Rubik Asatryan - Academia.edu (original) (raw)
Papers by Rubik Asatryan
Journal of Structural Chemistry, 1983
Bioresource Technology Reports, 2019
This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
The Journal of Physical Chemistry A, 2018
Diol radicals (DRs) are important intermediates in biocatalysis, atmospheric chemistry and biomas... more Diol radicals (DRs) are important intermediates in biocatalysis, atmospheric chemistry and biomass combustion. They are particularly generated from photolysis of halogenated diols and a barrierless addition of hydroxyl radical to a double bond of unsaturated alcohols, such as lignols. The energized DRs further isomerize / decompose to form products, including water. Aqueous-phase dehydration in radiolytic and biomimetic systems typically occurs at low temperatures, with or without catalysis, whereas the gas-phase dehydration is usually considered energetically unfavorable. In the present study, we propose a new low-energy, roaming-like mechanism based on a detailed dispersion-corrected DFT and ab initio level analysis of the gas-phase dehydration of DRs obtained from the combination of OH radicals with allyl alcohol (AA, CH 2 =CHCH 2 OH)-the simplest relevant model of the unsaturated alcohols. The roaming pathways involve a nearly dissociated OH-group, which subsequently abstracts an H-atom of the remaining fragment to form water and [C 3 H 5 O] radical via a transition state (TS) with energy close to the CO bond fission asymptote. Two types of roaming-like first-order saddle points (SP) are identified for unimolecular dehydration of 1,2-and 1,3-DR radical adducts involving either both hydroxyl groups of diol radicals to generate an oxygen-centered radical, or β-OH-group and a skeletal α-hydrogen atom of the 1,2-DR to form a resonantly stabilized hydroxyallyl radical. Two higher energy conventional (tight) transition states, along with the pathways to 1,2-OH-migration, as well as direct H-abstraction, are also identified and analyzed. Most of the traditional DFT methods that have been successfully employed in literature to locate so-farknown roaming SPs, were also able to identify presented here roaming SPs, in accord with dispersioncorrected double hybrid B2PLYP-D3(BJ) and mPW2PLYPD methods involving MP2-correlation corrections. However, the MP2 method itself failed to locate any of them, which seems to be typical for
Polymer Science U.S.S.R., 1985
Semi-empirical SCF MO LCAO methods have been used to investigate the possible paths of formation ... more Semi-empirical SCF MO LCAO methods have been used to investigate the possible paths of formation of the polyconjugated portions during radical polymerization of vinylacetylene derivatives. The active centres responsible for the mechanism of chain growth have been modelled. It is shown that the relative changes in the spin densities of the most probable centres localized on the p~ orbitals of the skeletal atoms C2 and C4 explain the influnce of the nonpolar substituent on the structure of the polymers formed. Experimental data on the realization of the diene regions correlate with the calculated values of the dipole moments of the monomer radicals, the systems not containing a substituent at the terminal C4 atom forming a separate series. It is concluded that the electrostatic interactions play a dominant role in the formation of the polyconjugatedregions.
Bulletin of the Academy of Sciences of the USSR Division of Chemical Science, 1982
ABSTRACT According to the data from the calculations by the semiempirical SCF method in the MINDO... more ABSTRACT According to the data from the calculations by the semiempirical SCF method in the MINDO/3 all-valence electron approximation and by a nonempirical method in the STO-4-31G basis, the reaction of hot T atoms in the T+CH3NH2 system most probably takes place according to a mechanism involving the abstraction of an H atom. In the case of “hot” T atoms there is also a possibility of the replacement of the NH2 group according to a Waiden inversion mechanism or its direct abstraction.
