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At least 973 records · Page 54Linked to original sources
PubMed2006

Induction of an aromatic six-membered nitrogen ring via cation-pi interaction.

Nitrogen clusters have been intensively studied for their potential application as high-energy density materials, but a six-membered nitrogen ring (N6) was not found to be stable and aromatic. To explore the possibility of inducing an aromatic N6 ring via cation-pi interaction, quantum chemistry calculations were performed on the systems of Ca2N6, CaN6, CaN6(2-), N6, and N6(4-) at the B3LYP/6-311+G level. The optimized geometries reveal that the planar structure of the N6 ring is stable only in the Ca2N6 complex. The computed NBO and CHelpG charges demonstrate that the planar N6 moiety in the Ca2N6 complex is almost a 10pi-electron system. The predicted nucleus-independent chemical shift (NICS) values demonstrate that the N6 moiety is aromatic in comparison with the NICS values of benzene. The estimated enthalpy of formation for the Ca2N6 complex is 100.4 kcal/mol for the reaction of 2Ca and 3N2. The binding energy between the Ca2+ cation and the N6(4-) moiety is -1928.8 kcal/mol, with electrostatic interaction serving as the predominant component. When all the calculated results are taken into account, including the planar structure, 10pi-electron system, identical bond length, and negative NICS value of the N6(4-) moiety in the Ca2N6 complex, it is deduced that the alkaline earth metal Ca is capable of inducing an aromatic N6 ring through the cation-pi interaction formed by electron transfer from the Ca atom to the N6 ring.

Benzene↗
PubMed2006

Amphiphilic character of the hydrated proton in methanol-water solutions.

The hydrated proton was studied in methanol-water solutions of varying methanol concentrations using the multistate empirical valence bond simulation method. Amphiphile-like behavior of the hydrated proton was noted from its anisotropic association with the methanol methyl groups. Molecular length immiscibility was also characterized through the enumeration of water and protonated water clusters. Excess proton diffusion was calculated across the varying methanol concentrations and found to be in good agreement with experiment after correcting for nuclear quantum effects.

Anisotropy↗
PubMed2002

Efficient classical simulation of optical quantum information circuits.

We identify a broad class of physical processes in an optical quantum circuit that can be efficiently simulated on a classical computer: this class includes unitary transformations, amplification, noise, and measurements. This simulatability result places powerful constraints on the capability to realize exponential quantum speedups as well as on inducing an optical nonlinear transformation via linear optics, photodetection-based measurement, and classical feedforward of measurement results, optimal cloning, and a wide range of other processes.

Journal Article↗
PubMed1984

Noise analysis of a digital radiography system.

The sources of noise in a digital video subtraction angiography system were identified and analyzed. Signal-to-noise ratios of digital radiography systems were measured using the digital image data recorded in the computer. The major sources of noise include quantum noise, TV camera electronic noise, quantization noise from the analog-to-digital converter, time jitter, structure noise in the image intensifier, and video recorder electronic noise. A new noise source was identified, which results from the interplay of fixed pattern noise and the lack of image registration. This type of noise may result from image-intensifier structure noise in combination with TV camera time jitter or recorder time jitter. A similar noise source is generated from the interplay of patient absorption inhomogeneities and patient motion or image re-registration. Signal-to-noise ratios were measured for a variety of experimental conditions using subtracted digital images. The measured signal-to-noise ratios were found to fluctuate on repeat trials with about a 10% standard deviation. Averaging of video frames was found to reduce the noise level by the expected square root N relation, where N is the number of frames averaged. Image-intensifier structure noise was shown to be a dominant noise source in unsubtracted images at medium to high radiation exposure levels. A total-system signal-to-noise ratio (SNR) of 750:1 was measured for an input exposure of 1 mR/frame at the image intensifier input. The effect of scattered radiation on subtracted image SNR was found to be greater than previously reported. The detail SNR was found to vary approximately as one plus the scatter degradation factor. Quantization error noise with 8-bit image processors (signal-to-noise ratio of 890:1) was shown to be of increased importance after recent improvements in TV cameras. The results of the analysis are useful both in the design of future digital radiography systems and the selection of optimum clinical techniques.

Angiography↗
PubMed2000

Strategies to improve the signal and noise performance of active matrix, flat-panel imagers for diagnostic x-ray applications.

