Browse
Submit Data
Databases
API
Help

Dataset Information

20 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Two Tautomers of Thiobarbituric Acid in One Crystal: The Experimental Charge Density Perspective.

ABSTRACT: High-quality crystals of a certain polymorphic form of thiobarbituric acid containing both keto and enol tautomers in the asymmetric unit were obtained. High-resolution X-ray diffraction data up to sinθ/λ = 1.0 Å^-1 were collected and subsequently successfully used for the refining of the multipolar model of electron density distribution. The use of a crystal containing both ketone and enol forms allowed a direct comparison of the topological analysis results and a closer look at the differences between these two forms. The similarities and differences between the deformation densities, electrostatic potentials, Laplacian maps and bond characteristics of the tautomers were analysed. Additionally, the spectrum of the intermolecular interactions was identified and studied from classical, relatively strong N-H···O and O-H···O hydrogen bonds through weaker N-H···S hydrogen bonds to weak interactions (for instance, C-H···O, C-H···S and N···O). The results of these studies point toward the importance of including both the geometrical features and the details of the electron density distribution in the analysis of such weak interactions.

SUBMITTER: Grzeskiewicz AM

PROVIDER: S-EPMC8745894 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Priority Choice Experimental Two-Qubit Tomography: Measuring One by One All Elements of Density Matrices.

Project description:In standard optical tomographic methods, the off-diagonal elements of a density matrix ? are measured indirectly. Thus, the reconstruction of ?, even if it is based on linear inversion, typically magnifies small errors in the experimental data. Recently, an optimal tomography solution measuring all the elements of ? one-by-one without error magnification has been theoretically proposed. We implemented this method for two-qubit polarization states. For comparison, we also experimentally implemented other well-known tomographic protocols, either based solely on local measurements (of, e.g., the Pauli operators and James-Kwiat-Munro-White projectors) or with mutually unbiased bases requiring both local and global measurements. We reconstructed seventeen separable, partially and maximally entangled two-qubit polarization states. Our experiments show that our method has the highest stability against errors in comparison to other quantum tomographies. In particular, we demonstrate that each optimally-reconstructed state is embedded in an uncertainty circle of the smallest radius, both in terms of trace distance and disturbance. We explain how to experimentally estimate uncertainty radii for all the implemented tomographies and show that, for each reconstructed state, the relevant uncertainty circles intersect indicating the approximate location of the corresponding physical density matrix.

| S-EPMC4726363 | biostudies-literature

Experimental charge density from electron microscopic maps.

Project description:The charge density (CD) distribution of an atom is the difference per unit volume between the positive charge of its nucleus and the distribution of the negative charges carried by the electrons that are associated with it. The CDs of the atoms in macromolecules are responsible for their electrostatic potential (ESP) distributions, which can now be visualized using cryo-electron microscopy at high resolution. CD maps can be recovered from experimental ESP density maps using the negative Laplacian operation. CD maps are easier to interpret than ESP maps because they are less sensitive to long-range electrostatic effects. An ESP-to-CD conversion involves multiplication of amplitudes of structure factors as Fourier transforms of these maps in reciprocal space by 1/d2 , where d is the resolution of reflections. In principle, it should be possible to determine the charges carried by the individual atoms in macromolecules by comparing experimental CD maps with experimental ESP maps.

| S-EPMC5521614 | biostudies-literature

Chitosan-Thiobarbituric Acid: A Superadsorbent for Mercury.

