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PubMed1991

Computer studies on the stereostructure and quantum chemical properties of 6-pyruvoyl tetrahydropterin, the key intermediate of tetrahydrobiopterin biosynthesis.

The optimized geometry of the conformation of atoms constituting the 6-pyruvoyl tetrahydropterin molecule, the labile key intermediate of tetrahydrobiopterin biosynthesis, was obtained by molecular orbital calculations within the MINDO/3 framework. The stereostructure of the molecule showing the preferred mode for binding to sepiapterin reductase or pyruvoyl tetrahydropterin reductase was drawn in perspective. The resulting structure with the equatorial staggered configuration of the 6-1',2'-dioxopropyl (pyruvoyl) side chain indicated that O(1') and H(6) were located in the trans position around the C(6)-C(1') bond and that the two vicinal carbonyls in the side chain were fixed in the incomplete trans form. The calculation of atomic charges and LUMO coefficients of these carbonyls suggests that the C2'-carbonyl may be more reactive toward NADPH than the C1'-carbonyl in the enzymatic reaction.

Alcohol Oxidoreductases↗
PubMed1999

Subsecond multi-slice computed tomography: basics and applications.

The recent advent of multislice-scanning is the first real quantum leap in computed tomography since the introduction of spiral CT in the early 90s. We discuss basic theoretical considerations important for the design of multislice scanners. Then, specific issues, like the design of the detector and spiral interpolation schemes are addressed briefly for the SOMATOM PLUS 4 Volume Zoom. The theoretical concepts are validated with phantom measurements. We finally show the large potential of the new technology for clinical applications. The concurrent acquisition of multiple slices results in a dramatic reduction of scan time for a given scan technique. This allows scanning volumes previously inaccessible. Similarly, given volumes can be scanned at narrower collimation, i.e. higher axial resolution in a given time. From data acquired at narrow collimation, both high-resolution studies and standard images can be reconstructed in the so-called Combi-Mode. This on the one hand reduces dose exposure to the patient because repeated scanning of a patient is no longer required. On the other hand, standard reconstructions benefit from narrow collimation as Partial Volume Artifacts are drastically suppressed. The rotational speed of 0.5 s of the SOMATOM PLUS 4 Volume Zoom furthermore opens up a whole range of new applications in cardiac CT. For the first time, virtually motion-free images can be acquired even for large volumes in a single breathhold by the combination of fast rotation and ECG triggering, respectively gating. We explain the underlying concepts and present initial results. The paper concludes with a brief discussion of the impact of the new technique on image display and postprocessing.

Artifacts↗
PubMed2005

A neural networks-based drug discovery approach and its application for designing aldose reductase inhibitors.

A novel approach that combines neural networks, computer docking and quantum mechanical method is developed to design potent aldose reductase inhibitors (ARIs). Neural networks is employed to determine the quantitative structure-activity relationship (QSAR) among the known ARIs. The physical descriptors of the neural networks, such as electronegativity and molar volume, are evaluated with first-principles quantum mechanical method. Based on the QSAR, new candidates for ARI are predicted, and subsequently screened via computer docking technique. The surviving candidates are further tested via quantum mechanical calculation for their bindings to aldose reductase. We find that the best 49 predicted ARI candidates have better calculated binding energies than those of experimentally known drug candidates.

Aldehyde Reductase↗
PubMed2001

Electronic structure of 3d[M(H2O)6](3+) ions from Sc(III) to Fe(III): a quantum mechanical study based on DFT computations and natural bond orbital analyses.