A theoretical investigation of factors limiting the detective quantum efficiency (DQE) of active matrix flat-panel imagers (AMFPIs), and of methods to overcome these limitations, is reported. At the higher exposure levels associated with radiography, the present generation of AMFPIs is capable of exhibiting DQE performance equivalent, or superior, to that of existing film-screen and computed radiography systems. However, at exposure levels commonly encountered in fluoroscopy, AMFPIs exhibit significantly reduced DQE and this problem is accentuated at higher spatial frequencies. The problem applies both to AMFPIs that rely on indirect detection as well as direct detection of the incident radiation. This reduced performance derives from the relatively large magnitude of the square of the total additive noise compared to the system gain for existing AMFPIs. In order to circumvent these restrictions, a variety of strategies to decrease additive noise and enhance system gain are proposed. Additive noise could be reduced through improved preamplifier, pixel and array design, including the incorporation of compensation lines to sample external line noise. System gain could be enhanced through the use of continuous photodiodes, pixel amplifiers, or higher gain x-ray converters such as lead iodide. The feasibility of these and other strategies is discussed and potential improvements to DQE performance are quantified through a theoretical investigation of a variety of hypothetical 200 microm pitch designs. At low exposures, such improvements could greatly increase the magnitude of the low spatial frequency component of the DQE, rendering it practically independent of exposure while simultaneously reducing the falloff in DQE at higher spatial frequencies. Furthermore, such noise reduction and gain enhancement could lead to the development of AMFPIs with high DQE performance which are capable of providing both high resolution radiographic images, at approximately 100 microm pixel resolution, as well as variable resolution fluoroscopic images at 30 fps.

Feasibility Studies↗
PubMed2000

Fast and stable method for simulating quantum electron dynamics

A fast and stable method is formulated to compute the time evolution of a wave function by numerically solving the time-dependent Schrodinger equation. This method is a real-space-real-time evolution method implemented by several computational techniques such as Suzuki's exponential product, Cayley's form, the finite differential method, and an operator named adhesive operator. This method conserves the norm of the wave function, manages periodic conditions and adaptive mesh refinement technique, and is suitable for vector- and parallel-type supercomputers. Applying this method to some simple electron dynamics, we confirmed the efficiency and accuracy of the method for simulating fast time-dependent quantum phenomena.

Journal Article↗
PubMed2004

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations.

Computational studies of proteins based on empirical force fields represent a powerful tool to obtain structure-function relationships at an atomic level, and are central in current efforts to solve the protein folding problem. The results from studies applying these tools are, however, dependent on the quality of the force fields used. In particular, accurate treatment of the peptide backbone is crucial to achieve representative conformational distributions in simulation studies. To improve the treatment of the peptide backbone, quantum mechanical (QM) and molecular mechanical (MM) calculations were undertaken on the alanine, glycine, and proline dipeptides, and the results from these calculations were combined with molecular dynamics (MD) simulations of proteins in crystal and aqueous environments. QM potential energy maps of the alanine and glycine dipeptides at the LMP2/cc-pVxZ//MP2/6-31G* levels, where x = D, T, and Q, were determined, and are compared to available QM studies on these molecules. The LMP2/cc-pVQZ//MP2/6-31G* energy surfaces for all three dipeptides were then used to improve the MM treatment of the dipeptides. These improvements included additional parameter optimization via Monte Carlo simulated annealing and extension of the potential energy function to contain peptide backbone phi, psi dihedral crossterms or a phi, psi grid-based energy correction term. Simultaneously, MD simulations of up to seven proteins in their crystalline environments were used to validate the force field enhancements. Comparison with QM and crystallographic data showed that an additional optimization of the phi, psi dihedral parameters along with the grid-based energy correction were required to yield significant improvements over the CHARMM22 force field. However, systematic deviations in the treatment of phi and psi in the helical and sheet regions were evident. Accordingly, empirical adjustments were made to the grid-based energy correction for alanine and glycine to account for these systematic differences. These adjustments lead to greater deviations from QM data for the two dipeptides but also yielded improved agreement with experimental crystallographic data. These improvements enhance the quality of the CHARMM force field in treating proteins. This extension of the potential energy function is anticipated to facilitate improved treatment of biological macromolecules via MM approaches in general.

Algorithms↗
PubMed2003

Imaging of quantum array structures with coherent and partially coherent diffraction.

Recent achievements in experimental and computational methods open the possibility of measuring and inverting the diffraction pattern from a finite object of submicrometer size. In this paper the possibilities of such experiments for two-dimensional arrays of quantum dots are discussed. The diffraction pattern corresponding to coherent and partial coherent illumination of a sample was generated. Test calculations based on the iterative algorithms were applied to reconstruct the shape of the individual islands in such a quantum structure directly from its diffraction pattern. It is demonstrated that, in the case of coherent illumination, the correct shape and orientation of an individual island can be obtained. In the case of partially coherent illumination, the correct shape of the particle can be obtained only when the coherence of the incoming beam is reduced to match the size of the island.

