| Year |
Citation |
Score |
| 2022 |
Roy D, Kovalenko A. Understanding the Liquid States of Cyclic Hydrocarbons Containing N, O, and S Atoms via the 3D-RISM-KH Molecular Solvation Theory. Molecules (Basel, Switzerland). 27. PMID 36235097 DOI: 10.3390/molecules27196563 |
0.337 |
|
| 2021 |
Roy D, Kovalenko A. Biomolecular Simulations with the Three-Dimensional Reference Interaction Site Model with the Kovalenko-Hirata Closure Molecular Solvation Theory. International Journal of Molecular Sciences. 22. PMID 34064655 DOI: 10.3390/ijms22105061 |
0.392 |
|
| 2020 |
Kovalenko A, Neburchilov V. Density functional theory and 3D-RISM-KH molecular theory of solvation studies of CO reduction on Cu-, CuO-, Fe-, and FeO-based nanocatalysts. Journal of Molecular Modeling. 26: 267. PMID 32918619 DOI: 10.1007/S00894-020-04529-8 |
0.404 |
|
| 2020 |
Roy D, Kovalenko A. Application of the Approximate 3D-RISM Molecular Solvation Theory to Acetonitrile as Solvent. The Journal of Physical Chemistry. B. PMID 32392049 DOI: 10.1021/Acs.Jpcb.0C03230 |
0.444 |
|
| 2019 |
Omelyan I, Kovalenko A. Enhanced solvation force extrapolation for speeding up molecular dynamics simulations of complex biochemical liquids. The Journal of Chemical Physics. 151: 214102. PMID 31822083 DOI: 10.1063/1.5126410 |
0.37 |
|
| 2019 |
Hinge VK, Roy D, Kovalenko A. Prediction of P-glycoprotein inhibitors with machine learning classification models and 3D-RISM-KH theory based solvation energy descriptors. Journal of Computer-Aided Molecular Design. PMID 31745705 DOI: 10.1007/S10822-019-00253-5 |
0.371 |
|
| 2019 |
Hinge VK, Blinov N, Roy D, Wishart DS, Kovalenko A. The role of hydration effects in 5-fluorouridine binding to SOD1: insight from a new 3D-RISM-KH based protocol for including structural water in docking simulations. Journal of Computer-Aided Molecular Design. PMID 31686367 DOI: 10.1007/S10822-019-00239-3 |
0.364 |
|
| 2019 |
Roy D, Kovalenko A. Application of the 3D-RISM-KH molecular solvation theory for DMSO as solvent. Journal of Computer-Aided Molecular Design. PMID 31637566 DOI: 10.1007/S10822-019-00238-4 |
0.465 |
|
| 2019 |
Nguyen C, Yamazaki T, Kovalenko A, Case DA, Gilson MK, Kurtzman T, Luchko T. A molecular reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site. Plos One. 14: e0219473. PMID 31291328 DOI: 10.1371/Journal.Pone.0219473 |
0.423 |
|
| 2019 |
Hinge VK, Roy D, Kovalenko A. Predicting skin permeability using the 3D-RISM-KH theory based solvation energy descriptors for a diverse class of compounds. Journal of Computer-Aided Molecular Design. PMID 31087228 DOI: 10.1007/S10822-019-00205-Z |
0.377 |
|
| 2019 |
Roy D, Kovalenko A. Performance of 3D-RISM-KH in Predicting Hydration Free Energy: Effect of Solute Parameters. The Journal of Physical Chemistry. A. PMID 30993994 DOI: 10.1021/Acs.Jpca.9B01623 |
0.391 |
|
| 2019 |
Blinov N, Wishart DS, Kovalenko A. Solvent Composition Effects on Structural Properties of the A β42 Monomer From the 3D-RISM-KH Molecular Theory of Solvation. The Journal of Physical Chemistry. B. PMID 30811210 DOI: 10.1021/Acs.Jpcb.9B00480 |
0.374 |
|
| 2018 |
Kovalenko A, Gusarov S. Multiscale methods framework: self-consistent coupling of molecular theory of solvation with quantum chemistry, molecular simulations, and dissipative particle dynamics. Physical Chemistry Chemical Physics : Pccp. 20: 2947-2969. PMID 28967656 DOI: 10.1039/C7Cp05585D |
0.351 |
|
| 2018 |
Lage MR, Dedzo GK, Stoyanov SR, Huang W, Gusarov S, Carneiro JWdM, Detellier C, Kovalenko A. Computational and Experimental Investigations of the Role of Water and Alcohols in the Desorption of Heterocyclic Aromatic Compounds from Kaolinite in Toluene Journal of Physical Chemistry C. 122: 10377-10391. DOI: 10.1021/Acs.Jpcc.7B12655 |
0.365 |
|
| 2017 |
Roy D, Blinov N, Kovalenko A. Predicting Accurate Solvation Free Energy in n-Octanol Using 3D-RISM-KH Molecular Theory of Solvation - Making Right Choices. The Journal of Physical Chemistry. B. PMID 28880087 DOI: 10.1021/Acs.Jpcb.7B06375 |
0.421 |
|
