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Zahra Homayoon

Bio: Zahra Homayoon is an academic researcher from Emory University. The author has contributed to research in topics: Potential energy surface & Dissociation (chemistry). The author has an hindex of 13, co-authored 23 publications receiving 476 citations. Previous affiliations of Zahra Homayoon include University of Santiago de Compostela & Texas Tech University.

Papers
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Journal ArticleDOI
TL;DR: Direct dynamics simulation studies are described for bimolecular SN2 nucleophilic substitution, unimolecular decomposition, post-transition-state dynamics, mass spectrometry experiments, and semiclassical vibrational spectra.
Abstract: In a direct dynamics simulation, the technologies of chemical dynamics and electronic structure theory are coupled so that the potential energy, gradient, and Hessian required from the simulation are obtained directly from the electronic structure theory. These simulations are extensively used to (1) interpret experimental results and understand the atomic-level dynamics of chemical reactions; (2) illustrate the ability of classical simulations to correctly interpret and predict chemical dynamics when quantum effects are expected to be unimportant; (3) obtain the correct classical dynamics predicted by an electronic structure theory; (4) determine a deeper understanding of when statistical theories are valid for predicting the mechanisms and rates of chemical reactions; and (5) discover new reaction pathways and chemical dynamics. Direct dynamics simulation studies are described for bimolecular SN2 nucleophilic substitution, unimolecular decomposition, post-transition-state dynamics, mass spectrometry experiments, and semiclassical vibrational spectra. Also included are discussions of quantum effects, the accuracy of classical chemical dynamics simulation, and the methodology of direct dynamics.

118 citations

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TL;DR: An isomerization-roaming pathway to the CH3ONO isomer and then to theCH3O + NO products is found, which supports the supposition of such a pathway based on locating a loose first-order saddle point and associated IRC, reported previously by Zhu and Lin.
Abstract: We report a global potential energy surface (PES) for CH3NO2 based on fitting roughly 114 000 density functional theory (UB3LYP/6-311+g(d,p)) electronic energies. The PES is a precise, permutationally invariant fit to these energies. Properties of the PES are described, as are some preliminary quasiclassical trajectory calculations. An isomerization-roaming pathway to the CH3ONO isomer and then to the CH3O + NO products is found. Although the pathway occurs at larger distances than a related loose saddle-point on the PES, the pathway supports the supposition of such a pathway based on locating a loose first-order saddle point and associated IRC, reported previously by Zhu and Lin [Zhu, R. S. and Lin, M. C. Chem. Phys. Lett. 2009, 478, 11].

52 citations

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TL;DR: The observation of distinct methoxy vibrational excitation for trajectories from nitromethane and methyl nitrite dissociation at the same total energy show that the nitromETHane dissociation bears a nonstatistical signature of the roaming isomerization pathway, and this is possibly responsible for the nitROMethane Λ-doublet propensity as well.
Abstract: We combine the techniques of infrared multiphoton dissociation (IRMPD) with state selective ion imaging to probe roaming dynamics in the unimolecular dissociation of nitromethane and methyl nitrite Recent theoretical calculations suggest a “roaming-mediated isomerization” pathway of nitromethane to methyl nitrite prior to decomposition State-resolved imaging of the NO product coupled with infrared multiphoton dissociation was carried out to examine this unimolecular decomposition near threshold The IRMPD images for the NO product from nitromethane are consistent with the earlier IRMPD studies that first suggested the importance of an isomerization pathway A significant Λ-doublet propensity is seen in nitromethane IRMPD but not methyl nitrite The experimental observations are augmented by quasiclassical trajectory calculations for nitromethane and methyl nitrite near threshold for each dissociation pathway The observation of distinct methoxy vibrational excitation for trajectories from nitromethane and methyl nitrite dissociation at the same total energy show that the nitromethane dissociation bears a nonstatistical signature of the roaming isomerization pathway, and this is possibly responsible for the nitromethane Λ-doublet propensity as well

