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.

Theoretical investigation on the linear and nonlinear optical properties of DAPSH crystal

The linear polarizability, first and second hyperpolarizabilities of the asymmetric unit of DAPSH crystal are studied and compared with available experimental results. The polarization effects are included using an iterative polarization procedure, which ensures the convergence of the dipole moment of DAPSH embedded within a polarization field generated by the surrounding asymmetric units whose atomic sites are considered as point charges. We estimate macroscopic susceptibilities from the results of the polarized asymmetric units in the unit cell, considering the significant contribution of the electrostatic interactions in crystal packing. The results show that the influence of the polarization effects leads to a marked decrease of the first hyperpolarizability, compared with the respective isolated counterpart, which improves the concordance with the experiment. There is a minor influence of polarization effects on the second hyperpolarizability but our estimated result for the third-order susceptibility, related to the NLO process of the intensity dependent refractive index, is significant as compared with the results for other organic crystals, such as chalcone-derivatives. In addition, supermolecule calculations are conducted for explicit dimers in presence of the electrostatic embedding to illustrate the role played by the electrostatic interactions in the hyperpolarizabilities of the DAPSH crystal.

Remarkable Nonlinear Properties of a Novel Quinolidone Derivative: Joint Synthesis and Molecular Modeling

A novel 4(1H) quinolinone derivative (QBCP) was synthesized and characterized with single crystal X-ray diffraction. Hirshfeld surfaces (HS) analyses were employed as a complementary tool to evaluate the crystal intermolecular interactions. The molecular global reactivity parameters of QBCP were studied using HOMO and LUMO energies. In addition, the molecular electrostatic potential (MEP) and the UV-Vis absorption and emission spectra were obtained and analyzed. The supermolecule (SM) approach was employed to build a bulk with 474,552 atoms to simulate the crystalline environment polarization effect on the asymmetric unit of the compound. The nonlinear optical properties were investigated using the density functional method (DFT/CAM-B3LYP) with the Pople's 6-311++G(d,p) basis set. The quantum DFT results of the linear polarizability, the average second-order hyperpolarizability and the third-order nonlinear susceptibility values were computed and analyzed. The results showed that the organic compound (QBCP) has great potential for application as a third-order nonlinear optical material.

Molecular modeling and nonlinear optical properties of new isostructural halogenated dihydroquinolinones

Two new isostructural halogenated dihydroquinolinones were synthesized and characterized by single crystal X-ray diffraction.

Synthesis and structural studies on (E)-3-(2,6-difluorophenyl)-1-(4-fluorophenyl)prop-2-en-1-one: a promising nonlinear optical material

A new fluorinated chalcone (E)-3-(2,6-difluorophenyl)-1-(4-fluorophenyl)prop-2-en-1-one was synthesized in 90% yield and crystallized by a slow evaporation technique. Its full structural characterization and purity were determined by scanning electron microscopy, infrared spectroscopy, gas chromatography-mass spectrometry, 1H, 13C and 19F nuclear magnetic resonance, thermal gravimetric analysis (TGA), differential scanning calorimetry (DSC), Raman microspectroscopy, UV-Vis absorption spectroscopy, single crystal X-ray diffraction (XRD) and Hirshfeld surface (HS) analysis. The fluorinated chalcone crystallized in centrosymmetric space group P21/c stabilized by the C-H⋯O and C-H⋯F interactions and the π⋯π contact. The crystalline environment was simulated through the supermolecule approach where a bulk with 378 000 atoms was built. The electric parameters were calculated at the DFT/CAM-B3LYP/6-311++G(d,p) level as function of the electric field frequency. The macroscopic parameters such as linear refractive index and third-order nonlinear susceptibility (χ (3)) were calculated, and the results were compared with experimental data obtained from the literature. The χ (3)-value for the chalcone crystal is 369.294 × 10-22 m2 V-2, higher than those obtained from a few similar types of molecule, showing that the chalcone crystal can be considered as a nonlinear optical material. Also, molecular theoretical calculations such as infrared spectrum assignments, frontier molecular orbital analysis and MEP were implemented, revealing that the most positive region is around the hydrogen atoms of the aromatic rings, and electrophilic attack occurs on the carbonyl group.

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.

Hyperpolarizability studies and Hirshfeld surface analysis of two heterocyclic chalcones

In this work, the nonlinear optical (NLO) properties of two heterocyclic chalcones, (E)-1-(5-chlorothiophen-2-yl)-3-(thiophen-2yl)-2-propen-1-one (CLTT) and (E)-1-(5-methylfuran-2-yl)-3-(5-methylthiophen-2-yl)prop-2en-1-one (2MFT), are investigated. Using an iterative electrostatic embedding approach via the Møller-Plesset perturbation (MP2) theory, the chalcone crystals were simulated and the polarization effects on the isolated molecules are investigated. The electrical parameters of CLTT and 2MFT as dipole moment and linear polarizability were calculated via MP2/6-311++G(d) and the second hyperpolarizability was obtained via DFT/CAM-B3-LYP/6-311++G(d) level. A significant influence of the molecular packing on the chalcone electric parameters was observed. The static linear refractive index and the third-order electric susceptibility of the compounds were calculated and compared with experimental results available for other chalcone derivatives, indicating the CLTT crystal as a promising candidate for NLO applications in photonic and optoelectronic devices. The Hirshfeld surface analysis has been used to quantify the intermolecular interactions of the molecular crystals. Additionally, the solvent medium effects on the electrical properties of the heterocyclic chalcones were also studied.

A novel dihydrocoumarin under experimental and theoretical characterization

Coumarins are natural and synthetic active ingredients widely applied in diverse types of medicinal treatments, such as cancer, inflammation, infection, and enzyme inhibition (monoamine oxidase B). Dihydrocoumarin compounds are of great interest in organic chemistry due to their structural versatilities and, as part of our investigations concerning the structural characterization of small molecules, this work focuses on crystal structure and spectroscopic characterization of the synthesized and crystallized compound 4-(4-methoxyphenyl)-3,4-dihydro-chromen-2-one (C₁₆H₁₄O₃). Additionally, a theoretical calculation was performed using density functional theory to analyze the sites where nucleophilic or electrophilic attack took place and to examine the molecular electrostatic potential surface. Throughout all of these calculations, both density functional theory and Car-Parrinello molecular dynamics were performed by fully optimized geometry. The spectroscopic analysis indicated the presence of aromatic carbons and hydrogen atoms, and also the carbonyl and methoxy groups that were confirmed by the crystallographic structure. The C₁₆H₁₄O₃ compound has a non-classical intermolecular interaction of type C-H⋅⋅⋅O that drives the molecular arrangement and the crystal packing. Moreover, the main absorbent groups were characterized throughout calculated harmonic vibrational frequencies. Also, natural bond orbital analysis successfully locates the molecular orbital with π-bonding symmetry and the molecular orbital with π* antibonding symmetry. Finally, the gap between highest occupied and lowest unoccupied molecular orbitals implies in a high kinetic stability and low chemical reactivity of title molecule.