95Mo nuclear magnetic resonance parameters of molybdenum hexacarbonyl from density functional theory: appraisal of computational and geometrical parameters

Solid-state (95)Mo nuclear magnetic resonance (NMR) properties of molybdenum hexacarbonyl have been computed using density functional theory (DFT) based methods. Both quadrupolar coupling and chemical shift parameters were evaluated and compared with parameters of high precision determined using single-crystal (95)Mo NMR experiments. Within a molecular approach, the effects of major computational parameters, i.e. basis set, exchange-correlation functional, treatment of relativity, have been evaluated. Except for the isotropic parameter of both chemical shift and chemical shielding, computed NMR parameters are more sensitive to geometrical variations than computational details. Relativistic effects do not play a crucial part in the calculations of such parameters for the 4d transition metal, in particular isotropic chemical shift. Periodic DFT calculations were tackled to measure the influence of neighbouring molecules on the crystal structure. These effects have to be taken into account to compute accurate solid-state (95)Mo NMR parameters even for such an inorganic molecular compound.     

Finite-element calculations on the behaviour of a DSC in temperature-modulated mode

The influence of changes of sample properties on the amplitude and phase shift of the differential-temperature signal as well as the influence of frequency changes has been calculated for a one-dimensional model of a temperature-modulated DSC (TMDSC) using a computer program for finite-element-method (FEM) calculations. Amplitude and phase shift of the measured signal ΔT (which is proportional to the differential heat-flow rate) is strongly influenced by the heat capacity of the sample. The connection is only linear for rather small heat capacities. The influence of the heat-transfer coefficient between sample and sample pan on amplitude and phase shift of the signal is not so large and linear (within the framework of our calculations). The influence of the heat-transfer coefficient between sample and sample pan on amplitude and phase shift of the signal is not so large and linear (within the framework of our calculations). For precise measurements, a very careful “calibration” is needed, which must take all the aforementioned influences into account.     

Effects of hydrogen bond and solvent polarity on the C=O stretching of bis(2-thienyl)ketone in solution

The optimized structural parameters, the absorption and the resonance Raman spectra have been investigated for the bis(2-thienyl)ketone in gas phase, in cyclohexane, methanol, and acetonitrile solvents by means of time dependent density functional theory calculations, the solvent electronic polarization effect on the solvation shift is examined and in well accordance with the calculation. The effect of increasing the polarity of the solvent is well represented by the polarizable continuum model, both for the absorption spectra and resonance Raman intensities. The Raman spectra of the C=O stretching mode, which is sensitive to the intermolecular interaction for bis(2-thienyl)ketone dissolved in solvents, were systematically studied. It was found that the hydrogen bond effect plays an important role in reducing the carbonyl stretching wavenumbers. The results of Raman shifts were interpreted through the dilution effect, solvation effects, and hydrogen bond-forming effects. Furthermore, the excitation profiles of several important Raman bands of bis(2-thienyl)ketone molecule in different solvents have been critically analyzed. The solvent effects on structural and symmetry properties of the molecule in S2 electronic state as well as the short-time photo relaxation dynamics have been discussed.     

The Xe shielding surfaces for Xe interacting with linear molecules and spherical tops

The 129Xe nuclear magnetic resonance spectrum of xenon in gas mixtures of Xe with other molecules provides a test of the ab initio surfaces for the intermolecular shielding of Xe in the presence of the other molecule. We examine the electron correlation contributions to the Xe-CO2, Xe-N2, Xe-CO, Xe-CH4, and Xe-CF4 shielding surfaces and test the calculations against the experimental temperature dependence of the density coefficients of the Xe chemical shift in the gas mixtures at infinite dilution in Xe. Comparisons with the gas phase data permit the refinement of site-site potential functions for Xe-N2, Xe-CO, and Xe-CF4 especially for atom-Xe distances in the range 3.5-6 A. With the atom-atom shielding surfaces and potential parameters obtained in the present work, construction of shielding surfaces and potentials for applications such as molecular dynamics averaging of Xe chemical shifts in liquid solvents containing CH3, CH2, CF3, and CF2 groups is possible.     

NMR chemical shifts of the rhodopsin chromophore in the dark state and in bathorhodopsin: a hybrid QM/MM molecular dynamics study

We investigate nuclear magnetic resonance (NMR) parameters of the rhodopsin chromophore in the dark state of the protein and in the early photointermediate bathorhodopsin via first-principles molecular dynamics simulations and NMR chemical shift calculations in a hybrid quantum/classical (QM/MM) framework. NMR parameters are particularly sensitive to structural properties and to the chemical environment, which allows us to address different questions about the retinal chromophore in situ. Our calculations show that both the 13C and the 1H NMR chemical shifts are rather insensitive to the protonation state of Glu181, an ionizable amino acid side chain located in the vicinity of the isomerizing 11-cis bond. Thus, other techniques should be better suited to establish its protonation state. The calculated chemical shifts for bathorhodopsin further support our previously published theoretical structure, which is in very good agreement with more recent X-ray data.     

