Vibrational coupled cluster theory

The theory and first implementation of a vibrational coupled cluster (VCC) method for calculations of the vibrational structure of molecules is presented. Different methods for introducing approximate VCC methods are discussed including truncation according to a maximum number of simultaneous mode excitations as well as an interaction space order concept is introduced. The theory is tested on calculation of anharmonic frequencies for a three-mode model system and a formaldehyde quartic force field. The VCC method is compared to vibrational self-consistent-field, vibrational M?ller-Plesset perturbation theory, and vibrational configuration interaction (VCI). A VCC calculation typically gives higher accuracy than a corresponding VCI calculation with the same number of parameters and the same formal operation count.     

The temperature dependence of the zero-field splitting of trimethylenemethane

Trimethylenemethane was generated by γ-irradiating polycrystalline methylenecyclopropane, and studied by EPR at various temperatures. The zero-field splitting constant, D, was observed to change from 0.0260 cm^?1 at 4 K to 0.0212 cm^?1 at 126 K, though the hyperfine coupling showed little temperature dependence.     

Ionic conductivity in three crystalline phases of LiBH4 under pressure

The AC electrical conductivity of LiBH₄ was investigated below 2 GPa between 1 Hz and 1.6 MHz. The high-temperature phase has an ionic conductivity of up to 0.01 S cm^?1, while the low-temperature phases have conductivities two orders of magnitude lower. All phases show an Arrhenius behaviour with activation energies E _a between 0.5 and 0.7 eV, in good agreement with earlier data except for phase III, which is found to have the highest activation energy of the phases studied. The high-temperature phase has a minimum in E _a near 1 GPa, close to the triple point, correlated with a sudden change in activation volume. These features may indicate an isostructural phase transition. The conductivities of the ambient temperature phases increase temporarily by an order of magnitude after transitions between these phases, probably due to new diffusion channels via structural defects. The phase diagram agrees well with earlier results.     

A low-temperature high-pressure apparatus with a temperature control system

Abstract

A low-temperature high-pressure apparatus was designed using commercial cryogenic equipment. Pressures up to 1 GPa and temperatures down to 40 K can be obtained in a volume of up to 30 cm³. The apparatus is of the piston-cylinder type with a piston diameter of 45 mm, and the pressure can be varied at all temperatures, An adaptive temperature control system keeps the temperature inside the pressure cylinder constant to within ±0.1 K.     

Efficient computation of the Gauss-Newton direction when fitting NURBS using ODR

We consider a subproblem in parameter estimation using the Gauss-Newton algorithm with regularization for NURBS curve fitting. The NURBS curve is fitted to a set of data points in least-squares sense, where the sum of squared orthogonal distances is minimized. Control-points and weights are estimated. The knot-vector and the degree of the NURBS curve are kept constant. In the Gauss-Newton algorithm, a search direction is obtained from a linear overdetermined system with a Jacobian and a residual vector. Because of the properties of our problem, the Jacobian has a particular sparse structure which is suitable for performing a splitting of variables. We are handling the computational problems and report the obtained accuracy using different methods, and the elapsed real computational time. The splitting of variables is a two times faster method than using plain normal equations.     

Unraveling the similarity of the photoabsorption of deprotonated p-coumaric acid in the gas phase and within the photoactive yellow protein

Using advanced QM/MM methods, the surprisingly negligible shift of the lowest-lying bright electronic excitation of the deprotonated p-coumaric acid (pCA(-)) within the photoactive yellow protein (PYP) is shown to stem from a subtle balance between hypsochromic and bathochromic effects. More specifically, it is found that the change in the excitation energy as a consequence of the disruption of the planarity of pCA(-) inside PYP is nearly canceled out by the shift induced by the intermolecular interactions of the chromophore and the protein as a whole. These results provide important insights about the primary absorption and the tuning of the chromophore by the protein environment in PYP.     

Volume dependence of thermal conductivity and bulk modulus for poly(propylene glycol)