Project description:In the present investigation, chitosan (CH) was supramolecularly cross-linked with thiobarbituric acid to form CT. CT was well characterized by UV, scanning electron microscopy-energy-dispersive X-ray analysis, Fourier transform infrared, NMR, differential scanning calorimetry, thermogravimetric analysis, and X-ray diffraction analyses, and its adsorption potential for elemental mercury (Hg0), inorganic mercury (Hg2+), and methyl mercury (CH3Hg+) was investigated. Adsorption experiments were conducted to optimize the parameters for removal of the mercury species under study, and the data were analyzed using Langmuir, Freundlich, and Temkin adsorption isotherm models. CT was found to have high adsorption capacities of 1357.69, 2504.86, and 2475.38 mg/g for Hg0, Hg2+, and CH3Hg+, respectively. The adsorbent CT could be reused up to three cycles by eluting elemental mercury using 0.01 N thiourea, inorganic mercury using 0.01 N perchloric acid, and methyl mercury with 0.2 N NaCl.

| S-EPMC6644366 | biostudies-literature

Experimental charge density of grossular under pressure - a feasibility study.

Project description:X-ray diffraction studies of crystals under pressure and quantitative experimental charge density analysis are among the most demanding types of crystallographic research. A successful feasibility study of the electron density in the mineral grossular under 1?GPa pressure conducted at the CRISTAL beamline at the SOLEIL synchrotron is presented in this work. A single crystal was placed in a diamond anvil cell, but owing to its special design (wide opening angle), short synchrotron wavelength and the high symmetry of the crystal, data with high completeness and high resolution were collected. This allowed refinement of a full multipole model of experimental electron distribution. Results are consistent with the benchmark measurement conducted without a diamond-anvil cell and also with the literature describing investigations of similar structures. Results of theoretical calculations of electron density distribution on the basis of dynamic structure factors mimic experimental findings very well. Such studies allow for laboratory simulations of processes which take place in the Earth's mantle.

| S-EPMC7201277 | biostudies-literature

Application of charge density methods to a protein model compound: calculation of Coulombic intermolecular interaction energies from the experimental charge density.

Project description:A combined experimental and theoretical charge density study of the pentapeptide Boc-Gln-d-Iva-Hyp-Ala-Phol (Boc, butoxycarbonyl; Gln, glutamine; Iva, isovaline; Hyp, hydroxyproline; Ala, ethylalanine; Phol, phenylalaninol) is described. The experimental analysis, based on synchrotron x-ray data collected at 20 K, is combined with ab initio theoretical calculations. The topologies of the experimental and theoretical densities are analyzed in terms of the atoms in molecules quantum theory. Topological parameters, including atomic charges and higher moments integrated over the atomic basins, have been evaluated with the program topxd and are used to calculate the electrostatic interactions between the molecules in the crystal. The interaction energies obtained after adding dispersive and repulsive van der Waals contributions agree quite well with those based on M-B3LYP/6-31G** dimer calculations for two of the three dimers in the crystal, whereas for the third a larger stabilization is obtained than predicted by the calculation. The agreement with theory is significantly better than that obtained with multipole moments derived directly from the aspherical atom refinement. The convergence of the interaction as a function of addition of successively higher moments up to and including hexadecapoles (l = 4) is found to be within 2-3 kJ/mol. Although shortcomings of both the theoretical and experimental procedures are pointed out, the agreement obtained supports the potential of the experimental method for the evaluation of interactions in larger biologically relevant molecules.

| S-EPMC129410 | biostudies-literature

Validation of experimental charge-density refinement strategies: when do we overfit?

Project description:A cross-validation method is supplied to judge between various strategies in multipole refinement procedures. Its application enables straightforward detection of whether the refinement of additional parameters leads to an improvement in the model or an overfitting of the given data. For all tested data sets it was possible to prove that the multipole parameters of atoms in comparable chemical environments should be constrained to be identical. In an automated approach, this method additionally delivers parameter distributions of k different refinements. These distributions can be used for further error diagnostics, e.g. to detect erroneously defined parameters or incorrectly determined reflections. Visualization tools show the variation in the parameters. These different refinements also provide rough estimates for the standard deviation of topological parameters.

| S-EPMC5571805 | biostudies-other

Charge mobility calculation of organic semiconductors without use of experimental single-crystal data.

