Journal of Theoretical and Computational Chemistry

Carbodiimides have been widely used for different purposes, such as an intermediary to form peptides bonds and esters, which have generated industrial, organic and biological applications. Diisoproylcarbodiimide (DIC), (3-(dimethylamino) propyl)ethylcarbodiimide (EDC) and N,N′-dicyclohexylcarbodiimide (DCC) are the most common carbodiimides, however, there exist other carbodiimides that are not normally used. Twelve carbodiimides including the above mentioned were chosen to study their chemical reactivity as well as their nucleophilic and electrophilic attack sites. Geometry optimization in gas and solution phases was obtained using Density Functional Theory (DFT) through B3LYP with 6-31G(d) and 6-311$++$G(d,p) level. Global and local reactivity descriptors were calculated and analyzed such as chemical hardness, ionization potential, electron affinity, Fukui functions, dual descriptor and hypersoftness. The results obtained for geometrical parameters do not have significant differences for gas and solution phase. The introduction of diffuse functions has great impact in electron affinity, modifying notably the values of reactivity descriptors, but didn’t show qualitative differences, since the results found for both basis set calculations show that Cyanamide or CD1 is the most stable and CD11 present greater reactivity of all studied molecules. Also, the hypersoftness results obtained with 6-31G(d) are in agreement with the general affirmation that carbodiimides are easily attacked by nucleophiles and electrophiles in the central carbon–nitrogen double bond.

Alkali-metal hydrazinidoboranes have been recently investigated as a new stable high-capacity material for hydrogen storage, necessitating an exploration of the dehydrogenation mechanism for further developments in this field. Herein, we present a first systematic study of the structure and dehydrogenation mechanism of sodium hydrazinidoborane (NaHB) with three possible pathways considered: pathway A, corresponding to unimolecular dehydrogenation; pathway B, featuring dehydrogenation of the (NaHB)₂ dimer via two different sub-pathways, and pathway C, corresponding to direct dehydrogenation (as compared to B). The calculated rate of the most probable dehydrogenation pathway (B, 3.28min${}^{-1})$ is similar to that obtained experimentally (12.26min${}^{-1})$, supporting the validity of our findings.

Antibodies play a significant role in the immunotherapy, basic research and the pharmaceutical industry. Nowadays, both DNA recombinant technology and antibody engineering technology are widely used in many fields such as diagnostics, therapeutics, drug targeted delivery, and research reagents. Computational docking of antigen-antibody complexes and analysis of atomic interactions are important to find effective B-cell epitopes and new antibodies with appropriate properties. In the present study, by using ClusPro 2.0 webserver, docking the antigen (factor H binding protein (fHbp)) to the novel-selected scFv antibody was performed. By analyzing the fHbp-scFv complexes, important amino acids were identified. After docking, peptides Ala192-His198, Asp 211-216, and Gly229-Ser228 of the fHbp antigen were recognized as essential interactive regions to the scFv antibody. Results obtained from our bioinformatics study are important and give us the basis for the favored designs of new molecules such as effective B-cell epitopes targeted by neutralizing antibodies for vaccine design.

This article communicates the study of magnetohydrodynamic (MHD) stagnation point flow of Casson liquid towards a stretched surface. Chemical reaction model involving both heat and mass transfer is established. Effects of viscous dissipation and Joule heating are also considered. Appropriate transformations yield strong nonlinear ordinary differential system. The obtained nonlinear systems have been solved through built-in shooting method. Velocity field shows decreasing behavior for higher estimation of magnetic parameter while temperature field shows increasing behavior for larger homogeneous heat parameter. Graphical behaviors of velocity, temperature and concentration are analyzed comprehensively corresponding to various pertinent parameters.

The vibrational structure of 2-ethyl-1-hexanol is of great interest because of its industrial and military applications. However, detailed spectral analysis is challenging due to its flexibility. This paper reports a detailed analysis of the gas and liquid phase vibrational spectra of 2-ethyl-1-hexanol using the Fourier transform infrared spectroscopy and Raman experimental data. By performing a detailed exploration of the conformational space in this work, the theoretical spectra reproduced almost all experimental details observed, and assigned internal valence coordinates to all of the experimentally observed bands in the floppy 2-ethyl-1-hexanol molecule. Relative contributions from the various internal valence coordinates to the experimental vibrational bands are directly compared between the liquid phase Raman band and the gas and liquid phase infrared band.

