Synthesis, crystal structure analysis, spectral investigations, DFT computations and molecular dynamics and docking study of 4-benzyl-5-oxomorpholine-3-carbamide, a potential bioactive agent

Study of Nonlinear Optical Properties of a Self-Healing Organic Crystal

Recently a noncentrosymmetric single crystal of a dibenzoate derivative, namely, dimethyl-4,4'-(methylenebis(azanediyl))dibenzoate, with second harmonic generation activities at 405 nm and ultrafast self-healing activity was reported by Mondal et al. in Nature Communications in 2023. Here, the linear and nonlinear optical properties of this notable molecular crystal were simulated using 1,611,464 atoms in the Supermolecule approach at the DFT/CAM-B3LYP/aug-cc-pVTZ level. Our results for the second order nonlinear optical properties of dimethyl-4,4'-(methylenebis(azanediyl))dibenzoate show that the second harmonic generation is more significant at 532 nm. In addition, the density functional theory calculations of the electro-optical parameters for the crystals in the pristine state and after the fracture mechanical self-healing process show small differences, confirming the efficiency of the self-healing process. Additionally, the crystal displays significant third-order nonlinear optical properties, particularly pronounced at a shorter wavelength of 330 nm. Thus, the self-healing dimethyl-4,4'-(methylenebis(azanediyl))dibenzoate crystal shows relevant second and third order nonlinear optical properties which make it a very interesting material for optical applications.

Design of Novel Membranes for the Efficient Separation of Bee Alarm Pheromones in Portable Membrane Inlet Mass Spectrometric Systems

Bee alarm pheromones are essential molecules that are present in beehives when some threats occur in the bee population. In this work, we have applied multilevel modeling techniques to understand molecular interactions between representative bee alarm pheromones and polymers such as polymethyl siloxane (PDMS), polyethylene glycol (PEG), and their blend. This study aimed to check how these interactions can be manipulated to enable efficient separation of bee alarm pheromones in portable membrane inlet mass spectrometric (MIMS) systems using new membranes. The study involved the application of powerful computational atomistic methods based on a combination of modern semiempirical (GFN2-xTB), first principles (DFT), and force-field calculations. As a fundamental work material for the separation of molecules, we considered the PDMS polymer, a well-known sorbent material known to be applicable for light polar molecules. To improve its applicability as a sorbent material for heavier polar molecules, we considered two main factors-temperature and the addition of PEG polymer. Additional insights into molecular interactions were obtained by studying intrinsic reactive properties and noncovalent interactions between bee alarm pheromones and PDMS and PEG polymer chains.

Exploring the nonlinear optical properties of hypoxanthinium salts: a structural and computational analysis

CONTEXT

In this study, we detail the synthesis and crystallographic characterization of an unprecedented structure, specifically hypoxanthinium chloride monohydrate ((I) hereafter), which crystallizes in the monoclinic P21/c space group. A comparative analysis was conducted with four related hypoxanthinium salts: hypoxanthinium bromide monohydrate (II), 9-methylhypoxanthinium chloride monohydrate (III), hypoxanthinium nitrate monohydrate (IV), and hypoxanthinium perchlorate monohydrate (V). This analysis has focused mainly on their crystal packing, hydrogen-bonding networks, and non-classical intermolecular interactions, as elucidated by comprehensive Hirshfeld surface and topological analyses. Theoretical investigation of the nonlinear optical (NLO) properties of the hypoxanthinium derivatives (I-V) was performed using the Density Functional Theory (DFT).

METHODS

The crystalline environment was simulated using the iterative Supermolecule method (SM), and the static and dynamics linear refractive index, linear polarizability, second-order hyperpolarizability, and the third-order nonlinear susceptibility at the DFT/CAM-B3LYP/6-311++G(d,p) level were computed. The results for the macroscopic third-order nonlinear susceptibility of (II) was found to equalχ 3 = 0.81 × 10 - 20 m 2 / V 2 . By replacing the bromine atom in (II) with a chlorine atom as in (III), theχ 3 value will be multiplied by 2.16, and therefore these results are large enough to suggest the potential application of these crystals as NLO materials.

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.

Interaction between a photoisomerizable azobenzene compound and alpha-lactalbumin: Spectroscopic and computational simulation studies

The combination of light and photoresponsive compounds provides a peculiar way of regulating biological systems. Azobenzene is a classical organic compound with photoisomerization properties. Exploring the interactions between azobenzene and proteins can deepen the biochemical applications of the azobenzene compounds. In this paper, the interaction of 4-[(2,6-dimethylphenyl)diazenyl]-3,5-dimethylphenol with alpha-lactalbumin was investigated by UV-Vis absorption spectra, multiple fluorescence spectra, computer simulations, and circular dichroism spectra. Most critically, the interaction differences between proteins and the trans- and cis-isomer of ligands have been analyzed and compared. Results showed that both isomers of ligands were bound to alpha-lactalbumin to form ground state complexes and statically quenched the steady-state fluorescence of alpha-lactalbumin. The van der Waals forces and hydrogen bonding dominated the binding; the difference is that the binding of the cis-isomer to alpha-lactalbumin is more rapidly stabilized, and the binding strength is greater than the trans-isomer. These binding differences were modeled and analyzed by molecular docking and kinetic simulations, and we found that both isomers bind through the hydrophobic aromatic cluster 2 of alpha-lactalbumin. However, the bent structure of the cis-isomer is more closely aligned with the construction of the aromatic cluster and may have contributed to the above differences.

Synthesis, Anti-Bacterial and Anti-Oxidant Activity of Azo-Oxazolone and Their Ring Opening Azo-Benzamide Derivatives

This article describes the controlled synthesis and characterization of azo oxazolone scaffold compounds containing multifunctional groups such as carbonyl group, imine and carbon-carbon double bond. The reaction of the azo-oxazolone with aromatic amines led to the ring-opening of the azo-oxazolone into the corresponding azo-benzamide derivatives in a short time (average 10 min), resulting in high yield (>90%). All newly synthesized compounds were characterized by the common spectral analysis such as UV, IR, ¹H-NMR, ¹³CNMR, Elemental analysis and MS spectrometry.

OBJECTIVE

The aim of the study was to synthesize new bioactive azo-benzamides by using azo-oxazolone as a synthon utilizing its ring-opening function.

MATERIALS AND METHODS

Azo-benzamide derivatives were prepared in very good yield via ring-opening reaction of azo-oxazolone with aromatic amines in the presence of acetic acid under reflux for few minutes.

RESULTS AND DISCUSSION

Chemical structures of the newly synthesized compounds were characterized by UV, IR, ¹H-NMR, ¹³C-NMR, Elemental analysis and MS spectrometry.

CONCLUSION

The new azo-oxazolone 4 and azo-benzamide compounds 5a, 5c, 5f, 5h, 5j were screened against Escherichia coli as G(-ve) and Staphylococcus aureus as G(+ve) using ciprofloxacin as a standard. All compounds showed high inhibition potency against E-Coli but low inhibition for S-aureus. Compounds 4, 5c, and 5J showed more reactivity against E-coli. Others: Also, the compounds were tested for their anti-oxidant activity by both DPPH and FRAP methods. The results showed that some compounds possessed moderate anti-oxidant activity in comparison to ascorbic acid as control, typically the compounds bearing OCH₃ and OCH₂CH₃ groups.

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.