Biomedical subjects

Diego Troya

Publications and source records attributed to Diego Troya.

17 recordsLinked to original sources

PubMed2006

Theoretical study of the Ar-, Kr-, and Xe-CH4, -CF4 intermolecular potential-energy surfaces.

We present a theoretical study of the intermolecular potentials for the Ar, Kr, and Xe-CH4, -CF4 systems. The potential-energy surfaces of these systems have been calculated utilizing second-order Möller-Plesset perturbation theory and coupled-cluster theory in combination with correlation-consistent basis sets (aug-cc-pvnz; n = d, t, q). The calculations show that the stabilizing interactions between the rare gases and the molecules are slightly larger for CF4 than for CH4. Moreover, the rare-gas-CX4 (X = H, F) potentials are more attractive for Xe than for Kr and Ar. Our highest quality ab initio data (focal-point-CCSD(T) extrapolated to the complete basis set limit) have been used to develop pairwise analytical potentials for rare-gas-hydrocarbon (-fluorocarbon) systems. These potentials can be applied in classical-trajectory studies of rare gases interacting with hydrocarbon surfaces.

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PubMed2006

H + CD4 abstraction reaction dynamics: product energy partitioning.

This paper presents experimental and theoretical studies of the product energy partitioning associated with the H + CD4 (nu = 0) --> HD + CD3 reaction for the collision energy range 0.5-3.0 eV. The theoretical results are based on quasiclassical trajectories from (1) first principles direct dynamics calculations (B3LYP/6-31G), (2) an empirical surface developed by Espinosa-García [J. Chem. Phys. 2002, 116, 10664] (EG), and (3) two semiempirical surfaces (MSINDO and reparametrized MSINDO). We find that most of the energy appears in product translation at energies just above the reactive threshold; however, HD vibration and rotation become quite important at energies above 1 eV, each accounting for over 20% of the available energy above 1.5 eV, according to the B3LYP calculations. The barrier on the B3LYP surface, though being later than that on EG, predicts significantly higher HD vibrational excitation than EG. This deviation is contradictory to what would be expected on the basis of the Polanyi rules and derives from modest differences in the potential energy surfaces. The CD3 internal energy is generally quite low, and we present detailed rotational state distributions which show that the CD3 rotational distribution is largely independent of collision energy in the 0.75-1.95 eV range. The most populated rotational levels are N = 5 and 6 on B3LYP, with most of that excitation being associated with motion about the C2 axes, rather than C3 axis, of the CD3 product, in good agreement with the experimental results. Through our extensive studies in this and previous work concerning the scattering dynamics, we conclude that B3LYP/6-31G provides the best available description of the overall dynamics for the title reaction at relatively high collision energies.

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PubMed2006

Ab initio and direct quasiclassical-trajectory study of the Cl + CH4-->HCl + CH3 reaction.

We present an electronic structure and dynamics study of the Cl + CH(4)--> HCl + CH(3) reaction. We have characterized the stationary points of the ground-state potential-energy surface using various electronic structure methods and basis sets. Our best calculations, CCSD(T) extrapolated to the complete basis-set limit based on geometries and harmonic frequencies obtained at the CCSD(T)/aug-cc-pvtz level, are in agreement with the experimental reaction energy and indirect measurements of the barrier height. Using ab initio information, we have reparametrized a semiempirical Hamiltonian so that the predictions of the improved Hamiltonian agree with the higher-level calculations in various regions of the potential-energy surface. This improved semiempirical Hamiltonian is then used to propagate quasiclassical trajectories and characterize the reaction dynamics. The good agreement of the calculated HCl rotational and angular distributions with the experiment indicates that reparametrizing semiempirical Hamiltonians is a promising approach to derive accurate potential-energy surfaces for polyatomic reactions. However, excessive energy leakage from the initial vibrational energy of the CH(4) molecule to the reaction coordinate in the trajectory calculations calls into question the suitability of the standard quasiclassical-trajectory method to describe energy partitioning in polyatomic reactions.

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PubMed2006

Theoretical study of the effect of surface density on the dynamics of Ar + alkanethiolate self-assembled monolayer collisions.

