Chemical Physics Letters (v.365, #1-2)
Geometry and dynamics of formic and acetic acids adsorbed on ice by M Compoint; C Toubin; S Picaud; P.N.M Hoang; C Girardet (1-7).
Energy optimization at 0 K and constrained molecular dynamics simulations at 250 K have been carried out to study adsorption and incorporation of formic and acetic acids on/in ice. The results show that the adsorption and incorporation processes are highly influenced by the formation of two H-bonds between the carboxyl function and two water molecules. The free energy profiles indicate that the two acid molecules are strongly trapped at the ice surface and that the incorporation of formic acid is favored when compared to acetic acid. These data are discussed within the context of tropospheric conditions.
A theory of fluorescence depolarization in mesophases with tilted distribution of directors by Alberto Arcioni; Riccardo Tarroni; Claudio Zannoni (8-14).
We develop a theory of fluorescence depolarization for a probe molecule reorienting in a mesophase with local uniaxial symmetry and a random distribution of directors tilted with respect to the axis of the structure. The theory should be applicable, e.g., to probes dissolved in a pyramidic liquid crystal or to chromophores attached to a side chain polymer brush. We work out expressions for the polarized fluorescence intensities as a function of the cone opening and show how these depend on the orientational correlation functions and on the order parameters for a uniaxial or biaxial probe.
Electronic spectra of indolyl radicals: a time-dependent DFT study by Alejandro Crespo; Adrián G Turjanski; Darı́o A Estrin (15-21).
Neutral and cationic indolyl radicals, such as those arising from tryptophan and melatonin, are involved in a variety of physiological situations. Due to their short life times, experimental characterization of these species is incomplete. We have performed density functional theory (DFT) calculations in order to provide information of the electronic spectral properties of indole, melatonin and tryptophan radical and radical cations. We predict that the neutral and cationic radicals exhibit absorption ranges from 450 to 500 nm and from 520 to 570 nm, respectively.
Ultrafine and uniform silicon nanowires grown with zeolites by C.P Li; X.H Sun; N.B Wong; C.S Lee; S.T Lee; Boon K Teo (22-26).
Ultrafine and uniform silicon nanowires (SiNWs), with a Si crystalline core of 1–5 nm (average 3 nm) in diameter and a SiO2 outer layer of 10–20 nm thick, were synthesized by the oxide-assisted growth method via the disproportionation of thermally evaporated SiO using zeolite as a template/precursor. From transmission and secondary electron microscopic characterizations, we deduced that the zeolite acted to limit the lateral growth of the Si crystalline core and supply the excess oxide to form the thick oxide outer layer. The ultrafine SiNWs exhibited strong photoluminescence that peaked at 720 nm.
Locally strong polarity in the solvent effect of nonpolar solvent carbon tetrachloride: the role of atomic quadrupoles by Hajime Torii (27-33).
The solvent effect of CCl4 on the CO stretching mode of acetone is studied by carrying out ab initio MO calculations for an acetone–(CCl4)4 cluster. It is shown that the electric field operating on the CO bond of acetone is significantly larger than that expected for the reaction field induced by the dipole moment of acetone, and is in the direction that the chlorine atoms look as if they had large positive charges. It is suggested that the atomic quadrupoles of the chlorine atoms, generated by the covalent bonds with the carbon atom, give rise to this effect.
Nucleus-independent chemical shifts and local aromaticities in large polycyclic aromatic hydrocarbons by Jun-ichi Aihara (34-39).
Central rings of coronene and kekulene are known to be paratropic with small positive nucleus-indepedent chemical shift (NICS) values at the centers although they are (4n + 2)-membered rings. However, careful inspection of the bond resonance energy (BRE) pattern in each π-system revealed that all constituent rings are aromatic in nature. Individual rings were found to sustain diatropic currents even if some bond currents are vanishingly small. Thus, NICS values at the ring centers of large polycyclic π-systems, including fullerenes, cannot always be used as indicators of local aromaticity. BRE is better suited for estimating the degree of local aromaticity in polycyclic π-systems.
