Structural and vibrational studies of molecular conductors using quantum mechanical methods: 1,3-Dithiole-2-thione, 1,3-dithiole-2-one, 1,3-dioxole-2-one and 1,3-dioxole-2-thione

Computations were carried out by employing the RHF and density functional theory (DFT) methods to investigate the geometries, atomic charges, harmonic vibrational frequencies for the 1,3-dithiole-2-thione (DTT), 1,3-dithiole-2-one (DTO), 1,3-dioxole-2-thione (DOT) and 1,3-dioxole-2-one (DOO) molecules and their radical cations. The geometrical parameters and atomic charges on various atomic sites of the DTT and DOT molecules and their radical cations suggest extended conjugation in these systems. Contrary to this, for the DOO⁺ and DTO⁺ ions there is no evidence in favour of such conjugation, however, the neutral molecules exhibit some conjugation. Harmonic forced field and vibrational mode calculations provided convincing theoretical evidence for the reassignment of some fundamental vibrational modes for all the four molecules. In going from the neutral species to the charged ions for all the four cases the CC stretching frequency is found to decrease drastically. The CS stretching frequency reduces drastically for the DTT and DOT molecules as compared to their radical cations whereas the CO stretching frequency is found to increase in going from the neutral molecule to its radical cation for the DOO and DTO molecules. The ring stretching mode with a₁ symmetry and CC and CO/S stretching modes in these molecules appear to help in conversion of neutral molecule into respective radical cation and neighbouring radical cation into respective neutral molecule. Thus, there appears the feasibility of stretching vibrational mode coupling with electron transfer.     

Raman microscopy of the mixite mineral BiCu6(AsO4)3(OH)6·3H2O from the Czech Republic

Raman microscopy of the mixite mineral BiCu₆(AsO₄)₃(OH)₆·3H₂O from Jáchymov and from Smrkovec (both Czech Republic) has been used to study their molecular structure. The presence of (AsO₄)³⁻, (AsO₃OH)²⁻, (PO₄)³⁻ and (PO₃OH)²⁻ units, as well as molecular water and hydroxyl ions, was inferred. O H···O hydrogen bond lengths were calculated from the Raman and infrared spectra using Libowitzky's empirical relation. Small differences in the Raman spectra between both samples were observed and attributed to compositional and hydrogen‐bonding network differences. Copyright © 2009 John Wiley & Sons, Ltd.     

ICLAS of HDO between 13,020 and 14,115 cm

The high resolution absorption spectrum of monodeuterated water, HDO, has been recorded by Intracavity Laser Absorption Spectroscopy (ICLAS) in the 13,020–14,115 cm⁻¹ region dominated by the 4ν₃ band. The achieved noise equivalent absorption (α_min10⁻⁹ cm⁻¹) allowed detecting transitions with line strengths as small as 2×10⁻²⁷ cm/molecule which is about 10 times lower than the smallest line intensities previously detected in the region.The rovibrational assignment of the spectrum was based on the results of the variational calculations of Schwenke and Partridge (SP) as well as recent calculations using a new potential energy surface performed by Voronin, Tolchenov and Tennyson (VTT). 2157 transitions involving 21 upper vibrational states were assigned to HD¹⁶O while only four bands were previously reported in the region. A set of 157 new energy levels could be derived. It includes rotational levels of several highly excited bending states, in particular the (0 11 0) pure bending state. For some states like the (1 0 3) and (0 2 3) Fermi dyad, effective Hamiltonian modelling was needed to establish the vibrational assignments of some rotational levels. VTT calculations were found to significantly improve the SP results, the rms deviation of the calculated and observed energies being decreased from 0.23 to 0.06 cm⁻¹.Finally, 79 transitions of the 4ν₃ band of the HD¹⁸O isotopologue were assigned, leading to the derivation of 48 levels, which are the most excited energy levels reported so far for this isotopologue.     

Temperature-dependent absorption cross-sections of HCFC-142b

Following the recent detection of HCFC-142b (1-chloro-1,1-difluoroethane) from space, laboratory infrared absorption cross-section spectra of this molecule in a pure vapour phase have been recorded in the spectral region using Fourier transform spectroscopy. The spectra have been recorded at a resolution of and a range of temperatures from 223 to 283 K. The resulting data show good agreement with the harmonic frequencies and intensities calculated using density functional theory as well as with the integrated absorption intensities of the spectral bands available in the literature. The new cross-sections will allow more accurate retrieval of atmospheric HCFC-142b concentrations using infrared spectroscopic techniques.     

Raman and infrared spectroscopic study of the molybdate‐containing uranyl mineral calcurmolite

Raman and infrared spectra of calcurmolite were recorded and interpreted from the uranium and molybdenum polyhedra, water molecules and hydroxyls point of view. U O bond lengths in uranyl and Mo O bond lengths in MoO₆ octahedra were calculated and O H…O bond lengths were inferred from the spectra. The mineral calcurmolite is characterised by bands assigned to the vibrations of the UO₂ units. These units provide intense Raman bands at 930, 900 and 868 and 823 cm⁻¹. These bands are attributed to the anti‐symmetric and symmetric stretching modes of the UO₂ units, respectively. Raman bands at 794, 700, 644, 378 and 354 cm⁻¹ are attributed to vibrations of the MoO₄ units. The bands at 693 and 668 cm⁻¹ are assigned to the anti‐symmetric and symmetric A_g modes of the terminal MO₂ units. Similar bands are observed at 797 and 773 cm⁻¹ for koechlinite and 798 and 775 cm⁻¹ for lindgrenite. It is probable that some of the bands in the low wavenumber region are attributable to the bending modes of MO₂ units. Copyright © 2008 John Wiley & Sons, Ltd.     