We present a classical-trajectory study of energy transfer in collisions of Ar atoms with alkanethiolate self-assembled monolayers (SAMs) of different densities. The density of the SAMs is varied by changing the distance between the alkanethiolate chains in the organic monolayers. Our calculations indicate that SAMs with smaller packing densities absorb more energy from the impinging Ar atoms, in agreement with recent molecular-beam scattering experiments. We find that energy transfer is enhanced by a decrease in the SAM density because (1) less dense SAMs increase the probability of multiple encounters between Ar and the SAM, (2) the vibrational frequencies of large-amplitude motions of the SAM chains decrease for less dense SAMs, which makes energy transfer more efficient in single-encounter collisions, and (3) increases in the distance between chains promote surface penetration of the Ar atom. Analysis of angular distributions reveals that the polar-angle distributions do not have a cosine shape in trapping-desorption processes involving penetration of the Ar atom into the alkanethiolate self-assembled monolayers. Instead, there is a preference for Ar atoms that penetrate the surface to desorb along the chain-tilt direction.

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PubMed2006

Experimental and theoretical investigations of the inelastic and reactive scattering dynamics of O(3p) + D2.

This paper presents a combined experimental and theoretical study of the dynamics of O((3)P) + D(2) collisions, with emphasis on a center-of-mass (c.m.) collision energy of 25 kcal mol(-1). The experiments were conducted with a crossed-molecular-beams apparatus, employing a laser detonation source to produce hyperthermal atomic oxygen and mass spectrometric detection to measure the product angular and time-of-flight distributions. The novel beam source, which enabled these experiments to be conducted, contributed unique challenges to the experiments and to the analysis, so the experimental methods and approach to the analysis are discussed in detail. Three different levels of theory were used: (1) quasiclassical trajectories (QCT), (2) time-independent quantum scattering calculations based on high-quality potential surfaces for the two lower-energy triplet states, and (3) trajectory-surface-hopping (TSH) studies that couple the triplet surfaces with the lowest singlet surface using a spin-orbit Hamiltonian derived from ab-initio calculations. The latter calculations explore the importance of intersystem crossing in the dynamics. Both experiment and theory show that inelastically scattered O atoms scatter almost exclusively in the forward direction, with little or no loss of translational energy. For the reaction, O((3)P) + D(2) --> OD + D, the experiment shows that, on average, approximately 50% of the available energy goes into product translation and that the OD product angular distributions are largely backward-peaked. These results may be interpreted in light of the QCT and TSH calculations, leading to the conclusion that the reaction occurs mainly on triplet potential energy surfaces with, at most, minor intersystem crossing to a singlet surface. Reaction on either of the two low-lying reactive triplet surfaces proceeds through a rebound mechanism in which the angular distributions are backward-peaked and the product OD is both vibrationally and rotationally excited. The quantum scattering results are in good agreement with QCT calculations, indicating that quantum effects are relatively small for this reaction at a collision energy of 25 kcal mol(-1).

Deuterium↗

PubMed2006

H + CD4 abstraction reaction dynamics: excitation function and angular distributions.

We compare experimental photoloc measurements and quasi-classical trajectory calculations of the integral cross sections, lab-frame speed distributions, and angular distributions associated with the CD3 products of the H + CD4(nu = 0) --> CD3 + HD reaction at collision energies ranging from 0.5 to 3.0 eV. Of the potential energy surfaces (PES) we explored, the direct dynamics calculations using the B3LYP/6-31G** density functional theory PES provide the best agreement with the experimental measurements. This agreement is likely due to the better overall description that B3LYP provides for geometries well removed from the minimum energy path, even though its barrier height is low by approximately 0.2 eV. In contrast to previous theoretical calculations, the angular distributions on this surface show behavior associated with a stripping mechanism, even at collision energies only approximately 0.1 eV above the reaction barrier. Other potential energy surfaces, which include an analytical potential energy surface from Espinosa-García and a direct dynamics calculation based on the MSINDO semiempirical Hamiltonian, are less accurate and predict more rebound dynamics at these energies than is observed. Reparametrization of the MSINDO surface, though yielding better agreement with the experiment, is not sufficient to capture the observed dynamics. The differences between these surfaces are interpreted using an analysis of the opacity functions, where we find that the wider cone of acceptance on the B3LYP surface plays a crucial role in determining the integral cross sections and angular distributions.

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PubMed2005

Ab initio and direct quasiclassical-trajectory study of the F+CH4-->HF+CH3 reaction.

