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Molecular geometry

About: Molecular geometry is a(n) research topic. Over the lifetime, 8246 publication(s) have been published within this topic receiving 170635 citation(s). The topic is also known as: molecular structure.

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Journal ArticleDOI
Karin Eichkorn1, Oliver Treutler1, Holger Öhm1, Marco Häser1  +1 moreInstitutions (1)
30 Jun 1995-
Abstract: We demonstrate accuracy and computational efficiency resulting from an approximate treatment of Coulomb operators which is based on the expansion of molecular electron densities in atom-centered auxiliary basis sets. This is of special importance in density functional methods which separate the treatment of Coulomb and exchange-correlation terms. Auxiliary basis sets are optimized as much as possible for isolated atoms and then augmented for use in molecular electronic structure calculations. For molecules involving atoms up to Br this typically affects energies by only 10−4 au per atom, and computed structure constants by less than 0.1 pm in bond distances and 0.1° in bond angles.

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2,376 citations


Journal ArticleDOI
Abstract: The approximate self‐consistent molecular orbital theory with complete neglect of differential overlap (CNDO) presented in earlier papers has been modified in two ways. (a) Atomic matrix elements are chosen empirically using data on both atomic ionization potentials and electron affinities. (b) Certain penetration‐type terms, which led to excess bonding between formally nonbonded atoms in the previous treatment, have been omitted. The new method (denoted by CNDO/2) has been applied to symmetrical triatomic (AB2) and tetratomic (AB3) molecules, for a range of bond angles. The theory leads to calculated equilibrium angles, dipole moments, and bending force constants which are in reasonable agreement with experimental values in most cases.

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1,769 citations


Journal ArticleDOI
TL;DR: The main-chain bond lengths and bond angles of protein structures are analysed as a function of resolution and differences in means are found to be highly statistically significant, suggesting that the different target values used by the different methods leave their imprint on the structures they refine.

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Abstract: The main-chain bond lengths and bond angles of protein structures are analysed as a function of resolution. Neither the means nor standard deviations of these parameters show any correlation with resolution over the resolution range investigated. This is as might be expected as bond lengths and bond angles are likely to be heavily influenced by the geometrical restraints applied during structure refinement. The size of this influence is then investigated by performing an analysis of variance on the mean values across the five most commonly used refinement methods. The differences in means are found to be highly statistically significant, suggesting that the difference target values used by the different methods leave their imprint on the structures they refine. This has implications concerning the actual target values used during refinement and stresses the importance of the values being not only accurate but also consistent from one refinement method to another.

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1,184 citations


Journal ArticleDOI
TL;DR: Polymorphism is the ability of any element or compound to crystallize as more than one distinct crystal species (e.g., carbon as cubic diamond or hexagonal graphite).

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Abstract: A polymorph is a solid crystalline phase of a given compound resulting from the possibility of at least two different arrangements of the molecules of that compound in the solid state. The molecule itself may be of different shape in the two polymorphs, but that is not necessary and, indeed, certain changes in shape (involving dynamic isomerism or tautomerism) involve formation of different molecules and hence do not constitute polymorphism. Geometrical isomers or tautomers, even though interconvertible and reversibly so, cannot be called polymorphs although they may behave in a confusingly similar manner. Shape changes, permissible in the molecule crystallizing in two or more polymorphic forms, include resonance structures, rotation of parts of the molecule about certain bonds, and minor distortions of bond distances and angles. These distortions of molecular shape result from polarizability effects of one molecule on another due to the change in relative positions of adjacent molecules in the two different crystalline arrangements. A safe criterion for classification of a system as polymorphic is the following. Two polymorphs will be different in crystal structure but identical in the liquid and vapor states. Dynamic isomers will melt at different temperatures, as do polymorphs, but will give melts of different composition. In time each of these melts changes to an equilibrium mixture of the two isomers with temperature-dependent composition. Some reported cases of polymorphism are undoubtedly dynamic isomerism, since the two behave quite similarly, especially if the equilibrium between the two isomers is very rapidly established. Polymorphism is the ability of any element or compound to crystallize as more than one distinct crystal species (e.g., carbon as cubic diamond or hexagonal graphite). Different polymorphs of a given compound are, in general, as different in structure and properties as the crystals of two different compounds. Solubility, melting point, density, hardness, crystal shape, optical and electrical properties, vapor pressure, etc., all vary with the polymorphic form. In general, it should be possible to obtain different crystal forms of a drug and thus modify the performance properties for that compound. To do so requires a knowledge of the behavior of polymorphs. Mitscherlich (1) is generally given credit for first using the term polymorphism during his work on the isomorphous sulfates of iron (ferrous), cobalt, nickel, magnesium, copper, zinc, and manganese. It is, however, obvious that the idea was not new at that time, since Humphrey Davy in 1809 pointed out that diamond and graphite are both carbon and that the two differ only in their arrangement of carbon atoms in the solid phase. Indeed, Klaproth may have been the first to be aware of polymorphism when he observed (1788) that calcium carbonate crystallizes both as calcite and as aragonite. Since that time a very large number of compounds, organic and inorganic, as well as the elements themselves, have been shown to crystallize in two or more different crystalline arrangements-chemically identical, physically different. Besides graphite and diamond there are, to name a few in the mineral field, wurtzite and sphalerite (ZnS) ; calcite, aragonite, and vaterite (CaC03) ; rutile, brookite, and anatase (TiO,). Most polymorphs, especially those of organic compounds, do not have special names; instead they are referred to as a,

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863 citations


Journal ArticleDOI
Abstract: We present the theory, computational implementation, and applications of a density functional Gaussian‐type‐orbital approach called DGauss. For a range of typical organic and small inorganic molecules, it is found that this approach results in equilibrium geometries, vibrational frequencies, bond dissociation energies, and reaction energies that are in many cases significantly closer to experiment than those obtained with Hartree–Fock theory. On the local spin density functional level, DGauss predicts equilibrium bond lengths within about 0.02 A or better compared with experiment, bond angles, and dihedral angles to within 1–2°, and vibrational frequencies within about 3%–5%. While Hartree–Fock optimized basis sets such as the 6‐31 G** set can be used in DGauss calculations to give good geometries, the accurate prediction of reaction energies requires the use of density functional optimized Gaussian‐type basis sets. Nonlocal corrections as proposed by Becke and Perdew for the exchange and correlation ener...

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838 citations


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Performance
Metrics
No. of papers in the topic in previous years
YearPapers
202223
2021191
2020176
2019201
2018207
2017244

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Topic's top 5 most impactful authors

István Hargittai

80 papers, 1.6K citations

Magdolna Hargittai

32 papers, 591 citations

David W. H. Rankin

26 papers, 408 citations

Yusuf Atalay

26 papers, 349 citations

Svein Samdal

25 papers, 329 citations