Marat Valiev

Marat Valiev
Staff Member Title: 
Senior Research Scientist
Phone: 
(509) 371-6459
Contact Email: 
marat.valiev@pnnl.gov
Overview: 
  • Development QM/MM capabilities for NWChem
  • Development of hybrid ab-initio and quasicontinuum methods
  • Development of integrated software suite for chemical dynamics
  • Study of microbially-mediated metal reduction processes
  • Study of phosphorylation reaction in protein kinases
  • Study of ion solvation processes
Details: 

1997-2001 Postgraduate Researcher, UCSD, La Jolla, CA 2001-2003 Project Scientist, UCSD, La Jolla, CA

Education: 

University of Connecticut M.S. 1994 Physics University of Connecticut Ph.D. 1997 Physics

Research Interests: 

Hybrid quantum mechanical and molecular mechanics approaches to large scale biochemical simulations Multiscale methods Mixed plane wave and local basis methods for periodic systems (PAW) Effective action methods

Capabilities: 
Molecular Science Computing

Publications

2016

  • M Valiev, S Deng, XB Wang. 2016. "How Anion Chaotrope Changes the Local Structure of Water: Insights from Photoelectron Spectroscopy and Theoretical Modeling of SCN− Water Clusters." Journal of Physical Chemistry B 120(8)1518-1525. 10.1021/acs.jpcb.5b07257
  • GL Hou, XT Kong, M Valiev, L Jiang, XB Wang. 2016. "Probing the Early Stages of Solvation of cis-Pinate Dianions by Water, Acetonitrile, and Methanol: A Photoelectron Spectroscopy and Theoretical Study." Physical Chemistry Chemical Physics. PCCP 18(5)3628-3637. 10.1039/C5CP05974G
  • GL Hou, M Valiev, XB Wang. 2016. "Deprotonated Dicarboxylic Acid Homodimers: Hydrogen Bonds and Atmospheric Implications." Journal of Physical Chemistry A 120(15)2342-2349. 10.1021/acs.jpca.6b01166

2015

  • K Bhaskaran-Nair, M Valiev, S Deng, WA Shelton, K Kowalski, XB Wang. 2015. "Probing microhydration effect on the electronic structure of the GFP chromophore anion: Photoelectron spectroscopy and theoretical investigations." Journal of Chemical Physics 143(22)Article No. 224301 .

2014

  • N Shaikh, M Valiev, SV Lymar. 2014. "Decomposition of Amino Diazeniumdiolates (NONOates): Molecular Mechanisms ." Journal of Inorganic Biochemistry 14128-35. 10.1016/j.jinorgbio.2014.08.008
  • S Deng, GL Hou, X Kong, M Valiev, XB Wang. 2014. "Examining the Amine Functionalization in Dicarboxylates: Photoelectron Spectroscopy and Theoretical Studies of Aspartate and Glutamate." Journal of Physical Chemistry A 118(28)5256-5262. 10.1021/jp505439b

2013

  • BE Van Kuiken, M Valiev, SL Daifuku, C Bannan, ML Strader, H Cho, N Huse, RW Schoenlein, N Govind, M Khalil. 2013. "Simulating Ru L3-edge X-ray Absorption Spectroscopy with Time-Dependent Density Functional Theory: Model Complexes and Electron Localization in Mixed-Valence Metal Dimers." Journal of Physical Chemistry A 117(21)4444-4454.
  • H Wen, GL Hou, SM Kathmann, M Valiev, XB Wang. 2013. "Communication: Solute Anisotropy Effects in Hydrated Anion and Neutral Clusters." Journal of Chemical Physics 138(3)Article No. 031101. 10.1063/1.4776766
  • J Chen, H Yin, D Wang, M Valiev. 2013. "Water Assisted Reaction Mechanism of OH- with CCl4 in Aqueous Solution - Hybrid Quantum Mechanical and Molecular Mechanics Investigation ." Chemical Physics Letters 55930-34.
  • B Sellner, M Valiev, SM Kathmann. 2013. "Charge and Electric Field Fluctuations in Aqueous NaCl Electrolytes ." Journal of Physical Chemistry B 117(37)10869-10882. 10.1021/jp405578w

2012

  • G Murdachaew, M Valiev, SM Kathmann, XB Wang. 2012. "Study of Ion Specific Interactions of Alkali Cations with Dicarboxylate Dianions." Journal of Physical Chemistry A 116(9)2055-2061. 10.1021/jp3012848
  • GN Chuev, M Valiev, MV Fedotova. 2012. "Integral Equation Theory of Molecular Solvation Coupled with Quantum Mechanical/Molecular Mechanics Method in NWChem Package." Journal of Chemical Theory and Computation 8(4)1246-1254. 10.1021/ct2009297
  • T Wang, H Yin, D Wang, M Valiev. 2012. "Hybrid Quantum Mechanical and Molecular Mechanics Study of the SN2 Reaction of CCl4 + OH− in Aqueous Solution: The Potential of Mean Force, Reaction Energetics, and Rate Constants." Journal of Physical Chemistry A 116(9)2371-2376. 10.1021/jp3005986

