Browse
Submit Data
Databases
API
Help

Dataset Information

17 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Intermolecular Forces Driving Hexamethylenetetramine Co-Crystal Formation, a DFT and XRD Analysis.

ABSTRACT: Interest in co-crystals formation has been constantly growing since their discovery, almost a century ago. Such success is due to the ability to tune the physical-chemical properties of the components in solid state by avoiding a change in their molecular structure. The properties influenced by the co-crystals formation range from an improvement of mechanical features and chemical stability to different solubility. In the scientific research area, the pharmacological field is undoubtedly one of those in which an expansion of the co-crystal knowledge can offer wide benefits. In this work, we described the crystalline structure of hexamethylenetetramine co-crystallized with the isophthalic acid, and we compared it with another co-crystal, showing the same components but different stoichiometry. To give a wider overview on the nature of the interactions behind the observed crystal packing and to rationalize the reasons of its formation, a computational analysis on such structures was carried out.

SUBMITTER: Bella G

PROVIDER: S-EPMC8510214 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Deciphering the driving forces in crystal packing by analysis of electrostatic energies and contact enrichment ratios.

Project description:Hirshfeld surface analysis is a widely used tool for identifying the types of intermolecular contacts that contribute most significantly to crystal packing stabilization. One useful metric for analyzing these contacts is the contact enrichment descriptor, which indicates the types of contacts that are over- or under-represented. In this statistical study, enrichment ratios were combined with electrostatic energy (Eelec) data for a variety of compound families. To compute the electrostatic interaction energy between atoms, charge density models from the ELMAM2 database of multipolar atoms were used. As expected, strong hydrogen bonds such as O/N-H...N and O/N-H...O typically display large enrichment values and have the most negative (i.e. favorable) electrostatic energies. Conversely, contacts that are repulsive from an electrostatic perspective are usually the most under-represented. Analyzing the enrichment ratio and electrostatic energy indicators was shown to help identify which favorable contacts are the most competitive with each other. For weaker interactions, such as hydrophobic contacts, the behavior is less clear cut and can depend on other factors such as the chemical content of the molecule. The anticorrelation between contact enrichment and Eelec is generally lost for weaker contacts. However, we observed that C...C contacts are often enriched in crystal structures containing heterocycles, despite the low electrostatic attraction. For molecules with only weak hydrogen bond donors/acceptors and hydrophobic groups, the correlation between contact enrichment and Eelec is still evident for the strongest of these interactions. However, there are some exceptions where the most favorable contacts from an electrostatic perspective are not the most over-represented. This can occur in cases where the shape of the molecule is complex or elongated, favoring dispersion forces and shape complementarity in the packing.

| S-EPMC10478513 | biostudies-literature

Unravelling the Supramolecular Driving Forces in the Formation of CO<sub>2</sub>-Responsive Pseudopeptidic Low-Molecular-Weight Hydrogelators.

Project description:A new family of C2-symmetric pseudopeptides with a high functional density for supramolecular interactions has been synthetized through the attachment of four amino acid subunits to a diamino aliphatic spacer. The resulting open-chain compounds present remarkable properties as low-molecular-weight hydrogelators. The self-assembled 3D networks were characterized by SEM analyses, observing regular nanofibres with 80-100 nm diameters. Spectroscopic and molecular modelling experiments revealed the presence of strong synergic effects between the H-bonding and π-π interactions, with the best results obtained for the homoleptic tetra-pseudopeptide derived from l-Phe. In addition, these bioinspired hydrogels possessed pH- and CO2-responsive sol-gel transitions. The formation of ammonium carbamate derivatives in the presence of carbon dioxide led to a detrimental change in its adequate self-assembly. CO2 desorption temperatures of ca. 70 °C were assigned to the thermodynamically favoured recovery of the supramolecular gel.

| S-EPMC9222431 | biostudies-literature

Crystal structure of new formamidinium triiodide jointly refined by single-crystal XRD, Raman scattering spectroscopy and DFT assessment of hydrogen-bond network features.

