Olexandr Isayev | Case Western Reserve University (original) (raw)
Papers by Olexandr Isayev
J. Phys. Chem. A, Jan 1, 2007
Reduction of nitro-aromatic compounds (NACs) proceeds through intermediates with a partial electr... more Reduction of nitro-aromatic compounds (NACs) proceeds through intermediates with a partial electron transfer into the nitro group from a reducing agent. To estimate the extent of such a transfer and, therefore, the activity of various model ferrous-containing reductants toward NAC degradation, the unrestricted density functional theory (DFT) in the basis of paired Löwdin-Amos-Hall orbitals has been applied to complexes of nitrobenzene (NB) and model Fe(II) hydroxides including cationic [FeOH]+, then neutral Fe(OH)2, and finally anionic [Fe(OH)3]-. Electron transfer is considered to be a process of unpairing electrons (without the change of total spin projection Sz) that reveals itself in a substantial spin contamination of the unrestricted solution. The unrestricted orbitals are transformed into localized paired orbitals to determine the orbital channels for a particular electron-transfer state and the weights of idealized charge-transfer and covalent electron structures. This approach allows insight into the electronic structure and bonding of the {Fe(PhNO2)}6 unit (according to Enemark and Feltham notation) to be gained using model nitrobenzene complexes. The electronic structure of this unit can be expressed in terms of pi-type covalent bonding [Fe+2(d6, S = 2) - PhNO2(S = 0)] or charge-transfer configuration [Fe+3(d5, S = 5/2) - {PhNO2}- ((pi*)1, S = 1/2)].
The 2008 Annual …, Jan 1, 2008
These simulations provide a detailed description of the chemical processes in the initial stages ... more These simulations provide a detailed description of the chemical processes in the initial stages of thermal decomposition of condensed CL-20. We elucidated key features of this process: composition of primary reaction products, reaction timing, Arrhenius behavior of the system, etc. They ...
Molecular diversity, Jan 1, 2006
Journal of Computational …, Jan 1, 2007
The theoretical study has been performed to refine the procedure for calculations of Gibbs free e... more The theoretical study has been performed to refine the procedure for calculations of Gibbs free energy with a relative accuracy of less than 1 kcal/mol. Three benchmark intermolecular complexes are examined via several quantum-chemical methods, including the second-order Moller-Plesset perturbation (MP2), coupled cluster (CCSD(T)), and density functional (BLYP, B3LYP) theories augmented by Dunnings correlation-consistent basis sets. The effects of electron correlation, basis set size, and anharmonicity are systematically analyzed, and the results are compared with available experimental data. The results of the calculations suggest that experimental accuracy can be reached only by extrapolation of MP2 and CCSD(T) total energies to the complete basis set. The contribution of anharmonicity to the zero point energy and TDeltaSint values is fairly small. The new, economic way to reach chemical accuracy in the calculations of the thermodynamic parameters of intermolecular interactions is proposed. In addition, interaction energy (De) and free energy change (DeltaA) for considered species have been evaluated by Carr-Parrinello molecular dynamics (CPMD) simulations and static BLYP-plane wave calculations. The free energy change along the reaction paths were determined by the thermodynamic integration/"Blue Moon Ensemble" technique. Comparison between obtained values, and available experimental and conventional ab initio results has been made. We found that the accuracy of CPMD simulations is affected by several factors, including statistical uncertainty and convergence of constrained forces (TD integration), and the nature of DFT (density functional theory) functional. The results show that CPMD technique is capable of reproducing interaction and free energy with an accuracy of 1 kcal/mol and 2-3 kcal/mol respectively.
J. Phys. Chem. B, Jan 1, 2007
J. Phys. Chem. B, Jan 1, 2008
CL-20 (2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane or HNIW) is a high-energy nitra... more CL-20 (2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane or HNIW) is a high-energy nitramine explosive. To improve atomistic understanding of the thermal decomposition of CL-20 gas and solid phases, we performed a series of ab initio molecular dynamics simulations. We found that during unimolecular decomposition, unlike other nitramines (e.g., RDX, HMX), CL-20 has only one distinct initial reaction channelhomolysis of the N-NO2 bond. We did not observe any HONO elimination reaction during unimolecular decomposition, whereas the ring-breaking reaction was followed by NO 2 fission. Therefore, in spite of limited sampling, that provides a mostly qualitative picture, we proposed here a scheme of unimolecular decomposition of CL-20. The averaged product population over all trajectories was estimated at four HCN, two to four NO2, two to four NO, one CO, and one OH molecule per one CL-20 molecule. Our simulations provide a detailed description of the chemical processes in the initial stages of thermal decomposition of condensed CL-20, allowing elucidation of key features of such processes as composition of primary reaction products, reaction timing, and Arrhenius behavior of the system. The primary reactions leading to NO2, NO, N 2O, and N2 occur at very early stages. We also estimated potential activation barriers for the formation of NO2, which essentially determines overall decomposition kinetics and effective rate constants for NO2 and N2. The calculated solid-phase decomposition pathways correlate with available condensed-phase experimental data.
