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PubMed2003

Hydride transfer catalyzed by xylose isomerase: mechanism and quantum effects.

We have applied molecular dynamics umbrella-sampling simulation and ensemble-averaged variational transition state theory with multidimensional tunneling (EA-VTST/MT) to calculate the reaction rate of xylose-to- xylulose isomerization catalyzed by xylose isomerase in the presence of two Mg2+ ions. The calculations include determination of the free energy of activation profile and ensemble averaging in the transmission coefficient. The potential energy function is approximated by a combined QM/MM/SVB method involving PM3 for the quantum mechanical (QM) subsystem, CHARMM22 and TIP3P for the molecular mechanical (MM) environment, and a simple valence bond (SVB) local function of two bond distances for the hydride transfer reaction. The simulation confirms the essential features of a mechanism postulated on the basis of kinetics and X-ray data by Whitlow et al. (Whitlow, M.; Howard, A. J.; Finzel, B. C.; Poulos, T. L.; Winborne, E.; Gilliland, G. L. Proteins 1991, 9, 153) and Ringe, Petsko, and coworkers (Labie, A.; Allen, K.-N.; Petsko, G. A.; Ringe, D. Biochemistry 1994, 33, 5469). This mechanism involves a rate-determining 1,2-hydride shift with prior and post proton transfers. Inclusion of quantum mechanical vibrational energy is important for computing the free energy of activation, and quantum mechanical tunneling effects are essential for computing kinetic isotope effects (KIEs). It is found that 85% of the reaction proceeds by tunneling and 15% by overbarrier events. The computed KIE for the ratio of hydride to deuteride transfer is in good agreement with the experimental results. The molecular dynamics simulations reveal that proton and hydride transfer reactions are assisted by breathing motions of the mobile Mg2+ ion in the active site, providing evidence for concerted motion of Mg2+ during the hydride transfer step.

Aldose-Ketose Isomerases↗
PubMed2004

Spin-mediated consciousness theory: possible roles of neural membrane nuclear spin ensembles and paramagnetic oxygen.

A novel theory of consciousness is proposed in this paper. We postulate that consciousness is intrinsically connected to quantum spin since the latter is the origin of quantum effects in both Bohm and Hestenes quantum formulism and a fundamental quantum process associated with the structure of space-time. That is, spin is the "mind-pixel". The unity of mind is achieved by entanglement of the mind-pixels. Applying these ideas to the particular structures and dynamics of the brain, we theorize that human brain works as follows: through action potential modulated nuclear spin interactions and paramagnetic O2/NO driven activations, the nuclear spins inside neural membranes and proteins form various entangled quantum states some of which survive decoherence through quantum Zeno effects or in decoherence-free subspaces and then collapse contextually via irreversible and non-computable means producing consciousness and, in turn, the collective spin dynamics associated with said collapses have effects through spin chemistry on classical neural activities thus influencing the neural networks of the brain. Our proposal calls for extension of associative encoding of neural memories to the dynamical structures of neural membranes and proteins. Thus, according our theory, the nuclear spin ensembles are the "mind-screen" with nuclear spins as its pixels, the neural membranes and proteins are the mind-screen and memory matrices, and the biologically available paramagnetic species such as O2 and NO are pixel-activating agents. Together, they form the neural substrates of consciousness. We also present supporting evidence and make important predictions. We stress that our theory is experimentally verifiable with present technologies. Further, experimental realizations of intra-/inter-molecular nuclear spin coherence and entanglement, macroscopic entanglement of spin ensembles and NMR quantum computation, all in room temperatures, strongly suggest the possibility of a spin-mediated mind.

Action Potentials↗
PubMed2004

Looking for design in materials design.

Despite great advances in computation, materials design is still science fiction. The construction of structure-property relations on the quantum scale will turn computational empiricism into true design.

Computer Simulation↗
PubMedDate not supplied

Semiempirical quantum chemical method and artificial neural networks applied for lambdamax computation of some azo dyes.

