The calculation of molecular volumes and the use of volume analysis in the investigation of structured media and of solid-state organic reactivity
01 Aug 1983-Journal of the American Chemical Society (American Chemical Society)-Vol. 105, Iss: 16, pp 5220-5225
TL;DR: In this article, a methode de calcul, rapide et precise, des volumes moleculaires a partir des geometries Moleculaires and des rayons atomiques.
Abstract: Proposition d'une methode de calcul, rapide et precise, des volumes moleculaires a partir des geometries moleculaires et des rayons atomiques. Application au calcul du volume de la cavite dans des composes de type cage, a la prevision de la stœchiometrie et de la stabilite de composes d'inclusion dans des matrices solides, a l'analyse des facteurs steriques agissant sur la reactivite de composes organiques a l'etat solide
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TL;DR: Due to wide application of MolProbity validation and corrections by the research community, in Phenix, and at the worldwide Protein Data Bank, newly deposited structures have continued to improve greatly as measured by Mol probity's unique all‐atom clashscore.
Abstract: This paper describes the current update on macromolecular model validation services that are provided at the MolProbity website, emphasizing changes and additions since the previous review in 2010. There have been many infrastructure improvements, including rewrite of previous Java utilities to now use existing or newly written Python utilities in the open-source CCTBX portion of the Phenix software system. This improves long-term maintainability and enhances the thorough integration of MolProbity-style validation within Phenix. There is now a complete MolProbity mirror site at http://molprobity.manchester.ac.uk. GitHub serves our open-source code, reference datasets, and the resulting multi-dimensional distributions that define most validation criteria. Coordinate output after Asn/Gln/His "flip" correction is now more idealized, since the post-refinement step has apparently often been skipped in the past. Two distinct sets of heavy-atom-to-hydrogen distances and accompanying van der Waals radii have been researched and improved in accuracy, one for the electron-cloud-center positions suitable for X-ray crystallography and one for nuclear positions. New validations include messages at input about problem-causing format irregularities, updates of Ramachandran and rotamer criteria from the million quality-filtered residues in a new reference dataset, the CaBLAM Cα-CO virtual-angle analysis of backbone and secondary structure for cryoEM or low-resolution X-ray, and flagging of the very rare cis-nonProline and twisted peptides which have recently been greatly overused. Due to wide application of MolProbity validation and corrections by the research community, in Phenix, and at the worldwide Protein Data Bank, newly deposited structures have continued to improve greatly as measured by MolProbity's unique all-atom clashscore.
2,355 citations
TL;DR: In this paper, the authors summarized the available data on the van der Waals radii of atoms in molecules and crystals and discussed the mechanisms of transformations between these types of chemical bonding.
Abstract: The available data on the van der Waals radii of atoms in molecules and crystals are summarized. The nature of the continuous variation in interatomic distances from van der Waals to covalent values and the mechanisms of transformations between these types of chemical bonding are discussed.
1,361 citations
TL;DR: The method chosen is a set of two-parameter correlations of Bondi's radii with repulsive-wall distances calculated by relativistic coupled-cluster electronic structure calculations, which results in new atomic radii for 16 main-group elements in the periodic table.
Abstract: Atomic radii are not precisely defined but are nevertheless widely used parameters in modeling and understanding molecular structure and interactions. The van der Waals radii determined by Bondi from molecular crystals and data for gases are the most widely used values, but Bondi recommended radius values for only 28 of the 44 main-group elements in the periodic table. In the present Article, we present atomic radii for the other 16; these new radii were determined in a way designed to be compatible with Bondi's scale. The method chosen is a set of two-parameter correlations of Bondi's radii with repulsive-wall distances calculated by relativistic coupled-cluster electronic structure calculations. The newly determined radii (in A) are Be, 1.53; B, 1.92; Al, 1.84; Ca, 2.31; Ge, 2.11; Rb, 3.03; Sr, 2.49; Sb, 2.06; Cs, 3.43; Ba, 2.68; Bi, 2.07; Po, 1.97; At, 2.02; Rn, 2.20; Fr, 3.48; and Ra, 2.83.
1,215 citations
TL;DR: The analysis of more than five million interatomic "non-bonded" distances has led to the proposal of a consistent set of van der Waals radii for most naturally occurring elements, and its applicability to other element pairs has been tested.
Abstract: The distribution of distances from atoms of a particular element E to a probe atom X (oxygen in most cases), both bonded and intermolecular non-bonded contacts, has been analyzed. In general, the distribution is characterized by a maximum at short E⋯X distances corresponding to chemical bonds, followed by a range of unpopulated distances – the van der Waals gap – and a second maximum at longer distances – the van der Waals peak – superimposed on a random distribution function that roughly follows a d3 dependence. The analysis of more than five million interatomic “non-bonded” distances has led to the proposal of a consistent set of van der Waals radii for most naturally occurring elements, and its applicability to other element pairs has been tested for a set of more than three million data, all of them compared to over one million bond distances.
1,030 citations
TL;DR: It was determined that, in general, methyl groups pack well in the default staggered conformation, except for the terminal methyl groups of methionine residues, which required rotational optimization, and high-resolution structures show impressively well-fitted packing interactions.
545 citations
Cites background or methods from "The calculation of molecular volume..."
...Those radii were decreased both for theoretical reasons of charge polarization (see Gavezzotti, 1983) and also because the larger radii produced signi®cant internal clashes for all possible arginine rotamers....
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...nucleus positions) in Reduce, since they are more consistent with the data which was used to derive van der Waals radii (Bondi, 1964; Gavezzotti, 1983)....
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...We use the longer values (i.e. nucleus positions) in Reduce, since they are more consistent with the data which was used to derive van der Waals radii (Bondi, 1964; Gavezzotti, 1983)....
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