Physical Chemistry …, Jan 1, 2010
Comprehensive study on interactions between nucleic acid bases (NABs) and bulk water environment ... more Comprehensive study on interactions between nucleic acid bases (NABs) and bulk water environment has been performed with use of Car-Parrinello molecular dynamics. Detailed analysis of average number, lifetimes and mobility of water molecules, orientation and 3D organization of hydrogen bond network in the first hydration shell of adenine, guanine, cytosine and thymine has been carried out. Effect of hydration by bulk water environment has been compared with the data from polyhydrated complexes of NABs. During bulk water hydration the presence of mixed Hw...N/Hw...pi type of bonding is detected for imino nitrogen atoms. The formation of three hydrogen bonds to carbonyl groups reflects the significance of polarizing effects of aqueous environments. Hydration of hydrophobic sites revealed the presence of extremely weak bonding. Hydration of C6-H6 site of thymine is standing significantly apart from the hydration of other hydrophobic sites. An average coordination numbers of adenine, guanine, cytosine and thymine in bulk water environment are 6.87, 8.52, 6.12 and 6.42 water molecules, correspondingly. The lifetime of water molecules in the first hydration shell varies from 1 to 3 ps. Some differences in hydration studied by CPMD (bulk water) and quantum chemical (less than 20 water molecules) methods indicate a significant effect of the second hydration shell on structure and properties of the first hydration shell for the considered compounds.
rsc.org
The correlation between hydration of Nucleic Acid Bases (NABs) and their conformational flexibili... more The correlation between hydration of Nucleic Acid Bases (NABs) and their conformational flexibility was analyzed based on the results of Car-Parrinello Molecular Dynamics (CPMD) simulations of NABs in bulk water environment. Correlations with quantum chemical results were drawn whenever it was possible. Statistical analysis confirmed that hydration causes bond length alteration in NABs and formation of zwitter-ionic resonance structures. In contrast to the gas phase, bulk hydration results in restricted mobility of amino group and increase in population of its planar-like conformations. At the same time, rings of all NABs become almost equally flexible in the dynamic aqueous environment. Therefore, each NAB possesses a non-planar effective conformation of pyrimidine ring despite the fact that planar geometry corresponds to minimum on the potential energy surface.
The Journal of …, Jan 1, 2004
... Zilberberg. Boreskov Institute of Catalysis, Novosibirsk 630090, Russia. Mykola Ilchenko. Ins... more ... Zilberberg. Boreskov Institute of Catalysis, Novosibirsk 630090, Russia. Mykola Ilchenko. Institute of Cell Biology and Genetic Engineering, NAS of Ukraine, pr. Zabolotnogo, 148, Kiev 03143, Ukraine. Olexandr Isayev, Leonid ...
Phys. Chem. Chem. …, Jan 1, 2011
The Journal of Physical …, Jan 1, 2011
The effect of hydration on the vertical ionization energy (VIE) of thymine was characterized usin... more The effect of hydration on the vertical ionization energy (VIE) of thymine was characterized using equation-of-motion ionization potential coupled-cluster (EOM-IP-CCSD) and effective fragment potential (EFP) methods. We considered several microsolvated clusters as well as thymine solvated in bulk water. The VIE in bulk water was computed by averaging over solvent−solute configurations obtained from equilibrium molecular dynamics trajectories at 300 K. The effect of microsolvation was analyzed and contrasted against the combined effect of the first solvation shell in bulk water. Microsolvation reduces the ionization energy (IE) by about 0.1 eV per water molecule, while the first solvation shell increases the IE by 0.1 eV. The subsequent solvation lowers the IE, and the bulk value of the solvent-induced shift of thymine’s VIE is approximately −0.9 eV. The combined effect of the first solvation shell was explained in terms of specific solute−solvent interactions, which were investigated using model structures. The convergence of IE to the bulk value requires the hydration sphere of approximately 13.5 Å radius. The performance of the EOM-IP-CCSD/EFP scheme was benchmarked against full EOM-IP-CCSD using microhydrated structures. The errors were found to be less than 0.01−0.02 eV. The relative importance of the polarization and higher multipole moments in EFP model was also investigated.
