scholarly journals Intermolecular Interactions Between Serine and C60, C59Si, and C59Ge: A DFT Study

2021 ◽  
Author(s):  
Mohsen Doust Mohammadi ◽  
Hewa Y. Abdullah
Keyword(s):  
Amino Acid ◽  
Intermolecular Interactions ◽  
Density Functional ◽  
Physical Adsorption ◽  
Amino Acid Molecule ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
Structure Of Nanomaterials ◽  
Silicon And Germanium ◽  
D Model

Abstract The study of intermolecular interactions is of great importance. This study attempted to quantitatively examine the interactions between Serine (C3H7NO3) and fullerene nanocages, C60, in vacuum. As the frequent introduction of elements as impurities into the structure of nanomaterials can increase the intensity of intermolecular interactions, nanocages doped with silicon and germanium have also been studied as adsorbents, C59Si and C59Ge. Quantum mechanical studies of such systems are possible in the density functional theory (DFT) framework. For this purpose, various functionals, such as B3LYP-D3, ωB97XD, and M062X, have been used. One of the most suitable basis functionals for the systems studied in this research is 6-311G (d), which has been used in both optimization calculations and calculations related to wave function analyses. The main part of this work is the study of various analyses that reveal the nature of the intermolecular interactions between the two components introduced above. The results of conceptual DFT, natural bond orbital, non-covalent interactions, and quantum theory of atoms in molecules were consistent and in favor of physical adsorption in all systems. Germanium had more adsorption energy than other dopants. The HOMO–LUMO energy gaps were as follows: C60: 5.996, C59Si: 5.309, and C59Ge: 5.188 eV at B3LYP-D3/6-311G (d) model chemistry. The sensitivity of the adsorption increased when an amino acid molecule interacted with doped C60, and this capability could be used to design nanocarrier to detect Serine amino acid.

scholarly journals Non-covalent interactions of Cysteine onto C60, C59Si, and C59Ge: A DFT study

2021 ◽  
Author(s):  
Mohsen Doust Mohammadi ◽  
hewa Y abdullah
Keyword(s):  
Intermolecular Interactions ◽  
Density Functional ◽  
Physical Adsorption ◽  
Amino Acid Molecule ◽  
The Density Functional Theory ◽  
Structure Of Nanomaterials ◽  
Non Covalent Interactions ◽  
Silicon And Germanium ◽  
D Model ◽  
Covalent Interactions

Abstract The study of intermolecular interactions is of great importance. This study attempted to quantitatively examine the interactions between Cysteine (C3H7NO2S) and fullerene nanocages, C60, in a vacuum. As the frequent introduction of elements as impurities into the structure of nanomaterials can increase the intensity of intermolecular interactions, nanocages doped with silicon and germanium have also been studied as adsorbents C59Si and C59Ge. Quantum mechanical studies of such systems are possible in the density functional theory (DFT) framework. For this purpose, various functionals, such as B3LYP-D3, ωB97XD, and M062X, have been used. One of the most suitable basis functionals for the systems studied in this research is 6-311G (d), which has been used in both optimization calculations and calculations related to wave function analyses. The main part of this work is the study of various analyses that reveal the nature of the intermolecular interactions between the two components introduced above. The results of conceptual DFT, natural bond orbital, non-covalent interactions, and quantum theory of atoms in molecules were consistent and favored physical adsorption in all systems. Germanium had more adsorption energy than other dopants. The HOMO–LUMO energy gaps were as follows: C60: 5.996, C59Si: 5.309, and C59Ge: 5.188 eV at B3LYP-D3/6-311G (d) model chemistry. The adsorption sensitivity increased when an amino acid molecule interacted with doped C60, and this capability could be used to design a nanocarrier to detect Cysteine amino acids.

scholarly journals Explaining SARS-CoV-2 3CL Mpro binding to peptidyl Michael acceptor and a ketone-based inhibitors using Molecular fractionation with conjugate caps method

2020 ◽  
Author(s):  
C Solis-Calero ◽  
PA Morais ◽  
FF Maia Jr ◽  
VN Freire ◽  
HF Carvalho
Keyword(s):  
Amino Acid ◽  
Density Functional ◽  
Radial Distance ◽  
Amino Acid Residues ◽  
Functional Theory ◽  
Main Protease ◽  
The Density Functional Theory ◽  
Michael Acceptor ◽  
Total Interaction ◽  
Molecular Fractionation

