Journal of Computational Biophysics and Chemistry

During the past decade, deep eutectic solvents (DESs), emerging as green, versatile and adjustable alternatives to traditional solvents, have attracted intensive interests and immense research in various research fields. Especially DESs show quite a remarkable potential dissolving capability, due to their ability to donate as well as accept protons and electrons. A thorough and deep understanding of the microstructure, interactions and dissolving mechanism within DESs plays a key role in acquiring a task-specific DES. Quantum chemistry (QC) calculations provide structure-property-function relationship based on the molecular description and make up for the limitations of the current experimental techniques, showing promises for DESs screening and design. This paper summarizes the current research involving QC calculations and combined experiments, on investigating the structure, physicochemical properties and dissolving capability of DESs from the macroscopic and microcosmic perspective. This paper highlights and discusses the dissolving mechanism of various compounds in DESs, covering the recent successes in applying QC calculations to select the appropriate DESs as dissolving media. Furthermore, a brief analysis of perspectives and challenges for the future research in this field is presented. It is expected that this paper will inspire the future development of DESs from synthesis design to various designated applications.

The FT-IR and FT-Raman spectra of 3-(4-nitrophenoxy)-9,9a-dihydro-4aH-carbazole (9HCNP) molecule were recorded. The theoretical wavenumbers are in proper agreement with the observed results. The electronic properties, such as natural bond orbital study of the molecule, were confirmed using the inter/intra molecular interactions, molecular electrostatic potential, and Mulliken population analyses on the atomic charge distribution, performed by the Becke-3–Lee–Yang–Parr (CAM-B3LYP) method utilizing Gaussian 09 software. The oscillator strength of electronic transitions and energies of HOMO and LUMO molecular orbitals were carried out to evaluate the global chemical reactivity descriptors of 9HCNP. The molecular docking evaluation was carried out to evaluate the structure–activity relationship and the binding affinity of the molecule, which shows that the molecule can perform as an inhibitor of breast cancer-causing human topoisomerase-I and II-DNA receptors. The result of the conjugation was found to play a significant role in bioactivity and drug-likeliness properties, which can be supported by the molecular docking analysis of those compounds. In addition, the morphological changes in control and in vitro cytotoxicity of 9HCNP confirm the anticancer activity of 9HCNP against human breast cancer cell lines was assessed in 24-h tetrazolium-dye (MTT) cytotoxicity assays and also analyzed in terms of the role of reactive oxygen species (ROS) in cell life. Hence, the results show the in vitro anticancer activity of the molecule for the development of human breast cancer drugs.

In this study, in-silico interaction analysis between Human serum albumin (HSA) and serum protein acidic and rich in cysteine (SPARC)–Collagen complex was performed to determine the binding affinity between the two proteins. Structure-based molecular interaction studies of the HSA–SPARC–Collagen complex were performed using ClusPro 2.0, ZDOCK and PatchDock servers. Molecular dynamics analysis was performed for the first-ranked complex structure (HSA–SPARC–Collagen complex) using GROMACS for a period of 125 nanoseconds to determine the stability of the complex. The results show higher structural interactive cumulative scores between the HSA and SPARC–Collagen complex. HSA–SPARC–Collagen complex predominantly has the Pi-alkyl and Pi-sigma interactions. The root mean square fluctuation (RMSF), root mean square deviation, solvent accessible surface area, radius of gyration and the number of hydrogen bonds show that formed complex is stable. In conclusion, our study provides an add-on for tuning drugs concerning albumin as a drug carrier by targeting the SPARC–Collagen complex for treating different ailments.

Graphene has been widely studied in many fields due to its excellent physical and chemical properties. In this paper, we focus on the electronic structure and adsorption behavior of Al atoms and X ($\mathrm{\text{X}}=\mathrm{\text{B}}$, N, Si, S) atoms co-adsorption on the surface of pure graphene and Al atom adsorption on the surface of X ($\mathrm{\text{X}}=\mathrm{\text{B}}$, N, Si, S) atoms-doped graphene systematically. The adsorption energy, adsorption distance, bond length, bond angle, and electronic structure were studied using density functional theory (DFT) theoretical calculation. The results show that the adsorption capacity of (Al, X) atoms co-adsorbed on the graphene surface is significantly improved compared to the Al atoms on the pure graphene surface. The adsorption energy of Al and B atoms co-adsorbed on the graphene surface is basically the same as that of Al atoms on the B-doped graphene surface. The calculation results also show that the adsorption capacity of Al atoms and X ($\mathrm{\text{X}}=\mathrm{\text{N}}$, Si, S) atoms co-adsorbed on the surface of graphene is better than that of Al atoms on the surface of graphene doped with X (X = N, Si, S) atoms. Compared with N atom and S atom-doped systems, the Si-doped graphene surface has a stronger adsorption capacity for Al atoms than pure graphene. However, due to the doping of N and S atoms, the adsorption capacity of Al atoms on the graphene surface is somewhat reduced. Our calculation results provide a theoretical basis for further selection of Al-based graphene composite materials.

