Chemical Physics Letters (v.467, #4-6)

Contents (iii-xiv).

Simple Hofmeister series by Johannes Lyklema (217-222).
Hofmeister effect for alkali ions on AgI.Hofmeister, or lyotropic, series date back to 1888, when the founder arranged a large number of electrolytes in sequences with respect to their effectiveness salting out egg white. Since then the name has been applied to various phenomena involving ion specificity. In order to isolate effects attributable to single ionic species an interpretational step has to be taken, because only effects of electroneutral combinations of ions can be measured. The resulting sequence depends on the particular phenomenon studied. As a result, a variety of observations have been reported without a clear organizing principle. Here we describe Hofmeister sequences for well-defined systems which allow clear definition and unambiguous interpretation. Hofmeister sequences are not unique, they depend on the system and are the result of pair interactions.

Electronic structure of Bi 3 Ga y ( - ) semiconductor clusters and the special stability of Bi 3 Ga 2 - – A gas phase Zintl analogue by Ujjwal Gupta; J. Ulises Reveles; Joshua J. Melko; Shiv N. Khanna; A.W. Castleman (223-229).
It is shown that Bi3Ga, Bi 3 Ga 2 - , Bi3Ga3, Bi 3 Ga 4 - and Bi3Ga5 all are stable species with a HOMO–LUMO gap varying from 1.12 to 1.89 eV.Here we present evidence that the gap between the highest occupied and lowest unoccupied molecular orbitals (HOMO–LUMO gap) can be tuned (1.12–1.89 eV) by changing the Ga composition of Bi3Gay anionic and neutral clusters, some of which display special stability. Collaboratively, mass spectrometry, photoelectron spectroscopy and computational results show that Bi 3 Ga 2 - is a very stable cluster with a large calculated HOMO–LUMO gap of 1.89 eV, and can be viewed as a gas phase Zintl analogue of Sn 5 2 - , already synthesized in the solution phase. The stability of Bi 3 Ga 2 - is further attributed to the fact that it has 12 valence electrons and possesses a closo structure in agreement with Wade’s rules.

High-level ab-initio methods allows to calculate the NMR chemical shifts and secondary isotope shifts of methanol with near quantitative accuracy.In this contribution high-level ab-initio calculations of the chemical shifts of methanol including zero-point vibrational and temperature corrections are presented. For the first time, secondary isotope effects have been calculated via second order vibrational perturbation theory. In comparison with recent experimental gas-phase data and in contrast to other quantum-chemical methods the results are consistent and in very good agreement with the experimental 13C, 17O and 1H chemical shifts reported by Makulski [W. Makulski, J. Mol. Struct. 872 (2008) 81]. Secondary isotope effects can be calculated with remarkable accuracy of a few hundredths of a ppm in comparison to experiment.

Cavity ring-down spectroscopy of singlet oxygen generated in microwave plasma by T. Földes; P. Čermák; M. Macko; P. Veis; P. Macko (233-236).
The Letter reports the observation of new absorption lines of the reactive specie singlet O2 generated in microwave discharge.The absorption spectrum of the (1–0) band of the b 1 Σ g + ← a 1 Δ g Noxon system near 1505 nm has been recorded by cw-CRDS in afterglow of a microwave discharge. The details of this method are presented along with spectroscopic data of 29 recorded lines of which 21 have been observed for the first time. The measured line positions are compared with positions calculated from rotational constants available in the literature. The density and the temperature of the generated singlet molecular oxygen O 2 ( a 1 Δ g ) are presented.

Ab initio interaction potential of methane and nitrogen by Muhammad Shadman; Saeed Yeganegi; Farhood Ziaie (237-242).
A new global potential for the CH4–N2 derived at the MP2 level of theory.A new global interaction potential for the CH4 and N2 complex has been derived at the MP2 level of theory and correlation consistent basis sets. The potential energy surface has been computed on a large grid of molecular geometries. In the most stable conformation, the nitrogen is below the methane pyramid base while the N–N bond axes and one of the methane C–H bonds are coplanar. The complete basis set limit of the interaction energies have been fitted to well-known analytical functions. Then the second virial coefficients were calculated for fitted potentials which agrees well with the experimental values.

