Coherent X‐Ray Scattering for the Hydrogen Atom in the Hydrogen Molecule
01 May 1965-Journal of Chemical Physics (American Institute of PhysicsAIP)-Vol. 42, Iss: 9, pp 3175-3187
TL;DR: In this paper, the x-ray form factors for a bonded hydrogen in the hydrogen molecule have been calculated for a spherical approximation to the bonded atom, and the corresponding complex scattering factors have also been calculated.
Abstract: The x‐ray form factors for a bonded hydrogen in the hydrogen molecule have been calculated for a spherical approximation to the bonded atom. These factors may be better suited for the least‐squares refinement of x‐ray diffraction data from organic molecular crystals than those for the isolated hydrogen atom. It has been shown that within the spherical approximation for the bonded hydrogens in H2, a least‐squares refinement of the atomic positions will result in a bond length (Re value) short of neutron diffraction or spectroscopic values. The spherical atoms are optimally positioned 0.07 A off each proton into the bond. A nonspherical density for the bonded hydrogen atom in the hydrogen molecule has also been defined and the corresponding complex scattering factors have been calculated. The electronic density for the hydrogen molecule in these calculations was based on a modified form of the Kolos—Roothaan wavefunction for H2. Scattering calculations were made tractable by expansion of a plane wave in spheroidal wavefunctions.
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TL;DR: In the last few years, the analysis of molecular crystal structures using tools based on Hirshfeld surfaces has rapidly gained in popularity as mentioned in this paper, which represents an attempt to venture beyond the current paradigm of nuclear distances and angles, crystal packing diagrams with molecules represented via various models, and to view molecules as organic wholes.
Abstract: In the last few years the analysis of molecular crystal structures using tools based on Hirshfeld surfaces has rapidly gained in popularity. This approach represents an attempt to venture beyond the current paradigm—internuclear distances and angles, crystal packing diagrams with molecules represented via various models, and the identification of close contacts deemed to be important—and to view molecules as “organic wholes”, thereby fundamentally altering the discussion of intermolecular interactions through an unbiased identification of all close contacts.
4,930 citations
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: It is shown that the AMOEBA force field is in fact a significant improvement over fixed charge models for small molecule structural and thermodynamic observables in particular, although further fine-tuning is necessary to describe solvation free energies of drug-like small molecules, dynamical properties away from ambient conditions, and possible improvements in aromatic interactions.
Abstract: Molecular force fields have been approaching a generational transition over the past several years, moving away from well-established and well-tuned, but intrinsically limited, fixed point charge models toward more intricate and expensive polarizable models that should allow more accurate description of molecular properties. The recently introduced AMOEBA force field is a leading publicly available example of this next generation of theoretical model, but to date, it has only received relatively limited validation, which we address here. We show that the AMOEBA force field is in fact a significant improvement over fixed charge models for small molecule structural and thermodynamic observables in particular, although further fine-tuning is necessary to describe solvation free energies of drug-like small molecules, dynamical properties away from ambient conditions, and possible improvements in aromatic interactions. State of the art electronic structure calculations reveal generally very good agreement with...
1,113 citations
TL;DR: The authors would like to thank M. Chabinyc, H. Ade, B. Noriega, K. Vandewal, and D. Duong for fruitful discussions in the preparation of this review and the Center for Advanced Molecular Photovoltaics for funding.
Abstract: The authors would like to thank M. Chabinyc, H. Ade, B. Collins, R. Noriega, K. Vandewal, and D. Duong for fruitful discussions in the preparation of this review. Stanford Synchrotron Radiation Lightsource (SSRL) is a national user facility operated by Stanford University on behalf of the U.S. Department of Energy, Office of Basic Energy Sciences. This publication was partially supported by the Center for Advanced Molecular Photovoltaics (Award No. KUS-C1-015-21), made by King Abdullah University of Science and Technology (KAUST).
1,072 citations
TL;DR: For nearly spherical molecules, the x-ray scattering from liquids yields structure and correlation functions for molecular scattering centers as discussed by the authors, which provide a sensitive test for future work on a molecular theory of liquid water.
Abstract: For nearly spherical molecules the x‐ray scattering from liquids yields structure and correlation functions for molecular scattering centers. The distribution of electron density in a water molecule is very nearly spherical, and orientational correlation between molecules in the liquid is not ``seen'' by x rays. Structure and correlation functions for molecular scattering centers are derived from x‐ray data on water and tabulated. They provide a sensitive test for future work on a molecular theory of liquid water.
618 citations
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TL;DR: The indicated trend for this compound, along with other results, provides the basis for a possible explanation of the anomolous values that have been obtained for hydrogen atom thermal parameters.
Abstract: Isotropic hydrogen atom thermal parameters for N,N'- hexamethylenebispropionamide have been determined. They show a definite trend and vary from approximately the same as the mean thermal parameters for atoms other than hydrogen near the center of the molecule to appreciably greater for atoms near the end. The indicated trend for this compound, along with other results, provides the basis for a possible explanation of the anomolous values that have been obtained for hydrogen atom thermal parameters.
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