The main protease SARS-CoV-2 3CL Mpro (3CL-Mpro) is an attractive target for developing antiviral inhibitors due to its essential role in processing the polyproteins translated from viral coronavirus RNA. In this work, it was obtained non-covalent complexes of this protease with two distinct ligands, a peptidyl Michael acceptor (N3) and a ketone-based compound (V2M). The complexes were modeled from processed crystallographic data (PDB id: 6LU7 and 6XHM respectively) using combined quantum mechanics/molecular mechanics (QM/MM) calculations. The QM region was treated at the PBE-def2-SV(P) level, while the Amber-ff19SB force field was used to describe the MM region. The obtained models were used to perform calculations for describing the protease/ligand binding, based in the framework of the Density Functional Theory (DFT) and within the Molecular Fractionation with Conjugated Caps (MFCC) scheme. Our results have shown values for the total interaction energies of -111.84 and -111.64 kcal mol-1 having as ligands a N3 and V2M, respectively. Most importantly, it was possible to assess the relative individual amino acid energy contribution for the binding of both ligands considering residues around them up to 10 Å of radial distance. Residues Gln189, Met165, Glu166, His164, and Asn142 were identified as main interacting amino acid residues for both complexes, being their negative interaction energy contributions higher than -5.0 kcal mol-1. In the case of 3CL-Mpro/ V2M complex, we should add His41, Ser144, and Cys145 as main contributing residues. Our data also have shown that interactions of type π-amide, π-alkyl and alkyl-alkyl and carbon hydrogen bonds should be also considered in order to explain the binding of 3CL-Mpro with the selected inhibitors. Our results also determined that the carbonyl-L-leucinamide scaffold of both inhibitors is its main determinant of binding with a contribution to the energy of interaction of 54.51 and 50.69 kcal mol-1 for N3 and V2M, respectively.

scholarly journals First-Principles Study on the Adsorption and Dissociation of Impurities on Copper Current Collector in Electrolyte for Lithium-Ion Batteries

Materials ◽  
2018 ◽  
Vol 11 (7) ◽  
pp. 1256 ◽  
Author(s):  
Jian Chen ◽  
Chao Li ◽  
Jian Zhang ◽  
Cong Li ◽  
Jianlin Chen ◽  
...  
Keyword(s):  
Lithium Ion Batteries ◽  
First Principles ◽  
Density Functional ◽  
Physical Adsorption ◽  
Lithium Ion ◽  
Current Collector ◽  
Residual Water ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
Adsorption And Dissociation

The copper current collector is an important component for lithium-ion batteries and its stability in electrolyte impacts their performance. The decomposition of LiPF6 in the electrolyte of lithium-ion batteries produces the reactive PF6, which reacts with the residual water and generates HF. In this paper, the adsorption and dissociation of H2O, HF, and PF5 on the Cu(111) surface were studied using a first-principles method based on the density functional theory. The stable configurations of HF, H2O, and PF5 adsorbed on Cu(111) and the geometric parameters of the admolecules were confirmed after structure optimization. The results showed that PF5 can promote the dissociation reaction of HF. Meanwhile, PF5 also promoted the physical adsorption of H2O on the Cu(111) surface. The CuF2 molecule was identified by determining the bond length and the bond angle of the reaction product. The energy barriers of HF dissociation on clean and O-atom-preadsorbed Cu(111) surfaces revealed that the preadsorbed O atom can promote the dissociation of HF significantly.

scholarly journals Strain Investigation on Spin-Dependent Transport Properties of γ-Graphyne Nanoribbon Between Gold Electrodes

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Yun Li ◽  
Xiaobo Li ◽  
Shidong Zhang ◽  
Liemao Cao ◽  
Fangping Ouyang ◽  
...  
Keyword(s):  
Transport Properties ◽  
High Performance ◽  
Density Functional ◽  
Strain Engineering ◽  
Molecular Junctions ◽  
Spin Splitting ◽  
Functional Theory ◽  
Spin Dependent Transport ◽  
The Density Functional Theory ◽  
Dependent Transport

AbstractStrain engineering has become one of the effective methods to tune the electronic structures of materials, which can be introduced into the molecular junction to induce some unique physical effects. The various γ-graphyne nanoribbons (γ-GYNRs) embedded between gold (Au) electrodes with strain controlling have been designed, involving the calculation of the spin-dependent transport properties by employing the density functional theory. Our calculated results exhibit that the presence of strain has a great effect on transport properties of molecular junctions, which can obviously enhance the coupling between the γ-GYNR and Au electrodes. We find that the current flowing through the strained nanojunction is larger than that of the unstrained one. What is more, the length and strained shape of the γ-GYNR serves as the important factors which affect the transport properties of molecular junctions. Simultaneously, the phenomenon of spin-splitting occurs after introducing strain into nanojunction, implying that strain engineering may be a new means to regulate the electron spin. Our work can provide theoretical basis for designing of high performance graphyne-based devices in the future.

scholarly journals Electron-phonon interaction in In-induced √7 ×√3 structures on Si(111) from first-principles

