Biomedical subjects

Mark A Spackman

Publications and source records attributed to Mark A Spackman.

9 recordsLinked to original sources

PubMed2006

Effective molecular polarizabilities and crystal refractive indices estimated from x-ray diffraction data.

Although it was proposed some time ago that (hyper)polarizabilities might be estimated from the results of x-ray charge density refinements, early results were unconvincing. In this work we show that the one particle density obtained from the usual multipole refinement model does not contain sufficient information to determine these response properties and instead pursue the "constrained wave function" approach of fitting to x-ray structure factors. Simplified sum-over-states expressions are derived for determining the dipole polarizability from these wave functions, and these clearly show that the earlier work ignored important two-electron expectation values for the dipole polarizability, and two- and three-electron terms for Beta, etc. Correction factors for the simplified sum-over-states polarizability tensors from the constrained wave function are obtained by calibration against coupled Hartree-Fock ab initio results to yield in-crystal effective polarizability tensors. Results obtained for benzene, urea, and 2-methyl-4-nitroaniline demonstrate that the effective molecular polarizabilities clearly include the effects of intermolecular interactions and electron correlation, especially for urea where the effects on the polarizability are known to be quite large. We also carefully consider the way in which the linear bulk susceptibility, chi((1)), and refractive indices are determined from the x-ray fitted polarizabilities, employing three models based on a rigorous treatment of the local field. Incorrect results are obtained for the sort of molecules that are of interest in nonlinear optical applications if the molecules are approximated by single point dipoles. In contrast, the use of Lorentz-factor tensors averaged over several sites yields excellent results, with refractive indices obtained using this model in remarkably good agreement with optical measurements extrapolated to zero frequency.

Aniline Compounds↗

PubMed2006

Invariom-model refinement of L-valinol.

The structure of L-valinol [(S)-(+)-2-amino-3-methylbutan-1-ol or hydroxylated L-valine], C5H13NO, has been determined at 100 K by single-crystal X-ray diffraction. The independent atom model geometry, Flack parameter and figures of merit are compared with results from an invariom structure refinement. The latter provides H-atom positions free of independent atom model bias and therefore yields a more accurate hydrogen-bond pattern, and the geometry from invariom refinement shows an improved agreement with results from a quantum chemical geometry optimization.

Chemistry, Organic↗

PubMed2006

Anisotropic displacement parameters for H atoms using an ONIOM approach.

X-ray diffraction data cannot provide anisotropic displacement parameters (ADPs) for H atoms, a major outstanding problem in charge-density analysis of molecular crystals. Although neutron diffraction experiments are the preferred source of this information, for a variety of reasons they are possible only for a minority of materials of interest. To date, approximate procedures combine rigid-body analysis of the molecular heavy-atom skeleton, based on ADPs derived from the X-ray data, with estimates of internal motion provided by spectroscopic data, analyses of neutron diffraction data on related compounds, or ab initio calculations on isolated molecules. Building on these efforts, an improved methodology is presented, incorporating information on internal vibrational motion from ab initio cluster calculations using the ONIOM approach implemented in GAUSSIAN03. The method is tested by comparing model H-atom ADPs with reference values, largely from neutron diffraction experiments, for a variety of molecular crystals: benzene, 1-methyluracil, alpha-glycine, xylitol and 2-methyl-4-nitroaniline. The results are impressive and, as the method is based on widely available software, and is in principle widely applicable, it offers considerable promise in future charge-density studies of molecular crystals.

Journal Article↗

PubMed2006

Electric field-derived point charges to mimic the electrostatics in molecular crystals.

Because of the way the electrostatic potential is defined in a crystal, it is not possible to determine potential-derived charges for atoms in a crystal. To overcome this limitation, we present a novel method for determining atomic charges for a molecule in a crystal based on a fit to the electric field at points on a surface around the molecule. Examples of fits to the electric field at points on a Hirshfeld surface, using crystal Hartree-Fock electron densities computed with a DZP basis set are presented for several organic molecular crystals. The field-derived charges for common functional groups are transferable, and reflect chemical functionality as well as the subtle effects of intermolecular interactions. The charges also yield an excellent approximation to the electric field surrounding a molecule in a crystal for use in cluster calculations on molecules in solids.

Crystallization↗

PubMed2006

Reassessment of large dipole moment enhancements in crystals: a detailed experimental and theoretical charge density analysis of 2-methyl-4-nitroaniline.

The molecular dipole moment of MNA in the crystal has been critically reexamined, to test the conclusion from an earlier experimental charge density analysis that it was substantially enhanced due to a combination of strong intermolecular interactions and crystal field effects. X-ray and neutron diffraction data have been carefully measured at 100 K and supplemented with ab initio crystal Hartree-Fock calculations. Considerable care taken in the measurement and reduction of the experimental data excluded most systematic errors, and sources of error and their effects on the experimental electron density have been carefully investigated. The electron density derived from a fit to theoretical structure factors assisted in the determination of the scale and thermal motion model. The dipole moment enhancement for MNA in the crystal is much less than that reported previously and only on the order of 30-40% (approximately 2.5 D). In addition to the dipole moment, experimental deformation electron density maps, bond critical point data, electric field gradients at hydrogen nuclei, and atomic and group charges all agree well with theoretical results and trends. Anisotropic modeling of the motion of hydrogen atoms, integral use of periodic ab initio calculations, and improved data quality are all aspects of this study that represent a considerable advance over previous work.

