Non-adiabatic coupling in the potential energy surfaces of SO2 molecule.

To investigate the potential energy surfaces and the coupling between the adiabatic states of SO2 molecules, it is necessary to consider the non-adiabatic coupling terms (NACTs), where the Born-Oppenheimer approximation breaks down. In this work, we analyze the conical intersections between 1 1A1 and 1 1B2 states (the A' states in Cs symmetry) and 1 1A2 and 1 1B1 states (the A'' states in Cs symmetry) using NACTs and adiabatic-to-diabatic transformation (ADT) angles. Our results confirm reasonable interaction between 1 1A1 and 1 1B2 states and strong interaction between 1 1A2 and 1 1B1 states.

Theoretical aspects of interaction of the anticancer drug cytarabine with human serum albumin.

Despite diagnostic and therapeutic methods, cancer is a major cause of death worldwide. Since anticancer drugs affect both normal and cancer cells, targeted drug delivery systems can play a key role in reducing the destructive effects of anticancer drugs on normal cells. In this regard, the use of stimulus-sensitive polymers has increased in recent years. This study has attempted to investigate interaction of the anticancer drug cytarabine with a stimuli-sensitive polymer, human serum albumin (HSA), one of the most abundant protein in blood plasma, via computational methods at both body temperature and tumor temperature. For this purpose, molecular docking was performed using Molegro virtual Docker software to select the best ligand in terms of binding energy to simulate molecular dynamics. Then, molecular dynamics simulation was performed on human serum albumin with code (1Ao6) and cytarabine with code (AR3), using Gromacs software and the results were presented in the graphs. The simulations were performed at 310 K (normal cell temperature) and 313 K (cancer cell temperature) in 100 ns. Results showed drug release occurred at a temperature of 313 K. These findings demonstrated the sensitivity of human serum albumin to temperature.

Computational study on transfer of L-ascorbic acid by UlaA through Escherichia coli membrane.

In this study, the transfer of L-ascorbic acid by UlaA through Escherichia coli (E. coli) membrane was evaluated using density functional theory (DFT), molecular docking, and molecular dynamics (MD) simulation methods. DFT calculations at the B3lyp/6[Formula: see text]311[Formula: see text]G(p,d) level were performed to investigate the interaction properties and molecular descriptors. The physical properties, such as chemical potential, chemical hardness, and chemical electrophilicity of all studied molecules, were investigated. Natural population analysis was employed to describe the state of charge transfer between interactions using the natural bond orbital (NBO). The atoms in molecules (AIM) theory was used to examine the properties of the bond critical points such as their electron densities and Laplacians. Molecular docking studies showed that L-ascorbic acid was bounded to the internal cavity of UlaA. It was found that there were some hydrogen bond interactions between L-ascorbic acid and active sites of UlaA. The results of the MD simulation showed that the root mean square deviation (RMSD) of UlaA and L-ascorbic acid bound-UlaA reached equilibrium after 3.7[Formula: see text]ns. An evaluation of the radius of gyration ([Formula: see text]) revealed that UlaA and L-ascorbic acid bound-UlaA were stabilized around 10,000[Formula: see text]ns. Finally, analysis of the RMS fluctuations suggested that the structure of the L-ascorbic acid binding site remained approximately rigid during simulation. All obtained results shed light on the special manner of L-ascorbic acid transfer through E. coli membrane, and confirmed the results of previous studies on this issue.

Effects of Displacement-Distortion of Potential Energy Surfaces on Nonadiabatic Electron Transfers via Conical Intersections: Application to SO2 and trans-1,3,5-Hexatriene.

We show that the time-correlation function formalism can be applied to calculate nonadiabatic electronic population dynamics on the two vibronically coupled diabatic displaced-distorted harmonic potential energy surfaces through conical intersection. We present general formulas for the time-evolved electronic populations at finite temperature with initial sampling from both initial thermal equilibrium and nonequilibrium nuclear distributions. The validity of our formalism is verified through comparison with previous work in a certain limit of our results for case of displaced harmonic oscillator. Finally for illustration, the derived expressions have been applied to determine the electronic population dynamics at conical intersections for SO2 and trans-1,3,5-hexatriene molecules.