Theoretical study of the dynamics of H + alkane reactions by Joshua P. Layfield; Diego Troya (243-248).
Sample calculated dynamics properties in the H + C3H8  → H2  +  i-C3H7 reaction.We have investigated the dynamics of the H + RH → H2  + R (R = CH3, C2H5, C3H7) reactions via direct quasiclassical trajectories propagated with a recently derived semiempirical Hamiltonian specific to H + alkane systems. Cross-sections, opacity functions, angular distributions, and energy partitioning in products are examined with a focus on understanding the role that the structure of the reagent alkane molecule plays in the reaction dynamics. In general, there are only subtle differences in the dynamics of the various reactions, except for the amount of energy channeled to the alkyl product, which increases with the size of the molecule.

Theoretical study of cocaine and ecgonine methyl ester in gas phase and in aqueous solution by David A. Rincón; M. Natália D.S. Cordeiro; Ricardo A. Mosquera; Fernanda Borges (249-254).
The conformational preferences of cocaine and ecgonine methyl ester explain why ecgonine methyl ester is the principal metabolite of cocaine.The conformational preferences of cocaine and ecgonine methyl ester were determined through ab initio and density functional theory calculations. They share the same preferred orientation of the acetate group with a hydrogen bond between the amine and carbonyl groups, and s-cis conformation for the methoxyl group. The benzoyloxy group of cocaine defines a specific accessible conformational region. In solution the most stable conformers are stabilized by internal hydrogen bonds in contrast to the lesser stables, which are stabilized by solute/solvent interactions. Overall, these conformational features explain why ecgonine methyl ester is the principal metabolite of cocaine in a human environment.

IR–UV double resonance spectra of pyrazine dimers: Competition between CH ⋯ π , π ⋯ π and CH ⋯ N interactions by Matthias Busker; Yuriy N. Svartsov; Thomas Häber; Karl Kleinermanns (255-259).
Pyrazine forms planar CH⋯N bonded and cross-displaced, stacked dimers in supersonic jets.We present size- and isomer-selective IR–UV double resonance spectra of two pyrazine dimer isomers. The most stable isomer has a planar structure, stabilized by two CH ⋯ N contacts. The other isomer has a stacked, cross-displaced structure. Our assignment is supported by B3LYP-D calculations. RI-MP2 calculations tend to overestimate the stability of the stacked and T-shaped isomers.

Evidence for a non-Rydberg molecular doubly excited state of Ca2 by M.-A. Gaveau; J.-M. Mestdagh; T. Bouissou; G. Durand; M.-C. Heitz; F. Spiegelman (260-264).
Experimental and theoretical evidence of a non-Rydberg molecular doubly excited state of Ca2.We report experimental and theoretical evidence of a non-Rydberg molecular doubly excited state of Ca2 involving excited molecular orbitals mixing 4p and 3d characters. The excitation spectrum of Ca2, carried by helium or argon clusters, is recorded experimentally in the range 25 600–27 800 cm−1, displaying a bimodal structure. The latter is interpreted from ab initio calculation and analysis of the adiabatic states of Ca2 up to doubly excited asymptotes Ca(4p3d1D) + Ca(4s2 1S) and Ca(4s3d3D) + Ca(4s4p3P), and the relevant dipole transition moments. The bimodal structure is assigned as resulting from the avoided crossing between adiabatic states 31Πu and 41Πu, reflecting the mixing of doubly excited configurations and absorbing singly excited configurations.

Theoretical characters of the ground states of YbX (X = F, Cl, Br, I, At) by Tao Su; Chuan-Lu Yang; Xin-Qiang Wang; Feng-Juan Bai; Mei-Shan Wang (265-269).
The spectroscopic constants of the ground states of YbX (X = F, Cl, Br, I, At) molecules are determined with potential energy curves based on ab initio calculations.The potential energy curves (PECs) of the ground states of YbX (X = F, Cl, Br, I, At) are investigated using the unrestricted coupled cluster singles and doubles method with perturbative treatment of triple excitations. The relativistic effective core potentials basis sets and full electron Huzinaga’s well tempered basis sets for Yb are used. The present spectroscopic constants calculated based on the PECs are in good agreement with the experimental data available at present. Isotopic effects on spectroscopic constants are also examined.

Quantum sieving in organic frameworks by Giovanni Garberoglio (270-275).
Isotope separation factors are calculated for T2/H2 and D2/H2 mixtures in various organic frameworks using path integral Monte Carlo simulations. The results are in good agreement with recent experimental data and are used to clarify the mechanisms responsible for the isotopic selectivity in these materials.The isotopic separation factors for T2/H2 and D2/H2 mixtures adsorbed in various organic frameworks have been calculated using path integral Monte Carlo simulations. The results are in fair agreement with the available experimental data, and show a very strong dependence on temperature.The selectivity shows a less pronounced dependence on the external pressure, but different behaviours are found for different materials. They are analyzed from the point of view of the solid–fluid potential energy surface.

