Biomedical subjects

David R Yarkony

Publications and source records attributed to David R Yarkony.

15 recordsLinked to original sources

PubMed2006

Towards a highly efficient theoretical treatment of Jahn-Teller effects in molecular spectra: the 1 2A and 2 2A electronic states of the ethoxy radical.

Nonadiabatic effects in the two lowest electronic states of the ethoxy radical, the 1 (2)A and 2 (2)A states, are considered, using multireference configuration interaction (MRCI) wave functions comprised of over 15x10(6) configuration state functions. The lowest point on the seam of conical intersection is located. Using this point as the origin, a quasidiabatic Hamiltonian suitable for use in a multimode vibronic coupling treatment of the coupled 1 (2)A and 2 (2)A electronic states is determined. The Hamiltonian includes all contributions from all internal coordinates through second order in displacements from the origin and is comprised of over 500 parameters. By using the average energy gradient, the energy difference gradients, and the derivative couplings, all of which are obtained at little additional cost once the requisite eigenstates are known, the second order Hamiltonian is determined from MRCI calculations at only 35 nuclear configurations. This is essentially the same number of points required to obtain the frequencies for the ground state equilibrium structure using centered differences of gradients. The diabatic Hamiltonian provides a good description of the seam space, the (N(int)-2)-dimensional space of conical intersection points, continuously connected to the minimum energy crossing point, enabling, for the first time, an analysis of the changes in the branching plane induced by seam curvature in the full seam space. Comparing the diabatic representation and MRCI results we find a good agreement for the ground state equilibrium structure, R(eq)(1 (2)A), as well as the ground state energy and vertical excitation energy. In good agreement with the available experimental data are the ground state equilibrium structure and the excitation energy to the A (2)A state, predicted here to involve a cone state level. Agreement between the harmonic frequencies at R(eq)(1 (2)A) computed from the MRCI wave function and from the diabatic Hamiltonian is excellent for all but the three lowest energy normal modes where significant deviations are observed indicating the need for selected cubic and/or quartic terms. For the low-lying vibrational levels, the diabatic representation can be used to partition the normal modes into two groups, those that involve inter(diabatic) state coupling and those that are spectators as far as nonadiabatic effects are concerned. The spin-orbit coupling interaction is determined using the Breit-Pauli approximation and its incorporation into the diabatic Hamiltonian is discussed.

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PubMed2006

On the characterization of three-state conical intersections using a group homomorphism approach: the two-state degeneracy spaces.

Second-order degenerate perturbation theory, in conjunction with the group homomorphism method for describing a similarity transformation, are used to characterize the subspace of two-state conical intersections contained in the branching space of a three-state conical intersection. It is shown by explicit calculation, using the lowest three-state conical intersection of (CH)3N2, that a second-order treatment yields highly accurate absolute energies, even at significant distances from the reference point of three-state intersection. The excellent agreement between the second order and ab initio results depends on the average energy component, which is computed using 5 first-order terms and 15 second-order terms. The second-order absolute energy change over the range rho = 0.0-0.3 au, where rho is the distance from the three-state conical intersection in the branching space coordinates, is approximately 6500 and 9500 cm(-1) for the E(1=2) and E(2=3) seams, respectively, with the maximum ab initio energy deviation from degeneracy of 200 cm(-1) occurring at rho = 0.3 au. The characteristic parameters gIJ and hIJ are also predicted to great accuracy, even at large rho, with the error growing to only 10-15% at rho = 0.3 au.

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PubMed2006

On the characterization of three state conical intersections using a group homomorphism approach: mapping the full N-5 dimensional seam space.

A method for characterizing the degeneracy preserving seam space in the vicinity of a three state conical intersection is introduced. Second order degenerate perturbation theory is used to construct an approximately diabatic Hamiltonian whose eigenenergies and eigenstates accurately describe the vicinity of the three state conical intersection in its full dimensionality. The perturbative analysis enables the large number, 6(N(int)(N(int)+1)2), of unique second order parameters needed to construct this accurate Hamiltonian to be determined from ab initio data at a limited number of nuclear configurations, with (N(int)+10) being minimal. Using the minimum energy three state conical intersection of the pyrazolyl radical (N(int) = 18), the potential of this approach is illustrated. A Hamiltonian comprised of the ten characteristic (linear) parameters and over 1440 second order parameters is constructed and used to determine the locus of the conical intersection seam as well as to describe the 18 dimensional space in the vicinity of that point of intersection. Our results demonstrate the ability of this methodology to quantitatively reproduce the ab initio potential energy surfaces near a three state conical intersection.

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PubMed2006

On the characterization of three state conical intersections: a quasianalytic theory using a group homomorphism approach.

