scholarly journals A computational study of cysteine and glutathione binding to Au8 cluster

10.29007/8c3l ◽  
2020 ◽  
Author(s):  
Thanh Si Nguyen ◽  
Vu Nhat Pham
Keyword(s):  
Gas Phase ◽  
Potential Energy Surfaces ◽  
Density Functional ◽  
Computational Study ◽  
Gold Cluster ◽  
Basis Set ◽  
Functional Theory ◽  
Metal Atoms ◽  
Energy Surfaces ◽  
Optimized Geometries

The interaction between the Au8 cluster with cysteine (Cys) and glutathione (GSH) is investigated by means of density functional theory (DFT) using the PBE functional in conjunction with the cc-pVTZ basis set for non-metal atoms and the cc-pVTZ-PP basis set for gold. Harmonic vibrational frequencies are also calculated to confirm optimized geometries as local minima or transition states on the potential energy surfaces. The computed results show that these molecules prefer to anchor on the gold cluster via the sulfur atom with the adsorption energies of 20.3 and 30.8 kcal/mol for CYS and GSH, respectively, in the gas phase. In water, such values are considerably reduced, namely 19.0 kcal/mol for CYS and 26.4 kcal/mol for GSH. If a visible light with a frequency of v = 6x1014 Hz (500 nm) is applied, the time for the recovery of CYS and GSH from the most stable complexes will be about 1.24 and 6.03x107 seconds at 298 K in the gas phase. Such values significantly reduce to 0.14 and 4.08x104 in water. Thus, the Au8 cluster could be a promising material for designing tiny sensors in CYS and GSH selective detection.

scholarly journals A computational study of cysteine and glutathione binding to small gold cluster Au8

2020 ◽  
Vol 23 (1) ◽  
Author(s):  
Si Thanh Nguyen ◽  
Pham Nhat Vu
Keyword(s):  
Gas Phase ◽  
Potential Energy Surfaces ◽  
Density Functional ◽  
Computational Study ◽  
Gold Cluster ◽  
Gold Surface ◽  
Basis Set ◽  
Functional Theory ◽  
Adsorption Behaviors ◽  
Energy Surfaces

Introduction: Understanding the binding mechanism between gold and is a fundamental step for numerous applications in biosensors and targeted drug delivery. This study aims to clarify the adsorption behaviors of CYS and GSH on the gold surface using a small gold Au8 cluster as a model reactant. Methods: Here, we examine in details the molecular interaction between Au8 cluster with (CYS) and (GSH) by means of density functional theory (DFT). The PBE functional is employed in combination with the basis set for non-metal atoms and the basis set for gold. Harmonic frequencies are also computed to confirm optimized geometries as local minima or transition states on the potential energy surfaces. Results: The calculated results show that these molecules prefer to anchor on the gold cluster via the sulfur atom with the adsorption energies of 20.3 and 30.8 / for CYS and GSH, respectively, in gas phase. In water, such values are considerably reduced, namely 19.0 / for CYS and 26.4 / for GSH. If a visible light with a frequency of v = 6x1014 Hz (500 nm) is applied, the time for the recovery of CYS and GSH from the most stable complexes will be about 1.24 and 6.03x107 seconds at 298 K in gas phase. Conclusion: The Au8 cluster could be a promising material for designing sensor in CYS and GSH selective detection.

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.

A computational study of the SNAr reaction of 2-ethoxy-3,5-dinitropyridine and 2-methoxy-3,5-dinitropyridine with piperidine

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Oluwakemi A. Oloba-Whenu ◽  
Idris O. Junaid ◽  
Chukwuemeka Isanbor
Keyword(s):  
Hydrogen Bonding ◽  
Gas Phase ◽  
Density Functional ◽  
Computational Study ◽  
Density Functional Theory Method ◽  
Basis Set ◽  
Slow Step ◽  
Functional Theory ◽  
Snar Reaction ◽  
Hybrid Density Functional

AbstractA computational study of the chemical kinetics and thermodynamics study of the SNAr between 3,5-dinitroethoxypyridine 1a and 3,5-dinitromethoxypyridine 1b with piperidine 2 in the gas phase is reported using hybrid density functional theory method B3PW91 and 6–31G(d,p) basis set. The reaction was modeled via both the catalyzed and base-catalyzed pathways which proceeded with the initial attack of the nucleophile 2 on the substrates 1 to yield the Meisenheimer complex intermediate that is stabilized with hydrogen bonding. Calculations show that the reaction goes via the formation and decomposition of a Meisenheimer complex, which was observed to be stabilized by hydrogen bonding. Along the uncatalyzed pathway, the decomposition of the Meisenheimer complex was the slow step and requires about 28 kcal/mol. This barrier was reduced to about 14.8 kcal/mol with the intervention of the base catalyst, thus making the formation of the Meisenheimer complex rate determining. All reactions were calculated to be exothermic, about −6.5 kcal/mol and −0.6 kcal/mol, respectively, for the reaction of 1a and 1b with 2.