Structure and protonation of some indolizine derivatives studied by ab initio MO calculations

Some gauge invariant atomic orbitals-coupled-perturbed Hartree-Fock (GIAO-CPHF) calculations were performed for seven indolizine derivatives and their monoprotonated forms. Chemical shift, molecular geometry, and charge distribution data are reported for each molecule. The calculations support the results of nuclear magnetic resonance (NMR) spectroscopy measurements showing that protonation occurs preferentially at N1. The good agreement between the calculated and observed ¹³C and ¹⁵N chemical shifts show that such calculations can be used for chemical shift assignment purposes. Cation structures and probable sites for electrophilic reaction or second protonation are also discussed.     

Dispersion relations for liquid crystals using the anisotropic Lorentz model with geometrical effects

The dispersion relations for the refraction indices and extinction coefficients of an ordered system of anisotropic molecules are derived, taking into account absorption near the resonance frequencies and the molecular geometrical form factor. The derivation is based on a combination of the anisotropic Lorentz oscillator dispersion model and the generalized Lorentz-Lorentz (LL) relationship. This relationship is shown to be consistent with the isotropic limit. The geometrical form tensor (GFT) distinguishes this relationship from the LL and the Calusius-Mossotti equations valid for isotropic media. Far from the absorption bands the dispersion relationships are shown to converge to those of Sellmeier-type dispersion relationships for transparent dielectrics that can be expanded into generalized Cauchy-type series. The principal values of the GFT are shown to cause a red shift to the resonance wavelengths that can be found from measurements in the disordered phase. Experimental data are presented based on published works as well as measurements using a spectroscopic retardation technique, and excellent agreement is obtained with the theoretical calculations on several LC materials.     

Ab initio calculations of NMR chemical shifts

The nuclear magnetic resonance chemical shift is one of the most powerful properties available for structure determination at the molecular level. A review of advances made in the ab initio calculation of chemical shielding during the past five years is presented. Specifically, progress in the areas including the effects of an unpaired electron, electron correlation, and relativistic effects into ab initio chemical shielding calculations, the tensor nature of the chemical shift, and intramolecular and intermolecular effects on the chemical shift will be covered.     

Quantum chemical study and infrared spectroscopy of hydrogen-bonded CHCl(3)-NH(3) in the gas phase

Molecular association of chloroform with ammonia is studied by high-level quantum chemical calculations including correlated MP2 and CCSD(T) calculations with basis sets up to6-311++G(d,p) and counterpoise corrected energies, geometries, and frequencies. The calculations predict an eclipsed hydrogen-bonded complex of C(3v) symmetry (DeltaE(0)=-15.07 kJ mol(-1)) with 225.4 pm intermolecular CHcdots, three dots, centeredN distance. Intermolecular interactions are analysed by Kitaura-Morokuma [Int. J. Quantum Chem. 10, 325 (1976)] interaction energy decomposition. Compared to the monomer, the C-H bond is elongated, and the CH-stretching fundamental shifts to lower wave numbers and has a marked approximately 340-fold increase of its intensity. Based on these predictions, the complex is observed by infrared spectroscopy in the gas phase at room temperature. A subtraction procedure isolates its spectrum, and a dilution series confirms the presence of a 1:1 complex. The CHCl(3)cdots, three dots, centeredNH(3) complex has an experimental -17.5 cm(-1) shift of its CH-stretching vibration, and CDCl(3)cdots, three dots, centeredNH(3) a -12.5 cm(-1) shift of the CD-stretching vibration. After a deperturbation of the CH-stretching/bending mode Fermi resonance system, this indicates a "redshifting" or more appropriately, a "C-H elongating" hydrogen bond in agreement with the ab initio calculations. An estimate of the complex concentration gives the equilibrium constant K(p)=0.024 (p(theta)=10(5) Pa) at 295 K for the dimerization, providing one of the few examples where a hydrogen-bonded gas phase complex at room temperature could be quantitatively studied by infrared spectroscopy.     

