Browse
Submit Data
Databases
API
Help

Dataset Information

22 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Impact of arsenic/phosphorus substitution on the intrinsic conformational properties of the phosphodiester backbone of DNA investigated using ab initio quantum mechanical calculations.

ABSTRACT: Deoxyribonucleic acid (DNA) is composed of five major elements carbon, hydrogen, nitrogen, oxygen, and phosphorus. The substitution of any of these elements in DNA would be anticipated to have major biological implications. However, recent studies have suggested that the substitution of arsenic into DNA (As-DNA) in bacteria may be possible. To help evaluate this possibility, ab initio quantum mechanical calculations are used to show that arsenodiester and phosphodiester linkages have similar geometric and conformational properties. Based on these results, it is suggested that the As-DNA will have similar conformational properties to phosphorus-based DNA, including the maintenance of base stacking.

SUBMITTER: Denning EJ

PROVIDER: S-EPMC3076535 | biostudies-literature | 2011 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Impact of arsenic/phosphorus substitution on the intrinsic conformational properties of the phosphodiester backbone of DNA investigated using ab initio quantum mechanical calculations.

Denning Elizabeth J EJ Mackerell Alexander D AD

Journal of the American Chemical Society 20110328 15

Deoxyribonucleic acid (DNA) is composed of five major elements carbon, hydrogen, nitrogen, oxygen, and phosphorus. The substitution of any of these elements in DNA would be anticipated to have major biological implications. However, recent studies have suggested that the substitution of arsenic into DNA (As-DNA) in bacteria may be possible. To help evaluate this possibility, ab initio quantum mechanical calculations are used to show that arsenodiester and phosphodiester linkages have similar geo ...[more]

PMID: 21443192

Similar Datasets

Polydopamine and eumelanin molecular structures investigated with <i>ab initio</i> calculations.

Project description:A set of computational methods that contains a brute-force algorithmic generation of chemical isomers, molecular dynamics (MD) simulations, and density functional theory (DFT) calculations is reported and applied to investigate nearly 3000 probable molecular structures of polydopamine (PDA) and eumelanin. All probable early-polymerized 5,6-dihydroxyindole (DHI) oligomers, ranging from dimers to tetramers, have been systematically analyzed to find the most stable geometry connections as well as to propose a set of molecular models that represents the chemically diverse nature of PDA and eumelanin. Our results indicate that more planar oligomers have a tendency to be more stable. This finding is in good agreement with recent experimental observations, which suggested that PDA and eumelanin are composed of nearly planar oligomers that appear to be stacked together via π-π interactions to form graphite-like layered aggregates. We also show that there is a group of tetramers notably more stable than the others, implying that even though there is an inherent chemical diversity in PDA and eumelanin, the molecular structures of the majority of the species are quite repetitive. Our results also suggest that larger oligomers are less likely to form. This observation is also consistent with experimental measurements, supporting the existence of small oligomers instead of large polymers as main components of PDA and eumelanin. In summary, this work brings an insight into the controversial structure of PDA and eumelanin, explaining some of the most important structural features, and providing a set of molecular models for more accurate modeling of eumelanin-like materials.

| S-EPMC5364519 | biostudies-literature

Stable GaSe-Like Phosphorus Carbide Monolayer with Tunable Electronic and Optical Properties from Ab Initio Calculations.

Project description:On the basis of density functional theory (DFT) calculations, we propose a stable two-dimensional (2D) monolayer phosphorus carbide (PC) with a GaSe-like structure, which has intriguing electronic and optical properties. Our calculated results show that this 2D monolayer structure is more stable than the other allotropes predicted by Tománek et al. [Nano Lett., 2016, 16, 3247⁻3252]. More importantly, this structure exhibits superb optical absorption, which can be mainly attributed to its direct band gap of 2.65 eV. The band edge alignments indicate that the 2D PC monolayer structure can be a promising candidate for photocatalytic water splitting. Furthermore, we found that strain is an effective method used to tune the electronic structures varying from direct to indirect band-gap semiconductor or even to metal. In addition, the introduction of one carbon vacancy in such a 2D PC structure can induce a magnetic moment of 1.22 µB. Our findings add a new member to the 2D material family and provide a promising candidate for optoelectronic devices in the future.

| S-EPMC6213067 | biostudies-literature

Ab initio calculations of conduction band effective mass parameters of thermoelectric

Project description:Since there are still research interests in the physical properties of quasi-binary thermoelectric

| S-EPMC7529947 | biostudies-literature

Dynamics Studies of Nitrogen Interstitial in GaN from Ab Initio Calculations.

Project description:Understanding the properties of defects is crucial to design higher performance semiconductor materials because they influence the electronic and optical properties significantly. Using ab initio calculations, the dynamics properties of nitrogen interstitial in GaN material, including the configuration, migration, and interaction with vacancy were systematically investigated in the present work. By introducing different sites of foreign nitrogen atom, the most stable configuration of nitrogen interstitial was calculated to show a threefold symmetry in each layer and different charge states were characterized, respectively. In the researches of migration, two migration paths, in-plane and out-of-plane, were considered. With regards to the in-plane migration, an intermediated rotation process was observed first time. Due to this rotation behavior, two different barriers were demonstrated to reveal that the migration is an anisotropic behavior. Additionally, charged nitrogen Frenkel pair was found to be a relatively stable defect complex and its well separation distance was about 3.9 Å. Part of our results are in good agreement with the experimental results, and our work provides underlying insights of the identification and dynamics of nitrogen interstitial in GaN material. This study of defects in GaN material is useful to establish a more complete theory and improve the performance of GaN-based devices.

| S-EPMC7475889 | biostudies-literature

Electronic properties of several two dimensional halides from ab initio calculations.

