638 research outputs found
Biomolecular Simulations with the Three-Dimensional Reference Interaction Site Model with the Kovalenko-Hirata Closure Molecular Solvation Theory
No full textThe statistical mechanics-based 3-dimensional reference interaction site model with the Kovalenko-Hirata closure (3D-RISM-KH) molecular solvation theory has proven to be an essential part of a multiscale modeling framework, covering a vast region of molecular simulation techniques. The successful application ranges from the small molecule solvation energy to the bulk phase behavior of polymers, macromolecules, etc. The 3D-RISM-KH successfully predicts and explains the molecular mechanisms of self-assembly and aggregation of proteins and peptides related to neurodegeneration, protein-ligand binding, and structure-function related solvation properties. Upon coupling the 3D-RISM-KH theory with a novel multiple time-step molecular dynamic (MD) of the solute biomolecule stabilized by the optimized isokinetic Nosé–Hoover chain thermostat driven by effective solvation forces obtained from 3D-RISM-KH and extrapolated forward by generalized solvation force extrapolation (GSFE), gigantic outer time-steps up to picoseconds to accurately calculate equilibrium properties were obtained in this new quasidynamics protocol. The multiscale OIN/GSFE/3D-RISM-KH algorithm was implemented in the Amber package and well documented for fully flexible model of alanine dipeptide, miniprotein 1L2Y, and protein G in aqueous solution, with a solvent sampling rate ~150 times faster than a standard MD simulation in explicit water. Further acceleration in computation can be achieved by modifying the extent of solvation layers considered in the calculation, as well as by modifying existing closure relations. This enhanced simulation technique has proven applications in protein-ligand binding energy calculations, ligand/solvent binding site prediction, molecular solvation energy calculations, etc. Applications of the RISM-KH theory in molecular simulation are discussed in this work
Benchmarking Free Energy Calculations in Liquid Aliphatic Ketone Solvents Using the 3D-RISM-KH Molecular Solvation Theory
No full textThe three-dimensional reference interaction site model of the molecular solvation theory with the Kovalenko–Hirata closure is used to calculate the free energy of solvation of organic solutes in liquid aliphatic ketones. The ketone solvent sites were modeled using a modified united-atom force field. The successful application of these solvation models in calculating ketone–water partition coefficients of a large number of solutes supports the validation and benchmarking reported here
Bondar Andriy Danylovych
No full textУ статті відображено життєвий і творчий шлях Андрія Даниловича Бондаря, вченого-дослідника, у полі зору якого були проблеми історії освіти та виховання, дидактики вищої школи. Представлено науковий доробок автора та його вклад у розбудову освіти в Україні за радянських часів.The article deals with the life and creative way of Andriy Danilovich Bondar, a researcher and scientist, who studied issues of the history of education, didactics of higher education. The scientific contributions of the author and his contribution to the development of education in Ukraine during the Soviet times are presented in article
Microscopic Theory of Liquid Interfaces in Molecular Systems
No full textA statistical-mechanical theory of inhomogeneous polyatomic fluids is proposed. It enables microscopic description of liquid interfaces in molecular systems with both non-polar and polar species. The method introduces a site-site generalization of the Lovett-Mow-Buff-Wertheim integro-differential equation for the one-particle density distributions to polyatomic fluids. It uses the inhomogeneous site-site direct correlation functions of molecular fluid consistently constructed by nonlinear interpolation between the homogeneous ones. The site-site correlations of the coexisting bulk phases are obtained from the reference interaction site model (RISM) integral equation with the closure approximation proposed by Kovalenko and Hirata. The theory is applied to the planar liquid-vapor as well as liquid-liquid interfaces of n-hexane and methanol in ambient conditions.Peer reviewed: YesNRC publication: Ye
Understanding the Liquid States of Cyclic Hydrocarbons Containing N, O, and S Atoms via the 3D-RISM-KH Molecular Solvation Theory
No full textThe 3D-reference interaction site model (3D-RISM) molecular solvation theory in combination with the Kovalenko–Hirata (KH) closure is extended to seven heterocyclic liquids to understand their liquid states and to test the performance of the theory in solvation free energy (SFE) calculations of solutes in select solvents. The computed solvent site distribution profiles were compared with the all-atom molecular dynamics (MD) simulations, showing comparable performances. The computational results were compared against the structural parameters for liquids, whenever available, as well as against the experimental SFEs. The liquids are found to have local ordered structures held together via weak interactions in both the RISM and MD simulations. The 3D-RISM-KH computed SFEs are in good agreement with the benchmark values for the tetrahydrothiophene-S,S-dioxide, and showed comparatively larger deviations in the case of the SFEs in the tetrahydrofuran continuum
Predicting 1,9-Decadiene−Water Partition Coefficients Using the 3D-RISM-KH Molecular Solvation Theory
No full textThe Three-Dimensional Reference Interaction Site Model (3D-RISM) with Kovalenko−Hirata (KH) closure is applied to calculate the 1,9-Decadiene/Water partition coefficients for a diverse class of compounds. The liquid state of 1,9-Decadiene is represented with the united atom TraPPE force field parameters. The 3D-RISM-KH computed partition functions are in good agreement with the experimental results. Our computational scheme can be used for a quantitative structure partitioning prediction for decadiene-water system, which has been used in membrane-mimicking of the egg-lecithin/water permeability experiments
Performance of 3D-RISM-KH in Predicting Hydration Free Energy: Effect of Solute Parameters
No full textThe three-dimensional
reference interaction site model molecular
solvation theory with the Kovalenko–Hirata closure relation
