Vasiliy Serafimovich Znamenskiy

@bmcc.cuny.edu

Borough of Manhattan Community College, Science Department
The City University of New York

Vasiliy Serafimovich Znamenskiy


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https://researchid.co/znamenski
10

Scopus Publications

736

Scholar Citations

9

Scholar h-index

9

Scholar i10-index

Scopus Publications

  • Electronic spectroscopy and computational studies of glutathionylco(III) balamin
    Azaria S. Eisenberg, Iya V. Likhtina, Vasiliy S. Znamenskiy, Ronald L. Birke
    Journal of Physical Chemistry A, 2012
    We have studied glutathionylcobalamin (GS-Cbl) by optical spectroscopy and with density functional theory (DFT) and time-dependent DFT (TD-DFT) electronic structure methods of truncated geometric models. We examined the geometric structure of the models by comparison of DFT calculations with recent high-resolution experimental X-ray structure data ( Hannibal, L. et al. Inorg. Chem. 2010, 49, 9921) for GS-Cbl, and we examined the TD-DFT excitation simulations by comparison of the models with measured optical spectra. The calculations employed the B3LYP hybrid functional and the nonhybrid BP86 functional in both vacuum and water (conductor polarized continuum model (cpcm)) with the 6-311G(d,p) basis set. The optimized geometric structure calculations for six truncated models were made by varying the chemical structure, solvent model, and the two DFT functionals. All showed similar geometry. Charge decomposition analysis (CDA) and extended charge decomposition analysis (ECDA), especially with BP86 shows the similar charge transfer nature of the Co-S bond in GS-Cbl and the Co-C bond in CH(3)Cbl. Mayer and Wiberg bond orders illustrate the similar covalent nature of the two bonds. Finally, absolute optical spectral simulation calculations were compared with the experimental UV-visible extinction spectrum and the electronic circular dichroism (ECD) differential extinction spectrum. The BP86 method shows more spectral features, and the best fit was found for a GS-Cbl model with 5,6-dimethylbenzimidazole at the BP86/6-311G(d,p) level with a water cpcm solvent model. The excited state transitions were investigated with Martin's natural transition orbitals (NTOs). The BP86 calculations also showed π bonding interactions between Co and the axial S of the GS- ligand in the molecular orbitals (MOs) and NTOs.
  • A charge-transfer surface enhanced Raman scattering model from time-dependent density functional theory calculations on a Ag10 -pyridine complex
    Ronald L. Birke, Vasiliy Znamenskiy, John R. Lombardi
    Journal of Chemical Physics, 2010
    Vibrational frequency calculations were made for a Ag10-pyridine vertex complex with density functional theory (DFT) for static simulated spectra and with time-dependent DFT (TD-DFT) for preresonance and resonance simulated spectra using both B3LYP/LANL2DZ and BP86/TZP methodologies. In addition, 40 excited states of the complex were calculated and assigned symmetry based on a C2v symmetry of the optimized complex found with B3LYP/LANL2DZ. Molecular orbital isosurfaces show that the excited states involve both Ag10 intercluster excitations and charge-transfer (CT) excitations between the Ag nanocluster and the pyridine molecule. An excitation around 500 nm involving CT from the Ag cluster to pyridine was found in both calculations. For free pyridine, the relative average deviations between unscaled calculated and experimental results were 1.5 cm−1 for BP86 and 3.1 cm−1 for the B3LYP calculations. For the complex, simulated spectra at a variety of excitation wavelengths were calculated. In the case of 514 nm excitation, the simulated Raman cross section from the TD-DFT calculations (near the CT resonance) was plotted versus Raman shift frequency and compared with an experimental surface enhanced Raman scattering (SERS) spectrum obtained on an oxidation-reduction cycle, ORC roughened Ag electrode. The BP86 TD-DFT calculation with finite damping term showed a better fit to experimental spectrum with respect to both relative intensities and frequencies. The average deviation of the unscaled BP86 calculations for 16 bands in the experimental spectrum was 13.0 cm−1. The calculated spectrum