| 2017 |
Hlushak S, Kovalenko A. Effective Interactions and Adsorption of Heterocyclic Aromatic Hydrocarbons in Kaolinite Organic Solutions Studied by 3D-RISM-KH Molecular Theory of Solvation Journal of Physical Chemistry C. 121: 22092-22104. DOI: 10.1021/Acs.Jpcc.7B06414 |
0.376 |
|
| 2016 |
Luchko T, Blinov N, Limon GC, Joyce KP, Kovalenko A. SAMPL5: 3D-RISM partition coefficient calculations with partial molar volume corrections and solute conformational sampling. Journal of Computer-Aided Molecular Design. 30: 1115-1127. PMID 27585474 DOI: 10.1007/S10822-016-9947-7 |
0.397 |
|
| 2016 |
Kobryn AE, Gusarov S, Kovalenko A. A closure relation to molecular theory of solvation for macromolecules. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 28: 404003. PMID 27549008 DOI: 10.1088/0953-8984/28/40/404003 |
0.43 |
|
| 2016 |
Johnson J, Case DA, Yamazaki T, Gusarov S, Kovalenko A, Luchko T. Small molecule hydration energy and entropy from 3D-RISM. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 28: 344002. PMID 27367817 DOI: 10.1088/0953-8984/28/34/344002 |
0.365 |
|
| 2016 |
Silveira RL, Stoyanov SR, Kovalenko A, Skaf MS. Cellulose Aggregation Under Hydrothermal Pretreatment Conditions. Biomacromolecules. PMID 27301535 DOI: 10.1021/Acs.Biomac.6B00603 |
0.358 |
|
| 2016 |
Hlushak S, Stoyanov SR, Kovalenko A. A 3D-RISM-KH Molecular Theory of Solvation Study of the Effective Stacking Interactions of Kaolinite Nanoparticles in Aqueous Electrolyte Solution Containing Additives Journal of Physical Chemistry C. 120: 21357. DOI: 10.1021/Acs.Jpcc.6B03786 |
0.433 |
|
| 2016 |
Holovko M, Kovalenko A, Hirata F. Partial molar volume of nonionic surfactants in aqueous solution studied by the KB/3D-RISM–KH theory Journal of Molecular Liquids. 217: 103-111. DOI: 10.1016/J.Molliq.2016.02.016 |
0.402 |
|
| 2016 |
Kovalenko A. Solvation Structure and Quasidynamics of Biomolecules Steered with Effective Solvation Forces Obtained From Molecular Theory of Solvation Biophysical Journal. 110: 645. DOI: 10.1016/J.Bpj.2015.11.3452 |
0.469 |
|
| 2015 |
Omelyan I, Kovalenko A. MTS-MD of Biomolecules Steered with 3D-RISM-KH Mean Solvation Forces Accelerated with Generalized Solvation Force Extrapolation. Journal of Chemical Theory and Computation. 11: 1875-95. PMID 26574393 DOI: 10.1021/Ct5010438 |
0.378 |
|
| 2015 |
Silveira RL, Stoyanov SR, Gusarov S, Skaf MS, Kovalenko A. Supramolecular Interactions in Secondary Plant Cell Walls: Effect of Lignin Chemical Composition Revealed with the Molecular Theory of Solvation. The Journal of Physical Chemistry Letters. 6: 206-11. PMID 26263115 DOI: 10.1021/Jz502298Q |
0.371 |
|
| 2015 |
Lyubimova O, Stoyanov SR, Gusarov S, Kovalenko A. Electric Interfacial Layer of Modified Cellulose Nanocrystals in Aqueous Electrolyte Solution: Predictions by the Molecular Theory of Solvation. Langmuir : the Acs Journal of Surfaces and Colloids. 31: 7106-16. PMID 26053228 DOI: 10.1021/Acs.Langmuir.5B00680 |
0.357 |
|
| 2015 |
Huang W, Blinov N, Kovalenko A. Octanol-Water Partition Coefficient from 3D-RISM-KH Molecular Theory of Solvation with Partial Molar Volume Correction. The Journal of Physical Chemistry. B. 119: 5588-97. PMID 25844645 DOI: 10.1021/Acs.Jpcb.5B01291 |
0.445 |
|
| 2015 |
Huang W, Blinov N, Wishart DS, Kovalenko A. Role of water in ligand binding to maltose-binding protein: insight from a new docking protocol based on the 3D-RISM-KH molecular theory of solvation. Journal of Chemical Information and Modeling. 55: 317-28. PMID 25545470 DOI: 10.1021/Ci500520Q |
0.322 |
|
| 2015 |
Kondratenko M, Stoyanov SR, Gusarov S, Kovalenko A, McCreery RL. Theoretical modeling of tunneling barriers in carbon-based molecular electronic junctions Journal of Physical Chemistry C. 119: 11286-11295. DOI: 10.1021/Jp5128332 |
0.327 |
|
| 2015 |
Lage MR, Stoyanov SR, Carneiro JWDM, Dabros T, Kovalenko A. Adsorption of bitumen model compounds on kaolinite in liquid and supercritical carbon dioxide solvents: A study by periodic density functional theory and molecular theory of solvation Energy and Fuels. 29: 2853-2863. DOI: 10.1021/Ef502202Q |
