Browse
Submit Data
Databases
API
Help

Dataset Information

21 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Crystalline Moduli of Polymers, Evaluated from Density Functional Theory Calculations under Periodic Boundary Conditions.

ABSTRACT: A theoretical methodology based on quantum chemistry to calculate mechanical properties of polymer crystals has been developed and applied to representative polymers. By density functional theory calculations including a dispersion force correction under three-dimensional periodic boundary conditions, crystal structures of poly(methylene oxide) (PMO), polyethylene (PE), poly(ethylene terephthalate) (PET), poly(trimethylene terephthalate) (PTT), and poly(butylene terephthalate) (PBT) were optimized and their mechanical properties, such as crystalline moduli and linear and volume compressibilities, were calculated. The optimized crystal structures were proved to be fully consistent with those determined by X-ray and neutron diffraction. The crystalline moduli (E _∥) parallel to the chain axis were calculated to be 114 GPa (PMO), 333 GPa (PE), 182 GPa (PET), 7.1 GPa (PTT), and 20.8 GPa (PBT) and compared with those determined from X-ray diffraction, Raman spectroscopy, and neutron inelastic scattering experiments. Herein, the E _∥ values thus determined are interpreted in terms of conformational characteristics of the polymeric chains and the validity of the homogeneous stress hypothesis adopted in the X-ray diffraction method is also discussed.

SUBMITTER: Kurita T

PROVIDER: S-EPMC6641976 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Vibrational Dynamics of Crystalline 4-Phenylbenzaldehyde from INS Spectra and Periodic DFT Calculations.

Project description:The present work emphasizes the value of periodic density functional theory (DFT) calculations in the assessment of the vibrational spectra of molecular crystals. Periodic calculations provide a nearly one-to-one match between the calculated and observed bands in the inelastic neutron scattering (INS) spectrum of crystalline 4-phenylbenzaldehyde, thus validating their assignment and correcting previous reports based on single molecule calculations. The calculations allow the unambiguous assignment of the phenyl torsional mode at ca. 118-128 cm-1, from which a phenyl torsional barrier of ca. 4000 cm-1 is derived, and the identification of the collective mode involving the antitranslational motion of CH···O bonded pairs, a hallmark vibrational mode of systems where C-H···O contacts are an important feature.

| S-EPMC7144378 | biostudies-literature

Antioxidant Properties of Kynurenines: Density Functional Theory Calculations.

Project description:Kynurenines, the main products of tryptophan catabolism, possess both prooxidant and anioxidant effects. Having multiple neuroactive properties, kynurenines are implicated in the development of neurological and cognitive disorders, such as Alzheimer's, Parkinson's, and Huntington's diseases. Autoxidation of 3-hydroxykynurenine (3HOK) and its derivatives, 3-hydroxyanthranilic acid (3HAA) and xanthommatin (XAN), leads to the hyperproduction of reactive oxygen species (ROS) which damage cell structures. At the same time, 3HOK and 3HAA have been shown to be powerful ROS scavengers. Their ability to quench free radicals is believed to result from the presence of the aromatic hydroxyl group which is able to easily abstract an electron and H-atom. In this study, the redox properties for kynurenines and several natural and synthetic antioxidants have been calculated at different levels of density functional theory in the gas phase and water solution. Hydroxyl bond dissociation enthalpy (BDE) and ionization potential (IP) for 3HOK and 3HAA appear to be lower than for xanthurenic acid (XAA), several phenolic antioxidants, and ascorbic acid. BDE and IP for the compounds with aromatic hydroxyl group are lower than for their precursors without hydroxyl group. The reaction rate for H donation to *O-atom of phenoxyl radical (Ph-O*) and methyl peroxy radical (Met-OO*) decreases in the following rankings: 3HOK ~ 3HAA > XAAOXO > XAAENOL. The enthalpy absolute value for Met-OO* addition to the aromatic ring of the antioxidant radical increases in the following rankings: 3HAA* < 3HOK* < XAAOXO* < XAAENOL*. Thus, the high free radical scavenging activity of 3HAA and 3HOK can be explained by the easiness of H-atom abstraction and transfer to O-atom of the free radical, rather than by Met-OO* addition to the kynurenine radical.

| S-EPMC5115656 | biostudies-literature

Double-Hybrid Density Functional Theory for Core Excitations: Theory and Benchmark Calculations.

