The electrostatic potential for the phosphodiester group determined from X-ray diffraction

Biopolymers ◽  
1992 ◽  
Vol 32 (9) ◽  
pp. 1141-1154 ◽  
Author(s):  
W. T. Klooster ◽  
B. M. Craven
Keyword(s):  
Electrostatic Potential ◽  
X Ray Diffraction ◽  
X Ray ◽  
Phosphodiester Group

Topological characterization of electron density, electrostatic potential and intermolecular interactions of 2-nitroimidazole: an experimental and theoretical study

2016 ◽  
Vol 72 (5) ◽  
pp. 775-786 ◽  
Author(s):  
Chinnasamy Kalaiarasi ◽  
Mysore S Pavan ◽  
Poomani Kumaradhas
Keyword(s):  
Electron Density ◽  
Intermolecular Interactions ◽  
Electrostatic Potential ◽  
Theoretical Calculations ◽  
Topological Analysis ◽  
X Ray Diffraction ◽  
Topological Characterization ◽  
Data Set ◽  
X Ray ◽  
Charge Concentration

An experimental charge density distribution of 2-nitroimidazole was determined from high-resolution X-ray diffraction and the Hansen–Coppens multipole model. The 2-nitroimidazole compound was crystallized and a high-angle X-ray diffraction intensity data set has been collected at low temperature (110 K). The structure was solved and further, an aspherical multipole model refinement was performed up to octapole level; the results were used to determine the structure, bond topological and electrostatic properties of the molecule. In the crystal, the molecule exhibits a planar structure and forms weak and strong intermolecular hydrogen-bonding interactions with the neighbouring molecules. The Hirshfeld surface of the molecule was plotted, which explores different types of intermolecular interactions and their strength. The topological analysis of electron density at the bond critical points (b.c.p.) of the molecule was performed, from that the electron density ρbcp(r) and the Laplacian of electron density ∇2ρbcp(r) at the b.c.p.s of the molecule have been determined; these parameters show the charge concentration/depletion of the nitroimidazole bonds in the crystal. The electrostatic parameters like atomic charges and the dipole moment of the molecule were calculated. The electrostatic potential surface of the molecule has been plotted, and it displays a large electronegative region around the nitro group. All the experimental results were compared with the corresponding theoretical calculations performed usingCRYSTAL09.

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.

X-ray Diffraction and the Electrostatic Potential

1997 ◽  
Author(s):  
Philip Coppens
Keyword(s):  
Electric Field ◽  
Electrostatic Potential ◽  
Chemical Reactivity ◽  
Lattice Energy ◽  
X Ray Diffraction ◽  
X Ray ◽  
Positive Unit ◽  
Molecular Potential ◽  
Structure Factors ◽  
Drug Receptor

The distribution of positive and negative charge in a crystal fully defines physical properties like the electrostatic potential and its derivatives, the electric field, and the gradient of the electric field. The electrostatic potential at a point in space, defined as the energy required to bring a positive unit of charge from infinite distance to that point, is an important function in the study of chemical reactivity. As electrostatic forces are relatively long-range forces, they determine the path along which an approaching reactant will travel towards a molecule. A nucleophilic reagent will first be attracted to the regions where the potential is positive, while an electrophilic reagent will approach the negative regions of the molecule. As the electrostatic potential is of importance in the study of intermolecular interactions, it has received considerable attention during the past two decades (see, e.g., articles on the molecular potential of biomolecules in Politzer and Truhlar 1981). It plays a key role in the process of molecular recognition, including drug-receptor interactions, and is an important function in the evaluation of the lattice energy, not only of ionic crystals. This chapter deals with the evaluation of the electrostatic potential and its derivatives by X-ray diffraction. This may be achieved either directly from the structure factors, or indirectly from the experimental electron density as described by the multipole formalism. The former method evaluates the properties in the crystal as a whole, while the latter gives the values for a molecule or fragment “lifted” out of the crystal. Like other properties derived from the charge distribution, the experimental electrostatic potential will be affected by the finite resolution of the experimental data set. But as the contribution of a structure factor F(H) to the potential is proportional to H−2, as shown below, convergence is readily achieved. A summary of the dependence of electrostatic properties of the magnitude of the scattering vector H is given in Table 8.1, which shows that the electrostatic potential is among the most accessible of the properties listed.

scholarly journals Application of maximum-entropy electrostatic potential in Materials Science.