Journal Article↗

PubMed2006

Dipole and quadrupole moments of molecules in crystals: a novel approach based on integration over Hirshfeld surfaces.

Elegant expressions are derived for the computation of dipole and quadrupole moments of molecules using the electrostatic potential and electric field evaluated on an oriented molecular surface. These expressions are implemented for Hirshfeld surfaces, applied to various molecular crystals, and compared with the results from the quantum theory of atoms in molecules. The effect of intermolecular interactions is also explored by examining the differences between electrostatic moments derived from a periodic Hartree-Fock electron density and an electron density resulting from a superposition of noninteracting molecules. The enhancement of the dipole moment for hydrogen bonded molecular crystals is typically 30%-40% and shown to be largely independent of the partitioning scheme. Dipole moments calculated from Hirshfeld surfaces systematically underestimate those from zero-flux surfaces, a result attributed to the translation of the Hirshfeld surface relative to the zero-flux surfaces for these molecules. For acetylene and benzene, the differences between a crystal calculation and the sum of noninteracting molecules are small, and both partitioning schemes yield quadrupole and second moment results in close agreement.

Journal Article↗

PubMed2004

Novel tools for visualizing and exploring intermolecular interactions in molecular crystals.

A new way of exploring packing modes and intermolecular interactions in molecular crystals is described, using Hirshfeld surfaces to partition crystal space. These molecular Hirshfeld surfaces, so named because they derive from Hirshfeld's stockholder partitioning, divide the crystal into regions where the electron distribution of a sum of spherical atoms for the molecule (the promolecule) dominates the corresponding sum over the crystal (the procrystal). These surfaces reflect intermolecular interactions in a novel visual manner, offering a previously unseen picture of molecular shape in a crystalline environment. Surface features characteristic of different types of intermolecular interactions can be identified, and such features can be revealed by colour coding distances from the surface to the nearest atom exterior or interior to the surface, or by functions of the principal surface curvatures. These simple devices provide a striking and immediate picture of the types of interactions present, and even reflect their relative strengths from molecule to molecule. A complementary two-dimensional mapping is also presented, which summarizes quantitatively the types of intermolecular contacts experienced by molecules in the bulk and presents this information in a convenient colour plot. This paper describes the use of these tools in the compilation of a pictorial glossary of intermolecular interactions, using identifiable patterns of interaction between small molecules to rationalize the often complex mix of interactions displayed by large molecules.

Journal Article↗

PubMed2003

Charge density analysis of two polymorphs of antimony(III) oxide.

High-resolution X-ray diffraction data have been collected on the cubic polymorph of antimony(III) oxide (senarmontite) to determine the charge distribution in the crystal. The results are in quantitative agreement with crystal Hartree-Fock calculations for this polymorph, and have been compared with theoretical calculations on the orthorhombic polymorph (valentinite). Information about the nature of bonding and relative bond strengths in the two polymorphs has been extracted in a straightforward manner via topological analysis of the electron density. All the close contacts in both polymorphs are found to be similar in nature based on the value of the Laplacian, the magnitude of the electron density and the local energy density at the bond critical points, and these characterise the observed interactions as substantially polar covalent, similar to molecular calculation results on Si-O and Ge-O. Electrostatic potential isosurfaces reveal the octopolar nature of this function for senarmontite, and shed light on the observed packing arrangement of Sb4O6 molecules in the crystal.

Journal Article↗

PubMed2002

Electron distribution and molecular motion in crystalline benzene: an accurate experimental study combining CCD X-ray data on C6H6 with multitemperature neutron-diffraction results on C6D6.

The electronic properties of the benzene molecule, for example its quadrupole moment and the electric field gradients (EFG's) at the H nuclei, are of fundamental importance in theoretical and experimental chemistry. With this in mind, single-crystal X-ray diffraction data on C(6)H(6) were collected with a charge-coupled device detector at T approximately 110 K. As accurate modelling of the thermal motion in the crystal was regarded as vital, especially for the hydrogen atoms, anisotropic-displacement parameters (ADP's) for the C and H atoms in C(6)H(6) were derived in a straightforward fashion from analysis of the temperature dependence of ADP's for the C and D atoms in C(6)D(6) at 15 K and 123 K obtained by neutron diffraction. Agreement between C-atom ADP's derived from thermal-motion analysis of neutron data and those obtained from multipole refinement by using the X-ray data is extraordinarily good; this gives confidence in the modelling of vibrational motion for the H atoms. The molecular quadrupole moment derived from the total charge density of the molecule in the crystal is (-29.7+/-2.4)x10(-40) C m(2), in excellent agreement with measurements made in the gas phase and in solution. The average deuterium nuclear quadrupole coupling constant (DQCC) derived from EFG tensors at H atoms is 182+/-17 kHz, also in excellent agreement with independent measurements. The strategy employed in this work may be of more general applicability for future accurate electron density studies.

Benzene↗