scholarly journals Sodium potassium hydrogen citrate, NaKHC6H5O7

2016 ◽  
Vol 72 (2) ◽  
pp. 170-173 ◽  
Author(s):  
Alagappa Rammohan ◽  
James A. Kaduk
Keyword(s):  
Hydrogen Bonds ◽  
Density Functional ◽  
Bond Valence ◽  
Bond Energies ◽  
Functional Theory ◽  
Sodium Potassium ◽  
X Ray ◽  
Potassium Hydrogen ◽  
Bond Valence Sum ◽  
Hydrogen Bond Energies

The crystal structure of sodium potassium hydrogen citrate has been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional theory techniques. The Na+cation is six-coordinate, with a bond-valence sum of 1.17. The K+cation is also six-coordinate, with a bond-valence sum of 1.08. The distorted [NaO6] octahedra share edges, forming chains along theaaxis. The likewise distorted [KO6] octahedra share edges with the [NaO6] octahedra on either side of the chain, and share corners with other [KO6] octahedra, resulting in triple chains along theaaxis. The most prominent feature of the structure is the chain along [111] of very short, very strong hydrogen bonds; the O...O distances are 2.414 and 2.400 Å. The Mulliken overlap populations in these hydrogen bonds are 0.138 and 0.142 e, which correspond to hydrogen-bond energies of 20.3 and 20.6 kcal mol−1.

scholarly journals Sodium rubidium hydrogen citrate, NaRbHC6H5O7, and sodium caesium hydrogen citrate, NaCsHC6H5O7: crystal structures and DFT comparisons

2019 ◽  
Vol 75 (2) ◽  
pp. 223-227 ◽  
Author(s):  
Andrew J. Cigler ◽  
James A. Kaduk
Keyword(s):  
Hydrogen Bonds ◽  
Density Functional ◽  
Bond Valence ◽  
X Ray Diffraction ◽  
Bond Energies ◽  
Coordination Polyhedra ◽  
X Ray ◽  
Axis Direction ◽  
Bond Valence Sum ◽  
Hydrogen Bond Energies

The crystal structure of sodium rubidium hydrogen citrate, NaRbHC6H5O7 or [NaRb(C6H6O7)] n , has been solved and refined using laboratory powder X-ray diffraction data, and optimized using density functional techniques. This compound is isostructural to NaKHC6H5O7. The Na atom is six-coordinate, with a bond-valence sum of 1.16. The Rb atom is eight-coordinate, with a bond-valence sum of 1.17. The distorted [NaO6] octahedra share edges to form chains along the a-axis direction. The irregular [RbO8] coordination polyhedra share edges with the [NaO6] octahedra on either side of the chain, and share corners with other Rb atoms, resulting in triple chains along the a-axis direction. The most prominent feature of the structure is the chain along [111] of very short, very strong hydrogen bonds; the O...O distances are 2.426 and 2.398 Å. The Mulliken overlap populations in these hydrogen bonds are 0.140 and 0.143 electrons, which correspond to hydrogen-bond energies of about 20.3 kcal mol−1. The crystal structure of sodium caesium hydrogen citrate, NaCsHC6H5O7 or [NaCs(C6H6O7)] n , has also been solved and refined using laboratory powder X-ray diffraction data, and optimized using density functional techniques. The Na atom is six-coordinate, with a bond-valence sum of 1.15. The Cs atom is eight-coordinate, with a bond-valence sum of 0.97. The distorted trigonal–prismatic [NaO6] coordination polyhedra share edges to form zigzag chains along the b-axis direction. The irregular [CsO8] coordination polyhedra share edges with the [NaO6] polyhedra to form layers parallel to the (101) plane, unlike the isolated chains in NaKHC6H5O7 and NaRbHC6H5O7. A prominent feature of the structure is the chain along [100] of very short, very strong O—H...O hydrogen bonds; the refined O...O distances are 2.398 and 2.159 Å, and the optimized distances are 2.398 and 2.347 Å. The Mulliken overlap populations in these hydrogen bonds are 0.143 and 0.133 electrons, which correspond to hydrogen-bond energies about 20.3 kcal mol−1.