The maximum absorption wavelengths of 31 azo dyes have been calculated by two comprehensive methods using the semiempirical quantum chemical method, PM3, and the weight decay based artificial neural network (WD-ANN) or the early stopping based artificial neural network (ES-ANN). The average absolute errors of WD-ANN and that of ES-ANN are 10.07 nm and 12.40 nm, respectively. These results are much better than the results using ZINDO/S with the default value (0.585) only.

Journal Article↗
PubMed2006

Majority logic gate for magnetic quantum-dot cellular automata.

We describe the operation of, and demonstrate logic functionality in, networks of physically coupled, nanometer-scale magnets designed for digital computation in magnetic quantum-dot cellular automata (MQCA) systems. MQCA offer low power dissipation and high integration density of functional elements and operate at room temperature. The basic MQCA logic gate, that is, the three-input majority logic gate, is demonstrated.

Journal Article↗
PubMed2005

Computational studies of the cationic aluminium(chloro) hydroxides by quantum chemical ab initio methods.

Cationic aluminium(chloro) hydroxide complexes with two to four aluminium atoms were studied using quantum chemical methods. Complexes were studied in both gas and liquid phase. The liquid environment was modeled by using a conductor-like screening model (COSMO). COSMO calculations were carried out as a single point calculation at the optimized gas phase structures. Water (epsilon = 78.54) was used as the solvent. The minimum energy structures obtained from the gas phase studies were mostly compact cyclic structures. Aluminium preferred to be five-coordinated in oxygen rich clusters. Core oxygen preferred three-fold coordination but in the largest clusters the four-coordinated oxygen was observed. Water reacted dissociatively with hydrogen poor clusters. The COSMO calculations showed that the optimal structures of cationic aluminium(chloro) hydroxides tend to be more open in the liquid than in the gas phase.

Aluminum↗
PubMed2004

Dephasing representation: Employing the shadowing theorem to calculate quantum correlation functions.

Due to the Heisenberg uncertainty principle, various classical systems differing only on the scale smaller than Planck's cell correspond to the same quantum system. We use this fact to find a unique semiclassical representation without the Van Vleck determinant, applicable to a large class of correlation functions expressible as quantum fidelity. As in the Feynman path integral formulation of quantum mechanics, all contributing trajectories have the same amplitude: that is why we denote it the "dephasing representation." By relating our approach to the problem of existence of true trajectories near numerically-computed chaotic trajectories, we make the approximation rigorous for any system in which the shadowing theorem holds. Numerical implementation only requires computing actions along the unperturbed trajectories and not finding the shadowing trajectories. While semiclassical linear-response theory was used before in quasi-integrable and chaotic systems, here its validity is justified in the most generic, mixed systems. Dephasing representation appears to be a rare practical method to calculate quantum correlation functions in nonuniversal regimes in many-dimensional systems where exact quantum computations are impossible.

Journal Article↗
PubMed2005

Combining fixed- and moving-grid methods to study direct dissociation processes involving nonadiabatic transitions.

We present a novel quantum-dynamics approach suitable for computing direct dissociation processes, including electronic transitions. This approach combines quantum trajectories in the Lagrangian reference frame with standard fixed-grid wave packets in order to overcome the limitations and difficulties of both techniques. As a model application, we consider the ultrafast photodissociation of H2 excited by a femtosecond extreme UV laser pulse.

Journal Article↗
PubMed1992

Computer simulations of enzymatic reactions: examination of linear free-energy relationships and quantum-mechanical corrections in the initial proton-transfer step of carbonic anhydrase.

Computer simulation approaches can provide a powerful tool for correlating the structure of enzymes with their catalytic activity. One of the most effective ways of simulating enzymatic reactions is provided by the empirical valence bond method. The general applicability of this method has been demonstrated in several enzymatic reactions and it is reexamined here in a study of the initial proton-transfer step in the catalytic reaction of carbonic anhydrase. The simulations produce a rate constant which is in agreement with the observed kinetic data and emphasizes the importance of the electrostatic effect associated with the catalytic zinc ion. The calculations are also used to examine the validity of linear free-energy relationships (LFERs) in enzyme catalysis and to evaluate quantum-mechanical corrections of the calculated rate constant. It is found that LFERs are valid in the present case and it is argued that this reflects the fact that the protein responds linearly to the development of electrostatic forces during the reaction. It is concluded that the present approach can be used to augment experimental studies in establishing the general validity of LFERs. It is noted, however, that such relationships are much more valid for transitions between different resonance structures than for transitions between reactants and product states.

