A. Nemukhin

发表

Photoinduced Chemistry in Fluorescent Proteins: Curse or Blessing?

Konstantin A Lukyanov, Anna I Krylov, Alexander V Nemukhin, 2017, Chemical reviews.

Triple-Decker Motif for Red-Shifted Fluorescent Protein Mutants.

Anna I Krylov, Alexander V Nemukhin, I. Polyakov, 2013, The journal of physical chemistry letters.

FLIM-FRET Imaging of Caspase-3 Activity in Live Cells Using Pair of Red Fluorescent Proteins

Alexander P. Savitsky, Maria G. Khrenova, Alexander V. Nemukhin, 2012, Theranostics.

Quantum chemistry behind bioimaging: insights from ab initio studies of fluorescent proteins and their chromophores.

Anna I Krylov, Alexander V Nemukhin, A. Krylov, 2012, Accounts of chemical research.

Modeling of biomolecular systems with the quantum mechanical and molecular mechanical method based on the effective fragment potential technique: Proposal of flexible fragments

B. Grigorenko, A. Nemukhin, I. Topol, 2002 .

On the Origin of Potential Barrier for the Reaction OH- + CO2 → HCO3- in Water: Studies by Using Continuum and Cluster Solvation Methods

B. Grigorenko, A. Nemukhin, I. Topol, 2002 .

Effect of protein environment on electronically excited and ionized states of the green fluorescent protein chromophore.

A. Krylov, B. Grigorenko, K. Bravaya, 2011, The journal of physical chemistry. B.

Rigid-Body Molecular Dynamics of Fullerene-Based Nanocars on Metallic Surfaces.

A. Kolomeisky, A. Akimov, A. Nemukhin, 2010, Journal of chemical theory and computation.

The photoreaction mechanism in the bacterial blue light receptor BLUF according to metadynamics modeling

A. Nemukhin, M. Khrenova, V. Mironov, 2014, Moscow University Chemistry Bulletin.

Improving the Design of the Triple-Decker Motif in Red Fluorescent Proteins.

I. Polyakov, A. Krylov, B. Grigorenko, 2017, The journal of physical chemistry. B.

On photoabsorption of the neutral form of the green fluorescent protein chromophore.

I. Polyakov, J. Collins, B. Grigorenko, 2009, Biophysical chemistry.

Dynamical properties of enzyme-substrate complexes disclose substrate specificity of the SARS-CoV-2 main protease as characterized by the electron density descriptors.

V. Tsirelson, A. Nemukhin, M. Khrenova, 2020, Physical chemistry chemical physics : PCCP.

Natural bond orbitals in multiconfigurational expansions: Local treatment of electron correlation in molecules

F. Weinhold, A. Nemukhin, 1992 .

CAS SCF calculations of potential enregy curves for the BO− ion

J. Almlöf, A. Nemukhin, A. Heiberg, 1982 .

Modeling reactivation of the phosphorylated human butyrylcholinesterase by QM(DFTB)/MM calculations

B. Grigorenko, A. Nemukhin, A. Kulakova, 2015 .

Cryosynthesis and properties of metal-organic nanomaterials

G. Sergeev, A. Nemukhin, V. V. Zagorskii, 1999 .

Many‐body potentials and dynamics based on diatomics‐in‐molecules: Vibrational frequency shifts in ArnHF (n=1–12,62) clusters

V. A. Apkarian, B. Grigorenko, A. Nemukhin, 1996 .

Computational Challenges in Modeling of Representative Bioimaging Proteins: GFP-Like Proteins, Flavoproteins, and Phytochromes.

A. Krylov, B. Grigorenko, A. Nemukhin, 2019, The journal of physical chemistry. B.

Potential Energy Landscape of the Electronic States of the GFP Chromophore in Different Protonation Forms: Electronic Transition Energies and Conical Intersections.

I. Polyakov, A. Krylov, B. Grigorenko, 2010, Journal of chemical theory and computation.

Toward Molecular-Level Characterization of Photoinduced Decarboxylation of the Green Fluorescent Protein: Accessibility of the Charge-Transfer States.

I. Polyakov, A. Krylov, B. Grigorenko, 2012, Journal of chemical theory and computation.

trans and cis Chromophore structures in the kindling fluorescent protein asFP595

B. Grigorenko, A. Nemukhin, A. Savitsky, 2006 .

Gas phase absorption studies of photoactive yellow protein chromophore derivatives.

O. Christiansen, K. Bravaya, A. Nemukhin, 2009, The journal of physical chemistry. A.

Quantum chemical modelling of reactivity and selectivity of 1, 2-dithiolanes towards retroviral and cellular zinc fingers

A. Nemukhin, I. Topol, S. Burt, 2002 .

Modeling Structures and Spectra of Fluorescent Proteins in the Coordinate-Locking Cluster Approach: Application to the Photoswitchable Protein AsFP595

J. Collins, A. Nemukhin, I. Topol, 2012 .

Understanding the non-catalytic behavior of human butyrylcholinesterase silent variants: Comparison of wild-type enzyme, catalytically active Ala328Cys mutant, and silent Ala328Asp variant.

P. Masson, A. Nemukhin, S. Varfolomeev, 2016, Chemico-biological interactions.

Modeling the Interplay of Poor Inhibitor Binding and Efficient Formation of a Covalent Adduct upon the Interaction of ARS Compounds with KRASᴳ¹²ᶜ

A. Nemukhin, M. Khrenova, A. M. Kulakova, 2019 .

Quantum mechanical/molecular mechanical analysis of mechanisms of enzyme action. Human acetylcholinesterase

B. Grigorenko, A. Nemukhin, S. Varfolomeev, 2011 .

Role of Protein Dimeric Interface in Allosteric Inhibition of N-Acetyl-Aspartate Hydrolysis by Human Aspartoacylase.

