Application of semi-empirical and ab initio quantum mechanical calculations.
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Computer Simulation↗
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Quantum Andreev map: a paradigm of quantum chaos in superconductivity.
We introduce quantum maps with particle-hole conversion (Andreev reflection) and particle-hole symmetry, which exhibit the same excitation gap as quantum dots in the proximity to a superconductor. Computationally, the Andreev maps are much more efficient than billiard models of quantum dots. This makes it possible to test analytical predictions of random-matrix theory and semiclassical chaos that were previously out of reach of computer simulations. We have observed the universal distribution of the excitation gap for a large Lyapunov exponent and the logarithmic reduction of the gap when the Ehrenfest time becomes comparable to the quasiparticle dwell time.
Journal Article↗
Two-electron integrations in the quantum theory of atoms in molecules.
A method to compute two-electron integrals over arbitrary regions of space is introduced and particularized to the basins appearing in the quantum theory of atoms in molecules. The procedure generalizes the conventional multipolar approach to account for overlapping densities. We show that the approach is always convergent and computationally efficient, scaling as N(4) in the worst, two-center case. Several numerical results supporting our claims are also presented.
Journal Article↗
Image quality evaluation of a desktop computed radiography system.
The modulation transfer function (MTF), noise power spectrum (NPS), and detective quantum efficiency (DQE) of the Lumisys ACR-2000 desktop computed radiography (CR) reader were measured and compared to equivalent measurements acquired from a Fuji AC-3 CR system. The one-dimensional (1D) MTF was measured from an image of a sharp edge and the 1D NPS was derived from a 2D NPS measured from a uniform field exposure. The energy dependent ideal input signal to noise ratio of the incident x-ray beams was estimated using published x-ray spectra and attenuation coefficients. Measurements were acquired using Agfa, Fuji, and Kodak storage phosphor plates and it was concluded that use of the Fuji plates resulted in the highest system DQE for the ACR-2000. The DQE was measured using exposures of 0.10, 1.0, and 10.0 mR from 70 and 120 kVp x-ray beams filtered with aluminum. The DQE of the Lumisys ACR-2000 was lower than that of the Fuji AC-3.
Computers↗
Computer simulations of organic reactions in solution.
Quantum and statistical mechanics have been used to determine energy profiles for the SN2 reaction of Cl- + CH3Cl in the gas phase, in aqueous solution, and in liquid DMF. The energy profile in the gas phase has the characteristic double-well form featuring unsymmetrical ion-dipole complexes as minima and a symmetrical transition state. Hydration causes the reaction surface to become almost unimodal and increases the barrier significantly. The reaction profile in DMF is intermediate between those for the gas phase and aqueous solution. The ion-dipole complexes are still free energy minima in DMF. Thus, the reaction in DMF involves initial formation of the complex before the rate-determining step. The computed results are shown to be in good accord with experimental free energies of activation. The same technique has been applied to the addition reaction of OH- + H2C = O in the gas phase and aqueous solution. Ab initio 6-31 + G* calculations indicate that the reaction proceeds essentially without activation in the gas phase. Hydration introduces a substantial energy barrier. The transition state in water has been located at a C-O separation of roughly 2 A. A key finding for both reactions is that the activation barriers induced by hydration result primarily from change in strengths rather than in numbers of solute-water hydrogen bonds along the reaction paths.
Chemical Phenomena↗
Efficient classical simulation of continuous variable quantum information processes.
We obtain sufficient conditions for the efficient simulation of a continuous variable quantum algorithm or process on a classical computer. The resulting theorem is an extension of the Gottesman-Knill theorem to continuous variable quantum information. For a collection of harmonic oscillators, any quantum process that begins with unentangled Gaussian states, performs only transformations generated by Hamiltonians that are quadratic in the canonical operators, and involves only measurements of canonical operators (including finite losses) and suitable operations conditioned on these measurements can be simulated efficiently on a classical computer.
Journal Article↗
Theoretical predictions of chemical degradation reaction mechanisms of RDX and other cyclic nitramines derived from their molecular structures.
Analysis of environmental degradation pathways of contaminants is aided by predictions of likely reaction mechanisms and intermediate products derived from computational models of molecular structure. Quantum mechanical methods and force-field molecular mechanics were used to characterize cyclic nitramines. Likely degradation mechanisms for hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) include hydroxylation utilizing addition of hydroxide ions to initiate proton abstraction via 2nd order rate elimination (E2) or via nucleophilic substitution of nitro groups, reductive chemical and biochemical degradation, and free radical oxidation. Due to structural similarities, it is predicted that, under homologous circumstances, certain RDX environmental degradation pathways should also be effective for octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) and similar cyclic nitramines. Computational models provided a theoretical framework whereby likely transformation mechanisms and transformation products of cyclic nitramines were predicted and used to elucidate in situ degradation pathways.