Carbonic Anhydrases↗
PubMed2006

Computation of relative bond dissociation enthalpies (DeltaBDE) of phenolic antioxidants from quantum topological molecular similarity (QTMS).

A recently proposed method called quantitative topological molecular similarity (QTMS) generated a model for the computation of the relative substituent effects on the bond dissociation enthalpies (DeltaBDEs) for a set of 39 phenols. The data set includes a diverse set of substituents with monosubstituted and poly-substituted derivatives that exhibit different electronic and steric effects. Many share common structural features with already well-established antioxidants. QTMS reveals the active region of the substituted phenols and identifies the electronic descriptors that best explain the range of DeltaBDEs observed. For substituents in the 4-X position (para) we find that our model requires a correction for radical stabilization enthalpy (RSE). Application of the QTMS methodology yields an unrivalled QSAR with r(2) = 0.98 and q(2) = 0.85 for the bond dissociation enthalpies of this phenolic antioxidant data set.

Journal Article↗
PubMed2001

Quantum mechanical quantitative structure activity relationships to avoid mutagenicity in dental monomers.

The objective of this study was to identify through quantum mechanical quantitative structure activity relationships (Q-QSARs) chemical structures in dental monomers that influence their mutagenicity. AMPAC, a semiempirical computer program that provides quantum mechanical information for chemical structures, was applied to three series of reference chemicals: a set of methacrylates, a set of aromatic and a set of aliphatic epoxy compounds. QSAR models were developed using this chemical information together with mutagenicity data (Salmonella TA 100, Ames Test). CODESSA, a QSAR program that calculates quantum chemical descriptors from information generated by AMPAC and statistically matches these descriptors with observed biological properties was used. QSARs were developed which had r2 values exceeding 0.90 for each study series. These QSARs were used to accurately predict the mutagenicity of BISGMA. a monomer commonly used in dentistry, and two epoxy monomers with developing use in dentistry, GY-281 and UVR-6105. The Q-QSAR quantum mechanical descriptors correctly predicted the level of mutagenicity for all three compounds. The descriptors in the correlation equation pointed to components of structure that may contribute to mutagenesis. The QSARs also provided 'dose windows' for testing mutagenicity, circumventing the need for extensive dose exploration in the laboratory. The Q-QSAR method promises an approach for biomaterials scientists to predict and avoid mutagenicity from the chemicals used in new biomaterial designs.

Dental Enamel↗
PubMed2004

Computational study of the amination of halobenzenes and phenylpentazole. A viable route to isolate the pentazolate anion?

Amination of halobenzenes, which proceeds via the benzyne intermediate (1), has been studied using quantum chemical methods. The computational data are in agreement with experimentally observed trends in reactivity and provide a qualitative explanation for the observed hydrogen isotope effects. To investigate if this is a viable way to isolate the pentazolate anion (2), the reactivities of the halobenzenes have been compared to phenylpentazole (3). The reaction energetics for phenylpentazole become favorable after complexation with Zn(2+).

Journal Article↗
PubMed1993

Experimental detection of multiple-quantum coherence transfer in coupled spin solids by multi-dimensional NMR experiments.

Three-dimensional multiple-quantum coherence experiments in coupled 1/2 spin solids have been designed to directly detect coherence transfers among all the accessible coherence orders during irradiation. The experiments have been performed on the coupled four-spin polycrystalline sample 1,2,3,4-tetrachloronaphthalene-bis(hexachlorocyclopentadiene) adduct. The experimental results reveal how the coherences transfer in this spin system, which support the theoretically deduced selection rules and can be used to assist more precise description of multiple-quantum coherence dynamics.

Hydrocarbons, Chlorinated↗
PubMed2005

Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 1. Implementation.

