All-trans- and t,T,t,C,t,T,t-deca-1,3,5,7,9-Pentaenes: Ab Initio Structures,Vibrational Analyses,and Some Regularities in the Series of Related Molecules

Total geometry optimization and calculation of the force constants for all-transand t,T,t,C,t,T,tdeca-1,3,5,7,9-pentaene were carried out at the ab initio, HF/6-31G level. The HF/6-31G//HF/ 6-31G force fields were modified using empirical scale factors transferred from trans-buta-1,3-diene augmented by an additional scale factor for the central formal carbon-carbon double bond coordinates (determined previously for all-trans-hexa-1,3,5-triene). The total number of scale factors was seven. The vibrational problems for both decapentaenes were solved using the respective scaled HF/6-31G//HF/6-31G force field. Infrared intensities and Raman activities were calculated from the unscaled HF/6-31G//HF/6-31G force fields. Complete assignment of all the fundamental vibrational frequencies is given. Geometrical parameters, vibrational frequencies and force constants are compared with the corresponding values of buta-1,3-diene, hexa-1,3,5-triene and octa-1,3,5,7-tetraene. Regularities in the properties of this molecular series are discussed. Special attention is given to the possibility of using the vibrational spectra for detection of distortions from the regular trans structure of these oligoenes.     

On the self-condensation of aminoguanidine leading to 1,1,4,10,10-pentaamino-2,3,5,6,8,9-hexaazadeca-1,3,5,7,9-pentaene (structure elucidation through X-ray powder diffraction)

Chemical and spectroscopic (UV; ¹H, ¹³C, ¹⁵N NMR; HRMS) studies determined the structure of 1,1,4,10,10-pentaamino-2,3,5,6,8,9-hexaazadeca-1,3,5,7,9-pentaene for the red-violet compound, which was obtained by treating aminoguanidine hydrochloride with KOH. X-ray powder diffraction and lattice-constrained PBC-DFT optimization confirmed this structure and defined a linear all-trans configuration.     

X-ray and density functional theory structural study of 1,3,5,7,9-penta-tert-butylcorannulene, C40H50

The first X-ray structural characterization of an alkyl-substituted corannulene, namely, 1,3,5,7,9-penta-tert-butylcorannulene (C40H50), has been accomplished. The addition of bulky tert-butyl groups to the corannulene core flattens the bowl and affects the solid-state packing. The presence of two enantiomers, in addition to positional disorder of the C40H50 bowls in the solid-state structure, has prevented the acquisition of accurate geometric parameters of this open geodesic polyarene. Therefore, DFT calculations have been used to describe its molecular geometry and to access bond lengths, bond angles, and a bowl depth.     

Structural,vibrational and thermodynamics propertiesof Zn-based semiconductors

We have preformed first-principle calculations for the structural, vibrational and thermodynamic properties of the IIB–VIA Zn-based semiconductor compounds ZnX (X = O, S, Se, Te). The phonon dispersion curves along several high-symmetry lines at the Brillouin zone together with the corresponding phonon density of states are calculated using density-functional perturbation theory. The calculated phonon frequencies at the Γ, X, and L points of the Brillouin zone show good agreement with the experimental values and other calculations. The thermodynamics properties including the phonon contribution to the Helmholtz free energy ΔF, the phonon contribution to the internal energy ΔE, the entropy S, and the constant-volume specific heat C_V are determined within the harmonic approximation based on the calculated phonon dispersion relations. If 298 K is taken as a reference temperature, the difference values of H ? H₂₉₈ have been also calculated and compared with the available experimental data.     

Structural, electronic, and vibrational properties of amino-adamantane and rimantadine isomers

We performed a first principles total energy investigation on the structural, electronic, and vibrational properties of adamantane molecules, functionalized with amine and ethanamine groups. We computed the vibrational signatures of amantadine and rimantadine isomers with the functional groups bonded to different carbon sites. By comparing our results with recent infrared and Raman spectroscopic data, we discuss the possible presence of different isomers in experimental samples.     

Monothiodibenzoylmethane: Structural and vibrational assignments

The vibrational structure of the title compound (1,3-diphenyl-3-thioxopropane-1-one, TDBM) was studied by a variety of experimental and theoretical methods. The stable ground state configuration of TDBM was investigated by infrared (IR) absorption measurements in different media, by linear dichroism (LD) polarization spectroscopy of samples partially aligned in a stretched polymer matrix, and by Raman spectroscopy. The investigation of the metastable photoproduct of TDBM was based on the previously published spectrum of the product trapped in argon matrix [Y. Posokhov, A. Gorski, J. Spanget-Larsen, F. Duus, P.E. Hansen, J. Waluk, Chem. Phys. Lett. 350 (2001) 502]. The observed vibrational spectra were compared with theoretical transitions obtained with B3LYP/cc-pVTZ density functional theory (DFT). The results leave no doubt that the stable ground state configuration of TDBM corresponds to the intramolecularly hydrogen bonded-enol form (e-CCC), and that the photoproduct corresponds to an “open”, non-chelated enethiol form (t-TCC), thereby supporting the previous conclusions by Posokhov et al. No obvious indications of the contribution of other forms to the observed spectra could be found.     