in both cases shows many contributions from nontotally symmetric as well as totally symmetric modes, indicating the contribution of Herzberg–Teller (HT) scattering. The simulated intensities of the Raman modes of different symmetry from Ag10-pyridine can be correlated with HT intensity borrowing from excited states of given symmetry and decent oscillator strength. These results explain the appearance of the a2 mode at 388 cm−1 and the moderately strong b2 mode at 1573 cm−1 found in the SERS experimental spectrum. The good agreement between experimental and simulated results indicates that a small Ag nanocluster-pyridine vertex complex can be used to simulate spectra with good relative intensities, if not absolute intensities, and accurate frequencies for most of the SERS bands for adsorbed pyridine on roughened bulk Ag.
  • Quantum mechanical calculations of charge effects on gating the KcsA channel
    Alisher M. Kariev, Vasiliy S. Znamenskiy, Michael E. Green
    Biochimica Et Biophysica Acta Biomembranes, 2007
  • Quantum calculations on hydrogen bonds in certain water clusters show cooperative effects
    Vasiliy S. Znamenskiy, Michael E. Green
    Journal of Chemical Theory and Computation, 2007
    Water molecules in clefts and small clusters are in a significantly different environment than in bulk water. We have carried out ab initio calculations that demonstrate this in a series of clusters, showing that cooperative effects must be taken into account in the treatment of hydrogen bonds and water clusters in such bounded systems. Hydrogen bonds between water molecules in simulations are treated most frequently by using point charge water potentials, such as TIP3P or SPC, sometimes with a polarizable extension. These produce excellent results in bulk water, for which they are calibrated. Clefts are different from bulk; it is necessary to look at smaller systems, and investigate the effect of limited numbers of neighbors. We start with a study of isolated clusters of water with varying numbers of neighbors of a hydrogen bonded pair of water molecules. The cluster as a whole is in vacuum. The clusters are defined so as to provide the possible arrangements of nearest neighbors of a central hydrogen bonded pair of water molecules. We then scan the length and angles of the central hydrogen bond of the clusters, using density functional theory, for each possible arrangement of donor and acceptor hydrogen bonds on the central hydrogen bonding pair; the potential of interaction of two water molecules varies with the number of donor and of acceptor neighbors. This also involves changes in charge on the water molecules as a function of bond length, and changes in energy and length as a function of number of neighboring donor and acceptor molecules. Energy varies by approximately 6 k(B)T near room temperature from the highest to the lowest energy when bond length alone is varied, enough to seriously affect simulations.
  • Charge reduction in electrosprays: Slender nanojets as intermediates J
    Ioan Marginean, Vasiliy Znamenskiy, Akos Vertes
    Journal of Physical Chemistry B, 2006
    Molecular dynamics simulations were used to study charge reduction in electrosprayed liquids through the formation of slender nanojet intermediates. The dynamics of shape relaxation and disintegration were followed as a function of charge in cylindrical water nanojets containing protonated diglycine molecules. Depending on the overall charge, simulations showed three basic scenarios for nanojet evolution. Moderately charged nanojets reduced to spheres, whereas nanojets charged close to the Rayleigh limit divided into two offspring droplets. Due to the large Coulomb interaction between ions, highly charged nanojets suffered repeated fission until the resulting droplets were charged below the Rayleigh limit. We demonstrated the role of surface fluctuations and Maxwell stress distributions in the disintegration process. The relaxation dynamics of the moderately charged systems to spherical geometry followed a damped oscillator behavior. Compared to neutral water jets, the presence of charges in subcritical nanojets resulted in a stiffer system with longer relaxation times to spherical geometry. Interparticle forces acting between the separating offspring droplets in nanojet breakup were also determined. Due to the increased role of fluctuations in nanojets, the Rayleigh limit was shown to overestimate the maximum charge on stable systems indicating higher nanodroplet production efficiency than one would expect from macroscopic theories alone.
