Fourier transform infrared spectra of H2CS and D2CS

Infrared spectra of thoformaldehyde, H2CS and D2CS, were observed in the gas phase at a resolution of better than 0.1 cm−1 from 4000 to 400 cm−1 using a Nicolet FTIR system. Vibrational band origins and rotational constants were determined for ν2, ν3, ν4, and ν6 of H2CS and for ν1, ν2, ν3, ν4, and ν6 of D2CS. The ν3, ν4, and ν6 bands of H2CS were analyzed as a set of three Coriolis interacting bands, and three Coriolis constants were determined; similarly the ν4 and ν6 bands of D2CS were analyzed as a pair of interacting bands and one Coriolis constant was determined. A general harmonic force field was determined, without constraints, to fit the vibrational wavenumbers, Coriolis constants, and centrifugal distortion constants. A zero-point (rz) structure was determined from the ground-state rotational constants, and the equilibrium (re) bond lengths were estimated.

Normal coordinates for the planar vibrations of benzene

Force constants and normal coordinates have been recalculated for all of the in-plane vibrations of benzene, making use of the recently observed data on one of the Coriolis constants in the E2g species from the work of Callomon et al. The extent to which the force field is uniquely determined by the data is reviewed for each symmetry species in turn, and the results of a force constant refinement calculation are reported in which a modified valency force field was used based on the hybrid orbital model. The results show considerable differences from Whiffen's normal coordinates for benzene, but somewhat smaller differences from Scherer's recent calculations.

A potential energy surface for the ground state of acetylene, C2H2

A potential energy function has been derived for the ground state surface of C2H2 as a many-body expansion. The 2- and 3-body terms have been obtained by preliminary investigation of the ground state surfaces of CH2( 3B1) and C2H( 2Σ+). A 4-body term has been derived which reproduces the energy, geometry and harmonic force field of C2H2. The potential has a secondary minimum corresponding to the vinylidene structure and the geometry and energy of this are in close agreement with predictions from ab initio calculations. The saddle point for the HCCH-H2CC rearrangement is predicted to lie 2•530 eV above the acetylene minimum.

Vibrational overtone spectra of monofluoroacetylene: a preliminary report

High-resolution infrared and near-infrared spectra have been observed for more than 80 overtone bands of the HCCF molecule, including two CH stretching overtones in the visible region. Many of these have been analysed, and many more are in the course of analysis and will be reported later. All fundamentals have now been rotationally analysed and the equilibrium rotational constant determined. These data provide a testing ground for anharmonic force-field analyses, and they are discussed briefly in this connection.

The infra-red spectra of silyl fluoride and silyl fluoride-d3

Infra-red spectra have been recorded for silyl fluoride and silyl fluoride-d3 at a resolution of circa 0·3 cm-1. Rotational structure has been observed for parallel fundamentals in both molecules, and for all perpendicular fundamentals. In both SiH3F and SiD3F the A1 and E species deformation modes interact strongly via a Coriolis perturbation; this has been analysed, and the band origin of v5 for SiH3F is reassigned. A hybrid-orbital force field based on the experimental data is also reported.

A potential energy surface for the ground state of formaldehyde, H2CO(1A1)

A model potential energy function for the ground state of H2CO has been derived which covers the whole space of the six internal coordinates. This potential reproduces the experimental energy, geometry and quadratic force field of formaldehyde, and dissociates correctly to all possible atom, diatom and triatom fragments. Thus there are good reasons for believing it to be close to the true potential energy surface except in regions where both hydrogen atoms are close to the oxygen. It leads to the prediction that there should be a metastable singlet hydroxycarbene HCOH which has a planar trans structure and an energy of 2•31 eV above that of equilibrium formaldehyde. The reaction path for dissociation into H2 + CO is predicted to pass through a low symmetry transition state with an activation energy of 4•8 eV. Both of these predictions are in good agreement with recently published ab initio calculations.