Journal of Structural Chemistry, 1979
Chemico-Biological Interactions, 2008
Our goal was to design, synthesize, and evaluate new cholinesterase inhibitors. Fourteen dehydroa... more Our goal was to design, synthesize, and evaluate new cholinesterase inhibitors. Fourteen dehydroamino acids esterified to choline and to its ternary analog were synthesized by a new method that gave a yield of 84-93%. The potency of the amino acid ester derivatives was tested by measuring K i values for inhibition of human red cell acetylcholinesterase and human plasma butyrylcholinesterase. The most potent compound was a choline ester of dehydrophenylalanine where the amine group of the amino acid was derivatized with a benzoyl group containing a methoxy in the 2-position, CH 3 O(C 6 H 4)CONHC(CHC 6 H 5)COOCH 2 CH 2 N + (CH 3) 3. This compound was a strong inhibitor of both human acetylcholinesterase and human butyrylcholinesterase, with K i values of 10 M and 0.08 M, respectively. These K i values are comparable to that of Rivastigmine. Docking of the most potent compound into the active site of human butyrylcholinesterase showed that the lowest energy model had two benzene rings oriented towards Trp 82 and Tyr 332 whereas the positively charged nitrogen group was stabilized by Trp 231. This orientation placed the ester group 3.89Å from the active site Ser 198, a distance too far for covalent bonding, explaining why the esters are inhibitors rather than substrates. This class of anticholinesterase agents has the potential for therapeutic utility in the treatment of disorders of the cholinergic system.
Chemosphere, 2002
SCF-MO computations have been performed on tetra-to octa-chlorinated dibenzo-p-dioxin congeners (... more SCF-MO computations have been performed on tetra-to octa-chlorinated dibenzo-p-dioxin congeners (PCDD) using an MNDO-PM3 Hamiltonian. Qualitative relationships were developed between empirical, international-toxic equivalence factors for PCDD congeners and their relative (specific) polarizabilities and mean values of second hyperpolarizabilities estimated using finite-field theory.
The Journal of Physical Chemistry A, 2004
ABSTRACT A 30-reaction core kinetic model has been developed that accounts for the major features... more ABSTRACT A 30-reaction core kinetic model has been developed that accounts for the major features in the homogeneous formation of polychlorinated dibenzofurans (PCDF) from the high-temperature oxidation of 2,4,6- trichlorophenol (TCP). The core, purely gas-phase scheme provides agreement within a factor of 1.5 - 2 between experimental and calculated yields of PCDD/Fs using the REACT kinetic program. It is demonstrated that the formation of PCDF is due to the conversion of TCP to 2,4-dichlorophenol (DCP), which subsequently forms a keto resonance structure of the 2,4-dichlorophenoxyl radical (DCP • ). The conversion of TCP to DCP provides an ortho hydrogen that is necessary for the formation of PCDF. Ab initio calculations were utilized to calculate the activation energies of the key reactions involved in the gas-phase formation of PCDF
A pressure dependent kinetic sub-mechanism for HxOxC1 species is developed based on literature da... more A pressure dependent kinetic sub-mechanism for HxOxC1 species is developed based on literature data for reactions of the hydrogen-oxygen subset and paths involving abstraction of hydrogen atoms. Pressure and temperature dependent rate constants are determined for bimolecular, chemical activation (association and addition) and unimolecular (thermal) dissociation reactions using multi-frequency QRRK analysis for k(E) and master Equation analysis for fall-off. Pressure and temperature dependent rate constants are expressed in the form of 7x3 Chebyshev polynomials over 0.01 to 100 atm and 300 to 3000K. The chemical activation systems include reactions of OH, HO2, O • , O2 with the following carbon species: CO, HC • =O, CH2=O, C • H2OH, CH3O, CH3 plus selected C2 species, with dissociation analysis for stabilized adducts. Improved rate constants are used for HO2 + CO reaction (near pressure independent) expressed as k1a= 8.45 x10 8 xT 1.21 exp(17267cal/RT) and k1b=7.14x10 7 xT 1.57 exp(1...
The Journal of Physical Chemistry A
Chem. Sci.
New rearrangement mechanism prototypes are introduced to account for the non-ideal coordination a... more New rearrangement mechanism prototypes are introduced to account for the non-ideal coordination and fluxional behavior of five-coordinate metalo-complexes.