2014 ◽  
Vol 70 (a1) ◽  
pp. C101-C101
Author(s):  
Eiji Nishibori
Keyword(s):  
Maximum Entropy ◽  
Electrostatic Potential ◽  
Diffraction Data ◽  
Materials Science ◽  
Structural Information ◽  
Entropy Method ◽  
Atomic Scale ◽  
X Ray Diffraction ◽  
X Ray ◽  
Adsorption Sites

Charge density (CD) studies by Maximum Entropy Method (MEM) (Sakata & Sato, 1990) from x-ray diffraction data have been widely applied to solve problems and questions in materials science during past two decades. Encapsulations of metal atoms (Takata et al, 1995), gas molecules, as well as protein molecules in the materials have been visualized as MEM CDs. The MEM CD technique is now regarded as a sophisticated technique for visualization in atomic scale. Electrostatic potential (EP) and electric field (EF) from x-ray diffraction data using MEM have been developed in 2006 (Tanaka et al, 2006). The EP & EF successfully applied to ferroelectric material PbTiO3 and a charge ordered manganite system. The method has huge potential in materials science since interaction in the non-atomic region can be visualized experimentally. One of the promising target for EP & EF analysis is host-guest systems, such as porous coordination polymers (PCPs), zeolites, clathrates as well as endohedral metallofullerenes[3]. In the case of host-guest systems, the guest atom(s) or molecule(s) are located in spatially wider sites in comparison to other type of materials. Therefore the detailed structural information in the spatially wider sites is one of the most important issues. In the present study, I present an application of MEM EP & EF analysis to host-guest related system, icosahedral B12 cluster materials and hydrogen adsorbed PCP. The EP studies clearly visualize doping sites in B12 based superconductor and adsorption sites in PCP. The EF enables us to estimate quantitative interaction from host to guest. The quantitative evaluation really bridges between experiment and theory in materials science.

Electrostatic Properties of Ions in Crystals from X-Ray Diffraction Data

1993 ◽  
Vol 48 (1-2) ◽  
pp. 81-84 ◽  
Author(s):  
Niels K. Hansen
Keyword(s):  
Density Distribution ◽  
Charge Density ◽  
Electrostatic Potential ◽  
Diffraction Data ◽  
Reciprocal Space ◽  
Electrostatic Energy ◽  
X Ray Diffraction ◽  
Charge Density Distribution ◽  
X Ray ◽  
Space Approach

Abstract A procedure for calculating the electrostatic potential and the electrostatic energy of an ion in a crystal is presented. It is based on a mixed direct and reciprocal space approach, and it takes into account the detailed charge density distribution in the crystal which can be obtained from accurate X-ray diffraction measurements.

scholarly journals The Cyclobutanocucurbit[5–8]uril Family: Electronegative Cavities in Contrast to Classical Cucurbituril while the Electropositive Outer Surface Acts as a Crystal Packing Driver

Molecules ◽  
2021 ◽  
Vol 26 (23) ◽  
pp. 7343
Author(s):  
Minghua Chen ◽  
Naixia Lv ◽  
Weiwei Zhao ◽  
Anthony I. Day
Keyword(s):  
Single Crystal ◽  
Electrostatic Potential ◽  
Outer Surface ◽  
Crystal Packing ◽  
Structural Parameters ◽  
Near Neighbor ◽  
X Ray Diffraction ◽  
X Ray ◽  
Dipole Interactions

The structural parameters for the cyclobutanoQ[5–8] family were determined through single crystal X-ray diffraction. It was found that the electropositive cyclobutano methylene protons (CH2) are important in forming interlinking crystal packing arrangements driven by the dipole–dipole interactions between these protons and the portal carbonyl O of a near neighbor. This type of interaction was observed across the whole family. Electrostatic potential maps also confirmed the electropositive nature of the cyclobutano CH2 but, more importantly, it was established that the cavities are electronegative in contrast to classical Q[5–8], which are near neutral.

Two mefenamic acid derivatives: structural study using powder X-ray diffraction, Hirshfeld surface and molecular electrostatic potential calculations

2017 ◽  
Vol 232 (5) ◽  
pp. 385-394 ◽  
Author(s):  
Paramita Chatterjee ◽  
Tanusri Dey ◽  
Sarbani Pal ◽  
Alok K. Mukherjee
Keyword(s):  
Electrostatic Potential ◽  
Mefenamic Acid ◽  
Molecular Electrostatic Potential ◽  
Three Dimensional ◽  
Molecular Geometry ◽  
Hirshfeld Surface ◽  
X Ray Diffraction ◽  
Potential Surfaces ◽  
X Ray ◽  
Surface Areas

AbstractTwo mefenamic acid (1) derivatives, prop-2-ynyl 2-(2,3-dimethylphynylamino)benzoate (2) and N′-(dihydro-2H-pyran-4(3H)-ylidene)-2-((2,3-dimethylphenyl)amino)benzohydrazide (3), have been synthesized and their crystal structures have been determined from laboratory powder X-ray diffraction data. The DFT optimized molecular geometry in 2 and 3 agrees closely to that obtained from the crystallographic study. The nature of intermolecular interactions in 2 and 3 has been analyzed through Hirshfeld surfaces and two-dimensional fingerprint plots, and compared with that in the mefenamic acid polymorphs. Intermolecular N–H···N, C–H···O/N and C–H···π(arene) interactions in 2 and 3 assemble molecules into two and three-dimensional supramolecular frameworks, respectively. Hydrogen-bond based interactions in 2 and 3 have been complimented by calculating molecular electrostatic potential surfaces. Hirshfeld surface analyses of 2, 3, three mefenamic acid polymorphs and a few related mefenamic acid derivatives retrieved from the Cambridge Structural Database (CSD) indicate that about 80% of the Hirshfeld surface areas in these compounds are due to H···H and C···H/H···C contacts.

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