Browse
Submit Data
Databases
API
Help

Dataset Information

31 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Novel Imidazole Liquid Crystals; Experimental and Computational Approaches.

ABSTRACT: The liquid crystalline materials named (E)-4-(2-(4-oxo-5,5-diphenyl-4,5-dihydro-1H-imidazol-2-yl)hydrazineylidene)methyl)phenyl and 4-(alkoxy)benzoate, In, were synthesized and their mesomorphic behaviors were examined. The chemical structures of the produced compounds were confirmed by Fourier-transform infrared spectroscopy (FT-IR), NMR, and elemental analysis. Differential scanning calorimetry (DSC) and polarized optical microscopy were used to investigate the mesomorphic properties of designed heterocyclic derivatives. All the compounds tested had suitable thermal stability and enantiotropic behavior of smectogenic temperature ranges. Furthermore, the enantiotropic smectic C phases were observed to cover all the homologues. Moreover, computational investigations corroborated the experimental findings of the mesomorphic behavior. The reactivity parameters were computed for the derivatives and linked with the experimental data. Theoretical calculations revealed that the polarizability of the studied series increases with the chain length, whereas the HOMO-LUMO energy gap or other reactivity descriptors were less sensitive to the size of the system. On the other hand, the predicted thermodynamic parameters revealed the size dependence of thermal stability of the compounds.

SUBMITTER: Al-Kadhi NS

PROVIDER: S-EPMC9316631 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Three Rings Schiff Base Ester Liquid Crystals: Experimental and Computational Approaches of Mesogenic Core Orientation Effect, Heterocycle Impact.

Project description:Three rings 2-hydroxypyridine liquid crystalline compounds have been prepared and fully characterized. The mesomorphic behavior of the prepared compounds has been investigated in terms of differential scanning calorimetry (DSC) and polarized optical microscopy (POM). Moreover, a comparative study between the prepared compounds and previously reported analogs has been discussed in terms of the orientation and position of the mesogenic core, in addition to the direction of the terminal alkyl chains. Furthermore, a detailed computational approach has been studied to illustrate the effect of geometrical and dimensional parameters on the type of the enhanced texture and the mesomorphic range and stability. The results of the DFT study revealed that the orientation of the mesogen could affect the mesomorphic behavior and this has been attributed in terms of the degree of the polarizability of the linking groups. This result has been confirmed by calculation of the net dipole moment and the molecular electrostatic potential that show how the mesogen orientation and position could impact the molecular charge separation. Finally, the effect of the pyridyl group has been also investigated in terms of the calculated aromaticity index and the π-π stacking.

| S-EPMC9000867 | biostudies-literature

Experimental and computational characterization of biological liquid crystals: a review of single-molecule bioassays.

Project description:Quantitative understanding of the mechanical behavior of biological liquid crystals such as proteins is essential for gaining insight into their biological functions, since some proteins perform notable mechanical functions. Recently, single-molecule experiments have allowed not only the quantitative characterization of the mechanical behavior of proteins such as protein unfolding mechanics, but also the exploration of the free energy landscape for protein folding. In this work, we have reviewed the current state-of-art in single-molecule bioassays that enable quantitative studies on protein unfolding mechanics and/or various molecular interactions. Specifically, single-molecule pulling experiments based on atomic force microscopy (AFM) have been overviewed. In addition, the computational simulations on single-molecule pulling experiments have been reviewed. We have also reviewed the AFM cantilever-based bioassay that provides insight into various molecular interactions. Our review highlights the AFM-based single-molecule bioassay for quantitative characterization of biological liquid crystals such as proteins.

| S-EPMC2769145 | biostudies-literature

Experimental and Theoretical Approaches of New Nematogenic Chair Architectures of Supramolecular H-Bonded Liquid Crystals.

Project description:New four isomeric chair architectures of 1:1 H-bonded supramolecular complexes were prepared through intermolecular interactions between 4-(2-(pyridin-4-yl)diazenyl-(2-(or 3-)chlorophenyl) 4-alkoxybenzoates and 4-n-alkoxybenzoic acids. The H-bond formation of all complexes was confirmed by differential scanning calorimetry (DSC) and Fourier-transform infrared spectroscopy (FTIR). Mesomorphic characterization was carried by DSC and polarized optical microscopy (POM). It was found that all prepared laterally chloro-substituted supramolecular complexes were nematogenic, and exhibited nematic phase and low melting temperature. The thermal stability of the nematic mesophase observed depends upon the location and spatial orientation of the lateral Cl- atom in as well as the length of terminal chains. Theoretical calculations were carried out within the paradigm of the density functional theory (DFT) in order to establish the molecular conformation for the formed complexes and estimate their thermal parameters. The results of the computational calculations revealed that the H-bonded complexes were in a chair form molecular geometry. Additionally, out of the acquired data, it was possible to designate the influence of the position and orientation of the lateral group as well as the alkoxy chain length on the stability of the nematic phase.

| S-EPMC7024265 | biostudies-literature

Novel sulphonic acid liquid crystal derivatives: experimental, computational and optoelectrical characterizations.

