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PubMed2004

Density of phonon states in solid parahydrogen from inelastic neutron scattering.

We have measured the inelastic neutron scattering spectrum of solid parahydrogen (at low pressure and T=13.3 K) using the thermal original spectrometer with cylindrical analyzers spectrometer at the ISIS pulsed neutron source (UK). From the experimental spectrum we have obtained the parahydrogen density of phonon states which has been compared with the estimates available in the literature. The present determination improves substantially the previous experimental scenario from the point of view of both statistics and accuracy. The comparison with the most recent estimate obtained from a quantum mechanical simulation of the molecular dynamics calls for an improvement of the computational methods..

Journal Article↗
PubMed2004

Effect of time-dependent basis functions and their superposition error on atom-centered density matrix propagation (ADMP): connections to wavelet theory of multiresolution analysis.

We present a rigorous analysis of the primitive Gaussian basis sets used in the electronic structure theory. This leads to fundamental connections between Gaussian basis functions and the wavelet theory of multiresolution analysis. We also obtain a general description of basis set superposition error which holds for all localized, orthogonal or nonorthogonal, basis functions. The standard counterpoise correction of quantum chemistry is seen to arise as a special case of this treatment. Computational study of the weakly bound water dimer illustrates that basis set superposition error is much less for basis functions beyond the 6-31+G(*) level of Gaussians when structure, energetics, frequencies, and radial distribution functions are to be calculated. This result will be invaluable in the use of atom-centered Gaussian functions for ab initio molecular dynamics studies using Born-Oppenheimer and atom-centered density matrix propagation.

Journal Article↗
PubMed2005

Properties of nearly one-electron molecules. II. Application to the Rydberg spectrum of CaF.

The ab initio K matrix method described in the preceding paper (Part I) is applied to the Rydberg electronic structure of calcium monofluoride. The spectroscopic quantum defects for the 2Sigma+, 2Pi, 2Delta, and 2Phi states of CaF are computed using the effective potential of Arif et al. [M. Arif, Ch. Jungen, and A. L. Roche, J. Chem. Phys. 106, 4102 (1997)]. Satisfactory agreement with the experimental values is obtained. The eigenquantum defects obtained from the reaction matrix for the CaF++e- system are found to be strongly energy dependent. The analysis shows that the main features of the energy-dependent structure in the eigenphases are a consequence of a broad molecular shape resonance. Partial-l (orbital angular momentum) characters of two interacting collision eigenchannels vary rapidly as a function of increasing collision energy. This prominent variation leads to interference structure in the intensities for transitions into the ionization continuum, manifesting nodal points in the total ionization cross section in the continuum above the shape resonance. The usefulness of this structure in the ionization cross section as a direct probe of the l-character of the bound state is discussed. In addition, ab initio results for the photoelectron angular distribution and the anisotropy parameter are presented. These computed results are susceptible to direct experimental verification.

Journal Article↗
PubMed2000

Studies on the structure of crescent-shaped GaAs quantum wires by combination of electron microscopy and photoluminescence spectroscopy

Crescent-shaped GaAs quantum wires were fabricated on a V-grooved GaAs(001) substrate using a flow rate modulation epitaxy technique in metalorganic chemical vapor phase deposition method. The microstructures of the quantum wires were investigated using electron microscopy. The optimum growth conditions for the quantum wire superlattice structures were discussed from the observed microstructures. The optical properties of the fabricated single quantum wires were also investigated using photoluminescence spectroscopy. The relationship between the microstructures of the quantum wires and the observed optical properties is discussed on the basis of computer simulations of the electronics structure.

Journal Article↗
PubMed1995

The first solvation shell of magnesium and calcium ions in a model nucleic acid environment: an ab initio study.

The interaction of organophosphate anions with divalent metal ions is central to many biological catalytic events. While experimental structural studies can give insight into the likely geometries that can be adopted, quantum mechanics allows for a more complete exploration of the competing forms. Ab initio quantum mechanical calculations have been performed on a series of complexes comprised of dimethyl phosphate, a divalent metal ion (either Mg(II) or Ca(II)) and water of hydration. An additional series of complexes were studied that included a Cl(I) ion to provide for charge neutrality. The most stable orientation of the hydrated metal ion complexed with the phosphate anion occurs when the metal ion is in a unidentate, rather than bidentate, orientation. The question of whether the divalent metal ion is located in the phosphinyl (-PO2(-)-) plane depends on the identity of the divalent metal ion and on the charge state of the complex.