Anharmonicity and local mode effects in the vibrational spectrum of NiCO4 and Co(CO)3NO

Previously published data on the vibrational fundamentals and overtones of the carbonyl stretching modes of Ni(CO)4 and Co(CO)3NO are reinterpreted using the recent model of Mills and Robiette, including Darling-Dennison resonances and local mode effects. The harmonic wavenumber θm and anharmonicity constant xm associated with the carbonyl and nitrosyl stretching modes are derived, and the 13C and 18O isotopic shifts are discussed in relation to the harmonic and anharmonic force field.

Quartic anharmonic resonances in acetylene molecules

Formulas are derived for the quartic anharmonic resonance coefficients observed to be important between C–H stretching and the combination of one quantum of C≡C stretching and two quanta of H–C≡C bending in a number of acetylene molecules. Examples of this resonance are ν3 with ν2+ν4+ν5 in 12C2H2, ν1 with ν2+2ν5 in 13C2H2, and ν1 with ν2+2ν4 in monofluoroacetylene and monochloroacetylene. The coefficients characterizing the resonances in these examples, which we denote K3,245, K1,255, and K1,244, arise from cubic and quartic terms in the anharmonic force field, in the normal coordinate representation, through second order and first order perturbation treatments respectively, where the second order resonances are calculated by a Van Vleck resonance formalism. The experimentally determined values of these coefficients are compared with values calculated from model anharmonic force fields.

The infrared spectrum of the ν2 and ν3 bands of H16OF, H18OF, and D16OF

Fourier transform IR spectra in the ν2 and ν3 regions between 800 and 1500 cm−1 have been measured of H16OF with a resolution of 0.007 cm−1 and of H18OF and DOF with a resolution of 0.040 cm−1. Ground state constants have been improved for H16OF and have been obtained for the first time for H18OF. Parameters of the v2 = 1 and v3 = 1 excited states have been determined from rovibrational analyses of ca. 1000 ν2/ν3 lines which were fitted with σ 0.36, 4.5, and 7.6 × 10−3 cm−1 for H16OF, H18OF, and D16OF, respectively. Band centers of ν2/ν3 are 1353.40466(5)/889.07974(6), 1350.3976(5)/862.2967(7), and 1002.0083(9)/891.0014(15) cm−1, respectively, for the three isotopic species. While ν2 and ν3 are sufficiently separated in HOF to be treated independently, a Coriolis resonance is evident in DOF, the interaction constant ξ23c = 0.19073(16) cm−1 being in agreement with the prediction from the harmonic force field.

Tests of MULTIMODE calculations of rovibrational energies of CH4

We report variational calculations of rovibrational energies of CH4 using the code MULTIMODE and an ab initio force field of Schwenke and Partridge. The systematic convergence of the energies with respect to the level of mode coupling is presented. Converged vibrational energies calculated using the five-mode representation of the potential for zero total angular momentum are compared with previous, benchmark calculations based on Radau coordinates using this force field for zero total angular momentum and for J = 1. Very good agreement with the previous benchmark calculations is found. (c) 2006 Elsevier B.V. All rights reserved.

Molecular dynamics simulations of proteins: can the explicit water model be varied?

In molecular mechanics simulations of biological systems, the solvation water is typically represented by a default water model which is an integral part of the force field. Indeed, protein nonbonding parameters are chosen in order to obtain a balance between water-water and protein-water interactions and hence a reliable description of protein solvation. However, less attention has been paid to the question of whether the water model provides a reliable description of the water properties under the chosen simulation conditions, for which more accurate water models often exist. Here we consider the case of the CHARMM protein force field, which was parametrized for use with a modified TIP3P model. Using quantum mechanical and molecular mechanical calculations, we investigate whether the CHARMM force field can be used with other water models: TIP4P and TIP5P. Solvation properties of N-methylacetamide (NMA), other small solute molecules, and a small protein are examined. The results indicate differences in binding energies and minimum energy geometries, especially for TIP5P, but the overall description of solvation is found to be similar for all models tested. The results provide an indication that molecular mechanics simulations with the CHARMM force field can be performed with water models other than TIP3P, thus enabling an improved description of the solvent water properties.

