scholarly journals Effect of arsenate substitution on phosphate repository of cell: a computational study

2018 ◽  
Vol 5 (11) ◽  
pp. 181565
Author(s):  
Amit Singh ◽  
Kousik Giri
Keyword(s):  
Molecular Mechanics ◽  
Density Functional ◽  
Computational Study ◽  
Basis Set ◽  
Phosphate Esters ◽  
Amber Force Field ◽  
Structural Differences ◽  
Phosphate Species ◽  
Structural Analogy ◽  
The Stability

The structural analogy with phosphate derives arsenate into various metabolic processes associated with phosphate inside the organisms. But it is difficult to evaluate the effect of arsenate substitution on the stability of individual biological phosphate species, which span from a simpler monoester form like pyrophosphate to a more complex phosphodiester variant like DNA. In this study, we have classified the physiological phosphate esters into three different classes on the basis of their structural differences. This classification has helped us to present a concise theoretical study on the kinetic stability of phosphate analogue species of arsenate against hydrolysis. All the calculations have been carried out using QM/MM methods of our Own N-layer Integrated molecular Orbital molecular Mechanics (ONIOM). For quantum mechanical region, we have used M06-2X density functional with 6-31+G(2d,2p) basis set and for molecular mechanics we have used the AMBER force field. The calculated rate constants for hydrolysis show that none of the phosphate analogue species of arsenate has a reasonable stability against hydrolysis.

A Computational Study of Catalytic Platinum Nanoparticles With and Without OH Chemisorption During Reactions

2008 ◽  
Author(s):  
Mikhail Sekachev ◽  
Cheng-Xian Lin ◽  
Zhiyu Hu ◽  
Don Dareing
Keyword(s):  
Binding Energy ◽  
Total Energy ◽  
Platinum Nanoparticles ◽  
Cluster Size ◽  
Density Functional ◽  
Energy Gap ◽  
Computational Study ◽  
Basis Set ◽  
Functional Theory ◽  
The Stability

In this paper, various energies and geometries of pure platinum nanoparticles and those of platinum nanoparticles with adsorbed OH were investigated. Ten different platinum clusters of up to 28 atoms were studied using spin-unrestricted density functional theory (DFT) with a double numerical plus polarization basis set. Three different shapes were presented, and the effect of cluster size on binding energy, total energy, and HOMO-LUMO energy gap was investigated. The same set of calculations was performed for selected clusters with OH adsorbate on the Pt(111) surface. The results show that the stability of both the pure clusters and the clusters with adsorbed OH molecule increases with an increase of cluster size. This fact indicates that direct influence of the size of Pt cluster on the reaction rate is possible, and the understanding of how cluster size would affect binding energy is important. The effect of cluster size on total energy of molecule was shown to be a linear function independent of cluster type, as expected. We also found that optimized (stable) Pt clusters were bigger in size than that of the initial clusters, or clusters with bulk geometry.

scholarly journals Density Functional Theory and Complete Basis Set Ab Initio Computational Study of Five-, Six-, Seven- and Eight-hydrogen Coordinated Carbon Cations

1999 ◽  
Vol 23 (8) ◽  
pp. 502-503
Author(s):  
Branko S. Jursic
Keyword(s):  
Density Functional Theory ◽  
Ab Initio ◽  
Density Functional ◽  
Computational Study ◽  
Basis Set ◽  
Functional Theory ◽  
Complete Basis ◽  
Complete Basis Set ◽  
High Level

High level ab initio and density functional theory studies are performed on highly protonated methane species.

Computational study of polarizability anisotropies

2018 ◽  
Vol 96 (10) ◽  
pp. 934-938
Author(s):  
Delano P. Chong
Keyword(s):  
Small Molecules ◽  
Density Functional ◽  
Computational Study ◽  
Chem Phys ◽  
Basis Set ◽  
Functional Theory ◽  
Exchange Correlation ◽  
Exchange Correlation Potential ◽  
Correlation Potential ◽  
Definition Of

The dipole polarizabilities (α) and polarizability anisotropies (Δα) of over 20 molecules are calculated to search for negative Δα. The geometry of each molecule is first optimized at the level of CCSD(T)/cc-pVQZ. Then, the α tensors are computed both with CCSD(T)/daug-cc-pVTZ in Gaussian 09 and with the exchange-correlation potential Vxc known as SAOP in the Amsterdam density functional theory program called ADF and a large basis set called QZ3P-3DIFFUSE. In addition to the popular formula of the ΔαRaman connected with Raman spectroscopy, we also present values of an alternative definition of the polarizability anisotropy ΔαKerr connected with Kerr spectroscopy, recently proposed by Kampfrath and colleagues (2018. Chem. Phys. Lett. 692: 319). On one hand, the signs of many ΔαRaman are undetermined; on the other hand, we obtain negative ΔαKerr for more than one-half of the small molecules studied. Of the 24 molecules studied, 18 have negative ΔαKerr.