Azocines↗
A quantitative method for the detection and localization of quantum-limited events from radionuclides in cells and tissue sections by computer-enhanced video microscopy.
Cellular dynamics often involve extremely low concentrations of biologically active substances, which can be radiolabeled and detected, localized and quantitated by autoradiography. The latter may require exposures from a few days to many months. The objective of this research was to demonstrate the feasibility of reducing this long period of data collection by one to two orders of magnitude, while maintaining or improving the spatial resolution and localization in tissues and the quantitative characteristics inherent in autoradiography. A mathematical model describing the complete system was generated using energy partition calculations to estimate photon production via scintillant per H3 beta particle emission and to estimate the subsequent photon capture based upon imaging system parameters and microscope geometry. Calculations showed that, typically, a single tritium beta particle produces a maximum of 5.8 X 10(3) photons. A photon-limited camera and microscope imaging system were selected and optimized in conjunction with a specially developed physical scintillation model. Results showed that the number of detected photoevents increases monotonically with both signal integration time and, independently, with the concentration of the radionuclide. Consequently, this work demonstrates that video microscopy imaging methods can spatially and temporally quantify very low concentrations of radiolabeled substances and can reduce data acquisition times.
Beta Particles↗
From computation to black holes and space-time foam.
We show that quantum mechanics and general relativity limit the speed nu of a simple computer (such as a black hole) and its memory space I to I(nu2) less, similar(t(-2))P, where t(P) is the Planck time. We also show that the lifetime of a simple clock and its precision are similarly limited. These bounds and the holographic bound originate from the same physics that governs the quantum fluctuations of space-time. We further show that these physical bounds are realized for black holes, yielding the correct Hawking black hole lifetime, and that space-time undergoes much larger quantum fluctuations than conventional wisdom claims-almost within range of detection with modern gravitational-wave interferometers.
Journal Article↗
Quantum backreaction through the Bohmian particle.
A novel solution to the quantum backreaction problem in a mixed quantum-classical simulation is provided using the Bohmian interpretation of quantum mechanics. The Bohmian backreaction is unique, computationally simple, features reaction channel branching, and easily gives the full classical limit. The Bohmian quantum-classical method is illustrated by application to a model of O2 interacting with a Pt surface.
Journal Article↗
On the role of Glu-68 in alcohol dehydrogenase.
Theoretical computations (molecular dynamics and combined quantum chemical and molecular mechanical geometry optimizations) have been performed on horse liver alcohol dehydrogenase. The results provide evidence that Glu-68, a highly conserved residue located 0.47 nm from the catalytic zinc ion, may intermittently coordinate to the zinc ion. Structures with Glu-68 coordinated to the zinc ion are almost as stable as structures with Glu-68 at the crystal position and the barrier between the two configurations of Glu-68 is so low that it can readily be bypassed at room temperature. There is a cavity behind the zinc ion that seems to be tailored to allow such coordination of Glu-68 to the zinc ion. It is suggested that Glu-68 may facilitate the exchange of ligands in the substrate site by coordinating to the zinc ion when the old ligand dissociates.
Alcohol Dehydrogenase↗
Computer experiments on xenon-containing molecules
Quantum chemical calculations have been performed on xenon-containing rare gas molecules. The novel HXeY molecules are best characterised as HXe+Y- where Y can be at least H, Cl, Br, I, CN, SH, OH or NCO. A good agreement of MP2/LJ18/6-311 + + G(2d,2p) results is obtained with respect to the trend in experimental data for the Xe-H stretching wavenumbers of the HXeY molecules. Predictions concerning compounds between Xe and carboxylic acids are made. It is shown that Xe can bind to the carboxy group of the side chains of amino acids, thus, allowing in principle Xe to bind to proteins.
Journal Article↗
Treatment of substitution and rearrangement mechanisms of transition metal complexes with quantum chemical methods.
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Computer Simulation↗
Insights into the regioselectivity and RNA-binding affinity of HIV-1 nucleocapsid protein from linear-scaling quantum methods.
Human immunodeficiency virus type 1 (HIV-1) nucleocapsid protein (NC) plays several important roles in the viral life-cycle and presents an attractive target for rational drug design. Here, the macromolecular reactivity of NC and its binding to RNA is characterized through determination of electrostatic and chemical descriptors derived from linear-scaling quantum calculations in solution. The computational results offer a rationale for the experimentally observed susceptibility of the Cys49 thiolate toward small-molecule electrophilic agents, and support the recently proposed stepwise protonation mechanism of the C-terminal Zn-coordination complex. The distinctive binding mode of NC to SL2 and SL3 stem-loops of the HIV-1 genomic RNA packaging signal is studied on the basis of protein side-chain contributions to the electrostatic binding energies. These results indicate the importance of several basic residues in the 3(10) helical region and the N-terminal zinc finger, and rationalize the presence of several evolutionarily conserved residues in NC. The combined reactivity and RNA-binding study provides new insights that may contribute toward the structure-based design of anti-HIV therapies.