Quantitative prediction of vibrational spectra of free radicals by means of hybrid models (harmonic CCSD(T) frequencies coupled to anharmonic DFT contributions).The accuracy of anharmonic frequencies for semirigid free radicals obtained by a second order perturbative treatment based on CCSD(T) force fields is investigated for the prototypical H2CN and F2CN radicals. B3LYP computations show that most of the DFT errors are related to the harmonic part of the force field, so that hybrid models in which harmonic frequencies computed by coupled-cluster methods are coupled to anharmonic contributions obtained by proper density functionals perform very well. This finding paves the route toward the computation of accurate vibrational frequencies for quite large unstable open-shell species of current biological and/or technological interest.

The ejection anisotropy of Coulomb explosion fragments released from alkyl halide molecules (C2H5X, 1-C3H7X and 1-C4H9X, where X = Br, Cl) under strong 35 ps laser irradiation is studied by means of time-of-flight mass spectrometry. The ejection anisotropy of the alkylhalide fragments under ps laser irradiation depends on the size of the molecular chain.The ejection anisotropy of Coulomb explosion fragments released from alkyl halide molecules (C2H5X, 1-C3H7X and 1-C4H9X, where X = Br, Cl) under strong 35 ps laser irradiation is studied by means of time-of-flight mass spectrometry. By comparing the angular distributions widths of the halogen fragment ions originating from multiply charged molecular ions it is concluded that the ejection anisotropy presents a weak dependence on the mass of the halogen atom, observed especially in the case of ethyl halide molecules, while a stronger dependence is found on the size of the alkyl chain.

Density functional study of aqueous uranyl(VI) fluoride complexes by Michael Bühl; Nicolas Sieffert; Georges Wipff (287-293).
An approach based on Car–Parrinello molecular dynamics simulations can reproduce the free binding energy between aqueous uranyl hydrate and fluoride ion very well, in contrast to static continuum models. It is predicted that the pristine tetrafluoride should not bind an additional water ligand in aqueous solution, suggesting significant population of four-coordinate [UO2F4]2− under experimental (EXAFS) conditions.Mixed uranyl aquo fluoro complexes [UO2(H2O) x F y ]2− y (y  = 1–4; x  +  y  = 4, 5) have been optimized with BLYP and B3LYP density functionals in vacuo and in a polarizable continuum modeling bulk water, and have been studied at the BLYP level with Car–Parrinello molecular dynamics (MD) simulations. Using constrained MD simulations and thermodynamic integration, the computed free binding energy between aqueous uranyl and fluoride, affording [UO2(H2O)4F]+, is in excellent agreement with experiment. With the same technique, five-coordinate [UO2F4(H2O)]2− is indicated to be unstable against loss of the water ligand, as the free energy for dissociation is computed to be ca. −7 kcal/mol in aqueous solution.

Local MP2 periodic study of rare-gas crystals by Migen Halo; Silvia Casassa; Lorenzo Maschio; Cesare Pisani (294-298).
The Crystal and Cryscor codes (which solve the HF + MP2 equations for periodic systems) have been applied to fcc rare-gas crystals Ne through Xe, the figure reports the cohesive energy versus lattice parameter, both scaled with respect to the experimental value, obtained with the best basis set. Open and filled symbols refer to two techniques for correcting MP2 energies for BSSE.The Cryscor code, a computational tool which solves the second-order Møller–Plesset local equations for periodic systems, is applied to fcc rare-gas crystals Ne through Xe. Cohesive energies, equilibrium lattice parameters and bulk moduli are calculated; DFT calculations have been performed for purposes of comparison.

Stability of growth rate of sodium chlorate by M.M. Mitrović; A.A. Žekić; Z.Z. Baroš (299-303).
The time dependence of the growth rate.The constancy of stabilized sodium chlorate crystal growth rate is investigated. After the growth rate stabilization, solution supersaturation was altered and then the initial one was restored, which resulted in fast restoring of the growth rate existing prior to the supersaturation change. It is thereby shown that stabilized growth rate is indeed very stable. The majority of crystals decrease the growth rates during the 3–4 growth hours, even if the process develops at the constant experimental conditions all the time. The new crystals introduced into the cell, continue to grow as the already growing crystals, with higher initial growth rates.

