M. R. Johnson

The vibrational spectrum of crystalline benzoic acid: Inelastic neutron scattering and density functional theory calculations

Vibrational spectra of several isotopomers of benzoic acid (BA) crystals have been recorded by inelastic neutron scattering and are compared with spectra calculated for different potential energy surfaces (PES). These PES were obtained within the harmonic approximation from quantum chemical density functional theory (DFT) calculations made for the monomer, the isolated dimer, and the crystal using different codes and different levels of basis functions. Without refinement of the force constants, agreement between calculated and observed spectra is already sufficient for an unambiguous assignment of all vibrational modes. The best agreement was obtained with periodic DFT calculations. The most prominent discrepancy between calculated and observed frequencies was found for the out-of-plane O–H bending modes. For these modes (as well as for the in-plane bending and the O–H stretching modes) the anharmonicity of the potential was calculated, and the anharmonic correction was shown to account for about one-thi...

Structure and vibrational dynamics of the strongly hydrogen-bonded model peptide: N-methyl acetamide

Density functional theory-based methods have been used to calculate the vibrations, in the harmonic approximation, of n-methyl acetamide in the solid state. Good agreement is obtained with previously published inelastic neutron scattering spectra. The starting point for the calculation is the crystal structure, which has to be measured at the same temperature as the vibrational spectra. Unit cell and atomic coordinates have been obtained using powder neutron diffraction on the methyl-deuterated material at 2 K. The controversial assignment of the N–H stretch mode at ∼1600 cm−1, made in the original analysis of the vibrational spectra, is not supported by the calculations presented here. Neither is evidence found for the proposed double-well potential for the proton in the hydrogen bond.

Modelling molecular vibrations in extended hydrogen-bonded networks - crystalline bases of RNA and DNA and the nucleosides

Crystalline bases of RNA and DNA and nucleosides provide a topical set of compounds showing extended hydrogen bond networks in up to three dimensions. In order to understand the structure and dynamics, such as molecular vibrations, in these systems, accurate potential energy calculations based on solid state molecular models are required. First-principles calculations based on density functional theory (DFT), which employ periodic boundary conditions have been shown in recent work on van der Waals solids and solids including hydrogen-bonded dimers and one-dimensional hydrogen-bonded chains to be most appropriate. Periodic calculations allow small molecular models based on the crystalline unit cell, which naturally include all features of any hydrogen bond network, to be constructed. Periodic DFT calculations of structure and molecular vibrations of the bases and nucleosides in the solid state, based on published crystallographic data, have been performed. The vibrational spectra are compared with recently published inelastic neutron scattering (INS) measurements and the analysis of this data based on single-molecule first-principles calculations. Solid state calculations are shown to be significantly better, offering a reliable description of vibrational modes of atoms involved in hydrogen bonds, without any refinement of calculated force constants.

Structure and dynamics of the keto and enol forms of acetylacetone in the solid state

The tunneling and librational dynamics of the methyl groups of acetyl-acetone were investigated by inelastic and quasielastic neutron scattering at ambient and high pressure (4 kbar) for a variety of isotopic compounds. Samples, prepared by quenching the liquid, are shown to consist of a mixture of keto and enol forms of the molecule. This fact explains difficulties in the data analysis of previous studies. In the present work the contributions of the two forms could be separated, by preparing pure enol samples as well as keto-enriched samples. Two inequivalent methyl groups are identified for the enol form with barrier heights of the hindering potential in the range of 220–800 K. These potential barriers are fairly sensitive to deuteration of the nonmethyl protons and to disorder in the crystal. In contrast, for the keto form the potential is insensitive to these factors. These differences reflect the influence of the hydrogen-bonded proton on the methyl group dynamics in the enol molecule.

The origin and temperature dependence of the single particle, methyl-group rotational potential in acetic acid

Abstract Inelastic neutron scattering (INS) is used to obtain a direct measurement of the tunnel frequency of the methyl groups at 2 K in acetic acid ( ν 0 = 1.52 μ eV) and its temperature dependence up to 38 K. Corresponding measurements of the libration frequency up to 90 K are also reported. In conjunction with a new 2 K crystal-structure determination, a recently published method for calculating rotational potentials of methyl groups from crystal structures is re-examined. Crystal structures at four different temperatures, and the improved calculation, are used to predict the temperature dependence of the rotational potential correctly.

