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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 G., J. Zhang, M. Valiev, and X. Wang. 2017. "Structures and energetics of hydrated deprotonated cis-pinonic acid anion clusters and their atmospheric relevance." Physical Chemistry Chemical Physics. PCCP 19, no. 16:10676-10684. PNNL-SA-123107. doi:10.1039/c6cp08834a
  • Hou G., X. Wang, and M. Valiev. 2017. "Formation of (HCOO-)(H2SO4) Anion Clusters: Violation of Gas Phase Acidity Predictions." Journal of the American Chemical Society 139, no. 33:11321-11324. PNNL-SA-127350. doi:10.1021/jacs.7b05964
  • Pirojsirikul T., A.W. Goetz, J.H. Weare, R.C. 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, no. 18:1631-1639. PNNL-SA-122946. doi:10.1002/jcc.24804
  • Sun J., M. Konda, R. Parthasarathi, T. Dutta, M. Valiev, F. Xu, and B.A. Simmons, et al. 2017. "One-pot integrated biofuel production using low-cost biocompatible protic ionic liquids." Green Chemistry 19, no. 13:3152-3163. PNNL-SA-127956. doi:10.1039/c7gc01179b

2016

  • Hou G., M. Valiev, and X.B. Wang. 2016. "Deprotonated Dicarboxylic Acid Homodimers: Hydrogen Bonds and Atmospheric Implications." Journal of Physical Chemistry A 120, no. 15:2342-2349. PNNL-SA-115831. doi:10.1021/acs.jpca.6b01166
  • Hou G., X. Kong, M. Valiev, L. Jiang, and X.B. 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, no. 5:3628-3637. PNNL-SA-113280. doi:10.1039/C5CP05974G
  • Qin Z., G. Hou, Z. Yang, M. Valiev, and X. 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, no. 21:4969076. PNNL-SA-121206. doi:10.1063/1.4969076
  • Valiev M., S. Deng, and X.B. 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, no. 8:1518-1525. PNNL-SA-111663. doi:10.1021/acs.jpcb.5b07257

2015

  • Bhaskaran-Nair K., M. Valiev, S. Deng, W.A. Shelton, K. Kowalski, and X.B. Wang. 2015. "Probing microhydration effect on the electronic structure of the GFP chromophore anion: Photoelectron spectroscopy and theoretical investigations." Journal of Chemical Physics 143, no. 22:Article No. 224301. PNNL-SA-113513.

2014

  • Deng S., G. Hou, X. Kong, M. Valiev, and X.B. Wang. 2014. "Examining the Amine Functionalization in Dicarboxylates: Photoelectron Spectroscopy and Theoretical Studies of Aspartate and Glutamate." Journal of Physical Chemistry A 118, no. 28:5256-5262. PNNL-SA-103080. doi:10.1021/jp505439b
  • Shaikh N., M. Valiev, and S.V. Lymar. 2014. "Decomposition of Amino Diazeniumdiolates (NONOates): Molecular Mechanisms." Journal of Inorganic Biochemistry 141. PNNL-SA-89482. 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. PNNL-SA-94799.
  • Sellner B., M. Valiev, and S.M. Kathmann. 2013. "Charge and Electric Field Fluctuations in Aqueous NaCl Electrolytes." Journal of Physical Chemistry B 117, no. 37:10869-10882. PNNL-SA-96493. doi:10.1021/jp405578w
  • Van Kuiken B.E., M. Valiev, S.L. Daifuku, C. Bannan, M.L. Strader, H. Cho, and N. Huse, et al. 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, no. 21:4444-4454. PNNL-SA-91804.
  • Wen H., G. Hou, S.M. Kathmann, M. Valiev, and X.B. Wang. 2013. "Communication: Solute Anisotropy Effects in Hydrated Anion and Neutral Clusters." Journal of Chemical Physics 138, no. 3:Article No. 031101. PNNL-SA-91019. doi:10.1063/1.4776766