The metal-donor atom bonding along the series of 3d[M(H2O)6](3+) ions from Sc(3+) to Fe(3+) has been investigated by density-functional calculations combined with natural localized bond orbital analyses. The M-OH(2) bonds were considered as donor-acceptor bonds, and the contributions coming from the metal ion's 3d sigma-, 3d pi-, and 4s sigma-interactions were treated individually. In this way, the total amount of charge transferred from the water oxygen-donor atoms toward the appropriate metal orbitals could be analyzed in a straightforward manner. One result obtained along these lines is that the overall extent of ligand-to-metal charge transfer shows a strong correlation to the hydration enthalpies of the aqua metal ions. If the contributions to the total ligand-to-metal ion charge transfer are divided into sigma- and pi-contributions, it turns out that Cr(3+) is the best sigma-acceptor, but its pi-accepting abilities are the weakest along the series. Fe(3+) is found to be the best pi-acceptor among the 3d hexaaqua ions studied. Its aptitude to accept sigma-electron density is the second weakest along the series and only slightly higher than that of Sc(3+) (the least sigma-acceptor of all ions) because of the larger involvement of the Fe(3+) 4s orbital in sigma-bonding. The strengths of the three types of bonding interactions have been correlated with the electron affinities of the different metal orbitals. Deviations from the regular trends of electron affinities along the series were found for those [M(H2O)6](3+) ions that are subject to Jahn-Teller distortions. In these cases (d(1) = [Ti(H2O)6](3+), d(2) = [V(H2O)6](3+), and d(4) = [Mn(H2O)6](3+)), ligand-to-metal charge transfer is prevented to go into those metal orbitals that contain unpaired d electrons. A lowering of the complex symmetry is observed and coupled with the following variations: The Ti(3+)- and V(3+)-hexaaqua ions switch from T(h)() to C(i)() symmetry while the Mn(3+)-hexaaqua ion moves to D(2)(h)() symmetry. The loss of orbital overlap leading to a diminished ligand-to-metal charge transfer toward the single occupied metal orbitals is compensated by amplified bonding interactions of the ligand orbitals with the unoccupied metal orbitals to some extent.

Journal Article↗
PubMed2005

Nonadiabatic quantum-classical reaction rates with quantum equilibrium structure.

Time correlation function expressions for quantum reaction-rate coefficients are computed in a quantum-classical limit. This form for the correlation function retains the full quantum equilibrium structure of the system in the spectral density function but approximates the time evolution of the operator by quantum-classical Liouville dynamics. Approximate analytical expressions for the spectral density function, which incorporate quantum effects in the many-body environment and reaction coordinate, are derived. The results of numerical simulations of the reaction rate are presented for a reaction model in which a two-level system is coupled to a bistable oscillator which is, in turn, coupled to a bath of harmonic oscillators. The nonadiabatic quantum-classical dynamics is simulated in terms of an ensemble of surface-hopping trajectories and the effects of the quantum equilibrium structure on the reaction rate are discussed.

Journal Article↗
PubMed1995

Rational design of anticonvulsants: a quantum pharmacologic study of the ion channel-modulating FMRFamide tetrapeptide as an endogenous anticonvulsant.

We applied the computational techniques of quantum pharmacology to examine molecular conformations (shapes and geometries) of the tetrapeptide FMR-Famide (L-Phe-L-Met-L-Arg-L-Phe-NH2), determining the geometric features necessary for anticonvulsant activity. The rigorous tiered hierarchical approach used molecular mechanics, molecular dynamics, and semiempirical quantum mechanics calculational methods. Low-energy conformations showed pertinent conformational information to be considered in the rational design of novel anticonvulsants. The FMRFamide peptide backbone assumes a bent but primary planar geometry. Distinct polar and nonpolar regions are created as the two Phe residues occupy one "face" of the bent conformation, while the Met and Arg residues occupy the opposite face. The aromatic rings point away from each other along the backbone, and this separation is consistent among the low-energy conformations at approximately 11-12 A. The Met side chain interacts with neither the peptide backbone nor the side chains of other residues. Molecular mechanics and semiempirical quantum mechanics calculations predict limited variation in the orientation of the Arg side chain.

Algorithms↗
PubMed2001

Quantitative structure-property relationships (QSPRs) on direct photolysis of PCDDs.

