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PubMed2006

Theoretical prediction of condensed phase heat of formation of nitramines, nitrate esters, nitroaliphatics and related energetic compounds.

An empirical approach is presented for calculation heats of formation of nitramines, nitrate esters, nitroaliphatics and related energetic compounds which contain at least one of the functional groups including N-NO(2), C-ONO(2) or nonaromatic C-NO(2). This approach is based on elemental composition and various structural and functional group parameters of C(a)H(b)N(c)O(d) energetic compounds. Heat of formation for 78 nitrocompounds including nitramines, nitrate esters, nitroaliphatics and the data obtained is compared with experimental data. Root mean square (rms) of deviation for 19 well known of mentioned energetic compounds are also compared with complex quantum mechanical computations which show 23.8 and 21.3 kJ/mol for new and quantum mechanical methods, respectively. Predicted condensed phase heats of formation for remainder 59 energetic molecules with complex molecular structures have a rms deviation from experiment of 42.3 kJ/mol.

Aniline Compounds↗
PubMed2006

Globally controlled quantum wires for perfect qubit transport, mirroring, and computing.

We describe a new design for a q wire with perfect transmission using a uniformly coupled Ising spin chain subject to global pulses. In addition to allowing for the perfect transport of single qubits, the design also yields the perfect "mirroring" of multiply encoded qubits within the wire. We further utilize this global-pulse generated perfect mirror operation as a "clock cycle" to perform universal quantum computation on these multiply encoded qubits where the interior of the q wire serves as the quantum memory while the q-wire ends perform one- and two-qubit gates.

Journal Article↗
PubMed2007

Computational approach to nuclear magnetic resonance in 1-Alkyl-3-methylimidazolium ionic liquids.

A quantum-chemical computational approach to accurately predict the nuclear magnetic resonance (NMR) properties of 1-alkyl-3-methylimidazolium ionic liquids has been performed by the gauge-including atomic orbitals method at the B3LYP/6-31++G** level using different simulated ionic liquid environments. The first molecular model chosen to describe the ionic liquid system includes the gas-phase optimized structures of ion pairs and separated ions of a series of imidazolium salts containing methyl, butyl, and octyl substituents and PF6-, BF4-, and Br- anions. In addition, a continuum polarizable model of solvation has been applied to predict the effects of the medium polarity on the molecular properties of 1,3-dimethylimidazolium hexafluorophosphate (MmimPF6). Furthermore, the specific acidic and basic solute-solvent interactions have been simulated by a discrete solvation model based on molecular clusters formed by MmimPF6 species and a discrete number of water molecules. The computational prediction of the NMR spectra allows a consistent interpretation of the dispersed experimental evidence in the literature. The following are main contributions of this work: (a) Theoretical results state the presence of a chemical equilibrium between ion-pair aggregates and solvent-separated counterions of 1-alkyl-3-methylimidazolium salts which is tuned by the solvent environment; thus, strong specific (acidic and basic) and nonspecific (polarity and polarizability) solvent interactions are predicted favoring the dissociated ionic species. (b) The calculated 1H and 13C NMR properties of these ionic liquids are revealed as highly dependent on the nature of solute-solvent interactions. Thus, the chemical shift of the hydrogen atom in position two of the imidazolium ring is deviated to high values by the specific interactions with water molecules, whereas nonspecific interaction with water (as a solvent) affects, in the opposite direction, this 1H NMR parameter. (c) Last, current calculations support the presence of hydrogen bonding between counterions, suggesting the importance of this interaction in the properties of the solvent in the 1-alkyl-3-methylimidazolium ionic liquids.

Journal Article↗
PubMed2003

Demonstration of an all-optical quantum controlled-NOT gate.