The Journal of Physical Chemistry a, 2010
exo-Tricyclo[5.2.1.0(2,6)]decane (TCD) or exo-tetrahydrodicyclopentadiene is the principal compon... more exo-Tricyclo[5.2.1.0(2,6)]decane (TCD) or exo-tetrahydrodicyclopentadiene is the principal component of the high-energy density hydrocarbon fuel commonly identified as JP-10. Thermodynamic parameters for the parent TCD molecule and of all the tricyclodecyl radicals corresponding to the loss of hydrogen atoms from different carbons sites (TCD-Ri with i indicating the given carbon center) are determined using several density functional theory and G3MP2B3 and CBS-QB3 higher level composite computational chemistry methods. Five isodesmic work reactions, three involving bridged hydrocarbon reference molecules with similar ring strains, are employed to produce a cancelation of systematic calculation errors in evaluation of standard, gas-phase formation enthalpies at 298 K. Delta(f)H degrees (298) for TCD is found to be -19.5 +/- 1.3 kcal mol(-1), which is several kcal mol(-1) lower than the commonly used values. C(i)-H bond energies for corresponding TCD carbon sites are evaluated as follows: TCD-R1, 107.2; TCD-R2, 100.1; TCD-R3, 98.0; TCD-R4, 98.5; TCD-R9, 98.7; TCD-R10, 104.1 kcal mol(-1). Results from use of five different DFT methods are in very good agreement with composite level values for all work reactions used for the radicals. The exo and endo isomers of TCD are both determined to have chair and boat conformers.
Chem Phys Lett, 2011
Transport of hydrogen atoms plays a key role in chemical and biological processes involving metab... more Transport of hydrogen atoms plays a key role in chemical and biological processes involving metabolism of molecular hydrogen. Several 'gas-phase' and more intricate organometallic models (mimics of the hydrogenase enzyme) are developed to show the intriguing role of the molecular hydrogen as a third party in the pass-on transfer of hydrogen atoms. This hydrogen assisted transport (HAT) mechanism is based on the current understanding of the hydrogen exchange reactions and it is believed to be applicable to certain H/D-isotope exchange processes and remote transport of H-atoms.
The Journal of Physical Chemistry a, 2010
Association of alkyl radicals with ground-state oxygen 3 Σ g + (O 2) generates chemically activat... more Association of alkyl radicals with ground-state oxygen 3 Σ g + (O 2) generates chemically activated peroxy intermediates, which can isomerize or further react to form new products before collisional stabilization. The lowest-energy reaction (∼19 kcal mol-1) for alkylperoxy derivatives of C 3 and larger n-hydrocarbons is an isomerization (intramolecular H-atom transfer) that forms a hydroperoxide alkyl radical, and there is a ∼30 kcal mol-1 barrier path to olefin plus HO 2 , which is a termination step at lower temperatures. The lowenergy-barrier product, hydroperoxide alkyl radical intermediate, can experience additional chemical activation via association with a second oxygen molecule, where there are three important paths that result in chain branching. The competition between this HO 2 + olefin termination step of the first O 2 association and the chain branching processes from the second chemical activation step plays a dominant role at temperatures below 1000 K. Secondary n-pentyl radicals are used in this study as surrogates to analyze the thermochemistry and detailed kinetics of the chemical activation and stabilized adduct reactions important to chain branching and termination. As these radicals provide six-member ring transition states for H-atom transfer between secondary carbons, they represent the detailed kinetics of larger alkane radicals, such as the common fuel components n-heptane and n-decane. Comprehensive potential energy diagrams developed from multilevel CBS-QB3, G3MP2, and CBS-APNO and single-level ab initio and density functional theory methods are used to analyze secondary 2-pentyl (n-pentan-2-yl) and interrelated 2-hydroperoxide-pentan-4-yl radical interactions with O 2. The thermochemistry and kinetics of the chemical activation and stabilized adduct reactions important to chain branching and termination are reported and discussed. Results show that the chain branching reactions have faster kinetics in this system because the barriers are lower than those observed in ethyl and propyl radical plus O 2 reactions; consequently, the branching is predicted to be more important. The lower barriers for branching result in less competition from the termination (HO 2 + olefin) path in this larger radical. Several nontraditional reaction channels not previously considered in the literature are identified. A pathway is suggested to explain the formation of a unique trioxane product observed experimentally.
