scholarly journals Charge distribution as a tool to investigate structural details. II. Extension to hydrogen bonds, distorted and hetero-ligand polyhedra

2001 ◽  
Vol 57 (5) ◽  
pp. 652-664 ◽  
Author(s):  
Massimo Nespolo ◽  
Giovanni Ferraris ◽  
Gabriella Ivaldi ◽  
Rudolf Hoppe
Keyword(s):  
Hydrogen Bonds ◽  
Charge Distribution ◽  
Empirical Parameter ◽  
Coordination Polyhedra ◽  
Scale Factors ◽  
Iterative Calculation ◽  
Structural Details ◽  
Contraction Parameter ◽  
Bond Strengths ◽  
Dynamic Structures

It is shown that one of the main reasons for most failures of the methods for calculating distance-dependent bond strengths is related to the distortion of the coordination polyhedra. The charge distribution (CD) method which depends on only one universal empirical parameter (contraction parameter) is modified to include: (i) an iterative calculation of the effective coordination number (ECoN), to deal with structures containing very distorted coordination polyhedra; (ii) a specific contraction parameter to treat structures containing any type of hydrogen bond; (iii) scale factors for coordination subshells, to treat structures with hetero-ligand polyhedra. The contraction parameter for the hydrogen bonds was obtained from 119 well refined structures based on neutron diffraction data. Examples of the application of the iterative charge distribution (CD-IT) are presented to show the efficiency of the new method in dealing with distorted (including hydrogen bonding) and hetero-ligand polyhedra. In particular, analysis of a series of 74 structures with pentacoordinated cations shows that deviations from overall trends are related to structure instability. The possible failure of the method with polyionic structures and `dynamic' structures is discussed.

Charge distribution as a tool to investigate structural details. IV. A new route to heteroligand polyhedra

2016 ◽  
Vol 72 (1) ◽  
pp. 51-66 ◽  
Author(s):  
Massimo Nespolo
Keyword(s):  
Charge Distribution ◽  
A Priori ◽  
Total Charge ◽  
Ionic Radii ◽  
Empirical Parameter ◽  
Coordination Polyhedra ◽  
New Approach ◽  
Bonding Effect ◽  
Structural Details ◽  
Previous Algorithm

A new route to apply the charge distribution (CHARDI) method to structures based on heteroligand coordination polyhedra is presented. The previous algorithm used scale factors computed in an iterative way based on the assumption (which turned out to be not always correct) that a real over–under bonding effect affects mainly the anionic charges of each single anion, without grossly modifying the total charge of each type of anion. The new, more general approach is not based on anya prioriassumption but treats separately the homoligand sub-polyhedra and attributes to each type of atom a fraction of the charge of the atom coordinated to it, computed in a self-consistent iterative way. The distinction between the bonding and non-bonding contact is also redefined in terms of the mean fictive ionic radii (MEFIR), without the need of an empirical parameter, used in the previous algorithm. CHARDI equations are generalized in terms of the new approach and a series of examples is presented.

Charge distribution as a tool to investigate structural details. III. Extension to description in terms of anion-centred polyhedra

2015 ◽  
Vol 71 (1) ◽  
pp. 34-47 ◽  
Author(s):  
Jean-Guillaume Eon ◽  
Massimo Nespolo
Keyword(s):  
Charge Distribution ◽  
Mixed Valence ◽  
Theoretical Description ◽  
Oxidation Number ◽  
Acta Cryst ◽  
Coordination Polyhedra ◽  
Structural Details ◽  
Mixed Valence Compounds ◽  
Experimental Geometry ◽  
Insight Into

