Quantum-mechanical calculations of vibrationally resolved cross sections for non-dissociative charge transfer of O3+ with H-2

Charge transfer due to collisions of ground state O3+ (2s(2)2p P-2) ions with molecular hydrogen is investigated using the quantum-mechanical molecular-orbital close-coupling (MOCC) method, and electronic and vibrational state-selective cross sections along with the corresponding differential cross sections are calculated for projectile energies of 100, 500, 1000 and 5000 eV/u at the orientation angles of 25 degrees,45 degrees and 89 degrees. The adiabatic potentials and radial coupling matrix elements utilized in the QMOCC calculations were obtained with the spin-coupled valence-bond approach. The infinite order sudden approximation (IOSA) and the vibrational sudden approximation (VSA) are utilized to deal with the rotation of H-2 and the coupling between the electron and the vibration of H-2. It is found that the distribution of vibrationally resolved cross sections with the vibrational quantum number upsilon' of H-2(+) (upsilon') varies with the increment of the projectile energy; and the electronic and vibrational stateselective differential cross sections show similar behaviors: there is a highest platform within a very small scattering angle, beyond which the differential cross sections decrease as the scattering angle increases and lots of oscillating structures appear, where the scattering angle of the first structure decreases as E-P(-1/2) with the increment of the projectile energy E-P; and the structure and amplitude of the differential cross sections are sensitive to the orientation of molecule H-2, which provides a possibility to identify the orientations of molecule H-2 by the vibrational state-selective differential scattering processes.

New insights into NO-carbon and N2O-carbon reactions from quantum mechanical calculations

Density functional theory calculations were used to investigate the mechanisms of NO-carbon and N2O-carbon reactions. It was the first time that the importance of surface nitrogen groups was addressed in the kinetic behaviors of the NO-carbon reaction. It was found that the off-plane nitrogen groups that are adjacent to the zigzag edge sites and in-plane nitrogen groups that are located on the armchair sites make the bond energy of oxygen desorption even ca. 20% lower than that of the off-plane epoxy group adjacent to zigzag edge sites and in-plane o-quinone oxygen atoms on armchair sites; this may explain the reason why the experimentally obtained activation energy of the NO-carbon reaction is ca. 20% lower than that of the O-2-carbon reaction over 923 K. A higher ratio of oxygen atoms can be formed in the N2O-carbon reaction, because of the lower dissociation energy of N2O, which results in a higher ratio of off-plane epoxy oxygen atoms. The desorption energy of semiquinone with double adjacent off-plane oxygen groups is ca. 20% less than that of semiquinone with only one adjacent off-plane oxygen group. This may be the reason why the activation energy of N2O is also ca. 20% less than that of the O-2-carbon reaction. The new mechanism can also provide a good qualitative comparison for the relative reaction rates of NO-, N2O-, and O-2-carbon reactions. The anisotropic characters of these gas-carbon reactions can also be well explained.

Quantum mechanical simulation of nanosized metal-oxide-semiconductor field-effect transistor using empirical pseudopotentials: A comparison for charge density occupation methods

The atomistic pseudopotential quantum mechanical calculations are used to study the transport in million atom nanosized metal-oxide-semiconductor field-effect transistors. In the charge self-consistent calculation, the quantum mechanical eigenstates of closed systems instead of scattering states of open systems are calculated. The question of how to use these eigenstates to simulate a nonequilibrium system, and how to calculate the electric currents, is addressed. Two methods to occupy the electron eigenstates to yield the charge density in a nonequilibrium condition are tested and compared. One is a partition method and another is a quasi-Fermi level method. Two methods are also used to evaluate the current: one uses the ballistic and tunneling current approximation, another uses the drift-diffusion method. (C) 2009 American Institute of Physics. [doi:10.1063/1.3248262]

Quantum mechanical effects in nanometer field effect transistors

The atomistic pseudopotential quantum mechanical calculations for million atom nanosized metal-oxide-semiconductor field-effect transistors (MOSFETs) are presented. When compared with semiclassical Thomas-Fermi simulation results, there are significant differences in I-V curve, electron threshold voltage, and gate capacitance. In many aspects, the quantum mechanical effects exacerbate the problems encountered during device minimization, and it also presents different mechanisms in controlling the behaviors of a nanometer device than the classical one. (c) 2007 American Institute of Physics.

Accurate quantum mechanical calculation for the N+OH reaction

Accurate three-dimensional time-dependent quantum wave packet calculations for the N+OH reaction on the (3)A' potential energy surface [Guadagnini, Schatz, and Walch, J. Chem. Phys. 102, 774 (1995)] have been carried out. The calculations show for the first time that the initial state-selected reaction probabilities are dominated by resonance structures, and the lifetime of the resonance is generally in the subpicosecond time scale. The calculated reaction cross sections indicate that they are a decreasing function of the translational energy, which is in agreement qualitatively with the quasiclassical trajectory calculations. The rate constants obtained from the quantum mechanical calculations are consistent with the quasiclassical trajectory results and the experimental measurements. (C) 2003 American Institute of Physics.