Structural, vibrational and DSC investigations of the tetraethylammonium hydrogenselenate crystal

The X-ray structure of tetraethylammonium hydrogenselenate, [N(C₂H₅)₄]HSeO₄, was determined at room temperature. The crystal belongs to the P space group of triclinic system, Z=2, a=8.290(2), b=9.073(2), c=9.517(2) Å, =76.75(3), β=74.31(3) and γ=63.92(3)°. The hydrogenselenate anions are joined into cyclic dimers by two identical (equivalent by C_i) strong hydrogen bonds O(2)–H(02)O(1^a); the O(2)O(1^a) distance equals 2.611(5) Å. Powder IR and Raman spectra are discussed with respect to the crystal structure. The DSC reveals two phase transitions at 328 and 358 K.     

Structural characterization, thermal, dielectric, vibrational properties and molecular motions in

[C₃N₂H₅]₆[Bi₄Br₁₈] has been synthesized and characterized by the X-ray (at 293 and 110 K), calorimetric, dilatometric and dielectric measurements. At room temperature it crystallizes in the monoclinic space group, C2/m. A crystal structure consists of disordered imidazolium cations and ordered discrete tetramers of [Bi₄Br₁₈]^6-. This compound reveals a rich polymorphism in a solid state. It undergoes three solid–solid phase transitions: from phase I to II at 426/423 K (heating–cooling), II→III at 227 K and III→IV at 219.5/219 K. A clear dielectric relaxation process is found in the room temperature phase II. Infrared studies of the polycrystalline [C₃N₂H₅]₆[Bi₄Br₁₈] showed that the ν(N–H), δ(ring) and δ(C–H) modes of the imidazolium cations appeared to be very sensitive to the IV→III phase transition. ¹H NMR measurements confirmed a key role of the imidazolium cations in the phase transitions mechanisms at low temperatures.     

Structural, electronic, and vibrational characterization of Fe-HNO porphyrinates by density functional theory

A recent report of the structural and vibrational properties of heme-bound HNO in myoglobin, MbHNO, revealed a long Fe-N(HNO) bond with the hydrogen atom bonded to the coordinated N atom. The Fe-N(H)-O moiety was reported to exhibit an unusually high Fe-N(HNO) stretching frequency relative to those of the corresponding [FeNO]6 and [FeNO]7 porphyrinates, despite the Fe-N(HNO) bond being longer than either of its Fe-N(NO) counterparts. Herein, we present results from density functional theory calculations of an active site model of MbHNO that support the previous assignment and clarify this seemingly contradictory result. The results are consistent with the experimental evidence for a ground-state Fe-N(H)-O structure having a long Fe-N(HNO) bond and a uniquely high nu(Fe)(-)(N(HNO)) frequency. This high frequency is the result of the correspondingly low reduced mass of the normal mode, which is largely attributable to significant motion of the N-bound hydrogen atom. Additionally, the calculations show the Fe-N(H)O bonding in this complex to be remarkably insensitive to whether the HNO and ImH ligand planes are parallel or perpendicular. This is attributed to insensitivities of the Fe-L(axial) characters of molecular orbitals to the relative HNO and ImH orientation in both the parallel and perpendicular conformers.     

Structural, vibrational, and thermal properties of densified silicates: Insights from molecular dynamics

Structural, vibrational, and thermal properties of densified sodium silicate (close to NS2) are investigated with classical molecular dynamics simulations of the glass and the liquid state. A systematic investigation of the glass structure with respect to density was performed. We observe a repolymerization of the network manifested by a transition from a tetrahedral to an octahedral silicon environment, the decrease of the amount of non-bridging oxygen atoms and the appearance of threefold coordinated oxygen atoms (triclusters). Anomalous changes in the medium range order are observed, the first sharp diffraction peak showing a minimum of its full-width at half maximum according to density. Generic vibrational trends are observed, such as the shift of the Boson peak intensity to higher frequencies and the decrease of its intensity. Finally, we show that the thermal behavior of the liquid can be reproduced by the Birch-Murnaghan equation of states, thus allowing us to compute the isothermal compressibility.     

Structural and polarized vibrational studies of pentacaesium trihydrogentetraselenate monohydrate

Polarized IR and Raman spectra of single crystal were measured at room and at low temperature. The polarized IR spectra were measured by transmission and specular reflection method. The IR-microscope was used for vibrational measurement of small monocrystals. Assignment of the bands is proposed on the basis of oriented gas model approximation. The polarized vibrational spectra are discussed in relation to the crystal structure and possible proton conductivity and phase transition.     

Conformational analyses of peptides and proteins by vibrational Raman optical activity

Recent developments of vibrational Raman optical activity (ROA) spectroscopy enabled the detailed analyses of the backbone and side chain conformations of peptides and proteins in solution phases. ROA can be used as a powerful analytical technique for determining not only the structures of conformers, but also their populations even for systems in fast conformational equilibria where NMR spectroscopy is difficult to be applied. ROA enabled the monitoring of the secondary structures of denatured or unfolded proteins, such as an amyloid fibril and its prefibril intermediates.     