A. Nemukhin, S. Varfolomeev, S. Lushchekina, 2017, Journal of chemical information and modeling.

Molecular Mechanism of Light-Induced Acceleration of the Adenosine Triphosphate Conversion to the Cyclic Adenosine Monophosphate Catalyzed by the Photoactivated Adenylyl Cyclase bPAC

A. Nemukhin, M. Khrenova, A. M. Kulakova, 2020 .

Interactions of Azodicarbonamide (ADA) Species with the Model Zinc Finger Site: Theoretical Support of the Zinc Finger Domain Destruction in the HIV-1 Nucleocapsid Protein (NCp7) by ADA

A. Nemukhin, I. Topol, S. Burt, 2001 .

Quantum Chemical Studies of Reactions of the Cyclic Disulfides with the Zinc Finger Domains in the HIV-1 Nucleocapsid Protein (NCp7)

A. Nemukhin, I. Topol, S. Burt, 2000 .

Hydrogen bonding at the diatomics-in-molecules level: Water clusters

B. Grigorenko, A. Nemukhin, I. Topol, 2000 .

On the Mechanism of Carborane Diffusion on a Hydrated Silica Surface

A. Kolomeisky, A. Nemukhin, I. Kupchenko, 2011 .

Simulated 18O kinetic isotope effects in enzymatic hydrolysis of guanosine triphosphate

B. Grigorenko, A. Nemukhin, X. Du, 2009, Biochemistry (Moscow).

Modeling Spectral Tuning in Red Fluorescent Proteins Using the Dipole Moment Variation upon Excitation

A. Nemukhin, M. Khrenova, F. Mulashkin, 2021, J. Chem. Inf. Model..

Modeling the Complete Catalytic Cycle of Aspartoacylase.

B. Grigorenko, A. Nemukhin, M. Khrenova, 2016, The journal of physical chemistry. B.

Quantum chemical modeling of reaction mechanism for 2-oxoglutarate dependent enzymes: effect of substitution of iron by nickel and cobalt.

Y. Abashkin, R. Cachau, A. Nemukhin, 2006, The journal of physical chemistry. A.

Interaction of phenol with xenon and nitrogen: spectroscopic and computational characterization.

Qian Cao, M. Räsänen, L. Khriachtchev, 2012, The Journal of chemical physics.

TOWARDS QUANTITATIVE DIATOMICS-IN-MOLECULES MODEL FOR THE WATER MOLECULE

V. A. Apkarian, B. Grigorenko, A. Nemukhin, 1998 .

A Light-Induced Reaction with Oxygen Leads to Chromophore Decomposition and Irreversible Photobleaching in GFP-Type Proteins.

I. Polyakov, A. Krylov, B. Grigorenko, 2015, The journal of physical chemistry. B.

On the use of restricted CI for correlation energy calculations: Application to BH

N. F. Stepanov, A. Nemukhin, V. I. Pupyschev, 1985 .

Dipole Moment Variation Clears Up Electronic Excitations in the π-Stacked Complexes of Fluorescent Protein Chromophores

A. Nemukhin, M. Khrenova, F. Mulashkin, 2020, J. Chem. Inf. Model..

Treatment of excited states in the CASSCF method: Application to BO

J. Almlöf, A. Nemukhin, A. Heiberg, 1981 .

The molecular structure and computed vibrational spectrum of B2O3

J. E. Boggs, J. Almlöf, A. Nemukhin, 1981 .

Potential curves of BO and LiO calculated with the complete active space SCF (CASSCF) method

J. Almlöf, A. Nemukhin, A. Heiberg, 1981 .

SCF and CASSCF studies of geometrical rearrangements in LiBO

J. Almlöf, A. Nemukhin, A. Heiberg, 1981 .

Potential curves for BLi and BLi

J. Almlöf, A. Nemukhin, A. Heiberg, 1980 .

Interplay between Locally Excited and Charge Transfer States Governs the Photoswitching Mechanism in the Fluorescent Protein Dreiklang.

I. Polyakov, A. Krylov, B. Grigorenko, 2020, The journal of physical chemistry. B.

Diatomics-in-molecules studies of the Li + H2O interaction

N. F. Stepanov, A. Nemukhin, S. V. Ljudkovski, 1983 .

Diatomics-in-molecules study of alkali hydroxides

N. F. Stepanov, A. Nemukhin, 1980 .

Origin of the π-stacking induced shifts in absorption spectral bands of the green fluorescent protein chromophore

V. Tsirelson, A. Nemukhin, M. Khrenova, 2019, Chemical Physics.

Interaction of aromatic compounds with xenon: spectroscopic and computational characterization for the cases of p-cresol and toluene.

Qian Cao, M. Räsänen, L. Khriachtchev, 2015, The journal of physical chemistry. A.

PROPERTIES OF THE NBR MOLECULE IN ARGON CLUSTERS

B. Grigorenko, A. Nemukhin, 1995 .

AB initio estimation of solvation shifts in the vibrational spectra of gold thiocomplexes

A. Nemukhin, R. Orlov, V. V. Togonidze, 1998 .

How Reproducible Are QM/MM Simulations? Lessons from Computational Studies of the Covalent Inhibition of the SARS-CoV-2 Main Protease by Carmofur.

A. Krylov, B. Grigorenko, A. Nemukhin, 2022, Journal of chemical theory and computation.

Free Energy Barriers for the N-Terminal Asparagine to Succinimide Conversion: Quantum Molecular Dynamics Simulations for the Fully Solvated Model.