Binding Sites↗
PubMed2006

Effective Hamiltonians by optimal control: solid-state NMR double-quantum planar and isotropic dipolar recoupling.

We report the use of optimal control algorithms for tailoring the effective Hamiltonians in nuclear magnetic resonance (NMR) spectroscopy through sophisticated radio-frequency (rf) pulse irradiation. Specifically, we address dipolar recoupling in solid-state NMR of powder samples for which case pulse sequences offering evolution under planar double-quantum and isotropic mixing dipolar coupling Hamiltonians are designed. The pulse sequences are constructed numerically to cope with a range of experimental conditions such as inhomogeneous rf fields, spread of chemical shifts, the intrinsic orientation dependencies of powder samples, and sample spinning. While the vast majority of previous dipolar recoupling sequences are operating through planar double-or zero-quantum effective Hamiltonians, we present here not only improved variants of such experiments but also for the first time homonuclear isotropic mixing sequences which transfers all I(x), I(y), and I(z) polarizations from one spin to the same operators on another spin simultaneously and with equal efficiency. This property may be exploited to increase the signal-to-noise ratio of two-dimensional experiments by a factor of square root 2 compared to conventional solid-state methods otherwise showing the same efficiency. The sequences are tested numerically and experimentally for a powder of (13)C(alpha),(13)C(beta)-L-alanine and demonstrate substantial sensitivity gains over previous dipolar recoupling experiments.

Algorithms↗
PubMed2006

An integrated instrumental setup for the combination of atomic force microscopy with optical spectroscopy.

In recent years, the study of single biomolecules using fluorescence microscopy and atomic force microscopy (AFM) techniques has resulted in a plethora of new information regarding the physics underlying these complex biological systems. It is especially advantageous to be able to measure the optical, topographical, and mechanical properties of single molecules simultaneously. Here an AFM is used that is especially designed for integration with an inverted optical microscope and that has a near-infrared light source (850 nm) to eliminate interference between the optical experiment and the AFM operation. The Tip Assisted Optics (TAO) system consists of an additional 100 x 100-microm(2) X-Y scanner for the sample, which can be independently and simultaneously used with the AFM scanner. This allows the offset to be removed between the confocal optical image obtained with the sample scanner and the simultaneously acquired AFM topography image. The tip can be positioned exactly into the optical focus while the user can still navigate within the AFM image for imaging or manipulation of the sample. Thus the tip-enhancement effect can be maximized and it becomes possible to perform single molecule manipulation experiments within the focus of a confocal optical image. Here this is applied to simultaneous measurement of single quantum dot fluorescence and topography with high spatial resolution.

Image Processing, Computer-Assisted↗
PubMed2002

Reaction mechanism of the HGXPRTase from Plasmodium falciparum: a hybrid potential quantum mechanical/molecular mechanical study.

Parasites lack the ability to synthesize purines de novo. Instead, they use an enzyme, hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRTase), to salvage host purine and to construct their own nucleotides. In this paper, we investigate the reaction mechanism of the HGXPRTase from Plasmodium falciparum using free-energy simulations and a hybrid potential QM/MM description of the enzyme. The possibility of both dissociative and associative nucleophilic substitutions is discussed, as contradictory hypotheses have been postulated on the basis of crystallographic data and kinetic isotope effect experiments. The preferred pathway is predicted to be stepwise with a rapid proton transfer from the hypoxanthine to the protein followed by a rate-limiting glycosyl transfer. This latter step has a D(N)A(N) mechanism with a transition state in which the pyrophosphate leaving group is more closely bound than the attacking hypoxanthine nucleophile. The energy barrier is comparable to the experimentally observed one.

Animals↗
PubMed2005

Relaxation of pseudo pure states: the role of cross-correlations.

In quantum information processing by NMR one of the major challenges is relaxation or decoherence. Often it is found that the equilibrium mixed state of a spin system is not suitable as an initial state for computation and a definite initial state is required to be prepared prior to the computation. As these preferred initial states are non-equilibrium states, they are not stationary and are destroyed with time as the spin system relaxes toward its equilibrium, introducing error in computation. Since it is not possible to cut off the relaxation processes completely, attempts are going on to develop alternate strategies like quantum error correction codes or noiseless subsystems. Here we study the relaxation behavior of various pseudo pure states and analyze the role of cross-terms between different relaxation processes, known as cross-correlation. It is found that while cross-correlations accelerate the relaxation of certain pseudo pure states, they retard that of others.