Evaluation of N—H...S and N—H...π interactions inO,O′-diethylN-(2,4,6-trimethylphenyl)thiophosphate: a combination of X-ray crystallographic and theoretical studies

2018 ◽  
Vol 74 (7) ◽  
pp. 847-855 ◽  
Author(s):  
Elham Torabi Farkhani ◽  
Mehrdad Pourayoubi ◽  
Mohammad Izadyar ◽  
Pavel V. Andreev ◽  
Ekaterina S. Shchegravina
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Density Functional ◽  
Natural Bond Orbital ◽  
Crystal Packing ◽  
Hirshfeld Surface ◽  
Basis Set ◽  
Theoretical Studies ◽  
Functional Theory ◽  
X Ray

In the crystal structure ofO,O′-diethylN-(2,4,6-trimethylphenyl)thiophosphate, C13H22NO2PS, two symmetrically independent thiophosphoramide molecules are linked through N—H...S and N—H...π hydrogen bonds to form a noncentrosymmetric dimer, withZ′ = 2. The strengths of the hydrogen bonds were evaluated using density functional theory (DFT) at the M06-2X level within the 6-311++G(d,p) basis set, and by considering the quantum theory of atoms in molecules (QTAIM). It was found that the N—H...S hydrogen bond is slightly stronger than the N—H...π hydrogen bond. This is reflected in differences between the calculated N—H stretching frequencies of the isolated molecules and the frequencies of the same N—H units involved in the different hydrogen bonds of the hydrogen-bonded dimer. For these hydrogen bonds, the corresponding charge transfers,i.e.lp (or π)→σ*, were studied, according to the second-order perturbation theory in natural bond orbital (NBO) methodology. Hirshfeld surface analysis was applied for a detailed investigation of all the contacts participating in the crystal packing.

π-Electron delocalization in 2-benzoyl-5-phenylpyrazolidin-3-one

2018 ◽  
Vol 73 (8) ◽  
pp. 577-582
Author(s):  
Monika Olesiejuk ◽  
Agnieszka Kudelko ◽  
Katarzyna Gajda ◽  
Błażej Dziuk ◽  
Krzysztof Ejsmont
Keyword(s):  
Hydrogen Bonds ◽  
Density Functional ◽  
Heterocyclic Ring ◽  
Molecular Structures ◽  
Electron Delocalization ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray ◽  
Benzene Rings ◽  
Subsequent Cyclization

AbstractThe crystal and molecular structures of 2-benzoyl-5-phenylpyrazolidin-3-one have been characterized by X-ray diffraction along with density functional theory studies. Cinnamic acid chloride was reacted with benzhydrazide, yielding 2-benzoyl-5-phenylpyrazolidin-3-one. This product was formed in the transformation comprising the nucleophilic addition of benzhydrazide to the styryl fragment of the α,β-unsaturated arrangement and subsequent cyclization. The molecule contains two benzene rings and one five-membered heterocyclic ring with an N–N single bond. The five-membered ring is composed of three atoms of sp3 hybridization and two atoms of sp2 hybridization, which cause the flattening of the heterocyclic ring. The Harmonic Oscillator Model of Aromaticity and Nucleus-Independent Chemical Shift indexes, calculated for the benzene rings, demonstrate that there are no substantial interactions between the regions of π-electron delocalization in the molecule. In the crystal structure, there are N–H···O hydrogen bonds that link the molecules along the crystallographic c axis and weak intermolecular C–H···O hydrogen bonds.

