The structure of DNA fragments: Quantum-chemical modelling.

In this review, we analyze and systematize our computational studies of the nucleic acid duplex formations and thermodynamic stability under the different factors of investigation. The proposed structural models of mini-helix contains N nucleobase pairs (N = 3-5); QM structural data suggest that the helical conformations of mini-helix adopt geometrical parameters comparable to those of natural A- and B-DNA forms under specific conditions as micro hydration and charge compensation. The gas-phase models adopt non regular conformations between the helical form and a ladder form.

Auto3D: Automatic Generation of the Low-Energy 3D Structures with ANI Neural Network Potentials.

Computational programs accelerate the chemical discovery processes but often need proper three-dimensional molecular information as part of the input. Getting optimal molecular structures is challenging because it requires enumerating and optimizing a huge space of stereoisomers and conformers. We developed the Python-based Auto3D package for generating the low-energy 3D structures using SMILES as the input.

Machine learned Hückel theory: Interfacing physics and deep neural networks.

The Hückel Hamiltonian is an incredibly simple tight-binding model known for its ability to capture qualitative physics phenomena arising from electron interactions in molecules and materials. Part of its simplicity arises from using only two types of empirically fit physics-motivated parameters: the first describes the orbital energies on each atom and the second describes electronic interactions and bonding between atoms. By replacing these empirical parameters with machine-learned dynamic values, we vastly increase the accuracy of the extended Hückel model.

Development of Multimodal Machine Learning Potentials: Toward a Physics-Aware Artificial Intelligence.

Machine learning interatomic potentials (MLIPs) are widely used for describing molecular energy and continue bridging the speed and accuracy gap between quantum mechanical (QM) and classical approaches like force fields. In this Account, we focus on the out-of-the-box approaches to developing transferable MLIPs for diverse chemical tasks. First, we introduce the "Accurate Neural Network engine for Molecular Energies," ANAKIN-ME, method (or ANI for short).

Effect of Microenvironment on the Geometrical Structure of d(A) d(T) and d(G) d(C) DNA Mini-Helixes and the Dickerson Dodecamer: A Density Functional Theory Study.

We report a comprehensive quantum-chemical study on d(A)·d(T) and d(G)·d(C) DNA mini-helixes and the Dickerson dodecamer d[CGCGAATTCGCG]. The research was performed to model the evolution of the spatial structure of d(A)·d(T) and d(G) d(C) DNA mini-helixes all the way from vacuum to water bulk. The influence of external factors such as the presence of counterions and the extent of hydration was included.

How water affects mercury-halogen interaction in the atmosphere.

The solvation of mercury and halogens ions in water is essential for studying the reaction kinetics of various mercury depletion reactions in the atmosphere. Here, we use two approaches. The first one is the implementation of transition state theory to study the recombination reactions of Hgand Hal with the introduction of a water molecule as a third body part.

Structure and Binding Energy of Double-Stranded A-DNA Mini-helices: Quantum-Chemical Study.

A-DNA is thought to play a significant biological role in gene expression due to its specific conformation and binding features. In this study, double-stranded mini-helices (dA:dT)3 and (dG:dC)3 in A-like DNA conformation were investigated. M06-2X/6-31G(d,p) method has been utilized to identify the optimal geometries and predict physicochemical parameters of these systems.

Structural waters in the minor and major grooves of DNA--a major factor governing structural adjustments of the A-T mini-helix.

The role of microhydration in structural adjustments of the AT-tract in B-DNA was studied at the B97-D/def2-SV(P) level. The (dA:dT)5 complexes with 10 water molecules in minor and 15 water molecules in major grooves were studied. The obtained network of hydrogen bonds revealed the dependence between the groove width and the types of water patterns.

B-DNA characteristics are preserved in double stranded d(A)3·d(T)3 and d(G)3·d(C)3 mini-helixes: conclusions from DFT/M06-2X study.

We report the results of the first comprehensive DFT study on the d(A)3·d(T)3 and d(G)3·d(C)3 nucleic acid duplexes. The ability of mini-helixes to preserve the conformation of B-DNA in the gas phase and under the influence of such factors as: solvent, uncompensated charge, and counter-ions was evaluated using M06-2X functional with 6-31G(d,p) basis set. The accuracy of the models was ascertained based on their ability to reproduce key structural features of natural B-DNA.