Project description:A novel liquid crystal homologous series based on the benzene sulphonic acid moiety, namely (E)-4-((4-((4-(alkoxy)benzoyl)oxy)benzylidene)amino)benzenesulfonic acid (Sn), was synthesized and examined via different experimental and theoretical measurements. The four synthesized members have terminally connected alkoxy chain groups, which vary between 6 and 12 carbons. FT-IR and NMR spectroscopy, as well as elemental analyses, were used to confirm their molecular structures. Mesomorphic and optical investigations of the prepared homologues were also conducted using differential scanning calorimetry (DSC) and polarized optical microscopy (POM). The DSC and POM characterization revealed that all of the synthesized sulphonic acid members are monomorphic, exhibiting a pure smectic A (SmA) mesophase with enantiotropic properties. Moreover, all compounds in the group have high thermal transition temperatures. The terminal electron-withdrawing group -SO3H plays a considerable role in the stabilization of the molecule, which in return resulted in high thermal SmA stability. Furthermore, the experimental data relating to the mesophase behavior were substantiated via computational studies using the DFT approach. In addition, the terminal -SO3H moiety has an essential impact on the thermal and physical parameters of possible geometries. All members of the synthesized Sn series exhibit ohmic behavior with electrical resistance in the GΩ range, as revealed by electrical measurements. The S10 electrode had the highest electrical conductivity: 35.16 pS. It also showed two direct optical band gaps of 3.58 and 3.23 eV with Urbach energies of 1261.1 and 502.4 meV. Upon decreasing the number of carbon atoms to n = 6, the main bandgap for S6 reduced to 3.3 eV. The highest conductivity, good absorption, and two large bandgaps recorded for the chain derivative S10 make it suitable for investigations relating to energy-based applications.

| S-EPMC9039420 | biostudies-literature

Dyes in Liquid Crystals: Experimental and Computational Studies of a Guest-Host System Based on a Combined DFT and MD Approach.

Project description:Practical applications of guest-host liquid crystal systems are critically dependent on the alignment of the guest species within the liquid crystal host. UV/Vis absorption spectroscopy shows that the 1,5-dihydroxy-2,6-bis-(4-propylphenyl)-9,10-anthraquinone dye aligns within the E7 nematic host, giving an experimental dichroic ratio of 9.40 and dye order parameter of 0.74. This alignment was modelled by using a combination of density functional theory (DFT) and molecular dynamics (MD) computational approaches that do not require the input of experimental data. Time-dependent DFT calculations show that the electronic transition dipole moment is highly aligned with the long molecular axis of the dye. Fully atomistic MD simulations show that the long axis of the dye is less highly aligned within the E7 host, indicating that this contribution limits the overall dye alignment and, thereby, the potential practical applications of this particular system. Importantly, this study demonstrates an experimental and combined DFT and MD computational approach that may be applied generally to guest-host systems, providing a potential route to their rational design.

| S-EPMC4515093 | biostudies-literature

Computational and Experimental Approaches to Controlling Bacterial Microcompartment Assembly.

Project description:Bacterial microcompartments compartmentalize the enzymes that aid chemical and energy production in many bacterial species. They are postulated to help bacteria survive in hostile environments. Metabolic engineers are interested in repurposing these organelles for non-native functions. Here, we use computational, theoretical, and experimental approaches to determine mechanisms that effectively control microcompartment self-assembly. We find, via multiscale modeling and mutagenesis studies, the interactions responsible for the binding of hexamer-forming proteins in a model system, the propanediol utilization bacterial microcompartments from Salmonella enterica serovar Typhimurium LT2. We determine how the changes in the microcompartment hexamer protein preferred angles and interaction strengths can modify the assembled morphologies. We demonstrate that such altered strengths and angles are achieved via amino acid mutations. A thermodynamic model provides guidelines to design microcompartments of various morphologies. These findings yield insight in controlled protein assembly and provide principles for assembling microcompartments for biochemical or energy applications as nanoreactors.

| S-EPMC8155464 | biostudies-literature

Ionic Liquid Solvation versus Catalysis: Computational Insight from a Multisubstituted Imidazole Synthesis in [Et2NH2][HSO4].