Glucose transporter 1 (GLUT1) plays an important role in the transport of glucose into cells. Studies found that GLUT1 is highly expressed in a variety of tumor cells, and it’s the rate-limiting transporter for tumor cells to uptake glucose, meaning that GLUT1 is a potential target for tumor treatment. Thus, the inhibition of GLUT1 by novel small compounds to lower glucose levels for cancer cells has become an emerging strategy. In this study, potential GLUT1 inhibitors were discovered by pharmacophore-based high-throughput virtual screening. First, 96 GLUT1 inhibitors were used to establish common pharmacophore hypotheses. The best pharmacophore model ADHRRR_1 was used to screen the ZINC database. Then, ADMET was launched to predict the pharmacokinetics of hit compounds from virtual screening. After that, the standard docking and precise docking were employed to dock these compounds with 4PYP protein; five molecules were selected as candidates of GLUT1 inhibitors for further analysis. Molecular Dynamic (MD) simulations and Molecular Mechanics/Poisson Boltzmann Surface Area (MM/PBSA) method were applied to evaluate the binding stability and affinity of the five protein–ligand composites. Finally, Zinc000068152777 and Zinc000141918576 with lower docking scores and binding free energy emerged as the potential GLUT1 inhibitors. Taken together, these results in our study may provide valuable information for cancer therapeutics by disturbing the energy metabolism of tumors.

Chronic Myeloid Leukemia (CML) is known as clonal myeloproliferative disorder resulted by the proliferative and deregulated expression of the BCR-ABL gene. Although targeting the BCR-ABL gene is an effective treatment for CML, the development of drug intolerance and drug resistance is still an issue for BCR-ABL targeted therapy. With an aim to develop novel BCR-ABL inhibitors with fewer side effects, we started with the anti-cancerous natural compound coumestrol as the lead. Chalcone and pyrazole are the well-exploited scaffolds in the anticancer domain; hence, in this work, we designed novel coumestrol derivatives with these structures. In order to quantify the structural changes, we employed in silico methods. The new drug leads were compared with the FDA-approved CML drug bosutinib. The molecular orbital analysis of the selected lead compounds was assessed by Density Functional Theory (DFT) approach. Molecular Dynamic (MD) computations were performed on the most promising leads to find the stability. Following which, the pharmacokinetics parameters of the screened compounds were also analyzed to check the drug-like property.

The development of an effective building blocks considered the boon in constructing highly efficient nonfullerene electron acceptors (NFEAs). The first theoretical design and investigation of environmental-friendly groups for changing potential end-capped electron acceptor molecules for high-performance environmental-friendly OSCs is proposed in this study. We developed BTT-based $A$–$\pi$–$D$–$\pi$–$A$ (acceptor–bridge–core–bridge–acceptor) type, neoteric Bat-shaped environmental-friendly acceptor molecules (K1–K6) for the first time by replacing the electronegative –F group of BTT with four electron-withdrawing (–CN, –COOCH₃, –NO₂, –Cl) groups. K1–K6 has its exciton-binding energy ($E_b$), open-circuit voltage ($V_{\mathrm{\text{oc}}}$), frontier molecular orbital analysis (FMO), transition density matrix (TDM) analysis, electron and hole reorganization energy ($\lambda$e, $\lambda$h), density of state (DOS) graphs, and transition energy Ex values computed and compared to the recently proposed high-performance BTT molecule. According to the research, the photovoltaic, photo-physical and electrical applications of proposed molecules K1–K6 are comparable to those of $R$. When compared to reference $R$ and proposed molecules, K6 tested to be the proverbial optoelectronic compound for OSCs due to its low $E_g$ (2.05eV), lowest $E_x$ (1.57eV), highest $\lambda$ max values of 790.61nm in CHCl₃, 0.95V value for $V_{\mathrm{\text{oc}}}$ and comparable $E_b$ (0.482eV). The superposition of orbitals and lucrative charge shift from the highest occupied molecular orbital (HOMO) (PTB7-Th) to the lowest unoccupied molecular orbital (LUMO) were verified by charge transfer study among the K6: PTB7-Th combine. As a result, the proposed molecules (K1–K6) with exceptional optoelectronic capabilities are suggested as the best harmless alternative materials for creating proficient and environmental-friendly OSCs.

This research is focused on the sensor properties of pure and X-decorated ($\mathrm{\text{X}}=\mathrm{\text{B}}$, N, P and S) magnesium oxide (Mg${}_{12}$O${}_{12}$) nanocages for melamine (C₃H₆N₆) molecule detection using density functional theory (DFT) electronic structure approach. Comparative adsorption study was carried out on four distinct computational models of hybrid functionals: $\omega$B97XD, PBE0-D3BJ, M062X-D3BJ and DSDPBEP86 with the double-hybrid (DSDPBEP86), being the superior model at the fifth rung of the Jacobi’s ladder, was used as the reference. The atoms-in-molecule (AIM), alongside with the non-covalent interactions (NCIs) as visual extension had been utilized in the study of weak interactions and to affirm the degree of interactions between the clusters and the toxin. In all cases, this study suggests that the adsorption phenomena are best described as chemisorption due to the negative adsorption enthalpy observed. The mean absolute deviation (MAD) and root mean square deviation (RMSD) statistical approaches suggest the behavior of the possible adsorptions to be ranked as follows: PBE0-D3BJ (first rank), $\omega$B97XD (second rank) and finally, M062X-D3BJ (third rank) with ($\mathrm{\text{MAD}}=0.7846$, 0.7870 and 0.8402) and ($\mathrm{\text{RMSD}}=0.8924$, 0.8946 and 0.9560), respectively. These results are consistent with those of the topological and the sensing parameters, hence, arriving at a conclusive scientific report that Mg${}_{12}$O${}_{12}$ and Mg${}_{12}$PO${}_{11}$ surfaces exhibit relatively better sensing performances for the trapping of melamine (MB).