The charge distribution (CHARDI) method is a self-consistent generalization of Pauling's concept of bond strength which does not make use of empirical parameters but exploits the experimental geometry of the coordination polyhedra building a crystal structure. In the two previous articles of this series [Nespoloet al.(1999).Acta Cryst.B55, 902–916; Nespoloet al.(2001).Acta Cryst.B57, 652–664], we have presented the features and advantages of this approach and its extension to distorted and heterovalent polyhedra and to hydrogen bonds. In this third article we generalize CHARDI to structures based on anion-centred polyhedra, which have drawn attention in recent years, and we show that computations based on both descriptions can be useful to obtain a deeper insight into the structural details, in particular for mixed-valence compounds where CHARDI is able to give precise indications on the statistical distribution of atoms with different oxidation number. A graph-theoretical description of the structures rationalizes and gives further support to the conclusions obtainedviathe CHARDI approach.

scholarly journals Electronic origin of the dependence of hydrogen bond strengths on nearest-neighbor and next-nearest-neighbor hydrogen bonds in polyhedral water clusters (H2O)n, n = 8, 20 and 24

2016 ◽  
Vol 18 (29) ◽  
pp. 19746-19756 ◽  
Author(s):  
Suehiro Iwata ◽  
Dai Akase ◽  
Misako Aida ◽  
Sotiris S. Xantheas
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Nearest Neighbor ◽  
Water Clusters ◽  
Hydrogen Donor ◽  
Donor And Acceptor ◽  
Bond Strengths

Comparison of the sum of the characteristic factors for some of the typical hydrogen donor and acceptor pairs with the CT term/kJ mol−1 (the upper value) and the O⋯O distance/in cubic (H2O)8.

Transuranium Element Incorporation into the β-U3O8 Uranyl Sheet

1996 ◽  
Vol 465 ◽  
Author(s):  
M. L. Miller ◽  
P. C. Burns ◽  
R. J. Finch ◽  
R. C. Ewing
Keyword(s):  
Crystal Structure ◽  
Spent Nuclear Fuel ◽  
Chemical Characteristics ◽  
Transuranium Element ◽  
Limited Data ◽  
Charge Balance ◽  
Coordination Polyhedra ◽  
Structural Details ◽  
Structure Determinations ◽  
Shared Edge

ABSTRACTSpent nuclear fuel (SNF) is unstable under oxidizing conditions. Although recent studies have determined the paragenetic sequence for uranium phases that result from the corrosion of SNF, there are only limited data on the potential of alteration phases for the incorporation of transuranium elements. The crystal chemical characteristics of transuranic elements (TUE) are to a certain extent similar to uranium; thus TUE incorporation into the sheets of uranyl oxide hydrate structures can be assessed by examination of the structural details of the β-U3O8 sheet type.The sheets of uranyl polyhedra observed in the crystal structure of β-U3O8 also occur in the mineral billietite (Ba[(UO2)3O2(OH)3]2(H2O)4), where they alternate with α-U3O8 type sheets. Preliminary crystal structure determinations for the minerals ianthinite, ([U24+(HO2)4O6(HO)4(H2O)4](H2O)5), and “wyartite II” (mineral name not approved by IMA committee on mineral names), {CaCo3}[U4+(UO2)2O3(OH)2](H2O)4, indicate that these phases also contain β-U3O8 type sheets. The β-U3O8sheet anion topology contains triangular, rhombic, and pentagonal sites in the proportions 2: 1:2. In all structures containing β-U3O8 type sheets, the triangular sites are vacant. The pentagonal sites are filled with U6+O2 forming pentagonal bipyramids. The rhombic dipyramids filling the rhombic sites contain U6+O2 in billietite, U4+O2 in β-U3O8U4+(H2O)2 in ianthinite, and U4+O3 in “wyartite-II” (in which one apical anion is replaced by two O atoms forming a shared edge with a carbonate triangle of the interlayer). Interlayer species include: H2O (billietite, “wyartite II”, and ianthinite), Ba2+ (billietite) Ca2+ (”wyartite II”), and CO3−2 (”wyartite II”); there is no interlayer in β-U3O8. The similarity of known TUE coordination polyhedra with those of U suggests that the β-U3O8 sheet will accommodate TUE substitution coupled with variations in apical anion configuration and interlayer population providing the required charge balance.

