Biomedical subjects

Josep M Luis

Publications and source records attributed to Josep M Luis.

13 recordsLinked to original sources

PubMed2006

Linear response functions for a vibrational configuration interaction state.

Linear response functions are implemented for a vibrational configuration interaction state allowing accurate analytical calculations of pure vibrational contributions to dynamical polarizabilities. Sample calculations are presented for the pure vibrational contributions to the polarizabilities of water and formaldehyde. We discuss the convergence of the results with respect to various details of the vibrational wave function description as well as the potential and property surfaces. We also analyze the frequency dependence of the linear response function and the effect of accounting phenomenologically for the finite lifetime of the excited vibrational states. Finally, we compare the analytical response approach to a sum-over-states approach.

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PubMed2006

Redox-controlled molecular flipper based on a chiral Cu complex.

A molecular bipaddled flipper based on a tetradentate chiral Cu complex has been designed. The paddling motion of this unprecedented molecular-scale machine can be controlled by reversible oxidation of the metal center. Kinetic and computational (density functional theory) analyses provide a detailed picture of the flipper motion at the molecular scale, rationalize the switching role of the metal-ion oxidation state, and pose the basis for the fine-tuning of the dynamic motion of this new class of molecular-scale devices.

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PubMed2006

A variational approach for calculating Franck-Condon factors including mode-mode anharmonic coupling.

We have implemented our new procedure for computing Franck-Condon factors utilizing vibrational configuration interaction based on a vibrational self-consistent field reference. Both Duschinsky rotations and anharmonic three-mode coupling are taken into account. Simulations of the first ionization band of ClO(2) and C(4)H(4)O (furan) using up to quadruple excitations in treating anharmonicity are reported and analyzed. A developer version of the MIDASCPP code was employed to obtain the required anharmonic vibrational integrals and transition frequencies.

Journal Article↗

PubMed2006

Analysis of electron delocalization in aromatic systems: individual molecular orbital contributions to para-delocalization indexes (PDI).

Our research group has recently defined two new aromaticity indexes based on the analysis of electron delocalization in aromatic species using the quantum theory of atoms-in-molecules. One of these indexes is the para-delocalization index (PDI) that measures the electronic delocalization between para-related carbon atoms in six-membered rings. In this paper, we show that this index can be partitioned into individual molecular orbital contributions. We have applied this PDI decomposition to several polycyclic aromatic hydrocarbons showing that this partitioning provides new insight into the origin of aromaticity.

Journal Article↗

PubMed2006

Simulation of photoelectron spectra with anharmonicity fully included: Application to the X 2A2<--X 1A1 band of furan.

Using a new unconventional procedure for calculating Franck-Condon factors with anharmonicity fully included the X 2A2<--X 1A1 band in the photoelectron spectrum of furan (and deuterated furan) was simulated at the second-order perturbation theory level. All 21 vibrational modes were considered but, in the end, only 4 are required to accurately reproduce the spectrum. Except for our own recent work on ethylene such calculations have been previously limited to tri- or tetraatomic molecules. Most of the effect of anharmonicity is accounted for in first order, although second-order corrections to the vibrational frequencies are important. Based on these simulations we were able to improve upon and extend previous assignments as well as suggest further measurements.

Journal Article↗

PubMed2005

Aromaticity analysis of lithium cation/pi complexes of aromatic systems.

The changes in the local aromaticity of aromatic rings on complexation with lithium cation are discussed for a series of polycyclic aromatic hydrocarbons by using, as probes of aromaticity, the para-delocalization index (PDI), the aromatic fluctuation index (FLU), the harmonic oscillator model of aromaticity index (HOMA), and the nucleus-independent chemical shift (NICS). In most cases, changes in the electronically based PDI and FLU indices are almost irrelevant. For this reason, the analysis is carried out mainly with the more sensitive HOMA and NICS descriptors. These indices indicate that changes in the local aromatic character of the different rings are small. In general, Li+ interacts more favorably with the ring having the largest pi charge, but there is no correlation between these magnitudes. The ring directly interacting with the lithium cation suffers a slight but significant reduction of aromaticity, while the reduction of the local aromaticity of the adjacent rings is minor. For those rings located further away from the ring directly connected to Li+, we found generally a small increase in aromaticity. Although there is no clear correlation between aromaticity and Li+ binding enthalpies, there is a rough correlation between the latter and the change in the aromaticity of the ring directly interacting with the metal cation.

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PubMed2005

The breakdown of the minimum polarizability principle in vibrational motions as an indicator of the most aromatic center.

The vibrational motions that disobey the minimum polarizability principle (MPP) in pi-conjugated molecules are distortions of the equilibrium geometry that produce a reduction in the polarizability due to the localization of pi electrons. For aromatic species, this electronic localization is responsible for the subsequent reduction in the aromaticity of the system. In the present work, we diagonalize the Hessian matrix of the polarizability with respect to the vibrational nontotally symmetric normal coordinates, to calculate the nontotally symmetric distortions that produce the maximum breakdown of the MPP in a series of twenty polycyclic aromatic hydrocarbons. It is shown that the nuclear displacements that break the MPP have larger components in those rings that possess the highest local aromaticity. Thus, these vibrational motions can be used as an indicator of local aromaticity.

