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Bad language in stereochemistry-and elsewhere-can lead to sloppy thinking. In this Essay I review the history of stereochemical concepts and vocabulary in the hope that it may contribute a little to better thinking and communication.
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Some questions are raised concerning the interpretation of distances between atoms of neighbouring molecules in crystals.
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Although listed in organic chemistry textbooks as one of the strongest carbon acids, and in spite of more than a hundred years of attempts to prepare the compound, tricyanomethane (cyanoform) has resisted isolation and characterization, either as the carbon-acid 1 or as the dicyanoketenimine tautomer 2. Only in the vapor phase at very low pressure has the compound been identified from its microwave spectrum. Here we review and partially repeat the preparative work. With the aid of spectroscopic and diffraction methods (including powder diffraction) we have identified some of the products obtained as: hydronium tricyanomethanide (3), (Z)-3-amino-2-cyano-3-iminoacrylimide (4), a co-crystal of 4 with sulfuric acid (or corresponding iminium salt), and an addition product of 2 with hydrochloric acid (5/6). Quantum-mechanical calculations at the MP2/6-311++g(2d,2p) level have been made to assess the relative energies of some of the molecules involved.
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This tutorial review introduces the fundamentals of intermolecular interactions in terms of the underlying physics and goes on to illustrate the most popular methods for the computer simulation of intermolecular interactions, from atom-atom potentials to ab initio methods, including intermediate, hybrid methods, with an appreciation of their relative merits and costs. Typical results are critically presented, culminating in the most difficult exercise of all, the computer prediction of crystal structures. Perspectives on our present and future ability to understand and exploit intermolecular interactions are given.
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The crystal structure of fluorobenzene is compared with isomorphous crystal structures of molecules of roughly similar shape. The lowest-energy fluorobenzene dimers are identified by theoretical calculations. Molecular pair analysis of the crystal structure of fluorobenzene and of an isomorphous virtual low-energy polymorph of benzene suggests that the important intermolecular interactions in the two structures are closely similar. In particular, the intermolecular C-H...F interactions in the fluorobenzene crystal have approximately the same structure-directing ability and influence on the intermolecular energy as the corresponding C-H...H interactions in benzene. Molecular pair analysis of the isomorphous crystal structures of benzonitrile, alloxan, and cyclopentene-1,2,3-trione indicates that essentially the same crystal structure can be adopted with quite different patterns of pair energies and atom-atom interactions. The question as to whether the packing radius of organic fluorine is larger or smaller than that of hydrogen, is addressed, but not answered.
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Factors influencing quantum mechanical calculations of nonbonded interactions between organic molecules are still imperfectly understood. Much effort has gone into efforts to calculate the structures and binding energies of stable benzene dimers. However, little experimental evidence is available for comparison with theoretical results. As a benchmark for assessing the reliability and accuracy of such calculations, the benzene crystal structure seems a more suitable target than the elusive dimer structures.
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Molecules are held together mainly by forces acting between individual atoms. Does the same apply to molecular clusters? Does intermolecular cohesion depend on weak bonds between individual atoms in different molecules or on less localized, more diffuse interactions between molecules? We discuss these questions from several viewpoints and in particular compare interpretations based on the extension of Bader's atoms in molecules (AIM) theory to cover closed-shell intermolecular interactions with interpretations based on the new pixel method for the calculation of coulombic, polarization, dispersion, and repulsion energies from the electron density of molecular clusters.
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The transformation of ammonium cyanate into urea, first studied over 170 years ago by Wöhler and Liebig, has an important place in the history of chemistry. To understand the nature of this solid state reaction, knowledge of the crystal structure of ammonium cyanate is a prerequisite. Employing neutron powder diffraction, we demonstrate conclusively that, in the structure of ammonium cyanate, the NH(4)(+) cation forms N-H...N hydrogen bonds to four cyanate N atoms at alternate corners of a distorted cube, rather than our previously proposed alternative arrangement with N-H...O hydrogen bonds to cyanate O atoms at the other four corners.
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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.