Charge distribution from infrared intensities: Which CH bonds form hydrogen bonds?

1985 ◽  
Vol 117 (3) ◽  
pp. 263-265 ◽  
Author(s):  
M. Gussoni ◽  
C. Castiglioni ◽  
G. Zerbi
Keyword(s):  
Hydrogen Bonds ◽  
Charge Distribution ◽  
Infrared Intensities

STRUCTURAL IMPLICATIONS OF O—H⋯O HYDROGEN BONDS IN INORGANIC CRYSTALS

2009 ◽  
Vol 23 (31n32) ◽  
pp. 3951-3958 ◽  
Author(s):  
FANGFANG ZHANG ◽  
DONGFENG XUE
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Spatial Frequency ◽  
Frequency Distribution ◽  
Structural Characteristics ◽  
Scatter Plot ◽  
Inorganic Crystal ◽  
Inorganic Crystals ◽  
Bond Strengths ◽  
Crystal Design

Structural characteristics of O — H ⋯ O hydrogen bonds in inorganic crystals were comprehensively investigated on the basis of a database study. It is shown that the multi-furcated hydrogen bonds are very common, therefore, the structures of hydrogen bonds in inorganic crystals are extremely flexible. The direction and distance preferences of hydrogen bonds were systematically analyzed through frequency distribution histograms and normalized spatial frequency distribution scatter plot. In addition, new bond valence parameters were proposed for O — H ⋯ O bonds in inorganic crystals fully taking into account the multi-furcated hydrogen bonds, which can be used to properly evaluate hydrogen bond strengths in inorganic crystals. The current work sheds some light on the usage of hydrogen bonds in inorganic crystal design.

scholarly journals Unveiled electric profiles within hydrogen bonds suggest DNA base pairs with similar bond strengths

PLoS ONE ◽  
2017 ◽  
Vol 12 (10) ◽  
pp. e0185638 ◽  
Author(s):  
Y. B. Ruiz-Blanco ◽  
Y. Almeida ◽  
C. M. Sotomayor-Torres ◽  
Y. García
Keyword(s):  
Hydrogen Bonds ◽  
Base Pairs ◽  
Dna Base ◽  
Dna Base Pairs ◽  
Bond Strengths

scholarly journals The methanol sesquisolvate of sodium naproxen

2018 ◽  
Vol 74 (11) ◽  
pp. 1624-1627
Author(s):  
Helene Kriegner ◽  
Matthias Weil ◽  
Matthew J. Jones
Keyword(s):  
Hydrogen Bonds ◽  
Coordination Number ◽  
Sodium Cation ◽  
Asymmetric Unit ◽  
Coordination Polyhedra ◽  
Oh Groups ◽  
Sodium Cations ◽  
Polymeric Chains ◽  
Sodium Naproxen ◽  
Molecular Salt

The asymmetric unit of the methanol solvate of sodium naproxen, systematic name: sodium (2S)-2-(6-methoxynaphthalen-2-yl)propanoate methanol sesquisolvate, Na+·C14H13O3 −·1.5CH3OH, comprises two formula units of the molecular salt and three methanol molecules. One of the sodium cations exhibits a coordination number of six and is bonded to three carboxylate O atoms and three methanol OH groups whereas the second sodium cation has a coordination number of seven, defined by five carboxylate O atoms and two methanol OH groups. Both coordination polyhedra around the sodium cations are considerably distorted. The two types of cations are bridged into polymeric chains extending parallel to [010]. This arrangement is stabilized by intrachain O—H...O hydrogen bonds between methanol ligands as donor and carboxylate O atoms as acceptor groups. The hydrophobic 6-methoxynaphthyl moieties flank the hydrophilic sodium oxygen chains into ribbons parallel to [010]. There are no noticeable intermolecular interactions between these ribbons. One of the 6-methoxynaphthyl moieties is disordered over two sets of sites in a 0.723 (3):0.277 (3) ratio.

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