Fermi resonance in aqueous methanol

The damped coupled oscillator model is used to study the Fermi resonance between the methyl stretching mode (v_s) and the first overtone of the symmetric deformation (2δ_s) in methanol as a function of concentration in aqueous solution. After removal of other non-resonant bands from the spectrum, the isotropic lineshape is fitted by the model using four adjustable parameters. The calculated resonance shift is approximately two times greater than that reported earlier for methanoi in an inert matrix, reflecting the enhanced interactions in the liquid phase.The magnitude of the resonance interaction parameter remains unchanged upon dilution in water, indicating that the vibrational anharmonicity is relatively insensitive to variations in the hydrogen bonding. The uncoupled frequency of the methyl stretching mode, on the other hand, is observed to increase markedly in solution. This shift, together with a concomitant decrease in the C-O stretching frequency, demonstrates that there is a significant electronic charge redistribution as methanol-methanol hydrogen bonds are replaced by methanol-water bonding interactions.     

Dispersion relations for liquid crystals using the anisotropic Lorentz model with geometrical effects

The dispersion relations for the refraction indices and extinction coefficients of an ordered system of anisotropic molecules are derived, taking into account absorption near the resonance frequencies and the molecular geometrical form factor. The derivation is based on a combination of the anisotropic Lorentz oscillator dispersion model and the generalized Lorentz–Lorentz (LL) relationship. This relationship is shown to be consistent with the isotropic limit. The geometrical form tensor (GFT) distinguishes this relationship from the LL and the Calusius–Mossotti equations valid for isotropic media. Far from the absorption bands the dispersion relationships are shown to converge to those of Sellmeier‐type dispersion relationships for transparent dielectrics that can be expanded into generalized Cauchy‐type series. The principal values of the GFT are shown to cause a red shift to the resonance wavelengths that can be found from measurements in the disordered phase. Experimental data are presented based on published works as well as measurements using a spectroscopic retardation technique, and excellent agreement is obtained with the theoretical calculations on several LC materials.     

Theoretical analysis of the intermolecular interaction effects on the excitation energy of organic pigments: solid state quinacridone

Quinacridones (QAs) are organic hydrogen-bonded pigments, which are yellow in solution and become reddish to violet in solid phase depending on the crystal structure. We have carried out regular and fragment molecular orbital (FMO) based time-dependent density functional theory (TDDFT) calculations of the alpha (I), beta, and gamma crystalline phases of QA to examine the origin of the spectral shift in the solid phase. On the basis of the TDDFT calculations, we have found that the spectral shift from gas to solid phase in QA is dominated by the interplay of the structural deformation, electrostatic potential (crystal field), and intermolecular interactions, and each contribution is of the same order of magnitude. The spectral shift induced by the structural deformation is mainly caused by the stretch of the CO bond. The individual intermolecular interactions contribute to bathochromic and hypsochromic shifts depending on the spatial orientation, and their sums result in the bathochromic shift overall.     

Theoretical investigation of the EPR parameters and local structure for trigonal Yb3+ ion in Bi4Ge3O12 crystal

Bi4Ge3O12 single crystals are of great interest for science research and engineering applications. In this paper, the electron paramagnetic resonance (EPR) g factors g||, gperpendicular of Yb3+ and hyperfine structure constants A||, Aperpendicular of 171Yb3+ and 173Yb3+ isotopes in Bi4Ge3O12 crystal are calculated from the perturbation formulas of these parameters. The crystal-field parameters are obtained from the superposition model and the crystal structure data. The EPR parameters for trigonal Yb3+ centers in Bi4Ge3O12 are reasonably explained by involving the defect structures of impurity Yb3+ centers. Based on the calculations, Yb3+ ion is found not to occupy exactly the host Bi3+ site, but to shift away from the center of oxygen octahedron by a distance DeltaZ approximately 0.317 A along C3 axis. The results are discussed.     

Localized surface plasmon resonance spectroscopy near molecular resonances

The peak location of the localized surface plasmon resonance (LSPR) of noble metal nanoparticles is highly dependent upon the refractive index of the nanoparticles' surrounding environment. In this study, new phenomena are revealed by exploring the influence of interacting molecular resonances and nanoparticle resonances. The LSPR peak shift and line shape induced by a resonant molecule vary with wavelength. In most instances, the oscillatory dependence of the peak shift on wavelength tracks with the wavelength dependence of the real part of the refractive index, as determined by a Kramers-Kronig transformation of the molecular resonance absorption spectrum. A quantitative assessment of this shift based on discrete dipole approximation calculations shows that the Kramers-Kronig index must be scaled in order to match experiment.     

Charge exchange in collisions of beryllium with its ion

Close-coupling calculations of the resonance and near resonance charge exchange in ion-atom collisions of Be at low and intermediate energies are presented. Accurate ab initio calculations are carried out of the Born-Oppenheimer potentials and the non-adiabatic couplings that are due to the finite nuclear masses and drive the near resonance charge exchange. We show that the near resonance charge exchange cross section follows Wigner's threshold law of inelastic processes for energies below 10(-8) eV and that the zero temperature rate constant for it is 4.5 × 10(-10) cm(3) s(-1). At collision energies much larger than the isotope shift of the ionization potentials of the atoms, we show that the near resonance charge exchange process is equivalent to the resonance charge exchange with cross sections having a logarithmic dependence. We also investigate the perturbation to the charge exchange process due to the non-adiabatic interaction to an electronic excited state. We show that the influence is negligible at low temperatures and still small at intermediate energies despite the presence of resonances.     