Two-dimensional Penning ionization electron spectroscopy of carbon disulfide: spectral assignments and anisotropic interactions with a He *(23 S) metastable atom by Shan Xi Tian; Naoki Kishimoto; Koichi Ohno (40-48).
Collision-energy-resolved Penning ionization electron spectra are measured for carbon disulfide (CS2) by collision with a He *(23 S) metastable atom. Assignments in Penning ionization electron spectrum are made on the basis of collision energy dependence of the partial ionization cross sections (CEDPICS). CEDPICS for the X 2Π g , A 2Π u , B 2Σ u + and C 2Σ g + states demonstrates that interactions for the He* access perpendicular to the molecular axis are more attractive than those for the collinear access, which is supported by the model calculations of the interaction potential energies. It is found that the perpendicular access plays an important role in a formation of the intermediate He++CS2 − state.
Emission characteristics of CdS nanoparticles induced by confinement within MCM-41 nanotubes by Weon-Sik Chae; Ju-Hye Ko; In-Wook Hwang; Yong-Rok Kim (49-56).
Nanosize CdS particles confined in siliceous MCM-41 channels were prepared by using reversed micelles as an insertion carrier. As-made CdS in MCM-41 host shows photoluminescence (PL) signals from both band-edge and surface defect state recombination. Calcinated CdS in the host, however, presents relatively suppressed surface defect state emission compared with band-edge emission. Such emission characteristics after calcination is ascribed to the reduced probability of recombination through deeply trapped surface defect states compared with direct excitonic recombination, which is possibly due to surface capping of the CdS nanoparticles by the host nanochannels.
Algebraic analysis of bent-from-linear transition intensities: the vibronically resolved emission spectrum of methinophosphide (HCP) by H. Ishikawa; H. Toyosaki; N. Mikami; F. Pérez-Bernal; P.H. Vaccaro; F. Iachello (57-68).
Emission spectra obtained from bulk-gas methinophosphide (HCP) have been interpreted by means of a Lie algebraic theory that describes explicit non-rigidity of the molecular framework. Fluorescence accompanying selective excitation of A ̃ 1 A″– X ̃ 1Σ+ vibronic bands was dispersed under moderate resolution, with substantial activity of the ν 2 H–C–P bending mode reflecting the bent-from-linear nature of the A ̃ ← X ̃ transition. Aside from furnishing an economical parameterization for energy level patterns, the algebraic treatment permits Franck–Condon intensities to be evaluated quantitatively. The equilibrium structure deduced for the A ̃ 1 A″ state is in good accord with quantum chemistry calculations except for substantially less than predicted elongation of the C–P bond upon electron promotion.
Pore structure of raw and purified HiPco single-walled carbon nanotubes by Martin Cinke; Jing Li; Bin Chen; Alan Cassell; Lance Delzeit; Jie Han; M Meyyappan (69-74).
Very high purity single-walled carbon nanotubes (SWNTs) were obtained from HiPco SWNT samples containing Fe particles by a two-step purification process. The raw and purified samples were characterized using high resolution transmission electron microscopy (HRTEM), Raman spectroscopy and thermogravimetric analysis (TGA). The purified sample consists of ∼0.4% Fe and the process does not seem to introduce any additional defects. The N2 adsorption isotherm studies at 77 K reveal that the total surface area of the purified sample increases to 1587 m2/g from 567 m2/g for the raw material, which is the highest value reported for SWNTs.
Stability and bandgap of semiconductor clusters by Jan-Ole Joswig; Sudip Roy; Pranab Sarkar; Michael Springborg (75-81).
Using a parameterized density-functional method we have studied the structural and electronic properties of different II–VI and III–V semiconductor clusters. We studied finite parts of the zincblende and wurtzite crystal structure for CdS, CdSe, InP, and ZnO and allowed the structures to relax to the closest total-energy minimum. Both stoichiometric and non-stoichiometric naked clusters were considered. We found (i) that the relative stability of the zincblende- and the wurtzite-derived clusters depends on the size of the structure, (ii) that the total-energy per atom is a non-smooth function of the size, and (iii) a correlation between the size of the HOMO–LUMO bandgap and the stability of the cluster. The implications of these results for the experimental analysis of the size distributions are discussed.
