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Postdoctoral, 2002-2005
Los Alamos National Lab, Theoretical Division, Adviser: Sergei Tretiak

Postdoctoral, 2000-2002
City College of New York, Computational Biophysical Chemistry, Adviser: Themis Lazaridis

Ph.D., 2000 (Thesis)
City University of New York, Adviser: J. J. Dannenberg

B.S./M.S., 1988 (Diploma)
Moscow State University, Adviser: Peter M. Zorkii


  • Fall 2008, Nanophotonics
  • Fall 2008, Special Topics in Physics (Theory and computations of molecular wavefunction)
  • Spring 2008, Honors Chemistry Fundamentals II
  • Fall 2007, Honors Chemistry Fundamentals I
  • Fall 2006, Honors Chemistry Fundamentals I
  • Spring 2005, Physical Chemistry II
  • Fall 2005, Honors Chemistry Fundamentals I


Multiscale simulations of the H-bonded aggregation: toward rational control over amyloid fibril formation

Density Functional Theory in Design of Fatigue-resistant Photochromic Materials for Optical Switching and Data Storage

Photochromic compounds change their color upon irradiation owing to the transition from open to closed ring isomers (photocyclization). They have prospective applications in optical switches and data storage applications, which require design of chromophores with enhanced properties of interest. Prediction of these properties based on the molecular structure is an important component of rational design strategy. We apply Density Functional Theory methods to predict kinetics of cycloreversion of thermal stability, fatigue resistance and the mechanism of byproduct formation for in dithienyl perfluorocyclopentenes.

Comparison of Sum over States (SOS) and Coupled Electronic Oscillator (CEO) formalisms used for computational design of Two Photon Absorbing materials with Time-Dependent Density Functional Theory

Two-photon absorption (2PA) and subsequent processes may be localized in space with a tightly focused laser beam. This property is used in a wide range of applications, including three dimensional data storage. We report theoretical studies of 3 conjugated chromophores experimentally shown to have large 2PA crosssections. We use Time Dependent Density Functional Theory (TD-DFT) to describe the electronic structure. A third order coupled electronic oscillator formalism is applied to calculate the frequency-dependent second order hyperpolarizability. Alternatively, sum over states formalism using state-to-state transition dipoles provided by a posteriory Tamm-Dancoff approximation is employed. It provides new venues for qualitative interpretation and rational design of 2PA chromophores.

Development and Application of Density Functional Theory in Design of Two-Photon Absorbing Photochromic Materials for Optical Data Storage

Diarylethenes are able to undergo light-induced transition from the open to closed ring isomer (photocyclization) accompanied by the change in optical properties (photochromism). This ability holds a great promise for photonic applications, including optical data storage and ultrafast optical switching. Photocyclization initiated by two photon absorption (2PA) could drastically increase the density of these devices. We analyze the Kohn-Sham orbitals responsible for photocyclization, and suggest the molecular structures that are expected to have both 2PA and photochromic activity. The proposed modifications are validated using the potential energy surfaces of the excited states and two-photon absorbing profiles, predicted using Time-Dependent Density Functional Theory (TD-DFT).

Reliability of Density Functional Theory for Estimation of the Molecular Hyperpolarizability

This work presents application of Density Functional Theory (DFT) to study electronic first hyperpolarizability (β ) of conjugated molecules, used for second harmonic generation (SHG). We use Donor/Acceptor-substituted benzenes and stilbenes as reference molecules, calculate β with four DFT functionals, HF and MP2 methods, and compare to the experimental data. Three main questions are addressed: 1) choice of the basis set, 2) choice of the method, and 3) the accurate way to compare calculated results to each other and to experiment. Instead of the absolute values, we propose to use relative ones (ratios of β) for comparison between the theory and experiment. We also recommend to rescale the ratios obtained at BMK/6- 31+G* level of theory for the rational design of SHG materials.