0.351 |
|
| 2015 |
Yesudas JP, Blinov N, Dew SK, Kovalenko A. Calculation of binding free energy of short double stranded oligonucleotides using MM/3D-RISM-KH approach Journal of Molecular Liquids. 201: 68-76. DOI: 10.1016/J.Molliq.2014.11.017 |
0.382 |
|
| 2014 |
Kobryn AE, Nikoli? D, Lyubimova O, Gusarov S, Kovalenko A. Dissipative particle dynamics with an effective pair potential from integral equation theory of molecular liquids. The Journal of Physical Chemistry. B. 118: 12034-49. PMID 25162701 DOI: 10.1021/Jp503981P |
0.4 |
|
| 2014 |
Moreira da Costa L, Stoyanov SR, Gusarov S, Seidl PR, Walkimar de M Carneiro J, Kovalenko A. Computational study of the effect of dispersion interactions on the thermochemistry of aggregation of fused polycyclic aromatic hydrocarbons as model asphaltene compounds in solution. The Journal of Physical Chemistry. A. 118: 896-908. PMID 24432843 DOI: 10.1021/Jp408005H |
0.337 |
|
| 2014 |
Huang W, Dedzo GK, Stoyanov SR, Lyubimova O, Gusarov S, Singh S, Lao H, Kovalenko A, Detellier C. Molecule–Surface Recognition between Heterocyclic Aromatic Compounds and Kaolinite in Toluene Investigated by Molecular Theory of Solvation and Thermodynamic and Kinetic Experiments Journal of Physical Chemistry C. 118: 23821-23834. DOI: 10.1021/Jp507393U |
0.425 |
|
| 2014 |
Blinov N, Huang W, Nikolic D, Wishart DS, Kovalenko A. Biomolecular Recognition Based on 3D Molecular Theory of Solvation Biophysical Journal. 106: 411a. DOI: 10.1016/J.Bpj.2013.11.2312 |
0.428 |
|
| 2013 |
Omelyan I, Kovalenko A. Multiple time step molecular dynamics in the optimized isokinetic ensemble steered with the molecular theory of solvation: accelerating with advanced extrapolation of effective solvation forces. The Journal of Chemical Physics. 139: 244106. PMID 24387356 DOI: 10.1063/1.4848716 |
0.378 |
|
| 2013 |
Pagadala NS, Bjorndahl TC, Blinov N, Kovalenko A, Wishart DS. Molecular docking of thiamine reveals similarity in binding properties between the prion protein and other thiamine-binding proteins. Journal of Molecular Modeling. 19: 5225-35. PMID 24126825 DOI: 10.1007/S00894-013-1979-5 |
0.318 |
|
| 2013 |
Nikoli? D, Moffat KA, Farrugia VM, Kobryn AE, Gusarov S, Wosnick JH, Kovalenko A. Multi-scale modeling and synthesis of polyester ionomers. Physical Chemistry Chemical Physics : Pccp. 15: 6128-38. PMID 23507929 DOI: 10.1039/C3Cp44285C |
0.328 |
|
| 2013 |
Kovalenko A. Multiscale modeling of solvation in chemical and biological nanosystems and in nanoporous materials Pure and Applied Chemistry. 85: 159-199. DOI: 10.1351/Pac-Con-12-06-03 |
0.462 |
|
| 2013 |
Fafard J, Lyubimova O, Stoyanov SR, Dedzo GK, Gusarov S, Kovalenko A, Detellier C. Adsorption of indole on kaolinite in nonaqueous media: Organoclay preparation and characterization, and 3D-RISM-KH molecular theory of solvation investigation Journal of Physical Chemistry C. 117: 18556-18566. DOI: 10.1021/Jp4064142 |
0.376 |
|
| 2012 |
Nikolić D, Blinov N, Wishart D, Kovalenko A. 3D-RISM-Dock: A New Fragment-Based Drug Design Protocol. Journal of Chemical Theory and Computation. 8: 3356-72. PMID 26605742 DOI: 10.1021/Ct300257V |
0.42 |
|
| 2012 |
Omelyan IP, Kovalenko A. Overcoming the Barrier on Time Step Size in Multiscale Molecular Dynamics Simulation of Molecular Liquids. Journal of Chemical Theory and Computation. 8: 6-16. PMID 26592867 DOI: 10.1021/Ct200157X |
0.346 |
|
| 2012 |
Gusarov S, Pujari BS, Kovalenko A. Efficient treatment of solvation shells in 3D molecular theory of solvation. Journal of Computational Chemistry. 33: 1478-94. PMID 22522583 DOI: 10.1002/Jcc.22974 |
0.398 |
|
| 2012 |
Omelyan I, Kovalenko A. Interpretation of atomic motion in flexible molecules: accelerating molecular dynamics simulations. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 85: 026706. PMID 22463356 DOI: 10.1103/Physreve.85.026706 |
0.341 |
|
| 2012 |