A cluster model of liquid water and its IR spectroscopic response by Petr Bouř (82-88).
IR spectra of liquid water were modeled for a cluster of 214 molecules, using combined MD and ab initio DFT-BPW91/6-31G** computations. The model reproduced well the experimental absorption profile in the range of 0–4000 cm −1 , positions, bandwidths and magnitudes of the absorption maxima for the OH stretching, bending and molecular librational modes. A band corresponding to the transitional motion is reproduced with a bigger error. The procedure can be applied universally and was also used for simulation of absorption spectra of liquid methanol.
On the convergence of the (ΔE CCSD(T)−ΔE MP2) term for complexes with multiple H-bonds by Petr Jurečka; Pavel Hobza (89-94).
The MP2 and CCSD(T) interaction energies of the following cyclic complexes were studied: formic acid dimer (FO–FO), formamide dimer (FA–FA), formamidine dimer (FI–FI), formamide⋯formamidine complex (FA–FI) and the formamidinoaldehyde⋯amidinoformamide (FL–AF) complex. Various AO basis sets up to the cc-pVTZ were investigated. It was shown that the (ΔE CCSD(T)−ΔE MP2) correction term evaluated with the 6-31G* basis set is overestimated while rather accurate values were obtained with 6-31G*(0.25) and cc-pVDZ (0.25, 0.15) basis sets. Because the latter one performs well also for stacked complexes it can be recommended for evaluation of the correction term of extended complexes possessing both H-bonded and stacked structures.
Mechanical and electrical properties of carbon nanotube ribbons by Yan-Hui Li; Jinquan Wei; Xianfeng Zhang; Cailu Xu; Dehai Wu; Li Lu; Bingqing Wei (95-100).
We have measured the Young’s modulus of long aligned carbon nanotube ribbons using a special stress–strain puller designed for whisker-like materials. The Young’s modulus of the graphitized carbon nanotube ribbons is about 60 GPa, which is 2.5 times higher than that of the as-grown ribbons. This suggests that the graphitization is an effective way to improve the mechanical properties of the ribbons. Most of the measured ribbons are semiconductor and their resistivities are in the range of 4.4–12.6×10−4 Ω cm . An interesting phenomenon appeared in one ribbon is that the electrical property of the ribbon changes from metallic to non-metallic with decreasing the temperature.
On the O(1D) + HX reactions (X=Cl, Br): a density functional theory analysis by Abraham F Jalbout (101-109).
The singlet potential energy surface of the O(1D) + HX → OH + X, and the O(1D) + HX →H+XO reactions, (X=Cl, Br) were explored with the B3LYP and B1LYP hybrid density functional theory methods. When these methods are coupled to the 6-311++G (3df, 3pd) basis set, very reliable information about the relative energies can be obtained (i.e., barrier heights, dissociation energies, etc.). We have examined the above-mentioned reactions, the HOX → HXO isomerization, and multiple dissociation pathways for both HOX and HXO (X=Cl, Br). The results of our calculations are presented.
K+/Na+ selectivity of KcsA potassium channel analyzed by reference interaction site model (RISM) integral equation theory by Qizhi Cui; Vedene H Smith (110-116).
We have analyzed K+/Na+ selectivity of the KcsA potassium channel from the point of view of solvation structure and solvation energetics at the atomic level by using the reference interaction site model (RISM) integral equation theory. Our results indicate that K+ is better dehydrated and has lower binding free energy in the four-site selectivity filter of the KcsA potassium channel than Na+. Thus the selectivity filter favors K+ over Na+ to enter and pass through the channel. A good agreement between our energetic results and those from simulation has been obtained.
Wavelength dependence of ultrafast and large third-order non-linear optical response of polyacetylene nanoparticles by X.Y Pan; N.V Chigarev; H.B Jiang; W.T Huang; Qihuang Gong; C.L Liu; V.M Kobryanskii; D.Yu Paraschuk (117-121).
