Biomedical subjects

John M Herbert

Publications and source records attributed to John M Herbert.

9 recordsLinked to original sources

PubMed2006

Charge penetration and the origin of large O-H vibrational red-shifts in hydrated-electron clusters, (H2O)n-.

The origin of O-H vibrational red-shifts observed experimentally in (H2O)n(-) clusters is analyzed using electronic structure calculations, including natural bond orbital analysis. The red-shifts are shown to arise from significant charge transfer and strong donor-acceptor stabilization between the unpaired electron and O-H sigma* orbitals on a nearby water molecule in a double hydrogen-bond-acceptor ("AA") configuration. The extent of e(-) --> sigma* charge transfer is comparable to the n --> sigma* charge transfer in the most strongly hydrogen-bonded X(-)(H2O) complexes (e.g., X = F, O, OH), even though the latter systems exhibit much larger vibrational red-shifts. In X(-)(H2O), the proton affinity of X(-) induces a low-energy XH...(-)OH diabatic state that becomes accessible in v = 1 of the shared-proton stretch, leading to substantial anharmonicity in this mode. In contrast, the H + (-)OH(H2O)(n-1) diabat of (H2O)n(-) is not energetically accessible; thus, the O-H stretching modes of the AA water are reasonably harmonic, and their red-shifts are less dramatic. Only a small amount of charge penetrates beyond the AA water molecule, even upon vibrational excitation of these AA modes. Implications for modeling of the aqueous electron are discussed.

Journal Article↗

PubMed2006

First-principles, quantum-mechanical simulations of electron solvation by a water cluster.

Despite numerous experiments and static electronic structure calculations, the nature of hydrated-electron clusters, (H2O)(n)(-), remains poorly understood. Here, we introduce a hybrid ab initio molecular dynamics scheme, balancing accuracy against feasibility, to simulate vibrational and photoelectron spectra of (H(2)O)(n)(-), treating all electrons quantum-mechanically. This methodology provides a computational tool for understanding the spectra of weakly bound and supramolecular anions and for elucidating the fingerprint of dynamics in these spectra. Simulations of (H2O)(4)(-) provide quantitative agreement with experimental spectra and furnish direct evidence of the nonequilibrium nature of the cluster ensemble that is probed experimentally. The simulations also provide an estimate of the cluster temperature (T approximately 150-200 K) that is not available from experiment alone. The "double acceptor" electron-binding motif is found to be highly stable with respect to thermal fluctuations, even at T = 300 K, whereas the extra electron stabilizes what would otherwise be unfavorable water configurations.

Journal Article↗

PubMed2006

Advances in methods and algorithms in a modern quantum chemistry program package.

Advances in theory and algorithms for electronic structure calculations must be incorporated into program packages to enable them to become routinely used by the broader chemical community. This work reviews advances made over the past five years or so that constitute the major improvements contained in a new release of the Q-Chem quantum chemistry package, together with illustrative timings and applications. Specific developments discussed include fast methods for density functional theory calculations, linear scaling evaluation of energies, NMR chemical shifts and electric properties, fast auxiliary basis function methods for correlated energies and gradients, equation-of-motion coupled cluster methods for ground and excited states, geminal wavefunctions, embedding methods and techniques for exploring potential energy surfaces.

Algorithms↗

PubMed2005

Accuracy and limitations of second-order many-body perturbation theory for predicting vertical detachment energies of solvated-electron clusters.

Vertical electron detachment energies (VDEs) are calculated for a variety of (H(2)O)(n)(-) and (HF)(n)(-) isomers, using different electronic structure methodologies but focusing in particular on a comparison between second-order Møller-Plesset perturbation theory (MP2) and coupled-cluster theory with noniterative triples, CCSD(T). For the surface-bound electrons that characterize small (H(2)O)(n)(-) clusters (n< or = 7), the correlation energy associated with the unpaired electron grows linearly as a function of the VDE but is unrelated to the number of monomers, n. In every example considered here, including strongly-bound "cavity" isomers of (H(2)O)(24)(-), the correlation energy associated with the unpaired electron is significantly smaller than that associated with typical valence electrons. As a result, the error in the MP2 detachment energy, as a fraction of the CCSD(T) value, approaches a limit of about -7% for (H(2)O)(n)(-) clusters with VDEs larger than about 0.4 eV. CCSD(T) detachment energies are bounded from below by MP2 values and from above by VDEs calculated using second-order many-body perturbation theory with molecular orbitals obtained from density functional theory. For a variety of both strongly- and weakly-bound isomers of (H(2)O)(20)(-) and (H(2)O)(24)(-), including both surface states and cavity states, these bounds afford typical error bars of +/-0.1 eV. We have found only one case where the Hartree-Fock and density functional orbitals differ qualitatively; in this case the aforementioned bounds lie 0.4 eV apart, and second-order perturbation theory may not be reliable.

Electrons↗

PubMed2005

Stabilization and rovibronic spectra of the T-shaped and linear ground-state conformers of a weakly bound rare-gas-homonuclear dihalogen complex: He...Br2.