The present paper describes the extension of a recently developed smooth conductor-like screening model for solvation to a d-orbital semiempirical framework (MNDO/d-SCOSMO) with analytic gradients that can be used for geometry optimizations, transition state searches, and molecular dynamics simulations. The methodology is tested on the potential energy surfaces for separating ions and the dissociative phosphoryl transfer mechanism of methyl phosphate. The convergence behavior of the smooth COSMO method with respect to discretization level is examined and the numerical stability of the energy and gradient are compared to that from conventional COSMO calculations. The present method is further tested in applications to energy minimum and transition state geometry optimizations of neutral and charged metaphosphates, phosphates, and phosphoranes that are models for stationary points in transphosphorylation reaction pathways of enzymes and ribozymes. The results indicate that the smooth COSMO method greatly enhances the stability of quantum mechanical geometry optimization and transition state search calculations that would routinely fail with conventional solvation methods. The present MNDO/d-SCOSMO method has considerable computational advantages over hybrid quantum mechanical/molecular mechanical methods with explicit solvation, and represents a potentially useful tool in the arsenal of multi-scale quantum models used to study biochemical reactions.

Algorithms↗
PubMed2006

Quasi-classical trajectories study of Ne79Br2(B) vibrational predissociation.

A full-dimensional quasi-classical trajectories study on the vibrational predissociation (VP) of the Ne79Br2(B) complex is presented. Following the most recent experiments, the Br2(B) vibrational levels v'=16-29 were explored. The total angular momentum, J, was taken to be zero, and a semiclassical Franck-Condon model to compute initial conditions from quantum distributions was employed. Predissociation lifetimes were extracted from Ne79Br2 population decay by using two different exponential laws. Predicted lifetimes are in excellent agreement with the last experimental results [J. A. Cabrera, C. R. Bieler, B. C. Olbricht, W. E. van der Veer and K. C. Janda, J. Chem. Phys., 2005, 123, 054311]. The Br2 fragment ro-vibrational distributions resulting from the VP of the molecule were obtained from the statistics of classical magnitudes using the standard binning procedure. Computed rotational distributions (for the Deltav'=-1, -2 channels) are also in very good agreement with the experimental results [M. Nejad-Sattari and T. A. Stephenson, J. Chem. Phys., 1997, 106 5454]. The influence of two quantum effects-the closing of the Deltav'=-1 dissociation channel and the intramolecular vibrational relaxation (IVR) mechanism-on the agreement with experimental rotational distributions, is discussed. Due to the classical character of our calculations and the binning procedure we used, the agreement of computed vibrational distributions with experimental and quantum theoretical is qualitative. For instance, for v'=28-for which the Deltav'=-1 channel is experimentally found to be closed-the Deltav'=-2 channel becomes statistically more significant. A discussion on the viability of similar quasi-classical methods to model the VP dynamics of analogous clusters is presented.

Journal Article↗
PubMed2006

Worm algorithm and diagrammatic Monte Carlo: a new approach to continuous-space path integral Monte Carlo simulations.

A detailed description is provided of a new worm algorithm, enabling the accurate computation of thermodynamic properties of quantum many-body systems in continuous space, at finite temperature. The algorithm is formulated within the general path integral Monte Carlo (PIMC) scheme, but also allows one to perform quantum simulations in the grand canonical ensemble, as well as to compute off-diagonal imaginary-time correlation functions, such as the Matsubara Green function, simultaneously with diagonal observables. Another important innovation consists of the expansion of the attractive part of the pairwise potential energy into elementary (diagrammatic) contributions, which are then statistically sampled. This affords a complete microscopic account of the long-range part of the potential energy, while keeping the computational complexity of all updates independent of the size of the simulated system. The computational scheme allows for efficient calculations of the superfluid fraction and off-diagonal correlations in space-time, for system sizes which are orders of magnitude larger than those accessible to conventional PIMC. We present illustrative results for the superfluid transition in bulk liquid 4He in two and three dimensions, as well as the calculation of the chemical potential of hcp 4He.

Journal Article↗