Numerical illustration of finite pulse duration effects on third-order nonlinear spectroscopies, 3PEPS and S3PE.Effects of finite pulse duration on two different observables of the three pulse photon echo experiment, the peak shift (3PEPS) and short-time slope (S3PE), are studied by a numerical simulation. The usefulness of S3PE method originally suggested in an impulsive limit turned out to be greatly reduced by finite duration of laser pulses. Some aspects of two experimental scanning methods in the three pulse photon echo experiments are discussed.

Terahertz optical properties of the high explosive β -HMX by J. Hooper; E. Mitchell; C. Konek; J. Wilkinson (309-312).
The terahertz optical properties of the explosive β -HMX are studied by density functional perturbation theory and experimental time-domain spectroscopy.We have calculated the full dielectric function in the far-infrared for the high explosive β -HMX using density functional perturbation theory. Complementary time-domain terahertz spectroscopy measurements were performed on military-grade samples of HMX. The calculated absorption coefficient in the range 0.1–3.6 THz is in excellent quantitative agreement with our experimentally determined absorption coefficient in terms of both peak positions and magnitude. Our calculated refractive index below 1 THz is 1.68, very close to our measured value of 1.71. This computational method appears well suited for first-principles calculation of the terahertz optical properties of molecular crystals.

The oxygen contents in SrTiO3 thin films were deduced from lattice parameters and X-ray photoemission spectroscopy results.SrTiO3−x thin films with various oxygen vacancies were fabricated by laser molecular beam epitaxy. The out-of-plane and in-plane lattice constants of the films increase with increasing oxygen vacancies, which was attributed to the increase of Ti3+ ions in the films. Ti3+ ions are formed only in the film inner which is revealed from X-ray photoemission spectroscopy (XPS). With varying the oxygen content, a metal-to-semiconductor transition was observed. The oxygen contents in the films, determined from lattice parameters and XPS are very consistent with each other, which shows quasi-quantitative methods to measure oxygen content in thin films.

The phase coexistence curve (liquid branch), Zeno-line and critical parameters for Cu. The symbols are experimental data on the binodal. Lines are the results of present calculations.We make some predictions with respect to the critical parameters of Al, Cu and W (critical parameters of which lie in the phase domain still inaccessible for experiment) on the basis of the correspondence between the critical point and unit compressibility line (Zeno line) positions in the temperature–density plane using two new similarity relations. These ones rely on the fact that the Zeno line must be tangential to the extension of the liquid branch of the binodal at zero temperatures and correctly describe its low-temperature part. We show also that the compressibility factor at the critical point can not exceed 0.32 for the Lennard-Jones like systems.

The local-field correction factor based on the real-cavity model well accommodates the observed changes of the 4 f ↔ 4 f oscillator strengths of Dy3+ embedded in chalcogenide glasses.The Lorentz-type local-field correction factor based on the virtual-cavity model has been widely applied to describing absorption and emission of photons owing to the intra-4f-configurational transitions of rare earth ions embedded in chalcogenide glasses. From a comparison between the oscillator strengths of Dy3+ ions embedded in Ge–As–S and Ge–Ga–S glasses, however, we verify that the real-cavity model accommodates the observed changes of the oscillator strengths much better than the virtual-cavity model. In addition, effects of chemical environments on the oscillator strengths are discussed in connection with local structural information obtained from Dy L 3-edge extended X-ray absorption fine structure spectroscopic analysis.

High-aspect-ratio gold nanorods synthesized in a surfactant gel phase by Yoshiko Takenaka; Hiroyuki Kitahata (327-330).
High-aspect-ratio gold nanorods, with aspect-ratio of about 50, were synthesized in a gelled solution.One-dimensional gold nanorods can grow spontaneously in a surfactant solution. In this study, a mixture of hexadecyltrimethylammonium bromide (HTAB) and octadecyltrimethylammonium bromide (OTAB) was used as a surfactant solution. When the solution gelled, high-aspect-ratio gold nanorods, with an average long-axis length of ∼1100 nm and an aspect-ratio of ∼50, were synthesized with a yield of ∼90%, whereas no high-aspect-ratio gold nanorods were synthesized when the solution did not gel. This phenomenon indicates that there is a close relation between the gelation of a surfactant solution and the elongation of gold nanorods.