The promise of tremendous computational power, coupled with the development of robust error-correcting schemes, has fuelled extensive efforts to build a quantum computer. The requirements for realizing such a device are confounding: scalable quantum bits (two-level quantum systems, or qubits) that can be well isolated from the environment, but also initialized, measured and made to undergo controllable interactions to implement a universal set of quantum logic gates. The usual set consists of single qubit rotations and a controlled-NOT (CNOT) gate, which flips the state of a target qubit conditional on the control qubit being in the state 1. Here we report an unambiguous experimental demonstration and comprehensive characterization of quantum CNOT operation in an optical system. We produce all four entangled Bell states as a function of only the input qubits' logical values, for a single operating condition of the gate. The gate is probabilistic (the qubits are destroyed upon failure), but with the addition of linear optical quantum non-demolition measurements, it is equivalent to the CNOT gate required for scalable all-optical quantum computation.

Journal Article↗
PubMed2002

Symmetry-general ab initio computation of physical properties using quantum software integrated with crystal structure databases: results and perspectives.

The timely integration of crystal structure databases, such as CRYSTMET, ICSD etc., with quantum software, like VASP, OresteS, ElectrA etc., allows ab initio cell and structure optimization on existing pure-phase compounds to be performed seamlessly with just a few mouse clicks. Application to the optimization of rough structure models, and possibly new atomic arrangements, is detailed. The ability to reproduce observed cell data can lead to an assessment of the intrinsic plausibility of a structure model, even without a competing model. The accuracy of optimized atom positions is analogous to that from routine powder studies. Recently, the ab initio symmetry-general least-squares extraction of the coefficients of the elastic tensor for pure-phase materials using data from corresponding entries in crystal structure databases was automated. A selection of highly encouraging results is presented, stressing the complementarity of simulation and experiment. Additional physical properties also appear to be computable using existing quantum software under the guidance of an automation scheme designed following the above automation for the elastic tensor. This possibility creates the exciting perspective of mining crystal structure databases for new materials with combinations of physical properties that were never measured before. Crystal structure databases can accordingly be expected to become the cornerstone of materials science research within a very few years, adding immense practical value to the archived structure data.

Journal Article↗
PubMed2005

A potential from quantum chemistry for thermodynamic property predictions for methanethiol.

An ab initio potential for methanethiol is determined by computing quantum-chemical interaction energies for a range of orientations and center-of-mass separation distances. These energies are initially fitted to a pairwise-additive, site-site Morse-C6 intermolecular potential. Additional interaction energies were then calculated at separation distances determined to be important from the angle-averaged Mayer f function calculated with the initial potential. This expanded set of interaction energies is then fitted using Boltzmann-type weighting to obtain the final intermolecular potential. Although there are some discrepancies in the fit for a particular type of orientation, the phase behavior calculated from Gibbs ensemble Monte Carlo simulations using this final potential is in very good agreement with experimental data. The prescription used here for obtaining the optimum potential from quantum-chemical methods should be applicable to other systems.

Journal Article↗
PubMed2006

The generalized molecular fractionation with conjugate caps/molecular mechanics method for direct calculation of protein energy.

A generalized molecular fractionation with conjugate caps/molecular mechanics (GMFCC/MM) scheme is developed for efficient linear-scaling quantum mechanical calculation of protein energy. In this GMFCC/MM scheme, the interaction energy between neighboring residues as well as between non-neighboring residues that are spatially in close contact are computed by quantum mechanics while the rest of the interaction energy is computed by molecular mechanics. Numerical studies are carried out to calculate torsional energies of six polypeptides using the GMFCC/MM approach and the energies are shown to be in general good agreement with the full system quantum calculation. Among those we tested is a polypeptide containing 396 atoms whose energies are computed at the MP26-31G* level. Our study shows that using GMFCC/MM, it is possible to perform high level ab initio calculation such as MP2 for applications such as structural optimization of protein complex and molecular dynamics simulation.

Algorithms↗
PubMedDate not supplied

Experimental realization of Shor's quantum factoring algorithm using nuclear magnetic resonance.

The number of steps any classical computer requires in order to find the prime factors of an l-digit integer N increases exponentially with l, at least using algorithms known at present. Factoring large integers is therefore conjectured to be intractable classically, an observation underlying the security of widely used cryptographic codes. Quantum computers, however, could factor integers in only polynomial time, using Shor's quantum factoring algorithm. Although important for the study of quantum computers, experimental demonstration of this algorithm has proved elusive. Here we report an implementation of the simplest instance of Shor's algorithm: factorization of N = 15 (whose prime factors are 3 and 5). We use seven spin-1/2 nuclei in a molecule as quantum bits, which can be manipulated with room temperature liquid-state nuclear magnetic resonance techniques. This method of using nuclei to store quantum information is in principle scalable to systems containing many quantum bits, but such scalability is not implied by the present work. The significance of our work lies in the demonstration of experimental and theoretical techniques for precise control and modelling of complex quantum computers. In particular, we present a simple, parameter-free but predictive model of decoherence effects in our system.