Studying reactive processes with classical dynamics: rebinding dynamics in MbNO

A new surface-crossing algorithm suitable for describing bond-breaking and bond-forming processes in molecular dynamics simulations is presented. The method is formulated for two intersecting potential energy manifolds which dissociate to different adiabatic states. During simulations, crossings are detected by monitoring an energy criterion. If fulfilled, the two manifolds are mixed over a finite number of time steps, after which the system is propagated on the second adiabat and the crossing is carried out with probability one. The algorithm is extensively tested (almost 0.5 mu s of total simulation time) for the rebinding of NO to myoglobin. The unbound surface ((FeNO)-N-...) is represented using a standard force field, whereas the bound surface (Fe-NO) is described by an ab initio potential energy surface. The rebinding is found to be nonexponential in time, in agreement with experimental studies, and can be described using two time constants. Depending on the asymptotic energy separation between the manifolds, the short rebinding timescale is between 1 and 9 ps, whereas the longer timescale is about an order of magnitude larger. NO molecules which do not rebind within 1 ns are typically found in the Xenon-4 pocket, indicating the high affinity of NO to this region in the protein.

Molecular dynamics simulation of interactions between a sodium dodecyl sulfate micelle and a poly(ethylene oxide) polymer

We have performed atomistic molecular dynamics simulations of an anionic sodium dodecyl sulfate (SDS) micelle and a nonionic poly(ethylene oxide) (PEO) polymer in aqueous solution. The micelle consisted of 60 surfactant molecules, and the polymer chain lengths varied from 20 to 40 monomers. The force field parameters for PEO were adjusted by using 1,2-dimethoxymethane (DME) as a model compound and matching its hydration enthalpy and conformational behavior to experiment. Excellent agreement with previous experimental and simulation work was obtained through these modifications. The simulated scaling behavior of the PEO radius of gyration was also in close agreement with experimental results. The SDS-PEO simulations show that the polymer resides on the micelle surface and at the hydrocarbon-water interface, leading to a selective reduction in the hydrophobic contribution to the solvent-accessible surface area of the micelle. The association is mainly driven by hydrophobic interactions between the polymer and surfactant tails, while the interaction between the polymer and sulfate headgroups on the micelle surface is weak. The 40-monomer chain is mostly wrapped around the micelle, and nearly 90% of the monomers are adsorbed at low PEO concentration. Simulations were also performed with multiple 20-monomer chains, and gradual addition of polymer indicates that about 120 monomers are required to saturate the micelle surface. The stoichiometry of the resulting complex is in close agreement with experimental results, and the commonly accepted "beaded necklace" structure of the SDS-PEO complex is recovered by our simulations.

Temperature dependence of protein dynamics simulated with three different water models

The effect of variation of the water model on the temperature dependence of protein and hydration water dynamics is examined by performing molecular dynamics simulations of myoglobin with the TIP3P, TIP4P, and TIP5P water models and the CHARMM protein force field at temperatures between 20 and 300 K. The atomic mean-square displacements, solvent reorientational relaxation times, pair angular correlations between surface water molecules, and time-averaged structures of the protein are all found to be similar, and the protein dynamical transition is described almost indistinguishably for the three water potentials. The results provide evidence that for some purposes changing the water model in protein simulations without a loss of accuracy may be possible.

Highly efficient separation of actinides from lanthanides by a phenanthroline-derived bis-triazine ligand

The synthesis, lanthanide complexation, and solvent ex- traction of actinide(III) and lanthanide(III) radiotracers from nitric acid solutions by a phenanthroline-derived quadridentate bis-triazine ligand are described. The ligand separates Am(III) and Cm(III) from the lanthanides with remarkably high efficiency, high selectivity, and fast extraction kinetics compared to its 2,2'-bipyridine counterpart. Structures of the 1:2 bis-complexes of the ligand with Eu(III) and Yb(III) were elucidated by X-ray crystallography and force field calculations, respec-tively. The Eu(III) bis-complex is the first 1:2 bis-complex of a quadridentate bis-triazine ligand to be characterized by crystallography. The faster rates of extraction were verified by kinetics measurements using the rotating membrane cell technique in several diluents. The improved kinetics of metal ion extraction are related to the higher surface activity of the ligand at the phase interface. The improvement in the ligand's properties on replacing the bipyridine unit with a phenanthroline unit far exceeds what was anticipated based on ligand design alone.