da Costa LM, Hayaki S, Stoyanov SR, Gusarov S, Tan X, Gray MR, Stryker JM, Tykwinski R, Carneiro JW, Sato H, Seidl PR, Kovalenko A. 3D-RISM-KH molecular theory of solvation and density functional theory investigation of the role of water in the aggregation of model asphaltenes. Physical Chemistry Chemical Physics : Pccp. 14: 3922-34. PMID 22322391 DOI: 10.1039/C2Cp23131J |
0.425 |
|
| 2012 |
Kovalenko A, Kobryn AE, Gusarov S, Lyubimova O, Liu X, Blinov N, Yoshida M. Molecular theory of solvation for supramolecules and soft matter structures: application to ligand binding, ion channels, and oligomeric polyelectrolyte gelators Soft Matter. 8: 1508-1520. DOI: 10.1039/C1Sm06542D |
0.444 |
|
| 2012 |
Da Costa LM, Stoyanov SR, Gusarov S, Tan X, Gray MR, Stryker JM, Tykwinski R, De M. Carneiro JW, Seidl PR, Kovalenko A. Density functional theory investigation of the contributions of π-π Stacking and hydrogen-bonding interactions to the aggregation of model asphaltene compounds Energy and Fuels. 26: 2727-2735. DOI: 10.1021/Ef202010P |
0.343 |
|
| 2011 |
Omelyan IP, Kovalenko A. Multiple time scale molecular dynamics for fluids with orientational degrees of freedom. II. Canonical and isokinetic ensembles. The Journal of Chemical Physics. 135: 234107. PMID 22191864 DOI: 10.1063/1.3669385 |
0.323 |
|
| 2011 |
Omelyan IP, Kovalenko A. Multiple time scale molecular dynamics for fluids with orientational degrees of freedom. I. Microcanonical ensemble. The Journal of Chemical Physics. 135: 114110. PMID 21950853 DOI: 10.1063/1.3637035 |
0.333 |
|
| 2011 |
Imai T, Miyashita N, Sugita Y, Kovalenko A, Hirata F, Kidera A. Functionality mapping on internal surfaces of multidrug transporter AcrB based on molecular theory of solvation: implications for drug efflux pathway. The Journal of Physical Chemistry. B. 115: 8288-95. PMID 21526784 DOI: 10.1021/Jp2015758 |
0.329 |
|
| 2011 |
Stumpe MC, Blinov N, Wishart D, Kovalenko A, Pande VS. Calculation of local water densities in biological systems: a comparison of molecular dynamics simulations and the 3D-RISM-KH molecular theory of solvation. The Journal of Physical Chemistry. B. 115: 319-28. PMID 21174421 DOI: 10.1021/Jp102587Q |
0.429 |
|
| 2011 |
Yamazaki T, Kovalenko A. Spatial decomposition of solvation free energy based on the 3D integral equation theory of molecular liquid: application to miniproteins. The Journal of Physical Chemistry. B. 115: 310-8. PMID 21166382 DOI: 10.1021/Jp1082938 |
0.423 |
|
| 2011 |
Borzsonyi G, Beingessner RL, Yamazaki T, Cho JY, Myles AJ, Kovalenko A, Fenniri H. Self-assembly of a water-soluble tricyclic heterocycle into J-type Rosette Nanotubes Materials Research Society Symposium Proceedings. 1312: 485-490. DOI: 10.1557/Opl.2011.135 |
0.302 |
|
| 2011 |
Blinov N, Dorosh L, Wishart D, Kovalenko A. 3D-RISM-KH approach for biomolecular modelling at nanoscale: thermodynamics of fibril formation and beyond Molecular Simulation. 37: 718-728. DOI: 10.1080/08927022.2010.544306 |
0.405 |
|
| 2011 |
Kobryn AE, Kovalenko A. Slip boundary conditions in nanofluidics from the molecular theory of solvation Molecular Simulation. 37: 733-737. DOI: 10.1080/08927022.2010.538055 |
0.379 |
|
| 2011 |
Kovalenko A, Blinov N. Multiscale methods for nanochemistry and biophysics in solution Journal of Molecular Liquids. 164: 101-112. DOI: 10.1016/J.Molliq.2011.09.011 |
0.422 |
|
| 2010 |
Genheden S, Luchko T, Gusarov S, Kovalenko A, Ryde U. An MM/3D-RISM approach for ligand binding affinities. The Journal of Physical Chemistry. B. 114: 8505-16. PMID 20524650 DOI: 10.1021/Jp101461S |
0.425 |
|
| 2010 |
Luchko T, Gusarov S, Roe DR, Simmerling C, Case DA, Tuszynski J, Kovalenko A. Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber. Journal of Chemical Theory and Computation. 6: 607-624. PMID 20440377 DOI: 10.1021/Ct900460M |
0.421 |
|
| 2010 |
Kaminski JW, Gusarov S, Wesolowski TA, Kovalenko A. Modeling solvatochromic shifts using the orbital-free embedding potential at statistically mechanically averaged solvent density. The Journal of Physical Chemistry. A. 114: 6082-96. PMID 20420454 DOI: 10.1021/Jp100158H |