Algorithms↗
PubMed2002

Reactivity and binding energies of transition metal halide ions with benzene.

We have generated novel halogen-ligated transition metal ions MX(n)+ (M = Sc, Ti, V, and Fe, X = Cl, Br and I, n = 1-3). We have explored their reactions with benzene, a typical aromatic hydrocarbon. Attachment of one benzene molecule is usually rapid, whereas attachment of a second benzene molecule is generally much slower. The kinetics were analyzed to estimate binding energies, modeling the attachment reaction as a radiative association process. In all cases the Standard Hydrocarbon semiquantitative estimation approach was employed, and in some cases the more accurate variational transition state (VTST) kinetic modeling approach was also applied. Density functional (DFT) quantum calculations were also performed to give computed binding energies for some of the complexes. Taking previously determined binding energies for halogen-ligated alkaline-earth ions as benchmarks, it is concluded that binding of the first benzene molecule to the transition-metal species is strongly enhanced by specific chemical interactions, while binding of the second benzene molecule is more nearly electrostatic. The binding energies are not strongly dependent on the identity of the transition metal ion, and the metal-ion dependences can be rationalized in terms of valence-orbital occupations of the metals. The binding energies are nearly independent of the identity of the halogen ligands.

Journal Article↗
PubMed2000

Stability of complexes of aromatic amides with bromide anion: quantitative structure--property relationships

Most of the theoretical studies published to-date on the structural and electronic properties of supramolecules have been devoted to the neutral or cationic complexes, while little is known about anionic systems. A detailed theoretical study of the interaction between simple aromatic amides and the bromide anion has recently been published (Cajan, M.; Stibor, I.; Koca, J. J. Phys. Chem. A 1999, 103, 3778). The present work focuses on the structural and physicochemical parameters of simple aromatic amides related to their ability to form the 1:1 complex with a bromide anion. A quantitative structure-property relationships (QSPR) model for the prediction of association constants is proposed. The model based on 22 complexes and nine molecular descriptors explained 96% (84% cross-validated) of the variance in association constants. The descriptors employed in this model included parameters for the characterization of conformational behavior and the 3D structure of amide molecules, distribution of electron density on the amidic functional group, and parameters for substitution on aromatic units. The quantitative structure-property relationship approach predicted the association constants with comparable quality, but significantly lower computational demand, than molecular modeling or standard quantum chemistry calculations.

Journal Article↗
PubMedDate not supplied

On the possibility of detecting low barrier hydrogen bonds with kinetic measurements.

Recent experimental evidence has pointed to the possible presence of a short, strong hydrogen bond in the enzyme-substrate transition states in some biochemical reactions. To date, most experimental measures of these short, strong hydrogen bonds have monitored their equilibrium properties. In this work we show that kinetic measurements can also be used to detect the presence of short, strong hydrogen bonds. In particular, we find nontrivial differences among rate constant ratios of protonated to deuterated hydrogen bonds between strong and weak hydrogen bonds for proton transfer between donor-acceptor sites. We quantify this kinetic isotope effect by performing dynamical calculations of these rate constants by computing reactive flux through a dividing surface. This reactive flux is computed by evolving trajectories on an effective quantum mechanical potential energy surface.

Journal Article↗
PubMed2004

Factors governing the protonation state of Zn-bound histidine in proteins: a DFT/CDM study.

We have performed systematic theoretical studies to elucidate the factors governing the His protonation/deprotonation state in Zn-binding sites, especially those containing the ubiquitous Zn-His-Asp/Glu triad. Specifically, we have addressed the following three questions: (1) How does the transfer of the Zn-bound His imidazole proton to the second-shell Asp/Glu carboxylate oxygen depend on the composition of the other first-shell ligands and the solvent accessibility of the metal-binding site? (2) Can any second-shell ligand with a proton acceptor group such as the backbone carbonyl oxygen also act as a proton acceptor? (3) What is the effect of the Asp/Glu in the Zn-His-Asp/Glu triad on the Zn-bound water protonation state? To address these questions, we used a combination of quantum mechanical and continuum dielectric methods to compute the free energies for deprotonating a Zn-bound imidazole/water in various Zn complexes. The calculations show that whether the Zn-bound His is protonated or deprotonated depends on (1) the solvent accessibility of the metal-binding site, and (2) the Lewis acid ability of Zn, which is indirectly determined by both the first- and the second-shell Zn ligands. The calculations also show that the effect of the Zn-His-Asp/Glu interaction on the nucleophilicity of the Zn-bound water depends on the solvent accessibility of the catalytic Zn site. Furthermore, they show that the Asp/Glu side chain in the Zn-His-Asp/Glu triad can increase the negative charge of its partner, His, and create an anionic hole that may stabilize a cation in buried cavities, provided that the Zn complex is cationic/neutral. The findings of this work are in accord with available experimental data.