50 citations

Journal ArticleDOI
TL;DR: New, full-dimensional potential energy surfaces (PESs), obtained using precise least-squares fitting of high-level electronic energy databases, are reported for intrinsic H2(H2O) two-body and H2 (H2 O)2 three-body potentials.
Abstract: New, full-dimensional potential energy surfaces (PESs), obtained using precise least-squares fitting of high-level electronic energy databases, are reported for intrinsic H2(H2O) two-body and H2(H2O)2 three-body potentials. The database for H2(H2O) consists of approximately 44 000 energies at the coupled cluster singles and doubles plus perturbative triples (CCSD(T))-F12a/haQZ (aug-cc-pVQZ for O and cc-pVQZ for H) level of theory, while the database for the three-body interaction consists of more than 36 000 energies at the CCSD(T)-F12a/haTZ (aug-cc-pVTZ for O, cc-pVTZ for H) level of theory. Two precise potentials are based on the invariant-polynomial technique and are compared to computationally faster ones obtained via "purified" symmetrization. All fits use reduced permutational symmetry appropriate for these non-covalent interactions. These intrinsic potentials are employed together with existing ones for H2, H2O, and (H2O)2, to obtain full PESs for H2(H2O) and H2(H2O)2. Properties of these full PESs are presented, including a diffusion Monte Carlo calculation of the zero-point energy and wavefunction, and dissociation energy of the H2(H2O) dimer. These PESs together with an existing one for water clusters are used in a many-body representation of the PES of hydrogen clathrate hydrates, illustrated for H2@(H2O)20. An analysis of this hydrate is presented, including the electronic dissociation energy to remove H2 from the calculated equilibrium structure.

38 citations

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TL;DR: Direct dynamics simulations, utilizing the RM1 semiempirical electronic structure theory, were performed to study the thermal dissociation of the doubly protonated tripeptide threonine-isoleucine-lysine ion, TIK(H+)2, for temperatures of 1250-2500 K, corresponding to classical energies of 1778-3556 kJ/mol.
Abstract: Direct dynamics simulations, utilizing the RM1 semiempirical electronic structure theory, were performed to study the thermal dissociation of the doubly protonated tripeptide threonine–isoleucine–lysine ion, TIK(H+)2, for temperatures of 1250–2500 K, corresponding to classical energies of 1778–3556 kJ/mol. The number of different fragmentation pathways increases with increase in temperature. At 1250 K there are only three fragmentation pathways, with one contributing 85% of the fragmentation. In contrast, at 2500 K, there are 61 pathways, and not one dominates. The same ion is often formed via different pathways, and at 2500 K there are only 14 m/z values for the product ions. The backbone and side-chain fragmentations occur by concerted reactions, with simultaneous proton transfer and bond rupture, and also by homolytic bond ruptures without proton transfer. For each temperature the TIK(H+)2 fragmentation probability versus time is exponential, in accord with the Rice–Ramsperger–Kassel–Marcus and transit...

33 citations


Cited by
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TL;DR: This review focuses on the NA-MQC dynamics methods and programs developed in the last 10 years, and stresses the relations between approaches and their domains of application.
Abstract: Nonadiabatic mixed quantum–classical (NA-MQC) dynamics methods form a class of computational theoretical approaches in quantum chemistry tailored to investigate the time evolution of nonadiabatic phenomena in molecules and supramolecular assemblies. NA-MQC is characterized by a partition of the molecular system into two subsystems: one to be treated quantum mechanically (usually but not restricted to electrons) and another to be dealt with classically (nuclei). The two subsystems are connected through nonadiabatic couplings terms to enforce self-consistency. A local approximation underlies the classical subsystem, implying that direct dynamics can be simulated, without needing precomputed potential energy surfaces. The NA-MQC split allows reducing computational costs, enabling the treatment of realistic molecular systems in diverse fields. Starting from the three most well-established methods—mean-field Ehrenfest, trajectory surface hopping, and multiple spawning—this review focuses on the NA-MQC dynamics...

396 citations

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TL;DR: This review describes recent results from quantum chemical and theoretical kinetic studies of relevance to atmospheric chemistry and examines the VOC oxidation initiation channels by OH, O(3), NO(3) and Cl, followed by the reactions of the alkyl, alkoxy,Alkylperoxy and Criegee intermediates active in the subsequent oxidation steps.
Abstract: The chemistry of the atmosphere encompasses a vast number of reactions acting on a plethora of intermediates. These reactions, occurring sequentially and in parallel, give rise to intertwined and irreducible mechanisms describing the complex chemical transformations of organic and inorganic compounds in the atmosphere. The complexity of this system is that it requires combined experimental, theoretical, and modeling approaches to elucidate the characteristics of the individual reactions, and their mutual interaction. In this review, we describe recent results from quantum chemical and theoretical kinetic studies of relevance to atmospheric chemistry. The review first summarizes the most commonly used theoretical methodologies. It then examines the VOC oxidation initiation channels by OH, O(3), NO(3) and Cl, followed by the reactions of the alkyl, alkoxy, alkylperoxy and Criegee intermediates active in the subsequent oxidation steps. Specific systems such as the oxidation of aromatics and the current state of knowledge on OH-regeneration in VOC oxidation are also discussed, as well as some inorganic reactions.

