Theoretical study of fMet-tRNA and fAla-tRNA structures by using quantum calculation

AbstractIn the prokaryotes, protein synthesis always starts with N-formylmethionine amino acid. Comparison of this amino acid with other amino acids is attempted and that is why formylmethionine is always the first amino acid to begin protein synthesis, in this paper we added a formyl group to alanine amino acid and then studied it when attached to the tRNA molecule and compared this structure with formylmethionine-tRNA structure. The quantum chemical calculations have performed using Gaussian 03 suite of programs. The fAla-tRNA and fMet-tRNA structures have fully optimized at the HF and B3LYP levels with 3–21G∗ and 6–31G∗ basis sets as well as MP2/3–21G∗ level and theoretically solvent effects on the structures were investigated. Then we studied electronic structures of the compounds using Natural Bond Orbital (NBO) analysis and calculated NMR parameters at the gas-phase. Frequency analysis was also calculated at the HF and B3LYP/3-21G∗ levels in the different solvents in 298.15K, 310.15K temperatures and 1.00 atmosphere pressure

ZnO Fullerene-like Cage as a Potential Sensor for SO Detection

A computational study based on density functional theory calculations was performed to investigate the potential possibility of using Zn 12 O 12 fullerene-like cage as an electronic sensor for SO 2 detection. For adsorption of SO 2 on the Zn 12 O 12 nanocage, three stable configurations were identified. The energy gap of Zn 12 O 12 nanocage is very sensitive to the presence of SO 2 molecule. The energy gap decreases from 4.19 eV in the free nanocage to 1.88 eV in the SO 2 -adsorbed form. This phenomenon increases the electrical conductivity of the nanocage. Considerable changes in the highest occupied molecular orbital/lowest unoccupied molecular orbital energy gap, short recovery time, high sensitivity, high electrical conductivity and also energetic favourability of the Zn 12 O 12 nanocage suggest that Zn 12 O 12 may be a potential sensor for SO 2 detection

Effects of Zinc Binding on the Structure and Stability of Glycylglycine Dipeptide: A Computational Study

Energies and structures of six different isomers resulted of complex between glycylglycine dipeptide and zinc cation were calculated at the BLYP and B3LYP levels of theory with 6-311G** and 6-311++G** basis sets. The energies of the glycylglycine-Zn2+ different complexes at the BLYP/6-311++G** obtained more stable than another methods. In this method, the most stable complex was zinc cation bound to the two oxygen sites of the glycylglycine zwitterion and acted as a bidentate ligand. The vibrational frequencies, thermodynamic and electronic properties, HOMO, LUMO, and energy gap for the most stable isomer in different solvents were calculated at the BLYP/6-311++G** level of theory

Novel coupling reactions of phytochemicals with sulfa drugs and their applications in the determination of nitrite at trace level in environmental samples

Twelve spectrophotometric methods based on new reactions for the determination of trace amounts of nitrite in environmental samples were developed. Replacement of toxic reagents was explored to attain the standards of clean chemistry. These methods utilize two classes of compounds namely; phytochemicals and sulfonamides, in the presence of limited amounts of sodium hydroxide. The methods were based on the oxidation of sulfanilamide (SAA), sulfadoxine (SDX), sulfamethoxazole (SMX) or sulfadiazine (SDZ) by nitrite in sodium hydroxide medium and coupling with cardol, cardanol or anacardic acid which yielded yellow, orange and orange red color derivatives having an absorbance maximum in the range 430, 460 and 470nm, respectively. The colors developed were stable for about 3h. Beer’s law was obeyed for nitrite in the concentration range 0.08–0.90, 0.16–1.04, 0.08–0.80 and 0.08–0.80μgml−1 for cardol; 0.80–4.40, 1.60–5.72, 0.52–5.20 and 0.80–4.40μgml−1 for cardanol and 0.80–5.70, 1.04–6.20, 1.30–5.20 and 0.80–4.00μgml−1 for anacardic acid, respectively. The reaction conditions and other important analytical parameters were optimized to enhance the sensitivity of the methods. Interference if any, by non-target ions was also investigated. The methods were applied determining nitrite in environmental samples. The performances of these methods were evaluated in terms of Student’s t-test and variance ratio F-test to find out the significance of the proposed methods over the reference spectrophotometric method