A. Nemukhin, S. Varfolomeev, I. Kaliman, 2010, Journal of chemical theory and computation.

On the potential-energy surface of the Mg + CO2 (C2v) system

A. Nemukhin, A. Granovsky, E. Polikarpov, 2001 .

QM/MM Approaches Shed Light on GFP Puzzles

B. Grigorenko, A. Nemukhin, 2020 .

Excited-state site effects in luminescence spectroscopy of SH radicals in krypton matrices: Experiment and simulations

M. Pettersson, M. Räsänen, L. Khriachtchev, 1999 .

Theoretical modeling of the heterobimetallic complex [La(pta)3Cu(salen)] and its precursors

A. Nemukhin, N. Kuzmina, A. Rogachev, 2004 .

The molecular spectra and structure of the oxides of boron and aluminium

A. Nemukhin, L. V. Serebrennikov, 1993 .

Intermolecular complexes of HXeOH with water: stabilization and destabilization effects.

M. Pettersson, M. Räsänen, L. Khriachtchev, 2002, Journal of the American Chemical Society.

STRUCTURE OF MAGNESIUM CLUSTER GRIGNARD REAGENTS

F. Weinhold, A. Nemukhin, I. Topol, 1995 .

Structure and spectra of methylmagnesium Grignard complexes

V. N. Solov'ev, G. Sergeev, A. Nemukhin, 1996 .

Experimental and theoretical studies of the products of reaction between Ln(hfa) 3 and Cu(acac) 2 (Ln = La, Y; acac = acetylacetonate, hfa = hexafluoroacetylacetonate)

A. Nemukhin, A. Rogachev, A. Mironov, 2007 .

Amide-imide tautomerization in the glutamine side chain in enzymatic and photochemical reactions in proteins.

B. Grigorenko, A. Nemukhin, M. Khrenova, 2018, Physical chemistry chemical physics : PCCP.

Mixed-ligand complexes based on asymmetric gadolinium β-diketonates: Synthesis, crystal structure, and theoretical modeling

A. Nemukhin, A. Rogachev, V. Sergienko, 2007 .

Why does mutation of Gln61 in Ras by the nitro analog NGln maintain activity of Ras‐GAP in hydrolysis of guanosine triphosphate?

B. Grigorenko, A. Nemukhin, M. Khrenova, 2015, Proteins.

Spectroscopic study of low temperature interactions in metal-organic co-condensates.

V. N. Solov'ev, G. Sergeev, A. Nemukhin, 2000, Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy.

Theoretical characterization of the 1,3-diazaazulene molecule and its derivatives

B. Grigorenko, K. Bravaya, A. Nemukhin, 2008 .

Photochemistry of disulphide radical anions in the solid phase

M. Mel’nikov, A. Nemukhin, S. Bogdanova, 1989 .

Stretching vibrations and structure of (HF)n (n=4–8) clusters

A. Nemukhin, G. V. Yukhnevich, E. Tarakanova, 1997 .

Model of the RNA Polymerase Complex of the SARS-CoV-2 Virus with Favipiravir

I. Polyakov, B. Grigorenko, A. Nemukhin, 2021, Russian Journal of Physical Chemistry B.

Catalytic Cycle of Penicillin Acylase from Escherichia coli: QM/MM Modeling of Chemical Transformations in the Enzyme Active Site upon Penicillin G Hydrolysis

V. Svedas, B. Grigorenko, A. Nemukhin, 2014 .

Photoinduced electron transfer facilitates tautomerization of the conserved signaling glutamine side chain in BLUF protein light sensors.

A. Nemukhin, M. Khrenova, A V Nemukhin, 2013, The journal of physical chemistry. B.

Molecular models predict light-induced glutamine tautomerization in BLUF photoreceptors.

Alexander V Nemukhin, Ilme Schlichting, Tatiana Domratcheva, 2008, Biophysical journal.

Studies on the conformational state of the chromophore group (11-cis-retinal) in rhodopsin by computer molecular simulation methods

A. Nemukhin, M. Khrenova, M. Ostrovsky, 2009, Biofizika.

Hydrogen bonding described through diatomics-in-ionic-systems: The HF dimer

V. A. Apkarian, B. Grigorenko, A. Nemukhin, 1998 .

Influence of correlation corrections on the relative stability of conformations of the C4 molecule

N. F. Stepanov, A. Nemukhin, A. Dement'ev, 1984 .

Nonempirical CI calculations of vertical electronic transition energies in linear C2, C3, C4 molecules

A. A. Safonov, A. Nemukhin, N. F. Stepanov, 1983 .

Two-centre model potential energy calculations for the 2Σ and 2Π states of Li+2, Na+2, K+2, Rb+2 and Cs+2

A. Nemukhin, N. F. Stephanov, 1979 .

Ab initio potential functions for the ionic states of OH

B. Grigorenko, A. Nemukhin, 1997 .

Emission of SH radicals in solid krypton : mixed quantum-classical molecular dynamics simulations

M. Räsänen, L. Khriachtchev, B. Grigorenko, 2001 .

Hybrid DIM-based QM/MM approach applied to vibrational spectra and trapping site structures of HArF in solid argon

A. Nemukhin, D. Firsov, A. Bochenkova, 2005 .

Modeling Structures and Spectra of Trapped Species in Low-Temperature Matrices

B. Grigorenko, A. Nemukhin, 2011, Physics and Chemistry at Low Temperatures.

MD–DIM simulations of the 3Πg(ion-pair)→3Πu(valence) red-shifted transitions of Cl2 in neon matrices

B. Grigorenko, A. Nemukhin, N. V. Ozhegova, 1998 .

Molecular polymorphism of human enzymes as the basis of individual sensitivity to drugs. Supercomputer-assisted modeling as a tool for analysis of structural changes and enzymatic activity of proteins

P. Masson, O. Lockridge, A. Nemukhin, 2016, Russian Chemical Bulletin.

An opsin shift in rhodopsin: retinal S0-S1 excitation in protein, in solution, and in the gas phase.

K. Bravaya, A. Nemukhin, A. Granovsky, 2007, Journal of the American Chemical Society.

Reaction Mechanism of Guanosine Triphosphate Hydrolysis by the Vision-Related Protein Complex Arl3-RP2.