The third-order optical non-linearity was measured in nanopolyacetylene using femtosecond optical Kerr effect technique at wavelength from 790 to 860 nm. The ultrafast non-resonant effective second-order hyperpolarizibility for single polyacetylene nanoparticle was estimated to be as large as 1.0×10−27 esu, which corresponding to the γ c of single carbon atom contribution equals to 5.0×10−33 esu. We ascribed the observations to the highly ordered structure of nanopolyacetylene and delocalization of the π electrons along the conjugated chains was supposed to be responsible for such properties.
Theory of covalent heterodinuclear magnetic exchange interaction and its application to MnIIIFeIII and FeIIFeII spin clusters in complex molecules by Kuang Xiao-Yu; Zhou Kang-Wei (122-128).
A covalent heterodinuclear magnetic exchange interaction formula has been established and the antiferromagnetic coupling phenomena of both heterodinuclear MnIIIFeIII and homodinuclear FeIIFeII spin-clusters in complex molecules have been studied. It is demonstrated that the antiferromagnetic phenomenon of transition-metal ion-pairs in molecules should be attributed to the combined effect of the direct-exchange interaction, the kinetic exchange interaction and the covalent effect; the strong antiferromagnetic characteristic of MnIIIFeIII cluster in [L′MnIII(μ-O)(μ-CH3CO2)2FeIIIL′] is mainly due to the d xz –d xz and d yz –d yz orbital exchange interactions, while the weak antiferromagnetic coupling in deoxyhemerythrin should be attributed to a μ-OH−–FeIIFeII cluster with a long Fe–O bond length in its active site. The theoretical results agree well with the experimental findings.
Electronic structure and STM images of self-assembled styrene lines on a Si(1 0 0) surface by W.A. Hofer; A.J. Fisher; G.P. Lopinski; R.A. Wolkow (129-134).
First principles electronic structure calculations are applied to styrene lines on a Si(1 0 0) surface grown via a recently reported ‘self-directed’ growth process. It is found that the delocalized π states of the molecule lie at the bandedge of the valence band, which makes them potentially suitable as carrier channels for hole transport along the styrene line. By contrast, the unoccupied π* states are situated well above the bandedge of the conduction band. In this case electron transport along the lines seems highly improbable. Finally, scanning tunneling microscope (STM) topographies of occupied states are simulated within a perturbation approach. While the experimental result of vanishing corrugation for the molecule at low bias voltages cannot be accounted for, good agreement is obtained between experiments and simulations for voltages below −2 V.
The extended Wiener index by X.H Li (135-139).
Comparison with the Wiener number and the molecular connectivity index, a novel set of Wiener indexes ( mWp , mWpc , mWc and mWch ) were defined, which are named the extended Wiener index. The potential usefulness of the extended Wiener index in QSAR/QSPR is evaluated by its correlation with a number of C3–C8 alkanes and by a favorable comparison with models based on molecular connectivity index.
Theoretical study of the reaction mechanism of platinum oxide with methane by Der-Yan Hwang; Alexander M Mebel (140-147).
Density functional B3LYP calculations have been employed to investigate the reaction of platinum oxide with methane. PtO is shown to form a molecular complex with CH4 bound by ∼13 kcal/mol. At elevated temperatures, direct abstraction of a hydrogen atom is possible leading to PtOH and free methyl radical with a barrier of ∼26 kcal/mol. A minor reaction channel is insertion into a C–H bond to produce a CH3PtOH molecule, which can be also formed by recombination of PtOH and CH3. CH3PtOH would preferably dissociates through a mechanism involving 1,2-CH3 migration to produce a PtCH3OH complex and eventually Pt+CH3OH.
A simulation protocol to study proteins in vacuo. Controlled re-folding and re-unfolding transitions by Gustavo A Arteca; O Tapia (148-156).