  • Solvation dynamics of room-temperature ionic liquids: Evidence for collective solvent motion on sub-picosecond timescales
    Mark N. Kobrak, Vasiliy Znamenskiy
    Chemical Physics Letters, 2004
  • Topological changes of hydrogen bonding of water with acetic acid: AIM and NBO studies
    Vasiliy S. Znamenskiy, Michael E. Green
    Journal of Physical Chemistry A, 2004
    Hydrogen bonding has been studied in a model system, originally devised for the KcsA K+ ion channel, using density functional calculations. The model was to represent the putative gating region of the channel. Four acetic acids here are fixed at approximately 4-fold symmetry; six water molecules are added. Initial configurations had two water molecules in the center of the near-square defined by the carboxyls of the acetic acids, plus one water at each corner on the outside. Certain configurations of the acetic acids allow an extra water molecule to move into the center of the group; a move of 0.1 A by the acetic acids suffices to produce this jump (>2 A). In certain cases, the inner and outer water positions were nearly isoenergetic. Atoms in molecules (AIM) and natural bond orbital (NBO) provide complementary techniques for studying the changes in bonding and in electron density that accompany the different positions of the water molecules, including discontinuous changes in the topology of bonding. Two...
  • Molecular dynamics study of polarity in room-temperature ionic liquids
    Vasiliy Znamenskiy, Mark N. Kobrak
    Journal of Physical Chemistry B, 2004
    In this work, we use molecular dynamics simulation to explore the physical principles governing the polarity of room-temperature ionic liquids. We use the calculated absorption spectrum of the solvatochromic dye molecule betaine-30 as a proxy for polarity and characterize the solute-solvent interactions responsible for the solvatochromic shift. We analyze specific solute-solvent interactions and discuss the complications posed by the proximity of counterions in solution. We also explore the question of competition between solutesolvent and solvent-solvent interactions and find evidence supporting a recently proposed scheme for control of solvent polarity. Finally, we show that nonspecific electrostatic solute -solvent interactions are screened by the ionic solvent, dictating that the thermodynamic properties of solvation are determined by local interactions. However, thermal fluctuations create transient long-ranged solute -solvent interactions that could be important for chemical kinetics.
  • Solvated Ion Evaporation from Charged Water Nanodroplets
    Vasiliy Znamenskiy, Ioan Marginean, Akos Vertes
    Journal of Physical Chemistry A, 2003
    The behavior of electrified droplets in an atmospheric environment and the mechanism of ion formation in electrospray ionization are the subject of continuing debate. Experimental evidence to decide between the various models of ion formation (e.g., ion evaporation, Coulomb explosion, and charge residue model) is not readily available and is especially scarce for nanometer-sized droplets. Even the morphology, the structure, and the dynamics of aqueous nanodroplets containing ionic solutes are poorly understood. Classical molecular dynamics simulations were used to explore the effect of ions on the shape and structure of these droplets. We also followed the gas-phase formation of hydronium and glycine homologue ions from the disintegrating nanodroplets. Droplets up to 6.5 nm in diameter were studied using potentials for the peptides and water that accounted for their internal degrees of freedom. Validity testing of the model indicated good agreement between the calculated radial distribution functions for ...
  • Molecular dynamics of ion formation from charged nanodroplets in electrospray ionization
    Proceedings 50th Asms Conference on Mass Spectrometry and Allied Topics, 2002