Cysteine↗
Fluorinated imidazoles as proton carriers for water-free fuel cell membranes.
We propose an alternative new material (2,4,5-trifluoroimidazole impregnated Nafion) for use as a high-temperature, water-free membrane for proton-exchange membrane fuel cells. This material has been tested computationally using molecular dynamics and quantum mechanics techniques, leading to an estimated conductivity of approximately 0.06 S/cm at 177 degrees C. This material overcomes the weakness of the imidazole-impregnated membranes, i.e., the poisoning of the Pt electrode. We find that 2,4,5-trifluoroimidazole binds weakly to platinum surfaces, so poisoning is not expected.
Bioelectric Energy Sources↗
Structural versatility of oxalamide-based compounds: a computational study on the isomerization of the oxalamide group and the structural preferences of the polyoxalamides.
The conformational properties of the oxalamide group and crystal structure of several polyoxalamides have been investigated by computational methods. First, a detailed quantum mechanical study of the conformational preferences of N,N'-dimethyloxalamide is reported. Results, which were obtained at the MP2/6-31G(d) level, provide not only the minimum energy conformations but also a description of the energetics and structural changes associated to the isomerization process of the oxalamide group. These quantum mechanical results together with those obtained from additional calculations have been used to develop a set of force-field parameters for the oxalamide group. Molecular mechanics calculations have been performed to test the parameters and to provide new information in terms of energy contributions about the isomerization of the oxalamide group. On the other hand, the new set of parameters has been used to investigate the structural preferences of polyoxalamides (-[NH-CO-CO-NH-(CH(2))(n)]-) by PCSP calculations. Results indicated that polyoxalamides with an even number of methylene groups adopt a structure with one hydrogen bonding direction, whereas polymers with an odd number of methylene groups prefer a structure with two hydrogen bonding directions. The latter crystal structure is completely different from that observed in conventional polyamides and has been investigated in detail through Monte Carlo simulations.
Crystallization↗
Conformational analysis of a 4-hydroxyequilenin Guanine adduct using density functional theory.
Equilenin, a component of the drug Premarin (Wyeth), can be metabolized to a quinonoid, 4-hydroxyequilenin (4-OHEN). 4-OHEN can react with 2'-deoxynucleosides to form unusual cyclic adducts, among which 4-hydroxyequilenin-2'-deoxyguanosine (4-OHEN-dG) is the major product under physiological conditions. The structure and stereochemistry of one stereoisomer, 4-OHEN-dG1, has been obtained previously using electrospray mass spectrometry and NMR methods [Shen et al. (1997) J. Am. Chem. Soc. 119, 11126-11127]; however, details of the conformations around the linkage site have not yet been investigated. The objective of this paper was to determine the conformation at the five-membered ring linkage site for this adduct. We have carried out a computational investigation involving high level quantum mechanical geometry optimization using density functional theory (DFT) for the 4-hydroxyequilenin-guanine adduct (4-OHEN-G1). Our results reveal that there are three conformational families which differ in the puckering of the five-membered ring at the linkage site and in the cyclohexene-type A ring conformation. The overall structures of all three families are "V"-shaped; however, two are quite compact while the third is more open. The lowest energy structure contains a half chair-type cyclohexene A ring, while two structures whose energies are approximately 3-4 kcal/mol higher are boat-type. Since the Watson-Crick hydrogen bonding edge of the modified guanine is obstructed by the formation of this bulky nonplanar adduct, it likely would reside in a groove of the DNA double helix.
Equilenin↗
The nature and transport mechanism of hydrated hydroxide ions in aqueous solution.
Compared to other ions, protons (H(+)) and hydroxide ions (OH(-)) exhibit anomalously high mobilities in aqueous solutions. On a qualitative level, this behaviour has long been explained by 'structural diffusion' the continuous interconversion between hydration complexes driven by fluctuations in the solvation shell of the hydrated ions. Detailed investigations have led to a clear understanding of the proton transport mechanism at the molecular level. In contrast, hydroxide ion mobility in basic solutions has received far less attention, even though bases and base catalysis play important roles in many organic and biochemical reactions and in the chemical industry. The reason for this may be attributed to the century-old notion that a hydrated OH(-) can be regarded as a water molecule missing a proton, and that the transport mechanism of such a 'proton hole' can be inferred from that of an excess proton by simply reversing hydrogen bond polarities. However, recent studies have identified OH(-) hydration complexes that bear little structural similarity to proton hydration complexes. Here we report the solution structures and transport mechanisms of hydrated hydroxide, which we obtained from first-principles computer simulations that explicitly treat quantum and thermal fluctuations of all nuclei. We find that the transport mechanism, which differs significantly from the proton hole picture, involves an interplay between the previously identified hydration complexes and is strongly influenced by nuclear quantum effects.
Journal Article↗