We present an electronic structure and dynamics study of the F+CH4-->HF+CH3 reaction. CCSD(T)/aug-cc-pVDZ geometry optimizations, harmonic-frequency, and energy calculations indicate that the potential-energy surface is remarkably isotropic near the transition state. In addition, while the saddle-point F-H-C angle is 180 degrees using MP2 methods, CCSD(T) geometry optimizations predict a bent transition state, with a 153 degrees F-H-C angle. We use these high-quality ab initio data to reparametrize the parameter-model 3 (PM3) semiempirical Hamiltonian so that calculations with the improved Hamiltonian and employing restricted open-shell wave functions agree with the higher accuracy data. Using this specific-reaction-parameter PM3 semiempirical Hamiltonian (SRP-PM3), we investigate the reaction dynamics by propagating quasiclassical trajectories. The results of our calculations using the SRP-PM3 Hamiltonian are compared with experiments and with the estimates of two recently reported potential-energy surfaces. The trajectory calculations using the SRP-PM3 Hamiltonian reproduce quantitatively the measured HF vibrational distributions. The calculations also agree with the experimental HF rotational distributions and capture the essential features of the excitation function. The results of the SRP semiempirical Hamiltonian developed here clearly improve over those using the two prior potential-energy surfaces and suggest that reparametrization of semiempirical Hamiltonians is a promising strategy to develop accurate potential-energy surfaces for reaction dynamics studies of polyatomic systems.

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PubMed2005

A reinterpretation of the mechanism of the simplest reaction at an sp3-hybridized carbon atom: H + CD4 --> CD3 + HD.

A comparison between theory and experiment for the benchmark H + CD4 --> HD + CD3 abstraction reaction yields a reinterpretation of the reaction mechanism and highlights the unexpected contribution of a stripping mechanism. Whereas the best analytic surface fails to reproduce experiment, a first-principles direct-dynamics (on the fly) treatment is in good agreement, showing that the H + CD4 reaction exhibits extreme sensitivity to modest differences in the potential energy surface. We find that bent H-D-C transition state geometries play an important role in the dynamics. A simple model that relates the scattering angle impact parameter and cone of acceptance accounts well for the overall reaction dynamics.

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PubMed2005

Quasiclassical trajectory study of energy transfer and collision-induced dissociation in hyperthermal Ar + CH4 and Ar + CF4 collisions.

We present a study of energy transfer in collisions of Ar with methane and perfluoromethane at hyperthermal energies (E(coll) = 4-10 eV). Quasiclassical trajectory calculations of Ar + CX(4) (X = H, F) collisions indicate that energy transfer from reagents' translation to internal modes of the alkane molecule is greatly enhanced by fluorination. The reasons for the enhancement of energy transfer upon fluorination are shown to emerge from a decrease in the hydrocarbon vibrational frequencies of the CX(4) molecule with increasing the mass of the X atom, and to an increase of the steepness of the Ar-CX(4) intermolecular potential. At high collision energies, we find that the cross section of Ar + CF(4) collisions in which the amount of energy transfer is larger than needed to break a C-F bond is at least 1 order of magnitude larger than the cross sections of Ar + CH(4) collisions producing CH(4) with energy above the dissociation limit. In addition, collision-induced dissociation is detected in short time scales in the case of the fluorinated species at E(coll) = 10 eV. These results suggest that the cross section for degradation of fluorinated hydrocarbon polymers under the action of nonreactive hyperthermal gas-phase species might be significantly larger than that of hydrogenated hydrocarbon polymers. We also illustrate a practical way to derive intramolecular potential energy surfaces for bond-breaking collisions by improving semiempirical Hamiltonians based on grids of high-quality ab initio calculations.

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PubMed2005

Classical trajectory study of collisions of Ar with alkanethiolate self-assembled monolayers: potential-energy surface effects on dynamics.

We have investigated collisions between Ar and alkanethiolate self-assembled monolayers (SAMs) using classical trajectory calculations with several potential-energy surfaces. The legitimacy of the potential-energy surfaces is established through comparison with molecular-beam data and ab initio calculations. Potential-energy surfaces used in previous work overestimate the binding of Ar to the SAM, leading to larger energy transfer than found in the experiments. New calculations, based on empirical force fields that better reproduce ab initio calculations, exhibit improved agreement with the experiments. In particular, polar-angle-dependent average energies calculated with explicit-atom potential-energy surfaces are in excellent agreement with the experiments. Polar- and azimuthal-angle-dependent product translational energies are examined to gain deeper insight into the dynamics of Ar+SAM collisions.

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PubMed2005

Five new zinc phosphite structures: tertiary building blocks in the construction of hybrid materials.