![Research paper thumbnail of Reaction of bicyclo [2.2. 1] hept‐5‐ene‐endo‐2‐ylmethylamine and nitrophenyl glycidyl ethers](https://attachments.academia-assets.com/51294254/thumbnails/1.jpg)
](
Journal of …
A number of density functionals was utilized for the calculation of electron attachment free ener... more A number of density functionals was utilized for the calculation of electron attachment free energy for nitrocompounds, quinones and azacyclic compounds. Different solvation models have been tested on the calculation of difference in free energies of solvation of oxidized and reduced forms of nitrocompounds in aqueous solution, quinones in acetonitrile, and azacyclic compounds in dimethylformamide. Gas-phase free energies evaluated at the mPWB1K/tzvp level and solvation energies obtained using SMD model to compute solvation energies of neutral oxidized forms and PCM(Pauling) to compute solvation energies of anion-radical reduced forms provide reasonable accuracy of the prediction of electron attachment free energy, difference in free solvation energies of oxidized and reduced forms, and as consequence yield reduction potentials in good agreement with experimental data (mean absolute deviation is 0.15 V). It was also found that SMD/M05-2X/tzvp method provides reduction potentials with deviation of 0.12 V from the experimental values but in cases of nitrocompounds and quinones this accuracy is achieved due to the cancelation of errors. To predict reduction ability of naturally occurred iron containing species with respect to organic pollutants we exploited experimental data within the framework of Pourbaix (Eh - pH) diagrams. We conclude that surface-bound Fe(II) as well as certain forms of aqueous Fe(II)aq are capable of reducing a variety of nitroaromatic compounds, quinones and novel high energy materials under basic conditions (pH > 8). At the same time, zero-valent iron is expected to be active under neutral and acidic conditions.
Energetic Materials: …, Jan 1, 2010
6 Mechanisms and Kinetics of CL-20 Modes of Transformation via Alkali Hydrolysis, via Photolysis,... more 6 Mechanisms and Kinetics of CL-20 Modes of Transformation via Alkali Hydrolysis, via Photolysis, Thermolysis, and Free Radical Reactions Mohammad Qasim, 1 Yana Kholod, 1 Sergiy Okovytyy, 1 Olexandr Isayev, 2 Leonid Gorb, 1 Veera M. Boddu, 3 Jerzy Leszxzynski1 1 ...
The Journal of Physical …
J. Phys. Chem. A, Jan 1, 2007
Reduction of nitro-aromatic compounds (NACs) proceeds through intermediates with a partial electr... more Reduction of nitro-aromatic compounds (NACs) proceeds through intermediates with a partial electron transfer into the nitro group from a reducing agent. To estimate the extent of such a transfer and, therefore, the activity of various model ferrous-containing reductants toward NAC degradation, the unrestricted density functional theory (DFT) in the basis of paired Löwdin-Amos-Hall orbitals has been applied to complexes of nitrobenzene (NB) and model Fe(II) hydroxides including cationic [FeOH]+, then neutral Fe(OH)2, and finally anionic [Fe(OH)3]-. Electron transfer is considered to be a process of unpairing electrons (without the change of total spin projection Sz) that reveals itself in a substantial spin contamination of the unrestricted solution. The unrestricted orbitals are transformed into localized paired orbitals to determine the orbital channels for a particular electron-transfer state and the weights of idealized charge-transfer and covalent electron structures. This approach allows insight into the electronic structure and bonding of the {Fe(PhNO2)}6 unit (according to Enemark and Feltham notation) to be gained using model nitrobenzene complexes. The electronic structure of this unit can be expressed in terms of pi-type covalent bonding [Fe+2(d6, S = 2) - PhNO2(S = 0)] or charge-transfer configuration [Fe+3(d5, S = 5/2) - {PhNO2}- ((pi*)1, S = 1/2)].
The 2008 Annual …, Jan 1, 2008
These simulations provide a detailed description of the chemical processes in the initial stages ... more These simulations provide a detailed description of the chemical processes in the initial stages of thermal decomposition of condensed CL-20. We elucidated key features of this process: composition of primary reaction products, reaction timing, Arrhenius behavior of the system, etc. They ...