2011

  • N Govind, EJ Bylaska, WA De Jong, K Kowalski, TP Straatsma, M Valiev, HJJ van Dam. 2011. "NWChem."
  • HJJ van Dam, WA De Jong, EJ Bylaska, N Govind, K Kowalski, TP Straatsma, M Valiev. 2011. "NWChem: scalable parallel computational chemistry." Wiley Interdisciplinary Reviews: Computational Molecular Science 1(6)888-894. 10.1002/wcms.62
  • D Wang, M Valiev, BC Garrett. 2011. "CH2Cl2 and OH− Reaction in Aqueous Solution: A Combined Quantum Mechanical and Molecular Mechanics Study." Journal of Physical Chemistry A 115(8)1380-1384. 10.1021/jp109287r
  • M Valiev, SV Lymar. 2011. "Structural and Mechanistic Analysis through Electronic Spectra: Aqueous Hyponitrite Radical (N2O2-) and Nitrosyl Hyponitrite Anion (N3O3-)." Journal of Physical Chemistry A 115(43)12004-12010. 10.1021/jp204967h
  • H Yin, D Wang, M Valiev. 2011. "Hybrid Quantum Mechanical/Molecular Mechanics Study of the SN2 Reaction of CH3Cl+OH− in Water." Journal of Physical Chemistry A 115(43)12047-12052. 10.1021/jp2076808

2010

  • M Valiev, EJ Bylaska, N Govind, K Kowalski, TP Straatsma, HJJ van Dam, D Wang, J Nieplocha, E Apra, TL Windus, WA De Jong. 2010. "NWChem: a Comprehensive and Scalable Open-Source Solution for Large Scale Molecular Simulations." Computer Physics Communications 181(9)1477-1489. 10.1016/j.cpc.2010.04.018
  • EL Cauet, M Valiev, JH Weare. 2010. "Vertical Ionization Potentials of Nucleobases in a Fully Solvated DNA Environment." Journal of Physical Chemistry B 114(17)5886-5894.

2009

  • N Govind, PV Sushko, WP Hess, M Valiev, K Kowalski. 2009. "Excitons in Potassium Bromide: A Study using Embedded Time-dependent Density Functional Theory and Equation-of-Motion Coupled Cluster Methods." Chemical Physics Letters 470(4-6)353-357. 10.1016/j.cplett.2009.01.073
  • N Govind, M Valiev, L Jensen, K Kowalski. 2009. "Excitation Energies of Zinc Porphyrin in Aqueous Solution Using Long-Range Corrected Time-Dependent Density Functional Theory." Journal of Physical Chemistry A 113(21)6041-6043. 10.1021/jp902118k
  • K Kowalski, M Valiev. 2009. "Extensive regularization of the coupled cluster methods based on the generating functional formalism: application to gas-phase benchmarks and to the S(N)2 reaction of CHCl3 and OH- in water." Journal of Chemical Physics 131(23)Article Number 234107.
  • BM Elsasser, M Valiev, JH Weare. 2009. "A Dianionic Phosphorane Intermediate and Transition States in an Associative AN+DN Mechanism for the RibonucleaseA Hydrolysis Reaction." Journal of the American Chemical Society 131(11)3869-3871. 10.1021/ja807940y
  • M Valiev, R D'Auria, DJ Tobias, BC Garrett. 2009. "Interactions of Cl- and OH Radical in Aqueous Solution." Journal of Physical Chemistry A 113(31)8823-8825.

2008

  • M Valiev, EJ Bylaska, M Dupuis, PG Tratnyek. 2008. "Combined Quantum Mechanical and Molecular Mechanics Studies of the Electron-Transfer Reactions Involving Carbon Tetrachloride in Solution." Journal of Physical Chemistry A 112(12)2713-2720. 10.1021/jp7104709
  • K Kowalski, M Valiev. 2008. "NonIterative Corrections to Equation-of-Motion Coupled-Cluster Excited State Energies Based on the Reduced Method of Moments of coupled cluster equation." International Journal of Quantum Chemistry 108(12)2178-2190. 10.1002/qua.21741
  • K Kowalski, M Valiev. 2008. "The Application of High-Level Iterative Coupled-Cluster Methods to the Cytosine Molecule." Journal of Physical Chemistry A 112(24)5538-5541.
  • PD Fan, M Valiev, K Kowalski. 2008. "Large-Scale Parallel Calculations with Combined Coupled Cluster and Molecular Mechanics Formalism: Excitation Energies of Zinc-porphyrin in Aqueous Solution." Chemical Physics Letters 458(1-3)205-209.
  • E Epifanovsky, K Kowalski, PD Fan, M Valiev, S Matsika, A Krylov. 2008. "On the Electronically Excited States of Uracil." Journal of Physical Chemistry A 112(40)9983-9992. 10.1021/jp803758q
  • AS Lipton, RW Heck, GR Staeheli, M Valiev, WA De Jong, PD Ellis. 2008. "A QM/MM Approach to Interpreting Zn-67 Solid-State NMR data in Zinc Proteins." Journal of the American Chemical Society 130(19)6224-6230.
  • M Kamiya, S Hirata, M Valiev. 2008. "Fast Electron Correlation Methods for Molecular Clusters without Basis Set Superposition Errors ." Journal of Chemical Physics 128(7)Art. No. 074103. 10.1063/1.2828517
  • J Nieplocha, S Krishnamoorthy, M Valiev, MK Krishnan, BJ Palmer, P Sadayappan. 2008. "Integrated Data and Task Management for Scientific Applications." 10.1007/978-3-540-69384-0_6