Journal Article↗
PubMed2004

Ab initio rate constants from hyperspherical quantum scattering: application to H + CH4 --> H2 + CH3.

A general and practical procedure is described for calculating rate constants for chemical reactions using a minimal number of ab initio calculations and quantum-dynamical computations. The method exploits a smooth interpolating functional developed in the hyperspherical representation. This functional is built from two Morse functions and depends on a relatively small number of parameters with respect to conventional functionals developed to date. Thus only a small number of ab initio points needs to be computed. The method is applied to the H + CH4 --> H2 + CH3 reaction. The quantum scattering calculations are performed treating explicitly the bonds being broken and formed. All the degrees of freedom except the breaking and forming bonds are optimized ab initio and harmonic vibrational frequencies and zero-point energies for them are calculated at the MP2(full) level with a cc-pVTZ basis set. Single point energies are calculated at a higher level of theory with the same basis set, namely CCSD(T, full). We report state-to-state cross sections and thermal rate constants for the title reaction and make comparisons with previous results. The calculated rate constants are in good agreement with experiments.

Journal Article↗
PubMed2000

Quantum information processing with semiconductor macroatoms.

An all optical implementation of quantum information processing with semiconductor macroatoms is proposed. Our quantum hardware consists of an array of quantum dots and the computational degrees of freedom are energy-selected interband optical transitions. The quantum-computing strategy exploits exciton-exciton interactions driven by ultrafast multicolor laser pulses. Contrary to existing proposals based on charge excitations, our approach does not require time-dependent electric fields, thus allowing for a subpicosecond, decoherence-free, operation time scale in realistic semiconductor nanostructures.

Journal Article↗
PubMedDate not supplied

[Input and output channels of quantum biocomputers].

It is proposed that "Quantum Molecular" computer of a neuron consists of the cell cytoskeleton serving as calculating media and input ionic channel sending a hypersound signal to observe these media. The sound spreads through the media travelling along microtubules and microfilaments and switching between those via molecular bridges which serve as elementary switches. The whole system works like a wave guiding net connecting input ionic channels (which generate different sound signals) and output ionic channels (which are controlled by the processed sound signals). Thus the output of such systems depends on the input (controlled by synaptic activity) and on the construction and state of these calculating media. We think that the sound waves spreading through different calculating media solve different physical problems. The construction of the calculating part of the cytoskeleton, according to the hypothesis, is different in different neurons. It is defined by special protein which is produced by DNA, RNA and protein molecular word processor (during brain development and, may be, education). We comment on how the existence of an extremal computer produces an impact on physics and mathematics exemplified by the optimality principle as substitution of physical relativity principle for a complex problem.

Brain↗
PubMed2006

Computational analysis of the proton translocation from Asp96 to schiff base in bacteriorhodopsin.

The potential energy change during the M --> N process in bacteriorhodopsin has been evaluated by ab initio quantum chemical and advanced quantum chemical calculations following molecular dynamics (MD) simulations. Many previous experimental studies have suggested that the proton transfer from Asp96 to the Schiff base occurs under the following two conditions: (1) the hydrogen bond between Thr46 and Asp96 breaks and Thr46 is detached from Asp96 and (2) a stable chain of four water molecules spans an area from Asp96 --> Schiff base. In this work, we successfully reproduced the proton-transfer process occurring under these two conditions by molecular dynamics and quantum chemical calculations. The quantum chemical computation revealed that the proton transfer from Asp96 to Shiff base occurs in two-step reactions via an intermediate in which an H(3)O(+) appears around Ala215. The activation energy for the proton transfer in the first reaction was calculated to be 9.7 kcal/mol, which enables fast and efficient proton pump action. Further QM/MM (quantum mechanical/molecular mechanical) and FMO (fragment molecular orbital) calculations revealed that the potential energy change during the proton transfer is tightly regulated by the composition and the geometry of the surrounding amino acid residues of bacteriorhodopsin. Here, we report in detail the Asp96 --> Schiff base proton translocation mechanism of bacteriorhodopsin. Additionally, we discuss the effectiveness of combining quantum chemical calculations with truncated cluster models followed by advanced quantum chemical calculations applied to a whole protein to elucidate its reaction mechanism.

