B.P. van Eijck

Crystal structure prediction of small organic molecules: a second blind test.

The first collaborative workshop on crystal structure prediction (CSP1999) has been followed by a second workshop (CSP2001) held at the Cambridge Crystallographic Data Centre. The 17 participants were given only the chemical diagram for three organic molecules and were invited to test their prediction programs within a range of named common space groups. Several different computer programs were used, using the methodology wherein a molecular model is used to construct theoretical crystal structures in given space groups, and prediction is usually based on the minimum calculated lattice energy. A maximum of three predictions were allowed per molecule. The results showed two correct predictions for the first molecule, four for the second molecule and none for the third molecule (which had torsional flexibility). The correct structure was often present in the sorted low-energy lists from the participants but at a ranking position greater than three. The use of non-indexed powder diffraction data was investigated in a secondary test, after completion of the ab initio submissions. Although no one method can be said to be completely reliable, this workshop gives an objective measure of the success and failure of current methodologies.

Influence of molecular vibrations on substitution coordinates

Abstract The consistency of the substitution method has been checked by examining the change of the planar moment of inertia upon substitution in those cases where this change should be zero by symmetry. From 438 literature data it was concluded that Costains estimate for the reliability of substitution coordinates is adequate except for the HD substitution where it is too optimistic by at least a factor of 2. A special case is formed by the substitution CH3CH2D, where absurdly large differences in the planar moments of inertia occur. It is shown that these differences can be largely eliminated when the effects of the torsion on parent and substituted molecules are properly accounted for. Approximate formulas for this purpose are derived and tested. It appears that neglect of these corrections is not justified when the geometry of a methyl group is to be determined accurately.

Acetic acid: Microwave spectra, internal rotation and substitution structure

Abstract The internal rotation splittings in the microwave spectrum of acetic acid have been re-examined, using both principal axis method (PAM) and internal axis method (IAM) treatments. It is shown how individual terms in the PAM equation can be correlated to the first terms in an expansion of the corresponding IAM formula. When centrifugal distortion was allowed for, both methods reproduced the A-type frequencies within experimental error. For the E-type lines the r.m.s. deviation was 1.64 MHz in the PAM (using Wvσ(n)-terms with n = 1, 2, …, 14, d, e, f) and 0.70 MHz in the IAM. To derive the substitution structure eight isotopic species were studied. The inertial moments of the molecules with various degrees of methyl group deuteration are not consistent with each other, so these data could not be fully used. Therefore, the structure was derived with the assumption of a cylindrically symmetric methyl group, although there is some evidence that the HCH angles differ by a few degrees. The geometry, which is in agreement with earlier electron diffraction results, is compared with the substitution structures of other carboxylic acids.

Attempted prediction of the crystal structures of six monosaccharides

A method is reported to generate possible crystal structures of the six hexopyranoses where comparison with an X-ray determination is possible. In these molecules, internal degrees of freedom are all-important. Using essentially only the information that the space group is P2 1 2 1 2 1 with one molecule in the asymmetric unit, a systematic search was made for all low-energy crystal structures of these substances. The energies were minimized with respect to nine lattice and rigid-body parameters and six intramolecular dihedral angles. The number of possible structures within the range 10 kcal mol −1 is of the order 1000. In all cases, the experimental structure was among them, and in four cases this was either the structure with the lowest energy or only a few tenths of a kcal mol −1 higher. However, in the two other cases the relative energy of the experimental structure was over 5 kcal mol −1 . Such calculations can provide a sensitive test for force fields

The rotational spectrum of acetone: Internal rotation and centrifugal distortion analysis

Abstract In the rotational spectrum of acetone, 52 new quartets (up to 300 GHz, J≤30) have been measured. Because the barrier hindering internal rotation is low (s = 21), a new computer program based on the Internal Axis Method has been developed. It has allowed us to satisfactorily fit the spectrum and to accurately determine the rotational constants, centrifugal distortion constants, and the three internal rotation parameters.

The millimeter-wave spectra of furan, pyrrole, and pyridine: Experimental and theoretical determination of the quartic centrifugal distortion constants

The ground state rotational spectra of furan, pyrrole, and pyridine have been investigated in the millimeter-wave range. High J transitions (J<60) have been measured and accurate rotational and centrifugal distortion constants have been determined. The results of the analysis are sufficiently accurate for the prediction of all strong transitions throughout the millimeter-wave range. The experimental quartic centrifugal distortion constants are compared with the values calculated from a quantum chemical force field.

Tunneling motion in ArH+3 and isotopomers from the analysis of their rotational spectra

The millimeter and submillimeter wave spectra of different H/D isotopomers of ArH+3 were investigated. The ionic clusters were produced inside a negative glow extended by a magnetic field, in Ar/H2/D2 mixtures. Most of the observed rotational lines were split by internal motion and spin statistical weights as well as intensity ratios for the components were determined from symmetry considerations. The splittings were interpreted in terms of internal motion of the H+3 triangle. In a first step, the usual rigid top‐rigid frame model was used to reproduce the order of magnitude of the splittings. In a second step, a more refined model, which accounts for the flexibility of the top and the frame, led to a better calculation of the observed splittings in ArH+3 and ArD+3.

Reformulation of quartic centrifugal distortion Hamiltonian

Abstract Some of Watsons quartic centrifugal distortion parameters have the undesirable property that they become infinite when two rotational constants are equal. A proposal is made for a redefinition of the parameters in such a way that they stay well defined in the symmetric top limit.

Microwave spectra and molecular structures of rotational isomers of fluoroacetic acid and fluoroacetyl fluoride

Abstract The molecular structures of both the trans - and the cis -conformations of fluoroacetic acid and fluoroacetyl fluoride have been redetermined from the microwave spectra of isotopically substituted species. For the fluoride the results of single and multiple D-substitutions are compared, and the effect of the torsional motion on substitution coordinates is discussed. From the fairly large geometry differences between rotational isomers the energy effect involved in geometry relaxation is estimated to be roughly 1–2 kcal mole −1 , which is more than the cis-trans energy differences themselves.

Hydrogen-bond geometry around sugar molecules: comparison of crystal statistics with simulated aqueous solutions

Abstract Hydrogen bonding in aqueous solutions of β-D-fructose and β-D-glucose was simulated by the molecular dynamics method. Hydroxyl groups were found to function as approximately one donor and one acceptor. The hydrogen bonding was found to occur predominantly in the acceptor lone pair plane, with large angular variations in that plane. These findings agree well with earlier results from crystal structure statistics.