Free energy calculation on enzyme reactions with an efficient iterative procedure to determine minimum energy paths on a combinedab initioQM/MM potential energy surface

2000 ◽  
Vol 112 (8) ◽  
pp. 3483-3492 ◽  
Author(s):  
Yingkai Zhang ◽  
Haiyan Liu ◽  
Weitao Yang
Keyword(s):  
Free Energy ◽  
Potential Energy ◽  
Potential Energy Surface ◽  
Iterative Procedure ◽  
Energy Surface ◽  
Minimum Energy ◽  
Free Energy Calculation ◽  
Energy Calculation ◽  
Enzyme Reactions ◽  
Minimum Energy Paths

scholarly journals Density functional theory study of the Jahn-Teller effect in cobaltocene

2009 ◽  
Vol 81 (8) ◽  
pp. 1397-1411 ◽  
Author(s):  
Matija Zlatar ◽  
Carl-Wilhelm Schläpfer ◽  
Emmanuel Penka Fowe ◽  
Claude A. Daul
Keyword(s):  
Density Functional Theory ◽  
Potential Energy ◽  
Potential Energy Surface ◽  
Density Functional ◽  
Energy Surface ◽  
Minimum Energy ◽  
Normal Modes ◽  
Coupling Coefficients ◽  
Functional Theory ◽  
Jahn Teller

A detailed discussion of the potential energy surface of bis(cyclopentadienyl)cobalt(II), cobaltocene, is given. Vibronic coupling coefficients are calculated using density functional theory (DFT). Results are in good agreement with experimental findings. On the basis of our calculation there is no second-order Jahn–Teller (JT) effect as predicted by group theory. The JT distortion can be expressed as a linear combination of all totally symmetric normal modes of the low-symmetry, minimum-energy conformation. The out-of-plane ring deformation is the most important mode. The JT distortion is analyzed by seeking the path of minimal energy of the adiabatic potential energy surface.

scholarly journals Neural Network Sampling of the Free Energy Landscape for Nitrogen Dissociation on Ruthenium

2020 ◽  
Author(s):  
Elizabeth Lee ◽  
Thomas Ludwig ◽  
Boyuan Yu ◽  
Aayush Singh ◽  
François Gygi ◽  
...  
Keyword(s):  
Neural Network ◽  
Free Energy ◽  
Heterogeneous Catalysis ◽  
Potential Energy ◽  
Potential Energy Surface ◽  
Energy Surface ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Enhanced Sampling ◽  
Elementary Reactions

<p>Reaction rates in heterogeneous catalysis are predicted using the free energy profiles of elementary reactions. Conventionally, the energetics are computed from critical points of the potential energy surface, with harmonic free energy corrections. Here we use <i>ab initio</i> molecular dynamics and neural network-assisted enhanced sampling simulations to directly calculate the free energy landscape of a prototypical heterogeneous catalysis reaction, the dissociation of molecular nitrogen on ruthenium. We show that accelerating force- and frequency-based enhanced sampling using neural networks can characterize reactive phenomena at density functional theory-level accuracy. A previously reported molecularly adsorbed metastable state is found in the potential energy surface but is absent in the free energy surface. The potential of mean force for the dissociation reaction shows significant temperature-dependent effects beyond the standard harmonic approximation. We demonstrate that these thermodynamic effects can be important for elementary reactions on transition metal surfaces.</p>

scholarly journals Synergistic approach to improve “alchemical” free energy calculation in rugged energy surface

2007 ◽  
Vol 126 (14) ◽  
pp. 144109 ◽  
Author(s):  
Donghong Min ◽  
Hongzhi Li ◽  
Guohui Li ◽  
Ryan Bitetti-Putzer ◽  
Wei Yang
Keyword(s):  
Free Energy ◽  
Energy Surface ◽  
Free Energy Calculation ◽  
Energy Calculation ◽  
Synergistic Approach ◽  
Alchemical Free Energy

THE PARTIAL POTENTIAL ENERGY SURFACE AND SCATTERING RESONANCE STATE OF THE STATE-TO-STATE REACTION Br + HBr(v) → BrH(v′) + Br

2006 ◽  
Vol 05 (spec01) ◽  
pp. 307-316 ◽  
Author(s):  
HUAYANG WANG ◽  
XIAOMIN SUN ◽  
DACHENG FENG ◽  
ZHENGTING CAI
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Energy Surface ◽  
Minimum Energy ◽  
Resonance State ◽  
Minimum Energy Path ◽  
Resonance States ◽  
One Dimensional ◽  
Well Model ◽  
The One

In this paper, the partial potential energy surface (PPESs) of the Br + HBr and Br - + HBr systems including the minimum energy path and the vibrational potential curves were constructed at MP2/6-311++G** level, based on the conception and constructing approach of the PPESs previously proposed. These results obtained from the PPESs were compared with those from the high resolved threshold photodetachment spectrum of the BrHBr - anion measured by Neumark et al., J Phys Chem94, 1377–1388, 1990. On the basis of the PPESs, the scattering resonance states of the Br + HBr (v) → BrH (v′) + Br state-to-state reaction were studied and the satisfactory results were obtained. Subsequently, we calculated the width and lifetime of the resonance states in this reaction by the one-dimensional square potential well model, and obtained some results consistent to the experiments.

scholarly journals Improved Potential Energy Surface of Ozone Constructed Using the Fitting by Permutationally Invariant Polynomial Function