Structural,vibrational, and energy characteristics of halide molecules of group II–V elements

Correlations between the internuclear distances r(M-X), the bond energies E(M-X), and the valence force constants f_r for di- and trihalides of Group II–V elements are established. Some missing values are estimated. Ivanovo State Chemical Technological Academy. Translated fromZhurnal Strukturnoi Khimii, Vol. 37, No. 5, pp. 859–875, September–October, 1996. Translated by L. Smolina Ivanovo State Chemical Technological Academy. Translated fromZhurnal Strukturnoi Khimii, Vol. 37, No. 5, pp. 859–875, September–October, 1996.     

Semiempirical vibrational and electronic structures of C60 and C70

The electronic and vibrational structures of C₆₀ and C₇₀ have been calculated at the PM3 semiempirical level. C₆₀ has a partially delocalized structure, while C₇₀ has both a localized set and a delocalized set of MOs. As with AM1 and MNDO, PM3 predicts the heat of formation of C₇₀ to be greater than that of C₆₀, and that C₇₀ is the thermodynamically more stable species. Calculation of the normal modes was accelerated over 40 times by limited use of symmetry theory.     

Structural, microstructural and vibrational characterization of apatite-type lanthanum silicates prepared by mechanical milling

Apatite-type lanthanum silicates have been successfully prepared at room temperature by dry milling hexagonal A-La₂O₃ and either amorphous or low cristobalite SiO₂. Milling a stochiometric mixture of these chemicals in a planetary ball mill with a moderate rotating disc speed (350 rpm), allows the formation of the target phase after only 3 h although longer milling times are needed to eliminate all SiO₂ and La₂O₃ traces. Thus, the mechanically activated chemical reaction proceeds faster when using amorphous silica instead of low cristobalite as silicon source and pure phases are obtained after only 9 and 18 h, respectively. As obtained powder phases are not amorphous and show an XRD pattern as well as IR and Raman bands characteristic of the lanthanum silicate. The domain size of the as-prepared phases varies gradually with the temperature of post-milling thermal treatment with activation energies of about 26(8) and 52(10) kJ mol⁻¹ K⁻¹ for the apatites obtained from amorphous silica and low-cristobalite, respectively. These values suggest crystallite growth to be favored when using amorphous silica as reactant.     

Tetrapropylammonium triiodomercurate(II). Structural and vibrational spectra

The crystals of the tetrapropylammonium triiodomercurate(II) are monoclinic, with a = 1775.5(11) pm, b = 1287.4(20) pm, c = 938.9(5) pm and β = 95.52(5)°, Z = 4, space group P2₁/n. The structure was solved by direct methods and refined by least-squares techniques to a conventional R 0.04 for 1520 independent reflections. The structure consists of dimeric HgI₃ units. Each mercury atom is tetrahedrally coordinated to four iodine atoms in such a way that both tetrahedra are linked by sharing an edge. The average mercury—iodine terminal bond distance is 268.7 pm, whereas the bridging distance is 293.2 pm. Far-IR and Raman spectra are also reported and tentatively assigned to D_2h symmetry.     

Structural, elastic constant, and vibrational properties of wurtzite gallium nitride: a first-principles approach

Perdew-Wang proposed generalized gradient approximation (GGA) is used in conjunction with ultrasoft pseudopotential to investigate the structural, elastic constant, and vibrational properties of wurtzite GaN. The equilibrium lattice parameters, axial ratio, internal parameter, bulk modulus, and its pressure derivative are calculated. The effect of pressure on equilibrium lattice parameters, axial ratio, internal parameter (u), relative volume, and bond lengths parallel and perpendicular to the c-axis are discussed. At 52 GPa, the relative volume change is observed to be 17.8%, with an abrupt change in bond length. The calculated elastic constants are used to calculate the shear wave speeds in the [100] and [001] planes. The finite displacement method is employed to calculate phonon frequencies and the phonon density of states. The first- and second-order pressure derivative and volume dependent Gruneisen parameter (γ(j)) of zone-center phonon frequencies are discussed. These phonon calculations calculated at theoretical lattice constants agree well with existing literature.     

Enhanced Raman spectrum of lawsone on Ag surface: vibrational analyses, frequency shifts, and molecular geometry

The surface-enhanced Raman spectrum of lawsone, a well known natural dye, has been investigated. Activation with KNO(3) or Na(2)SO(4) solution was necessary to enhance the Raman signal, whereas addition of NaCl solution depletes the effects. In the enhanced Raman spectrum, the strong double-bond stretching bands are most distinctive and show large red shifts from those in the infrared and FT-Raman spectra. The observed strong double-bond stretching bands reflect lawsone coordinated perpendicular to the Ag surface. DFT computations have been carried out for the plausible configurations of lawsone coordinated to an adatom on the Ag surface. Lawsone coordinated to an Ag(+) adatom with H(+) released best reproduces the observed vibrational characteristics.