Modeling the tetraphenylalanine-PEG hybrid amphiphile: from DFT calculations on the peptide to molecular dynamics simulations on the conjugate

The conformational properties of the hybrid amphiphile formed by the conjugation of a hydrophobic peptide with four phenylalanine (Phe) residues and hydrophilic poly(ethylene glycol), have been investigated using quantum mechanical calculations and atomistic molecular dynamics simulations. The intrinsic conformational preferences of the peptide were examined using the building-up search procedure combined with B3LYP/ 6-31G(d) geometry optimizations, which led to the identification of 78, 78, and 92 minimum energy structures for the peptides containing one, two, and four Phe residues. These peptides tend to adopt regular organizations involving turn-like motifs that define ribbon or helicallike arrangements. Furthermore, calculations indicate that backbone ... side chain interactions involving the N-H of the amide groups and the pi clouds of the aromatic rings play a crucial role in Phe-containing peptides. On the other hand,MD simulations on the complete amphiphile in aqueous solution showed that the polymer fragment rapidly unfolds maximizing the contacts with the polar solvent, even though the hydrophobic peptide reduce the number of waters of hydration with respect to an individual polymer chain of equivalent molecular weight. In spite of the small effect of the peptide in the hydrodynamic properties of the polymer, we conclude that the two counterparts of the amphiphile tend to organize as independent modules.

Synthesis, mechanism of formation, and molecular orbital calculations of arylamidoximes

A simple and easy synthesis of ten arylamidoximes from arylnitriles and hydroxylamine is described. The formation of the arylamides has been observed to a much lesser extent in the present work. A new mechanism for the formation of arylamidoximes, as well as arylamides, from arylnitriles and hydroxylamine is suggested. Quantum mechanical calculations have been carried out to support this mechanism. The enthalpy of formation in conjunction with atomic charges of the reactants and intermediates helped to understand more about the generation of the products.

First principles calculations on the origin of violet-blue and green light photoluminescence emission in SrZrO3 and SrTiO3 perovskites

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Ability of the PM3 Quantum Mechanical Method to Model Intermolecular Hydrogen Bonding between Neutral Molecules

The PM3 semiempirical quantum-mechanical method was found to systematically describe intermolecular hydrogen bonding in small polar molecules. PM3 shows charge transfer from the donor to acceptor molecules on the order of 0.02-0.06 units of charge when strong hydrogen bonds are formed. The PM3 method is predictive; calculated hydrogen bond energies with an absolute magnitude greater than 2 kcal mol-' suggest that the global minimum is a hydrogen bonded complex; absolute energies less than 2 kcal mol-' imply that other van der Waals complexes are more stable. The geometries of the PM3 hydrogen bonded complexes agree with high-resolution spectroscopic observations, gas electron diffraction data, and high-level ab initio calculations. The main limitations in the PM3 method are the underestimation of hydrogen bond lengths by 0.1-0.2 for some systems and the underestimation of reliable experimental hydrogen bond energies by approximately 1-2 kcal mol-l. The PM3 method predicts that ammonia is a good hydrogen bond acceptor and a poor hydrogen donor when interacting with neutral molecules. Electronegativity differences between F, N, and 0 predict that donor strength follows the order F > 0 > N and acceptor strength follows the order N > 0 > F. In the calculations presented in this article, the PM3 method mirrors these electronegativity differences, predicting the F-H- - -N bond to be the strongest and the N-H- - -F bond the weakest. It appears that the PM3 Hamiltonian is able to model hydrogen bonding because of the reduction of two-center repulsive forces brought about by the parameterization of the Gaussian core-core interactions. The ability of the PM3 method to model intermolecular hydrogen bonding means reasonably accurate quantum-mechanical calculations can be applied to small biologic systems.

Converged quantum calculations of HO2 bound states and resonances for J=6 and 10

Bound and resonance states of HO2 are calculated quantum mechanically using both the Lanczos homogeneous filter diagonalization method and the real Chebyshev filter diagonalization method for nonzero total angular momentum J=6 and 10, using a parallel computing strategy. For bound states, agreement between the two methods is quite satisfactory; for resonances, while the energies are in good agreement, the widths are in general agreement. The quantum nonzero-J specific unimolecular dissociation rates for HO2 are also calculated. (C) 2004 American Institute of Physics.