Derivation and Implementation of the Pairwise Spin-Contamination Correction and Application to Study Potential Energy Curves for 3D Transition Metal Hydrides from BS-DFT

Chemical bond between transition metal atom and hydrogen is important in surface chemistry and nanoparticle cluster catalysis, as the energetics of this bond breaking plays a critical role in hydrogen transfer process. The studies of Transition Metal (TM) systems present a challenge for theoretical description due to the presence of several electronic states close in energy which results in strong electron correlation. For this reason molecules containing TMs serve as an important testing ground for various methods in theoretical chemistry and molecular physics. Density functional theory (DFT) is the method of choice to study large systems, due to relatively low computational cost.

Biomedical use of two-photon absorption: computer-assisted design of non-linear optical materials for photodynamic therapy and fluorescent labels

Multiscale simulations of the H-bonded aggregation: toward rational control over amyloid fibril formation

Protein self-assembly into β-sheet structures is a critical factor of neurodegenerative diseases, such as Altzheimer’s. Accurate simulations of the thermodynamic and kinetic properties of this process may contribute to a better understanding and finding a cure. However, large molecular weight of the aggregates makes direct molecular dynamics (MD) simulation a challenge. Instead, we apply the multiscale approach where atomistic MD on the protein fragments produce pairwise potentials which are than used for coarse-grained simulations of self-assembly. As a first step toward this goal we obtained the potentials of mean force between various amino acid side chain pairs. Explicit solvent with umbrella sampling and the weighted histogram analysis method were used. The side chains were constrained in various orientations inside a spherical cluster of 200 water molecules, and Spherical Solvent Boundary Potential was used to account for the solvent outside this sphere. The strongest attraction (4.5 kcal/mol) was found for the coaxial Arg+…Glu- pair. Many neutral and like-charged side chains display a weak (c.a. 2 kcal/mol) attraction.

Quantum Chemistry of Quantum Dots

HOMO calculated at DFT level (B3PW91/ LANL2mb) in Cd32Se14(SeH)36(PH3)4, the cluster modeling colloidal quantum dot of 2 nm in diameter. Electronic structure of quantum dots strongly depends on passivating ligands. In a joined experimental and theoretical investigation, we have found that ligand removal does not change the absorption spectra, while oxidation shifts the maximum into IR region.

Computer Modeling for the Energy Conversion Technologies of the Future

One of the research directions in my group is theory and modeling of energy conversion processes and design of functional materials used for that purpose.

Current Funding

Past Funding

  • DOE LANL-UCSB Collaborative Research Program: Computationally guided control of nanomaterial synthesis: carbon nanotube growth catalyzed by metal nanoparticles
    Co-PI: Masunov
  • UCF Office of Research (ORC): Computer simulations of decomposition thermodynamics and kinetics of hydrogen clathrate hydrates as novel hydrogen storage materials
    PI: Masunov
  • NASA State University System Florida Turbine Initiative (SFTI Ph1): Composite cathodes for Intermediate Temperature Solid Oxide Fuel Cells: A comprehensive approach to designing materials for superior functionality
    Co-PI: Masunov
  • DOD U.S. Army Research, Development and Engineering Command/Simulation Technology Center (RDECOM-STC): High performance computing for simulation training systems
    Subcontract: Masunov

Select Publications

Yakovenko A. A.; Gallegos J. H.; Antipin M. Yu.; Masunov A.E.; Timofeeva T.V. “Crystal Morphology as an Evidence of Supramolecular Organization in Adducts of 1,2-bis(chloromercurio)tetrafluorobenzene with Organic Esters” Crystal Growth and Design, Published online June 22, 2011.

Gadzhiev, O. B.; Ignatov, S. K.; Gangopadhyay, S.; Masunov, A. E.; Petrov, A. I. “Mechanism of nitric oxide oxidation reaction (2NO+O2→2NO2) revisited.” Journal of Chemical Theory and Computation, Published online May 30, 2011.

Berhanu, W.M.; Masunov, A.E. “Unique example of amyloid aggregates stabilized by main chain H-bond instead of the steric zipper: molecular dynamics study of the amyloidogenic segment of amylin wild-type and mutants.” Journal of Molecular Modeling. Published online May 28, 2011.

Goel, S.; Masunov, A. E. “Density Functional Theory Study of Small Nickel Clusters.” Journal of Molecular Modeling. Published online May 20, 2011.