Molecular diversity, Jan 1, 2006
Journal of Computational …, Jan 1, 2007
The theoretical study has been performed to refine the procedure for calculations of Gibbs free e... more The theoretical study has been performed to refine the procedure for calculations of Gibbs free energy with a relative accuracy of less than 1 kcal/mol. Three benchmark intermolecular complexes are examined via several quantum-chemical methods, including the second-order Moller-Plesset perturbation (MP2), coupled cluster (CCSD(T)), and density functional (BLYP, B3LYP) theories augmented by Dunnings correlation-consistent basis sets. The effects of electron correlation, basis set size, and anharmonicity are systematically analyzed, and the results are compared with available experimental data. The results of the calculations suggest that experimental accuracy can be reached only by extrapolation of MP2 and CCSD(T) total energies to the complete basis set. The contribution of anharmonicity to the zero point energy and TDeltaSint values is fairly small. The new, economic way to reach chemical accuracy in the calculations of the thermodynamic parameters of intermolecular interactions is proposed. In addition, interaction energy (De) and free energy change (DeltaA) for considered species have been evaluated by Carr-Parrinello molecular dynamics (CPMD) simulations and static BLYP-plane wave calculations. The free energy change along the reaction paths were determined by the thermodynamic integration/"Blue Moon Ensemble" technique. Comparison between obtained values, and available experimental and conventional ab initio results has been made. We found that the accuracy of CPMD simulations is affected by several factors, including statistical uncertainty and convergence of constrained forces (TD integration), and the nature of DFT (density functional theory) functional. The results show that CPMD technique is capable of reproducing interaction and free energy with an accuracy of 1 kcal/mol and 2-3 kcal/mol respectively.
J. Phys. Chem. B, Jan 1, 2007
J. Phys. Chem. B, Jan 1, 2008
CL-20 (2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane or HNIW) is a high-energy nitra... more CL-20 (2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane or HNIW) is a high-energy nitramine explosive. To improve atomistic understanding of the thermal decomposition of CL-20 gas and solid phases, we performed a series of ab initio molecular dynamics simulations. We found that during unimolecular decomposition, unlike other nitramines (e.g., RDX, HMX), CL-20 has only one distinct initial reaction channelhomolysis of the N-NO2 bond. We did not observe any HONO elimination reaction during unimolecular decomposition, whereas the ring-breaking reaction was followed by NO 2 fission. Therefore, in spite of limited sampling, that provides a mostly qualitative picture, we proposed here a scheme of unimolecular decomposition of CL-20. The averaged product population over all trajectories was estimated at four HCN, two to four NO2, two to four NO, one CO, and one OH molecule per one CL-20 molecule. Our simulations provide a detailed description of the chemical processes in the initial stages of thermal decomposition of condensed CL-20, allowing elucidation of key features of such processes as composition of primary reaction products, reaction timing, and Arrhenius behavior of the system. The primary reactions leading to NO2, NO, N 2O, and N2 occur at very early stages. We also estimated potential activation barriers for the formation of NO2, which essentially determines overall decomposition kinetics and effective rate constants for NO2 and N2. The calculated solid-phase decomposition pathways correlate with available condensed-phase experimental data.
Physical Chemistry …, Jan 1, 2010
Comprehensive study on interactions between nucleic acid bases (NABs) and bulk water environment ... more Comprehensive study on interactions between nucleic acid bases (NABs) and bulk water environment has been performed with use of Car-Parrinello molecular dynamics. Detailed analysis of average number, lifetimes and mobility of water molecules, orientation and 3D organization of hydrogen bond network in the first hydration shell of adenine, guanine, cytosine and thymine has been carried out. Effect of hydration by bulk water environment has been compared with the data from polyhydrated complexes of NABs. During bulk water hydration the presence of mixed Hw...N/Hw...pi type of bonding is detected for imino nitrogen atoms. The formation of three hydrogen bonds to carbonyl groups reflects the significance of polarizing effects of aqueous environments. Hydration of hydrophobic sites revealed the presence of extremely weak bonding. Hydration of C6-H6 site of thymine is standing significantly apart from the hydration of other hydrophobic sites. An average coordination numbers of adenine, guanine, cytosine and thymine in bulk water environment are 6.87, 8.52, 6.12 and 6.42 water molecules, correspondingly. The lifetime of water molecules in the first hydration shell varies from 1 to 3 ps. Some differences in hydration studied by CPMD (bulk water) and quantum chemical (less than 20 water molecules) methods indicate a significant effect of the second hydration shell on structure and properties of the first hydration shell for the considered compounds.
rsc.org
The correlation between hydration of Nucleic Acid Bases (NABs) and their conformational flexibili... more The correlation between hydration of Nucleic Acid Bases (NABs) and their conformational flexibility was analyzed based on the results of Car-Parrinello Molecular Dynamics (CPMD) simulations of NABs in bulk water environment. Correlations with quantum chemical results were drawn whenever it was possible. Statistical analysis confirmed that hydration causes bond length alteration in NABs and formation of zwitter-ionic resonance structures. In contrast to the gas phase, bulk hydration results in restricted mobility of amino group and increase in population of its planar-like conformations. At the same time, rings of all NABs become almost equally flexible in the dynamic aqueous environment. Therefore, each NAB possesses a non-planar effective conformation of pyrimidine ring despite the fact that planar geometry corresponds to minimum on the potential energy surface.