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
Mehdi Ayouz ◽  
Dmitri Babikov
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Energy Surface ◽  
Polynomial Function ◽  
Minimum Energy ◽  
Basis Set ◽  
Invariant Polynomial ◽  
Complete Basis Set ◽  
Data Points ◽  
Small Set

New global potential energy surface for the ground electronic state of ozone is constructed at the complete basis set level of the multireference configuration interaction theory. A method of fitting the data points by analytical permutationally invariant polynomial function is adopted. A small set of 500 points is preoptimized using the old surface of ozone. In this procedure the positions of points in the configuration space are chosen such that the RMS deviation of the fit is minimized. New ab initio calculations are carried out at these points and are used to build new surface. Additional points are added to the vicinity of the minimum energy path in order to improve accuracy of the fit, particularly in the region where the surface of ozone exhibits a shallow van der Waals well. New surface can be used to study formation of ozone at thermal energies and its spectroscopy near the dissociation threshold.

scholarly journals Neural Network Sampling of the Free Energy Landscape for Nitrogen Dissociation on Ruthenium

2020 ◽  
Author(s):  
Elizabeth Lee ◽  
Thomas Ludwig ◽  
Boyuan Yu ◽  
Aayush Singh ◽  
François Gygi ◽  
...  
Keyword(s):  
Neural Network ◽  
Free Energy ◽  
Heterogeneous Catalysis ◽  
Potential Energy ◽  
Potential Energy Surface ◽  
Energy Surface ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Enhanced Sampling ◽  
Elementary Reactions

<p>Reaction rates in heterogeneous catalysis are predicted using the free energy profiles of elementary reactions. Conventionally, the energetics are computed from critical points of the potential energy surface, with harmonic free energy corrections. Here we use <i>ab initio</i> molecular dynamics and neural network-assisted enhanced sampling simulations to directly calculate the free energy landscape of a prototypical heterogeneous catalysis reaction, the dissociation of molecular nitrogen on ruthenium. We show that accelerating force- and frequency-based enhanced sampling using neural networks can characterize reactive phenomena at density functional theory-level accuracy. A previously reported molecularly adsorbed metastable state is found in the potential energy surface but is absent in the free energy surface. The potential of mean force for the dissociation reaction shows significant temperature-dependent effects beyond the standard harmonic approximation. We demonstrate that these thermodynamic effects can be important for elementary reactions on transition metal surfaces.</p>

scholarly journals Neural Network Sampling of the Free Energy Landscape for Nitrogen Dissociation on Ruthenium

2020 ◽  
Author(s):  
Elizabeth Lee ◽  
Thomas Ludwig ◽  
Boyuan Yu ◽  
Aayush Singh ◽  
François Gygi ◽  
...  
Keyword(s):  
Neural Network ◽  
Free Energy ◽  
Heterogeneous Catalysis ◽  
Potential Energy ◽  
Potential Energy Surface ◽  
Energy Surface ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Enhanced Sampling ◽  
Elementary Reactions

<p>Reaction rates in heterogeneous catalysis are predicted using the free energy profiles of elementary reactions. Conventionally, the energetics are computed from critical points of the potential energy surface, with harmonic free energy corrections. Here we use <i>ab initio</i> molecular dynamics and neural network-assisted enhanced sampling simulations to directly calculate the free energy landscape of a prototypical heterogeneous catalysis reaction, the dissociation of molecular nitrogen on ruthenium. We show that accelerating force- and frequency-based enhanced sampling using neural networks can characterize reactive phenomena at density functional theory-level accuracy. A previously reported molecularly adsorbed metastable state is found in the potential energy surface but is absent in the free energy surface. The potential of mean force for the dissociation reaction shows significant temperature-dependent effects beyond the standard harmonic approximation. We demonstrate that these thermodynamic effects can be important for elementary reactions on transition metal surfaces.</p>

scholarly journals Structures and stabilities of C2H2F3+ cations: an abinitio molecular orbital study

1987 ◽  
Vol 65 (3) ◽  
pp. 473-481 ◽  
Author(s):  
Micheline Charpentier ◽  
Jacques Fossey ◽  
Thomas T. Tidwell ◽  
Saul Wolfe
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Energy Surface ◽  
Atomic Orbital ◽  
Minimum Energy ◽  
Saddle Points ◽  
Lone Pair ◽  
Basis Set ◽  
Stationary Points ◽  
Energy Structure

Eleven stationary points on the singlet C2H2F3+ potential energy surface have been calculated using the 3-21G basis set, and characterized as minima (four structures) or first-order saddle points (seven structures) by vibrational analysis. To check the reliability of this basis set, three of the structures have also been optimized at the 6-31G* level; although the geometries change somewhat, the relative energies and nature (maxima, minima) of the structures remain the same. For CF3CH2+ the minimum energy structure has one C—F bond coplanar with the vacant p-atomic orbital at the cationic centre. The structure is 16.4 kcal/mol less stable than the lowest energy conformation of FCH2CF2+, and the barrier for the 1,2 fluorine migration which connects the two structures is low. The cation F2CHCHF+ has a conformation that is a minimum on the potential energy surface that is 16.9 kcal/mol higher in energy than FCH2CF2+; the two structures are separated by a barrier for 1,2 hydrogen migration of 23.5 kcal/mol. The electronic effects in the various structures have been studied using a quantitative PMO analysis of the interactions between the two carbon fragments of the ions. For CF3CH2+ the net effect of the fluorine is highly destabilizing; the principal stabilizing interactions between CF3+ and CH2 consist of π donation from CF3+ to CH2 and homoconjugation of a fluorine lone pair with the cationic centre. No net stabilization attributable to fluorine bridging could be found.

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