Experimental Charge Density and Electrostatic Potential of Triglycine

1998 ◽  
Vol 54 (4) ◽  
pp. 485-493 ◽  
Author(s):  
V. Pichon-Pesme ◽  
C. Lecomte
Keyword(s):  
Electrostatic Potential ◽  
Electron Density Distribution ◽  
Crystal Data ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
X Ray ◽  
A Charge ◽  
Net Charges ◽  
Experimental Electron Density ◽  
Experimental Charge Density

The experimental electron density distribution in triglycine has been determined using single-crystal X-ray diffraction data at 123 K to a resolution of (sin θ/λ)max = 1.1 Å−1. Several multipolar pseudo-atom density refinements were performed against the 7238 observed data in order to estimate the net charges on the atoms. The electrostatic potential around the two molecules is calculated from the parameters derived from these refinements. A charge transfer between the two triglycine molecules of the asymmetric unit is discussed. Crystal data: C6H11N3O4, Mr = 189.2, triclinic, P1¯, Z = 4 (two molecules in the asymmetric unit), T = 123 K, a = 11.585 (1), b = 14.603 (2), c = 4.800 (4) Å, α = 89.28 (3), β = 95.55 (2), γ = 104.484 (8)°, V = 782.5 (7) Å3, Dx = 1.61 g cm−3, μ = 1.5 cm−1 for λMo = 0.7107 Å.

Experimental charge density and electrostatic potential of glycyl-L-threonine dihydrate

2000 ◽  
Vol 56 (1) ◽  
pp. 155-165 ◽  
Author(s):  
Farid Benabicha ◽  
Virginie Pichon-Pesme ◽  
Christian Jelsch ◽  
Claude Lecomte ◽  
Ahmed Khmou
Keyword(s):  
Electron Density ◽  
Electrostatic Potential ◽  
Electron Density Distribution ◽  
Crystal Data ◽  
X Ray Diffraction ◽  
Topological Methods ◽  
X Ray ◽  
Molecular Electron ◽  
Experimental Electron Density ◽  
Experimental Charge Density

The experimental electron density distribution in glycyl-L-threonine dihydrate has been investigated using single-crystal X-ray diffraction data at 110 K to a resolution of (sin θ/λ) = 1.2 Å−1. Multipolar pseudo-atom refinement was carried out against 5417 observed data and the molecular electron density was analyzed using topological methods. The experimental electrostatic potential around the molecule is discussed in terms of molecular interactions. Crystal data: C6H12N2O4.2H2O, Mr = 212.2, orthorhombic, P212121, Z = 4, F(000) = 456 e, T = 110 K, a = 9.572 (3), b = 10.039 (3), c = 10.548 (2) Å, V = 1013.6 (4) Å3, Dx = 1.3 g cm−3, µ = 1.2 cm−1 for λMo = 0.7107 Å.

Submolecular partitioning of morphine hydrate based on its experimental charge density at 25 K

2005 ◽  
Vol 61 (4) ◽  
pp. 443-448 ◽  
Author(s):  
S. Scheins ◽  
M. Messerschmidt ◽  
P. Luger
Keyword(s):  
Electron Density ◽  
Electron Density Distribution ◽  
Theoretical Calculations ◽  
Topological Analysis ◽  
Theoretical Studies ◽  
X Ray Diffraction ◽  
X Ray ◽  
Resolution Single ◽  
Experimental Electron Density ◽  
Experimental Charge Density

The electron density distribution of morphine hydrate has been determined from high-resolution single-crystal X-ray diffraction measurements at 25 K. A topological analysis was applied and, in order to analyze the submolecular transferability based on an experimental electron density, a partitioning of the molecule into atomic regions was carried out, making use of Bader's zero-flux surfaces to yield atomic volumes and charges. The properties obtained were compared with the theoretical calculations of smaller fragment molecules, from which the complete morphine molecule can be reconstructed, and with theoretical studies of another opiate, Oripavine PEO, reported in the literature.