A. Nemukhin, M. Khrenova, E. Kots, 2016, The journal of physical chemistry. B.

Hydrolysis of Guanosine Triphosphate (GTP) by the Ras·GAP Protein Complex: Reaction Mechanism and Kinetic Scheme.

A. Kolomeisky, B. Grigorenko, A. Nemukhin, 2015, The journal of physical chemistry. B.

Computational characterization of the chemical step in the GTP hydrolysis by Ras‐GAP for the wild‐type and G13V mutated Ras

Maria G Khrenova, Alexander V Nemukhin, A. Nemukhin, 2015, Proteins.

QM/MM modeling of the glutathione?hydroxymethyl radical reaction in waterElectronic supplementary information (ESI) available: Parameters of all EFPs obtained in a series of preliminary ab initio calculations and Cartesian coordinates of all species. See http://www.rsc.org/suppdata/cp/b3/b311293d/

B. Grigorenko, A. Nemukhin, I. Topol, 2004 .

Quantum chemical modeling of the GTP hydrolysis by the RAS-GAP protein complex.

R. Cachau, B. Grigorenko, A. Nemukhin, 2004, Biochimica et biophysica acta.

Minimum energy reaction profiles for the hydrolysis reaction of the cyclic guanosine monophosphate in water: Comparison of the results of two QM/MM approaches

Maria G. Khrenova, Alexander V. Nemukhin, Bella L. Grigorenko, 2012 .

Mechanism of the myosin catalyzed hydrolysis of ATP as rationalized by molecular modeling

B. Grigorenko, A. Nemukhin, I. Topol, 2007, Proceedings of the National Academy of Sciences.

Optimization of Cholinesterase-Based Catalytic Bioscavengers Against Organophosphorus Agents

P. Masson, O. Lockridge, L. Schopfer, 2018, Front. Pharmacol..

Modeling the role of G12V and G13V Ras mutations in the Ras-GAP-catalyzed hydrolysis reaction of guanosine triphosphate.

Maria G Khrenova, Alexander V Nemukhin, B. Grigorenko, 2014, Biochemistry.

Proof of concept for poor inhibitor binding and efficient formation of covalent adducts of KRASG12C and ARS compounds.

A. Nemukhin, M. Khrenova, A. M. Kulakova, 2020, Organic & biomolecular chemistry.

Molecular Modeling Reveals the Mechanism of Ran-RanGAP-Catalyzed Guanosine Triphosphate Hydrolysis without an Arginine Finger

B. Grigorenko, A. Nemukhin, M. Khrenova, 2021, ACS Catalysis.

Theoretical Vibrational Spectra of Reaction Intermediates in the Active Site of Guanosine Triphosphate Binding Proteins

B. Grigorenko, A. Nemukhin, A. Nemukhin, 2020, Russian Journal of Physical Chemistry A.

Diversity of mechanisms in Ras-GAP catalysis of guanosine triphosphate hydrolysis revealed by molecular modeling.

B. Grigorenko, A. Nemukhin, E. Kots, 2019, Organic & biomolecular chemistry.

Theoretical vibrational spectroscopy of intermediates and the reaction mechanism of the guanosine triphosphate hydrolysis by the protein complex Ras-GAP.

B. Grigorenko, A. Nemukhin, M. Khrenova, 2016, Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy.

Mechanisms of enzymatic hydrolysis of nucleoside triphosphates by quantum and molecular mechanics

B. Grigorenko, A. Nemukhin, M. Shadrina, 2008 .

Mechanisms of guanosine triphosphate hydrolysis by Ras and Ras‐GAP proteins as rationalized by ab initio QM/MM simulations

B. Grigorenko, A. Nemukhin, I. Topol, 2006, Proteins.

QM/MM modeling the Ras–GAP catalyzed hydrolysis of guanosine triphosphate

R. Cachau, B. Grigorenko, A. Nemukhin, 2005, Proteins.

Computational study of a transition state analog of phosphoryl transfer in the Ras–RasGAP complex: AlFx versus MgF3–

R. Cachau, B. Grigorenko, A. Nemukhin, 2005, Journal of molecular modeling.

Modeling the Transient Kinetics of the L1 Metallo-β-Lactamase.

A. Nemukhin, M. Khrenova, 2018, The journal of physical chemistry. B.

Exploring structural and optical properties of fluorescent proteins by squeezing: modeling high-pressure effects on the mStrawberry and mCherry red fluorescent proteins.

Adèle D. Laurent, A. Krylov, A. Nemukhin, 2012, The journal of physical chemistry. B.

Modeling Light-Induced Chromophore Hydration in the Reversibly Photoswitchable Fluorescent Protein Dreiklang

B. Grigorenko, A. Nemukhin, Igor Polyakov, 2023, Molecules.

Protonation States of Molecular Groups in the Chromophore-Binding Site Modulate Properties of the Reversibly Switchable Fluorescent Protein rsEGFP2.

I. Polyakov, B. Grigorenko, A. Nemukhin, 2021, The journal of physical chemistry letters.

Intermediates of the Autocatalytic Reaction of the Formation of a Chromophore in a Green Fluorescent Protein

B. Grigorenko, A. Nemukhin, M. Khrenova, 2020, Russian Journal of Physical Chemistry B.

Mechanisms of ATP to cAMP Conversion Catalyzed by the Mammalian Adenylyl Cyclase: A Role of Magnesium Coordination Shells and Proton Wires.

I. Polyakov, B. Grigorenko, A. Nemukhin, 2019, The journal of physical chemistry. B.

Computational Modeling Reveals the Mechanism of Fluorescent State Recovery in the Reversibly Photoswitchable Protein Dreiklang.

I. Polyakov, A. Krylov, B. Grigorenko, 2019, The journal of physical chemistry. B.

Molecular Modeling Clarifies the Mechanism of Chromophore Maturation in the Green Fluorescent Protein.