A Theoretical Study of NBO,NICS, and 14N NQR Parameters of Adenine Tautomers in the Gas Phase via DFT

The natural bond orbital (NBO) analysis, nucleus independent chemical shift (NICS), and ¹⁴N NQR parameters of the most stable tautomers of adenine in the gas phase were predicted using density functional theory method. The NBO analysis revealed that the resonance interaction between lone pair of the nitrogen atom and empty non‐Lewis NBO increases with increasing the p character of the nitrogen lone pair. The present investigation indicated the π clouds in both the considered heterocyclic rings containing six electrons, and these tautomers has the aromatic character. The NICS study utilizing the gauge‐invariant atomic orbital method showed that there are diatropic currents in the heterocyclic rings of the tautomers, so we determined the order of overall aromaticity of these tautomers. The results of NQR parameter calculations showed three parameters are effective on nuclear quadrupole coupling constant; the p character value of lone pair electrons of nitrogens, and the related occupancies and whenever, the lone pair electrons of nitrogens participate in the formation of chemical bond and/or π system of the ring, the q_zz and consequently its χ decreases.     

Weak intramolecular interactions in ethylene glycol identified by vapor phase OH-stretching overtone spectroscopy

Vapor phase OH-stretching overtone spectra of ethylene glycol were recorded to investigate weak intramolecular hydrogen bonding. The spectra were recorded with conventional absorption spectroscopy and laser photoacoustic spectroscopy in the first to fourth OH-stretching overtone regions. The room-temperature spectra are dominated by two conformers that show weak intramolecular hydrogen bonding. A less abundant third conformer, with no sign of hydrogen bonding, is also observed. Vapor phase spectra of the ethylene-d(4) glycol isotopomer were also recorded and used to identify an interfering resonance between CH-stretching and OH-stretching states in the fourth overtone. Anharmonic oscillator local mode calculations of the OH-stretching transitions have provided an accurate simulation of the observed spectra. The local mode parameters were calculated with coupled cluster ab initio methods. The calculations facilitate assignment of the different conformers in the spectra and illustrate the effect of the intramolecular hydrogen bonding.     

Ionic core effects on the mie resonance in lithium clusters

We investigate the effects of the atomic cores on the Mie resonance in lithium metal clusters, perturbing a jellium Hamiltonian with zero-range pseudopotentials. The resonance is red-shifted with respect to the classical formula by core effects, most important of which is the increased effective mass due to the core potentials. Much of the large shift seen in lithium clusters is thereby explained if the strength of the pseudopotentials is taken from band structure calculations. However, such pseudopotentials cause the resonance to be greatly broadened, contrary to observation.     

Monte Carlo calculations of multiple scattering of resonance photons: phase matrix algorithm and its application to 3-dimensional radiative transfer and self reversal of spectral lines

We describe an algorithm for Monte Carlo calculations of multiple scattering of resonance photons by arbitrary atomic states. The angular dependence and the polarization of the scattered radiation are calculated using the phase matrix and the polarizations of the exciting and emitted photons are represented by Stokes parameters. Together with a new ansatz to solve the Holstein-Bibermann integro differential equation the formalism is applied to time dependent three-dimensional radiative transfer in a cyclindrical cell. As a further application it is shown that self reversal of spectral lines can occur in a homogeneous medium and in the case of complete frequency redistribution.     

Quasichemical interpretation of the ultrasonic velocity in ternary aqueous systems

The quasichemical model of hydration have been used to calculate the speed of ultrasound in binary solutions of water and nonelectrolyte. The model has been confined to systems that exhibit a maximum in the ultrasonic velocity vs. nonelectrolyte concentration. The parameters of the model are the hydration equilibrium constant, the nonelectrolyte hydration number, and the molar volume and compressibility of the hydrated nonelectrolyte. These have been fitted to experimental results by the method of least squares. The model calculations reproduce qualitatively the ultrasonic velocity as a function of nonelectrolyte concentration. The calculated maximum of the ultrasonic velocity is generally too low, but the nonelectrolyte concentration at which this maximum occurs agrees well with experiment.Addition of a third component shift the velocity maximum. The quasichemical model has also been used to calculate this shift. These calculations have been based on the parameters developed for the binary system. The shift on the nonelectrolyte concentration scale is reproduced satisfactorily, but the shift of the maximal value of the ultrasonic velocity is less accurately predicted by the model.