2007

  • EJ Bylaska, M Valiev, JR Rustad, JH Weare. 2007. "Structure and Dynamics of the Hydration Shells of the Al3+ Ion ." Journal of Chemical Physics 126(10)Art.no.104505.
  • JR Hammond, M Valiev, WA De Jong, K Kowalski. 2007. "Calculations of Molecular Properties in Hybrid Coupled-Cluster and Molecular Mechanics Approach." Journal of Physical Chemistry A 111(25)5492-5498. 10.1021/jp070553x
  • M Valiev, BC Garrett, MKang Tsai, K Kowalski, SM Kathmann, GK Schenter, M Dupuis. 2007. "Hybrid Approach for Free Energy Calculations with High-Level Methods: Application to the S(N)2 Reaction of CHCl3 and OH- in Water." Journal of Chemical Physics 127(5)51102 (1-4).
  • MKang Tsai, K Kowalski, M Valiev, M Dupuis. 2007. "Signature OH Absorption Spectrum from cluster Models of Solvation: a solvent-to-solute charge transfer state." Journal of Physical Chemistry A 111(42)10478-10482. 10.1021/jp074617f
  • SN Kerisit, KM Rosso, M Dupuis, M Valiev. 2007. "Molecular Computational Investigation of Electron Transfer Kinetics across Cytochrome-Iron Oxide Interfaces." Journal of Physical Chemistry C 111(30)11363-11375.
  • M Valiev, J Yang, J Adams, SS Taylor, JH Weare. 2007. "Phosphorylation Reaction in cAPK Protein Kinase - Free Energy Quantum Mechanic/Molecular Mechanics Simulations.." Journal of Physical Chemistry B 111(47)13455-13464. 10.1021/jp074853q

2006

  • M Valiev, K Kowalski. 2006. "Hybrid Coupled Cluster and Molecular Dynamics Approach: Application to the Excitation Spectrum of Cytosine in the Native DNA Environment." Journal of Chemical Physics 125(21)Art. No. 211101. 10.1063/1.2403847
  • K Kowalski, M Valiev. 2006. "Asymptotic Extrapolation Scheme for Large-Scale Calculations with Hybrid Coupled Cluster and Molecular Dynamic Simulations." Journal of Physical Chemistry A 110(48)13106-13111.
  • K Kowalski, M Valiev. 2006. "Multiscale Dynamical Framework for High-Level Calculations of Finite Temperature Ground and Excited State Properties." 10.1088/1742-6596/46/1/035
  • DMA Smith, KM Rosso, M Dupuis, M Valiev, TP Straatsma. 2006. "Electronic Coupling between Heme Electron-Transfer Centers and Its Decay with Distance Depends Strongly on Relative Orientation." Journal of Physical Chemistry B 110(31)15582-15588. 10.1021/jp057068r

2005

  • S Hirata, M Valiev, M Dupuis, SS Xantheas, SI Sugiki, H Sekino. 2005. "Fast Electron Correlation Methods for Molecular Clusters in the Ground and Excited States." Molecular Physics 103(15-16)2255-2265.

2003

  • M Valiev, EJ Bylaska, JH Weare. 2003. "Calculations of the Electronic Structure of 3d Transition Metal Dimers with Projector Augmented Plane Wave Method." Journal of Chemical Physics 119(12)5955-5964.
  • M Valiev, R Kawai, JA Adams, JH Weare. 2003. "The Role of the Putative Catalytic Base in the Phosphoryl Transfer Reaction in a Protein Kinase: First Principles Calculations." Journal of the American Chemical Society 125(33)9926-9927.

2002

  • EJ Bylaska, M Valiev, R Kawai, JH Weare. 2002. "Parallel Implementation of the Projector Augmented Plane Wave Method for Charged Systems." Computer Physics Communications 143(1)11-28.
  • M Valiev, EJ Bylaska, A Gramada, JH Weare. 2002. "First Principles Molecular Dynamics Simulations Using Density-Functional Theory."