A. Krylov, B. Grigorenko, A. Nemukhin, 2017, Journal of the American Chemical Society.

First-principles characterization of the energy landscape and optical spectra of green fluorescent protein along the A→I→B proton transfer route.

Anna I Krylov, Alexander V Nemukhin, I. Polyakov, 2013, Journal of the American Chemical Society.

Modeling absorption of the kindling fluorescent protein with the neutral form of the chromophore

J. Collins, A. Nemukhin, A. Savitsky, 2012 .

QM/MM Modeling of the Flavin Functionalization in the RutA Monooxygenase

B. Grigorenko, A. Nemukhin, T. Domratcheva, 2023, Molecules.

Computer-designed active human butyrylcholinesterase double mutant with a new catalytic triad.

P. Masson, O. Lockridge, L. Schopfer, 2019, Chemico-biological interactions.

Coupling between the BLUF and EAL domains in the blue light-regulated phosphodiesterase BlrP1

B. Grigorenko, A. Nemukhin, M. Khrenova, 2011, Journal of molecular modeling.

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

A. Nemukhin, M. Khrenova, F. Mulashkin, 2021, Molecules.

Exploration of the Zinc Finger Motif in Controlling Activity of Matrix Metalloproteinases

A. Nemukhin, A. Savitsky, M. Khrenova, 2014, The journal of physical chemistry. B.

Molecular Dynamics of Surface-Moving Thermally Driven Nanocars.

James M Tour, Anatoly B Kolomeisky, Alexander V Nemukhin, 2008, Journal of chemical theory and computation.

Tuning Electrostatic Gating of Semiconducting Carbon Nanotubes by Controlling Protein Orientation in Biosensing Devices

D. D. Jones, B. Grigorenko, A. Nemukhin, 2021, Angewandte Chemie.

This paper is published as part of a PCCP Themed Issue on: Physical Chemistry of Biomolecular Motors and Machines

Jianhua Xing, Hong Qian, Pei-Zhe Shi, 2009 .

The effect of oxidation on the electronic structure of the green fluorescent protein chromophore.

I. Polyakov, A. Krylov, B. Grigorenko, 2010, The Journal of chemical physics.

Quantum Chemical Benchmark Studies of the Electronic Properties of the Green Fluorescent Protein Chromophore. 1. Electronically Excited and Ionized States of the Anionic Chromophore in the Gas Phase.

Evgeny Epifanovsky, Anna I Krylov, I. Polyakov, 2009, Journal of chemical theory and computation.

Modeling the Solvation Sites in Rare-Gas Matrices with the Simulated Annealing Monte Carlo Technique

Alexander A. Moskovsky, Alexander Nemukhin, A. Nemukhin, 1999, J. Chem. Inf. Comput. Sci..

Modelling trapping sites of (HF)2 in argon clusters

B. Grigorenko, A. Nemukhin, 1997 .

Modeling properties of the HF dimer in argon clusters

B. Grigorenko, A. Nemukhin, 1997 .

Theoretical vibrational spectrum of (HF)(2) in argon matrices

B. Grigorenko, A. Nemukhin, A. Savin, 1996 .

Computational characterization of the all-atom structure and the calcium binding sites of the LH1-RC core complex from Thermochromatium tepidum

B. Grigorenko, A. Nemukhin, M. Khrenova, 2016 .

All-atom structures and calcium binding sites of the bacterial photosynthetic LH1-RC core complex from Thermochromatium tepidum

B. Grigorenko, A. Nemukhin, M. Khrenova, 2014, Journal of Molecular Modeling.

ArHF vibrational predissociation dynamics using the diatomics-in-molecule potential energy surface

B. Grigorenko, A. Nemukhin, A. Buchachenko, 1999 .

Boron oxides: Ab initio studies with natural bond orbital analysis

Frank Weinhold, F. Weinhold, A. Nemukhin, 1993 .

Structures of the aluminum oxides studied by ab initio methods with natural bond orbital analysis

F. Weinhold, A. Nemukhin, 1992 .

Matrix-isolation study of the phenol-water complex and phenol dimer

M. Räsänen, L. Khriachtchev, G. Gor, 2011 .

Theoretical Characterization of the Flavin-Based Fluorescent Protein iLOV and its Q489K Mutant.

A. Nemukhin, M. Khrenova, T. Domratcheva, 2015, The journal of physical chemistry. B.

Mutants of the Flavoprotein iLOV as Prospective Red-Shifted Fluorescent Markers.

Yulia I. Meteleshko, A. Nemukhin, M. Khrenova, 2017, The journal of physical chemistry. B.

Methodological aspects of QM/MM calculations: A case study on matrix metalloproteinase‐2

Walter Thiel, Tatiana Vasilevskaya, Maria G. Khrenova, 2016, J. Comput. Chem..

Mechanism of proteolysis in matrix metalloproteinase‐2 revealed by QM/MM modeling

Walter Thiel, Tatiana Vasilevskaya, Maria G. Khrenova, 2015, J. Comput. Chem..

Three Faces of N-Acetylaspartate: Activator, Substrate, and Inhibitor of Human Aspartoacylase.

Ekaterina D Kots, Maria G Khrenova, Alexander V Nemukhin, 2017, The journal of physical chemistry. B.

Analysis of proton wires in the enzyme active site suggests a mechanism of c‐di‐GMP hydrolysis by the EAL domain phosphodiesterases

M. A. Knyazeva, B. Grigorenko, A. Nemukhin, 2016, Proteins.

Estimating orientation factors in the FRET theory of fluorescent proteins: the TagRFP-KFP pair and beyond.

