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Fundamental and Computational Sciences Directorate

Staff information

Marat Valiev

Biosystms Dynamics & Simula
Scientist
Pacific Northwest National Laboratory
PO Box 999
MSIN: K8-91
Richland, WA 99352

PNNL Publications

2017

  • Hou GL, J Zhang, M Valiev, and XB Wang. 2017. "Structures and energetics of hydrated deprotonated cis-pinonic acid anion clusters and their atmospheric relevance." Physical Chemistry Chemical Physics. PCCP 19(16):10676-10684.  doi:10.1039/c6cp08834a
  • Hou GL, XB Wang, and M Valiev. 2017. "Formation of (HCOO-)(H2SO4) Anion Clusters: Violation of Gas Phase Acidity Predictions." Journal of the American Chemical Society 139(33):11321-11324.  doi:10.1021/jacs.7b05964
  • Pirojsirikul T, AW Goetz, JH Weare, RC Walker, K Kowalski, and M Valiev. 2017. "Combined Quantum-Mechanical Molecular Mechanics Calculations with NWChem and AMBER: Excited State Properties of Green Fluorescent Protein Chromophore Analogue in Aqueous Solution." Journal of Computational Chemistry 38(18):1631-1639.  doi:10.1002/jcc.24804
  • Sun J, M Konda, R Parthasarathi, T Dutta, M Valiev, F Xu, BA Simmons, and S Singh. 2017. "One-pot integrated biofuel production using low-cost biocompatible protic ionic liquids." Green Chemistry 19(13):3152-3163.  doi:10.1039/c7gc01179b

2016

  • Hou GL, M Valiev, and XB Wang. 2016. "Deprotonated Dicarboxylic Acid Homodimers: Hydrogen Bonds and Atmospheric Implications." Journal of Physical Chemistry A 120(15):2342-2349.  doi:10.1021/acs.jpca.6b01166
  • Hou GL, XT Kong, M Valiev, L Jiang, and 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.  doi:10.1039/C5CP05974G
  • Qin Z, GL Hou, Z Yang, M Valiev, and XB Wang. 2016. "Negative ion photoelectron spectra of ISO3-, IS2O3-, and IS2O4- intermediates formed in interfacial reactions of ozone and iodide/sulfite aqueous microdroplets." Journal of Chemical Physics 145(21):4969076.  doi:10.1063/1.4969076
  • Valiev M, S Deng, and 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.  doi:10.1021/acs.jpcb.5b07257

2015

  • Bhaskaran-Nair K, M Valiev, S Deng, WA Shelton, JR, K Kowalski, and 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

  • Deng S, GL Hou, X Kong, M Valiev, and 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.  doi:10.1021/jp505439b
  • Shaikh N, M Valiev, and SV Lymar. 2014. "Decomposition of Amino Diazeniumdiolates (NONOates): Molecular Mechanisms ." Journal of Inorganic Biochemistry 141:28-35.  doi:10.1016/j.jinorgbio.2014.08.008

2013

  • Chen J, H Yin, D Wang, and M Valiev. 2013. "Water Assisted Reaction Mechanism of OH- with CCl4 in Aqueous Solution - Hybrid Quantum Mechanical and Molecular Mechanics Investigation ." Chemical Physics Letters 559:30-34. 
  • Sellner B, M Valiev, and SM Kathmann. 2013. "Charge and Electric Field Fluctuations in Aqueous NaCl Electrolytes ." Journal of Physical Chemistry B 117(37):10869-10882.  doi:10.1021/jp405578w
  • Van Kuiken BE, M Valiev, SL Daifuku, C Bannan, ML Strader, H Cho, N Huse, RW Schoenlein, N Govind, and 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. 
  • Wen H, GL Hou, SM Kathmann, M Valiev, and XB Wang. 2013. "Communication: Solute Anisotropy Effects in Hydrated Anion and Neutral Clusters." Journal of Chemical Physics 138(3):Article No. 031101.  doi:10.1063/1.4776766

2012

  • Chuev GN, M Valiev, and 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.  doi:10.1021/ct2009297
  • Murdachaew G, M Valiev, SM Kathmann, and XB Wang. 2012. "Study of Ion Specific Interactions of Alkali Cations with Dicarboxylate Dianions." Journal of Physical Chemistry A 116(9):2055-2061.  doi: 10.1021/jp3012848
  • Wang T, H Yin, D Wang, and 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.  doi:10.1021/jp3005986

