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We describe the use of dipole lattice sums to estimate the electric field experienced by a molecule in a crystal, and apply it iteratively to ab initio calculations on a number of molecules of interest for nonlinear optical applications. The results demonstrate that it represents an efficient and reliable route to estimating molecular dipole moments in crystals. Typical dipole moment enhancements are in the range of 10-40%, agreeing well with the range resulting from partitioning of crystal Hartree-Fock electron densities, but much less than has been suggested in some previous work, and in particular from charge density analysis of X-ray diffraction data. © 2007 Elsevier B.V. All rights reserved.

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Chemistry

(SoNS) School of Natural Sciences

Chemical Physics Letters

The use of dipole lattice sums to estimate electric fields and dipole moment enhancement in molecular crystals

The crystal structure of the N,N,N′,N′- tetramethylethylenediammonium dithiocyanate salt has been examined by experimental charge density studies from high-resolution X-ray diffraction data. The corresponding results are compared with multipole refinements, using theoretical structure factors obtained from a periodic density functional theory calculation at the B3LYP level with a 6-31G** basis set. The salt crystallizes in space group P1̄ and contains only a single ion pair with an inversion center in the cation. The salt has thus one unique classical N +-H⋯(NCS)- hydrogen bond but also has six other weaker interactions: four C-H⋯S, one C-H⋯N, and one C-H⋯Cπ. The nature of all these interactions has been examined topologically using Bader's quantum theory of "atoms in molecules" and all eight of the Koch-Popelier criteria. The experimental and theoretical approaches agree well and both show that the inter-ion interactions, even in this simplest of systems, play an integrated and complex role in the packing of the ions in the crystal. Electrostatic potential maps are derived from experimental charge densities. This is the first time such a system has been examined in detail by these methods. © 2007 American Chemical Society.

Journal of Physical Chemistry A

Investigation of inter-ion interactions in N,N,N′N′- tetramethylethylenediammonium dithiocyanate via experimental and theoretical charge density studies

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. © 2006 International Union of Crystallography.

Acta Crystallographica Section C: Crystal Structure Communications

Invariom-model refinement of L-valinol

Detailed investigation of the charge density distribution in concomitant polymorphs of 3-acetylcoumarin in terms of experimental and theoretical densities shows significant differences in the intermolecular features when analyzed based on the topological properties via the quantum theory of atoms in molecules. The two forms, triclinic and monoclinic (Form A and Form B), pack in the crystal lattice via weak C-H⋯O and C-H⋯π interactions. Form A results in a head-to-head molecular stack, while Form B generates a head-to-tail stack. Form A crystallizes in P1̄ (Z′ = 2) and Form B crystallizes in P21/n (Z′ = 1). The electron density maps of the polymorphs demonstrate the differences in the nature of the charge density distribution in general. The charges derived from experimental and theoretical analysis show significant differences with respect to the polymorphic forms. The molecular dipole moments differ significantly for the two forms. The lattice energies evaluated at the HF and DFT (B3LYP) methods with 6-31G** basis set for the two forms clearly suggest that Form A is the thermodynamically stable form as compared to Form B. Mapping of electrostatic potential over the molecular surface shows dominant variations in the electronegative region, which bring out the differences between the two forms. © 2006 American Chemical Society.

Crystal Growth and Design

Topological analysis of charge density distribution in concomitant polymorphs of 3-acetylcoumarin, a case of packing polymorphism

In an attempt to investigate the putative S-H⋯N hydrogen bond, we have studied the title compound, 1-formyl-3-thiosemicarbazide, which was revealed in a CSD search as a crystal structure which might show such an interaction. However, a redetermination of the structure at room temperature and careful analysis showed that the earlier study [Saxena et al (1991). Acta Cryst. C47, 2374-2376] on which the CSD search was based was in error and that the possibility of an S-H⋯N hydrogen bond is negated. The presence of five other varieties of hydrogen bond (N-H⋯O, N-H⋯S, N-H⋯N, C-H⋯O, C-H⋯S) in the crystal packing prompted us to redirect our efforts and to undertake a study of the charge-density distribution at 90 K. The topological analysis of these five varieties of hydrogen bond was carried out with Bader's quantum theory of 'atoms in molecules' and by applying Koch-Popelier's criteria. The analysis reveals that the hydrogen-bond strength is highest for N-H⋯O and lowest for C-H⋯S with N-H⋯S, N-H⋯N and C-H⋯O forming the middle order. © 2006 International Union of Crystallography Printed in Great Britain - all rights reserved.

Acta Crystallographica Section B: Structural Science

Five varieties of hydrogen bond in 1-formyl-3-thiosemicarbazide: An electron density study

The topological features of the charge densities, ρ(r), of three bioactive molecules, 2-thiouracil [2,3-dihydro-2-thioxopyrimidin-4(1H)-one], cytosine [4-aminopyrimidin-2(1H)-one] monohydrate and salicylic acid (2-hydroxybenzoic acid), have been determined from high-resolution X-ray diffraction data at 90 K. The corresponding results are compared with the periodic theoretical calculations, based on theoretical structure factors, performed using DFT (density-functional theory) at the B3LYP/6-31G** level. The molecules pack in the crystal lattices via weak intermolecular interactions as well as strong hydrogen bonds. All the chemical bonds, including the intra- and intermolecular interactions in all three compounds, have been quantitatively described by topological analysis based on Bader's quantum theory of 'Atoms In Molecules'. The roles of interactions such as C-H⋯O, C-H⋯S, C-H⋯π and π⋯π have been investigated quantitatively in the presence of strong hydrogen bonds such as O-H⋯O, N-H⋯O and N-H⋯S, based on the criteria proposed by Koch and Popelier to characterize hydrogen bonds and van der Waals interactions. The features of weak intermolecular interactions, such as S⋯S in 2-thiouracil, the hydrogen bonds generated from the water molecule in cytosine monohydrate and the formation of the dimer via strong hydrogen bonds in salicylic acid, are highlighted on a quantum basis. Three-dimensional electrostatic potentials over the molecular surfaces emphasize the preferable binding sites in the structure and the interaction features of the atoms in the molecules, which are crucial for drug-receptor recognition. © 2006 International Union of Crystallography Printed in Great Britain - all rights reserved.