Berhanu, W. M.; Masunov, A. E. “Molecular dynamic simulation of wildtype and mutants of the polymorphic amyloid NNQNTF segments of elk prion: structural stability and thermodynamic of association.” Biopolymers, 95(9), 573-590, 2011.

Goel, S.; Masunov, A. E. “Dissociation Curves and Binding Energies of Diatomic Transition Metal Carbides from Density Functional Theory.” Int. J. Quant. Chem. Published online Jan. 18, 2011.

Liu, J.; Mikhaylov, I. A.; Zou, J.; Osaka, I.; Masunov, A. E.; McCullough, R. D.; Zhai, L. “Insight into how molecular structures of thiophene-based conjugated polymers affect crystallization behaviors.” Polymer, 52(10), 2302-2309, 2011.

Patel, P. D.; Masunov, A. E. “Theoretical Study of Photochromic Compounds: Part 3. Prediction of Thermal Stability.” J. Phys. Chem. C 115(20), 10292-10297, 2011.

Borowska, L.; Fritzsche, S.; Kik, P.; Masunov, A. E. “Near-field enhancement of infrared intensities for f-f transitions in Er3+ ions.” Journal of Molecular Modeling. 17 (3), 423-428, 2011.

Berhanu, W. M.; Masunov, A. E. “Can Molecular Dynamics Simulations assist in design of specific inhibitors and imaging agents of amyloid aggregation? Structure, stability and free energy predictions for amyloid oligomers of VQIVYK, MVGGVV and LYQLEN.” Journal of Molecular Modeling. Published online: Dec. 21, 2010. DOI 10.1007/s00894-010-0912-4

Mikhailov, I. A.; Masunov, A. E. “Theory and computations of two-photon absorbing photochromic chromophores.” European J. Chemistry. 1 (2), 142-161, 2010.

Hirsch-Kuchma, M.; Komanski, C. B.; Colon, J.; Teblum, A.; Masunov, A. E.; Seal, S.; Alvarado, B.; Summy, J.; Baker, C. H. “Phosphate ester hydrolysis by cerium oxide nanoparticles.” Nanomedicine: Nanotechnology, Biology and Medicine. 6 (6), 738-744, 2010.

Masunov, A. E. “Theoretical Spectroscopy of Carbocyanine Dyes Made Accurate by Frozen Density Correction to Excitation Energies obtained by TD-DFT.” International Journal of Quantum Chemistry. 110 (15), 3095-3100, 2010.

Passier, R.; Ritchie, J.P.; Toro, C.; Diaz, C.; Masunov, A.E.; Belfield, K.D.; Hernandez, F. E. “Thermally controlled preferential molecular aggregation state in a thiacarbocyanine dye.” J. Chem. Phys. 133(13), 134508, 2010.

Webster, S.; Peceli, D.; Hu, H.; Padilha, L. A.; Przhonska, O. V.; Masunov, A. E.; Gerasov, A. O.; Kachkovski, A. D.; Slominsky, Y. L.; Tolmachev, A. I.; Kurdyukov, V. V.; Viniychuk, O. O.; Barrasso, E.; Lepkowicz, R.; Hagan, D. J.; Van Stryland, E. W. “Near-unity quantum yields for intersystem crossing and singlet oxygen generation in polymethine-like molecules: design and experimental realization.” J. Phys. Chem. Lett. 1(15), 2354-2360, 2010.

Belfield K.D.; Bondar M.V.; Frazer A.; Morales A.R.; Kachkovsky O.D.; Mikhailov I.A.; Masunov A.E.; Przhonska O.V. “Fluorene-Based Metal-Ion Sensing Probe with High Sensitivity to Zn2+ and Efficient Two-Photon Absorption.” J. Phys. Chem. C 114(28), 9313-9321, 2010.

Gangopadhyay, S.; Inerbaev, T. A.; Masunov, A. E.; Mesit, J.; Guha, R.; Sleiti, A.; Kapat, J. “Understanding of oxygen vacancy migration and clustering in barium/strontium ferrite/cobaltite.” Solid State Ionics. 181, 1067-1073, 2010.