Theoretical investigation of the stability, reactivity, and the interaction of methyl-substituted peridinium-based ionic liquids

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Emmanuel A. Bisong ◽  
Hitler Louis ◽  
Tomsmith O. Unimuke ◽  
Victoria M. Bassey ◽  
John A. Agwupuye ◽  
...  
Keyword(s):  
Ionic Liquids ◽  
Electron Density ◽  
Density Functional ◽  
Natural Bond Orbital ◽  
Stabilization Energy ◽  
Basis Set ◽  
Bond Critical Point ◽  
Electronic Interaction ◽  
Donor And Acceptor ◽  
The Stability

Abstract This research work focuses on the reactivity, stability, and electronic interaction of pyridinium hydrogen nitrate (PHN)-based ionic liquids and the influence of methyl substituent on this class of ionic liquids: Ortho- (O-MPHN), meta- (M-MPHN), and para- (P-MPHN) substitution. Natural bond orbital (NBO) calculations were performed at the density functional theory (DFT) with Becke’s Lee Yang and Parr functional (B3LYP) methods and DFT/B3LYP/6-311++G(d,p) as basis set using GAUSSIAN 09W and GAUSSVIEW 6.0 software and the most important interaction between donor (Filled Lewis-type NBO’s) and the acceptor (vacant non-Lewis NBOs) were observed. From our natural bond orbital (NBO) result, it could be deduced that the higher the stabilization energy value, the greater the interaction between the donor and acceptor NBOs. The stability of the studied compounds is said to follow the order from O-MPHN > PHN > P-MPHN > M-MPHN based on the hyperconjugative interaction (stabilization energy) of the most significant interaction. The result of the highest occupied molecular orbital (HOMO), shows that PHN has the highest HOMO while the substituted derivatives have similar HOMO values between −7.70 and −7.98 eV thus PHN complex is the best electron donor while the substituted derivatives act as electron acceptors due to the presence of methyl group substituent which is observed to be electron deficient as a result of its withdrawal effect from the aromatic ring. Furthermore, the electron density, real space functions such as energy density and Laplacian of electron density at bond critical point (BCP) of the hydrogen bond interaction of the studied compounds were analyzed using Multifunctional Wavefunction analyzer software version 3.7 and it was observed that the hydrogen at position 6 and oxygen at position 11 (H6–O11) of M-methyl pyridinium nitrate with bond distance of 4.59 (Å) gave binding energy with the strongest electrostatic interaction between the cation and anion of the compounds under investigation. We also observed from our results that, substitution at the ortho position enhances the stability and strengthen the extent of charge transfer. This therefore implies that substitution at ortho position is more favorable for inter- and intramolecular interactions resulting to stabilization of the studied molecules.

Computational Study of Tetrahedral Fullerenes Containing Fused Pentagon-Triples

2021 ◽  
Vol 21 (4) ◽  
pp. 2419-2426
Author(s):  
Csaba L. Nagy ◽  
Katalin Nagy
Keyword(s):  
Density Functional ◽  
Computational Study ◽  
Chemical Shifts ◽  
Point Group ◽  
Functional Theory ◽  
Global Strain ◽  
The Stability ◽  
Global And Local ◽  
Hybrid Density Functional ◽  
Electronic And Structural Properties

Fullerenes that violate the isolated pentagon rule are too reactive and were obtained only as endoor exohedral derivatives. Density functional theory using the B3LYP hybrid density functional was applied to investigate the electronic and structural properties of the ten smallest tetrahedral (Td or T point group) fullerenes containing four directly fused pentagon-triples. The influence of nitrogen doping and exohedral hydrogenation of the four reactive sites was also analyzed. Nucleus independent chemical shifts values computed using B3LYP/6-31G(d) are used as global and local aromaticity probe. The global strain energy is evaluated in terms of the pyramidalization (POAV) angle. The results show that the stability increases with the elimination of the energetically unfavorable strain.