The thermal conductivity λ and heat capacity per unit volume of poly(propylene glycol) PPG (0.4 and 4.0 kg·mol⁻¹ in number-average molecular weight) have been measured in the temperature range 150–295 K at pressures up to 2 GPa using the transient hot-wire method. At 295 K and atmospheric pressure, λ = 0.147 W m⁻¹K⁻¹ for PPG (0.4 kg·mol⁻¹) and λ = 0.151 W m⁻¹K⁻¹ for PPG (4.0 kg·mol⁻¹). The temperature dependence of λ is less than 4 × 10⁻⁴ W m⁻¹K⁻² for both molecular weights. The bulk modulus has been measured in the temperature range 215–295 K up to 1.1 GPa. At atmospheric pressure, the room temperature bulk moduli are 1.97 GPa for PPG (0.4 kg·mol⁻¹) and 1.75 GPa for PPG (4.0 kg·mol⁻¹). These data were used to calculate the volume dependence of $ \lambda ,g\, = - \left( {\frac{{\partial \lambda /\lambda }}{{\partial V/V}}} \right)_T $. At room temperature and atmospheric pressure (liquid phase) we find g = 2.79 for PPG (0.4 kg·mol⁻¹) and g = 2.15 for PPG (4.0 kg·mol⁻¹). The volume dependence of g, (∂g/∂ log V)_T varies between −19 to −10 for both molecular weights. Under isochoric conditions, g is nearly independent of temperature. The difference in g between the glassy state and liquid phase is small and just outside the inaccuracy of g of about 8%. The theoretical model for λ by Horrocks and McLaughlin yields an overestimate of g by up to 120%. © 1998 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 36 : 345–355, 1998     

Organically pillared layered zinc hydroxides

The two organically pillared layered zinc hydroxides [Zn₂(OH)₂(ndc)], CPO-6, and [Zn₃(OH)₄(bpdc)], CPO-7, were obtained in hydrothermal reactions between 2,6-naphthalenedicarboxylic acid (ndc) and zinc nitrate (CPO-6) and 4,4′biphenyldicarboxylate (bpdc) and zinc nitrate (CPO-7), respectively. In CPO-6, the tetrahedral zinc atoms are connected by two μ₂-OH groups and two carboxylate oxygen atoms, forming infinite layers extending parallel to the bc-plane. These layers are pillared by ndc to form a three-dimensional structure. In CPO-7, the zinc hydroxide layers are containing four-, five- and six coordinated zinc atoms, and the layers are built like stairways running along the [001] direction. Each step is composed of three infinite chains running in the [010] direction. Both crystal structures were solved from conventional single crystal data. Crystal data for CPO-6: Monoclinic space group P2₁/c (No. 14), a=11.9703(7), b=7.8154(5), c=6.2428(4) Å, β=90.816(2)°, V=583.97(6) Å³ and Z=4. Crystal data for CPO-7: Monoclinic space group C2/c (No. 15), a=35.220(4), b=6.2658(8), c=14.8888(17) Å, β=112.580(4)°, V=3033.8(6) Å³ and Z=8. The compounds were further characterized by thermogravimetric- and chemical analysis.     

Combinatorial synthesis of benztropine libraries and their evaluation as monoamine transporter inhibitors

A combinatorial synthesis of benztropine analogues is presented. Radical azidonation of 3-benzyloxy-8-azabicyclo[3.2.1]octane-8-carboxylic acid tert-butyl ester 3 to 3-(1-azidobenzyloxy)-8-azabicyclo[3.2.1]octane-8-carboxylic acid tert-butyl ester 4 was used as a key step in the synthesis. This step was optimized by adding 10% DMF to the reaction. Reaction of 4 with phenyl magnesium bromide followed by Boc removal and N-methylation gave benztropine 1. Reaction of five-component Grignard reagents with 4 was used to create a two-dimensional library of 25 N-normethylbenztropine analogues. Further reaction of this library with five alkyl bromides was carried out to create a three-dimensional library containing 125 compounds. Screening of the libraries towards binding and inhibition of uptake of the human dopamine (hDAT), serotonin (hSERT) and norepinephrine transporters (hNET) was carried out. None of the synthesized compounds were found to be stronger than benztropine, and none were selective for inhibition of binding over monoamine uptake.     

Density functional self-consistent quantum mechanics/molecular mechanics theory for linear and nonlinear molecular properties: Applications to solvated water and formaldehyde

A combined quantum mechanics/molecular mechanics (QM/MM) method is described, where the polarization between the solvent and solute is accounted for using a self-consistent scheme linear in the solvent polarization. The QM/MM method is implemented for calculation of energies and molecular response properties including the calculation of linear and quadratic response functions using the density-functional theory (DFT) and the Hartree-Fock (HF) theory. Sample calculations presented for ground-state energies, first-order ground-state properties, excitation energies, first-order excited state properties, polarizabilities, first-hyperpolarizabilities, and two-photon absorptions strengths of formaldehyde suggests that DFT may in some cases be a sufficiently reliable alternative to high-level theory, such as coupled-cluster (CC) theory, in modeling solvent shifts, whereas results obtained with the HF wave function deviate significantly from the CC results. Calculations carried out on water gives results that also are comparable with CC calculations in accuracy for ground-state and first-order properties. However, to obtain such accuracy an exchange-correlation functional capable of describing the diffuse Rydberg states must be chosen.