Pedro A. M. Vazquez

Cálculo ab initio de intensidades Raman dinâmicas utilizando a teoria da resposta linear

In this paper a methodology for the computation of Raman scattering cross-sections and depolarization ratios within the Placzek Polarizability Theory is described. The polarizability gradients are derived from the values of the dynamic polarizabilities computed at the excitation frequencies using ab initio Linear Response Theory. A sample application of the computational program, at the HF, MP2 and CCSD levels of theory, is presented for H2O and NH3. The results show that high correlated levels of theory are needed to achieve good agreement with experimental data.

Implementação computacional do modelo carga-fluxo de carga-fluxo de dipolo para cálculo e interpretação das intensidades do espectro infravermelho

The first computational implementation that automates the procedures involved in the calculation of infrared intensities using the charge-charge flux-dipole flux model is presented. The atomic charges and dipoles from the Quantum Theory of Atoms in Molecules (QTAIM) model was programmed for Morphy98, Gaussian98 and Gaussian03 programs outputs, but for the ChelpG parameters only the Gaussian programs are supported. Results of illustrative but new calculations for the water, ammonia and methane molecules at the MP2/6-311++G(3d,3p) theoretical level, using the ChelpG and QTAIM/Morphy charges and dipoles are presented. These results showed excellent agreement with analytical results obtained directly at the MP2/6-311++G(3d,3p) level of theory.

QTAIM charge–charge flux–dipole flux models for the fundamental infrared intensities of BF3 and BCl3

Quantum Theory of Atoms in Molecules Charge-Charge Flux-Dipole Flux (QTAIM/CCFDF) models have been determined for the BF3 and BCl3 molecules. Model parameters were obtained from MP2/6-31G(2d,2p) wave functions owing to their accurate estimations of the BF3 intensities and were found to be insensitive to changes in basis sets with polarization functions and to the level of electron correlation treatment, MP2, QCISD and DFT. The BF3 stretching intensity has a very dominant equilibrium charge contribution with small charge and dipole fluxes occurring in the opposite direction to the charge movement. Large equilibrium charge and small dynamic contributions are also characteristic of stretching vibrations in the ionic diatomic molecules, NaF, NaCl, LiF and LiCl. Furthermore the Laplacians of the electron density at the bond critical points of BF3 and these diatomics are all positive indicating electron depletion in their bonding regions relative to large electronic densities concentrated around their nuclei that is characteristic of ionic bonds. The MP2/6-31G(2d,2p) BCl3 stretching intensity can be accurately estimated by equilibrium charge movement since the charge and dipole fluxes almost exactly cancel one another. Both in-plane and out-of-plane BF3 and BCl3 bending deformations are described by equilibrium charge movements that are partially canceled by opposing dipole fluxes that measure the effect on the dipole moment change from electron densities polarized in the opposite direction. Charge fluxes are calculated to be small for the in-plane deformations and are zero by symmetry for the out-of-plane ones.

The Raman Spectrum of the Squarate (C4O4-2 ) Anion: An Ab Initio Basis Set Dependence Study

The Raman excitation profile of the squarate anion, C4O4-2 , was calculated using ab initio methods at the Hartree-Fock using Linear Response Theory (LRT) for six excitation frequencies: 632.5, 514.5, 488.0, 457.9, 363.8 and 337.1 nm. Five basis set functions (6-31G*, 6-31+G*, cc-pVDZ, aug-cc-pVDZ and Sadlejs polarizability basis set) were investigated aiming to evaluate the performance of the 6-31G* set for numerical convergence and computational cost in relation to the larger basis sets. All basis sets reproduce the main spectroscopic features of the Raman spectrum of this anion for the excitation interval investigated. The 6-31G* basis set presented, on average, the same accuracy of numerical results as the larger sets but at a fraction of the computational cost showing that it is suitable for the theoretical investigation of the squarate dianion and its complexes and derivatives.