RECENT SCHOLAR PUBLICATIONS

  • Tutoring Prompt for Personalized Self-Study Using Generative AI
    VS Znamenskiy
    2026
  • Historical Overview of Tissue Preservation by Low Temperatures Under Pressure, Eliminating Ice Formation
    V Znamenskiy
    No, this paper has not appeared, nor has it been accepted to appear, in any … , 2025
    2025
  • Measurement Lab Quiz – Exported as Brightspace Package
    V Znamenskiy
    https://doi.org/10.6084/m9.figshare.29247533.v1 , 2025
    2025
  • Integrating Universal Generative AI Platforms in Educational Labs to Foster Critical Thinking and Digital Literacy
    V Znamenskiy, R Niyazov, J Hernandez
    3rd International Conference on Computer Science, Engineering and Artificial … , 2025
    2025
    Citations: 4
  • Pattern Discovery Exercises: Fill-in-the-Blank Sequence Tasks
    V Znamenskiy
    https://doi.org/10.5281/zenodo.15252816. , 2025
    2025
  • Ideal Mathematical Pendulum: Examples of Physics Problem Conditions Expressed Primarily Through Diagrams
    V Znamenskiy
    2025
  • Challenges in Developing Physical Intuition in College General Physics Courses
    VS Znamenskiy, R Niyazov
    2025
  • CityTech Algebra based Physics Exam1 (Brightspace Quiz)
    VS Znamenskiy, R Niyazov
    2025
  • Charging and Discharging Capacitors: Brightspace Package of an Arithmetic Quiz
    V Znamenskiy
    2025
  • R12 Equivalent Resistance Reduction Steps
    VS Znamenskiy, R Niyazov
    2025
  • Principles for Physics Lab Reports Using Google Sheets
    V Znamenskiy
    2025
  • Artificial Intelligence and Astronomy: Lab Manual for Generative AI-Based Learning Activities
    V Znamenskiy
    2025
    Citations: 1
  • Formulas for Algebra-Based College Physics Ⅰ
    V Znamenskiy
    2025
  • Find the rule for constructing the row elements for each row and insert the missing elements instead of the “?” signs
    V Znamenskiy
    2025
  • Trying to Get the Chatgpt AI to Generate Educational Quizzes in a Specific Format Designed for Upload to Blackboard
    V Znamenskiy
    2nd Annual BMCC Assessment Day Colloquium Student Engagement Strategies … , 2023
    2023
  • Electronic spectroscopy and computational studies of glutathionylco (III) balamin
    AS Eisenberg, IV Likhtina, VS Znamenskiy, RL Birke
    The Journal of Physical Chemistry A 116 (25), 6851-6869 , 2012
    2012
    Citations: 25
  • A charge-transfer surface enhanced Raman scattering model from time-dependent density functional theory calculations on a Ag10-pyridine complex
    RL Birke, V Znamenskiy, JR Lombardi
    The Journal of chemical physics 132 (21) , 2010
    2010
    Citations: 89
  • Фейсбук группа "Физика": https://www.facebook.com/groups/PhysicsInRussian
    ВС Знаменский
    https://www.facebook.com/groups/PhysicsInRussian , 2008
    2008
  • Quantum mechanical calculations of charge effects on gating the KcsA channel
    AM Kariev, VS Znamenskiy, ME Green
    Biochimica et Biophysica Acta (BBA)-Biomembranes 1768 (5), 1218-1229 , 2007
    2007
    Citations: 27
  • Quantum calculations on hydrogen bonds in certain water clusters show cooperative effects
    VS Znamenskiy, ME Green
    Journal of chemical theory and computation 3 (1), 103-114 , 2007
    2007
    Citations: 60