Project description:The double-hybrid (DH) time-dependent density functional theory is extended to core excitations. Two different DH formalisms are presented utilizing the core-valence separation (CVS) approximation. First, a CVS-DH variant is introduced relying on the genuine perturbative second-order correction, while an iterative analogue is also presented using our second-order algebraic-diagrammatic construction [ADC(2)]-based DH ansatz. The performance of the new approaches is tested for the most popular DH functionals using the recently proposed XABOOM [J. Chem. Theory Comput.2021, 17, 1618] benchmark set. In order to make a careful comparison, the accuracy and precision of the methods are also inspected. Our results show that the genuine approaches are highly competitive with the more advanced CVS-ADC(2)-based methods if only excitation energies are required. In contrast, as expected, significant differences are observed in oscillator strengths; however, the precision is acceptable for the genuine functionals as well. Concerning the performance of the CVS-DH approaches, the PBE0-2/CVS-ADC(2) functional is superior, while its spin-opposite-scaled variant is also recommended as a cost-effective alternative. For these approaches, significant improvements are realized in the error measures compared with the popular CVS-ADC(2) method.

| S-EPMC9979613 | biostudies-literature

Structural Anisotropy in Polar Fluids Subjected to Periodic Boundary Conditions.

Project description:A heuristic model based on dielectric continuum theory for the long-range solvation free energy of a dipolar system possessing periodic boundary conditions (PBCs) is presented. The predictions of the model are compared to simulation results for Stockmayer fluids simulated using three different cell geometries. The boundary effects induced by the PBCs are shown to lead to anisotropies in the apparent dielectric constant and the long-range solvation free energy of as much as 50%. However, the sum of all of the anisotropic energy contributions yields a value that is very close to the isotropic one derived from dielectric continuum theory, leading to a total system energy close to the dielectric value. It is finally shown that the leading-order contribution to the energetic and structural anisotropy is significantly smaller in the noncubic simulation cell geometries compared to when using a cubic simulation cell.

| S-EPMC3269192 | biostudies-other

Challenging Density Functional Theory Calculations with Hemes and Porphyrins.

Project description:In this paper we review recent advances in computational chemistry and specifically focus on the chemical description of heme proteins and synthetic porphyrins that act as both mimics of natural processes and technological uses. These are challenging biochemical systems involved in electron transfer as well as biocatalysis processes. In recent years computational tools have improved considerably and now can reproduce experimental spectroscopic and reactivity studies within a reasonable error margin (several kcal·mol(-1)). This paper gives recent examples from our groups, where we investigated heme and synthetic metal-porphyrin systems. The four case studies highlight how computational modelling can correctly reproduce experimental product distributions, predicted reactivity trends and guide interpretation of electronic structures of complex systems. The case studies focus on the calculations of a variety of spectroscopic features of porphyrins and show how computational modelling gives important insight that explains the experimental spectra and can lead to the design of porphyrins with tuned properties.

| S-EPMC4848975 | biostudies-literature

The distribution of word matches between Markovian sequences with periodic boundary conditions.

Project description:Word match counts have traditionally been proposed as an alignment-free measure of similarity for biological sequences. The D(2) statistic, which simply counts the number of exact word matches between two sequences, is a useful test bed for developing rigorous mathematical results, which can then be extended to more biologically useful measures. The distributional properties of the D(2) statistic under the null hypothesis of identically and independently distributed letters have been studied extensively, but no comprehensive study of the D(2) distribution for biologically more realistic higher-order Markovian sequences exists. Here we derive exact formulas for the mean and variance of the D(2) statistic for Markovian sequences of any order, and demonstrate through Monte Carlo simulations that the entire distribution is accurately characterized by a Pólya-Aeppli distribution for sequence lengths of biological interest. The approach is novel in that Markovian dependency is defined for sequences with periodic boundary conditions, and this enables exact analytic formulas for the mean and variance to be derived. We also carry out a preliminary comparison between the approximate D(2) distribution computed with the theoretical mean and variance under a Markovian hypothesis and an empirical D(2) distribution from the human genome.

| S-EPMC3880068 | biostudies-literature

Electrically turning periodic structures in cholesteric layer with conical-planar boundary conditions.