Journal of Structural Chemistry, 1983
Bioresource Technology Reports, 2019
This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
The Journal of Physical Chemistry A, 2018
Diol radicals (DRs) are important intermediates in biocatalysis, atmospheric chemistry and biomas... more Diol radicals (DRs) are important intermediates in biocatalysis, atmospheric chemistry and biomass combustion. They are particularly generated from photolysis of halogenated diols and a barrierless addition of hydroxyl radical to a double bond of unsaturated alcohols, such as lignols. The energized DRs further isomerize / decompose to form products, including water. Aqueous-phase dehydration in radiolytic and biomimetic systems typically occurs at low temperatures, with or without catalysis, whereas the gas-phase dehydration is usually considered energetically unfavorable. In the present study, we propose a new low-energy, roaming-like mechanism based on a detailed dispersion-corrected DFT and ab initio level analysis of the gas-phase dehydration of DRs obtained from the combination of OH radicals with allyl alcohol (AA, CH 2 =CHCH 2 OH)-the simplest relevant model of the unsaturated alcohols. The roaming pathways involve a nearly dissociated OH-group, which subsequently abstracts an H-atom of the remaining fragment to form water and [C 3 H 5 O] radical via a transition state (TS) with energy close to the CO bond fission asymptote. Two types of roaming-like first-order saddle points (SP) are identified for unimolecular dehydration of 1,2-and 1,3-DR radical adducts involving either both hydroxyl groups of diol radicals to generate an oxygen-centered radical, or β-OH-group and a skeletal α-hydrogen atom of the 1,2-DR to form a resonantly stabilized hydroxyallyl radical. Two higher energy conventional (tight) transition states, along with the pathways to 1,2-OH-migration, as well as direct H-abstraction, are also identified and analyzed. Most of the traditional DFT methods that have been successfully employed in literature to locate so-farknown roaming SPs, were also able to identify presented here roaming SPs, in accord with dispersioncorrected double hybrid B2PLYP-D3(BJ) and mPW2PLYPD methods involving MP2-correlation corrections. However, the MP2 method itself failed to locate any of them, which seems to be typical for
Polymer Science U.S.S.R., 1985
Semi-empirical SCF MO LCAO methods have been used to investigate the possible paths of formation ... more Semi-empirical SCF MO LCAO methods have been used to investigate the possible paths of formation of the polyconjugated portions during radical polymerization of vinylacetylene derivatives. The active centres responsible for the mechanism of chain growth have been modelled. It is shown that the relative changes in the spin densities of the most probable centres localized on the p~ orbitals of the skeletal atoms C2 and C4 explain the influnce of the nonpolar substituent on the structure of the polymers formed. Experimental data on the realization of the diene regions correlate with the calculated values of the dipole moments of the monomer radicals, the systems not containing a substituent at the terminal C4 atom forming a separate series. It is concluded that the electrostatic interactions play a dominant role in the formation of the polyconjugatedregions.
Bulletin of the Academy of Sciences of the USSR Division of Chemical Science, 1982
ABSTRACT According to the data from the calculations by the semiempirical SCF method in the MINDO... more ABSTRACT According to the data from the calculations by the semiempirical SCF method in the MINDO/3 all-valence electron approximation and by a nonempirical method in the STO-4-31G basis, the reaction of hot T atoms in the T+CH3NH2 system most probably takes place according to a mechanism involving the abstraction of an H atom. In the case of “hot” T atoms there is also a possibility of the replacement of the NH2 group according to a Waiden inversion mechanism or its direct abstraction.