Project description:A novel triiodide phase of the formamidinium cation, CH5N2 +·I3 -, crystallizes in the triclinic space group P at a temperature of 110 K. The structure consists of two independent isolated triiodide ions located on inversion centers. The centrosymmetric character of I3 - was additionally confirmed by the observed pronounced peaks of symmetrical oscillations of I3 - at 115-116 cm-1 in Raman scattering spectra. An additional structural feature is that each terminal iodine atom is connected with three neighboring planar formamidinium cations by N-H⋯I hydrogen bonding with the N-H⋯I bond length varying from 2.81 to 3.08 Å, forming a deformed two-dimensional framework of hydrogen bonds. A Mulliken population analysis showed that the calculated charges of hydrogen atoms correlate well with hydrogen-bond lengths. The crystal studied was refined as a three-component twin with domain ratios of 0.631 (1):0.211 (1):0.158 (1).

| S-EPMC8382056 | biostudies-literature

Forces Driving Chaperone Action.

Project description:It is still unclear what molecular forces drive chaperone-mediated protein folding. Here, we obtain a detailed mechanistic understanding of the forces that dictate the four key steps of chaperone-client interaction: initial binding, complex stabilization, folding, and release. Contrary to the common belief that chaperones recognize unfolding intermediates by their hydrophobic nature, we discover that the model chaperone Spy uses long-range electrostatic interactions to rapidly bind to its unfolded client protein Im7. Short-range hydrophobic interactions follow, which serve to stabilize the complex. Hydrophobic collapse of the client protein then drives its folding. By burying hydrophobic residues in its core, the client's affinity to Spy decreases, which causes client release. By allowing the client to fold itself, Spy circumvents the need for client-specific folding instructions. This mechanism might help explain how chaperones can facilitate the folding of various unrelated proteins.

| S-EPMC4947014 | biostudies-literature

Forces driving epithelial wound healing.

Project description:A fundamental feature of multicellular organisms is their ability to self-repair wounds through the movement of epithelial cells into the damaged area. This collective cellular movement is commonly attributed to a combination of cell crawling and "purse-string" contraction of a supracellular actomyosin ring. Here we show by direct experimental measurement that these two mechanisms are insufficient to explain force patterns observed during wound closure. At early stages of the process, leading actin protrusions generate traction forces that point away from the wound, showing that wound closure is initially driven by cell crawling. At later stages, we observed unanticipated patterns of traction forces pointing towards the wound. Such patterns have strong force components that are both radial and tangential to the wound. We show that these force components arise from tensions transmitted by a heterogeneous actomyosin ring to the underlying substrate through focal adhesions. The structural and mechanical organization reported here provides cells with a mechanism to close the wound by cooperatively compressing the underlying substrate.

| S-EPMC4915550 | biostudies-literature

Driving forces of researchers mobility.

Project description:Starting from the dataset of the publication corpus of the APS during the period 1955-2009, we reconstruct the individual researchers trajectories, namely the list of the consecutive affiliations for each scholar. Crossing this information with different geographic datasets we embed these trajectories in a spatial framework. Using methods from network theory and complex systems analysis we characterise these patterns in terms of topological network properties and we analyse the dependence of an academic path across different dimensions: the distance between two subsequent positions, the relative importance of the institutions (in terms of number of publications) and some socio-cultural traits. We show that distance is not always a good predictor for the next affiliation while other factors like "the previous steps" of the career of the researchers (in particular the first position) or the linguistic and historical similarity between two countries can have an important impact. Finally we show that the dataset exhibit a memory effect, hence the fate of a career strongly depends from the first two affiliations.

| S-EPMC4014622 | biostudies-literature

Synthesis, single crystal (XRD), Hirshfeld surface analysis, computational study (DFT) and molecular docking studies of (E)-4-((2-hydroxy-3,5-diiodobenzylidene)amino)-N-(pyrimidine)-2-yl) benzenesulfonamide.

Project description:The Schiff base (E)-4-((2-hydroxy-3,5-diiodobenzylidene)amino)-N-(pyrimidine)-2-yl) benzene sulfonamide (DIDA) compound was synthesis with condensation of 3,5-diiodosalicylaldehyde and sulfadiazine. The compound characterized with FTIR, X-ray crystallography and electronic spectra. The titled compound associated with experimental and theoretical method, DFT used for the theoretical method. The IR was calculated from DFT mode with B3LYP/GENSEP basic set. The electronic spectra computed from TD-DFT method with CAM-B3LYP functional, with IEFPCM solvation model and DMSO used as the solvent. Wave function based properties like localized orbital locator, electron localization function and non-covalent interactions have been studied extensively. The ADMET properties of the compound DIDA indicated that the compound has excellent drug likeness properties and PASS studies showed that it has anti-infective properties, which is confirmed by a docking score of -7.4 kcal/mol.

| S-EPMC8379672 | biostudies-literature

Pan-Cancer Analysis of the Roles and Driving Forces of RAB42.