Freezing on heating of liquid solutions

We report a reversible liquid-solid transition upon heating of a simple solution composed of a-cyclodextrine (alpha CD), water, and 4-methylpyridine. These solutions are homogeneous and transparent at ambient temperature and solidify when heated to temperatures between 45 degrees and 75 degrees. Quasielastic and elastic neutron scattering show that molecular motions are slowed down in the solid and that crystalline order is established. The solution freezes on heating. This process is fully reversible, on cooling the solid melts. A rearrangement of hydrogen bonds is postulated to be responsible for the observed phenomenon.

Crystal structure and low-temperature methyl-group dynamics of cobalt and nickel acetates

The crystal structures of cobalt and nickel acetate tetrahydrate have been determined at room-temperature and liquid-helium temperature by neutron powder diffraction of the fully deuterated salts. Molecular mechanics and ab initio methods based on these structural results have then been used to calculate the rotational potentials experienced by the methyl groups. We have also used inelastic neutron scattering to measure the rotational potential via the rotational tunneling spectrum of the methyl groups, and this has enabled us to compare different methods for the calculation of partial charges in these ionic compounds. Good agreement between the observables and calculations has been obtained for both compounds when ab initio methods are used to recalculate partial charges at every step of the methyl rotation.

Crystallization on heating and complex phase behavior of α-cyclodextrin solutions

Solutions composed of α-cyclodextrin (α-CD), water, and various methylpyridines, in particular, 4-methylpyridine (4MP), undergo reversible liquid-solid transitions upon heating, the crystalline solid phases undergoing further phase transformations at higher temperatures. This unusual behavior has been characterized by an ensemble of measurements, including solubility, differential scanning calorimetry, quasielastic neutron scattering, as well as x-ray powder diffraction. For the α-CD/4MP system five crystalline phases have been identified. The unit cell parameters and corresponding changes with temperature indicate a scenario for the crystallization process. A simple model is proposed that mimics the observed disorder-order transition.

Molecular deformations of halogeno-mesitylenes in the crystal: structure, methyl group rotational tunneling, and numerical modeling

In crystals of halogeno-mesitylenes, steric hindrance between methyl groups and halogen atoms results in a small out-of-plane deformation of the heavy atoms. Even though these deformations are of very small amplitude, their effect on the rotational potential of the methyl groups is very large because the large threefold contributions to the potential due to the halogens next to a methyl group do not cancel as they do in a planar structure. An investigation of these effects by a combination of computational and experimental methods is presented here for compounds for which precise single crystal structure determinations at low temperatures are available, namely tribromomesitylene and triiodomesitylene, as well as dibromomesitylene for which such a determination was made recently. Information about the rotational potential of the methyl groups is derived from the observed proton densities as well from inelastic and quasi-elastic neutron scattering studies of the tunneling dynamics. DFT calculations reproduce well the molecular structures in the crystal, while a planar structure is predicted for the isolated molecules. The rotational potential of the methyl groups was characterized by DFT and force field calculations at different levels of approximation. The correct calculation of the amplitude of the rotational potential requires the inclusion of the relaxation of all atomic positions during the methyl group rotation, indicating that a one-dimensional model of the rotation is inadequate.

Rotation–libration and rotor–rotor coupling in 4-methylpyridine

The low temperature rotational dynamics of methyl groups in 4-methylpyridine is analyzed in terms of a model potential including rotation-libration and rotor-rotor coupling. The parameters of the model potential are adjusted by comparison of calculated with published and newly recorded inelastic neutron scattering spectra. Initial evaluations of the potential parameters of the model are obtained from molecular mechanics calculations. Experimental spectra are calculated from these potentials by numerical solution of Schrödingers equation for clusters of coupled rotors embedded in a bigger ensemble of rotors treated in the mean field approximation. Adjustment of the potential parameters leads to excellent agreement with the experimental spectra of protonated 4-methylpyridine, measured at well-defined spin temperatures. At higher levels of deuteration, agreement with experiment is qualitative, only. The observed deviations are attributed to the increasing frustration of the system of coupled methyl groups and mutual localization, effects leading to a phase transition around 5.5 K in isotopic mixtures, as shown in diffraction experiments.