scholarly journals A computational study of mercaptopurine and thioguanine binding to gold clusters Aun (n = 3, 4)

2021 ◽  
Vol 10 (3) ◽  
pp. xx-xx
Author(s):  
Si Nguyen Thanh ◽  
Huyen Duong Thi ◽  
Thao Pham Thi Bich ◽  
Kha Tran Ni ◽  
Nhat Pham Vu
Keyword(s):  
Density Functional ◽  
Computational Study ◽  
Density Functional Theory Calculations ◽  
Gold Surface ◽  
Gold Clusters ◽  
Drug Binding ◽  
Basis Set ◽  
Release Mechanism ◽  
Water Solvent ◽  
Protein Matrices

The density functional theory calculations are employed to elucidate the adsorption/desorption behaviours of mercaptopurine (MP) and thioguanine (TG) drugs on the gold surfaces, using Au3 and Au4 clusters as model reactants. The PBE functional in combination with the effective core potential cc-pVTZ-PP basis set for gold atoms and cc-pVTZ basis set for nonmetals have been used to investigated geometric structures, thermodynamic parameters and electronic properties of the obtained complexes. The IEF-PCM model with water solvent was used to include the effect of biological environment on the interactions. The computed results show that the binding is dominated by a covelant bond Au−S and by electrostatic effects, namely a hydrogen bond contribution NH∙∙∙Au. In addition, the drug binding to gold clusters is a reversible process and a drug release mechanism was also clarified. Accordingly, the drugs are willing to separate from the gold surface due to either a slight change of pH in tumor cells or the presence of cysteine residues in protein matrices.

Computational Study: Noncovalent Interaction of Cys-Ala Peptide with Alkaline Earth Metal Ions and its Conformation Changes

2021 ◽  
Vol 874 ◽  
pp. 128-135
Author(s):  
Mutiara Anisa Tresnoningtias ◽  
Andre Sasongko Nurwarrohman ◽  
Ihyar Kurnia ◽  
Christian Rinaldy ◽  
Asy’ari Mukhammad ◽  
...  
Keyword(s):  
Metal Ions ◽  
Density Functional ◽  
Alkaline Earth ◽  
Computational Study ◽  
Earth Metal ◽  
Basis Set ◽  
Alkaline Earth Metal ◽  
Interaction Energies ◽  
Water Solvent ◽  
Alkaline Earth Metal Ions

The study of the intermolecular interactions is important to explain the phenomenon occurred on the human body. One of the most important processes that can be studied is the interaction of the peptide with metal ions. In this study, a computational approach was harnessed to predict the interaction and the changes in peptide’s conformation between Cys-Ala peptide which is one of the important amino acids in e-cadherin with some of alkaline earth metal ions. Cys-Ala peptide (Ac-CA-NH2) was used as a molecular model in this calculation. All the molecular structure involved in the interaction was optimized by density functional theory DFT/M06-2X, and basis set 6-31G** to obtain minimum energy, the interaction energies, and the changes in its conformation. The results showed that the interaction energy of Ac-CA-NH2 with alkaline earth metal ions from top to bottom based on the Periodic table is getting higher in a row. The interaction energies of Ac-CA-NH2 with Be2+, Mg2+ and Ca2+ ions are -2.393kcal, -17.489 kcal, and -25.938 kcal respectively. These energies were obtained from the interaction of the peptide with ions in a water solvent. The changes in the peptide's bond length and dihedral angle indicate a conformational change in the Cys-Ala peptide, but it still maintains the trans conformation in its peptide bonds. The results and evaluations of this study may be used for further research considerations and may be applied to enzymes or other peptides that have the Cys-Ala residue.

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 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 Compressibility and Phase Stability of Iron-Rich Ankerite

Minerals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 607
Author(s):  
Raquel Chuliá-Jordán ◽  
David Santamaria-Perez ◽  
Javier Ruiz-Fuertes ◽  
Alberto Otero-de-la-Roza ◽  
Catalin Popescu
Keyword(s):  
High Pressure ◽  
Density Functional ◽  
Computational Study ◽  
Density Functional Theory Calculations ◽  
High Pressure Phase ◽  
Stable Phase ◽  
Pressure Derivative ◽  
Reversible Phase Transition ◽  
Murnaghan Equation ◽  
Pressure Phase

