scholarly journals Mechanism of Guanosine Triphosphate Hydrolysis by the Visual Proteins Arl3-RP2: Free Energy Reaction Profiles Computed with Ab Initio Type QM/MM Potentials

Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 3998
Author(s):  
Maria G. Khrenova ◽  
Egor S. Bulavko ◽  
Fedor D. Mulashkin ◽  
Alexander V. Nemukhin
Keyword(s):  
Molecular Dynamics ◽  
Reaction Mechanism ◽  
Ab Initio ◽  
Md Simulations ◽  
Human Vision ◽  
Basis Sets ◽  
Hydrolysis Rate ◽  
Guanosine Triphosphate ◽  
Gtp Hydrolysis ◽  
Energy Profiles

We report the results of calculations of the Gibbs energy profiles of the guanosine triphosphate (GTP) hydrolysis by the Arl3-RP2 protein complex using molecular dynamics (MD) simulations with ab initio type QM/MM potentials. The chemical reaction of GTP hydrolysis to guanosine diphosphate (GDP) and inorganic phosphate (Pi) is catalyzed by GTPases, the enzymes, which are responsible for signal transduction in live cells. A small GTPase Arl3, catalyzing the GTP → GDP reaction in complex with the activating protein RP2, constitute an essential part of the human vision cycle. To simulate the reaction mechanism, a model system is constructed by motifs of the crystal structure of the Arl3-RP2 complexed with a substrate analog. After selection of reaction coordinates, energy profiles for elementary steps along the reaction pathway GTP + H2O → GDP + Pi are computed using the umbrella sampling and umbrella integration procedures. QM/MM MD calculations are carried out, interfacing the molecular dynamics program NAMD and the quantum chemistry program TeraChem. Ab initio type QM(DFT)/MM potentials are computed with atom-centered basis sets 6-31G** and two hybrid functionals (PBE0-D3 and ωB97x-D3) of the density functional theory, describing a large QM subsystem. Results of these simulations of the reaction mechanism are compared to those obtained with QM/MM calculations on the potential energy surface using a similar description of the QM part. We find that both approaches, QM/MM and QM/MM MD, support the mechanism of GTP hydrolysis by GTPases, according to which the catalytic glutamine side chain (Gln71, in this system) actively participates in the reaction. Both approaches distinguish two parts of the reaction: the cleavage of the phosphorus-oxygen bond in GTP coupled with the formation of Pi, and the enzyme regeneration. Newly performed QM/MM MD simulations confirmed the profile predicted in the QM/MM minimum energy calculations, called here the pathway-I, and corrected its relief at the first elementary step from the enzyme–substrate complex. The QM/MM MD simulations also revealed another mechanism at the part of enzyme regeneration leading to pathway-II. Pathway-II is more consistent with the experimental kinetic data of the wild-type complex Arl3-RP2, whereas pathway-I explains the role of the mutation Glu138Gly in RP2 slowing down the hydrolysis rate.

scholarly journals The Influence of Gas–Wall and Gas–Gas Interactions on the Accommodation Coefficients for Rarefied Gases: A Molecular Dynamics Study

Micromachines ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 319 ◽  
Author(s):  
Shahin Mohammad Nejad ◽  
Silvia Nedea ◽  
Arjan Frijns ◽  
David Smeulders
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Rarefied Gas ◽  
Interaction Strength ◽  
Gold Surface ◽  
Md Simulations ◽  
Accommodation Coefficients ◽  
Experimental Values ◽  
Energy And Momentum ◽  
Gas Interactions

Molecular dynamics (MD) simulations are conducted to determine energy and momentum accommodation coefficients at the interface between rarefied gas and solid walls. The MD simulation setup consists of two parallel walls, and of inert gas confined between them. Different mixing rules, as well as existing ab-initio computations combined with interatomic Lennard-Jones potentials were employed in MD simulations to investigate the corresponding effects of gas-surface interaction strength on accommodation coefficients for Argon and Helium gases on a gold surface. Comparing the obtained MD results for accommodation coefficients with empirical and numerical values in the literature revealed that the interaction potential based on ab-initio calculations is the most reliable one for computing accommodation coefficients. Finally, it is shown that gas–gas interactions in the two parallel walls approach led to an enhancement in computed accommodation coefficients compared to the molecular beam approach. The values for the two parallel walls approach are also closer to the experimental values.