J. Collins, A. Nemukhin, M. Khrenova, 2015, Biophysical journal.

Characterization of a complete cycle of acetylcholinesterase catalysis by ab initio QM/MM modeling

A. Nemukhin, S. Varfolomeev, S. V. Lushchekina, 2008, Journal of molecular modeling.

Diatomics-in-molecules description of the Rg–Hal2 rare gas–halogen van der Waals complexes with applications to He–Cl2

N. F. Stepanov, B. Grigorenko, A. Nemukhin, 1997 .

Stalling chromophore synthesis of the fluorescent protein Venus reveals the molecular basis of the final oxidation step†

Gabriel dos Passos Gomes, I. Polyakov, P. Rizkallah, 2021, Chemical science.

Quantum Chemical Benchmark Studies of the Electronic Properties of the Green Fluorescent Protein Chromophore: 2. Cis-Trans Isomerization in Water.

Evgeny Epifanovsky, Anna I Krylov, I. Polyakov, 2009, Journal of chemical theory and computation.

Frontiers in Multiscale Modeling of Photoreceptor Proteins

Jógvan Magnus Haugaard Olsen, Y. M. Rhee, N. Ferré, 2020, Photochemistry and photobiology.

Toward molecular mechanism of xenon anesthesia: a link to studies of xenon complexes with small aromatic molecules.

M. Räsänen, L. Khriachtchev, A. Nemukhin, 2015, The journal of physical chemistry. A.

Hybrid diatomics-in-molecules-based quantum mechanical/molecular mechanical approach applied to the modeling of structures and spectra of mixed molecular clusters Arn(HCl)m and Arn(HF)m.

A. Nemukhin, M. Suhm, A. Bochenkova, 2004, The Journal of chemical physics.

Modeling spectral tuning in monomeric teal fluorescent protein mTFP1.

Jack Collins, J. Collins, A. Nemukhin, 2010, Biophysical chemistry.

Multiscale Simulations of the Covalent Inhibition of the SARS-CoV-2 Main Protease: Four Compounds and Three Reaction Mechanisms

A. Krylov, B. Grigorenko, A. Nemukhin, 2023, Journal of the American Chemical Society.

Structure of the Brain N-Acetylaspartate Biosynthetic Enzyme NAT8L Revealed by Computer Modeling.

I. Polyakov, B. Grigorenko, A. Nemukhin, 2020, ACS chemical neuroscience.

Allosteric Control of N-Acetyl-Aspartate Hydrolysis by the Y231C and F295S Mutants of Human Aspartoacylase

Ekaterina D Kots, Maria G Khrenova, Alexander V Nemukhin, 2018, J. Chem. Inf. Model..

Light-Induced Change of Arginine Conformation Modulates the Rate of Adenosine Triphosphate to Cyclic Adenosine Monophosphate Conversion in the Optogenetic System Containing Photoactivated Adenylyl Cyclase

Maria G. Khrenova, Alexander V. Nemukhin, Anna M. Kulakova, 2021, J. Chem. Inf. Model..

Theoretical investigations of AlO2

Jan Almlöf, J. Almlöf, A. Nemukhin, 1992 .

Implementation of a molecular dynamics approach with rigid fragments to simulation of chemical reactions in biomolecular systems

Bella L. Grigorenko, Alexey V. Akimov, A. Akimov, 2007 .

Two Sides of Quantum-Based Modeling of Enzyme-Catalyzed Reactions: Mechanistic and Electronic Structure Aspects of the Hydrolysis by Glutamate Carboxypeptidase

A. Nemukhin, M. Khrenova, A. V. Krivitskaya, 2021, Molecules.

MODELING STRUCTURE AND SPECTRA OF PROTEIN COMPLEXES BY USING MOLECULAR DYNAMICS AND QUANTUM CHEMISTRY METHODS : FROM SIMPLE TWO-DOMAIN UNITS TO PHOTOSYNTHETIC AGGREGATES

A. Nemukhin, M. Khrenova, 2012 .

Molecular dynamics of small magnesium clusters in argon matrices

B. Grigorenko, A. Nemukhin, N. V. Ozhegova, 1997 .

Competition between two cysteines in covalent binding of biliverdin to phytochrome domains.

A. Nemukhin, M. Khrenova, A. Kulakova, 2018, Organic & biomolecular chemistry.

Conformational partitioning in pH-induced fluorescence of the kindling fluorescent protein (KFP).

Alexander S. Goryashenko, B. Grigorenko, A. Nemukhin, 2011, The journal of physical chemistry. B.

Molecular mechanism of the dark-state recovery in BLUF photoreceptors

Maria G. Khrenova, Alexander V. Nemukhin, Tatiana Domratcheva, 2017 .

Modeling structure and excitation of biliverdin-binding domains in infrared fluorescent proteins

I. Polyakov, B. Grigorenko, A. Nemukhin, 2018, Chemical Physics Letters.

Minimum energy reaction profiles for ATP hydrolysis in myosin.

B. Grigorenko, A. Nemukhin, I. Kaliman, 2011, Journal of molecular graphics & modelling.

Opening the Arg-Glu salt bridge in myosin: computational study.

B. Grigorenko, A. Nemukhin, I. Kaliman, 2009, Physical chemistry chemical physics : PCCP.

Computational characterization of ketone-ketal transformations at the active site of matrix metalloproteinases.

A. Nemukhin, A. Savitsky, M. Khrenova, 2014, The journal of physical chemistry. B.

Semiempirical andab initio study of the structure of the alumophenylsiloxane complex and its fragments

A. Nemukhin, V. Vinokurov, I. Kolesnikov, 1995 .

Mechanism of the chemical step for the guanosine triphosphate (GTP) hydrolysis catalyzed by elongation factor Tu.

J. Collins, B. Grigorenko, A. Nemukhin, 2008, Biochimica et biophysica acta.

Simulation of Spectra of Red Fluorescent Protein Mutants

A. Nemukhin, M. G. Khrenova, A. Kulakova, 2018, Moscow University Chemistry Bulletin.

Reaction mechanism of matrix metalloproteinases with a catalytically active zinc ion studied by the QM(DFTB)/MM simulations

W. Thiel, T. Vasilevskaya, A. Nemukhin, 2016 .

Thermal isomerization of the chromoprotein asFP595 and its kindling mutant A143G: QM/MM molecular dynamics simulations.