By the use of partial least squares (PLS) method and 27 quantum chemical descriptors computed by PM3 Hamiltonian, a statistically significant QSPR were obtained for direct photolysis quantum yields (Y) of selected Polychlorinated dibenzo-p-dioxins (PCDDs). The QSPR can be used for prediction. The direct photolysis quantum yields of the PCDDs are dependent on the number of chlorine atoms bonded with the parent structures, the character of the carbonoxygen bonds, and molecular polarity. Increasing bulkness and polarity of PCDDs lead to decrease of log Y values. Increasing the frontier molecular orbital energies (Elumo and Ehomo) and heat of formation (HOF) values leads to increase of log Y values.

Carbon↗
PubMed2000

Quantitative structure-property relationships for direct photolysis quantum yields of selected polycyclic aromatic hydrocarbons

By the use of partial least squares (PLS) method and 11 quantum chemical descriptors computed by PM3 Hamiltonian, Quantitative Structure-Property Relationships (QSPRs) for direct photolysis quantum yields of selected polycyclic aromatic hydrocarbons (PAHs) were obtained. Direct photolysis quantum yields were predicted for PAHs for which experimental quantum yield values were lacking. Based on the QSPR models, significant PAH molecular characters governing their direct photolysis quantum yields were identified. It can generally be concluded that PAHs with large average molecular polarizability, molecular weight, and heat of formation values tend to have small photolysis quantum yields. PAHs with large values of the energy of the lowest unoccupied molecular orbital (Elumo), small values of the energy of the highest occupied molecular orbital (Ehomo), and large Elumo-Ehomo values, tend to have great photolysis quantum yields.

Journal Article↗
PubMed2005

Computational complexity and fundamental limitations to fermionic quantum Monte Carlo simulations.

Quantum Monte Carlo simulations, while being efficient for bosons, suffer from the "negative sign problem" when applied to fermions--causing an exponential increase of the computing time with the number of particles. A polynomial time solution to the sign problem is highly desired since it would provide an unbiased and numerically exact method to simulate correlated quantum systems. Here we show that such a solution is almost certainly unattainable by proving that the sign problem is nondeterministic polynomial (NP) hard, implying that a generic solution of the sign problem would also solve all problems in the complexity class NP in polynomial time.

Journal Article↗
PubMed2006

Quantum control of internal conversion in 24-vibrational-mode pyrazine.

Quantum control of the S(2)-->S(1) internal conversion in a complete 24-mode dimensionality model of pyrazine is demonstrated. The fully quantum mechanical study makes use of the recently developed "QP algorithm" for performing accurate computations of projected quantum dynamics and the role of overlapping resonances in control. The results are extremely encouraging, demonstrating active control over internal conversion so as to almost completely suppress the process over time scales of approximately 50-100 fs [well in excess of the natural internal conversion times (approximately 20 fs)] or to accelerate it to complete internal conversion in less than 5 fs. A number of new diagnostics are introduced to demonstrate the significance of overlapping-resonance contributions to control. Control is far better than for a reduced dimensionality model of pyrazine, presumably because of the increased degree of overlap between bound state resonances existing in the full dimensionality case.

Journal Article↗
PubMed2006

SER-HIS-ASP catalytic triad in model non-aqueous solvent environment: a computational study.

Emerging new properties and applications of enzymes in organic solvents and ionic liquids are unabating. By applying a combined Quantum Mechanics/Continuum Mechanics computation on a prototypical catalytic triad serine-histidine-aspartate (SER-HIS-ASP) interacting with ethanol or acetonitrile molecules, the major difference between protic and aprotic solvents in effecting transition-state stabilization has been analyzed. Moderately polar aprotic solvent acetonitrile is predicted to be unable to stabilize the transition state in replacing the role of the oxyanion-hole environment, whereas protic ethanol solvent molecules of similar polarity to acetonitrile are adequate in re-gaining the enzymatic activities.

Acetonitriles↗
PubMed2001

Quantitative structure-property relationships (QSPRs) on direct photolysis quantum yields of PCDDs.

