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Journal ArticleDOI

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

TL;DR: A redetermination of the structure at room temperature and careful analysis showed that the earlier study was in error and that the possibility of an S-H...N hydrogen bond is negated, resulting in a topological analysis of five varieties of hydrogen bond.
Abstract: 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
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TL;DR: It is shown that, contrary to widespread expectation, hydrogen atoms can be located very accurately using x-ray diffraction, yielding bond lengths involving hydrogen atoms (A–H) that are in agreement with results from neutron diffraction mostly within a single standard deviation.
Abstract: Precise and accurate structural information on hydrogen atoms is crucial to the study of energies of interactions important for crystal engineering, materials science, medicine, and pharmacy, and to the estimation of physical and chemical properties in solids. However, hydrogen atoms only scatter x-radiation weakly, so x-rays have not been used routinely to locate them accurately. Textbooks and teaching classes still emphasize that hydrogen atoms cannot be located with x-rays close to heavy elements; instead, neutron diffraction is needed. We show that, contrary to widespread expectation, hydrogen atoms can be located very accurately using x-ray diffraction, yielding bond lengths involving hydrogen atoms (A–H) that are in agreement with results from neutron diffraction mostly within a single standard deviation. The precision of the determination is also comparable between x-ray and neutron diffraction results. This has been achieved at resolutions as low as 0.8 A using Hirshfeld atom refinement (HAR). We have applied HAR to 81 crystal structures of organic molecules and compared the A–H bond lengths with those from neutron measurements for A–H bonds sorted into bonds of the same class. We further show in a selection of inorganic compounds that hydrogen atoms can be located in bridging positions and close to heavy transition metals accurately and precisely. We anticipate that, in the future, conventional x-radiation sources at in-house diffractometers can be used routinely for locating hydrogen atoms in small molecules accurately instead of large-scale facilities such as spallation sources or nuclear reactors.

131 citations

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TL;DR: The theoretical and practical aspects of the use of atomic energy in R Bader's theory 'Atoms in Molecules' for solving problems of physical and structural chemistry are considered in this article.
Abstract: The theoretical and practical aspects of the use of atomic energy in R Bader's theory 'Atoms in Molecules' for solving problems of physical and structural chemistry are considered

98 citations

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TL;DR: The deformation electron densities, electrostatic potentials and interaction energies calculated for several tripeptides and aromatic molecules are calculated using ELMam2 electron-density parameters and compared with the former ELMAM database and density functional theory calculations.
Abstract: ELMAM2 is a generalized and improved library of experimentally derived multipolar atom types. The previously published ELMAM database is restricted mostly to protein atoms. The current database is extended to common functional groups encountered in organic molecules and is based on optimized local axes systems taking into account the local pseudosymmetry of the molecular fragment. In this approach, the symmetry-restricted multipoles have zero populations, while others take generally significant values. The various applications of the database are described. The deformation electron densities, electrostatic potentials and interaction energies calculated for several tripeptides and aromatic molecules are calculated using ELMAM2 electron-density parameters and compared with the former ELMAM database and density functional theory calculations.

94 citations


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TL;DR: The structure, IR harmonic frequencies and intensities of normal vibrations of 20 molecular crystals with the X-Cl···Cl-X contacts of different types, and the obtained crystalline wave functions have been further used to define and describe quantitatively the Cl··· Cl interactions via the electron-density features at the Cl··Cl bond critical points.
Abstract: The structure, IR harmonic frequencies and intensities of normal vibrations of 20 molecular crystals with the X–Cl···Cl–X contacts of different types, where X = C, Cl, and F and the Cl···Cl distance varying from ∼3.0 to ∼4.0 A, are computed using the solid-state DFT method. The obtained crystalline wave functions have been further used to define and describe quantitatively the Cl···Cl interactions via the electron-density features at the Cl···Cl bond critical points. We found that the electron-density at the bond critical point is almost independent of the particular type of the contact or hybridization of the ipso carbon atom. The energy of Cl···Cl interactions, Eint, is evaluated from the linking Eint and local electronic kinetic energy density at the Cl···Cl bond critical points. Eint varies from 2 to 12 kJ/mol. The applicability of the geometrical criterion for the detection of the Cl···Cl interactions in crystals with two or more intermolecular Cl···Cl contacts for the unique chlorine atom is not str...