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.

scholarly journals The ANI-1ccx and ANI-1x Data Sets, Coupled-Cluster and Density Functional Theory Properties for Molecules

2020 ◽  
Author(s):  
Justin S. Smith ◽  
Roman Zubatyuk ◽  
Benjamin T. Nebgen ◽  
Nicholas Lubbers ◽  
Kipton Barros ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Potential Energy Surfaces ◽  
Density Functional ◽  
Atomic Charge ◽  
Density Functional Theory Calculations ◽  
Coupled Cluster ◽  
Data Sets ◽  
Data Set ◽  
Functional Theory ◽  
Energy Surfaces

<p>Maximum diversification of data is a central theme in building generalized and accurate machine learning (ML) models. In chemistry, ML has been used to develop models for predicting molecular properties, for example quantum mechanics (QM) calculated potential energy surfaces and atomic charge models. The ANI-1x and ANI-1ccx ML-based eneral-purpose potentials for organic molecules were developed through active learning; an automated data diversification process. Here, we describe the ANI-1x and ANI-1ccx data sets. To demonstrate data set diversity, we visualize them with a dimensionality reduction scheme, and contrast against existing data sets. The ANI-1x data set contains multiple QM properties from 5M density functional theory calculations, while the ANI-1ccx data set contains 500k data points obtained with an accurate CCSD(T)/CBS extrapolation. Approximately 14 million CPU core-hours were expended to generate this data. Multiple QM properties from density functional theory and coupled cluster are provided: energies, atomic forces, multipole moments, atomic charges, and more. We provide this data to the community to aid research and development of ML models for chemistry.</p>

scholarly journals Stability and magnetic properties of isomorphous substituted Si7-xMnx+

2018 ◽  
Vol 56 (1) ◽  
pp. 64
Author(s):  
Nguyen Thanh Tung ◽  
Nguyen Thi Mai ◽  
Ngo Tuan Cuong
Keyword(s):  
Density Functional Theory ◽  
Magnetic Properties ◽  
Magnetic Moment ◽  
Density Functional ◽  
Basis Set ◽  
Pentagonal Bipyramid ◽  
Functional Theory ◽  
Electronic Configurations ◽  
Method Of Density Functional ◽  
Optimized Geometries

The optimized geometries, stability, and magnetic properties of cationic clusters Si7+, Si6Mn+, and Si5Mn2+ have been determined by the method of density functional theory using the B3P86/6-311+G(d) functional/basis set. Their electronic configurations have been analyzed to understand the influence of substituting Si atoms by Mn atoms on the structural and magnetic aspects of Si7+. It is shown that the manganese dopant does not alter the structure of the silicon host but significantly changes its stability and magnetism. In particular, while the magnetic moment of Si7+ is 1 mB, Si5Mn2+ exhibits a strong magnetic moment of 9 mB and that of Si6Mn+ takes a relatively high value of 4 mB. Among studied clusters, the pentagonal bipyramid Si5Mn2+ is assigned as the most stable one.

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.

Donor Functionalized Perylene and Different π-Spacers Based Sensitizers for DSSC Applications - A Theoretical Approach

2021 ◽  
Author(s):  
D. Nicksonsebastin ◽  
P. Pounraj ◽  
Prasath M
Keyword(s):  
Density Functional Theory ◽  
Solar Cell ◽  
Gas Phase ◽  
Density Functional ◽  
Basis Set ◽  
Dye Sensitized Solar Cell ◽  
Functional Theory ◽  
Dye Sensitized ◽  
Td Dft ◽  
Organic Sensitizers

Abstract Perylene based novel organic sensitizers for the Dye sensitized solar cell applications are investigated by using Density functional theory (DFT) and time dependant density functional theory (TD-DFT).The designed sensitizers have perylene and dimethylamine (DM) and N-N-dimethylaniline(DMA) functionalized perylene for the dssc applications.π-spacers are thiophene andcyanovinyl groups and cyanoacrylic acid is chosen as the acceptor for the designed sensitizers. The studied sensitizers were fully optimized by density functional theory at B3LYP/6-311G basis set on gas phase and DMF phase. The electronic absorption of the sensitizers is analyzed by TD-DFT at B3LYP/6-311G basis set in both gas and DMF phase.

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