Multifaceted Study of a Y-Shaped Pyrimidine Compound: Assessing Structural Properties, Docking Interactions, and Third-Order Nonlinear Optics

In this study, we report the synthesis of a new compound, N4,N4-dimethyl-2-(methylsulfanyl)-N6-(4-phenoxyphenyl)pyrimidine-4,6-diamine (DMS), and its comprehensive analysis through structural and spectroscopic characterizations, reactivity parameters, and nonlinear optical properties, utilizing a combination of experimental and computational techniques. The experimental aspect of the investigation encompassed structural characterization using X-ray diffraction and spectroscopic assessments employing Fourier-transform infrared, Raman, and nuclear magnetic resonance techniques, along with thermal analysis. Our computational approach involved density functional theory (DFT) calculations and molecular dynamics (MD) simulations to examine the local reactivity properties of DMS. We employed fundamental reactivity descriptors to evaluate DMS's local reactivity and utilized MD simulations to identify DMS atoms engaging in significant interactions with water molecules. We conducted periodic DFT calculations on DMS's crystal structure to investigate the contributions of specific atoms and groups to the compound's overall stability as well as to analyze noncovalent interactions between DMS molecules. We assessed the nonlinear optical properties through dynamic second hyperpolarizability and third-order nonlinear susceptibility calculations. Additionally, we conducted a comparative analysis of the static and dynamic second hyperpolarizability for the DMS molecule within the sum-over-states framework. The obtained value for the third-order nonlinear susceptibility, (λ = 1907 nm), exceeds those of other organic materials reported in previous studies, indicating that the DMS crystal holds promise as a nonlinear optical material for potential application in photonic device fabrication. Furthermore, molecular docking studies were performed with the 3E5A, 4EUT, and 4EUU proteins, yielding binding affinities of -8.1, -8.2, and -8.3 kcal/mol, respectively, in association with the ligand.

A comparative study of structural and spectroscopic properties of three structurally similar mechanically bending organic single crystals - 2-Amino-3-nitro-5-halo (halo = Cl, Br, or I) pyridine

In recent years, scientists have been very interested in single crystals of monoaromatic compounds with mechanical softness, but they are hard to find. The present work reports a comparative study of structural, spectroscopic, and quantum chemical investigations of three structurally similar mechanically bending monoaromatic compounds, namely, 2-amino-3-nitro-5-chloro pyridine (I), 2-amino-3-nitro-5-bromo pyridine (II), and 2-amino-3-nitro-5-iodo pyridine (III). The mechanical responses of the three organic crystals studied here are very intriguing due to the similarity of their chemical structures, which only differ in the presence of halogen atoms (Cl, Br, and I) at the fifth position of the pyridine ring and are explained through examining intermolecular interaction energies from energy frameworks analysis, slip layer topology, and Hirshfeld surface analysis. The crystals of all the three feature one dimensional ribbons comprising alternating NaminoH⋯Onitro and NaminoH⋯Npyridine hydrogen bonds that form R22(12) and R22(8) dimeric rings, respectively. In (III), weak I⋯I interactions link the adjacent ribbons forming a two dimensional sheet. Layer-like structures are observed in all three crystals, with no significant interactions between the adjacent architectures (ribbons or sheets). Energy framework calculations are used for estimating the bending ability of the three compounds, with the three following the order Cl ≪ Br < I. The iterative electrostatic scheme coupled with the supermolecule approach (SM) at the DFT/CAM-B3LYP/aug-cc-pVTZ level is used to calculate the third-order nonlinear susceptibility (χ3) values in a simulated crystalline environment for the static case as well as two typical electric field frequency values, (λ = 1064 nm) and (λ = 532 nm). In addition, estimates of the topological studies (localized orbital locator and electron localization function) and reactivity characteristics (global reactivity parameters, molecular electrostatic potential, and Fukui function) are made for the compounds under investigation. Docking studies done using AutoDock software with a protein target (PDB ID: 6CM4) revealed that three compounds could be used to treat Alzheimer's disease.

Y-shaped potential third-order nonlinear optical material – 3-(2-amino-2-oxoethyl)-5-methyl hexanoic acid: an analysis of structural, spectroscopic and docking studies

The merit of this work is that it has clearly established the structure and the nonlinear optical properties relationship of the title molecule and it could be helpful for developing new nonlinear optical materials.