Project description:The mechanisms of a tetrasubstituted imidazole [2-(2,4,5-triphenyl-1?H-imidazol-1-yl)ethan-1-ol] synthesis from benzil, benzaldehyde, ammonium acetate, and ethanolamine in [Et2NH2][HSO4] ionic liquid (IL) are studied computationally. The effects of the presence of the cationic and anionic components of the IL on transition states and intermediate structures, acting as a solvent versus as a catalyst, are determined. In IL-free medium, carbonyl hydroxylation when using a nucleophile (ammonia) proceeds with a Gibbs free energy (?G?) barrier of 49.4?kcal?mol-1. Cationic and anionic hydrogen-bond solute-solvent interactions with the IL decrease the barrier to 35.8?kcal?mol-1. [Et2NH2][HSO4] incorporation in the reaction changes the nature of the transition states and decreases the energy barriers dramatically, creating a catalytic effect. For example, carbonyl hydroxylation proceeds via two transition states, first proton donation to the carbonyl (?G?=9.2?kcal?mol-1) from [Et2NH2]+, and then deprotonation of ammonia (?G?=14.3) via Et2NH. Likewise, incorporation of the anion component [HSO4]- of the IL gives comparable activation energies along the same reaction route and the lowest transition state for the product formation step. We propose a dual catalytic IL effect for the mechanism of imidazole formation. The computations demonstrate a clear distinction between IL solvent effects on the reaction and IL catalysis.

| S-EPMC5062012 | biostudies-literature

Enhancers of host immune tolerance to bacterial infection discovered using linked computational and experimental approaches

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-06-16 | GSE196425 | GEO

Living liquid crystals.

Project description:Collective motion of self-propelled organisms or synthetic particles, often termed "active fluid," has attracted enormous attention in the broad scientific community because of its fundamentally nonequilibrium nature. Energy input and interactions among the moving units and the medium lead to complex dynamics. Here, we introduce a class of active matter--living liquid crystals (LLCs)--that combines living swimming bacteria with a lyotropic liquid crystal. The physical properties of LLCs can be controlled by the amount of oxygen available to bacteria, by concentration of ingredients, or by temperature. Our studies reveal a wealth of intriguing dynamic phenomena, caused by the coupling between the activity-triggered flow and long-range orientational order of the medium. Among these are (i) nonlinear trajectories of bacterial motion guided by nonuniform director, (ii) local melting of the liquid crystal caused by the bacteria-produced shear flows, (iii) activity-triggered transition from a nonflowing uniform state into a flowing one-dimensional periodic pattern and its evolution into a turbulent array of topological defects, and (iv) birefringence-enabled visualization of microflow generated by the nanometers-thick bacterial flagella. Unlike their isotropic counterpart, the LLCs show collective dynamic effects at very low volume fraction of bacteria, on the order of 0.2%. Our work suggests an unorthodox design concept to control and manipulate the dynamic behavior of soft active matter and opens the door for potential biosensing and biomedical applications.

| S-EPMC3910648 | biostudies-literature

Discovery of Amoebicidal Compounds by Combining Computational and Experimental Approaches.

Project description:Pathogenic and opportunistic free-living amoebae such as Acanthamoeba spp. can cause keratitis (Acanthamoeba keratitis [AK]), which may ultimately lead to permanent visual impairment or blindness. Acanthamoeba can also cause rare but usually fatal granulomatous amoebic encephalitis (GAE). Current therapeutic options for AK require a lengthy treatment with nonspecific drugs that are often associated with adverse effects. Recent developments in the field led us to target cAMP pathways, specifically phosphodiesterase. Guided by computational tools, we targeted the Acanthamoeba phosphodiesterase RegA. Computational studies led to the construction and validation of a homology model followed by a virtual screening protocol guided by induced-fit docking and chemical scaffold analysis using our medicinal and biological chemistry (MBC) chemical library. Subsequently, 18 virtual screening hits were prioritized for further testing in vitro against Acanthamoeba castellanii, identifying amoebicidal hits containing piperidine and urea imidazole cores. Promising activities were confirmed in the resistant cyst form of the amoeba and in additional clinical Acanthamoeba strains, increasing their therapeutic potential. Mechanism-of-action studies revealed that these compounds produce apoptosis through reactive oxygen species (ROS)-mediated mitochondrial damage. These chemical families show promise for further optimization to produce effective antiacanthamoebal drugs.

| S-EPMC7849001 | 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