In this work, degenerate perturbation theory through second order is used to characterize the vicinity of a three state conical intersection. This report extends our recent demonstration that it is possible to describe the branching space (in which the degeneracy is lifted linearly) and seam space (in which the degeneracy is preserved) in the vicinity of a two state conical intersection using second order perturbation theory. The general analysis developed here is based on a group homomorphism approach. Second order perturbation theory, in conjunction with high quality ab initio electronic structure data, produces an approximately diabatic Hamiltonian whose eigenenergies and eigenstates can accurately describe the three adiabatic potential energy surfaces, the interstate derivative couplings, and the branching and seam spaces in their full dimensionality. The application of this approach to the minimum energy three state conical intersection of the pyrazolyl radical demonstrates the potential of this method. A Hamiltonian comprised of the ten characteristic (linear) parameters and over 300 second order parameters is constructed to describe the branching space associated with a point of conical intersection. The second order parameters are determined using data at only 30 points. In the vicinity of the conical intersection the energy and derivative couplings are well reproduced and the singularity in the derivative coupling is analyzed.

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PubMed2005

On the connectivity of seams of conical intersection: seam curvature.

The seam of conical intersection of two electronic states is said to be curved when the span of the basis vectors describing the branching plane varies along the seam. In this work degenerate perturbation theory is used to determine an approximately diabatic Hamiltonian that can reliably reproduce the potential-energy surfaces in the vicinity of a point of conical intersection. This Hamiltonian provides a rigorous description of seam curvature, and a means for obtaining the full (N(int)-2)-dimensional seam of conical intersection connected to a point of conical intersection.

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PubMed2005

Escape from the double cone: optimized descriptions of the seam space using gateway modes.

The conceptual description of nuclear dynamics near a conical intersection generally focuses on the branching plane, the two-dimensional subspace in which the conical topography is evinced, to the exclusion of the seam coordinates, the remaining internal nuclear coordinates. Establishing the limits of the utility of this assumption is an important issue in nonadiabatic dynamics. To accomplish this a careful treatment of the nuclear dynamics near conical intersections is required. The coordinate systems generally available for describing conical intersections are not optimal for such studies. In this work we extend a perturbative description of a conical intersection to describe more general seam spaces. We develop a coordinate system that segregates the interactions coupling the branching plane to the seam space into a set of gateway modes. The size of this set does not increase with the size of the molecule. The gateway modes are illustrated for the 1,2 1A conical intersections in NH3. The connection between the gateway modes and the optimum coordinate system for locating and characterizing seam confluences, intersections of two branches of the same seam, is discussed.

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PubMed2005

A novel conical intersection topography and its consequences: the 1, 2 2A conical intersection seam of the vinoxy radical.

A region of the 1, 2 2A seam of accidental conical intersections in the vinoxy radical exhibits a novel topography which has important consequences for both upper-state to lower-state and lower-state to upper-state nonadiabatic transitions. The impact of this topography on these nonadiabatic transitions is described. We also considered the possibility that this conical intersection seam provides a dynamical bottleneck to the photodissociation of vinoxy to H+ketene by facilitating nonadiabatic recrossing. Our analysis of the conical topographies and the proximity of the conical intersections to the transition state for dissociation to H+ketene does not support nonadiabatic recrossing as an effective dynamical bottleneck blocking the H+ketene channel.

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PubMed2005

Statistical and nonstatistical nonadiabatic photodissociation from the first excited state of the hydroxymethyl radical.

Photodissociation of hydroxymethyl (H(2)COD) from the first excited state, a Rydberg 3s state, can produce either H+HCOD or H(2)CO+D. These processes involve a seam of conical intersections. An analysis of the seam is reported based on a pointwise determination of the three gradient vectors that characterize a conical intersection: the energy difference gradient and the coupling gradient, which span the branching space, and the gradient of the average energy. These data are used to understand why H, but not D is produced at energies near threshold, the difference in the recoil anisotropy for H and D dissociation, and whether H or D will be produced impulsively or after formation of an intermediate complex.

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PubMed2004

Exploring molecular complexity: conical intersections and NH3 photodissociation.

The role of conical intersections in the photodissociation of the A 1A2" state of NH3 is investigated using extended atomic basis sets and a configuration state function expansion of approximately 8.5 million terms. A previously unknown portion of the 1 1A-2 1A seam of conical intersections with only C(s) symmetry is located. This portion of the seam is readily accessible from the equilibrium geometry of the A 1A2" state. These conical intersections are expected to play a role in the competition between adiabatic and nonadiabatic pathways for NH3(A 1A2") photodissociation.

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PubMed2004

Quantitative detection of singlet O2 by cavity-enhanced absorption.