Growth kinetics of silicon nanowires by platinum assisted vapour–liquid–solid mechanism by H. Jeong; T.E. Park; H.K. Seong; M. Kim; U. Kim; H.J. Choi (331-334).
Growth rate of Si nanowires with temperature. Growth with Pt catalyst shows the smaller activation energy than that of Au catalyst.The growth kinetics of Si nanowires produced by a vapour–liquid–solid (VLS) mechanism in conjunction with Pt and Au catalysts, respectively, was investigated and compared. Pt was employed as a VLS catalyst for single-crystal Si nanowires in a SiCl4-based chemical vapour deposition process. The growth rates were higher with Pt than with Au under all processing conditions. The activation energy was measured as 80 and 130 kJ/mol with the Pt and Au catalysts, respectively. The present results suggest that the rate-determining step is the incorporation of Si atoms in the lattice at the liquid/solid interfaces and, furthermore, the metal catalysts affect this step, resulting in different activation energy.

Hyper-Rayleigh scattering from BaTiO3 and PbTiO3 nanocrystals by Ernesto V. Rodriguez; Cid B. de Araújo; Antonio M. Brito-Silva; V.I. Ivanenko; A.A. Lipovskii (335-338).
The hyper-Rayleigh scattering technique is used to determine the first-order hyperpolarizability of BaTiO3 and PbTiO3 nanoparticles.The hyper-Rayleigh scattering technique was applied to measure the first-order hyperpolarizability, β, of ferroelectric BaTiO3 and PbTiO3 nanoparticles (NPs) dissolved in methanol. The crystalline particles have average diameter of ≈50 nm as determined by scanning electron microscopy. A 8 ns pulsed laser operating at 1064 nm was used as the excitation source to generate the second harmonic scattered light. The results show that the per nanoparticle β value is 10−24  esu and the β value per unit volume of NPs is two orders of magnitude larger than that observed for antiferroelectric NaNbO3 nanoparticles.

After adding one OH group on the fullerene cage the highest spin density is localized at the first neighbor carbon site within a pentagon ring vertex.Work presented here applies density functional theory to investigate the chemical shifts and hyperfine coupling constants in fullerenols. The magnetic effects of adding one hydroxyl group on the carbon cage of C60 are carefully examined on this base. Calculations make evident that unpaired spins are highly localized on the fullerene surface. Also, the addition of three hydroxyl groups on C60 reveals a pattern of spin density distribution very similar to that obtained for C60OH, which can indicate a high radical reactivity of fullerenols containing an odd number of hydroxyl groups and, thus, a tendency to form polyhydroxylated systems.

Graphene-like nano-sheets for surface acoustic wave gas sensor applications by R. Arsat; M. Breedon; M. Shafiei; P.G. Spizziri; S. Gilje; R.B. Kaner; K. Kalantar-zadeh; W. Wlodarski (344-347).
The gas sensing properties of graphene-like nano-sheets deposited on 36° YX lithium tantalate (LiTaO3) surface acoustic wave (SAW) transducers are reported.The gas sensing properties of graphene-like nano-sheets deposited on 36° YX lithium tantalate (LiTaO3) surface acoustic wave (SAW) transducers are reported. The thin graphene-like nano-sheets were produced via the reduction of graphite oxide which was deposited on SAW interdigitated transducers (IDTs). Their sensing performance was assessed towards hydrogen (H2) and carbon monoxide (CO) in a synthetic air carrier gas at room temperature (25 °C) and 40 °C. Raman and X-ray photoelectron spectroscopy (XPS) revealed that the deposited graphite oxide (GO) was not completely reduced creating small, graphitic nanocrystals ∼2.7 nm in size.

Structures, stabilities and electronic properties of X@T12-POSS (X = transition metal atoms or ions) complexes.The geometries of the polyhedral oligomeric silsesquioxane (T12-POSS) cage, (HSiO3/2)12, containing the endohedral transition metal atoms or ions: Sc0,+1,+,2, Ti0,+2, Cr0,+1,+2, Mn0,+1,+2 Fe0,+1,+2, Co0,+1+,2, Ni0,+1,+2, Cu0,+1,+2, Zn0,+1,+2 Mo0 and W0,+1,+2 have been optimized at the B3LYP/6-311G(d,p) level of theory. The density functional theory (DFT) calculations predict that all these transition metal species form endohedral complexes within the T12-POSS cage. The inclusion energies, electronic properties, the HOMO–LUMO gaps, and ionization potentials of these endohedral transition metal T12-POSS complexes and their 31Si and 1H chemical shifts of (SiHO3/2)12 are predicted and discussed.