0.427 |
|
| 2010 |
Blinov N, Dorosh L, Wishart D, Kovalenko A. Association thermodynamics and conformational stability of beta-sheet amyloid beta(17-42) oligomers: effects of E22Q (Dutch) mutation and charge neutralization. Biophysical Journal. 98: 282-96. PMID 20338850 DOI: 10.1016/J.Bpj.2009.09.062 |
0.339 |
|
| 2010 |
Stoyanov SR, Yin CX, Gray MR, Stryker JM, Gusarov S, Kovalenko A. Computational and experimental study of the structure, binding preferences, and spectroscopy of nickel(II) and vanadyl porphyrins in petroleum. The Journal of Physical Chemistry. B. 114: 2180-8. PMID 20099931 DOI: 10.1021/Jp908641T |
0.339 |
|
| 2010 |
Yamazaki T, Fenniri H, Kovalenko A. Structural water drives self-assembly of organic rosette nanotubes and holds host atoms in the channel. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 11: 361-7. PMID 20017180 DOI: 10.1002/Cphc.200900324 |
0.355 |
|
| 2010 |
Yamazaki T, Kovalenko A, Murashov VV, Patey GN. Ion solvation in a water-urea mixture. The Journal of Physical Chemistry. B. 114: 613-9. PMID 19947642 DOI: 10.1021/Jp908814T |
0.385 |
|
| 2010 |
Santo KP, Kovalenko A, Stepanova M. Macromol. Theory Simul. 5/2010 Macromolecular Theory and Simulations. 19. DOI: 10.1002/Mats.201090007 |
0.727 |
|
| 2010 |
Santo KP, Kovalenko A, Stepanova M. Self-Consistent Field Modeling of Three-Dimensional Morphologies of Branched Lipid Surfactant at Air-Water Interface Macromolecular Theory and Simulations. 19: 228-239. DOI: 10.1002/Mats.200900076 |
0.724 |
|
| 2009 |
Yamazaki T, Kovalenko A. Spatial Decomposition Analysis of the Thermodynamics of Cyclodextrin Complexation. Journal of Chemical Theory and Computation. 5: 1723-30. PMID 26609997 DOI: 10.1021/Ct9000729 |
0.341 |
|
| 2009 |
Imai T, Kovalenko A, Hirata F, Kidera A. Molecular thermodynamics of trifluoroethanol-induced helix formation: analysis of the solvation structure and free energy by the 3D-RISM theory. Interdisciplinary Sciences, Computational Life Sciences. 1: 156-60. PMID 20640830 DOI: 10.1007/S12539-009-0037-6 |
0.417 |
|
| 2009 |
Yamazaki T, Blinov N, Wishart D, Kovalenko A. Essential role of hydration in aggregation of misfolded prion proteins: quantification by molecular theory of solvation. Journal of Toxicology and Environmental Health. Part A. 72: 1060-8. PMID 19697240 DOI: 10.1080/15287390903084462 |
0.37 |
|
| 2009 |
Imai T, Oda K, Kovalenko A, Hirata F, Kidera A. Ligand mapping on protein surfaces by the 3D-RISM theory: toward computational fragment-based drug design. Journal of the American Chemical Society. 131: 12430-40. PMID 19655800 DOI: 10.1021/Ja905029T |
0.33 |
|
| 2009 |
Danumah C, Beingessner RL, Haque A, Ban F, Richards JP, Kovalenko A, Fenniri H. Synthesis, properties, and mechanistic insight into the self-assembly of a lamellar fibrous superstructure from a synthetically simple discotic molecule. Langmuir : the Acs Journal of Surfaces and Colloids. 25: 11857-61. PMID 19555114 DOI: 10.1021/La901511V |
0.303 |
|
| 2009 |
Li Q, Gusarov S, Evoy S, Kovalenko A. Electronic structure, binding energy, and solvation structure of the streptavidin-biotin supramolecular complex: ONIOM and 3D-RISM study. The Journal of Physical Chemistry. B. 113: 9958-67. PMID 19545155 DOI: 10.1021/Jp902668C |
0.407 |
|
| 2009 |
Malvaldi M, Bruzzone S, Chiappe C, Gusarov S, Kovalenko A. Ab initio study of ionic liquids by KS-DFT/3D-RISM-KH theory. The Journal of Physical Chemistry. B. 113: 3536-42. PMID 19278268 DOI: 10.1021/Jp810887Z |
0.408 |
|
| 2009 |
Yoshida N, Imai T, Phongphanphanee S, Kovalenko A, Hirata F. Molecular recognition in biomolecules studied by statistical-mechanical integral-equation theory of liquids. The Journal of Physical Chemistry. B. 113: 873-86. PMID 19105732 DOI: 10.1021/Jp807068K |
0.429 |
|
| 2009 |
Kobryn AE, Ichiki K, Kovalenko A. Thermodynamic dependences of slip length for nanofluidic flows over crystalline surfaces: Predictions of molecular theory of solvation International Journal of Quantum Chemistry. 109: 1666-1671. DOI: 10.1002/Qua.22160 |