has been shown to produce excellent solvation characteristics for
a large class of (bio)chemical systems in solution. Correct calculation
of hydration free energy is central to successful application of any
solvation model. In order to find out the best possible force-field
parameters to be used for hydration free energy calculation with the
aforementioned theory, we have developed an extended database containing
a large number of experimental solvation free energies available in
the current literature and used a plethora of theoretical models for
assessment. The general Amber force field was found to perform satisfactorily,
whereas special care should be taken in solute charge assignment with
the universal force field
Performance of 3D-RISM-KH in Predicting Hydration Free Energy: Effect of Solute Parameters
No full textThe three-dimensional
reference interaction site model molecular
solvation theory with the Kovalenko–Hirata closure relation
has been shown to produce excellent solvation characteristics for
a large class of (bio)chemical systems in solution. Correct calculation
of hydration free energy is central to successful application of any
solvation model. In order to find out the best possible force-field
parameters to be used for hydration free energy calculation with the
aforementioned theory, we have developed an extended database containing
a large number of experimental solvation free energies available in
the current literature and used a plethora of theoretical models for
assessment. The general Amber force field was found to perform satisfactorily,
whereas special care should be taken in solute charge assignment with
the universal force field
Generalised canonical-isokinetic ensemble: speeding up multiscale molecular dynamics and coupling with 3D molecular theory of solvation
No full textWe have proposed a new canonical-isokinetic ensemble for efficient sampling of conformational space in molecular dynamics (MD) simulations which leads to the optimised isokinetic Nos\ue9-Hoover (OIN) chain algorithm for atomic and molecular systems. We applied OIN to multiple time step (MTS) MD simulations of the rigid and flexible models of water to demonstrate its advantage over the standard canonical, isokinetic and canonical-isokinetic ensembles. With the stabilising effect of OIN thermostatting in MTS-MD, gigantic outer time steps up to picoseconds can be employed to accurately calculate equilibrium and conformational properties. Furthermore, we developed the atomic version of OIN for MTS-MD of a biomolecule in a solvent potential of mean force obtained at sequential MD steps by using the molecular theory of solvation, aka three-dimensional reference interaction site model with the Kovalenko-Hirata closure (3D-RISM-KH). The solvation forces are obtained analytically by converging the 3D-RISM-KH integral equations once per several OIN outer time steps, and are calculated in between by using solvation force-coordinate extrapolation (SFCE) in the subspace of previous successive solutions to 3D-RISM-KH. For illustration, we applied the multiscale OIN/SFCE/3D-RISM-KH algorithm to a fully flexible model of alanine dipeptide in aqueous solution. Although the computational rate of solvent sampling in OIN/SFCE/3D-RISM-KH is already 20 times faster than standard MD with explicit solvent, further substantial acceleration of sampling stems from making solute evolution steps in a statistically averaged potential of mean force obtained from 3D-RISM-KH. The latter efficiently samples the phase space for essential events with rare statistics such as exchange and localisation of solvent and ligand molecules in confined spaces, pockets and at binding sites of the solute macromolecule, as distinct from MD with explicit solvent which requires enormous computational time and number of steps in such cases. \ua9 2013 Taylor & Francis Group, LLC.Peer reviewed: YesNRC publication: Ye
MTS-MD of biomolecules steered with 3D-RISM-KH mean solvation forces accelerated with generalized solvation force extrapolation
No full textWe developed a generalized solvation force extrapolation (GSFE) approach to speed up multiple time step molecular dynamics (MTS-MD) of biomolecules steered with mean solvation forces obtained from the 3D-RISM-KH molecular theory of solvation (three-dimensional reference interaction site model with the Kovalenko-Hirata closure). GSFE is based on a set of techniques including the non-Eckart-like transformation of coordinate space separately for each solute atom, extension of the force-coordinate pair basis set followed by selection of the best subset, balancing the normal equations by modified least-squares minimization of deviations, and incremental increase of outer time step in motion integration. Mean solvation forces acting on the biomolecule atoms in conformations at successive inner time steps are extrapolated using a relatively small number of best (closest) solute atomic coordinates and corresponding mean solvation forces obtained at previous outer time steps by converging the 3D-RISM-KH integral equations. The MTS-MD evolution steered with GSFE of 3D-RISM-KH mean solvation forces is efficiently stabilized with our optimized isokinetic Nos\ue9\u2013Hoover chain (OIN) thermostat. We validated the hybrid MTS-MD/OIN/GSFE/3D-RISM-KH integrator on solvated organic and biomolecules of different stiffness and complexity: asphaltene dimer in toluene solvent, hydrated alanine dipeptide, miniprotein 1L2Y, and protein G. The GSFE accuracy and the OIN efficiency allowed us to enlarge outer time steps up to huge values of 1\u20134 ps while accurately reproducing conformational properties. Quasidynamics steered with 3D-RISM-KH mean solvation forces achieves time scale compression of conformational changes coupled with solvent exchange, resulting in further significant acceleration of protein conformational sampling with respect to real time dynamics. Overall, this provided a 50- to 1000-fold effective speedup of conformational sampling for these systems, compared to conventional MD with explicit solvent. We have been able to fold the miniprotein from a fully denatured, extended state in about 60 ns of quasidynamics steered with 3D-RISM-KH mean solvation forces, compared to the average physical folding time of 4\u20139 \u3bcs observed in experiment.Peer reviewed: YesNRC publication: Ye
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