Papers by Keyword: Computational Chemistry

Abstract: 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.

Abstract: Feasibility of the sulfur-based construction materials is caused by properties, availability and low cost of sulfur. There exist numerous ways to improve the operational properties, including the ways that are based on nanotechnology, and ab initio (quantum chemistry) studies. Unfortunately, both application and verification of numerical simulation within the same research are quite complex. In the present case study we present typical scheme of survey involving both experimental and numerical studies. As a test subject we have selected orthorhombic sulfur crystals grown from the solution in toluene. It was clearly shown that good correspondence between experimental and numerical results can be achieved for offered methodology; Raman shifts for isolated S8 molecule mostly correspond to the shifts of sulfur crystal. Computed frequencies for all primary modes are close to the experimental data. Similar correspondences can serve as proofs of conformity between unknown molecular structures in nanomodified sulfur-based material and selected structural models

Abstract: onic Liquids (ILs) provide an alternative green solvent for separating aromatic from its mixture with aliphatic hydrocarbon. The present work demonstrates the screening of potential IL for separation of benzene (aromatic) from n-hexane (aliphatic) using COSMO-RS. A total of 10 imidazolium based cations and 52 different anions resulting in 520 possible combinations of ILs were studied. The COSMO-RS was used to theoretically calculate the activity coefficient at infinite dilution (γ) for benzene and n-hexane in each of the ILs. Consequently, from the activity coefficient (γ) value, the capacity (C) and selectivity (S) at infinite dilution for each ILs with regards to the benzene/n-heptane separation were calculated. The Performance Index (PI) which is the product of the capacity (C) and selectivity (S) is then determined and compared against sulfolane as the benchmarking solvent, used widely by industry for the separation of benzene and aliphatic hydrocarbon. The result showed 20 ILs with C, S, and PI value higher than sulfolane thus making them as potential candidate for the separation application.

Abstract: Based on the principle of using atomistic force field, and the use of ultra-flexible multi-scale modeling techniques to predict the polycarbonate and polyimide polymer molecular structure and the elastic properties of the system. The model combines molecular modeling and nonlinear continuum mechanics basic principles, to simulate and predict the behavior of the material properties of the polymer molecular structure. For the polymer structure and properties, using a plurality of force field simulation to predict the contrast, and binding experiments measured polymer performance value, using static and dynamic molecular simulation technology for molecular mechanics energy minimization to solve.

Abstract: The adsorption of hydrogen sulfide (H₂S), carbondioxide (CO₂) and methane (CH₄) on H-FER zeolite was investigated under computational chemistry using ONIOM (HF/6-31G (d,p):UFF) and ONIOM (B3LYP/6-31G (d,p):UFF) method. Compared to the H-FER zeolite induces much stronger binding of H₂S, CO₂ and CH₄ suggesting great enhancements in the adsorption selectivity. The order of binding energies of adsorbed molecules is H₂S > CO₂ > CH₄. It was found that the extended zeolitic framework covering the nanocavity was essential for describing the confinement effect of the zeolite. The results of these calculations show that the zeolite can be used to adsorb H₂S bester then CO₂ and CH₄. Carbondioxide and hydrogen sulfide are pollutant in biogas product from anaerobic digestion of biodegradable materials. There for, zeolite can be use to purified gas before using as fuel.

Abstract: The influence of sp² hybridization on friction and structure of diamond-like carbon (DLC) films was studied by first-principles molecular dynamics. First-principles calculations have been performed using the pseudo-potential plane wave method. Our results show that: 1) The buffer role of sp²-hybridized state carbon between grain boundaries greatly affected the residual stress of DLC film, and hence the friction decreased steadily with the increased in sp² hybridization content. 2) For thinner films, there was very greatly differences in stress between diamond-like carbon film (110) surfaces in <001> and<1-10> directions. The difference in friction force between soft and hard directions was nonexistent, when the sp²-hybridized state carbon atoms increased to 80%, perhaps because the originally hard C-C and C-H bonds changed, and steadily reject interaction was drive break.

Abstract: Geopolymer is a novel type of inorganic cementitious materials, which has become a hot topic across the world. Geopolymerization process of metakaolin in alkaline solutions shows important effects on final properties of hardened geopolymer. In this paper all the possible reaction pathways involved in the dissolution-reorientation-polycondensation process of metakaolin in alkaline solution were studied according to thermodynamic theory. The corresponding reaction energy of every possible pathway was also calculated using computation chemistry methodsemi- empirical AM1 calculation. The optimum reaction pathway was analysized based on the energy-minimized principle. The calculation results showed that highly alkaline accelerated the dissolution of 6-membered tetrahedron rings of SiO4 or AlO4 tetrahedron representing the molecular structure of metakaolin during dissolution process. Si-Al hybrid reorientation should theoretically be primary reorientation pathway during reorientation process. Framework clusters should be primary polycondensation products during polycondensation process. The above studies enhanced our understanding of formation mechanisms of metakaolin in alkaline solutions related to geopolymerization.