Aspartic Acid↗
PubMed2005

Structural and conformational properties of 1,1,1-trifluoro-2-propanol investigated by microwave spectroscopy and quantum chemical calculations.

The microwave spectrum of 1,1,1-trifluoro-2-propanol, CF(3)CH(OH)CH(3), and one deuterated species, CF(3)CH(OD)CH(3), have been investigated in the 20.0-62.0 GHz spectral region at about -50 degrees C. The rotational spectrum of one of the three possible rotameric forms was assigned. This conformer is stabilized by an intramolecular hydrogen bond formed between the hydrogen atom of the hydroxyl group and the nearest fluorine atoms. The hydrogen bond is weak and assumed to be mainly a result of attraction between the O-H and the C-F bond dipoles, which are nearly antiparallel. The identified rotamer is at least 3 kJ/mol more stable than any other rotameric form. Two vibrationally excited states belonging to two different normal modes were assigned for this conformer, and their frequencies were determined by relative intensity measurements. The microwave work has been assisted by quantum chemical computations at the MP2/cc-pVTZ and B3LYP/6-311++G** levels of theory, as well as by the infrared spectrum of the O-H stretching vibration.

Computer Simulation↗
PubMed2003

Spin dynamics from majorana fermions.

Using the Majorana fermion representation of spin-1/2 local moments, we show how the dynamic spin correlation and susceptibility are obtained directly from the one-particle Majorana propagator. We illustrate our method by applying it to the spin dynamics of a nonequilibrium quantum dot, computing the voltage-dependent spin relaxation rate and showing that, at weak coupling, the fluctuation-dissipation relation for the spin of a quantum dot is voltage dependent. We confirm the voltage-dependent Curie susceptibility recently found by Parcollet and Hooley [Phys. Rev. B 66, 085315 (2002)]].

Journal Article↗
PubMed2003

Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA-LF.

To account for the distortion of the coordination sphere that takes place in complexes containing open-shell metal cations such as Cu(II), we implemented, in sum of interactions between fragments ab initio computed (SIBFA) molecular mechanics, an additional contribution to take into account the ligand field splitting of the metal d orbitals. This term, based on the angular overlap model, has been parameterized for Cu(II) coordinated to oxygen and nitrogen ligands. The comparison of the results obtained from density functional theory computations on the one hand and SIBFA or SIBFA-LF on the other shows that SIBFA-LF gives geometric arrangements similar to those obtained from quantum mechanical computations. Moreover, the geometric improvement takes place without downgrading the energetic agreement obtained from SIBFA. The systems considered are Cu(II) interacting with six water molecules, four ammonia or four imidazoles, and four water plus two formate anions.

Journal Article↗
PubMed2005

Computational methods in coupled electron-ion Monte Carlo simulations.

In the last few years, we have been developing a Monte Carlo simulation method to cope with systems of many electrons and ions in the Born-Oppenheimer approximation: the coupled electron-ion Monte Carlo method (CEIMC). Electronic properties in CEIMC are computed by quantum Monte Carlo rather than by density functional theory (DFT) based techniques. CEIMC can, in principle, overcome some of the limitations of the present DFT-based ab initio dynamical methods. The new method has recently been applied to high-pressure metallic hydrogen. Herein, we present a new sampling algorithm that we have developed in the framework of the reptation quantum Monte Carlo method chosen to sample the electronic degrees of freedom, thereby improving its efficiency. Moreover, we show herein that, at least for the case of metallic hydrogen, variational estimates of the electronic energies lead to an accurate sampling of the proton degrees of freedom.

Computer Simulation↗