2021 ◽  
Author(s):  
I. Yu. Sklyadneva ◽  
Rolf Heid ◽  
Pedro Miguel Echenique ◽  
Evgueni Chulkov
Keyword(s):  
Density Functional Theory ◽  
Double Layer ◽  
First Principles ◽  
Linear Response ◽  
Density Functional ◽  
Single Layer ◽  
Phonon Interaction ◽  
Functional Theory ◽  
Electron Phonon Interaction ◽  
The Density Functional Theory

Electron-phonon interaction in the Si(111)-supported rectangular √(7 ) ×√3 phases of In is investigated within the density-functional theory and linear-response. For both single-layer and double-layer √(7 ) ×√3 structures, it...

scholarly journals Strain Effects on the Electronic and Thermoelectric Properties of n(PbTe)-m(Bi2Te3) System Compounds

Materials ◽  
2021 ◽  
Vol 14 (15) ◽  
pp. 4086
Author(s):  
Weiliang Ma ◽  
Marie-Christine Record ◽  
Jing Tian ◽  
Pascal Boulet
Keyword(s):  
Density Functional ◽  
Lattice Thermal Conductivity ◽  
Compressive Strain ◽  
Van Der Waals Interactions ◽  
Functional Theory ◽  
Band Engineering ◽  
Seebeck Coefficients ◽  
The Density Functional Theory ◽  
P Type ◽  
Narrow Band Gap Semiconductors

Owing to their low lattice thermal conductivity, many compounds of the n(PbTe)-m(Bi2Te3) homologous series have been reported in the literature with thermoelectric (TE) properties that still need improvement. For this purpose, in this work, we have implemented the band engineering approach by applying biaxial tensile and compressive strains using the density functional theory (DFT) on various compounds of this series, namely Bi2Te3, PbBi2Te4, PbBi4Te7 and Pb2Bi2Te5. All the fully relaxed Bi2Te3, PbBi2Te4, PbBi4Te7 and Pb2Bi2Te5 compounds are narrow band-gap semiconductors. When applying strains, a semiconductor-to-metal transition occurs for all the compounds. Within the range of open-gap, the electrical conductivity decreases as the compressive strain increases. We also found that compressive strains cause larger Seebeck coefficients than tensile ones, with the maximum Seebeck coefficient being located at −2%, −6%, −3% and 0% strain for p-type Bi2Te3, PbBi2Te4, PbBi4Te7 and Pb2Bi2Te5, respectively. The use of the quantum theory of atoms in molecules (QTAIM) as a complementary tool has shown that the van der Waals interactions located between the structure slabs evolve with strains as well as the topological properties of Bi2Te3 and PbBi2Te4. This study shows that the TE performance of the n(PbTe)-m(Bi2Te3) compounds is modified under strains.

scholarly journals Study on the interaction between catechin and cholesterol by the density functional theory

2020 ◽  
Vol 18 (1) ◽  
pp. 357-368
Author(s):  
Kaiwen Zheng ◽  
Kai Guo ◽  
Jing Xu ◽  
Wei Liu ◽  
Junlang Chen ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bond ◽  
Charge Transfer ◽  
Density Functional ◽  
Antioxidant Properties ◽  
Micelle Formation ◽  
Aromatic Rings ◽  
Hydrogen Bond Interaction ◽  
Functional Theory ◽  
The Density Functional Theory

AbstractCatechin – a natural polyphenol substance – has excellent antioxidant properties for the treatment of diseases, especially for cholesterol lowering. Catechin can reduce cholesterol content in micelles by forming insoluble precipitation with cholesterol, thereby reducing the absorption of cholesterol in the intestine. In this study, to better understand the molecular mechanism of catechin and cholesterol, we studied the interaction between typical catechins and cholesterol by the density functional theory. Results show that the adsorption energies between the four catechins and cholesterol are obviously stronger than that of cholesterol themselves, indicating that catechin has an advantage in reducing cholesterol micelle formation. Moreover, it is found that the molecular interactions of the complexes are mainly due to charge transfer of the aromatic rings of the catechins as well as the hydrogen bond interactions. Unlike the intuitive understanding of a complex formed by hydrogen bond interaction, which is positively correlated with the number of hydrogen bonds, the most stable complexes (epicatechin–cholesterol or epigallocatechin–cholesterol) have only one but stronger hydrogen bond, due to charge transfer of the aromatic rings of catechins.

A trinuclear chromium(III) chlorocarbyne

2021 ◽  
Author(s):  
Takashi Kurogi ◽  
Keiichi Irifune ◽  
Takahiro Enoki ◽  
Kazuhiko Takai
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Terminal Alkynes ◽  
Functional Theory ◽  
The Density Functional Theory

Reduction of CCl4 by CrCl2 in THF afforded a trinuclear chromium(III) carbyne [CrCl(thf)2)]3(μ3-CCl)(μ-Cl)3. The chlorocarbyne complex reacted with aldehydes to afford chloroallylic alcohols and terminal alkynes. The density functional theory...

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