Tris(dimethylphenylphosphine)ruthenium(0) Complexes of n4-Coordinated Polycyclic Aromatic Hydrocarbons

2000 ◽  
Vol 53 (6) ◽  
pp. 507 ◽  
Author(s):  
Martin A. Bennett ◽  
Mark Bown ◽  
David C. R. Hockless
Keyword(s):  
Coordination Geometry ◽  
Crystal Data ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Tertiary Phosphine ◽  
X Ray ◽  
Tertiary Phosphines ◽  
Polycyclic Aromatic ◽  
R Value ◽  
Axial Site

From the reaction of [Ru2Cl3(PMe2Ph)6] Cl with the appropriate radical anions, yellow complexes of general formula [Ru(PMe2Ph)3(η4-arene)] [arene = naphthalene (C10H8) (1), anthracene (C14H10) (2), and triphenylene (C18H12) (3)] have been isolated in poor yield and characterized by elemental analysis, n.m.r. (1H, 13C, 31P) spectroscopy and single-crystal X-ray diffraction. Crystal data: (1), monoclinic, C2/c, a 31.096(8), b 12.012(4), c 17.078(8) Å, β 104.41(3)˚, V 6178(4) Å3, ? 8, refined to final R value of 0.032 with use of 3641 reflections [I > 3σ(I)]; (2), monoclinic, C2/c, a 55.909(4), b 14.348(5), c 17.573(5) Å, β 105.41(1)˚, V 13590(6) Å3, Z 16 (two molecules per asymmetric unit), refined to final R value of 0.049 with use of 7770 reflections [I > 3σ(I)]; (3), mono-clinic, Pn, a 9.377(3), b 12.229(3), c 15.975(3) Å, β 103.51(2)˚, V 1781.2 (7) Å3, Z 2, refined to final R value of 0.026 with use of 2830 reflections [I > 3σ(I)]. In each case, coordination of the zerovalent metal fragment Ru(PMe2Ph)3 to the diene section of one of the terminal rings causes the aromatic molecule to be folded by c. 40˚ at the outer carbon atoms of the diene. The coordination geometry about ruthenium is approximately square pyramidal, with the diene and two tertiary phosphines in the equatorial plane and the remaining tertiary phosphine in the axial site.

Ideal and Real Structure of Ti5O4(PO4)4: X-ray and HRTEM Investigations

1998 ◽  
Vol 54 (6) ◽  
pp. 722-731 ◽  
Author(s):  
F. Reinauer ◽  
R. Glaum
Keyword(s):  
Crystal Structure ◽  
Electron Microscopy ◽  
Structure Refinement ◽  
Ideal Structure ◽  
Crystal Data ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
X Ray ◽  
Transmission Electron ◽  
The Ideal

The crystal structure of pentatitanium tetraoxide tetrakis(phosphate), Ti5O4(PO4)4, has been determined and refined from X-ray diffraction single-crystal data [P212121 (No. 19), Z = 4, a = 12.8417 (12), b = 14.4195 (13), c = 7.4622 (9) Å (from Guinier photographs); conventional residual R 1 = 0.042 for 2556 Fo > 4σ(Fo ), R 1 = 0.057 for all 3276 independent reflections; 282 parameters; 29 atoms in the asymmetric unit of the ideal structure]. The structure is closely related to those of β-Fe2O(PO4)-type phosphates and synthetic lipscombite, Fe3(PO4)4(OH). While these consist of infinite chains of face-sharing MO6 octahedra, in pentatitanium tetraoxide tetrakis(phosphate) only five-eighths of the octahedral voids are occupied according to □3Ti5O4(PO4)4. Four of the five independent Ti4+O6 show high radial distortion [1.72 ≤ d(Ti−O) ≤ 2.39 Å] and a typical 1 + 4 + 1 distance distribution. The fifth Ti4+O6 is an almost regular octahedron [1.91 ≤ d(Ti−O) ≤ 1.98 Å]. Partial disorder of Ti4+ over the available octahedral voids is revealed by the X-ray structure refinement. High-resolution transmission electron microscopy (HRTEM) investigations confirm this result.