B. Grigorenko, A. Nemukhin, A. Savitsky, 2013, The journal of physical chemistry. B.

Correlation between the substrate structure and the rate of acetylcholinesterase hydrolysis modeled with the combined quantum mechanical/molecular mechanical studies.

A. Nemukhin, D. Morozov, S. Varfolomeev, 2010, Chemico-biological interactions.

Computational Characterization of the Substrate Activation in the Active Site of SARS-CoV-2 Main Protease

Maria G. Khrenova, Alexander V. Nemukhin, Vladimir G. Tsirelson, 2020, Supercomput. Front. Innov..

Vibrational matrix shift simulations of SO2 in rare gases : importance of many-body effects

N. F. Stepanov, A. Nemukhin, A. I. Krylova, 1992 .

Unusual emitting states of the kindling fluorescent protein: appearance of the cationic chromophore in the GFP family.

I. Polyakov, B. Grigorenko, A. Nemukhin, 2013, The journal of physical chemistry. B.

Computational Characterization of Reaction Intermediates in the Photocycle of the Sensory Domain of the AppA Blue Light Photoreceptor †

Maria G Khrenova, Alexander V Nemukhin, Ilme Schlichting, 2011, Photochemistry and photobiology.

Stalling chromophore maturation of the fluorescent protein Venus reveals the molecular basis of the final oxidation step

I. Polyakov, P. Rizkallah, D. D. Jones, 2020 .

Modeling of the glycine tripeptide cyclization in the Ser65Gly/Tyr66Gly mutant of green fluorescent protein

A. Krylov, B. Grigorenko, A. Nemukhin, 2019, Mendeleev Communications.

Role of zwitterions in kindling fluorescent protein photochemistry.

Alexander V Nemukhin, K. Bravaya, A. Nemukhin, 2015, The journal of physical chemistry. B.

Conformation dependence of pKa's of the chromophores from the purple asFP595 and yellow zFP538 fluorescent proteins.

J. Collins, B. Grigorenko, A. Nemukhin, 2008, Theochem.

Modeling photoabsorption of the asFP595 chromophore.

K. Bravaya, A. Nemukhin, A. Savitsky, 2008, The journal of physical chemistry. A.

Ground-state structures and vertical excitations for the kindling fluorescent protein asFP595.

B. Grigorenko, A. Nemukhin, I. Topol, 2006, The journal of physical chemistry. B.

Electronic Excitations of the Chromophore from the Fluorescent Protein asFP595 in Solutions.

Alexander V Nemukhin, A. Nemukhin, I. Topol, 2006, Journal of chemical theory and computation.

Computational Modeling of the Neurofibromin-Stimulated Guanosine Triphosphate Hydrolysis by the KRas Protein

A. Nemukhin, I. Polyakov, 2023, Biophysica.

Theoretical characterization of the photochemical reaction CO2 + O(3P) → CO + O2 related to experiments in solid krypton

I. Polyakov, B. Grigorenko, A. Nemukhin, 2020 .

Hindered rotation of HArF in solid argon: Infrared spectroscopy and a theoretical model

M. Räsänen, L. Khriachtchev, A. Nemukhin, 2008 .

Investigation of matrix-isolated species: spectroscopy and molecular modelling

M. Räsänen, L. Khriachtchev, B. Grigorenko, 2007 .

Ab initio potential curves of the fragments and diatomics-in-molecules potential energy surfaces for the SH⋯Kr complex

B. Grigorenko, A. Nemukhin, A. Granovsky, 1999 .

An analysis of stationary points on the (HF)n potential surfaces (n≤6) predicted by the diatomics-in-ionic-systems model

B. Grigorenko, A. Nemukhin, A. Moskovsky, 2000 .

Supercomputer simulation of the covalent inhibition of the main protease of SARS-CoV-2

B. Grigorenko, A. Nemukhin, S. Varfolomeev, 2021, Russian Chemical Bulletin.

Quantum chemical modeling of the reduction of cis‐diammineplatinum(IV) tetrachloride [Pt(NH3)2Cl4] by methyl thiolate anion

Alexander V. Nemukhin, I. A. I. Dobrogorskaia-Mereau, A. Nemukhin, 2005, J. Comput. Chem..

Computational Modeling of the Interaction of Molecular Oxygen with the miniSOG Protein—A Light Induced Source of Singlet Oxygen

A. Nemukhin, A. Kulakova, Igor V. Polyakov, 2023, Biophysica.

Computational Modeling of the SARS-CoV-2 Main Protease Inhibition by the Covalent Binding of Prospective Drug Molecules

Bella L. Grigorenko, Igor V. Polyakov, Alexander V. Nemukhin, 2020, Supercomput. Front. Innov..

