Peptide model XXVIII: An exploratory ab initio and density functional study on the side-chain-backbone interaction in N-acetyl-L-cysteine- N-methylamide and N-formyl-L-cysteinamide in their γL-backbone conformations

2002 ◽  
Vol 80 (7) ◽  
pp. 832-844 ◽  
Author(s):  
M A Zamora ◽  
H A Baldoni ◽  
A M Rodriguez ◽  
R D Enriz ◽  
C P Sosa ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Potential Energy ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Energy Surface ◽  
Geometry Optimization ◽  
Intramolecular Hydrogen Bonding ◽  
Functional Study ◽  
Side Chain ◽  
Intramolecular Hydrogen

A conformational and electronic study on the energetically preferred conformations (γL) of N- and C-protected L-cysteine (P-CONH-CH(CH2SH)-CONH-Q, where P and Q may be H or Me) was carried out. After restraining the backbone (BB) conformation to its global minimum (γL or C7eq), all nine possible side-chain (SC) conformations were subjected to geometry optimization at the HF/3–21G and the B3LYP/6–31G(d,p) levels of theory. Seven of the nine side-chain conformers were located on the potential-energy surface. All conformers were subjected to an AIM (atoms in molecules) analysis. This study indicates that three of the seven optimized conformers exhibited either or both SC [Formula: see text] BB- or BB [Formula: see text] SC-type intramolecular hydrogen bonding. Five conformers, however, had distances between a proton and a heteroatom that suggested hydrogen bonding.Key words: L-cysteine diamides, side-chain potential-energy surface, ab initio and DFT geometry optimization, AIM analysis, intramolecular hydrogen bonding.

scholarly journals Desymmetrization in geometry optimization: application to an ab initio study of copper(I) hydration

2020 ◽  
Vol 92 (10) ◽  
pp. 1643-1654
Author(s):  
Cory C. Pye ◽  
Daniel C. M. Whynot ◽  
Christopher R. Corbeil ◽  
Darren J. W. Mercer
Keyword(s):  
Irreducible Representation ◽  
Potential Energy ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Coordination Number ◽  
Energy Surface ◽  
Geometry Optimization ◽  
Symmetry Reduction ◽  
Stationary Points ◽  
Ab Initio Study

AbstractGroup theoretical arguments are used to find the subgroup corresponding to symmetry reduction along a particular irreducible representation of a group. The results are used to guide the search for stationary points on the potential energy surface of hydrated copper(I) ion at the HF/6-31G∗, HF/6-31+G∗, HF/6-311+G∗, MP2/6-31G∗, MP2/6-31+G∗, MP2/6-311+G∗, B3LYP/6-31G∗, B3LYP/6-31+G∗, and B3LYP/6-311+G∗ levels. The better levels give the most stable coordination number of two. The effect of desymmetrization on the Cu-O distances and stretching frequencies has been examined.

An accurate, global, ab initio potential energy surface for the H + 3 molecule

2000 ◽  
Vol 98 (5) ◽  
pp. 261-273 ◽  
Author(s):  
Oleg L. Polyansky, Rita Prosmiti, Wim Kl
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Energy Surface

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.

scholarly journals Variational analysis of HF dimer tunneling rotational spectra using an ab initio potential energy surface

2021 ◽  
pp. 111481
Author(s):  
Oleg L. Polyansky ◽  
Roman I. Ovsyannikov ◽  
Jonathan Tennyson ◽  
Sergei P. Belov ◽  
Mikhail Yu. Tretyakov ◽  
...  
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Variational Analysis ◽  
Energy Surface ◽  
Rotational Spectra

An analytical six‐dimensional potential energy surface for (HF)2 from ab initio calculations

1988 ◽  
Vol 89 (5) ◽  
pp. 3002-3007 ◽  
Author(s):  
P. R. Bunker ◽  
Manfred Kofranek ◽  
Hans Lischka ◽  
Alfred Karpfen
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Ab Initio Calculations ◽  
Ab Initio ◽  
Energy Surface
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