Intra- and intermolecular interactions in small bioactive molecules: Cooperative features from experimental and theoretical charge-density analysis

Analysis of charge density distributions in molecular crystals has received considerable attention in the last decade both from high-resolution X-ray diffraction studies and from high-level theoretical calculations. An overview of the progress made in deriving one-electron properties, intermolecular interactions in terms of the Atoms in Molecule (AIM) approach (R.F.W. Bader. Atoms in Molecules-A Quantum Theory, Clarendon, Oxford (1990), R.F.W. Bader. J. Phys. Chem., A102, 7314 (1998)) is given with special emphasis on improvements in charge density models and development of both experimental and theoretical techniques to interpret and analyse the nature of weak intermolecular interactions. The significance of the derived results from the charge density of coumarin and its derivatives have been analysed to obtain insights into the nature of intermolecular C-H⋯O, C-H ⋯π, π⋯π, C-H⋯S, and S⋯S contacts. The appearance of a 'region of overlap' to segregate hydrogen bonds from van der Waals interactions based on the criteria proposed by Koch and Popelier (U. Koch, P.L.A. Popelier. J. Phys. Chem., 99, 9747 (1995), P.L.A. Popelier. Atoms in Molecules. An Introduction, pp. 150-153, Prentice Hall, UK (2000)) and the identification of differences in energy surfaces in concomitant polymorphs of 3-acetylcoumarin are described. © 2005 Taylor & Francis.

Crystallography Reviews

Evaluation of weak intermolecular interactions in molecular crystals via experimental and theoretical charge densities

Evaluation of intermolecular interactions in terms of both experimental and theoretical charge density analyses has produced a unified picture with which to classify strong and weak hydrogen bonds, along with van der Waals interactions, into three regions. © The Royal Society of Chemistry 2005.

Fulltext

CrystEngComm

Charge density based classification of intermolecular interactions in molecular crystals

Experimental electron densities in coumarin, 1-thiocoumarin, and 3-acetylcoumarin have been analyzed based on the X-ray diffraction data at 90 K. These compounds pack in the crystal lattice with weak C-H⋯O and C-H⋯π interactions, and variations in charge density properties and derived local energy densities have been investigated in the regions of intermolecular interactions. Theoretical charge density calculations on crystals using the B3LYP/6-3 IG** method show remarkable agreement with the derived properties and energy densities from the experiment. The intermolecular interactions follow an exponential dependence of electron density and energy densities at the bond critical points. The Laplacian follows a "Morse-like" dependence on the length of the interaction line. Based on the set of criteria defined using the theory of "atoms in molecules", it has become possible to distinguish between a hydrogen bond (C-H⋯O) and a van der Waals interaction (C-H⋯π). This has resulted in the identification of a "region of overlap" in terms of electron densities, energy densities, and mutual penetration of the hydrogen and acceptor atoms with respect to the interaction length. This approach suggests a possible tool to distinguish between the two types of interactions.

Exploring the lower limit in hydrogen bonds: Analysis of weak C-H⋯O and C-H⋯π interactions in substituted coumarins from charge density analysis

The crystal structure of the title compound (systematic name: 2H-1-benzothiopyran-2-thione), C9H6S2, also known as dithiocoumarin, has been determined. The molecule is essentially planar and the structure is stabilized via S⋯S and C-H⋯π interactions. © 2004 International Union of Crystallography Printed in Great Britain - all rights reserved.

Acta Crystallographica Section E: Structure Reports Online

2H-Thiochromene-2-thione

An analysis of structural features associated with polymorphism in 3-acetylcoumarin has been made in terms of morphology, infrared spectroscopy, crystal structure, powder X-ray diffraction, and differential scanning calorimetric measurements. The appearance of concomitant polymorphe is found to depend on the crystallization temperature in the 1:1 chloroform/hexane solvent system. C-H⋯O and C-H⋯π interactions stabilize one form in a head to head configuration, while only C-H⋯O interactions stabilize the other in a head to tail configuration of the molecules in the crystal lattice.

Concomitant polymorphism in 3-acetylcoumarin: Role of weak C-H⋯O and C-H⋯π interactions

Erratum: Electron density study of 2H-chromene-2-thione (Acta Crystallographica Section B: Structural Science (2002) B58 (1011-1017))

The charge-density distribution in 2H-chromene-2-thione (2-thiocoumarin), C9H6OS, has been determined from X-ray diffraction data measured at 90 K using a CCD detector, to a resolution of sinθ/λ &lt; 1.08 Å-1. A multipolar-atom density model was fitted against 6908 reflections with I &gt; 2σ(I) [R(F) = 0.021, wR(F) = 0.022, goodness of fit = 1.81] in order to generate the difference Fourier maps. The topological properties of the molecular electron density in terms of the bond critical points and the evaluation of the dipole moment show that the molecular dipole moment in the crystal is higher than the corresponding value derived from theoretical calculations.