Aspartoacylase: a central nervous system enzyme. Structure, catalytic activity and regulation mechanisms

A. Nemukhin, M. Khrenova, S. Varfolomeev, 2019, Russian Chemical Reviews.

Effect of solvation water shells on enzyme active sites in zinc-dependent hydrolases

B. Grigorenko, A. Nemukhin, M. Khrenova, 2018, Structural Chemistry.

Quantum chemical modelling in the research of molecular mechanisms of enzymatic catalysis

B. Grigorenko, A. Nemukhin, S. Varfolomeev, 2012 .

Reconstructing the Electron Density of Intermediates of the Hydrolysis of N-Acetylaspartate by Aspartoacylase

A. Nemukhin, M. Khrenova, E. Kots, 2019, Russian Journal of Physical Chemistry A.

Computer simulation in molecular medicine and drug design

A. Nemukhin, S. Varfolomeev, S. Lushchekina, 2016, Herald of the Russian Academy of Sciences.

Modeling chemical transformations at the active sites of cholinesterases by quantum-based simulations

A. Nemukhin, S. Varfolomeev, S. Lushchekina, 2015, Moscow University Chemistry Bulletin.

Quantumchemicalmodellingintheresearchofmolecularmechanisms of enzymatic catalysis

B. Grigorenko, A. Nemukhin, S. Varfolomeev, 2012 .

Quantum chemical justification of the specificity of enzyme catalysis: Correlations between the rate of enzyme catalysis by acetylcholinesterase and substrate structure

A. Nemukhin, D. Morozov, S. Varfolomeev, 2009 .

On the nature of oxoiron (IV) intermediate in dioxygen activation by non-heme enzymes

R. Cachau, A. Nemukhin, I. Topol, 2006 .

Modeling of serine protease prototype reactions with the flexible effective fragment potential quantum mechanical/molecular mechanical method

B. Grigorenko, A. Nemukhin, I. Topol, 2004 .

Modeling dioxygen binding to the non‐heme iron‐containing enzymes

B. Grigorenko, A. Nemukhin, I. Topol, 2006 .

On quantum mechanical--molecular mechanical (QM/MM) approaches to model hydrolysis of acetylcholine by acetylcholinesterase.

B. Grigorenko, A. Nemukhin, D. Morozov, 2013, Chemico-biological interactions.

Modeling of the mechanism of hydrolysis of succinylcholine in the active site of native and modified (Asp70Gly) human butyrylcholinesterase

I. Polyakov, B. Grigorenko, A. Nemukhin, 2010 .

Molecular Modeling the Reaction Mechanism of Serine-Carboxyl Peptidases.

B. Grigorenko, K. Bravaya, A. Nemukhin, 2006, Journal of chemical theory and computation.

Implementation of the replica-exchange molecular dynamics method for rigid bodies

A. Nemukhin, V. Vanovschi, S. S. Konyukhov, 2006 .

Serine hydrolase catalytic sites : geometry invariants and modeling catalytic activity

A. Nemukhin, S. Varfolomeev, A. Rogov, 2006 .

Impact of pyrophosphate and O-ethyl-substituted pyrophosphate groups on DNA structure.

A. Nemukhin, M. Saparbaev, S. Kuznetsova, 2007, The journal of physical chemistry. B.

Quantum Chemistry Calculations Provide Support to the Mechanism of the Light-Induced Structural Changes in the Flavin-Binding Photoreceptor Proteins.

B. Grigorenko, A. Nemukhin, M. Khrenova, 2010, Journal of chemical theory and computation.

Hydrolysis of Guanosine Triphosphate (GTP) by the Ras·GAP Protein Complex: Reaction Mechanism and Kinetic Scheme.

A. Kolomeisky, B. Grigorenko, A. Nemukhin, 2015, The journal of physical chemistry. B.

Reaction Mechanism of Guanosine Triphosphate Hydrolysis by the Vision-Related Protein Complex Arl3-RP2.

A. Nemukhin, M. Khrenova, E. Kots, 2016, The journal of physical chemistry. B.

Towards first-principles calculation of electronic excitations in the ring of the protein-bound bacteriochlorophylls

A. Nemukhin, M. Khrenova, A. Moskovsky, 2018 .

Mechanism of proteolysis in matrix metalloproteinase‐2 revealed by QM/MM modeling

W. Thiel, T. Vasilevskaya, A. Nemukhin, 2015, J. Comput. Chem..

Photoinduced Chemistry in Fluorescent Proteins: Curse or Blessing?

K. Lukyanov, A. Krylov, A. Bogdanov, 2017, Chemical reviews.

Optimization of molecular orbitals in calculations of excited states by CI and MC SCF methods

A. Nemukhin, N. F. Stepanov, 1984 .

Molecular Dynamics of Surface-Moving Thermally Driven Nanocars.

J. Tour, A. Kolomeisky, A. Nemukhin, 2008, Journal of Chemical Theory and Computation.

Modeling reaction routes from rhodopsin to bathorhodopsin

A. Nemukhin, M. Khrenova, A. Bochenkova, 2010, Proteins.

Spontaneous Reactivation of OPC-Inhibited BChE Mutants: Modeling of Mechanisms

P. Masson, B. Grigorenko, A. Nemukhin, 2022, Russian Journal of Physical Chemistry B.

QM/MM Simulations of the Covalent Inhibition of the SARS-CoV-2 Main Protease: Four Compounds and Three Reaction Mechanisms

A. Krylov, B. Grigorenko, A. Nemukhin, 2023 .

Unusual emitting states of the kindling fluorescent protein: appearance of the cationic chromophore in the GFP family.

B. Grigorenko, A. Nemukhin, A. Savitsky, 2013, The journal of physical chemistry. B.

Quantum Chemistry in Studies of Fluorescent and Photosensing Proteins

J. Collins, A. Nemukhin, M. Khrenova, 2013 .

Novel flavin-based fluorescent proteins with red-shifted emission bands: a computational study

Yulia I. Meteleshko, A. Nemukhin, M. Khrenova, 2019, Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology.

Computational Modeling Reveals the Mechanism of Fluorescent State Recovery in the Reversibly Photoswitchable Protein Dreiklang.

A. Krylov, B. Grigorenko, A. Nemukhin, 2019, The journal of physical chemistry. B.

Modeling of enzyme-catalyzed P–O bond cleavage in the adenosine triphosphate molecule

A. Nemukhin, M. Khrenova, T. I. Mulashkina, 2024, Mendeleev Communications.

Discrimination of enzyme–substrate complexes by reactivity using the electron density analysis: peptide bond hydrolysis by the matrix metalloproteinase-2

V. Tsirelson, A. Nemukhin, M. Khrenova, 2020 .