2012

  • Chuev G.N., M. Valiev, and M.V. 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, no. 4:1246-1254. PNNL-SA-84845. doi:10.1021/ct2009297
  • Murdachaew G., M. Valiev, S.M. Kathmann, and X.B. Wang. 2012. "Study of Ion Specific Interactions of Alkali Cations with Dicarboxylate Dianions." Journal of Physical Chemistry A 116, no. 9:2055-2061. PNNL-SA-82916. 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, no. 9:2371-2376. PNNL-SA-86625. doi:10.1021/jp3005986

2011

  • Govind N., E.J. Bylaska, W.A. De Jong, K. Kowalski, T. Straatsma, M. Valiev, and H.J. van Dam. 2011. "NWChem." In Encyclopedia of Parallel Computing, edited by D Padua. 1345-1353. New York, New York:Springer. PNNL-SA-75220.
  • Valiev M., and S.V. Lymar. 2011. "Structural and Mechanistic Analysis through Electronic Spectra: Aqueous Hyponitrite Radical (N2O2-) and Nitrosyl Hyponitrite Anion (N3O3-)." Journal of Physical Chemistry A 115, no. 43:12004-12010. PNNL-SA-80255. doi:10.1021/jp204967h
  • van Dam H.J., W.A. De Jong, E.J. Bylaska, N. Govind, K. Kowalski, T. Straatsma, and M. Valiev. 2011. "NWChem: scalable parallel computational chemistry." Wiley Interdisciplinary Reviews. Computational Molecular Science 1, no. 6:888-894. PNNL-SA-76231. doi:10.1002/wcms.62
  • Wang D., M. Valiev, and B.C. Garrett. 2011. "CH2Cl2 and OH- Reaction in Aqueous Solution: A Combined Quantum Mechanical and Molecular Mechanics Study." Journal of Physical Chemistry A 115, no. 8:1380-1384. PNNL-SA-75398. 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, no. 43:12047-12052. PNNL-SA-82050. doi:10.1021/jp2076808

2010

  • Cauet E.L., M. Valiev, and J.H. Weare. 2010. "Vertical Ionization Potentials of Nucleobases in a Fully Solvated DNA Environment." Journal of Physical Chemistry B 114, no. 17:5886-5894. PNNL-SA-66857.
  • Valiev M., E.J. Bylaska, N. Govind, K. Kowalski, T. Straatsma, H.J. van Dam, and D. Wang, et al. 2010. "NWChem: a Comprehensive and Scalable Open-Source Solution for Large Scale Molecular Simulations." Computer Physics Communications 181, no. 9:1477-1489. PNNL-SA-66553. doi:10.1016/j.cpc.2010.04.018

2009

  • Elsasser B.M., M. Valiev, and J.H. 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, no. 11:3869-3871. PNNL-SA-58125. doi:10.1021/ja807940y
  • 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, no. 21:6041-6043. PNNL-SA-65173. doi:10.1021/jp902118k
  • Govind N., P.V. Sushko, W.P. 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, no. 4-6:353-357. PNNL-SA-63223. doi:10.1016/j.cplett.2009.01.073
  • 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, no. 23:Article Number 234107. PNNL-SA-67688.
  • Valiev M., R. D'Auria, D.J. Tobias, and B.C. Garrett. 2009. "Interactions of Cl- and OH Radical in Aqueous Solution." Journal of Physical Chemistry A 113, no. 31:8823-8825. PNNL-SA-65411.

