: The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

We provide a simple explanation for X-H bond contraction and the associated blue shift and decrease of intensity in IR spectrum of the so-called improper hydrogen bonds This explanation organizes hydrogen bonds (HBs) with a seemingly random relationship between the X-H bond length (and IR frequency and its intensity) to its interaction energy The factors which affect the X-H bond in all X-H [midline ellipsis] Y HBs can be divided into two parts: (a) The electron affinity of X causes a net gain of electron density at the X-H bond region in the presence of Y and encourages an X-H bond contraction (b) The well understood attractive interaction between the positive H and electron rich Y forces an X-H bond elongation For electron rich, highly polar X-H bonds (proper HB donors) the latter almost always dominates and results in X-H bond elongation, whereas for less polar, electron poor X-H bonds (pro-improper HB donors) the effect of the former is noticeable if Y is not a very strong HB acceptor Although both the above factors increase with increasing HB acceptor ability of Y, the shortening effect dominates over a range of Ys for suitable pro-improper X-Hs resulting in a surprising trend of decreasing X-H bond length with increasing HB acceptor ability The observed frequency and intensity variations follow naturally The possibility of HBs which do not show any IR frequency change in the X-H stretching mode also directly follows from this explanation

Red-, blue-, or no-shift in hydrogen bonds: a unified explanation.

Ordinary differential equations of the first order linear differential equations complex numbers and linear algebra simultaneous linear differential equations numerical methods the descriptive theory of nonlinear differential equations mechanical systems and electric circuits Fourier series Fourier integrals and Fourier transforms the Laplace transformation partial differential equations Bessel functions and Legendre polynomials applications and further properties of matrices vector analysis the calculus of variations analytic functions of a complex variable infinite series in the complex plane the theory of residues conformal mapping.

Advanced Engineering Mathematics. By C. R. Wylie. Pp. xiv, 813. 1966. (McGraw-Hill.)

Pancě Naumov,*,† Stanislav Chizhik,‡,§ Manas K. Panda,† Naba K. Nath,† and Elena Boldyreva*,‡,§ †New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates ‡Institute of Solid State Chemistry and Mechanochemistry, Siberian Branch of Russian Academy of Sciences, ul. Kutateladze, 18, Novosibirsk 630128, Russia Novosibirsk State University, ul. Pirogova, 2, Novosibirsk 630090, Russia

Mechanically Responsive Molecular Crystals

Hydrophobic hydration is considered to have a key role in biological processes ranging from membrane formation to protein folding and ligand binding. Historically, hydrophobic hydration shells were thought to resemble solid clathrate hydrates, with solutes surrounded by polyhedral cages composed of tetrahedrally hydrogen-bonded water molecules. But more recent experimental and theoretical studies have challenged this view and emphasized the importance of the length scales involved. Here we report combined polarized, isotopic and temperature-dependent Raman scattering measurements with multivariate curve resolution (Raman-MCR) that explore hydrophobic hydration by mapping the vibrational spectroscopic features arising from the hydrophobic hydration shells of linear alcohols ranging from methanol to heptanol. Our data, covering the entire 0-100 °C temperature range, show clear evidence that at low temperatures the hydration shells have a hydrophobically enhanced water structure with greater tetrahedral order and fewer weak hydrogen bonds than the surrounding bulk water. This structure disappears with increasing temperature and is then, for hydrophobic chains longer than ~1 nm, replaced by a more disordered structure with weaker hydrogen bonds than bulk water. These observations support our current understanding of hydrophobic hydration, including the thermally induced water structural transformation that is suggestive of the hydrophobic crossover predicted to occur at lengths of ~1 nm (refs 5, 9, 10, 14).

Water structural transformation at molecular hydrophobic interfaces

Vibrational spectra of Cs2CaCl4·2H2O

Transmission of electrons via metal-molecule-metal junctions, involving rotor-stator anthracene aldehyde molecules is investigated. Two model barriers having input parameters evaluated from accurate ab initio calculations are proposed and the transmission coefficients are obtained by using the quasiclassical approximation. Transmission coefficients further enter in the integral for the net current, utilizing Simmons’ method. Conformational dependence of the tunneling processes is evident and the presence of the side groups enhances the functionality of the future single-molecule based electronic devices.

Electron transmission through a class of anthracene aldehyde molecules

Scientific applications perform numerical simulations of different natural phenomena in the filed of computational physics and chemistry, mathematics, informatics, mechanics, bioinformatics, etc. They are primarily developed for the scientific research community and usually they are used for simulating some I/O and data extensive experiments [Segal 2005]. The performance of such simulation experiments requires powerful supercomputers, high performance or Grid computing [Vecchiola et al. 2009]. Formally, a scientific application is a software applications which turns the object into mathematical models by simulating activities from the real world [Ziff Davis Publishing Holdings 1995]. Scientific applications are different from commercial application, especially in the process of testing and evaluation. They are developed for the specific research community and not evaluated by customers. Testing is usually performed by comparing the obtained results with theory or performed physical experiments. Also, scientists can decide for the correctness of the results visually, by comparing images. The absence of software engineering testing practices and documentation is confirmed by the results obtained in the survey we conducted among participants in the High Performance South East Europe

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Scientific Software Testing: A Practical Example.

Derivation of high-quality intermolecular potentials for molecular dynamics (MD) and Monte Carlo (MC) simulations is crucial for efficient modeling of molecular systems. Despite their overall complexity, the interactions potentials have often been derived in a semiempirical manner, though in certain cases, also ab initio techniques have been involved in their construction. In the present study, we aim to construct optimized intermolecular interaction potentials to be used for MD and MC simulations of pure molecular liquids and their mixtures. We have focused on one of the simplest forms of the potentials, namely the Lennard-Jones (LJ) + Coulomb electrostatic terms. Interaction between each pair of atoms in the molecular liquids has thus been characterized by the LJ parameters + atomic charges. The optimization has been performed by genetic algorithms. An in-depth analysis of the performances of both the standard, widely used (i.e. non-optimized), and the optimized interaction potentials was carried out. This analysis was carried out from various aspects related to their performances.

Optimization of intermolecular interaction potential energy parameters for monte-carlo and molecular dynamics simulations

A monocrystal of sucrose, cooled to the boiling temperature of liquid nitrogen and then left at ambient temperature, shows a pyroelectric effect that is very clearly manifested through the growth of ice crystals in the direction of the induced electric field lines of force.

Ljupčo Pejov

Papers

Vibrational spectra of Cs2CaCl4·2H2O

Electron transmission through a class of anthracene aldehyde molecules

Scientific Software Testing: A Practical Example.

Optimization of intermolecular interaction potential energy parameters for monte-carlo and molecular dynamics simulations

Pyroelectric Effect of a Sucrose Monocrystal