Laser-induced fluorescence spectra of Br(2) entrained in a He supersonic expansion have been recorded in the Br(2) B-X, 8-0, 12-0, and 21-0 spectral regions at varying downstream distances, and thus different temperature regimes. Features associated with transitions of the T-shaped and linear He...Br(2)(X,nu(") = 0) complexes are identified. The changes in the relative intensities of the T-shaped and linear features with cooling in the expansion indicate that the linear conformer is energetically more stable than the T-shaped conformer. A He + Br(2)(X,nu(") = 0) ab initio potential-energy surface, computed at the coupled cluster level of theory with a large, flexible basis set, is used to calculate the binding energies of the two conformers, 15.8 and 16.5 cm(-1) for the T-shaped and linear complexes, respectively. This potential and an excited-state potential [M. P. de Lara-Castells, A. A. Buchachenko, G. Delgado-Barrio, and P. Villareal, J. Chem. Phys. 120, 2182 (2004)] are used to calculate the excitation spectra of He...(79)Br(2)(X,nu(") = 0) in the Br(2) B-X, 12-0 region. The calculated spectra are used to make spectral assignments and to determine the energies of the excited-state intermolecular vibrational levels accessed in the observed transitions. Temperature-dependent laser-induced fluorescence spectra and a simple thermodynamic model [D. S. Boucher, J. P. Darr, M. D. Bradke, R. A. Loomis, and A. B. McCoy, Phys. Chem. Chem. Phys. 6, 5275 (2004)] are used to estimate that the linear conformer is 0.4(2) cm(-1) more strongly bound than the T-shaped conformer. Two-laser action spectroscopy experiments reveal that the binding energy of the linear He...(79)Br(2)(X,nu(") = 0) conformer is 17.0(8) cm(-1), and that of the T-shaped He...(79)Br(2)(X,nu(") = 0) conformer is then 16.6(8) cm(-1), in good agreement with the calculated values.

Journal Article↗

PubMed2005

Accelerated, energy-conserving Born-Oppenheimer molecular dynamics via Fock matrix extrapolation.

Born-Oppenheimer molecular dynamics calculations, especially those that exploit information retained from previous time steps in order to accelerate convergence of the electronic structure calculations, can suffer from systematic error in the energy gradient that manifests as a drift in the microcanonical energy. Here, we demonstrate that this is only the case when the self-consistent field (SCF) convergence criterion is set too low; using only a marginally tighter threshold (still two orders of magnitude lower than what is standard for geometry optimizations), the drift disappears completely, for a time scale of several picoseconds. Using a Fock matrix extrapolation technique, SCF convergence is achieved in as few as three iterations per time step, without sacrificing energy conservation. In test calculations for C2F4, (H2O4-, (H2O6, and [Fe(H2O6]2+, we demonstrate energy-conserving Fock matrix extrapolation that reduces the number of SCF cycles by up to 70% and reduces the computer time per molecular dynamics step by 45-55%, relative to simulations performed without extrapolation.

Algorithms↗

PubMed2005

Calculation of electron detachment energies for water cluster anions: an appraisal of electronic structure methods, with application to (H2O)20- AND (H2O)24-.

We present benchmark calculations of vertical electron detachment energies (VDEs) for various conformers of (H2O)n-, using both wave function and density functional methods, in sequences of increasingly diffuse Gaussian basis sets. For small clusters (n < or = 6), a systematic examination of VDE convergence reveals that it is possible to converge this quantity to within approximately 0.01 eV of the complete-basis limit, using a highly diffuse but otherwise economical Pople-style basis set of double-zeta quality, with 28 atom-centered basis functions per water molecule. Floating-center basis functions can be useful but are not required to obtain accurate VDEs. Second-order Møller-Plesset perturbation (MP2) theory suffices to obtain VDEs that are within 0.05 eV of the results from both experiment and coupled-cluster theory, and which always err toward underbinding the extra electron. In contrast to these consistent predictions, VDEs calculated using density functional theory (DFT) vary widely, according to the fraction of Hartree-Fock exchange in a given functional. Common functionals such as BLYP and B3LYP overestimate the VDE by 0.2-0.5 eV, whereas a variant of Becke's "half and half" functional is much closer to coupled-cluster predictions. Exploratory calculations for (H2O)20- and (H2O)24- cast considerable doubt on earlier calculations that were used to assign the photoelectron spectra of these species to particular cluster isomers.

Journal Article↗

PubMed2004

Curvy-steps approach to constraint-free extended-Lagrangian ab initio molecular dynamics, using atom-centered basis functions: convergence toward Born-Oppenheimer trajectories.

A dynamical extension of the "curvy-steps" approach to linear-scaling self-consistent field calculations is presented, which yields an extended-Lagrangian formulation of ab initio molecular dynamics. An exponential parametrization of the one-electron density matrix, expressed in terms of atom-centered Gaussian basis functions, facilitates propagation along the manifold of density matrices in a geometrically correct fashion that automatically enforces idempotency constraints. The extended Lagrangian itself is constraint free, thus neither density matrix purification nor expensive, iterative solution for Lagrange multipliers is required. Propagation is highly efficient, and time steps compare favorably to those used in Car-Parrinello molecular dynamics simulations. The behavior of the method, especially with regard to the maintenance of adiabatic decoupling of nuclei and electrons, is examined for a sequence of diatomic molecules, and comparison is made to trajectories propagated on the converged Born-Oppenheimer surface. Certain claims to the contrary notwithstanding, our results demonstrate that vibrational frequencies may depend on the value of the fictitious mass parameter, even in an atom-centered basis. Light-atom stretching frequencies can be significantly redshifted, even when the nuclear and electronic energy scales are well separated. With a sufficiently small fictitious mass and a short time step, accurate frequencies can be obtained; we characterize appropriate values of these parameters for a wide range of vibrational frequencies.

Journal Article↗

PubMed2002

Carbon-11 labeled radioligands for imaging brain cannabinoid receptors.

Two radioligands, [(11)C] SR149080 and its morpholino analog [(11)C] SR149568, were synthesized by reaction of the respective phenolic precursors with [(11)C] methyl iodide. Both radioligands had appropriate regional brain distribution for cannabinoid receptors in mice with peak target to non-target ratios of 2.2 for [(11)C] SR149080 and 1.6 for [(11)C] SR149568 at 90 and 30 minutes post-injection respectively. The uptake of both tracers was blocked with a 1 mg/kg dose of SR141716A.

Animals↗