Journal of Structural Chemistry, 1979
Chemico-Biological Interactions, 2008
Our goal was to design, synthesize, and evaluate new cholinesterase inhibitors. Fourteen dehydroa... more Our goal was to design, synthesize, and evaluate new cholinesterase inhibitors. Fourteen dehydroamino acids esterified to choline and to its ternary analog were synthesized by a new method that gave a yield of 84-93%. The potency of the amino acid ester derivatives was tested by measuring K i values for inhibition of human red cell acetylcholinesterase and human plasma butyrylcholinesterase. The most potent compound was a choline ester of dehydrophenylalanine where the amine group of the amino acid was derivatized with a benzoyl group containing a methoxy in the 2-position, CH 3 O(C 6 H 4)CONHC(CHC 6 H 5)COOCH 2 CH 2 N + (CH 3) 3. This compound was a strong inhibitor of both human acetylcholinesterase and human butyrylcholinesterase, with K i values of 10 M and 0.08 M, respectively. These K i values are comparable to that of Rivastigmine. Docking of the most potent compound into the active site of human butyrylcholinesterase showed that the lowest energy model had two benzene rings oriented towards Trp 82 and Tyr 332 whereas the positively charged nitrogen group was stabilized by Trp 231. This orientation placed the ester group 3.89Å from the active site Ser 198, a distance too far for covalent bonding, explaining why the esters are inhibitors rather than substrates. This class of anticholinesterase agents has the potential for therapeutic utility in the treatment of disorders of the cholinergic system.
Chemosphere, 2002
SCF-MO computations have been performed on tetra-to octa-chlorinated dibenzo-p-dioxin congeners (... more SCF-MO computations have been performed on tetra-to octa-chlorinated dibenzo-p-dioxin congeners (PCDD) using an MNDO-PM3 Hamiltonian. Qualitative relationships were developed between empirical, international-toxic equivalence factors for PCDD congeners and their relative (specific) polarizabilities and mean values of second hyperpolarizabilities estimated using finite-field theory.
The Journal of Physical Chemistry A, 2004
ABSTRACT A 30-reaction core kinetic model has been developed that accounts for the major features... more ABSTRACT A 30-reaction core kinetic model has been developed that accounts for the major features in the homogeneous formation of polychlorinated dibenzofurans (PCDF) from the high-temperature oxidation of 2,4,6- trichlorophenol (TCP). The core, purely gas-phase scheme provides agreement within a factor of 1.5 - 2 between experimental and calculated yields of PCDD/Fs using the REACT kinetic program. It is demonstrated that the formation of PCDF is due to the conversion of TCP to 2,4-dichlorophenol (DCP), which subsequently forms a keto resonance structure of the 2,4-dichlorophenoxyl radical (DCP • ). The conversion of TCP to DCP provides an ortho hydrogen that is necessary for the formation of PCDF. Ab initio calculations were utilized to calculate the activation energies of the key reactions involved in the gas-phase formation of PCDF
A pressure dependent kinetic sub-mechanism for HxOxC1 species is developed based on literature da... more A pressure dependent kinetic sub-mechanism for HxOxC1 species is developed based on literature data for reactions of the hydrogen-oxygen subset and paths involving abstraction of hydrogen atoms. Pressure and temperature dependent rate constants are determined for bimolecular, chemical activation (association and addition) and unimolecular (thermal) dissociation reactions using multi-frequency QRRK analysis for k(E) and master Equation analysis for fall-off. Pressure and temperature dependent rate constants are expressed in the form of 7x3 Chebyshev polynomials over 0.01 to 100 atm and 300 to 3000K. The chemical activation systems include reactions of OH, HO2, O • , O2 with the following carbon species: CO, HC • =O, CH2=O, C • H2OH, CH3O, CH3 plus selected C2 species, with dissociation analysis for stabilized adducts. Improved rate constants are used for HO2 + CO reaction (near pressure independent) expressed as k1a= 8.45 x10 8 xT 1.21 exp(17267cal/RT) and k1b=7.14x10 7 xT 1.57 exp(1...
The Journal of Physical Chemistry A
Chem. Sci.
New rearrangement mechanism prototypes are introduced to account for the non-ideal coordination a... more New rearrangement mechanism prototypes are introduced to account for the non-ideal coordination and fluxional behavior of five-coordinate metalo-complexes.