2011

  • Govind N, EJ Bylaska, WA De Jong, K Kowalski, TP Straatsma, M Valiev, and HJJ van Dam. 2011. "NWChem." In Encyclopedia of Parallel Computing, ed. D Padua, pp. 1345-1353.  Springer, New York, NY. 
  • Valiev M, and 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.  doi:10.1021/jp204967h
  • van Dam HJJ, WA De Jong, EJ Bylaska, N Govind, K Kowalski, TP Straatsma, and M Valiev. 2011. "NWChem: scalable parallel computational chemistry." Wiley Interdisciplinary Reviews: Computational Molecular Science 1(6):888-894.  doi:10.1002/wcms.62
  • Wang D, M Valiev, and 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.  doi:10.1021/jp109287r
  • Yin H, D Wang, and 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.  doi:10.1021/jp2076808

2010

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

2009

  • Govind N, M Valiev, L Jensen, and 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.  doi:10.1021/jp902118k
  • Govind N, PV Sushko, WP Hess, M Valiev, and 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.  doi:10.1016/j.cplett.2009.01.073
  • Valiev M, R D'Auria, DJ Tobias, and BC Garrett. 2009. "Interactions of Cl- and OH Radical in Aqueous Solution." Journal of Physical Chemistry A 113(31):8823-8825. 
  • Elsasser BM, M Valiev, and 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.  doi:10.1021/ja807940y
  • Kowalski K, and 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. 

2008

  • Fan PD, M Valiev, and 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. 
  • Valiev M, EJ Bylaska, M Dupuis, and 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.  doi:10.1021/jp7104709
  • Epifanovsky E, K Kowalski, PD Fan, M Valiev, S Matsika, and A Krylov. 2008. "On the Electronically Excited States of Uracil." Journal of Physical Chemistry A 112(40):9983-9992.  doi:10.1021/jp803758q
  • Kamiya M, S Hirata, and M Valiev. 2008. "Fast Electron Correlation Methods for Molecular Clusters without Basis Set Superposition Errors ." Journal of Chemical Physics 128(7):Art. No. 074103.  doi:10.1063/1.2828517
  • Kowalski K, and 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.  doi:10.1002/qua.21741
  • Kowalski K, and 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. 
  • Lipton AS, RW Heck, GR Staeheli, M Valiev, WA De Jong, and 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. 
  • Nieplocha J, S Krishnamoorthy, M Valiev, MK Krishnan, BJ Palmer, and P Sadayappan. 2008. "Integrated Data and Task Management for Scientific Applications." In Proceedings of ICCS: Lecture Notes in Computer Science, vol. 5101, pp. 20-31.  Springer-Verlag, Berlin, Germany.  doi:10.1007/978-3-540-69384-0_6

2007

  • Valiev M, BC Garrett, MK Tsai, K Kowalski, SM Kathmann, GK Schenter, and 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). 
  • Valiev M, J Yang, J Adams, SS Taylor, and 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.  doi:10.1021/jp074853q
  • Bylaska EJ, M Valiev, JR Rustad, and JH Weare. 2007. "Structure and Dynamics of the Hydration Shells of the Al3+ Ion ." Journal of Chemical Physics 126(10):Art.no.104505. 
  • Hammond JR, M Valiev, WA De Jong, and K Kowalski. 2007. "Calculations of Molecular Properties in Hybrid Coupled-Cluster and Molecular Mechanics Approach." Journal of Physical Chemistry A 111(25):5492-5498.  doi:10.1021/jp070553x
  • Kerisit SN, KM Rosso, M Dupuis, and M Valiev. 2007. "Molecular Computational Investigation of Electron Transfer Kinetics across Cytochrome-Iron Oxide Interfaces." Journal of Physical Chemistry C 111(30):11363-11375. 
  • Tsai MK, K Kowalski, M Valiev, and 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.  doi:10.1021/jp074617f

2006

  • Valiev M, and 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.  doi:10.1063/1.2403847
  • Kowalski K, and 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. 
  • Kowalski K, and M Valiev. 2006. "Multiscale Dynamical Framework for High-Level Calculations of Finite Temperature Ground and Excited State Properties." In Journal of Physics: Conference Series ; SciDAC 2006, SCIENTIFIC DISCOVERY THROUGH ADVANCED COMPUTING, 25-29 June 2006, Denver, Colorado, USA , vol. 46, pp. 244-248.  Institute of Phyics Publishing, Philadelphia, PA.  doi:10.1088/1742-6596/46/1/035
  • Smith DMA, KM Rosso, M Dupuis, M Valiev, and 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.  doi:10.1021/jp057068r

2005

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

2003

  • Valiev M, EJ Bylaska, and 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. 

2002

  • Valiev M, EJ Bylaska, A Gramada, and JH Weare. 2002. "First Principles Molecular Dynamics Simulations Using Density-Functional Theory." In Reviews of Modern Quantum Chemistry: A Celebration of the Contributions of Robert G Parr.  World Scientific Publishing Company, Inc., Singapore, River Edge, NJ. 
  • Bylaska EJ, M Valiev, R Kawai, and JH Weare. 2002. "Parallel Implementation of the Projector Augmented Plane Wave Method for Charged Systems." Computer Physics Communications 143(1):11-28. 

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