67 citations

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TL;DR: Experimental X-ray crystal structures of formaldehyde, acrolein and N-methylformamide have been determined in order to ascertain the role of C-H···O interactions in the crystal packing of formyl compounds.
Abstract: Structural and electronic properties of C–H⋯O contacts in compounds containing a formyl group are investigated from the perspective of both hydrogen bonding and dipole–dipole interactions, in a systematic and graded approach. The effects of α-substitution and self-association on the nature of the formyl H-atom are studied with the NBO and AIM methodologies. The relative dipole–dipole contributions in formyl C–H⋯O interactions are obtained for aldehyde dimers. The stabilities and energies of aldehyde clusters (dimer through octamer) have been examined computationally. Such studies have an implication in crystallization mechanisms. Experimental X-ray crystal structures of formaldehyde, acrolein and N-methylformamide have been determined in order to ascertain the role of C–H⋯O interactions in the crystal packing of formyl compounds.

66 citations

References
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TL;DR: In this article, a semi-empirical exchange correlation functional with local spin density, gradient, and exact exchange terms was proposed. But this functional performed significantly better than previous functionals with gradient corrections only, and fits experimental atomization energies with an impressively small average absolute deviation of 2.4 kcal/mol.
Abstract: Despite the remarkable thermochemical accuracy of Kohn–Sham density‐functional theories with gradient corrections for exchange‐correlation [see, for example, A. D. Becke, J. Chem. Phys. 96, 2155 (1992)], we believe that further improvements are unlikely unless exact‐exchange information is considered. Arguments to support this view are presented, and a semiempirical exchange‐correlation functional containing local‐spin‐density, gradient, and exact‐exchange terms is tested on 56 atomization energies, 42 ionization potentials, 8 proton affinities, and 10 total atomic energies of first‐ and second‐row systems. This functional performs significantly better than previous functionals with gradient corrections only, and fits experimental atomization energies with an impressively small average absolute deviation of 2.4 kcal/mol.

80,847 citations


"Five varieties of hydrogen bond in ..." refers methods in this paper

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TL;DR: Numerical calculations on a number of atoms, positive ions, and molecules, of both open- and closed-shell type, show that density-functional formulas for the correlation energy and correlation potential give correlation energies within a few percent.
Abstract: A correlation-energy formula due to Colle and Salvetti [Theor. Chim. Acta 37, 329 (1975)], in which the correlation energy density is expressed in terms of the electron density and a Laplacian of the second-order Hartree-Fock density matrix, is restated as a formula involving the density and local kinetic-energy density. On insertion of gradient expansions for the local kinetic-energy density, density-functional formulas for the correlation energy and correlation potential are then obtained. Through numerical calculations on a number of atoms, positive ions, and molecules, of both open- and closed-shell type, it is demonstrated that these formulas, like the original Colle-Salvetti formulas, give correlation energies within a few percent.

77,776 citations

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TL;DR: L Lists of software presented and~or reviewed in the Journal of Applied Crystallography are available on the World Wide Web at the above address, together with information about the availability of the software where this is known.
Abstract: Computer Program Abstracts The category Computer Program Abstracts provides a rapid means of communicating up-to-date information concerning both new programs or systems and significant updates to existing ones. Following normal submission, a Computer Program Abstract will be reviewed by one or two members of the IUCr Commission on Crystallographic Computing. It should not exceed 500 words in length and should follow the standard format given on page 189 of the June 1985 issue of the Journal [J. Appl. CrysL (1985). 18, 189190] and on the World Wide Web at http://www.iucr. ac. uk/journals/jac/software/. Lists of software presented and~or reviewed in the Journal of Applied Crystallography are available on the World Wide Web at the above address, together with information about the availability of the software where this is known. J. App/. CrysL (1997). 30, 565 ORTEP-3 for Windows a version of ORTEP-III with a Graphical User Interface (GUI)

19,153 citations


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15,916 citations


"Five varieties of hydrogen bond in ..." refers background in this paper

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Book

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01 Jan 1990
TL;DR: In this article, the quantum atom and the topology of the charge desnity of a quantum atom are discussed, as well as the mechanics of an atom in a molecule.
Abstract: List of symbols 1. Atoms in chemistry 2. Atoms and the topology of the charge desnity 3. Molecular structure and its change 4. Mathematical models of structural change 5. The quantum atom 6. The mechanics of an atom in a molecule 7. Chemical models and the Laplacian of the charge density 8. The action principle for a quantunm subsystem Appendix - Tables of data Index

11,422 citations


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