Exponential decay of relaxation effects at LaAlO3/SrTiO3 heterointerfaces by U. Schwingenschlögl; C. Schuster (354-357).
Schematic view of the LaAlO3/SrTiO3 heterostructure, in a projection along the [1 0 0] direction and perpendicular to the interface plane. Arrows show the directions of atomic shifts due to the interface lattice relaxation.We study the decay of interface induced structural and electronic relaxation effects in epitaxial LaAlO3/SrTiO3 heterostructures. The results are based on first-principles band structure calculations for a multilayer configuration with an ultrathin LaAlO3 layer sandwiched between bulk-like SrTiO3 layers. We carry out the structure optimization for the heterointerface and investigate the electronic states of the conducting interface layer, which is found to extend over two SrTiO3 unit cells. The decay of atomic displacements is analyzed as a function of the distance to the interface, and the resulting exponential law is evaluated quantitatively.

The diffusion of porphyrin molecules through nano-porous networks was found to be governed by an adsorption–desorption mechanism.The adsorption of porphyrin molecules out of ethanol solution onto TiO2 particles of nano-porous TiO2 films was studied by means of optical absorption (UV–Vis) spectroscopy. The process was found to be limited by aggregation of dye molecules. From the temperature dependence of the process, an activation energy of 0.18 ± 0.02 eV was deduced. It is correlated to the interaction energy of π-stacked porphyrin molecules. Aggregation-breaking additives change the up-take kinetics in a way that it becomes similar to the kinetics of non-aggregating molecules.

Graphene sheets via microwave chemical vapor deposition by G.D. Yuan; W.J. Zhang; Y. Yang; Y.B. Tang; Y.Q. Li; J.X. Wang; X.M. Meng; Z.B. He; C.M.L. Wu; I. Bello; C.S. Lee; S.T. Lee (361-364).
Graphene sheets (GSs) via microwave chemical vapor deposition (CVD) method: the preferential etching of the inter-planar carbon species/bonding by excited hydrogen atoms in the plasma was considered essential for the formation of graphene structure.High-quality graphene sheets (GS) were synthesized on stainless steel substrates at ∼500 °C by microwave plasma chemical vapor deposition (CVD) in an atmosphere of methane/hydrogen mixture. The GS product was characterized to contain mostly 1- or 2–3-layers using scanning electron microscopy, transmission electron microscopy/selective area electron diffraction, atomic force microscopy, and Raman spectroscopy. The present CVD approach is capable of producing graphenes with high yield and high purity with no carbon impurities such as carbon nanotubes.

Theoretical prediction of ring structures for ZnS quantum dots by Sougata Pal; Rahul Sharma; Biplab Goswami; Pranab Sarkar (365-368).
A new ring-like structures for ZnS quantum dots has been reported.The lowest energy structure of ZnS quantum dots of different sizes have been determined by using a search based on genetic algorithm (GA) coupled with the density-functional tight-binding method (DFTB). The GA search converges to a rather new ring-like configurations of ZnS quantum dots. These ring-like clusters have higher HOMO–LUMO gap values compared to other known structures (such as hollow, zinc-blende and wurtzite) of ZnS QDs.

Single-molecule DNA conductance in water solutions: Role of DNA low-frequency dynamics by E.B. Starikov; A. Quintilla; C. Nganou; K.H. Lee; G. Cuniberti; W. Wenzel (369-374).
Dependence of charge transmission through DNAs on their lowest-frequency acoustic modes, combined with picosecond molecular dynamics, has been studied.Dependence of charge transmission through several experimentally studied DNA duplexes on their lowest-frequency acoustic modes, combined with the molecular dynamics in picosecond characteristic time range, has been studied. Based on this analysis we were able to identify the specific acoustic modes responsible for the noticeable increase in DNA charge transmission. Other factors influencing electric properties of DNA duplexes are discussed.

Conformational dependence of the anharmonic NH stretch frequencies in glycine dipeptide has been predicted.Conformational dependence of the fundamental and overtone vibrational transition frequencies and anharmonicities for the NH stretch mode in glycine dipeptide has been examined theoretically using a second-order vibrational perturbation approach. It is found that unlike the diagonal and off-diagonal anharmonicities, both the harmonic and anharmonic vibrational frequencies exhibit clear sensitivity to peptide conformation, convincingly showing that the NH stretch mode can be used as peptide local structural probe. These results reflect the intrinsic localized nature of the NH stretch mode. Weak vibrational coupling is predicted between the two adjacent NH stretch modes, even though they are highly anharmonic.