Powder X-ray diffraction of pazopanib hydrochloride Form 1, C21H24N7O2SCl

2021 ◽  
pp. 1-3
Author(s):  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Density Functional ◽  
Lattice Energy ◽  
Powder Diffraction Data ◽  
X Ray Diffraction ◽  
Powder Diffraction File ◽  
Functional Theory ◽  
X Ray

The crystal structure of pazopanib hydrochloride Form 1 has been refined using synchrotron X-ray powder diffraction data and optimized using density functional theory techniques. Pazopanib hydrochloride crystallizes in space group P-1 (#2) with a = 8.45008(6), b = 8.71310(12), c = 16.05489(35) Å, α = 79.5996(9), β = 86.4784(5), γ = 87.3764(3)°, V = 1159.724(9) Å3, and Z = 2. The crystal structure is essentially identical to that of CSD Refcode CEVYEK. There are four strong N–H⋯Cl hydrogen bonds to the chloride anion. Several additional weaker N–H⋯Cl and C–H⋯Cl hydrogen bonds are also present. A variety of C–H⋯O, C–H⋯N, and N–H⋯S hydrogen bonds also contribute to the lattice energy. The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™.

scholarly journals Sodium dipotassium citrate, NaK2C6H5O7

2016 ◽  
Vol 72 (3) ◽  
pp. 403-406 ◽  
Author(s):  
Alagappa Rammohan ◽  
James A. Kaduk
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Density Functional ◽  
Three Dimensional ◽  
Bond Valence ◽  
Carboxylate Group ◽  
Powder Diffraction Data ◽  
X Ray ◽  
Dimensional Network ◽  
Bond Valence Sum

The crystal structure of sodium dipotassium citrate, Na+·2K+·C6H5O73−, has been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The Na+and one of the K+cations are six-coordinate, with bond-valence sums of 1.13 and 0.92 valence units, respectively, while another crystallographically independent K+cation is seven-coordinate with a bond-valence sum of 1.20. The [KO6] and [KO7] polyhedra share edges and corners to form layers perpendicular to thebaxis. The distorted [NaO6] octahedra share edges to form chains along theaaxis. The result is a three-dimensional network. The only O—H...O hydrogen bond is an intramolecular one between the hydroxy group and a terminal carboxylate group.

scholarly journals Use of bond-valence sums in modelling the diffuse scattering from PZN (PbZn1/3Nb2/3O3)

2014 ◽  
Vol 70 (6) ◽  
pp. 626-635 ◽  
Author(s):  
R. E. Whitfield ◽  
T. R. Welberry ◽  
M. Paściak ◽  
D. J. Goossens
Keyword(s):  
Diffuse Scattering ◽  
Density Functional ◽  
Minimum Energy ◽  
Bond Valence ◽  
Instability Index ◽  
Global Instability ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
Bond Valence Sum ◽  
Order Structures

This work extends previous efforts to model diffuse scattering from PZN (PbZn1/3Nb2/3O3). Earlier work [Welberryet al.(2005).J. Appl. Cryst.38, 639–647; Welberryet al.(2006).Phys. Rev. B,74, 224108] is highly prescriptive, using Monte Carlo simulation with very artificial potentials to induce short-range-order structures which were deduced as necessary from inspection of the data. While this gives valid results for the nature of the local structure, it does not strongly relate these structures to underlying crystal chemistry. In that work, the idea of the bond-valence sum was used as a guide to the expected behaviour of the atoms. This paper extends the use of the bond-valence sum from a qualitative guide to becoming a key aspect of the potential experienced by the atoms, through the idea of the global instability index, whose square has been shown to be proportional to the density functional theory energy of some systems when close to the minimum energy configuration.