350 citations

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TL;DR: The present results are an important cog in clarifying the atmospheric fate and oxidation processes of Criegee intermediates, and they also show how theoretical methods can provide reliable rate data for complex atmospheric processes.
Abstract: Criegee intermediates are produced in the ozonolysis of unsaturated hydrocarbons in the troposphere, and understanding their fate is a prerequisite to modeling climate-controlling atmospheric aerosol formation. Although some experimental and theoretical rate data are available, they are incomplete and partially inconsistent, and they do not cover the tropospheric temperature range. Here, we report quantum chemical rate constants for the reactions of stabilized formaldehyde oxide (CH2OO) and acetaldehyde oxide (syn-CH3CHOO and anti-CH3CHOO) with H2O and for their unimolecular reactions. Our results are obtained by combining post-CCSD(T) electronic structure benchmarks, validated density functional theory potential energy surfaces, and multipath variational transition state theory with multidimensional tunneling, coupled-torsions anharmonicity, and high-frequency anharmonicity. We consider two different types of reaction mechanisms for the bimolecular reactions, namely, (i) addition-coupled hydrogen transfe...

231 citations

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TL;DR: Comparisons with experiment suggest that the present dynamically corrected VRC-TST approach provides quantitatively accurate predictions for the capture rate, and the present approach should be applicable to a wide array of radical-radical combination reactions.
Abstract: An ab initio transition state theory based procedure for accurately predicting the combination kinetics of two alkyl radicals is described. This procedure employs direct evaluations of the orientation dependent interaction energies at the CASPT2/cc-pvdz level within variable reaction coordinate transition state theory (VRC-TST). One-dimensional corrections to these energies are obtained from CAS+1+2/aug-cc-pvtz calculations for CH3 + CH3 along its combination reaction path. Direct CAS+1+2/aug-cc-pvtz calculations demonstrate that, at least for the purpose of predicting the kinetics, the corrected CASPT2/cc-pvdz potential energy surface is an accurate approximation to the CAS+1+2/aug-cc-pvtz surface. Furthermore, direct trajectory simulations, performed at the B3LYP/6-31G* level, indicate that there is little local recrossing of the optimal VRC transition state dividing surface. The corrected CASPT2/cc-pvdz potential is employed in obtaining direct VRC-TST kinetic predictions for the self and cross combinations of methyl, ethyl, iso-propyl, and tert-butyl radicals. Comparisons with experiment suggest that the present dynamically corrected VRC-TST approach provides quantitatively accurate predictions for the capture rate. Each additional methyl substituent adjacent to a radical site is found to reduce the rate coefficient by about a factor of two. In each instance, the rate coefficients are predicted to decrease quite substantially with increasing temperature, with the more sterically hindered reactants having a more rapid decrease. The simple geometric mean rule, relating the capture rate for the cross reaction to those for the self-reactions, is in remarkably good agreement with the more detailed predictions. With suitable generalizations the present approach should be applicable to a wide array of radical–radical combination reactions.

200 citations

Journal ArticleDOI
TL;DR: The newly proposed sudden vector projection (SVP) model and its applications are reviewed, which are capable of treating the translational, rotational, and multiple vibrational modes in reactions involving polyatomic reactants.
Abstract: ConspectusMode specificity is defined by the differences in reactivity due to excitations in various reactant modes, while bond selectivity refers to selective bond breaking in a reaction. These phenomena not only shed light on reaction dynamics but also open the door for laser control of reactions. The existence of mode specificity and bond selectivity in a reaction indicates that not all forms of energy are equivalent in promoting the reactivity, thus defying a statistical treatment. They also allow the enhancement of reactivity and control product branching ratio. As a result, they are of central importance in chemistry.This Account discusses recent advances in our understanding of these nonstatistical phenomena. In particular, the newly proposed sudden vector projection (SVP) model and its applications are reviewed. The SVP model is based on the premise that the collision in many direct reactions is much faster than intramolecular vibrational energy redistribution in the reactants. In such a sudden li...

177 citations