By the use of partial least squares (PLS) method and 16 fundamental quantum chemical descriptors computed by PM3 Hamiltonian, quantitative structure-property relationships (QSPRs) were obtained for direct photolysis quantum yields of selected polychlorinated dibenzo-p-dioxins (PCDDs). Direct photolysis quantum yields for PCDDs without experimental quantum yield values were predicted. The QSPR results showed that it was mainly the number of chlorine atoms bonded to the parent structure, the largest positive atomic charge on a chlorine atom, the dipole moment, and the frontier molecular orbital energies (Ehomo and Elumo) that determine the direct photolysis quantum yields of the PCDDs. Increasing the number of chlorine atoms, dipole moment, and the largest positive atomic charge on a chlorine atom, leads to decrease of photolysis quantum yields. Increasing Elumo, Ehomo and Elumo - Ehomo values lead to increase of log Y values.

Chlorine↗
PubMed2005

Experimental implementation of heat-bath algorithmic cooling using solid-state nuclear magnetic resonance.

The counter-intuitive properties of quantum mechanics have the potential to revolutionize information processing by enabling the development of efficient algorithms with no known classical counterparts. Harnessing this power requires the development of a set of building blocks, one of which is a method to initialize the set of quantum bits (qubits) to a known state. Additionally, fresh ancillary qubits must be available during the course of computation to achieve fault tolerance. In any physical system used to implement quantum computation, one must therefore be able to selectively and dynamically remove entropy from the part of the system that is to be mapped to qubits. One such method is an 'open-system' cooling protocol in which a subset of qubits can be brought into contact with an external system of large heat capacity. Theoretical efforts have led to an implementation-independent cooling procedure, namely heat-bath algorithmic cooling. These efforts have culminated with the proposal of an optimal algorithm, the partner-pairing algorithm, which was used to compute the physical limits of heat-bath algorithmic cooling. Here we report the experimental realization of multi-step cooling of a quantum system via heat-bath algorithmic cooling. The experiment was carried out using nuclear magnetic resonance of a solid-state ensemble three-qubit system. We demonstrate the repeated repolarization of a particular qubit to an effective spin-bath temperature, and alternating logical operations within the three-qubit subspace to ultimately cool a second qubit below this temperature. Demonstration of the control necessary for these operations represents an important step forward in the manipulation of solid-state nuclear magnetic resonance qubits.

Journal Article↗
PubMed2006

Effect of quantum partial charges on the structure and dynamics of water in single-walled carbon nanotubes.

In this work, using quantum partial charges, computed from 6-31G(**)B3LYP density functional theory, in molecular dynamics simulations, we found that water inside (6,6) and (10,0) single-walled carbon nanotubes with similar diameters but with different chiralities has remarkably different structural and dynamical properties. Density functional calculations indicate that tubes with different chiralities have significantly different partial charges at the ends of tubes. The partial charges at the ends of a (10,0) tube are around 4.5 times higher than those of a (6,6) tube. Molecular dynamics simulations with the partial charges show different water dipole orientations. In the (10,0) tube, dipole vectors of water molecules at the end of the tube point towards the water reservoir resulting in the formation of an L defect in the center region. This is not observed in the (6,6) tube where dipole vectors of all the water molecules inside the tube point towards either the top or the bottom water reservoir. The water diffusion coefficient is found to increase in the presence of the partial charges. Water in the partially charged (10,0) tube has a lower diffusion coefficient compared to that of in the partially charged (6,6) tube.

Computer Simulation↗
PubMed2004

Computation of the equation of state of the quantum hard-sphere fluid utilizing several path-integral strategies.

The compressibility factor of the quantum hard-sphere fluid within the region (rho(N) (*)</=0.8,lambda(B) (*)</=0.9) is computed by following four distinct routes involving the three pair radial correlation functions that are significant in the path-integral context, namely, instantaneous, pair linear response, and centroids. These functions are calculated with path-integral Monte Carlo simulations involving the Cao-Berne propagator. The first route to the equation of state is the instantaneous standard one, i.e., the usual volume derivative of the partition function expressed in terms of the instantaneous pair radial correlations. The other three routes stem from the extended compressibility theorem, which associates the isothermal compressibility with the three pair radial structures mentioned above and involves the solving of appropriate Ornstein-Zernike equations. An analysis of the error bars in the quantities computed is reported, and it is proven the usefulness of the centroid pair correlations to fix quantum equations of state. Also, the regions where the fluid-solid changes of phase should take place are identified with the use of indicators sensitive to order in the sample. The consistency of the current results is assessed and comparison with data available in the literature is made wherever possible.