Binding Sites↗
PubMed2006

Condensed-phase relaxation of multilevel quantum systems. II. Comparison of path integral calculations and second-order relaxation theory for a nondegenerate three-level system.

An exactly solvable model of multisite condensed-phase vibrational relaxation was studied in Paper I (Peter, S.; Evans, D. G.; Coalson, R. D. J. Phys. Chem. B 2006, 110, 18758.), where it was shown that long-time steady-state site populations of a degenerate N-level system are not equal (hence, they are non-Boltzmann) and depend on the initial preparation of the system and the number of sites that it comprises. Here we consider a generalization of the model to the case of a nondegenerate three-level system coupled to a high-dimensional bath: such a model system has direct relevance to a large class of donor-bridge-acceptor electron transfer processes. Because the quantum dynamics of this system cannot be computed analytically, we compare numerically exact path integral calculations to the predictions of second-order time-local relaxation theory. For modest system-bath coupling strengths, the two sets of results are in excellent agreement. They show that non-Boltzmann long-time steady-state site populations are obtained when the level splitting is small but nonzero, whereas at larger values of the system bias (asymmetry) these populations become Boltzmann distributed.

Journal Article↗
PubMed2004

Semiclassical calculation of the vibrational echo.

The infrared echo measurement probes the time scales of the molecular motions that couple to a vibrational transition. Computation of the echo observable within rigorous quantum mechanics is problematic for systems with many degrees of freedom, motivating the development of semiclassical approximations to the nonlinear optical response. We present a semiclassical approximation to the echo observable, based on the Herman-Kluk propagator. This calculation requires averaging over a quantity generated by two pairs of classical trajectories and associated stability matrices, connected by a pair of phase-space jumps. Quantum, classical, and semiclassical echo calculations are compared for a thermal ensemble of noninteracting anharmonic oscillators. The semiclassical approach uses input from classical mechanics to reproduce the significant features of a complete, quantum mechanical calculation of the nonlinear response.

Journal Article↗
PubMed2004

Calculating expectations with time-dependent perturbations in quantum Monte Carlo.

We show that a small perturbation periodic in imaginary time can be used to compute expectation values of nondifferential operators that do not commute with the Hamiltonian within the framework of quantum diffusion Monte Carlo. Some results for the harmonic oscillator and the helium atom are presented showing the validity of the proposed method.

Journal Article↗
PubMed2006

A unified electrostatic and cavitation model for first-principles molecular dynamics in solution.

The electrostatic continuum solvent model developed by [Fattebert and Gygi J. Comput. Chem. 23, 662 (2002); Int. J. Quantum Chem. 93, 139 (2003)] is combined with a first-principles formulation of the cavitation energy based on a natural quantum-mechanical definition for the surface of a solute. Despite its simplicity, the cavitation contribution calculated by this approach is found to be in remarkable agreement with that obtained by more complex algorithms relying on a large set of parameters. Our model allows for very efficient Car-Parrinello simulations of finite or extended systems in solution and demonstrates a level of accuracy as good as that of established quantum-chemistry continuum solvent methods. We apply this approach to the study of tetracyanoethylene dimers in dichloromethane, providing valuable structural and dynamical insights on the dimerization phenomenon.

Journal Article↗
PubMed2001

Path-integral study of positronium decay in xenon.

We use path-integral Monte Carlo to study the properties of a quantum particle equilibrated in a classical Lennard-Jones fluid. By choosing 2m(e) for its mass, and potential parameters corresponding to xenon, we are able to model the behavior of thermalized positronium above the xenon critical temperature. We carefully study the local distortion of the fluid in the neighborhood of the quantum particle, and use this information to compute the annihilation rate as a function of density on two isotherms. The results compare favorably with experiment below the critical point density. Contrary to accepted views, we demonstrate that positronium remains in a self-trapped state at over twice the critical point density.

Journal Article↗