Magnetic Resonance Spectroscopy↗
PubMed2001

Computing the relative gas-phase populations of C60 and C70: beyond the traditional delta H(fo),298 scale.

Computations and experiments have shown that the relative heat of formation (i.e., the heat of formation per carbon atom) of C70 is lower than of C60. Moreover, various computations suggest that this is actually a general trend among fullerene cages. The relationship is particularly important for gas-phase fullerenes. Experiments have shown that C60 is typically more populated than C70 when produced in high-temperature gas-phase synthesis. It is not immediately obvious how to reconcile those two terms, or whether the relative heats of formation and the relative populations are in conflict or in agreement. This article deals with this problem, treating it as a general task of relative stabilities of gas-phase clusters of different dimensions (i.e., nonisomeric clusters) under different types of thermodynamic equilibria. The results are then applied to C60 and C70 and point out that the conventional standard pressure of 1 atm is considerably different from actual fullerene-synthesis conditions. Apparently, we should expect considerably lower cluster pressures in carbon-arc synthesis. At 1 atm, C70 is more populated than C60, but at the conditions of a saturated carbon vapor the stability order is reversed in favor of C60 so that an agreement with experiment is obtained already within the thermodynamic treatment. The pressure effects are modeled using the MNDO, AM1, PM3, and SAM1 quantum-chemical semi-empirical methods as well as the available experimental data. The computations consistently show that, if the pressure effects are considered, C60 becomes more populated than C70. Relationships of the thermodynamic treatment to more sophisticated but impractical kinetic analysis are also discussed.

Carbon↗
PubMed2006

Continuous distribution of emission states from single CdSe/ZnS quantum dots.

The photoluminescence dynamics of colloidal CdSe/ZnS/streptavidin quantum dots were studied using time-resolved single-molecule spectroscopy. Statistical tests of the photon-counting data suggested that the simple "on/off" discrete state model is inconsistent with experimental results. Instead, a continuous emission state distribution model was found to be more appropriate. Autocorrelation analysis of lifetime and intensity fluctuations showed a nonlinear correlation between them. These results were consistent with the model that charged quantum dots were also emissive, and that time-dependent charge migration gave rise to the observed photoluminescence dynamics.

Cadmium Compounds↗
PubMed2006

Ab initio determination of the ionization potentials of DNA and RNA nucleobases.

Quantum chemical high level ab initio coupled-cluster and multiconfigurational perturbation methods have been used to compute vertical and adiabatic ionization potentials of the five canonical DNA and RNA nucleobases: uracil, thymine, cytosine, adenine, and guanine. Several states of their cations have been also calculated. The present results represent a systematic compendium of these magnitudes, establishing theoretical reference values at a level not reported before, calibrating computational strategies, and guiding the assignment of the features in the experimental photoelectron spectra.

Adenine↗
PubMed2005

Density-matrix renormalization-group algorithms with nonorthogonal orbitals and non-Hermitian operators, and applications to polyenes.

We describe the theory and implementation of two extensions to the density-matrix renormalization-group (DMRG) algorithm in quantum chemistry: (i) to work with an underlying nonorthogonal one-particle basis (using a biorthogonal formulation) and (ii) to use non-Hermitian and complex operators and complex wave functions, which occur naturally in biorthogonal formulations. Using these developments, we carry out ground-state calculations on ethene, butadiene, and hexatriene, in a polarized atomic-orbital basis. The description of correlation in these systems using a localized nonorthogonal basis is improved over molecular-orbital DMRG calculations, and comparable to or better than coupled-cluster calculations, although we encountered numerical problems associated with non-Hermiticity. We believe that the non-Hermitian DMRG algorithm may further become useful in conjunction with other non-Hermitian Hamiltonians, for example, similarity-transformed coupled-cluster Hamiltonians.

Algorithms↗
PubMed2004

Eigenvalue problem of the Schrödinger equation via the finite-difference time-domain method.

We present a very efficient scheme to calculate the eigenvalue problem of the time-independent Schrödinger equation. The eigenvalue problem can be solved via an initial-value procedure of the time-dependent Schrödinger equation. First, the time evolution of the wave function is calculated by the finite-difference time-domain method. Then the eigenenergies of the electron system can be obtained through a fast Fourier transformation along the time axis of the wave function after some point. The computing effort for this scheme is roughly proportional to the total grid points involved in the structure and it is suitable for large scale quantum systems. We have applied this approach to the three-dimensional GaN quantum dot system involving one million grid points. It takes only 7 h to calculate the confined energies and the wave functions on a standard 2-GHz Pentium 4 computer. The proposed approach can be implemented in a parallel computer system to study more complex systems.