0.406 |
|
| 2008 |
Kobryn AE, Kovalenko A. Molecular theory of hydrodynamic boundary conditions in nanofluidics. The Journal of Chemical Physics. 129: 134701. PMID 19045110 DOI: 10.1063/1.2972978 |
0.357 |
|
| 2008 |
Yamazaki T, Blinov N, Wishart D, Kovalenko A. Hydration effects on the HET-s prion and amyloid-beta fibrillous aggregates, studied with three-dimensional molecular theory of solvation. Biophysical Journal. 95: 4540-8. PMID 18689456 DOI: 10.1529/Biophysj.107.123000 |
0.366 |
|
| 2008 |
Imai T, Kovalenko A, Hirata F, Kidera A. 1P-039 Theoretical identification of binding sites for benzene in T4 lysozyme mutants based on the 3D-RISM theory(The 46th Annual Meeting of the Biophysical Society of Japan) Seibutsu Butsuri. 48. DOI: 10.2142/Biophys.48.S26_6 |
0.331 |
|
| 2008 |
Stoyanov SR, Gusarov S, Kovalenko A. Multiscale modelling of asphaltene disaggregation Molecular Simulation. 34: 953-960. DOI: 10.1080/08927020802411711 |
0.469 |
|
| 2008 |
Stoyanov SR, Gusarov S, Kuznicki SM, Kovalenko A. Theoretical Modeling of Zeolite Nanoparticle Surface Acidity for Heavy Oil Upgrading The Journal of Physical Chemistry C. 112: 6794-6810. DOI: 10.1021/Jp075688H |
0.309 |
|
| 2007 |
Casanova D, Gusarov S, Kovalenko A, Ziegler T. Evaluation of the SCF Combination of KS-DFT and 3D-RISM-KH; Solvation Effect on Conformational Equilibria, Tautomerization Energies, and Activation Barriers. Journal of Chemical Theory and Computation. 3: 458-76. PMID 26637028 DOI: 10.1021/Ct6001785 |
0.405 |
|
| 2007 |
Imai T, Ohyama S, Kovalenko A, Hirata F. Theoretical study of the partial molar volume change associated with the pressure-induced structural transition of ubiquitin. Protein Science : a Publication of the Protein Society. 16: 1927-33. PMID 17660257 DOI: 10.1110/Ps.072909007 |
0.37 |
|
| 2007 |
Imai T, Harano Y, Kinoshita M, Kovalenko A, Hirata F. Theoretical analysis on changes in thermodynamic quantities upon protein folding: essential role of hydration. The Journal of Chemical Physics. 126: 225102. PMID 17581082 DOI: 10.1063/1.2743962 |
0.353 |
|
| 2007 |
Johnson RS, Yamazaki T, Kovalenko A, Fenniri H. Molecular basis for water-promoted supramolecular chirality inversion in helical rosette nanotubes. Journal of the American Chemical Society. 129: 5735-43. PMID 17417852 DOI: 10.1021/Ja0706192 |
0.306 |
|
| 2007 |
Imai T, Hiraoka R, Kovalenko A, Hirata F. Locating missing water molecules in protein cavities by the three-dimensional reference interaction site model theory of molecular solvation. Proteins. 66: 804-13. PMID 17186526 DOI: 10.1002/Prot.21311 |
0.44 |
|
| 2007 |
Drabik P, Gusarov S, Kovalenko A. Microtubule stability studied by three-dimensional molecular theory of solvation. Biophysical Journal. 92: 394-403. PMID 17056728 DOI: 10.1529/Biophysj.106.089987 |
0.42 |
|
| 2007 |
Hiraoka R, Imai T, Kovalenko A, Hirata F. 1P051 Molecular mechanism of the dissociation of carbon monoxide and oxygen from myoglobin studied by the 3D-RISM theory(Proteins-functions,Poster Presentations) Seibutsu Butsuri. 47. DOI: 10.2142/Biophys.47.S36_2 |
0.348 |
|
| 2007 |
Gusarov S, Fedorova TA, Dmitriev YY, Kovalenko A. On variational estimates for exchange‐correlation interaction obtained within super‐CI approach to MCSCF approximation International Journal of Quantum Chemistry. 109: 1672-1675. DOI: 10.1002/Qua.22007 |
0.302 |
|
| 2006 |
Imai T, Harano Y, Kinoshita M, Kovalenko A, Hirata F. A theoretical analysis on hydration thermodynamics of proteins. The Journal of Chemical Physics. 125: 24911. PMID 16848615 DOI: 10.1063/1.2213980 |
0.374 |
|
| 2006 |
Gusarov S, Ziegler T, Kovalenko A. Self-consistent combination of the three-dimensional RISM theory of molecular solvation with analytical gradients and the Amsterdam density functional package. The Journal of Physical Chemistry. A. 110: 6083-90. PMID 16671679 DOI: 10.1021/Jp054344T |
0.446 |
|
| 2006 |