2008

  • Epifanovsky E., K. Kowalski, P. Fan, M. Valiev, S. Matsika, and A. Krylov. 2008. "On the Electronically Excited States of Uracil." Journal of Physical Chemistry A 112, no. 40:9983-9992. PNNL-SA-60634. doi:10.1021/jp803758q
  • Fan P., 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, no. 1-3:205-209. PNNL-SA-58403.
  • 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, no. 7:Art. No. 074103. PNNL-SA-56634. 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, no. 12:2178-2190. PNNL-SA-53239. 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, no. 24:5538-5541. PNNL-SA-57526.
  • Lipton A.S., R.W. Heck, G.R. Staeheli, M. Valiev, W.A. De Jong, and P.D. Ellis. 2008. "A QM/MM Approach to Interpreting Zn-67 Solid-State NMR data in Zinc Proteins." Journal of the American Chemical Society 130, no. 19:6224-6230. PNWD-SA-8060.
  • Nieplocha J., S. Krishnamoorthy, M. Valiev, M. Krishnan, B.J. Palmer, and P. Sadayappan. 2008. "Integrated Data and Task Management for Scientific Applications." In Proceedings of ICCS: Lecture Notes in Computer Science, 5101, 20-31. Berlin:Springer-Verlag. PNNL-SA-59937. doi:10.1007/978-3-540-69384-0_6
  • Valiev M., E.J. Bylaska, M. Dupuis, and P.G. 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, no. 12:2713-2720. PNNL-SA-56528. doi:10.1021/jp7104709

2007

  • Bylaska E.J., M. Valiev, J.R. Rustad, and J.H. Weare. 2007. "Structure and Dynamics of the Hydration Shells of the Al3+ Ion." Journal of Chemical Physics 126, no. 10:Art.no.104505. PNNL-SA-52973.
  • Hammond J.R., M. Valiev, W.A. De Jong, and K. Kowalski. 2007. "Calculations of Molecular Properties in Hybrid Coupled-Cluster and Molecular Mechanics Approach." Journal of Physical Chemistry A 111, no. 25:5492-5498. PNNL-SA-53480. doi:10.1021/jp070553x
  • Kerisit S.N., K.M. 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, no. 30:11363-11375. PNNL-SA-54356.
  • Tsai M.K., 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, no. 42:10478-10482. PNNL-SA-55912. doi:10.1021/jp074617f
  • Valiev M., B.C. Garrett, M.K. Tsai, K. Kowalski, S.M. Kathmann, G.K. 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, no. 5:51102 (1-4). PNNL-SA-55381.
  • Valiev M., J. Yang, J. Yang, J. Adams, S.S. Taylor, and J.H. Weare. 2007. "Phosphorylation Reaction in cAPK Protein Kinase - Free Energy Quantum Mechanic/Molecular Mechanics Simulations." Journal of Physical Chemistry B 111, no. 47:13455-13464. PNNL-SA-53829. doi:10.1021/jp074853q

2006

  • 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, no. 48:13106-13111. PNNL-SA-50543.
  • 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, 46, 244-248. Philadelphia, Pennsylvania:Institute of Phyics Publishing. PNNL-SA-50655. doi:10.1088/1742-6596/46/1/035
  • Smith D.M., K.M. Rosso, M. Dupuis, M. Valiev, and T. 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, no. 31:15582-15588. PNNL-SA-51763. doi:10.1021/jp057068r
  • 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, no. 21:Art. No. 211101. PNNL-SA-49559. doi:10.1063/1.2403847

2005

  • Hirata S., M. Valiev, M. Dupuis, S.S. Xantheas, S. Sugiki, and H. Sekino. 2005. "Fast Electron Correlation Methods for Molecular Clusters in the Ground and Excited States." Molecular Physics 103, no. 15-16:2255-2265. PNNL-SA-42030.

2003

  • Valiev M., E.J. Bylaska, and J.H. Weare. 2003. "Calculations of the Electronic Structure of 3d Transition Metal Dimers with Projector Augmented Plane Wave Method." Journal of Chemical Physics 119, no. 12:5955-5964. PNNL-SA-36780.
  • Valiev M., R. Kawai, J.A. Adams, and J.H. 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, no. 33:9926-9927.

2002

  • Bylaska E.J., M. Valiev, R. Kawai, and J.H. Weare. 2002. "Parallel Implementation of the Projector Augmented Plane Wave Method for Charged Systems." Computer Physics Communications 143, no. 1:11-28. PNNL-SA-34313.
  • Valiev M., E.J. Bylaska, A. Gramada, and J.H. 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. Singapore, River Edge, New Jersey:World Scientific Publishing Company, Inc. PNNL-SA-35277.

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