Journal Article↗
PubMed1997

An accurate method for computer-generating tungsten anode x-ray spectra from 30 to 140 kV.

A tungsten anode spectral model using interpolating polynomials (TASMIP) was used to compute x-ray spectra at 1 keV intervals over the range from 30 kV to 140 kV. The TASMIP is not semi-empirical and uses no physical assumptions regarding x-ray production, but rather interpolates measured constant potential x-ray spectra published by Fewell et al. [Handbook of Computed Tomography X-ray Spectra (U.S. Government Printing Office, Washington, D.C., 1981)]. X-ray output measurements (mR/mAs measured at 1 m) were made on a calibrated constant potential generator in our laboratory from 50 kV to 124 kV, and with 0-5 mm added aluminum filtration. The Fewell spectra were slightly modified (numerically hardened) and normalized based on the attenuation and output characteristics of a constant potential generator and metal-insert x-ray tube in our laboratory. Then, using the modified Fewell spectra of different kVs, the photon fluence phi at each 1 keV energy bin (E) over energies from 10 keV to 140 keV was characterized using polynomial functions of the form phi (E) = a0[E] + a1[E] kV + a2[E] kV2 + ... + a(n)[E] kVn. A total of 131 polynomial functions were used to calculate accurate x-ray spectra, each function requiring between two and four terms. The resulting TASMIP algorithm produced x-ray spectra that match both the quality and quantity characteristics of the x-ray system in our laboratory. For photon fluences above 10% of the peak fluence in the spectrum, the average percent difference (and standard deviation) between the modified Fewell spectra and the TASMIP photon fluence was -1.43% (3.8%) for the 50 kV spectrum, -0.89% (1.37%) for the 70 kV spectrum, and for the 80, 90, 100, 110, 120, 130 and 140 kV spectra, the mean differences between spectra were all less than 0.20% and the standard deviations were less than approximately 1.1%. The model was also extended to include the effects of generator-induced kV ripple. Finally, the x-ray photon fluence in the units of photons/mm2 per mR was calculated as a function of HVL, kV, and ripple factor, for various (water-equivalent) patient thicknesses (0, 10, 20, and 30 cm). These values may be useful for computing the detective quantum efficiency, DQE(f), of x-ray detector systems. The TASMIP algorithm and ancillary data are made available on line at http:/(/)www.aip.org/epaps/epaps.html.

Algorithms↗
PubMed2005

Experimental implementation of local adiabatic evolution algorithms by an NMR quantum information processor.

Quantum adiabatic algorithm is a method of solving computational problems by evolving the ground state of a slowly varying Hamiltonian. The technique uses evolution of the ground state of a slowly varying Hamiltonian to reach the required output state. In some cases, such as the adiabatic versions of Grover's search algorithm and Deutsch-Jozsa algorithm, applying the global adiabatic evolution yields a complexity similar to their classical algorithms. However, using the local adiabatic evolution, the algorithms given by J. Roland and N.J. Cerf for Grover's search [J. Roland, N.J. Cerf, Quantum search by local adiabatic evolution, Phys. Rev. A 65 (2002) 042308] and by Saurya Das, Randy Kobes, and Gabor Kunstatter for the Deutsch-Jozsa algorithm [S. Das, R. Kobes, G. Kunstatter, Adiabatic quantum computation and Deutsh's algorithm, Phys. Rev. A 65 (2002) 062301], yield a complexity of order N (where N=2(n) and n is the number of qubits). In this paper, we report the experimental implementation of these local adiabatic evolution algorithms on a 2-qubit quantum information processor, by Nuclear Magnetic Resonance.

Journal Article↗