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PubMed2005

Variational calculation of vibrational linear and nonlinear optical properties.

A variational approach for reliably calculating vibrational linear and nonlinear optical properties of molecules with large electrical and/or mechanical anharmonicity is introduced. This approach utilizes a self-consistent solution of the vibrational Schrodinger equation for the complete field-dependent potential-energy surface and, then, adds higher-level vibrational correlation corrections as desired. An initial application is made to static properties for three molecules of widely varying anharmonicity using the lowest-level vibrational correlation treatment (i.e., vibrational Møller-Plesset perturbation theory). Our results indicate when the conventional Bishop-Kirtman perturbation method can be expected to break down and when high-level vibrational correlation methods are likely to be required. Future improvements and extensions are discussed.

Algorithms↗

PubMed2005

Calculation of Franck-Condon factors including anharmonicity: simulation of the C2H4+X2B3u<--C2H4X1A(g) band in the photoelectron spectrum of ethylene.

Our new simple method for calculating accurate Franck-Condon factors including nondiagonal (i.e., mode-mode) anharmonic coupling is used to simulate the C2H4+X2B3u<--C2H4X1A(g) band in the photoelectron spectrum. An improved vibrational basis set truncation algorithm, which permits very efficient computations, is employed. Because the torsional mode is highly anharmonic it is separated from the other modes and treated exactly. All other modes are treated through the second-order perturbation theory. The perturbation-theory corrections are significant and lead to a good agreement with experiment, although the separability assumption for torsion causes the C2D4 results to be not as good as those for C2H4. A variational formulation to overcome this circumstance, and deal with large anharmonicities in general, is suggested.

Journal Article↗

PubMed2005

Generalizing the breakdown of the maximum hardness and minimum polarizabilities principles for nontotally symmetric vibrations to non-pi-conjugated organic molecules.

In previous works we have shown that certain pi-conjugated organic molecules possess nontotally symmetric vibrations that break the maximum hardness (MHP) and minimum polarizability principles (MPP). We have also derived a set of simple rules to determine a priori without calculations whether a particular pi-conjugated organic molecule violates these two principles. In the present work, we generalize these results, and we show that not only pi-conjugated organic molecules but also other molecules without pi-conjugated structure or even pi-bonds can exhibit nontotally symmetric molecular distortions that do not follow these two principles. We have also found that the breakdowns of the MHP and the MPP are not necessarily connected, since the polarizability is not always proportional to the softness. Finally, we also introduced a methodology based on the diagonalization of the hardness Hessian matrix with respect to the vibrational normal coordinates to determine the nontotally symmetric molecular displacements that do not follow the MHP.

Aluminum↗

PubMed2004

The hardness profile as a tool to detect spurious stationary points in the potential energy surface.

In the present work, we have computed the energy and hardness profiles for a series of inter and intramolecular conformational changes at several levels of calculation. All processes studied have in common the fact that the choice of a weak methodology or a poor basis set results in the presence of spurious stationary points in the energy profile. At variance with the energy profiles, the hardness profiles calculated as the difference between the vertical ionization potential and electron affinity always show the correct number of stationary points independently of the basis set and methodology used. For this reason, we have concluded that hardness profiles can be used to check the reliability of the energy profiles for those chemical systems that, because of their size, cannot be treated with high level ab initio methods.

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PubMed2004

Basis set and electron correlation effects on initial convergence for vibrational nonlinear optical properties of conjugated organic molecules.

Using three typical pi-conjugated molecules (1,3,5-hexatriene, 1-formyl-6-hydroxyhexa-1,3,5- triene, and 1,1-diamino-6,6-dinitrohexa-1,3,5-triene) we investigate the level of ab initio theory necessary to produce reliable values for linear and nonlinear optical properties, with emphasis on the vibrational contributions that are known to be important or potentially important. These calculations are made feasible by employing field-induced coordinates in combination with a finite field procedure. For many, but not all, purposes the MP2/6-31+G(d) level is adequate. Based on our results the convergence of the usual perturbation treatment for vibrational anharmonicity was examined. Although this treatment is initially convergent in most circumstances, a problematic situation has been identified.

Electrons↗

PubMed2004

A different approach for calculating Franck-Condon factors including anharmonicity.

An efficient new procedure for calculating Franck-Condon factors, based on the direct solution of an appropriate set of simultaneous equations, is presented. Both Duschinsky rotations and anharmonicity are included, the latter by means of second-order perturbation theory. The critical truncation of basis set is accomplished by a build-up procedure that simultaneously removes negligible vibrational states. A successful test is carried out on ClO2 for which there are experimental data and other theoretical calculations.

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