Computed simulations suggest that denatured anhydrous proteins can re-fold into quasi-native structures unaided by water, in agreement with experimental evidence. Using a novel protocol for dynamics simulations, we report on in vacuo relaxation studies of a partly unfolded intermediate of apo-cytochrome c ′. We find a range of accessible paths that include direct native-like re-folding, reversible re-unfolding, and full unfolding. The timescale for these processes can be regulated by modifying the coupling to the simulated thermal bath. The simulation strategy and the tools developed to follow molecular shape changes provide a robust approach to study intrinsic properties of protein folds.
Energy exchange in reactive scattering of hydrogen molecules from a Cu surface by G.R Darling; Z.S Wang; S Holloway (157-163).
The energy exchange between a D2 molecule and the phonon states of a copper surface has been modelled using quantum wavepackets. For processes where the molecule gains internal energy, we predict a gain in molecular energy near the excitation threshold. This gain decreased with increasing translational energy, and was insensitive to the final state of the molecule. For non-activated processes, with a decrease in molecular internal energy, a net loss of energy to the substrate was found. This loss increased as the change in internal energy of the molecule increased. These results are in good agreement with experimental observation.
Resolution of overlapping charge-transfer transitions by a combined absorption-MCD–MLD approach by Jim Peterson; Terrence J Collins; Eckard Münck; Emile L Bominaar (164-169).
The general lack of resolution in molecular electronic absorption spectra has been a major obstacle to development in this field for decades, resulting in gradual loss of interest and effort compared to virtually all other areas of spectroscopy. Ironically, magnetic linear dichroism (MLD) has been known to atomic spectroscopists for more than a century, but ignored as a technique suitable for molecular studies. Here we demonstrate that the concerted application of MLD, in conjunction with magnetic circular dichroism and absorption spectroscopy, represents a significant advance in deconvoluting overlapping electronic transitions of randomly oriented chromophores.
First hyperpolarizability of the molecular excited states: Calculations for p-nitroaniline and comparison with experiments by W.M. Faustino; D.V. Petrov (170-175).
We calculated the first hyperpolarizability of the molecules with some fraction of both ground and excited state populations. We used a numerical procedure employed widely known software. The comparison with experimental data for para-nitroaniline molecule obtained by the Hyper-Rayleigh technique is done.
Intermetallic compounds of the heaviest elements: the electronic structure and bonding of dimers of element 112 and its homolog Hg by V Pershina; T Bastug; T Jacob; B Fricke; S Varga (176-183).
Fully relativistic (four-component) density-functional calculations were performed for the element 112 dimers (112)X (X = Pd, Cu, Ag and Au) and those of its lighter homolog, Hg. A relatively small decrease of about 15–20 kJ/mol in bonding was found from the HgX to (112)X compounds. Respectively, the bond lengths were increased by 0.06 Å on the average. The Mulliken population analysis has shown this effect to be a result of a decreasing contribution of the relativistically stabilized 7s-AO of element 112 to bonding. The following trend in the binding energies was predicted for (112)X as a function of X: Pd >Cu>Au>Ag, exactly as the trend obtained experimentally for adsorption of Hg on the corresponding metal surfaces.
Synthesis of SWNTs and MWNTs by a molten salt (NaCl) method by J.B Bai; A.-L Hamon; A Marraud; B Jouffrey; V Zymla (184-188).
A method to obtain the single-walled and multi-walled carbon nanotubes is presented. It consists of electrolytic conversion of graphite to carbon nanotubes in fused NaCl at 810 °C. The experimental conditions are given. The filling of the nanotubes is also possible if elements are added in the salt solution.
Accelerating the calculation of the rovibrational energies of tetraatomic molecules using a two-layer Lanczos algorithm by Hua-Gen Yu (189-196).
The two-layer Lanczos algorithm has been extended to study the rovibrational spectrum of four-atom molecules in a mixed grid/finite basis representation basis. This algorithm exploits the partitioning structure of the Hamiltonian in polyspherical coordinates, and calculates the eigenstates in a reduced-dimension (RD) way but exactly. It consists of the standard Lanczos method for the outer layer iteration and the guided spectral transform (GST) Lanczos for the inner layer. For H2CO, numerical results show that the two-layer Lanczos method is substantially efficient.