Fast analytical evaluation of intermolecular electrostatic interaction energies using the pseudoatom representation of the electron density. I. The Löwdin α-function method.

The previously reported [Volkov et al. (2004). Chem. Phys. Lett. 391, 170-175] exact potential and multipole moment (EP/MM) method for evaluation of intermolecular electrostatic interaction energies using the nuclei-centered pseudoatom representation of electron densities is significantly improved in terms of both speed and accuracy by replacing the numerical quadrature integration of the exact potential with a fully analytical technique. The resulting approach, incorporated in the XDPROP module of the software package XD, has been tested on several molecular systems ranging in size from water-water to dodecapeptide-dodecapeptide dimers using electron densities constructed via the University at Buffalo Aspherical Atom Databank. The improved hybrid method provides electrostatic interaction energies within the uncertainty of ≤0.2 kJ mol-1 for all benchmark systems. The running time for a dimer of a sizable, 225-atom dodecapeptide is under 4 s on a 2012 central processing unit (2.8 GHz AMD Opteron 6348) and under 3 s on a relatively modern processor (2.8 GHz Intel Xeon E3-1505M v5).

Investigation of the free volume changes in one day hydrogel and one day silicone-hydrogel contact lenses by means of positron annihilation lifetime spectroscopy.

UNLABELLED: PURPOSE OF JOB: The evolution of materials used to manufacture contact lenses, there is a need to increase comfort and visual acuity man while improving biocompatibility and minimizing the impact of the material on the physiology of the cornea. There is still a problem with limiting the level of oxygen available to the cornea, resulting in various diseases. Therefore, the aim of this work is to investigate the physical and structural properties of hydrogel and silicone-hydrogel contact lenses. MATERIALS AND METHODS: To achieve the main objective, the project involves the complete, systematic and comprehensive research methodology, techniques of positron lifetime spectroscopy PAL associated with polymerization, nanovoid natural structure of modern polymeric materials used in ophthalmology. This method is particularly sensitive to detect the structure of disordered materials with structural defects. Therefore it is reasonable to use PAL spectroscopy in studies of polymer nanostructures change contact lenses used in ophthalmology. RESULTS: As a result of the measurements obtained curve describing the dependence of the number of counts of acts of annihilation as a function of time. Distribution of positron lifetime spectra into three components, allows to extract the longest third component which gives information about the geometrical parameters of free volume. Clear changes were observed long-living component lifetimes of ortho-positronium and their intensities between the lenses tested. CONCLUSIONS: The measurements allowed us to isolate and calculate the value of long-living tau3 and its intensity I3, which values are component of positron lifetime associated with the formation of ortho-positronium (o-Ps) and is a measure of the density distribution of free volume creation. The results of these measurements indicate that the formation of free volume holes takes place both in the hydrogel lens and silicone-hydrogel. However, the size of free volume and the amount of free volume occurring for silicone-hydrogel lenses are greater than for hydrogel lenses. The study nanovoid structure of polymeric materials, their size and number suggest a relationship with the oxygen permeability of contact lenses, which implies a continuation and extension of the initial research.

Unified treatment of coherent and incoherent electronic energy transfer dynamics using classical electrodynamics.

Recent experiments on resonance energy transfer (RET) in photosynthetic systems have found evidence of quantum coherence between the donor and the acceptor. Under these conditions, Förster's theory of RET is no longer applicable and no theory of coherent RET advanced to date rivals the intuitive simplicity of Förster's theory. Here, we develop a framework for understanding RET that is based on classical electrodynamics but still captures the essence of the quantum coherence between the molecules. Our theory requires only a knowledge of the complex polarizabilities of the two molecules participating in the transfer as well as the distance between them. We compare our results to quantum mechanical calculations and show that the results agree quantitatively.

Excited states and electronic spectra of extended tetraazaporphyrins.

Electronic excited states, electronic absorption, and magnetic circular dichroism (MCD) spectra of free-base tetraazaporphyrin (TAP), phthalocyanine (Pc), naphthalocyanine (Nc), and anthracocyanine (Ac) were studied by quantum chemical calculations using the symmetry-adapted cluster-configuration interaction (SAC-CI) method. Not only optically allowed states including the Q- and B-bands but also optically forbidden states were calculated for transitions whose excitation energies were lower than 4.5 eV. The present SAC-CI calculations consistently assigned the absorption and MCD peaks as optically allowed π→π(∗) excitations, although these calculations using double-zeta basis limit quantitative agreement and discussion. For Nc and Ac, excited states beyond the four-orbital model appeared in the low-energy region. The low-energy shifts of the Q-bands with the extension of molecular size were explained by the orbital energies. The splitting of the Q-bands decreases with extension of the molecular size. This feature was reproduced by the SAC-CI calculations but the configuration interaction with single excitations and time-dependent density functional theory calculations failed to reproduce this trend. Electron correlation in the excited states is important in reproducing this splitting of the Q-bands and in describing the energy difference between the B(2u) and B(3u) states of free-base porphyrins.

A simple formula to calculate the ionization energies of two-, three-, and four-electron atomic ions.

We have previously proposed a simple equation that is able to reproduce literature values (Moore 1970) for the ionization energies of one-electron (Lang and Smith 1981) and two-electron (Sabir Ali et al. 1984) atomic ions with very good agreement. However, our proposed equation has no firm theoretical basis, only that we consider our potential energy approach a logical alternative to the usual kinetic relativistic/quantum mechanical methodology. The results calculated from the equation give excellent agreement with literature values and differ by less than 1 eV and less than 0.02% in all cases from hydrogen up to atomic number 20. This paper provides an updated version of the two-electron equation adapted to calculate the ionization energies of three and four electron ions. Our equation also gives fairly good estimates of first electron affinities. Comparisons are made with another published equation, sources of data are described, and the calculated results are discussed.

Dynamics of electron transfer reactions in the presence of mode mixing: comparison of a generalized master equation approach with the numerically exact simulation.

A generalized master equation approach is developed to describe electron transfer (ET) dynamics in the presence of mode mixing. Results from this approximate approach are compared to the numerically exact simulations using the multilayer multiconfiguration time-dependent Hartree theory. The generalized master equation approach is found to work well for nonadiabatic resonant ET. Depending on the specific situation, it is found that the introduction of mode mixing may either increase or decrease the ET time scale. The master equation fails in the adiabatic ET regime, where the introduction of mode mixing may lead to electron trapping. From both the approximate theory and the numerically exact simulation it is shown how neglecting mode mixing in practical calculations may lead to inaccurate predictions of the ET dynamics.

Reducing radiation damage in macromolecular crystals at synchrotron sources.

A new strategy is presented to reduce primary X-ray damage in macromolecular crystallography. The strategy is based on separating the diffracting and damaged regions as much as feasible. The source of the radiation damage to macromolecular crystals is from two primary mechanisms: the direct excitations of electrons by absorption, and inelastic scattering of the X-rays. The first produces photoelectrons with their accompanying Auger electrons from relaxation of the core hole and the second creates Compton electrons. The properties of these two mechanisms and calculations of primary X-ray damage quantify how to modify the spatial distribution of X-rays to reduce the deleterious effects of radiation damage. By focusing the incident X-rays into vertical stripes, it is estimated that the survival (the time during which quality diffraction data can be obtained with a given X-ray flux) of large crystals can be increased by at least a factor of 1.6, while for very small platelet crystals the survival can be increased by up to a factor of 14.