Project description:Electro-optical cell based on the cholesteric liquid crystal is studied with unique combination of the boundary conditions: conical anchoring on the one substrate and planar anchoring on another one. Periodic structures in cholesteric layer and their transformation under applied electric field are considered by polarizing optical microscopy, the experimental findings are supported by the data of the calculations performed using the extended Frank elastic continuum approach. Such structures are the set of alternating over- and under-twisted defect lines whose azimuthal director angles differ by [Formula: see text]. The [Formula: see text] and [Formula: see text]-defects of periodicity, which are the smooth transition between the defect lines, are observed at the edge of electrode area. The growth direction of defect lines forming a diffraction grating can be controlled by applying a voltage in the range of [Formula: see text] V during the process. Resulting orientation and distance between the lines don't change under voltage. However, at [Formula: see text] V [Formula: see text]-defects move along the defect lines away from the electrode edges, and, finally, the grating lines collapse at the cell's center. These results open a way for the use of such cholesteric material in applications with periodic defect structures where a periodicity, orientation, and configuration of defects should be adjusted.

| S-EPMC8052423 | biostudies-literature

Periodic Density Functional Theory Calculations of Uranyl Tetrachloride Compounds Engaged in Uranyl-Cation and Uranyl-Hydrogen Interactions: Electronic Structure, Vibrational, and Thermodynamic Analyses.

Project description:Solid-state uranyl hybrid structures are often formed through unique intermolecular interactions occurring between a molecular uranyl anion and a charge-balancing cation. In this work, solid-state structures of the uranyl tetrachloride anion engaged in uranyl-cation and uranyl-hydrogen interactions were studied using density functional theory (DFT). As most first-principles methods used for systems of this type focus primarily on the molecular structure, we present an extensive benchmarking study to understand the methods needed to accurately model the geometric properties of these systems. From there, the electronic and vibrational structures of the compounds were investigated through projected density of states and phonon analysis and compared to the experiment. Lastly, we present a DFT + thermodynamics approach to calculate the formation enthalpies (ΔHf) of these systems to directly relate to experimental values. Through this methodology, we were able to accurately capture trends observed in experimental results and saw good quantitative agreement in predicted ΔHf compared to the value calculated through referencing each structure to its standard state. Overall, results from this work will be used for future combined experimental and computational studies on both uranyl and neptunyl hybrid structures to delineate how varying intermolecular interaction strengths relates to the overall values of ΔHf.

| S-EPMC9832540 | biostudies-literature

Preferential Binding of Lanthanides to Methanol Dehydrogenase Evaluated with Density Functional Theory.

Project description:Methanol dehydrogenase (MDH) is an enzyme used by certain bacteria for the oxidation of methanol to formaldehyde, which is a necessary metabolic reaction. The discovery of a lanthanide-dependent MDH reveals that lanthanide ions (Ln3+) have a role in biology. Two types of MDH exist in methane-utilizing bacteria: one that is Ca2+-dependent (MxaF) and another that is Ln3+-dependent. Given that the triply charged Ln3+ are strongly hydrated, it is not clear how preference for Ln3+ is manifested and if the Ca2+-dependent MxaF protein can also bind Ln3+ ions. A computational approach was used to estimate the Gibbs energy differences between the binding of Ln3+ and Ca2+ to MDH using density functional theory. The results show that both proteins bind La3+ with higher affinity than Ca2+, albeit with a more pronounced difference in the case of Ln3+-dependent MDH. Interestingly, the binding of heavier lanthanides is preferred over the binding of La3+, with Gd3+ showing the highest affinity for both proteins of all Ln3+ ions that were tested (La3+, Sm3+, Gd3+, Dy3+, and Lu3+). Energy decomposition analysis reveals that the higher affinity of La3+ than Ca2+ to MDH is due to stronger contributions of electrostatics and polarization, which overcome the high cost of desolvating the ion.

| S-EPMC8028316 | biostudies-literature

Density functional theory calculations on Mossbauer parameters of nonheme iron nitrosyls.

Project description:Density Functional Theory (DFT) calculations on transition metal nitrosyls often reveal unusual spin density profiles, involving substantial spatial separation of majority and minority spin densities. Against this context, there is a significant lack of studies where DFT calculations have been quantitatively calibrated against experimental spectroscopic properties. Reported herein are DFT calculations of Mössbauer isomer shifts and quadrupole splittings for 21 nonheme iron complexes (26 distinct iron sites) including 9 iron nitrosyls. Low- (S = 1/2) and high-spin (S = 3/2) {FeNO}(7) complexes, S = 1/2 {Fe(NO)(2)}(9) species, and polynuclear iron nitrosyls are all represented within the set of compounds examined. The general conclusion with respect to isomer shifts is that DFT (OLYP/STO-TZP) performs comparably well for iron nitrosyls and for iron complexes in general. However, quadrupole splittings are less accurately reproduced for nitrosyl complexes.

| S-EPMC2777692 | 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