Project description:Using density functional theory, we study the electronic properties of several halide monolayers. We show that their electronic bandgaps, as obtained with the HSE hybrid functional, range between 3.0 and 7.5 eV and that their phonon spectra are dynamically stable. Additionally, we show that under an external electric field some of these systems exhibit a semiconductor-to-metal transition.

| S-EPMC6466728 | biostudies-literature

Enzyme active site interactions by Raman/FTIR, NMR, and ab initio calculations.

Project description:Characterization of enzyme active site structure and interactions at high resolution is important for the understanding of the enzyme catalysis. Vibrational frequency and NMR chemical shift measurements of enzyme-bound ligands are often used for such purpose when X-ray structures are not available or when higher resolution active site structures are desired. This review is focused on how ab initio calculations may be integrated with vibrational and NMR chemical shift measurements to quantitatively determine high-resolution ligand structures (up to 0.001 Å for bond length and 0.01 Å for hydrogen bonding distance) and how interaction energies between bound ligand and its surroundings at the active site may be determined. Quantitative characterization of substrate ionic states, bond polarizations, tautomeric forms, conformational changes and its interactions with surroundings in enzyme complexes that mimic ground state or transition state can provide snapshots for visualizing the substrate structural evolution along enzyme-catalyzed reaction pathway. Our results have shown that the integration of spectroscopic studies with theoretical computation greatly enhances our ability to interpret experimental data and significantly increases the reliability of the theoretical analysis.

| S-EPMC5484042 | biostudies-literature

Ab initio genotype-phenotype association reveals intrinsic modularity in genetic networks.

Project description:Microbial species express an astonishing diversity of phenotypic traits, behaviors, and metabolic capacities. However, our molecular understanding of these phenotypes is based almost entirely on studies in a handful of model organisms that together represent only a small fraction of this phenotypic diversity. Furthermore, many microbial species are not amenable to traditional laboratory analysis because of their exotic lifestyles and/or lack of suitable molecular genetic techniques. As an adjunct to experimental analysis, we have developed a computational information-theoretic framework that produces high-confidence gene-phenotype predictions using cross-species distributions of genes and phenotypes across 202 fully sequenced archaea and eubacteria. In addition to identifying the genetic basis of complex traits, our approach reveals the organization of these genes into generic preferentially co-inherited modules, many of which correspond directly to known enzymatic pathways, molecular complexes, signaling pathways, and molecular machines.

| S-EPMC1681479 | biostudies-literature

A compilation of ab-initio calculations of embrittling potencies in binary metallic alloys.

Project description:Segregation-induced changes in interfacial cohesion often control the mechanical properties of metals. The change in the work of separation of an interface upon segregation of a solute to the interface, termed the embrittling potency, is an atomic-level quantity used to predict and understand embrittlement phenomena. We present a compilation of calculations of embrittling potencies, along with references for these calculations. A discussion of this data is made in a separate article (Gibson and Schuh, 2016 [1]).

| S-EPMC4706572 | biostudies-literature

Ab initio calculations on structure and stability of BN/CC isosterism in azulene.

Project description:Herein, we investigated the thermodynamic stability and opto-electronic properties of a newly BN-doped azulene. The gas-phase formation enthalpies of 11 BN-doped azulene were calculated by the atomization energy method using three computational models (CBS-APNO, CBS-QB3, and G3MP2). The results suggest that AZ-1N9B exhibits the highest stability among the studied isomers. On the other hand, AZ-1B9N and AZ-9B10N display nearly equal stability with relative energies of 19.36 and 19.82 kcal/mol at CBS-QB3, respectively. These two isomers are considered the least stable among the investigated compounds. The frontier molecular orbitals (FMO), ionization energies (IE), and electron affinities (EA) of these isomers were discussed. Additionally, the electronic absorption spectra of the BN-doped azulenes were computed using the TD-B3LYP/6-31 + G(d,p) and TD-CAM-B3LYP level of theories, which using a long-range corrected hybrid functional in acetone. The computational results obtained in this research are align closely with the existing literature, thereby reinforcing the credibility and reliability of our findings.

| S-EPMC10290675 | biostudies-literature

Ab initio calculations of torsionally mediated hyperfine splittings in E states of acetaldehyde.

Project description:Quantum chemistry packages can be used to predict with reasonable accuracy spin-rotation hyperfine interaction constants for methanol, which contains one methyl-top internal rotor. In this work we use one of these packages to calculate components of the spin-rotation interaction tensor for acetaldehyde. We then use torsion-rotation wavefunctions obtained from a fit to the acetaldehyde torsion-rotation spectrum to calculate the expected magnitude of hyperfine splittings analogous to those observed at relatively high J values in the E symmetry states of methanol. We find that theory does indeed predict doublet splittings at moderate J values in the acetaldehyde torsion-rotation spectrum, which closely resemble those seen in methanol, but that the factor of three decrease in hyperfine spin-rotation constants compared to methanol puts the largest of the acetaldehyde splittings a factor of two below presently available Lamb-dip resolution.

| S-EPMC6508553 | 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