scholarly journals Structure, electronic properties, NBO, NLO and chemi-cal reactivity of bis (1, 4-dithiafulvalene) derivatives: functional density theory study

2017 ◽  
Vol 6 (1) ◽  
pp. 18
Author(s):  
Tahar Abbaz ◽  
Amel Bendjeddou ◽  
Didier Villemin
Keyword(s):  
Electronic Properties ◽  
Density Functional ◽  
Computational Study ◽  
Molecular Geometry ◽  
Basis Set ◽  
Frontier Molecular Orbital ◽  
Reactivity Descriptors ◽  
Nlo Property ◽  
Functional Density Theory ◽  
Nucleophilic Reactivity

In this work, through computational study based on density functional theory (DFT/B3LYP) using basis set 6-31G (d,p) a number of global and local reactivity descriptors for a series of molecules containing a TTF function which are bis (1,4-dithiafulvalene) derivatives. They were computed to predict the reactivity and the reactive sites on the molecules. The molecular geometry and the electronic properties in the ground state such as frontier molecular orbital (HOMO and LUMO), ionization potential (I) and electron affinity (A) were investigated to get a better insight of the molecular properties. Molecular electrostatic potential (MEP) for all compounds were determined to check their electrophilic or nucleophilic reactivity. Fukui index, polarizability, hyperpolarizability, second order NLO property and natural bond orbital (NBO) analyses have also employed to determine the reactivity of bis (1,4-dithiafulvalene) derivatives.

Homolytic bond-dissociation enthalpies of tin bonds and tin–ligand bond strengths — A computational study

2009 ◽  
Vol 87 (7) ◽  
pp. 974-983 ◽  
Author(s):  
Sarah R. Whittleton ◽  
Russell J. Boyd ◽  
T. Bruce Grindley
Keyword(s):  
Density Functional ◽  
Computational Study ◽  
Basis Set ◽  
Functional Theory ◽  
Bond Dissociation ◽  
Donor Acceptor ◽  
Bond Strengths ◽  
Moller Plesset ◽  
Effective Core Potentials ◽  
Ligand Bond

Density functional theory and second-order Møller–Plesset perturbation theory with effective core potentials have been used to calculate homolytic bond-dissociation enthalpies, D(Sn–X), of organotin compounds, and their performance has been assessed by comparison with available experimental bond enthalpies. The SDB-aug-cc-pVTZ basis set with its effective core potential was used to calculate the D(Sn–X) of a series of trimethyltin(IV) species, Me3Sn–X, where X = H, CH3, CH2CH3, NH2, OH, Cl, and F. This is the most comprehensive report to date of homolytic Sn–X bond-dissociation enthalpies (BDEs). Effective core potentials are then used to calculate thermodynamic parameters including donor–acceptor bond enthalpies, [Formula: see text], for a series of tin-ligand complexes, L2SnX4 (X = Br or Cl, L = py, dmf, or dmtf), which are compared with previous experimental and nonrelativistic computational results. Based on computational efficiency and accuracy, it is concluded that effective core potentials are appropriate computational methods to examine bonding in organotin systems.

scholarly journals Protonated heterocyclic derivatives of cyclopropane and cyclopropanone: classical species, alternate sites, and ring fragmentation

2015 ◽  
Vol 93 (7) ◽  
pp. 708-714 ◽  
Author(s):  
Margarida S. Miranda ◽  
Darío J.R. Duarte ◽  
Joaquim C.G. Esteves da Silva ◽  
Joel F. Liebman
Keyword(s):  
Density Functional Theory ◽  
Gas Phase ◽  
Density Functional ◽  
Computational Study ◽  
Basis Set ◽  
Proton Affinities ◽  
Functional Theory ◽  
Heterocyclic Derivatives ◽  
Gas Phase Basicities ◽  
Derivatives Of

A computational study has been performed for protonated oxygen- or nitrogen-containing heterocyclic derivatives of cyclopropane and cyclopropanone. We have searched for the most stable conformations of the protonated species using density functional theory with the B3LYP functional and the 6-31G(2df,p) basis set. More accurate enthalpy values were obtained from G4 calculations. Proton affinities and gas-phase basicities were accordingly derived.

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