MOST CITED SCHOLAR PUBLICATIONS

  • Molecular dynamics study of polarity in room-temperature ionic liquids
    V Znamenskiy, MN Kobrak
    The Journal of Physical Chemistry B 108 (3), 1072-1079 , 2004
    2004
    Citations: 172
  • Solvated ion evaporation from charged water nanodroplets
    V Znamenskiy, I Marginean, A Vertes
    The Journal of Physical Chemistry A 107 (38), 7406-7412 , 2003
    2003
    Citations: 152
  • Solvation dynamics of room-temperature ionic liquids: evidence for collective solvent motion on sub-picosecond timescales
    MN Kobrak, V Znamenskiy
    Chemical physics letters 395 (1-3), 127-132 , 2004
    2004
    Citations: 136
  • A charge-transfer surface enhanced Raman scattering model from time-dependent density functional theory calculations on a Ag10-pyridine complex
    RL Birke, V Znamenskiy, JR Lombardi
    The Journal of chemical physics 132 (21) , 2010
    2010
    Citations: 89
  • Quantum calculations on hydrogen bonds in certain water clusters show cooperative effects
    VS Znamenskiy, ME Green
    Journal of chemical theory and computation 3 (1), 103-114 , 2007
    2007
    Citations: 60
  • Charge reduction in electrosprays: slender nanojets as intermediates
    I Marginean, V Znamenskiy, A Vertes
    The Journal of Physical Chemistry B 110 (12), 6397-6404 , 2006
    2006
    Citations: 36
  • Quantum mechanical calculations of charge effects on gating the KcsA channel
    AM Kariev, VS Znamenskiy, ME Green
    Biochimica et Biophysica Acta (BBA)-Biomembranes 1768 (5), 1218-1229 , 2007
    2007
    Citations: 27
  • Electronic spectroscopy and computational studies of glutathionylco (III) balamin
    AS Eisenberg, IV Likhtina, VS Znamenskiy, RL Birke
    The Journal of Physical Chemistry A 116 (25), 6851-6869 , 2012
    2012
    Citations: 25
  • Topological changes of hydrogen bonding of water with Acetic Acid: AIM and NBO studies
    VS Znamenskiy, ME Green
    The Journal of Physical Chemistry A 108 (31), 6543-6553 , 2004
    2004
    Citations: 20
  • Integrating Universal Generative AI Platforms in Educational Labs to Foster Critical Thinking and Digital Literacy
    V Znamenskiy, R Niyazov, J Hernandez
    3rd International Conference on Computer Science, Engineering and Artificial … , 2025
    2025
    Citations: 4
  • Molecular dynamics of ion formation from charged nanodroplets in electrospray ionization
    VS Znamenskiy, A Vertes
    50th ASMS Conference on Mass Spectrometry and Allied Topics, 2-6 , 2002
    2002
    Citations: 3
  • Molecular Dynamics Study of Contact Melting in the KCl–KI System.
    VS Znamenskii, PF Zilberman, PA Savintsev, EA Goncharenko
    Inorganic Materials 32 (No. 5, 1996), pp. 536–540 , 1996
    1996
    Citations: 3
  • Molecular-dynamic simulation of external electromagnetic fields effect on the contact melting of ionic crystals
    EA Goncharenko, VS Znamenskij, PF Zil'berman
    Физика и химия обработки материалов, 94-99 , 1995
    1995
    Citations: 2
  • Характеристики контактного плавления при моделировании ионных систем методом молекулярной динамики с потенциалами по Полингу и Фуми-Този
    ВС Знаменский, ПА Савинцев, ПФ Зильберман, АП Савинцев
    Неорганические материалы 30 (4), 514-516 , 1994
    1994
    Citations: 2
  • Artificial Intelligence and Astronomy: Lab Manual for Generative AI-Based Learning Activities
    V Znamenskiy
    2025
    Citations: 1
  • Calculations of the strength of hydrogen bonds: Switching between short, strong hydrogen bonds and normal bonds in a system containing water and four carboxylic acids
    VS Znamenskiy, ME Green
    BIOPHYSICAL JOURNAL 86 (1), 633A-633A , 2004
    2004
    Citations: 1
  • Molecular dynamics study of ionic melts resulting from contact melting
    EA Goncharenko, TA Grechukha, PF ZiPberman, VS Znamenskii
    October 2000, Volume 36, Issue 10, pp 1056-1059 36 (10), pp 10 , 2000
    2000
    Citations: 1
  • Нанофизика контактного плавления: моделирование методом молекулярной динамики
    ПА Савинцев, ВС Знаменский, ПФ Зильберман, АП Савинцев
    Вестник Кабардино-Балкарского государственного университета. Серия … , 1996
    1996
    Citations: 1
  • Исследование контактного плавления методом молекулярной динамики
    ВС Знаменский
    1994
    Citations: 1
  • Tutoring Prompt for Personalized Self-Study Using Generative AI
    VS Znamenskiy
    2026