Gangopadhyay, S., Masunov,* A. E., Poalelungi, E., Leuenberger, M. “Weak magnetic coupling in Mn12 molecular magnet is predicted correctly at DFT+U theory level.” J. Chem. Phys. 132(24), 244104, 2010.

Vincent, A.; Inerbaev, T. M.; Babu, S.; Karakoti, A. S.; Self, W. T.; Masunov, A. E.; Seal, S. “Tuning Hydrated Nanoceria Surfaces: Experimental/Theoretical Investigations of Ion Exchange and Implications in Organic and Inorganic Interactions.” Langmuir. 26(10), 7188-7198, 2010.

Inerbaev, T. M.; Seal, S.; Masunov, A. E., “Density functional study of oxygen vacancy formation and spin density distribution in octahedral ceria nanoparticles.” Journal of Molecular Modeling. 16(10), 1617-1623, 2010.

Berhanu, W. M.; Mikhailov, I. A.; Masunov, A. E. “Are density functional theory predictions of the Raman spectra accurate enough to distinguish conformational transitions during amyloid formation?” Journal of Molecular Modeling. 16(6), 1093-1101, 2010.

Berhanu, W. M.; Masunov, A. E. “Natural polyphenols as inhibitors of amyloid aggregation. Molecular Dynamics study of GNNQQNY heptapeptide decamer.” Biophysical Chemistry. 149 (1-2), 12-21, 2010.

Satyender Goel and Artëm E. Masunov. (2008). “Potential energy curves and electronic structure of 3d transition metal hydrides and their cations.” J. Chem. Phys. 129, 214302.

Suponitsky KY, Masunov AE, Antipin MY. (2008). “Conformational dependence of the first molecular hyperpolarizability in the computational design of nonlinear optical materials for optical switching.” Mendeleev Communications 18(5), 265-267.

Zakharov A, Masunov AE, Dreuw A. (2008). “Catalytic Role of Calix[4]hydroquinone in Acetone-Water Proton Exchange: A Quantum Chemical Study of Proton Transfer via Keto-Enol Tautomerism.” Journal of Physical Chemistry A, 112(41), 10405-10412.

Yang P, Tretiak S, Masunov AE, et al. (2008). “Quantum chemistry of the minimal CdSe clusters.” Journal of Chemical Physics 129(7), article number 074709.

Suponitsky KY, Tafur S, Masunov AE. (2008). “Applicability of hybrid density functional theory methods to calculation of molecular hyperpolarizability.” Journal of Chemical Physics 129(4), article number 044109.

De Boni L, Toro C, Masunov AE, et al. (2008). “Untangling the excited states of DR1 in solution: An experimental and theoretical study.” Journal of Physical Chemistry A, 112(17), 3886-3890.

Mikhailov IA, Tafur S, Masunov AE. (2008). “Double excitations and state-to-state transition dipoles in pi-pi* excited singlet states of linear polyenes: Time-dependent density-functional theory versus multiconfigurational methods.” Physical Review A 77(1), article number 012510.

Toro C, Thibert A, De Boni L, et al. (2008). “Fluorescence emission of disperse red 1 in solution at room temperature.” Journal of Physical Chemistry B 112(3), 929-937.

Graduate Students

Students will have opportunities to apply their knowledge and widen their horizons in interdisciplinary filed of Nanoscience, including Biochemistry and Materials Science, Biology and Physics, Computers and Device Engineering. They will learn a wide variety of Computational Chemistry techniques including methodological developments, applications, or both. Students will have a choice of different projects, such as computer-assisted design of nonlinear optical materials (for bioimaging and photodynamic therapy), catalytic effects of ceria nanoparticles (to slow down biological aging), control over growth of carbon nanotubes (for microelectronics applications) and amyloid fibrils (Parkinson’s disease treatment), development of polarizable force fields to describe clathrates (hydrogen storage materials) and protein/lignad interactions (computational drug design), methodological developments of density functional theory (for description of strongly correlated systems) and implicit solvation models (for more accurate simulations of soft condensed matter). The acquired experience and problem-solving skills will open the doors to successful careers in industry and academia.