The Journal of Physical Chemistry a, 2010
exo-Tricyclo[5.2.1.0(2,6)]decane (TCD) or exo-tetrahydrodicyclopentadiene is the principal compon... more exo-Tricyclo[5.2.1.0(2,6)]decane (TCD) or exo-tetrahydrodicyclopentadiene is the principal component of the high-energy density hydrocarbon fuel commonly identified as JP-10. Thermodynamic parameters for the parent TCD molecule and of all the tricyclodecyl radicals corresponding to the loss of hydrogen atoms from different carbons sites (TCD-Ri with i indicating the given carbon center) are determined using several density functional theory and G3MP2B3 and CBS-QB3 higher level composite computational chemistry methods. Five isodesmic work reactions, three involving bridged hydrocarbon reference molecules with similar ring strains, are employed to produce a cancelation of systematic calculation errors in evaluation of standard, gas-phase formation enthalpies at 298 K. Delta(f)H degrees (298) for TCD is found to be -19.5 +/- 1.3 kcal mol(-1), which is several kcal mol(-1) lower than the commonly used values. C(i)-H bond energies for corresponding TCD carbon sites are evaluated as follows: TCD-R1, 107.2; TCD-R2, 100.1; TCD-R3, 98.0; TCD-R4, 98.5; TCD-R9, 98.7; TCD-R10, 104.1 kcal mol(-1). Results from use of five different DFT methods are in very good agreement with composite level values for all work reactions used for the radicals. The exo and endo isomers of TCD are both determined to have chair and boat conformers.
Chem Phys Lett, 2011
Transport of hydrogen atoms plays a key role in chemical and biological processes involving metab... more Transport of hydrogen atoms plays a key role in chemical and biological processes involving metabolism of molecular hydrogen. Several 'gas-phase' and more intricate organometallic models (mimics of the hydrogenase enzyme) are developed to show the intriguing role of the molecular hydrogen as a third party in the pass-on transfer of hydrogen atoms. This hydrogen assisted transport (HAT) mechanism is based on the current understanding of the hydrogen exchange reactions and it is believed to be applicable to certain H/D-isotope exchange processes and remote transport of H-atoms.
The Journal of Physical Chemistry a, 2010
Association of alkyl radicals with ground-state oxygen 3 Σ g + (O 2) generates chemically activat... more Association of alkyl radicals with ground-state oxygen 3 Σ g + (O 2) generates chemically activated peroxy intermediates, which can isomerize or further react to form new products before collisional stabilization. The lowest-energy reaction (∼19 kcal mol-1) for alkylperoxy derivatives of C 3 and larger n-hydrocarbons is an isomerization (intramolecular H-atom transfer) that forms a hydroperoxide alkyl radical, and there is a ∼30 kcal mol-1 barrier path to olefin plus HO 2 , which is a termination step at lower temperatures. The lowenergy-barrier product, hydroperoxide alkyl radical intermediate, can experience additional chemical activation via association with a second oxygen molecule, where there are three important paths that result in chain branching. The competition between this HO 2 + olefin termination step of the first O 2 association and the chain branching processes from the second chemical activation step plays a dominant role at temperatures below 1000 K. Secondary n-pentyl radicals are used in this study as surrogates to analyze the thermochemistry and detailed kinetics of the chemical activation and stabilized adduct reactions important to chain branching and termination. As these radicals provide six-member ring transition states for H-atom transfer between secondary carbons, they represent the detailed kinetics of larger alkane radicals, such as the common fuel components n-heptane and n-decane. Comprehensive potential energy diagrams developed from multilevel CBS-QB3, G3MP2, and CBS-APNO and single-level ab initio and density functional theory methods are used to analyze secondary 2-pentyl (n-pentan-2-yl) and interrelated 2-hydroperoxide-pentan-4-yl radical interactions with O 2. The thermochemistry and kinetics of the chemical activation and stabilized adduct reactions important to chain branching and termination are reported and discussed. Results show that the chain branching reactions have faster kinetics in this system because the barriers are lower than those observed in ethyl and propyl radical plus O 2 reactions; consequently, the branching is predicted to be more important. The lower barriers for branching result in less competition from the termination (HO 2 + olefin) path in this larger radical. Several nontraditional reaction channels not previously considered in the literature are identified. A pathway is suggested to explain the formation of a unique trioxane product observed experimentally.