Geometry of OH⋯O interactions in the liquid state of linear alcohols from ab initio molecular dynamics simulations

2020 ◽  
Vol 22 (12) ◽  
pp. 6690-6697 ◽  
Author(s):  
Aman Jindal ◽  
Sukumaran Vasudevan
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Liquid State ◽  
Crystalline State ◽  
Md Simulations ◽  
Ab Initio Molecular Dynamics ◽  
Linear Alcohols ◽  
Dynamics Simulations

Hydrogen bonding OH···O geometries in the liquid state of linear alcohols, derived from ab initio MD simulations, show no change from methanol to pentanol, in contrast to that observed in their crystalline state.

AB-INITIO MOLECULAR DYNAMICS IN THE FULL-POTENTIAL LMTO METHOD: DERIVATION OF A PRACTICAL FORCE THEOREM

1993 ◽  
Vol 07 (01n03) ◽  
pp. 262-265 ◽  
Author(s):  
M. METHFESSEL ◽  
M. VAN SCHILFGAARDE
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Local Density ◽  
Basis Set ◽  
Ab Initio Molecular Dynamics ◽  
Basis Sets ◽  
Full Potential ◽  
Major Advance ◽  
First Results ◽  
Lmto Method

A major advance in electronic structure calculations was the combination of local-density techniques with molecular dynamics by Car and Parrinello seven years ago. Unfortunately, application of the Car-Parrinello scheme has been limited essentially to sp materials because only in the plane-wave pseudopotential method forces are trivial to calculate. We present a systematic approach to derive force theorems with desired characteristics within complicated basis sets, which are applicable to all elements of the periodic table equally well. Application to the LMTO basis set yields an accurate force theorem, quite distinct from the Hellman-Feynman form, which is exceptionally insensitive to errors in the trial density. The forces were implemented in a new full-potential LMTO method which is suited to arbitrary geometries. First results for ab-initio molecular dynamics and simulated annealing runs are shown for some random small molecules and small clusters of silver atoms.

scholarly journals Polydopamine and eumelanin molecular structures investigated with ab initio calculations

2017 ◽  
Vol 8 (2) ◽  
pp. 1631-1641 ◽  
Author(s):  
Chun-Teh Chen ◽  
Francisco J. Martin-Martinez ◽  
Gang Seob Jung ◽  
Markus J. Buehler
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Dft Calculations ◽  
Ab Initio Calculations ◽  
Ab Initio ◽  
Density Functional ◽  
Md Simulations ◽  
Molecular Structures ◽  
Brute Force ◽  
Functional Theory

A set of computational methods that contains a brute-force algorithmic generation of chemical isomers, molecular dynamics (MD) simulations, and density functional theory (DFT) calculations is reported and applied to investigate nearly 3000 probable molecular structures of polydopamine (PDA) and eumelanin.

Force field development and simulations of senior dialkyl sulfoxides

2016 ◽  
Vol 18 (15) ◽  
pp. 10507-10515 ◽  
Author(s):  
Vitaly V. Chaban
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Ab Initio ◽  
Md Simulations ◽  
Field Development ◽  
Force Field Development ◽  
Structure And Dynamics ◽  
Ethyl Methyl ◽  
Methyl Sulfoxide ◽  
Diethyl Sulfoxide

Thermodynamics, structure, and dynamics of diethyl sulfoxide (DESO) and ethyl methyl sulfoxide (EMSO) were investigated using ab initio calculations and non-polarizable potential based molecular dynamics (MD) simulations.