The structure of a potential bioactive agent namely, 3-[($N$-methylanilino)methyl]-5-(thiophen-2-yl)-1,3,4-oxadiazole-2(3$H)$-thione was characterized by proton and carbon-13 nuclear magnetic resonance (NMR) chemical shifts, Fourier transform infrared (FT-IR) and Laser-Raman spectroscopic techniques. The quantum chemical computations of molecular structures (disorder I and disorder II forms), vibrational wavenumbers, carbon-13 and proton chemical shifts and UV-Vis spectroscopic parameters have been performed with DFT/B3LYP method at 6-311$++$G(d,p) basis set. The highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), nonlinear optical (NLO) properties and natural bond orbital (NBO) analyses have been theoretically examined with the mentioned calculation level. The calculated values have been compared with the recorded experimental data. The computed molecular geometric parameters, vibrational wavenumbers, NMR chemical shifts, and UV-Vis wavelengths have been found to be in a good harmony with the experimental values and spectral results of similar structures in the literature. We believe that the work will be of considerable interest to anyone working in the area of theoretical chemistry, whether in industry or academics.

Conformational, structural, vibrational spectroscopic properties and nuclear magnetic chemical shift values of 4-acetoxyphenethyl acrylate (4APA) were investigated using spectroscopic and theoretical approaches including FT-IR and NMR spectroscopes and quantum chemical calculations. FT-IR spectroscopic measurement was carried out between 3500cm${}^{-1}$–400cm${}^{-1}$. Geometric parameters, vibrational wavenumbers and nuclear magnetic chemical shift values were estimated using B3LYP hybrid density functional theory method with 6-311$++$G(d, p) basis set. ¹H, ${}^{13}$C, APT and HETCOR NMR experiments of 4APA were obtained in DMSO solution. For a quantitative description of vibrational wavenumbers, total energy distribution (TED) values with scaled quantum mechanical (SQM) method were calculated. Moreover, molecular docking study of title molecule was theoretically carried out using Auto Dock Vina Program.

Here, we have proposed a new scheme of the computational combinatorial design approach to identify potential inhibitor peptides. It consists of four steps: (i) using “multiple copy simultaneous search” (MCSS) procedure to locate specific functional groups on the protein surface; (ii) the peptide main chain is constructed based on the location of favored N-methylacetamide (NMA) groups; (iii) molecular dynamics simulations of the complex formed between the constructed peptides with the target protein in explicit water molecules are carried to select the peptides with strong binding to the protein and (iv) the sequences of the stable peptides selected from (iii) are aligned and the frequencies of the amino acids at each position of peptide are calculated. Sequence patterns of potential inhibitors are determined based on the frequency of amino acids at each position. It was applied to design peptide inhibitors that bind to the E2 protein of HPV16 so as to disrupt its transcriptional regulator of E1–E2 complex formation. The sequence pattern of these potential inhibitors is in agreement with known inhibitors obtained from phage display, and the MCSS calculations indicate that a hydrophobic pocket on HPV16 E2 plays a significant role in E1–E2 formation and inhibitor-E2 binding.

The gas phase studies on the electronic stabilities and thermochemical properties of metastable AC mismatches have been performed and the results are analyzed to explain the features of experimentally available AC mismatches. The hydrogen bonding patterns observed in these mismatches are relevant to the formation of stable AC mismatches. In these AC pairs, the H migration mechanism to generate other tautomeric forms is not observed, which shows the compatibility of H bonding capacity of the sites involved in H bonds. The presence of hydrogen bond type –N$\cdots$H–N– may contribute to better AC pairing, hence cisA1-1cisC2, transA2-cisC1 and transA1-1cisC2 are found to be more favorable pairs compared to other AC pairs.