Electron density distribution and Madelung potential in α-spodumene, LiAl(SiO3)2, from two-wavelength high-resolution X-ray diffraction data

1999 ◽  
Vol 55 (3) ◽  
pp. 273-284 ◽  
Author(s):  
Sandrine Kuntzinger ◽  
Nour Eddine Ghermani
Keyword(s):  
High Resolution ◽  
Density Distribution ◽  
Electron Density ◽  
Electron Density Distribution ◽  
Data Sets ◽  
X Ray Diffraction ◽  
Net Charge ◽  
X Ray ◽  
Madelung Potential ◽  
Net Charges

The electron density distribution in α-spodumene, LiAl(SiO3)2, was derived from high-resolution X-ray diffraction experiments. The results obtained from both Mo Kα- and Ag Kα-wavelength data sets are reported. The features of the Si—O and Al—O bonds are related to the geometrical parameters of the Si—O—Al and Si—O—Si bridges on the one hand and to the O...Li+ interaction on the other. Kappa refinements against the two data sets yielded almost the same net charges for the Si (+1.8 e) and O (−1.0 e) atoms in spodumene. However, the Al net charge obtained from the Ag Kα data (+1.9 e) is larger than the net charge derived from the Mo Kα data (+1.5 e). This difference correlates with a more contracted Al valence shell revealed by the shorter X-ray wavelength (κ = 1.4 for the Ag Kα data set). The derived net charges were used to calculate the Madelung potential at the spodumene atomic sites. The electrostatic energy for the chemical formula LiAl(SiO3)2 was −8.60 e2 Å−1 (−123.84 eV) from the net charges derived from the Ag Kα data and −6.97 e2 Å−1 (−100.37 eV) from the net charges derived from the Mo Kα data.

Electron Density Distribution in LiB3O5 at 293 K

1997 ◽  
Vol 53 (6) ◽  
pp. 870-879 ◽  
Author(s):  
C. Le Hénaff ◽  
N. K. Hansen ◽  
J. Protas ◽  
G. Marnier
Keyword(s):  
Density Distribution ◽  
Electron Density ◽  
Electron Density Distribution ◽  
X Ray Diffraction ◽  
X Ray ◽  
Hartree Fock ◽  
Density Maps ◽  
Symmetry Constraints ◽  
Net Charges ◽  
Good Agreement

The electron density distribution in lithium triborate LiB3O5 has been studied at room temperature by X-ray diffraction using Ag K \alpha radiation up to 1.02 Å−1 [1439 unique reflections with I > 3\sigma(I)]. Conventional refinements with a free-atom model yield R(F) = 0.0223, wR(F) = 0.0299, S = 1.632. Atom charge refinements show that the lithium should be considered a monovalent ion. Multipolar refinements were undertaken up to fourth order, imposing local non-crystallographic symmetry constraints in order to avoid phase problems leading to meaningless multipole populations due to the non-centrosymmetry of the structure (space group: Pn a21). The residual indices decreased to: R(F) = 0.0147, wR(F) = 0.0193, S = 1.106. The net charges are in good agreement with what can be expected in borate chemistry. Deformation density maps are analysed in terms of \sigma and \pi bonding. The experimental electron distribution in the p z orbitals of triangular B atoms and surrounding O atoms has been analysed by introducing idealized hybridized states. In parallel, the electron density has been determined from ab initio Hartree–Fock calculations on fragments of the structure. Agreement with the X-ray determination is very good and confirms the nature of bonding in the crystal. The amount of transfer of \pi electrons from the oxygen to the triangular B atoms is estimated to be 0.22 electrons by theory.

Experimental charge density study on FLPs and a FLP reaction product

2018 ◽  
Vol 233 (9-10) ◽  
pp. 723-731
Author(s):  
Christian Joseph Schürmann ◽  
Regine Herbst-Irmer ◽  
Thorsten Lennart Teuteberg ◽  
Daniel Kratzert ◽  
Gerhard Erker ◽  
...  
Keyword(s):  
Charge Transfer ◽  
Charge Density ◽  
Theoretical Calculations ◽  
X Ray Diffraction ◽  
Charge Density Distribution ◽  
X Ray ◽  
Charge Densities ◽  
A Charge ◽  
Density Study ◽  
Experimental Charge Density

Abstract The charge density distribution of the intramolecular frustrated Lewis pair (FLP) Mes2PCH2CH2B(C6F5)2 (1), the phosphinimine HNPMes2CH2CH2B(C6F5)2 (2), as well as a FLP homologue with nitrogen NEt2CHPhCH2B(C6F5)2 (3) were investigated with Bader’s quantum theory of atoms in molecules (QTAIM). The charge densities were derived from both experimental high-resolution X-ray diffraction data (2, 3) and theoretical calculations (1, 3). The QTAIM analysis for the FLPs 1 and 3 showed the prominent B-pnictogen interaction to be weak dative bonds without significant charge-transfer. This holds also true for the B–N–bond of 2. The nitrogen atom is negatively charged, due to a charge transfer from phosphorous and shows features of a sp2-hybridization. The bond is therefore best described as a non-hypervalent Pδ+–Nδ− moiety.