Anomalous reaction of oxide radical ion with 5-azacytosines: An experimental and theoretical study by Kavanal P. Prasanthkumar; Hari Mohan; Gopinathan Pramod; Cherumuttathu H. Suresh; Charuvila T. Aravindakumar (381-386).
Oxide radical ion ( • O - ) undergoes an unusual addition reaction with azacytosine. It is estimated that about 82% of the reaction proceeds via addition at the ring nitrogen and the remaining via electron transfer followed by elimination reaction.The reactions of oxide radical ion ( • O - ) with 5-azacytosine (5AC) and 5-azacytidine (5ACyd) in aqueous medium were studied using the pulse radiolysis technique and quantum chemical calculation using density functional theory (DFT). It is demonstrated that the major reaction pathway is the addition of • O - to the ring nitrogen of 5AC, followed by a fast protonation of adducts by water. Only a minor percentage (<18%) undergoes an electron transfer reaction. The similarity in the reaction mechanism of • O - (addition to azacytosine) and • OH (which generally participates in an addition reaction) is an interesting observation and is quite unusual in the case of heterocyclic compounds.

Interaction of Cd2+ with adenine and thymine and influence of metalation in base pairing are studied with high level DFT methods. Cd2+ binding to adenine nucleobases changes the equilibrium of tautomers and preferably supports the imino form rare tautomer.The influence of Cd2+ on nucleobases and base pairing has been studied systematically using high-level DFT method. Cd2+ strongly interacts with adenine (A), changing tautomer structures and affecting the tautomer equilibrium whereas the Cd2+-thymine (T) interaction barely shifts the equilibrium of T tautomers. The isoenergy of metal-bridged A–Cd2+–T base pair complexes in the same binding pattern reveals the absence of interaction between A and T. The effects of Cd2+ in H-bond base pairing have also been discussed to further understand the possible schemes in cadmium induced DNA mutations.

Theoretical studies on the nature of bonding in σ-hole complexes by A. Mohajeri; A.H. Pakiari; N. Bagheri (393-397).
Structural and electronic properties of σ-hole bonded complexes formed from the interaction between NH3, H2O and HF as nucleophile and molecules containing σ-hole atom of groups V–VII have been investigated.Density functional investigation has been performed to explore structural and electronic properties of σ-hole bonded complexes formed from the interaction between NH3, H2O and HF as nucleophile and molecules containing σ-hole atom of groups V–VII. It is found that the strength of interaction decreases in the order of Cl > S > P and Br > Se > As. This interaction is comparable or even stronger than the normal hydrogen bonding, however in the case where the nucleophile is not aligned in proper orientation with respect to the σ-hole atom the hydrogen bonding is preferred. The role of electrostatic potential in formation of σ-hole complex is also demonstrated and discussed.

‘Ex situ’ magnetic resonance volume imaging by Vasiliki Demas; John M. Franck; Louis S. Bouchard; Dimitris Sakellariou; Carlos A. Meriles; Rachel Martin; Pablo J. Prado; Alejandro Bussandri; Jeffrey A. Reimer; Alex Pines (398-401).
Frequency and phase encoded volume image of a fluorinated sample in an open 1 MHz electromagnet system.The portable NMR community has introduced advances that have allowed for a variety of studies. Imaging of static and moving objects has almost become standardized. The inherent static field gradients of portable systems have, however, limited such studies to imaging of slices perpendicular to the main gradient; full volume imaging in transportable, open systems has not been actively pursued. We present a true three-dimensional image of a phantom in an ex situ, electromagnet-based system. The basic concepts and designs put forth here extend in a straightforward fashion to higher fields and imaging of larger samples by ex situ methodologies.

The adiabatic electron affinities (EAs) for the heteroatomic molecule SO4: An MP2/CBS study by Wenxu Zheng; Kai-Chung Lau; Ning-Bew Wong; Wai-Kee Li (402-406).
An MP2/CBS approach has been proposed to calculate the adiabatic electron affinities (EAs) for the heteroatomic molecule SO4.An MP2/CBS approach has been proposed to calculate the adiabatic electron affinities (EAs) for the heteroatomic molecule SO4. The method involves the approximation to the complete basis set (CBS) limit at the MP2 level. The zero-point vibrational energy correction, the diagonal Born–Oppenheimer correction, and the scalar relativistic effect correction have been also made in the calculations. The present MP2/CBS predictions are found to be in good accord with the available experimental values.