Accurate ab initio Calculations of Methane Dimer Interaction Energies and Molecular Dynamics Simulation of Fluid Methane

2009 ◽  
Vol 1177 ◽  
Author(s):  
Arvin Huang-Te Li ◽  
Sheng Der Chao
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Binding Energy ◽  
Ab Initio ◽  
Bond Length ◽  
Dynamics Simulation ◽  
Basis Set ◽  
Basis Sets ◽  
Equilibrium Bond Length ◽  
Basis Size

AbstractIntermolecular interaction potentials of the methane dimers have been calculated for 12 symmetric conformations using the Hartree-Fock (HF) self-consistent theory, the second-order M�ller-Plesset (MP2) perturbation theory, and the coupled-cluster with single and double and perturbative triple excitations (CCSD(T)) theory. The HF calculations yield unbound potentials largely due to the exchange-repulsion interaction. In MP2 and CCSD(T) calculations, the basis set effects on the repulsion exponent, the equilibrium bond length, the binding energy, and the asymptotic behavior of the calculated intermolecular potentials have been thoroughly studied. We have employed basis sets from the Slater-type orbitals fitted with Gaussian functions, Pople�s medium size basis sets to Dunning�s correlation consistent basis sets. With increasing basis size, the repulsion exponent and the equilibrium bond length converge at the 6-31G** basis set and the 6-311++G(2d, 2p) basis set, respectively, while a large basis set (aug-cc-pVTZ) is required to converge the binding energy at a chemical accuracy (˜0.01 kcal/mol). We used the BSSE corrected results that systematically converge to the destined potential curve with increasing basis size. The binding energy calculated and the equilibrium bond length using the CCSD(T) method are close to the results at the basis set limit. For molecular dynamics simulation, a 4-site potential model with sites located at the hydrogen atoms was used to fit the ab initio potential data. This model stems from a hydrogen-hydrogen repulsion mechanism to explain the stability of the dimer structure. MD simulations using the ab initio PES show good agreement on both the atom-wise radial distribution functions and the self-diffusion coefficients over a wide range of experimental conditions.

Energetics and diffusion of liquid water and hydrated ions through nanopores in graphene: ab initio molecular dynamics simulation

2017 ◽  
Vol 19 (31) ◽  
pp. 20551-20558 ◽  
Author(s):  
Raúl Guerrero-Avilés ◽  
Walter Orellana
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Ab Initio Molecular Dynamics ◽  
Functional Theory ◽  
Hydrated Ions ◽  
And Diffusion

The energetics and diffusion of water molecules and hydrated ions (Na+, Cl−) passing through nanopores in graphene are addressed by dispersion-corrected density functional theory calculations and ab initio molecular dynamics (MD) simulations.

scholarly journals THEORETICAL STUDY ON THE REACTION MECHANISM OF CO2 FORMATION FROM ACYLOXY RADICALS

2018 ◽  
Vol 55 (6A) ◽  
pp. 105
Author(s):  
Nguyen Thi Minh Hue
Keyword(s):  
Reaction Mechanism ◽  
Density Functional ◽  
Basis Sets ◽  
Free Energies ◽  
Combustion Chemistry ◽  
Functional Theory ◽  
Mechanism Of Decomposition ◽  
Energy Profiles ◽  
The Density Functional Theory ◽  
Experimental Values

The decomposition mechanism of acyloxy radicals has been studied by the Density Functional Theory (DFT) using B3LYP functional in conjunction with the 6-311++G(d,p) and 6-311++G(3df,2p) basis sets. The potential energy profiles for reaction systems were generally established. Calculated results indicate that the formation of products including hydrocarbon radicals and CO2 molecule is energetically favored. The rate of decomposition increases with the number of carbon in non-cyclic saturated acyloxy radicals. Calculated enthalpies and Gibbs free energies of reactions well agree with experimental values. This study is a contribution to the understanding of the reaction mechanism of decomposition of acyloxy radicals in atmosphere and combustion chemistry. 

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