Fast Scanning Hadamard Spectrophotometer

A simple, low-cost, multiplexed Hadamard-type spectrophotometer based on a spinning disk containing 63 separated masks has been constructed to obtain spectral data in time intervals down to 50 ms. Each mask contains 63 resolution elements. Optical localization and identification of the masks were implemented in the disk to avoid misalignment problems. The control of the spectrophotometer and data acquisition was made by using a dedicated single-board microcomputer based on an 8085 CPU. The single board microcomputer sends the data, through an RS-232C interface, to an IBM-AT compatible microcomputer where the Hadamard transform is performed to recover and display the emission, transmittance, or absorbance spectrum. The instrument has been used in the visible range to obtain absorbance data for time-resolved flow injection analysis applications.

Electronic and Magnetic Properties of the [Ni(salophen)]: an Experimental and DFT Study

Graphical abstract

Core–valence correlation effects on IR calculations: the BF3 and BCl3 cases

The first theoretical results of core–valence correlation effects are presented for the infrared wavenumbers and intensities of the BF3 and BCl3 molecules, using (double– and triple–zeta) Dunning core–valence basis sets at the CCSD(T) level. The results are compared with those calculated in the frozen core approximation with standard Dunning basis sets at the same correlation level and with the experimental values. The general conclusion is that the effect of core–valence correlation is, for infrared wavenumbers and intensities, smaller than the effect of adding augmented diffuse functions to the basis set, e.g., cc–pVTZ to aug–cc–pVTZ. Moreover, the trends observed in the data are mainly related to the augmented functions rather than the core–valence functions added to the basis set. The results obtained here confirm previous studies pointing out the large descrepancy between the theoretical and experimental intensities of the stretching mode for BCl3.

Técnicas de análise do perfil de execução e otimização de programas em química computacional

In this paper we review the basic techniques of performance analysis within the UNIX environment that are relevant in computational chemistry, with particular emphasis on the execution profile using the gprof tool. Two case studies (in ab initio and molecular dynamics calculations) are presented in order to illustrate how execution profiling can be used to effectively identify bottlenecks and to guide source code optimization. Using these profiling and optimization techniques it was possible to obtain significant speedups (of up to 30%) in both cases.n this paper we review the basic techniques of performance analysis within the UNIX environment that are relevant in computational chemistry, with particular emphasis on the execution profile using the gprof tool. Two case studies (in ab initio and molecular dynamics calculations) are presented in order to illustrate how execution profiling can be used to effectively identify bottlenecks and to guide source code optimization. Using these profiling and optimization techniques it was possible to obtain significant speedups (of up to 30%) in both cases.

Técnicas para análise de desempenho de computadores

A series of open source benchmarks for computer performance analysis of personal computers with a focus on computational chemistry calculations is presented. The results returned by these tests are discussed and used to correlate with the actual performance of a set of computers available for research on two computing intensive fields of chemistry, quantum chemical and molecular simulation calculations.

Hydration structures of the squarate dianion C4O42−. A combined molecular dynamics simulation and quantum ab initio study

Abstract Molecular dynamics (MD) simulations are used to determine the structure of the first solvation shell around a single monocyclic oxocarbon dianion C4O42− in aqueous solution. The simulations were carried out using a fixed-geometry model for the oxocarbon with excess partial charges equally distributed over the oxygen atoms and the well-known SPC/E model for water. Quantum ab initio calculations for an isolated oxocarbon at different levels of approximation indicate that the such a description of the squarate dianion should be fairly accurate for the study of solvation structures. Analysis of a complete set of solute–solvent site–site radial distribution functions and hydrogen (H)-bonding distributions obtained from the MD simulations, indicates a well-defined first solvation shell consisting of approximately 18 water molecules. About 12 of these molecules are tightly H-bonded to the oxocarbon (an average of 3 molecules per oxygen atom) forming a highly symmetric solute–solvent complex, while the remaining six water molecules are more loosely distributed above and below the oxocarbon plane. The structure of a cluster consisting of a dianion and 12 water molecules was then examined through ab initio calculations at the Hartree–Fock 6-31G(d,p) level. The optimized ab initio structure of the cluster is in excellent agreement with the MD results.