The syntheses and structures of five new zinc phosphites [Zn(HPO(3))(C(4)H(6)N(2))] (1), [Zn(2)(HPO(3))(2)(C(10)H(10)N(2))(2)](2) (2), [Zn(HPO(3))(C(14)H(14)N(4))(0.5)] (3), [Zn(2)(HPO(3))(2)(C(14)H(14)N(4))].0.4H(2)O (4), and [Zn(2)(HPO(3))(2)(C(14)H(14)N(4))] (5) are reported. In compounds 1-3, the zinc atoms are ligated by 1-methylimidazole, 1-benzylimidazole, and 1,4-bis(imidazol-1-ylmethyl)benzene, respectively, while compounds 4 and 5 are synthesized in the presence of the same bifunctional ligand, 1,3-bis(imidazol-1-ylmethyl)benzene. The inorganic framework of compound 1 is composed of vertex-shared ZnO(3)N and HPO(3) tetrahedra that form 4-rings, which, in turn, are linked to generate a one-dimensional ladder structure. In 2, the inorganic framework is composed of 4-rings and 8-rings to form the well-known 4.8(2) 2D network. This is connected via C-H...pi interactions between 1-benzylimidazole ligand to generate a pseudo-pillared-layer structure. In 3, the inorganic framework again has the 4.8(2) topology pillared by the bis(imidazole) ligand, 1,3-bis(imidazol-1-ylmethyl)benzene. In 4, a new layer pattern is observed. Specifically, three edge-sharing 4-rings form triple-fused 4-rings. These tertiary building units are further connected to form 12-rings. The alternating triple 4-rings and 12-rings form a previously unknown 2D inorganic sheet. The sheets are joined together by the bis(imidazole) ligand, 1,3-bis(imidazol-1-ylmethyl)benzene, to generate a 3D pillared-layer structure. In 4, benzene rings and imidazole rings stack in a zigzag pattern in the interlayer space. A significant role for the triple 4-ring tertiary building unit in the formation of hybrid inorganic/organic metal phosphite structures is proposed for 4 and 5. In 5, the triple 4-rings fuse to give a 1D stair-step structure. Calculations show that the triple 4-ring pattern observed in the linear ladder structure of 1 is more stable than that in the stair step pattern of 5.

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PubMed2005

Quasiclassical trajectory study of the O(3P) + CH4 --> OH + CH3 reaction with a specific reaction parameters semiempirical Hamiltonian.

We present a theoretical study of the O(3P) + CH4 --> OH + CH3 reaction using electronic structure, kinetics, and dynamics calculations. We calculate a grid of ab initio points at the PMP2/AUG-cc-pVDZ level to characterize the potential energy surface in regions of up to 1.3 eV above reagents. This grid of ab initio points is used to derive a set of specific reaction parameters (SRP) for the MSINDO semiempirical Hamiltonian. The resulting SRP-MSINDO Hamiltonian improves the quality of the standard Hamiltonian, particularly in regions of the potential energy surface beyond the minimum-energy reaction path. Quasiclassical-trajectory calculations are used to study the reaction dynamics with the original and the improved MSINDO semiempirical Hamiltonians, and a prior surface. The SRP-MSINDO semiempirical Hamiltonian yields OH rotational distributions in agreement with experimental results, improving over the results of the other surfaces. Thermal rate constants estimated with Variational Transition State Theory using the SRP-MSINDO Hamiltonian are also in agreement with experiments. Our results indicate that reparametrized semiempirical Hamiltonians are a good alternative to generating potential energy surfaces for accurate dynamics studies of polyatomic reactions.

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PubMed2004

Crossed beams and theoretical studies of the dynamics of hyperthermal collisions between Ar and ethane.

Crossed molecular beams experiments and classical trajectory calculations have been used to study the dynamics of Ar+ethane collisions at hyperthermal collision energies. Experimental time-of-flight and angular distributions of ethane molecules that scatter into the backward hemisphere (with respect to their original direction in the center-of-mass frame) have been collected. Translational energy distributions, derived from the time-of-flight distributions, reveal that a substantial fraction of the collisions transfer abnormally large amounts of energy to internal excitation of ethane. The flux of the scattered ethane molecules increased only slightly from directly backward scattering to sideways scattering. Theoretical calculations show angular and translational energy distributions which are in reasonable agreement with the experimental results. These calculations have been used to examine the microscopic mechanism for large energy transfer collisions ("supercollisions"). Collinear ("head-on") or perpendicular ("side-on") approaches of Ar to the C-C axis of ethane do not promote energy transfer as much as bent approaches, and collisions in which the H atom is "sandwiched" in a bent Ar...H-C configuration lead to the largest energy transfer. The sensitivity of collisional energy transfer to the intramolecular potential energy of ethane has also been examined.

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PubMed2004

Theoretical studies of hyperthermal O(3P) collisions with hydrocarbon self-assembled monolayers.

