity, the average values will change from one vibrational state to the next and, in a molecular ensemble distributed over several states, they are temperature dependent. All these aspects dictate the need to make statistical definitions of various conceivable, different averages, or structure types. In addition, since the two main tools for quantitative structure determination in the vapor phase—gas electron diffraction and microwave spectroscopy—interact with molecular ensembles in different ways, certain operational definitions are also needed for a precise understanding of experimental structures. To illustrate how the operations of an experimental technique affect the nature of its observables, gas electron diffraction shall be used as an example.

An exploratory ab initio study on the conformations of ethylguanidine in its neutral [CH3-CH2-NH-C(=NH)NH2] and protonated [CH3-CH2-NH-C(NH2)2] forms

2000 ◽  
Vol 78 (5) ◽  
pp. 626-641 ◽  
Author(s):  
Melody L Mak ◽  
Salvatore J Salpietro ◽  
R Daniel Enriz ◽  
Imre G Csizmadia
Keyword(s):  
Dft Calculations ◽  
Conformational Analysis ◽  
Ab Initio ◽  
Internal Symmetry ◽  
Basis Sets ◽  
Side Chain ◽  
Torsional Angle ◽  
Ab Initio Study ◽  
Single Isomer ◽  
Arginine Side Chain

To explore the conformation intricacies of the guanidine group in the arginine side chain, ab initio computations have been carried out with ethylguanidine and the ethyl guanidinium ion. HF computations have been performed using 3-21G and 6-31G basis sets and DFT calculations were carried out at the B3LYP/6-31G(d) level of theory. The ethyl guanidinium ion has a single isomer due to its internal symmetry, although this structure has at least three conformations. However, several structures were found and optimized for ethylguanidine, involving the endo- and exo- orientation of the lone NH and torsional angle χ6, as well as the torsional modes associated with χ4 and χ5. Torsional angle χ5 gives rise to s-cis and s-trans structures.Key words: ethylguanidine, ethylguanidinium ion, ab initio MO, arginine side-chain, conformational analysis.

Active Learning Accelerates Ab Initio Molecular Dynamics on Pericyclic Reactive Energy Surfaces

2020 ◽  
Author(s):  
Shi Jun Ang ◽  
Wujie Wang ◽  
Daniel Schwalbe-Koda ◽  
Simon Axelrod ◽  
Rafael Gomez-Bombarelli
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Transition State ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Energy Surface ◽  
Computational Cost ◽  
Reactive Trajectories ◽  
Dynamics Simulations ◽  
Energy Surfaces

<div>Modeling dynamical effects in chemical reactions, such as post-transition state bifurcation, requires <i>ab initio</i> molecular dynamics simulations due to the breakdown of simpler static models like transition state theory. However, these simulations tend to be restricted to lower-accuracy electronic structure methods and scarce sampling because of their high computational cost. Here, we report the use of statistical learning to accelerate reactive molecular dynamics simulations by combining high-throughput ab initio calculations, graph-convolution interatomic potentials and active learning. This pipeline was demonstrated on an ambimodal trispericyclic reaction involving 8,8-dicyanoheptafulvene and 6,6-dimethylfulvene. With a dataset size of approximately</div><div>31,000 M062X/def2-SVP quantum mechanical calculations, the computational cost of exploring the reactive potential energy surface was reduced by an order of magnitude. Thousands of virtually costless picosecond-long reactive trajectories suggest that post-transition state bifurcation plays a minor role for the reaction in vacuum. Furthermore, a transfer-learning strategy effectively upgraded the potential energy surface to higher</div><div>levels of theory ((SMD-)M06-2X/def2-TZVPD in vacuum and three other solvents, as well as the more accurate DLPNO-DSD-PBEP86 D3BJ/def2-TZVPD) using about 10% additional calculations for each surface. Since the larger basis set and the dynamic correlation capture intramolecular non-covalent interactions more accurately, they uncover longer lifetimes for the charge-separated intermediate on the more accurate potential energy surfaces. The character of the intermediate switches from entropic to thermodynamic upon including implicit solvation effects, with lifetimes increasing with solvent polarity. Analysis of 2,000 reactive trajectories on the chloroform PES shows a qualitative agreement with the experimentally-reported periselectivity for this reaction. This overall approach is broadly applicable and opens a door to the study of dynamical effects in larger, previously-intractable reactive systems.</div>

Rotational de-excitations of C3H+ (1Σ+) by collision with He: new ab initio potential energy surface and scattering calculations

2020 ◽  
Vol 494 (4) ◽  
pp. 5675-5681 ◽  
Author(s):  
Sanchit Chhabra ◽  
T J Dhilip Kumar
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Cross Sections ◽  
Energy Surface ◽  
Molecular Ions ◽  
Basis Set ◽  
Rate Coefficients ◽  
Close Coupling ◽  
Collisional Rate Coefficients

ABSTRACT Molecular ions play an important role in the astrochemistry of interstellar and circumstellar media. C3H+ has been identified in the interstellar medium recently. A new potential energy surface of the C3H+–He van der Waals complex is computed using the ab initio explicitly correlated coupled cluster with the single, double and perturbative triple excitation [CCSD(T)-F12] method and the augmented correlation consistent polarized valence triple zeta (aug-cc-pVTZ) basis set. The potential presents a well of 174.6 cm−1 in linear geometry towards the H end. Calculations of pure rotational excitation cross-sections of C3H+ by He are carried out using the exact quantum mechanical close-coupling approach. Cross-sections for transitions among the rotational levels of C3H+ are computed for energies up to 600 cm−1. The cross-sections are used to obtain the collisional rate coefficients for temperatures T ≤ 100 K. Along with laboratory experiments, the results obtained in this work may be very useful for astrophysical applications to understand hydrocarbon chemistry.

Dynamics and kinetics of the Si(1D) + H2/D2 reactions on a new global ab initio potential energy surface

2021 ◽  
Vol 23 (10) ◽  
pp. 6141-6153
Author(s):  
Jianwei Cao ◽  
Yanan Wu ◽  
Haitao Ma ◽  
Zhitao Shen ◽  
Wensheng Bian
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Quantum Dynamics ◽  
Energy Surface ◽  
Molecular Dynamics Calculations ◽  
Ring Polymer ◽  
Ring Polymer Molecular Dynamics ◽  
Kinetics Of

Quantum dynamics and ring polymer molecular dynamics calculations reveal interesting dynamical and kinetic behaviors of an endothermic complex-forming reaction.

Sign in / Sign up

Export Citation Format

Share Document