Project description:Prediction of material properties of newly designed molecules is a long-term goal in organic electronics. In general, it is a difficult problem, because the material properties are dominated by the unknown packing structure. We present a practical method to obtain charge transport properties of organic single crystals, without use of experimental single-crystal data. As a demonstration, we employ the promising molecule C10-DNBDT. We succeeded in quantitative evaluation of charge mobility of the single crystal using our quantum wave-packet dynamical simulation method. Here, the single-crystal data is computationally obtained by searching possible packing structures from structural formula of the molecule. We increase accuracy in identifying the actual crystal structure from suggested ones by using not only crystal energy but also similarity between calculated and experimental powder X-ray diffraction patterns. The proposed methodology can be a theoretical design technique for efficiently developing new high-performance organic semiconductors, since it can estimate the charge transport properties at early stage in the process of material development.

| S-EPMC7026405 | biostudies-literature

Synthesis of Pyrazole-Thiobarbituric Acid Derivatives: Antimicrobial Activity and Docking Studies.

Project description:A one-pot reaction was described that results in various pyrazole-thiobarbituric acid derivatives as new pharmacophore agents. These new heterocycles were synthesized in high yields with a broad substrate scope under mild reaction conditions in water mediated by NHEt?. The molecular structures of the synthesized compounds were assigned based on different spectroscopic techniques. The new compounds were evaluated for their antibacterial and antifungal activity. Compounds 4h and 4l were the most active compounds against C. albicans with MIC = 4 µg/L. Compound 4c exhibited the best activity against S. aureus and E. faecalis with MIC = 16 µg/L. However, compounds 4l and 4o were the most active against B. subtilis with MIC = 16 µg/L. Molecular docking studies for the final compounds and standard drugs were performed using the OpenEye program.

| S-EPMC6274314 | biostudies-literature

Two tautomers in the same crystal: 3-(4-fluoro-phen-yl)-1H-pyrazole and 5-(4-fluoro-phen-yl)-1H-pyrazole.

Project description:The title co-crystal, 3-(4-fluoro-phen-yl)-1H-pyrazole-5-(4-fluoro-phen-yl)-1H-pyrazole (1/1), C9H7FN2, crystallizes with four independent mol-ecules (A, B, C and D) in the asymmetric unit exhibiting two tautomeric forms (A and D; B and C) due to N-H proton exchange between the two N atoms of the pyrazole ring. The dihedral angles between the mean planes of the pyrazole and benzene rings are 15.6?(1), 19.8?(9), 14.0?(1) and 10.7?(7)° in mol-ecules A, B, C and D, respectively. In the crystal, N-H?N hydrogen bonds link the four mol-ecules in the asymmetric unit into a ring with an R 4 (4)(12) motif. Furthermore, weak C-H?F inter-actions link the mol-ecules into a three-dimensional network.

| S-EPMC4186127 | biostudies-literature

Characterization of thiobarbituric acid derivatives as inhibitors of hepatitis C virus NS5B polymerase.

Project description:In an effort to find chemicals inhibiting the enzymatic activity of the hepatitis C virus (HCV) NS5B polymerase, a series of thiobarbituric acid derivatives were selected from a library provided by Korea Research Institute of Chemical Technology and characterized. The selected compounds exhibited IC50 values ranging from 1.7 to 3.8 ?M, and EC50 values ranging from 12.3 to 20.7 ?M against NS5B polymerase of type 1b strain. They showed little effect against type 2a polymerase. One of the compounds, G05, was selected and further characterized. It inhibited the synthesis of RNA by recombinant HCV NS5B polymerase in a dose dependent manner. The CC50 value was 77 ?M. The inhibition was in a noncompetitive manner with the substrate UTP. The compound did not inhibit the elongation step of RNA synthesis in a single-cycle processive polymerization assay. It inhibited the binding of NS5B polymerase to the template RNA in a dose-dependent manner.

| S-EPMC3032711 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data