D. Feil

Molecular-dynamics simulation of crystalline 18-crown-6: thermal shortening of covalent bonds

Molecular-dynamics simulations of crystalline 18-crown-6 have been performed in a study of the apparent thermal shortening of covalent bonds observed in crystal structures. At 100 K, a shortening of 0.006 _+ 0.001 A for C----C and C----O bonds was obtained. This result was found to be independent of details of the force field and the simulation. There was agreement between computational and experimental values for the thermal parameters, as well as for the molecular geometry (bond and dihedral angles) of 18-crown-6. Some differences are attributed to the inability of the force field to reproduce hydrogen-bonding geometries. Simulation at 295 K resulted in an estimated shortening of 0.019_+ 0.005 A. Thus at room temperature for C--C bonds (apparent) thermal shortening and (real) chemical shortening, resulting from the electronegative oxygen substituents, are of the same order of magnitude. In the simulation at 295 K occasional dihedral transitions were observed, which may reflect the proximity of the melting point (312 K).

Novel treatment of the experimental data in the application of the maximum-entropy method to the determination of the electron-density distribution from x-ray experiments

The maximum-entropy method (MEM) has been tested on a limited set of noisy Fourier data from a known electron-density distribution (EDD). It is shown that maximizing the entropy of the EDD under the usual condition of fitting the variance of the data set does not necessarily lead to a satisfactory error distribution of the calculated reflections. The MEM property of producing the flattest EDD consistent with the data causes the calculated values of strong reflections to deviate systematically as much as possible from their measured values. Calculated values of strong reflections are usually smaller than their measured values. The use of a novel constraint on the entropy maximization greatly improves the form of the error distribution and also the calculated EDD.

Modelling of the diffusion of carbon dioxide in polyimide matrices by computer simulation

Computer aided molecular modelling is used to visualize the motion of CO2 gas molecules inside a polyimide polymer matrix. The polymers simulated are two 6FDA-bases polyimides, 6FDA-4PDA and 6FDA-44ODA. These polymers have also been synthesized in our laboratory, and thus the simulated properties could directly be compared with “real-world” data. The simulation experiments have been performed using the GROMOS1 package. The polymer boxes were created using the soft-core method, with short (11 segments) chains. This results in highly relaxed and totally amorphous polyimide matrices. The motion of randomly placed CO2 molecules in the boxes during molecular dynamics runs was followed, revealing three types of motion: jumping, continuous- and trapped motion. The calculated diffusivities are unrealistic, but possible shortcomings in our model are given.

Crystal structure and charge distribution of pyrazine: effects of extinction, thermal diffuse scattering and series termination

The crystal structure and electronic charge distribution of pyrazine (1,4-diazabenzene) has been determined at 184 K by X-ray methods. The structural results of Wheatley [Acta Cryst. (1957), 10, 182-187] have been confirmed. A clear indication of bonding effects is obtained. Neither positional and thermal parameters nor difference-Fourier maps are affected by extinction. The effect of thermal diffuse scattering (TDS) on positional parameters is also negligible. However, after correction for TDS, thermal parameters increase significantly. The difference-Fourier map is influenced by TDS as well as the inclusion of high-order Fourier terms.

Potential of mean force by thermodynamic integration: molecular-dynamics simulation of decomplexation

“Umbrella sampling” has been incorporated in the thermodynamic integration method to obtain a potential of mean force by slow growth molecular-dynamics simulations. The method was tested for liquid argon, for which good agreement was obtained with a standard potential of mean force, as derived from the radial pair-correlation function. For a sodium chloride ion-pair in aqueous solution the calculations showed resonable agreement with a literature result. The method was also applied to the decomplexation of 18-crown-6 and a potassium cation in aqueous solution.

Molecular-dynamics simulations of interfaces between water and crystalline urea

Molecular-dynamics simulations of several water-crystalline urea interfaces have been performed. The structure and dynamics of water close to the urea crystal surface are discussed in terms of density profiles, positional and orientational distribution functions, and diffusion coefficients. The water structure close to the interface is strongly determined by the structure of the crystal surface: the (001) and (111) interfaces reveal strong adsorption of water while the (110) and () interfaces do so to a lesser extent. Assuming that the growth rate of a specific crystal face decreases with increasing solvent adsorption, the appearance of only (111) on the urea growth form is predicted. We argue that on the other hand the dominance of (110) over (001) cannot be explained using a simple layer growth model.

Project on comparison of structural parameters and electron density maps of oxalic acid dihydrate

Results obtained from four X-ray and five neutron data sets collected under a project sponsored by the Commission on Charge, Spin and Momentum Densities are analyzed by comparison of thermal parameters, positional parameters and X - N electron density maps. Three sets of theoretical calculations are also included in the comparison. Though several chemically significant features are reproduced in all the experimental density maps, differences in detail occur which caution against overinterpretation of the maps. Large differences between vibrational tensor elements Uij are observed which can often not be corrected by the scaling of all temperature parameters in a set. Positional parameters are reproducible to precisions of 0.001 A or better. The biggest discrepancies between theoretical and experimental deformation density maps occurs in the lone-pair regions where peaks are higher in the theoretical maps. However, this comparison may be affected by inadequacies in the thermal-motion formalism which must be invoked before experimental and theoretical maps can be compared in a quantitative way.

The crystal structure of urea nitrate

The structure of urea nitrate has been solved, by the use of three-dimensional X-ray data. Data were collected using Cu Ke and Mo K0~ radiations. The structure consists of layers with urea and nitrate groups held together by hydrogen bonds. The positions of all hydrogen atoms were found. The final R values for Cu and Mo measurements are 4.8% and 6.2% respectively. The agreement between the two sets of data is good.

Molecular dynamics of 18-crown-6 complexes with alkali-metal cations and urea: prediction of their conformations and comparison with data from the Cambridge Structural Database

Complexes of 18‐crown‐6 with alkali–metal cations (Na+, K+, and Rb+), urea, and the uncomplexed crown ether were studied in vacuo with the molecular dynamics method. Conformational data from these calculations (simulation times in the range from 6–15 ns) was compared with information from the Cambridge Structural Database. Despite the differences in condition between the simulations and the solid state, a number of interesting similarities are observed.

A local density‐functional study of the electron density distribution in the H2O dimer

Accurate local density‐functional calculations of the electron density distribution in the H2O dimer are performed and, in order to distinguish intramolecular charge shifts from intermolecular charge transfer, analyzed in terms of an expansion in atom‐centered multipole moments. The dependence on basis set and basis set superposition error of the electron density redistribution upon forming the hydrogen bonded complex has been examined. A model study reveals that only strong hydrogen bonds induce electron density redistributions large enough to be observable by means of x‐ray diffraction.