Hiraoka R, Imai T, Kovalenko A, Seto T, Hirata F. 2P415 Probing for hydrophobic molecules in cavities and clefts of a protein by the 3D-RISM theory(46. Water and bio-molecule,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006) Seibutsu Butsuri. 46. DOI: 10.2142/Biophys.46.S399_3 |
0.375 |
|
| 2006 |
Johnson RS, Yamazaki T, Kovalenko A, Fenniri H. Solvent-controlled helicity in self-assembling rosette nanotubes Materials Research Society Symposium Proceedings. 922: 25-28. DOI: 10.1557/Proc-0922-U04-03 |
0.316 |
|
| 2006 |
Imai T, Kovalenko A, Hirata F. Hydration structure, thermodynamics, and functions of protein studied by the 3D-RISM theory Molecular Simulation. 32: 817-824. DOI: 10.1080/08927020600779376 |
0.44 |
|
| 2005 |
Kovalenko A, Hirata F. A molecular theory of liquid interfaces. Physical Chemistry Chemical Physics : Pccp. 7: 1785-93. PMID 19787939 DOI: 10.1039/B416615A |
0.345 |
|
| 2005 |
Livadaru L, Kovalenko A. Self-consistent molecular theory of polymers in melts and solutions. The Journal of Physical Chemistry. B. 109: 10631-9. PMID 16852290 DOI: 10.1021/Jp044654W |
0.371 |
|
| 2005 |
Imai T, Kovalenko A, Hirata F. Partial molar volume of proteins studied by the three-dimensional reference interaction site model theory. The Journal of Physical Chemistry. B. 109: 6658-65. PMID 16851748 DOI: 10.1021/Jp045667C |
0.393 |
|
| 2005 |
Omelyan I, Hirata F, Kovalenko A. Criticality of a liquid-vapor interface from an inhomogeneous integral equation theory. Physical Chemistry Chemical Physics : Pccp. 7: 4132-7. PMID 16474878 DOI: 10.1039/B507761C |
0.374 |
|
| 2005 |
Imai T, Takekiyo T, Kovalenko A, Hirata F, Kato M, Taniguchi Y. Theoretical study of volume changes associated with the helix-coil transition of an alanine-rich peptide in aqueous solution. Biopolymers. 79: 97-105. PMID 16001396 DOI: 10.1002/Bip.20337 |
0.348 |
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| 2004 |
Livadaru L, Kovalenko A. Molecular description of the collapse of hydrophobic polymer chains in water. The Journal of Chemical Physics. 121: 4449-52. PMID 15332873 DOI: 10.1063/1.1789916 |
0.314 |
|
| 2004 |
Imai T, Kovalenko A, Hirata F. 3P080 Hydration thermodynamics of protein studied by the 3D-RISM theory Seibutsu Butsuri. 44. DOI: 10.2142/Biophys.44.S209_4 |
0.376 |
|
| 2004 |
Omelyan I, Kovalenko A, Hirata F. Microscopic description of a liquid–vapor interface by an inhomogeneous integral equation theory Chemical Physics Letters. 397: 368-373. DOI: 10.1016/J.Cplett.2004.08.114 |
0.331 |
|
| 2004 |
Imai T, Kovalenko A, Hirata F. Solvation thermodynamics of protein studied by the 3D-RISM theory Chemical Physics Letters. 395: 1-6. DOI: 10.1016/J.Cplett.2004.06.140 |
0.441 |
|
| 2003 |
Omelyan I, Kovalenko A, Hirata F. Compressibility of tert-Butyl Alcohol-Water Mixtures: The Rism Theory Journal of Theoretical and Computational Chemistry. 2: 193-203. DOI: 10.1142/S0219633603000501 |
0.335 |
|
| 2002 |
Kovalenko A, Hirata F. Towards A Molecular Theory For The Van Der Waals–Maxwell Description Of Fluid Phase Transitions Journal of Theoretical and Computational Chemistry. 1: 381-406. DOI: 10.1142/S0219633602000282 |
0.392 |
|
| 2002 |
Yoshida K, Yamaguchi T, Kovalenko A, Hirata F. Structure of tert-Butyl Alcohol−Water Mixtures Studied by the RISM Theory Journal of Physical Chemistry B. 106: 5042-5049. DOI: 10.1021/Jp013400X |
0.416 |
|
| 2001 |
Imai T, Harano Y, Kovalenko A, Hirata F. Theoretical study for volume changes associated with the helix-coil transition of peptides. Biopolymers. 59: 512-519. PMID 11745117 DOI: 10.1002/1097-0282(200112)59:7<512::Aid-Bip1056>3.0.Co;2-C |
0.312 |
|
| 2001 |
Hirata F, Kovalenko A. Description of a polar molecular liquid in a disordered microporous material with activating chemical groups by a replica RISM theory Condensed Matter Physics. 4: 643. DOI: 10.5488/Cmp.4.4.643 |
0.32 |
|
| 2001 |
Kovalenko A, Hirata F. A replica reference interaction site model theory for a polar molecular liquid sorbed in a disordered microporous material with polar chemical groups Journal of Chemical Physics. 115: 8620-8633. DOI: 10.1063/1.1409954 |
0.376 |
|
| 2001 |