Molecular descriptors issued from conceptual DFT have been used in the framework of a QSPR approach for the decomposition enthalpy of selected nitroaromatic compounds.Five molecular descriptors issued from the conceptual density functional theory (DFT), namely ionization potential, electron affinity, hardness, electronegativity and electrophilicity indexes, have been used for defining a QSPR model for the decomposition enthalpy of 22 nitroaromatic compounds. Two descriptors, electron affinity and electrophilicity, appeared to be linearly correlated with this property, but the best predictivity is obtained with a multi-linear correlation involving three descriptors. Beside the numerical aspects, our work points out the perspectives of using DFT indexes within QSPR framework, for the predictions of decomposition enthalpy, a property directly related to explosivity.

Second-order quadrupolar shifts as an NMR probe of fast molecular-scale dynamics in solids by Teresa Kurkiewicz; Michael J. Thrippleton; Stephen Wimperis (412-416).
Motionally averaged second-order quadrupolar shifts are revealed by 11B multiple-quantum NMR spectroscopy of solid ortho-carborane.Molecular-scale dynamics on the nanosecond timescale or faster can have a measurable influence on isotropic NMR frequencies of quadrupolar nuclei. Although previously studied in solution, where it is usually referred to as the ‘dynamic shift’, this effect is less well known in solids. Here we demonstrate that multiple-quantum NMR measurements of isotropic quadrupolar shifts are a simple way to probe nanosecond timescale motions in solids. We measure the 11B (spin I  = 3/2) shifts of the resolved boron sites in ortho-carborane as a function of temperature and interpret the results in terms of the known rapid tumbling dynamics.

Application of the fragment molecular orbital method for determination of atomic charges on polypeptides. II. Towards an improvement of force fields used for classical molecular dynamics simulations by Yoshio Okiyama; Hirofumi Watanabe; Kaori Fukuzawa; Tatsuya Nakano; Yuji Mochizuki; Takeshi Ishikawa; Kuniyoshi Ebina; Shigenori Tanaka (417-423).
Relative deviation of the electrostatic potentials determined by RESP charges from those obtained by FMO on sampling points for crambin protein, and also the relative deviation of the charge values from the Amber 94 charge ones, for a number of restraint weights.The restrained electrostatic potential (RESP) fitting method with a harmonic restraint toward target values is applied to determination of atomic charges on polypeptides on the basis of the fragment molecular orbital method. The present RESP charges are determined to be confined around the targeted Amber 94 charges with high-fitting quality, including structural specificity; an optimal value of restraint weight makes the fitted charges reliable and stable. We employ the optimally-weighted RESP charges for an improvement of force fields in molecular dynamics simulation and show that the charges keep good reproducibility of the electrostatic properties during the simulation.

Terahertz spectroscopy of l-proline in reverse aqueous micelles by Catherine C. Cooksey; Benjamin J. Greer; Edwin J. Heilweil (424-429).
Terahertz spectra of H2O, D2O and l-proline incorporated within reverse aqueous micelles reveals low-frequency internal and hydrogen-bonded modes.A new method for obtaining room-temperature terahertz (THz) absorption spectra of aqueous-phase biomolecules in the frequency range 1–21 THz (35 cm−1–700 cm−1) is reported. The spectrum for l-proline was acquired by solvating the amino acid within the nanometer-sized interior water pool of reverse micelles dispersed in transparent n-heptane. Terahertz spectra of H2O, D2O and the effect of l-proline concentration and micelle size are discussed, and the results are compared to spectra of solid-phase l-proline and Gaussian calculations.

Real-time correlation functions are expressed as integrals of smooth functions using single-step propagators.Using single-step approximations to the propagator, we show that real-time correlation functions can be expressed as integrals of smooth functions, and thus can be efficiently evaluated by Monte Carlo methods. This approach allows direct calculation of correlation functions at intermediate temperatures over short to intermediate time lengths.

Fluorescence emission anisotropy, three-component systems, excitation energy transfer, Monte-Carlo simulations.Hybrid Monte-Carlo simulation algorithm of fluorescence anisotropy decay for donor–mediator–acceptor systems has been proposed. The results of hybrid Monte-Carlo simulations are compared with the results of Monte-Carlo step by step simulations. Very good agreement between both Monte-Carlo simulations has been obtained. The hybrid Monte-Carlo simulation of emission anisotropy is characterized by very good accuracy and little time consumption. As an example the donor–mediator–acceptor system in uniaxially stretched polymer film has been studied.

Author Index (439-445).