The structure of the naturally occurring, iron-rich mineral Ca1.08(6)Mg0.24(2)Fe0.64(4)Mn0.04(1)(CO3)2 ankerite was studied in a joint experimental and computational study. Synchrotron X-ray powder diffraction measurements up to 20 GPa were complemented by density functional theory calculations. The rhombohedral ankerite structure is stable under compression up to 12 GPa. A third-order Birch–Murnaghan equation of state yields V0 = 328.2(3) Å3, bulk modulus B0 = 89(4) GPa, and its first-pressure derivative B’0 = 5.3(8)—values which are in good agreement with those obtained in our calculations for an ideal CaFe(CO3)2 ankerite composition. At 12 GPa, the iron-rich ankerite structure undergoes a reversible phase transition that could be a consequence of increasingly non-hydrostatic conditions above 10 GPa. The high-pressure phase could not be characterized. DFT calculations were used to explore the relative stability of several potential high-pressure phases (dolomite-II-, dolomite-III- and dolomite-V-type structures), and suggest that the dolomite-V phase is the thermodynamically stable phase above 5 GPa. A novel high-pressure polymorph more stable than the dolomite-III-type phase for ideal CaFe(CO3)2 ankerite was also proposed. This high-pressure phase consists of Fe and Ca atoms in sevenfold and ninefold coordination, respectively, while carbonate groups remain in a trigonal planar configuration. This phase could be a candidate structure for dense carbonates in other compositional systems.

Estimating the adsorption energy of element 113 on a gold surface

Open Physics ◽  
2013 ◽  
Vol 11 (11) ◽  
Author(s):  
Alexander Rusakov ◽  
Yuriy Demidov ◽  
Andréi Zaitsevskii
Keyword(s):  
Adsorption Energy ◽  
Cluster Size ◽  
Density Functional ◽  
Gold Surface ◽  
Gold Clusters ◽  
Basis Sets ◽  
Energy Estimates ◽  
First Principle ◽  
Gaussian Basis Sets ◽  
Functional Theory

AbstractWe report first-principle based studies of element 113 (E113) interactions with gold aimed primarily at estimating the adsorption energy in thermochromatographic experiments. The electronic structure of E113-Aun systems was treated within the accurate shape-consistent small core relativistic pseudopotential framework at the level of non-collinear relativistic density functional theory (RDFT) with specially optimised Gaussian basis sets. We used gold clusters with up to 58 atoms to simulate the adsorption site on the stable Au(111) surface. Stabilization of the E113-Aun binding energy and the net Bader charge of E113 and the neighboring Au atoms with respect to n indicated the cluster size used was appropriate. The resulting adsorption energy estimates lie within the 1.0–1.2 eV range, substantially lower than previously reported values.

scholarly journals Molecular Insights into Cage Occupancy of Hydrogen Hydrate: A Computational Study

Processes ◽  
2019 ◽  
Vol 7 (10) ◽  
pp. 699 ◽  
Author(s):  
Ma ◽  
Zhong ◽  
Liu ◽  
Zhong ◽  
Yan ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Storage ◽  
Molecular Dynamics Simulations ◽  
Density Functional ◽  
Storage Capacity ◽  
Computational Study ◽  
Density Functional Theory Calculations ◽  
Hydrogen Storage Capacity ◽  
Large Cage ◽  
Dynamics Simulations

Density functional theory calculations and molecular dynamics simulations were performed to investigate the hydrogen storage capacity in the sII hydrate. Calculation results show that the optimum hydrogen storage capacity is ~5.6 wt%, with the double occupancy in the small cage and quintuple occupancy in the large cage. Molecular dynamics simulations indicate that these multiple occupied hydrogen hydrates can occur at mild conditions, and their stability will be further enhanced by increasing the pressure or decreasing the temperature. Our work highlights that the hydrate is a promising material for storing hydrogen.

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.

Mechanistic Insight into Construction of Axially Chiral Biaryls via Palladium/Chiral Norbornene Cooperative Catalysis: a DFT-Based Computational Study

2021 ◽  
Author(s):  
Xuexiang Ma ◽  
Aili Feng ◽  
Chengbu Liu ◽  
Dongju Zhang
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Computational Study ◽  
Density Functional Theory Calculations ◽  
Functional Theory ◽  
Cooperative Catalysis ◽  
Mechanistic Insight ◽  
Aryl Bromides ◽  
Axially Chiral ◽  
Insight Into

Density functional theory calculations were performed on a prototype of three-component reactions involving aryl iodides, 2,6-substituted aryl bromides, and acrylates to understand the construction of axially chiral biaryls through the...

Computational study on epoxidation of propylene by dioxygen using the silanol-functionalized polyoxometalate-supported osmium oxide catalyst

2019 ◽  
Vol 6 (12) ◽  
pp. 3482-3492 ◽  
Author(s):  
Yun-Jie Chu ◽  
Xue-Mei Chen ◽  
Chun-Guang Liu
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Oxide Catalyst ◽  
Computational Study ◽  
Density Functional Theory Calculations ◽  
Single Site ◽  
Functional Theory ◽  
Epoxidation Of Propylene ◽  
Osmium Oxide

The silanol-functionalized POM-supported single-site Os oxide catalyst has been theoretically considered for epoxidation of propylene in the presence of dioxygen based on density functional theory calculations.

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