Harano Y, Imai T, Kovalenko A, Kinoshita M, Hirata F. Theoretical study for partial molar volume of amino acids and polypeptides by the three-dimensional reference interaction site model Journal of Chemical Physics. 114: 9506-9511. DOI: 10.1063/1.1369138 |
0.387 |
|
| 2001 |
Kovalenko A, Hirata F. Self-consistent, Kohn-Sham DFT and three-dimensional RISM description of a metal-molecular liquid interface Journal of Molecular Liquids. 90: 215-224. DOI: 10.1016/S0167-7322(01)00124-6 |
0.407 |
|
| 2001 |
Kovalenko A, Hirata F. First-principles realization of a van der Waals–Maxwell theory for water Chemical Physics Letters. 349: 496-502. DOI: 10.1016/S0009-2614(01)01241-6 |
0.445 |
|
| 2001 |
Kinoshita M, Imai T, Kovalenko A, Hirata F. Improvement of the reference interaction site model theory for calculating the partial molar volume of amino acids and polypeptides Chemical Physics Letters. 348: 337-342. DOI: 10.1016/S0009-2614(01)01129-0 |
0.377 |
|
| 2000 |
Kovalenko A, Hirata F. Potentials of mean force of simple ions in ambient aqueous solution. II. Solvation structure from the three-dimensional reference interaction site model approach, and comparison with simulations Journal of Chemical Physics. 112: 10403-10417. DOI: 10.1063/1.481677 |
0.429 |
|
| 2000 |
Kovalenko A, Hirata F. Potentials of mean force of simple ions in ambient aqueous solution. I. Three-dimensional reference interaction site model approach Journal of Chemical Physics. 112: 10391-10402. DOI: 10.1063/1.481676 |
0.383 |
|
| 2000 |
Sato H, Kovalenko A, Hirata F. Self-consistent field, ab initio molecular orbital and three-dimensional reference interaction site model study for solvation effect on carbon monoxide in aqueous solution Journal of Chemical Physics. 112: 9463-9468. DOI: 10.1063/1.481564 |
0.419 |
|
| 2000 |
Kovalenko A, Hirata F, Kinoshita M. Hydration structure and stability of Met-enkephalin studied by a three-dimensional reference interaction site model with a repulsive bridge correction and a thermodynamic perturbation method Journal of Chemical Physics. 113: 9830-9836. DOI: 10.1063/1.1321039 |
0.48 |
|
| 2000 |
Kovalenko A, Truong TN. Thermochemistry of solvation: A self-consistent three-dimensional reference interaction site model approach The Journal of Chemical Physics. 113: 7458-7470. DOI: 10.1063/1.1313388 |
0.458 |
|
| 2000 |
Kovalenko A, Hirata F. Hydration free energy of hydrophobic solutes studied by a reference interaction site model with a repulsive bridge correction and a thermodynamic perturbation method Journal of Chemical Physics. 113: 2793-2805. DOI: 10.1063/1.1305885 |
0.444 |
|
| 2000 |
Shapovalov V, Truong TN, Kovalenko A, Hirata F. Liquid structure at metal oxide–water interface: accuracy of a three-dimensional RISM methodology Chemical Physics Letters. 320: 186-193. DOI: 10.1016/S0009-2614(00)00191-3 |
0.42 |
|
| 1999 |
Kovalenko A, Hirata F. Self-consistent description of a metal–water interface by the Kohn–Sham density functional theory and the three-dimensional reference interaction site model Journal of Chemical Physics. 110: 10095-10112. DOI: 10.1063/1.478883 |
0.446 |
|
| 1999 |
Kovalenko A, Ten-no S, Hirata F. Solution of three-dimensional reference interaction site model and hypernetted chain equations for simple point charge water by modified method of direct inversion in iterative subspace Journal of Computational Chemistry. 20: 928-936. DOI: 10.1002/(Sici)1096-987X(19990715)20:9<928::Aid-Jcc4>3.0.Co;2-X |
0.392 |
|
| 1998 |
Kovalenko A, Pizio O. The structure and adsorption of the four bonding sites model for associating fluids in disordered porous media from replica Ornstein–Zernike integral equation theory Journal of Chemical Physics. 108: 8651-8661. DOI: 10.1063/1.476295 |
0.351 |
|
| 1998 |
Kovalenko A, Hirata F. Three-dimensional density profiles of water in contact with a solute of arbitrary shape: a RISM approach Chemical Physics Letters. 290: 237-244. DOI: 10.1016/S0009-2614(98)00471-0 |
0.381 |
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