Project description:RAB42 is a member of the RAS family. However, the roles and driving forces for RAB42 in tumors remain elusive. In this study, we performed a comprehensive pan-cancer analysis of the roles and regulatory mechanisms of RAB42 using bioinformatics and experiments. Online databases such as Sanger Box, ACLBI and TIDE were used to search for the expression levels, prognostic value and immune features of RAB42. We observed that RAB42 expression was upregulated in most tumors and was closely associated with poor prognosis. Enrichment analysis indicated that RAB42 was related to multiple biological functions, especially the immune process. RAB42 expression had a positive correlation with immune cell infiltration and immune checkpoint gene expression. RAB42 had a high predictive value for immunotherapy efficiency. Our study screened out susceptible drugs for the RAB42 protein by sensitivity analysis and virtual screening. Many key driver genes such as TP53 contributed to RAB42 expression. DNA methylation, super-enhancer and non-coding RNAs were the epigenetic factors responsible for RAB42 expression. In brief, RAB42 could serve as a diagnostic and prognostic biomarker in many tumor types. RAB42 might be a predictive biomarker and a new target for immunotherapy. Genetic and epigenetic factors were essential for RAB42 overexpression in tumors.

| S-EPMC9855782 | biostudies-literature

Elucidating the fundamental forces in protein crystal formation: the case of crambin.

Project description:Molecular simulations of proteins have been usually accomplished through empirical or semi-empirical potentials, due to the large size and inherent complexity of these biological systems. On the other hand, a theoretical description of proteins based on quantum-mechanical methods would however provide an unbiased characterization of their electronic properties, possibly offering a link between these and the ultimate biological activity. Yet, such approaches have been historically hindered by the large amount of requested computational power. Here we demonstrate the feasibility of periodic all-electron density functional theory calculations in the description of the crystal of the protein crambin (46 aminoacids), which is determined with exceptional structural accuracy. We have employed the hybrid B3LYP functional, coupled to an empirical description of London interactions (D*) to simulate the crambin crystal with an increasing amount of lattice water molecules in the cell (up to 172H2O per cell). The agreement with the experiment is good for both protein geometry and protein-water interactions. The energetics was computed to predict crystal formation energies, protein-water and protein-protein interaction energies. We studied the role of dispersion interactions which are crucial for holding the crambin crystal in place. B3LYP-D* electrostatic potential and dipole moment of crambin as well as the electronic charge flow from crambin to the solvating water molecules (0.0015e per H2O) have also been predicted. These results proved that quantum-mechanical simulations of small proteins, both free and in their crystalline state, are now feasible in a reasonable amount of time, by programs capable of exploiting high performance computing architectures, allowing the study of protein properties not easily amenable through classical force fields.

| S-EPMC5963673 | biostudies-literature

Driving forces of Antarctic krill abundance.

Project description:Antarctic krill, crucial to the Southern Ocean ecosystem and a vital fisheries resource, is endangered by climate change. Identifying drivers of krill biomass is therefore essential for determining catch limits and designating protection zones. We present a modeling approach to pinpointing effects of sea surface temperature, ice cover, chlorophyll levels, climate indices, and intraspecific competition. Our study reveals that larval recruitment is driven by both competition among age classes and chlorophyll levels. In addition, while milder ice and temperature in spring and summer favor reproduction and early larval survival, both larvae and juveniles strongly benefit from heavier ice and colder temperatures in winter. We conclude that omitting top-down control of resources by krill is only acceptable for retrospective or single-year prognostic models that use field chlorophyll data but that incorporating intraspecific competition is essential for longer-term forecasts. Our findings can guide future krill modeling strategies, reinforcing the sustainability of this keystone species.

| S-EPMC10848738 | 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