Journal Article↗
PubMed2007

The importance of the active site histidine for the activity of epoxide- or aziridine-based inhibitors of cysteine proteases.

In the present study the importance of the active site histidine residue (His) for the activity of epoxide- or aziridine-based cysteine protease inhibitors is examined theoretically. To account for all important effects, QM/MM hybrid approaches are employed which combine quantum mechanical (QM) methods that are necessary to describe bond-breaking and formation processes, with molecular mechanics (MM) methods that incorporate the influence of the protein environment. Using various model systems, the computations exclude a direct proton shift from the active site His residue to the inhibitor, but show that one water molecule is sufficient to establish a very efficient relay system. This relay system allows an easy proton transfer from the active site His residue to the inhibitor and is thus essential for the activity of both types of inhibitors. Differences between the epoxides and the aziridines are discussed, along with some implications for the rational design of optimized inhibitors. The work presented herein represents the first QM/MM study into the mode of action of these important inhibitor classes.

Aziridines↗
PubMed2006

Some introductory formalizations on the affine Hilbert spaces model of the origin of life. I. On quantum mechanical measurement and the origin of the genetic code: a general physical framework theory.

A physical (affine Hilbert spaces) frame is developed for the discussion of the interdependence of the problem of the origin (symbolic assignment) of the genetic code and a possible endophysical (a kind of "internal") quantum measurement in an explicite way, following the general considerations of Balázs (Balázs, A., 2003. BioSystems 70, 43-54; Balázs, A., 2004a. BioSystems 73, 1-11). Using the Everett (a dynamic) interpretation of quantum mechanics, both the individual code assignment and the concatenated linear symbolism is discussed. It is concluded that there arises a skewed quantal probability field, with a natural dynamic non-linearity in codon assignment within the physical model adopted (essentially corresponding to a much discussed biochemical frame of self-catalyzed binding (charging) of t RNA like proto RNAs (ribozymes) with amino acids). This dynamic specific molecular complex assumption of individual code assignment, and the divergence of the code in relation to symbol concatenation, are discussed: our frame supports the former and interpret the latter as single-type codon (triplet), also unambiguous and extended assignment, selection in molecular evolution, corresponding to converging towards the fixedpoint of the internal dynamics of measurement, either in a protein- or RNA-world. In this respect, the general physical consequence is the introduction of a fourth rank semidiagonal energy tensor (see also Part II) ruling the internal dynamics as a non-linear in principle second-order one. It is inferred, as a summary, that if the problem under discussion could be expressed by the concepts of the Copenhagen interpretation of quantum mechanics in some yet not quite specified way, the matter would be particularly interesting with respect to both the origin of life and quantum mechanics, as a dynamically supported natural measurement-theoretical split between matter ("hardware") and (internal) symbolism ("software") aspects of living matter.

Biological Evolution↗
PubMed2004

Dynamics of proton transfer in bacteriorhodopsin.

Proton transfer in bacteriorhodopsin from the cytoplasm to the extracellular side is initiated from protonated asp96 in the cytoplasmic region toward the deprotonated Schiff base. This occurs in the transition from the photocycle late M state to the N state. To investigate this proton-transfer process, a quantum mechanics/molecular mechanics (QM/MM) model is constructed from the bacteriorhodopsin E204Q mutant crystal structure. Three residues, asp96, asp85, and thr89, as well as most of the retinal chromophore and the Schiff base link of lys216 are treated quantum mechanically and connected to the remaining classical protein through linker atom hydrogens. Structural transformation in the M state results in the formation of a water channel between the Schiff base and asp96. Since a part of this channel is lined with hydrophobic residues, there has been a question on the mechanism of proton transfer in a hydrophobic channel. Ab initio dynamics using the CHARMM/GAMESS methodology is used to simulate the transfer of the proton through a partially hydrophobic channel. Once sufficient water molecules are added to the channel to allow the formation of a single chain of waters from asp96 to the Schiff base, the transfer occurs as a fast (less than a picosecond) concerted event irrespective of the protonation state of asp85. Dynamic transfer of the proton from asp96 to the nearest water initiates the organization of a strongly bonded water chain conducive to the transfer of the proton to the Schiff base nitrogen.

Bacteriorhodopsins↗