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Journal ArticleDOI: 10.1107/S0108768106017393

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

01 Aug 2006-Acta Crystallographica Section B-structural Science (International Union of Crystallography)-Vol. 62, Iss: 4, pp 612-626
Abstract: 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.

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Topics: Non-covalent interactions (64%), Intermolecular force (57%), Molecule (57%) ...read more
Citations
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Journal ArticleDOI: 10.1021/IC801402U
Abstract: A series of lanthanide adducts with different amounts of 1,10-phenanthroline, chloride ions, and water molecules in the inner and outer coordination spheres are investigated with the aim of relating the chemical bonding pattern in the crystals to the luminescence properties of the Eu ion: [LnCl1Phen2(H2O)3]Cl2(H2O) (Ln = Eu, 1Eu; Gd, 1Gd; Tb, 1Tb), [EuCl2Phen2(H2O)2]Cl1(H2O) (2), and [EuCl2Phen1(H2O)4]Cl1(H2O) (3). The influence of inner- versus outer-sphere ligands on the Ln−X bond lengths and angles in the structure is examined. A detailed topological analysis of the electron density function derived from the X-ray diffraction data for 1Gd is performed within the frame of the “atoms in molecule” theory for the first time for a lanthanide complex. The chemical bonding pattern is interpreted in terms of net atomic charges, bond energies, and electron transfers from the ligands to the metal ion. A noteworthy finding is that the energy of extended noncovalent interactions occurring in the second coordinatio...

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Topics: Outer sphere electron transfer (58%), Chemical bond (57%), Molecule (56%) ...read more

134 Citations


Open accessJournal ArticleDOI: 10.1126/SCIADV.1600192
01 May 2016-Science Advances
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.

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Topics: Neutron diffraction (56%), Bond length (54%), Neutron (52%) ...read more

131 Citations


Open accessJournal ArticleDOI: 10.1107/S0108767312008197
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.

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94 Citations


Journal ArticleDOI: 10.1021/JP405119X
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...

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Topics: Intermolecular force (53%), Charge density (52%)

67 Citations


Journal ArticleDOI: 10.1002/CPHC.200700339
08 Oct 2007-ChemPhysChem
Abstract: Although reliable determination of the molecular dipole moment from experimental charge density analyses on molecular crystals is a challenging undertaking, these values are becoming increasingly common experimental results. We collate all known experimental determinations and use this database to identify broad trends in the dipole moment enhancements implied by these measurements as well as outliers for which enhancements are pronounced. Compelling evidence emerges that molecular dipole moments from X-ray diffraction data can provide a wealth of information on the change in the molecular charge distribution that results from crystal formation. Most importantly, these experiments are unrivalled in their potential to provide this information in such detail and deserve to be exploited to a much greater extent. The considerable number of experimental determinations now available has enabled us to pinpoint those studies that merit further attention, either because they point unequivocally to a considerable enhancement in the crystal (of 50 % or more), or because the experimental determinations suggest enhancements of 100 % or more—much larger than independent theoretical estimates. In both cases further detailed experimental and theoretical studies are indicated.

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Topics: Dipole (55%)

62 Citations


References
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Journal ArticleDOI: 10.1063/1.464913
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.

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80,847 Citations


Journal ArticleDOI: 10.1103/PHYSREVB.37.785
Chengteh Lee1, Weitao Yang1, Robert G. Parr1Institutions (1)
15 Jan 1988-Physical Review B
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.

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77,776 Citations


Journal ArticleDOI: 10.1107/S0021889897003117
Louis J. Farrugia1Institutions (1)
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)

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19,153 Citations


Journal ArticleDOI: 10.1107/S0021889899006020
Louis J. Farrugia1Institutions (1)
Abstract: The category Computer Program Abstracts provides a rapid means of communicating up-to-date information concerning both new programs or systems and signi®cant 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. Cryst. (1985). 18, 189± 190] and on the World Wide Web at http://www.iucr. org/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.

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17,718 Citations


Journal ArticleDOI: 10.1021/J100785A001
Topics: Van der Waals strain (85%), Van der Waals surface (84%), Van der Waals radius (81%) ...read more

15,916 Citations


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No. of citations received by the Paper in previous years
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20217
20205
20196
20181
201711
20166