We present a dynamics study of inelastic and reactive scattering processes in collisions of hyperthermal (5 eV) O(3P) atoms with a hydrocarbon self-assembled monolayer (SAM). Molecular-dynamics simulations are carried out using a quantum mechanics/molecular mechanics (QM/MM) interaction potential that uses a high quality semiempirical Hamiltonian for the QM part and the MM3 force field for the MM part. A variety of products coming from reaction are identified, including H abstraction to generate OH, O atom addition to the SAM with subsequent elimination of H atoms, and direct C-C breakage. The C-C breakage mechanism provides a pathway for significant surface mass loss in single reactive events whereas the O addition-H elimination channel leads to surface oxidation. Reaction probabilities, product energy, and angular distributions are examined to gain insight on polymer erosion in low Earth orbit conditions and on fundamentals of inelastic and reactive hyperthermal gas-surface interactions.

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PubMed2004

Ab initio potential energy surface, variational transition state theory, and quasiclassical trajectory studies of the F+CH4-->HF+CH3 reaction.

In this work we present a study of the F+CH(4)-->HF+CH(3) reaction (DeltaHdegrees(298 K)=-32.0 kcal mol(-1)) using different methods of the chemical reaction theory. The ground potential energy surface (PES) is characterized using several ab initio methods. Full-dimensional rate constants have been calculated employing the variational transition state theory and using directly ab initio data. A triatomic analytical representation of the ground PES was derived from ab initio points calculated at the second- and fourth-order Møller-Plesset levels with the 6-311+G(2df,2pd) basis set, assuming the CH(3) fragment to be a 15 a.m.u. pseudoatom in the fitting process. This is suggested from experiments that indicate that the methyl group is uncoupled to the reaction coordinate. A dynamics study by means of the quasiclassical trajectory (QCT) method and employing this analytical surface was also carried out. The experimental data available on the HF internal states distributions are reproduced by the QCT results. Very recent experimental information about the reaction stereodynamics is also borne out by our QCT calculations. Comparisons with the benchmark F+H(2) and analogous Cl+CH(4) reactions are established throughout.

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PubMed2004

Quantum wave packet and quasiclassical trajectory studies of OH+CO: influence of the reactant channel well on thermal rate constants.

We study the OH+CO-->H+CO2 reaction with both six-dimensional quantum wave packets (QM) and quasiclassical trajectories (QCT), determining reaction probabilities and thermal rate constants (or coefficients), and studying the influence of the reactant channel hydrogen-bonded complex well on the reaction dynamics. The calculations use the recently developed Lakin-Troya-Schatz-Harding (LTSH) ground electronic state potential energy surface, along with a modified surface developed for this study (mod-LTSH), in which the reactant channel well is removed. Our results show that there can be significant differences between the QM and QCT descriptions of the reaction for ground-state reactants and for energies important to the thermal rate constants. Zero-point energy violation plays an important role in the QCT results, and as a result, the QCT reaction probability (for ground-state reactants and zero impact parameter) is much higher than its QM counterpart at moderate to low reagent translational energies. The influence of the reactant channel well in the QCT results is to enhance reactivity at moderate energies and to suppress reactivity at the very lowest collision energies. The QM results also show the enhancement at moderate energies but, while the very lowest translational energies cannot be adequately converged, they do not indicate any tendency toward suppression as energy is reduced. QCT calculations for excited rotational states of the reactants show that the suppression of reactivity associated with the reactant channel well is less important when the reactants are rotating, and as a result, the influence of the reactant channel well on the thermal rate coefficients is relatively small, being important below 200 K. Our results indicate that there still remain important discrepancies between experiment and theory in this low temperature regime and that further improvements of the potential are needed.

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PubMed2004

Crossed beams and theoretical studies of the O(3P)+CH4-->H+OCH3 reaction excitation function.

The excitation function for the reaction, O(3P)+CH4-->H+OCH3, has been measured in a crossed molecular beams experiment and determined with direct dynamics calculations that use the quasiclassical trajectory method in conjunction with a recently developed semiempirical Hamiltonian. Good agreement is found between experiment and theory, enabling us to address two fundamental issues for the O(3P)+CH4 reaction that arise for all O(3P)+saturated hydrocarbon reactions: (1) the importance of triplet excited states that correlate adiabatically to ground-state reactants and products and (2) the importance of intersystem crossing processes involving the lowest singlet surface [corresponding to reaction with O(1D)]. Our results indicate that the first excited triplet surface contributes substantially to the cross section when the collision energy exceeds the reaction barrier (approximately 2 eV) by more than 0.5 eV. Although triplet-singlet crossings may occur at all energies, we have found that their effect on the excitation function is negligible for the collision energies studied-up to 1.5 eV above threshold.

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