A method for the practical determination of the absolute concentration of single (a1delta(g)) oxygen is discussed. The method is based on sensitive off-axis integrated-cavity-output spectroscopy (ICOS). Off-axis ICOS allows narrowband, continuous-wave lasers to be used in conjunction with optical cavities to record sensitive absorption measurements. The details of the method as well as spectroscopic data confirming the first observation of the (1, 0) band of the b1sigma(g)(+) - a1delta(g) Noxon system are presented. The absolute transition probabilities for the b1sigma(g)(+) - a1delta(g) Noxon system, which are not known precisely from experiments, are determined by quantum chemistry theory.

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PubMed2004

Analytic evaluation of nonadiabatic coupling terms at the MR-CI level. I. Formalism.

An efficient and general method for the analytic computation of the nonandiabatic coupling vector at the multireference configuration interaction (MR-CI) level is presented. This method is based on a previously developed formalism for analytic MR-CI gradients adapted to the use for the computation of nonadiabatic coupling terms. As was the case for the analytic energy gradients, very general, separate choices of invariant orbital subspaces at the multiconfiguration self-consistent field and MR-CI levels are possible, allowing flexible selections of MR-CI wave functions. The computational cost for the calculation of the nonadiabatic coupling vector at the MR-CI level is far below the cost for the energy calculation. In this paper the formalism of the method is presented and in the following paper [Dallos et al., J. Chem. Phys. 120, 7330 (2004)] applications concerning the optimization of minima on the crossing seam are described.

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PubMed2004

Analytic evaluation of nonadiabatic coupling terms at the MR-CI level. II. Minima on the crossing seam: formaldehyde and the photodimerization of ethylene.

The method for the analytic calculation of the nonadiabatic coupling vector at the multireference configuration-interaction (MR-CI) level and its program implementation into the COLUMBUS program system described in the preceding paper [Lischka et al., J. Chem. Phys. 120, 7322 (2004)] has been combined with automatic searches for minima on the crossing seam (MXS). Based on a perturbative description of the vicinity of a conical intersection, a Lagrange formalism for the determination of MXS has been derived. Geometry optimization by direct inversion in the iterative subspace extrapolation is used to improve the convergence properties of the corresponding Newton-Raphson procedure. Three examples have been investigated: the crossing between the 1(1)B1/2(1)A1 valence states in formaldehyde, the crossing between the 2(1)A1/3(1)A1 pi-pi* valence and ny-3py Rydberg states in formaldehyde, and three crossings in the case of the photodimerization of ethylene. The methods developed allow MXS searches of significantly larger systems at the MR-CI level than have been possible before and significantly more accurate calculations as compared to previous complete-active space self-consistent field approaches.

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PubMed2004

Marching along ridges. An extrapolatable approach to locating conical intersections.

A conical intersection is a singular point in nuclear coordinate space. As result of this singularity the parameters used to search for energy minimized conical intersections, energy gradients, energy difference gradients and coupling vectors, vary irregularly along the search path. This irregular variation precludes the efficient use of extrapolation procedures to speed convergence. In this work we show how a previously introduced orthogonalization procedure for the branching or g-h space can be used to design search algorithms in which the key parameters are slowly varying functions of the search path. From a topographical perspective this approach amounts to walking along a path parallel the ridge of conical intersections.

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PubMed2003

Conical intersections of three electronic states affect the ground state of radical species with little or no symmetry: pyrazolyl.

Conical intersections of three states of the same symmetry are located in the pyrazolyl radical using wave functions of approximately 40 million configuration state functions. The three-state intersection is found to be only approximately 3400 cm-1 above the minimum energy structure on the ground electronic state. It is suggested that many organic radicals may also exhibit this feature.

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PubMed2003

Beyond two-state conical intersections. Three-state conical intersections in low symmetry molecules: the allyl radical.

Using multireference configuration interaction expansions comprised of over 7 million configuration state functions, three-state conical intersections are reported for the closely spaced, spectroscopically observed (tilde)B(2A1), (tilde)C(2B1), and (tilde)D(2B2) states (in C(2v) symmetry) of the allyl radical. These conical intersections of states which were previously assigned as the 3,4,5(2)A states and are here reassigned as the 4,5,6(2)A states, are expected to be accessible using optical probes. This conclusion is obtained from the structure of the minimum energy point on the 4,5,6(2)A three-state conical intersection seam which is similar to the equilibrium structure of the ground (tilde)X(2A2) state and only 1.1 eV above the (tilde)D(2B2) state at its equilibrium geometry. The seam of three-state degeneracies joins two two-state seams of conical intersection, the 4,5(2)A and 5,6(2)A conical intersection seams. The energy of the minimum energy point on the 4,5(2)A two-state seam is only 0.15 eV above that of the (tilde)D(2B2) state at its equilibrium structure. Three-state intersections are also reported for the 3,4,5(2)A states.

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