The Journal of …, Jan 1, 2004
... Zilberberg. Boreskov Institute of Catalysis, Novosibirsk 630090, Russia. Mykola Ilchenko. Ins... more ... Zilberberg. Boreskov Institute of Catalysis, Novosibirsk 630090, Russia. Mykola Ilchenko. Institute of Cell Biology and Genetic Engineering, NAS of Ukraine, pr. Zabolotnogo, 148, Kiev 03143, Ukraine. Olexandr Isayev, Leonid ...
Phys. Chem. Chem. …, Jan 1, 2011
The Journal of Physical …, Jan 1, 2011
The effect of hydration on the vertical ionization energy (VIE) of thymine was characterized usin... more The effect of hydration on the vertical ionization energy (VIE) of thymine was characterized using equation-of-motion ionization potential coupled-cluster (EOM-IP-CCSD) and effective fragment potential (EFP) methods. We considered several microsolvated clusters as well as thymine solvated in bulk water. The VIE in bulk water was computed by averaging over solvent−solute configurations obtained from equilibrium molecular dynamics trajectories at 300 K. The effect of microsolvation was analyzed and contrasted against the combined effect of the first solvation shell in bulk water. Microsolvation reduces the ionization energy (IE) by about 0.1 eV per water molecule, while the first solvation shell increases the IE by 0.1 eV. The subsequent solvation lowers the IE, and the bulk value of the solvent-induced shift of thymine’s VIE is approximately −0.9 eV. The combined effect of the first solvation shell was explained in terms of specific solute−solvent interactions, which were investigated using model structures. The convergence of IE to the bulk value requires the hydration sphere of approximately 13.5 Å radius. The performance of the EOM-IP-CCSD/EFP scheme was benchmarked against full EOM-IP-CCSD using microhydrated structures. The errors were found to be less than 0.01−0.02 eV. The relative importance of the polarization and higher multipole moments in EFP model was also investigated.
Journal of …
A number of density functionals was utilized for the calculation of electron attachment free ener... more A number of density functionals was utilized for the calculation of electron attachment free energy for nitrocompounds, quinones and azacyclic compounds. Different solvation models have been tested on the calculation of difference in free energies of solvation of oxidized and reduced forms of nitrocompounds in aqueous solution, quinones in acetonitrile, and azacyclic compounds in dimethylformamide. Gas-phase free energies evaluated at the mPWB1K/tzvp level and solvation energies obtained using SMD model to compute solvation energies of neutral oxidized forms and PCM(Pauling) to compute solvation energies of anion-radical reduced forms provide reasonable accuracy of the prediction of electron attachment free energy, difference in free solvation energies of oxidized and reduced forms, and as consequence yield reduction potentials in good agreement with experimental data (mean absolute deviation is 0.15 V). It was also found that SMD/M05-2X/tzvp method provides reduction potentials with deviation of 0.12 V from the experimental values but in cases of nitrocompounds and quinones this accuracy is achieved due to the cancelation of errors. To predict reduction ability of naturally occurred iron containing species with respect to organic pollutants we exploited experimental data within the framework of Pourbaix (Eh - pH) diagrams. We conclude that surface-bound Fe(II) as well as certain forms of aqueous Fe(II)aq are capable of reducing a variety of nitroaromatic compounds, quinones and novel high energy materials under basic conditions (pH > 8). At the same time, zero-valent iron is expected to be active under neutral and acidic conditions.
Energetic Materials: …, Jan 1, 2010
6 Mechanisms and Kinetics of CL-20 Modes of Transformation via Alkali Hydrolysis, via Photolysis,... more 6 Mechanisms and Kinetics of CL-20 Modes of Transformation via Alkali Hydrolysis, via Photolysis, Thermolysis, and Free Radical Reactions Mohammad Qasim, 1 Yana Kholod, 1 Sergiy Okovytyy, 1 Olexandr Isayev, 2 Leonid Gorb, 1 Veera M. Boddu, 3 Jerzy Leszxzynski1 1 ...
The Journal of Physical …