A general rigorous quantum dynamics algorithm to calculate vibrational energy levels of pentaatomic molecules

An exact variational algorithm is presented for calculating vibrational energy levels of pentaatomic molecules without any dynamical approximation. The quantum mechanical Hamiltonian of the system is expressed in a set of orthogonal coordinates defined by four scattering vectors in the body-fixed frame. The eigenvalue problem is solved using a two-layer Lanczos iterative diagonalization method in a mixed grid/basis set. A direct product potential-optimized discrete variable representation (PO-DVR) basis is used for the radial coordinates while a non-direct product finite basis representation (FBR) is employed for the angular variables. The two-layer Lanczos method requires only the actions of the Hamiltonian operator on the Lanczos vectors, where the potential-vector products are accomplished via a pseudo-spectral transform technique. By using Jacobi, Radau and orthogonal satellite vectors, we have proposed 21 types of orthogonal coordinate systems so that the algorithm is capable of describing most five-atom systems with small and/or large amplitude vibrational motions. Finally, an universal program (PetroVib) has been developed. Its applications to the molecules , and the van der Waals cluster He₃Cl₂ are also discussed.     

Adsorption characteristics of atomic nitrogen on ruthenium surfaces

We have studied the adsorption, vibration, and diffusion of N atoms on Ru(0 0 0 1), , and surfaces by means of the 5-parameter Morse potential (5-MP) of interaction between atomic nitrogen and a metal surface. The adsorption sites, adsorption geometry, binding energy and eigenvibration of atomic nitrogen on the different ruthenium surfaces are calculated. It is shown that atomic nitrogen always preferably occupies the high coordination sites on Ru surfaces. The 4-fold site is the preferable adsorption site for atomic nitrogen on both open and surfaces while 3-fold site is the most stable adsorption site for atomic nitrogen on both Ru(0 0 0 1) and surfaces. Moreover, we find the lowest energy pathway of diffusion and diffusion barriers of atomic nitrogen on the surfaces.     

Aromatic butenolides produced by a soil ascomycete Auxarthron sp. KCB15F070 derived from a volcanic island

LC/MS-based chemical screening of fungal extract fraction library led to identification of three 2,3-aryl substituted furanone metabolites (1–3), including one known butenolide glycoside (1) whose stereochemistry remained unsolved and two new compounds gotjawaside and gotjawalide (2 and 3), from Auxarthron sp. KCB15F070, a fungus isolated from a soil sample of the volcanic island Jeju, Korea. Their planar structures were elucidated by 1D- and 2D-NMR spectroscopic and HRESIMS spectrometric techniques, and the absolute configurations of three compounds were solved using a combination of chemical derivatizations and computational analysis of vibrational circular dichroism (VCD) spectra.     

CO分子振转光谱的理论研究

采用从头算的多参考组态相互作用(MRCI)方法并结合基组aug-cc-pCVQZ计算了CO分子基态(X1Σ+)的势能曲线和偶极矩曲线,得到的势能曲线、偶极矩曲线分别与RKR势、文献的偶极矩曲线吻合较好。利用所得的势能,求解双原子分子核运动的Schrdinger方程找到了CO分子X1Σ+态转动量子数J=0时的70个振动态,对于每一振动态,分别计算了其振动能级G(v)、转动惯性常数B_v和离心畸变常数D_v,并把计算结果与已知的42个实验值做了详细比较,结果表明,计算的振动能级G(v)、转动惯性常数B_v、离心畸变常数D_v与实验值符合较好。利用G(v),B_v导出的光谱常数[谐振频率ω_e(2 160.1 cm-1)、非谐振频率ω_eχ_e(13.1 cm-1)、转动常数B_e(1.918 cm-1)、振转耦合常数α_e(0.017 3 cm-1)]也与实验值的光谱常数[ω_e(2 169.8 cm-1),ω_eχ_e(13.3 cm-1),B_e(1.931 cm-1),α_e(0.017 5 cm-1)]较为符合,这在一定程度上证明了方法MRCI/Aug-cc-pCVQZ对CO分子基态性质的计算是合适而可靠的。利用乘积近似方法计算了CO分子在常温、中温、高温时的配分函数,在此基础上,计算了CO分子在T=296 K时的1-0跃迁带的谱线强度,通过比较发现,计算所得的线强度与HITRAN数据库符合较好。进一步计算的CO分子X1Σ+态1-0,2-0,3-0,4-0,2-1,3-1和4-1跃迁带的带强度也与实验值较为吻合,同时首次计算了CO分子X1Σ+态3-2跃迁带、4-2跃迁带的线强度及带强度。