Electron density study of 2H-chromene-2-thione.
01 Dec 2002-Acta Crystallographica Section B-structural Science (International Union of Crystallography)-Vol. 58, Iss: 6, pp 1011-1017
TL;DR: In this paper, the charge density distribution in 2H-chromene-2-thione (2thiocoumarin), C9H6OS, has been determined from X-ray diffraction data measured at 90ÅK using a CCD detector.
Abstract: 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 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.
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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.
181 citations
TL;DR: The identification of a "region of overlap" in terms of electron density, energy densities, and mutual penetration of the hydrogen and acceptor atoms with respect to the interaction length is suggested as a possible tool to distinguish between the two types of interactions.
Abstract: 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/6-31G** 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...
131 citations
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.
100 citations
TL;DR: 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 dif...
Abstract: 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 dif...
79 citations
TL;DR: This paper describes a group of around 25 phenylpropiolic acids in which the catemer is the default packing mode and shows that a supporting interaction, in this case a C-H...O hydrogen bond, is the essential condition for the formation of any carboxylic acid catemer.
Abstract: The catemer is an infinite one-dimensional pattern formed by the carboxylic acid group in crystals, and is constituted with O-H...O hydrogen bonds. The catemer is uncommon and may be contrasted with the ubiquitous carboxylic acid dimer, the favored mode of association of this functional group. Both catemers and dimers, however, have two O-H...O hydrogen bonds for each carboxy group, so the reasons for the rarity of the catemer must lie elsewhere. In this paper, we describe a group of around 25 phenylpropiolic acids in which the catemer is the default packing mode. Exceptionally, the particular catemer that is found in this family is of the very rare syn,anti variety. We show that a necessary ingredient in catemer formation is a supportive C-H...O hydrogen bond from a proximal C-H group, which is located on the phenyl ring, ortho to the ethynyl group, and suitably activated by electron withdrawing substituents. When steric factors become noteworthy, alternative patterns are adopted, such as the syn,syn catemer and, in one case, a rare cisoid dimer. When electron-donating groups, either through inductive effect such as methyl or through resonance such as halogens, are present on the phenyl ring, the dimer is formed in all but one case. Polymorphism seems not to be an issue in these carboxylic acids in that no compound would generally crystallize as both a dimer and a catemer. It may be concluded that a supporting interaction, in this case a C-H...O hydrogen bond, is the essential condition for the formation of any carboxylic acid catemer. Catemers are so rare because it is difficult to set up this type of supporting interaction in most carboxylic acids.
78 citations
References
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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)
19,468 citations
Book•
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
11,853 citations
"Electron density study of 2H-chrome..." refers background in this paper
...For every chemical bond in the structure there is a point at which the ®rst derivative of the charge density vanishes (Bader, 1990)....
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...The limitations in theory (Bader, 1990) to de®ne the topology of the molecular boundary could also in ̄uence the differences seen in theory and experiment....
[...]
...Also, the topology of the charge density is manifested as local maxima at the positions of the nuclei, as can be inferred from Bader's quantum theory (Bader, 1990)....
[...]
TL;DR: In this paper, a generalized aspherical-atom formalism is used to refine X-ray data on silicon, tetracyanoethylene, p-nitropyridine N-oxide and ammonium thiocyanate.
Abstract: X-ray data on silicon, tetracyanoethylene, p-nitropyridine N-oxide and ammonium thiocyanate are refined with a generalized aspherical-atom formalism as introduced by Stewart, but modified to have a spherical valence more similar to the unperturbed HF valence shell. Several types of radial dependences of the multipole functions are tested and criteria are developed for judging the adequacy of the aspherical-atom refinement. The aspherical-atom model leads to a significant decrease in the least-squares error function, a reduction of features in the residual map, and an improvement in thermal parameters when comparison is made with the neutron results or when the rigid-bond postulate proposed by Hirshfeld is applied. Positional parameters are often improved except in the case of terminal atoms for which discrepancies, attributed to correlation between dipole-population and positional parameters, are sometimes observed. Deformation maps based on the aspherical-atom least-squares parameters contain less noise than X -- N maps and benefit from inclusion of calculated values of weak structure amplitudes in the summation. In the cases studied, deformation maps including terms beyond the experimental resolution do not yield additional information.
1,417 citations
TL;DR: In this paper, a probe molecule coumarin 153 (Cu153) and picosecond spectroscopic techniques were used to examine the solvation dynamics in polar liquids and showed that the frequency of the electronic spectrum of this probe provides a convenient measure of solvation energetics.
Abstract: Solvation dynamics in polar liquids have been examined using the probe molecule coumarin 153 (Cu153) and picosecond spectroscopic techniques. Steady‐state absorption and fluorescence spectra of Cu153 as a function of solvent show that the frequency of the electronic spectrum of this probe provides a convenient measure of solvation energetics. Both nonspecific dipolar and to a smaller degree H‐bonding solute–solvent interactions are involved. Time‐correlated single photon counting was used to observe time‐dependent shifts of the fluorescence spectrum of Cu153 in a variety of alcohols, propylene carbonate, and N‐methylpropionamide solvents as a function of temperature. These time‐dependent spectral shifts provide a direct measure of the time dependence of the solvation process. Theoretical models that treat the solvent as a dielectric continuum do not adequately account for the observed solvation dynamics. In the solvents studied, such theories predict a single exponential shift of the fluorescence spectrum...
1,127 citations
TL;DR: In this article, the success of this separation can be tested by comparison of the vibration ellipsoids of bonded atom pairs, which should have equal amplitudes in the bond direction.
Abstract: The frequent practice of combining X-ray and neutron diffraction for distinguishing vibrational smearing from charge deformation due to chemical bonding is neither necessary nor completely satisfactory. The two effects occur principally in distinct regions of real and reciprocal space. They can be distinguished by X-ray data alone provided these extend to reciprocal radii d* > 2 A- 1 and provided the refinement program allows explicitly for the bonding deformation. The success of this separation can be tested by comparison of the vibration ellipsoids of bonded atom pairs, which should have equal amplitudes in the bond direction. Application of this 'rigid-bond' test to four recent refinements using the charge deformation model shows the vibration parameters to be largely unbiased, as those from parallel spherical-atom refinements are not. Hydrogen vibration parameters cannot be derived from X-ray data because of large deformation densities at the nuclei; nor do they satisfy the rigid-bond postulate.
675 citations