Unimolecular Rovibrational Bound and Resonance States for Large Angular Momentum: J=20 Calculations for HO2

We explore the calculation of unimolecular bound states and resonances for deep-well species at large angular momentum using a Chebychev filter diagonalization scheme incorporating doubling of the autocorrelation function as presented recently by Neumaier and Mandelshtam [Phys. Rev. Lett. 86, 5031 (2001)]. The method has been employed to compute the challenging J=20 bound and resonance states for the HO2 system. The methodology has firstly been tested for J=2 in comparison with previous calculations, and then extended to J=20 using a parallel computing strategy. The quantum J-specific unimolecular dissociation rates for HO2-> H+O-2 in the energy range from 2.114 to 2.596 eV have been reported for the first time, and comparisons with the results of Troe and co-workers [J. Chem. Phys. 113, 11019 (2000) Phys. Chem. Chem. Phys. 2, 631 (2000)] from statistical adiabatic channel method/classical trajectory calculations have been made. For most of the energies, the reported statistical adiabatic channel method/classical trajectory rate constants agree well with the average of the fluctuating quantum-mechanical rates. Near the dissociation threshold, quantum rates fluctuate more severely, but their average is still in agreement with the statistical adiabatic channel method/classical trajectory results.

Mechanisms of glycerol dehydration

Dehydration of neutral and protonated glycerol was investigated using quantum mechanical calculations (CBS-QB3). Calculations on neutral glycerol show that there is a high barrier for simple 1,2-dehydration, E-a = 70.9 kcal mol(-1), which is lowered to 65.2 kcal mol(-1) for pericyclic 1,3-dehydration. In contrast, the barriers for dehydration of protonated glycerol are much lower. Dehydration mechanisms involving hydride transfer, pinacol rearrangement, or substitution reactions have barriers between 20 and 25 kcal mol(-1). Loss of water from glycerol via substitution results in either oxirane or oxetane intermediates, which can interconvert over a low barrier. Subsequent decomposition of these intermediates proceeds via either a second dehydration step or loss of formaldehyde. The computed mechanisms for decomposition of protonated glycerol are supported by the gas-phase fragmentation of protonated glycerol observed using a triple-quadrupole mass spectrometer.

A computational study of Compton profiles of water - methanol solutions

The molecular level structure of mixtures of water and alcohols is very complicated and has been under intense research in the recent past. Both experimental and computational methods have been used in the studies. One method for studying the intra- and intermolecular bindings in the mixtures is the use of the so called difference Compton profiles, which are a way to obtain information about changes in the electron wave functions. In the process of Compton scattering a photon scatters inelastically from an electron. The Compton profile that is obtained from the electron wave functions is directly proportional to the probability of photon scattering at a given energy to a given solid angle. In this work we develop a method to compute Compton profiles numerically for mixtures of liquids. In order to obtain the electronic wave functions necessary to calculate the Compton profiles we need some statistical information about atomic coordinates. Acquiring this using ab-initio molecular dynamics is beyond our computational capabilities and therefore we use classical molecular dynamics to model the movement of atoms in the mixture. We discuss the validity of the chosen method in view of the results obtained from the simulations. There are some difficulties in using classical molecular dynamics for the quantum mechanical calculations, but these can possibly be overcome by parameter tuning. According to the calculations clear differences can be seen in the Compton profiles of different mixtures. This prediction needs to be tested in experiments in order to find out whether the approximations made are valid.

Structure, dynamics, and interactions of jacalin. Insights from molecular dynamics simulations examined in conjunction with results of X-ray studies

Molecular dynamics simulations have been carried out on all the jacalin-carbohydrate complexes of known structure, models of unliganded molecules derived from the complexes and also models of relevant complexes where X-ray structures are not available. Results of the simulations and the available crystal structures involving jacalin permit delineation of the relatively rigid and flexible regions of the molecule and the dynamical variability of the hydrogen bonds involved in stabilizing the structure. Local flexibility appears to be related to solvent accessibility. Hydrogen bonds involving side chains and water bridges involving buried water molecules appear to be important in the stabilization of loop structures. The lectin-carbohydrate interactions observed in crystal structures, the average parameters pertaining to them derived from simulations, energetic contribution of the stacking residue estimated from quantum mechanical calculations, and the scatter of the locations of carbohydrate and carbohydrate-binding residues are consistent with the known thermodynamic parameters of jacalin-carbohydrate interactions. The simulations, along with X-ray results, provide a fuller picture of carbohydrate binding by jacalin than provided by crystallographic analysis alone. The simulations confirm that in the unliganded structures water molecules tend to occupy the positions occupied by carbohydrate oxygens in the lectin-carbohydrate complexes. Population distributions in simulations of the free lectin, the ligands, and the complexes indicate a combination of conformational selection and induced fit. Proteins 2009; 77:760-777.

Origin of the Enhanced Photoluminescence from Semiconductor CdSeS Nanocrystals

Internal structures of extraordinarily luminescent semiconductor nanoparticles are probed with photoelectron spectroscopy, establishing a gradient alloy structure as an essential ingredient for the observed phenomenon. Comparative photoluminescence lifetime measurements provide direct evidence for a minimization of nonradiative decay channels because of the removal of interfacial defects due to a progressive change in the lattice parameters in such graded structures, exhibiting a nearly single exponential decay Quantum mechanical, calculations suggest a differential extent of spatial collapse of the electron and the hole wave functions in a way that helps to enhance the photoluminescence efficiency, while at the same time increasing the lifetime of the excited state, as observed in the experiments.