scholarly journals Charge density and electrostatic potential analyses in paracetamol

2009 ◽  
Vol 65 (3) ◽  
pp. 363-374 ◽  
Author(s):  
Nouzha Bouhmaida ◽  
François Bonhomme ◽  
Benoît Guillot ◽  
Christian Jelsch ◽  
Nour Eddine Ghermani
Keyword(s):  
Electron Density ◽  
Electrostatic Potential ◽  
Electrostatic Force ◽  
Nucleophilic Attack ◽  
Electrostatic Energy ◽  
Atomic Charges ◽  
X Ray Diffraction ◽  
X Ray ◽  
Maxwell Stress Tensor ◽  
Experimental Electron Density

The electron density of monoclinic paracetamol was derived from high-resolution X-ray diffraction at 100 K. The Hansen–Coppens multipole model was used to refine the experimental electron density. The topologies of the electron density and the electrostatic potential were carefully analyzed. Numerical and analytical procedures were used to derive the charges integrated over the atomic basins. The highest charge magnitude (−1.2 e) was found for the N atom of the paracetamol molecule, which is in agreement with the observed nucleophilic attack occurring in the biological media. The electric field generated by the paracetamol molecule was used to calculate the atomic charges using the divergence theorem. This was simultaneously applied to estimate the total electrostatic force exerted on each atom of the molecule by using the Maxwell stress tensor. The interaction electrostatic energy of dimers of paracetamol in the crystal lattice was also estimated.

Distribution and Topology of the Electron Density in an Aluminosilicate Compound from High-Resolution X-ray Diffraction Data: the Case of Scolecite

1998 ◽  
Vol 54 (6) ◽  
pp. 819-833 ◽  
Author(s):  
S. Kuntzinger ◽  
N. E. Ghermani ◽  
Y. Dusausoy ◽  
C. Lecomte
Keyword(s):  
High Resolution ◽  
Density Distribution ◽  
Electron Density ◽  
Critical Points ◽  
Diffraction Data ◽  
Electron Density Distribution ◽  
X Ray Diffraction ◽  
X Ray ◽  
And Topology ◽  
Experimental Electron Density

The experimental electron density distribution in scolecite, CaAl2Si3O10.3H2O, has been derived from single-crystal high-resolution Ag Kα X-ray diffraction data. A statistical method based on the prediction matrix has been used to discuss the estimation of the valence populations (P val) in the kappa least-squares refinements. The densities on the Si—O—Si and Si—O—Al bridges have been characterized using the topology of the electron density through its Laplacian at the bond critical points. The Si—O and Al—O bond features are related to the atomic environment and to the Si—O—T geometries (T = Si, Al).

Examination of Rabbit Fc Crystals

1968 ◽  
Vol 26 ◽  
pp. 140-141
Author(s):  
J. P. Robinson ◽  
P. G. Lenhert
Keyword(s):  
Molecular Weight ◽  
Flat Plate ◽  
Phosphate Buffer ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
X Ray ◽  
Neutral Ph ◽  
Small Crystals ◽  
Carbon Coated ◽  
Diffraction Patterns

Crystallographic studies of rabbit Fc using X-ray diffraction patterns were recently reported. The unit cell constants were reported to be a = 69. 2 A°, b = 73. 1 A°, c = 60. 6 A°, B = 104° 30', space group P21, monoclinic, volume of asymmetric unit V = 148, 000 A°3. The molecular weight of the fragment was determined to be 55, 000 ± 2000 which is in agreement with earlier determinations by other methods.Fc crystals were formed in water or dilute phosphate buffer at neutral pH. The resulting crystal was a flat plate as previously described. Preparations of small crystals were negatively stained by mixing the suspension with equal volumes of 2% silicotungstate at neutral pH. A drop of the mixture was placed on a carbon coated grid and allowed to stand for a few minutes. The excess liquid was removed and the grid was immediately put in the microscope.

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