Oxygen vacancy formation and the ion migration mechanism in layered perovskite (Sr,La)3Fe2O7−δ

2014 ◽  
Vol 16 (22) ◽  
pp. 10875-10882 ◽  
Author(s):  
Isao Kagomiya ◽  
Keigo Jimbo ◽  
Ken-ichi Kakimoto ◽  
Masanobu Nakayama ◽  
Olivier Masson
Keyword(s):  
Density Functional ◽  
Vacancy Formation ◽  
Layered Perovskite ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
Ion Migration ◽  
X Ray ◽  
Oxygen Vacancy Formation ◽  
Migration Mechanism ◽  
Bond Valence Sum

The characteristic ion migration mechanism for Sr2.46La0.54Fe2O7−δ was investigated by combination of experiments [X-ray diffraction, enthalpy investigations of vacancy formation] and computations [bond valence sum, ab initio density functional theory].

Crystal structure of lacosamide form I, C13H18N2O3

2015 ◽  
Vol 30 (3) ◽  
pp. 224-230
Author(s):  
James A. Kaduk ◽  
Kai Zhong ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Density Functional ◽  
Three Dimensions ◽  
Van Der Waals Interactions ◽  
Powder Diffraction File ◽  
Functional Theory ◽  
X Ray

The crystal structure of lacosamide form I has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques (density functional theory). Lacosamide form I crystallizes in space group P21 (#4) with a = 10.677 73(5), b = 4.799 68(2), c = 13.639 16(9) Å, β = 91.6331(10)̊, V = 698.719(6) Å3, and Z = 2. Van der Waals interactions are important in the crystal structure. Two N–H···O hydrogen bonds form C1,1(4) chains along the b-axis. Several weaker C–H···O hydrogen bonds to the ketone oxygens also contribute to the packing energy. These C–H···O extend both along the b-axis and in the ac-plane, and help link the molecules in three dimensions. The powder pattern has been submitted to International Centre for Diffraction Data for inclusion in the Powder Diffraction File™.

Electron density studies on hydrogen bonding in two chromone derivatives

2010 ◽  
Vol 66 (6) ◽  
pp. 687-695 ◽  
Author(s):  
Magdalena Małecka ◽  
Lilianna Chęcińska ◽  
Agnieszka Rybarczyk-Pirek ◽  
Wolfgang Morgenroth ◽  
Carsten Paulmann
Keyword(s):  
Hydrogen Bonds ◽  
Electron Density ◽  
Topological Analysis ◽  
Bond Energies ◽  
Synchrotron Diffraction ◽  
X Ray ◽  
Chromone Derivatives ◽  
Topological Parameters ◽  
Weak Hydrogen Bonds ◽  
Hydrogen Bond Energies

The experimental electron densities of two chromone derivatives have been determined from X-ray synchrotron diffraction data at low temperature (100 K). Topological analysis of the electron density has been used to analyze the formation of resonance-assisted hydrogen bonds (RAHBs). Geometrical and topological parameters confirm π-electron delocalization within the hydrogen-bonded ring. In addition, weak C—H...O interactions were identified in both structures. Hydrogen-bond energies allowed medium and weak hydrogen bonds to be distinguished.

Powder X-ray diffraction of daclatasvir dihydrochloride Form N-2 (Daklinza®), C40H52N8O6Cl2

2021 ◽  
pp. 1-4
Author(s):  
Ryan L. Hodge ◽  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Density Functional Theory ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Density Functional ◽  
Powder Diffraction Data ◽  
X Ray Diffraction ◽  
Powder Diffraction File ◽  
Functional Theory ◽  
X Ray

The crystal structure of daclatasvir dihydrochloride Form N-2 (Daklinza®) has been refined using synchrotron X-ray powder diffraction data and optimized using density functional theory techniques. Daclatasvir dihydrochloride, Form N-2, crystallizes in space group P1 (#1) with a = 7.54808 (15), b = 9.5566 (5), c = 16.2641 (11) Å, α = 74.0642 (24), β = 84.0026 (13), γ = 70.6322 (5)°, V = 1064.150(11) Å3, and Z = 1. The hydrogen bonds were identified and quantified. Strong N–H⋯Cl hydrogen bonds link the cations and anions in chains along the a-axis. The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™ (PDF®).

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