Effect of COF Presence on DNA Molecular Interactions: A QM/MM and MD Simulations Study

Abstract

Four models of DNA including A-DNA, B-DNA, Triple helix-DNA (T-DNA), and Z-DNA along with a COF molecule were prepared. Molecular dynamics simulations were performed on all DNAs and their complex with COF (embedded DNAs in the central hole of COF). Comprehensive analyses such as Base pair distance, hydrogen bonding, Van der Waals, and electrostatic interaction numbers were carried out to investigate the effect of COF molecule on DNA intermolecular interactions. Furthermore, quantum-mechanics studies were performed to explore the accuracy of intermolecular and intramolecular interactions. The results obtained based on promolecular density in two selected base pairs. Noncovalent interaction (NCI) analysis to investigate the strength of hydrogen bonds, Van der Waals interactions, and steric effect was done. Density Overlap Regions Indicator (DORI) analysis was accomplished to study the accuracy of π-π stacking interactions between adjacent bases. δg functions were evaluated to analyze the strength of chemical bonds, hydrogen bonds and also the steric effect. The average distance between O … H, N … H, and H … O that are contributing in H-bonding are ∼ 1.88, 1.97, and 1.95 Å in A-DNA, respectively. Also, the average number of H-bonding numbers in A-DNA calculated to be 14.43 and 13.04 in pure and complex form. All the achieved results showed that designed COF did not make any changes in DNA structures, but in some cases, had some effects on the interactions of DNAs.

Design of molecularly imprinted polymers (MIP) using computational methods: A review of strategies and approaches

“…In terms of non-covalent interactions, Van der Waals interactions by Lennard-Jones potential, hydrogen bonds by a variant with additional constants, and electrostatic interactions by Coulomb's law are calculated. [45][46][47][48] However, in the realm of computational statistical mechanics, probabilities of the system in a state are computed. The probability of the system existing in a particular state, with an energy level, is given by the "Boltzmann distribution."…”

“…Thus, interatomic potentials and molecular mechanics force fields are applied as descriptors to measure the forces between the atoms and their potential energies. In terms of non‐covalent interactions, Van der Waals interactions by Lennard‐Jones potential, hydrogen bonds by a variant with additional constants, and electrostatic interactions by Coulomb's law are calculated 45–48 …”

“…By this method, a subsystem is defined to be treated at the QM level while another part is simulated at the MM atomistic level. 45 Sequential MD/QM is another approach by which firstly, configurations are obtained by MD simulation statistically, and then QM calculation is applied to the whole system 58,59 PCA, a multivariate statistical technique, extracts the most important coordinates of atoms among trajectories (data sets) by using covariance matrix or correlation matrix. 60 However, clustering partitions have similar conformations found in the produced trajectories of MD simulation.…”