Synthesis, X-ray Structure, Conformational Analysis, and DFT Studies of a Giant s-Triazine bis-Schiff Base

The current work involves the synthesis of 2,2′-(6-(piperidin-1-yl)-1,3,5-triazine-2,4-diyl)bis(hydrazin-2-yl-1-ylidene))bis(methanylylidene))diphenol 4, characterization, and the DFT studies of the reported compound. The crystal unit cell parameters of 4 are a = 8.1139(2) Å, b = 11.2637(2) Å, c = 45.7836(8) Å. The unit cell volume is 4184.28(15) Å3 and Z = 4. It crystallized in the orthorhombic crystal system and Pbca space group. The O…H, N…H, C…H, H…H and C…C intermolecular contacts which affect the crystal stability were quantitatively analyzed using Hirshfeld calculations. Their percentages were calculated to be 9.8, 15.8, 23.7, 46.4, and 1.6% from the whole contacts occurred in the crystal, respectively. Conformational analysis was performed using DFT calculations for 17 suggested conformers and the most stable conformer was found to be the one which is stabilized by two intramolecular O-H…N hydrogen bonding interactions. This conclusion was further revealed by natural bond orbital calculations.

Hydrogen Delocalization in an Asymmetric Biomolecule: The Curious Case of alpha-Fenchol

Rotational microwave jet spectroscopy studies of the monoterpenol α-fenchol have so far failed to identify its second expected torsional conformer, despite computational predictions that it is only very slightly higher in energy than the most stable conformer. Vibrational FTIR and Raman jet spectroscopy investigations reveal unusually complex OH and OD stretching spectra compared to other alcohols. Via modelling of the torsional states, observed spectral splittings are explained by delocalization of the hydroxy hydrogen atom through quantum tunneling between the two non-equivalent but accidentally near-degenerate conformers separated by a low and narrow barrier. The energy differences between the torsional states are determined to be only 16(1) and 7(1) cm$^{−1}hc$ for the protiated and deuterated alcohol, respectively, which further shrink to 9(1) and 3(1) cm$^{−1}hc$ upon OH or OD stretch excitation. Comparisons are made with the more strongly asymmetric monoterpenols borneol and isopinocampheol as well as with the symmetric, rapidly tunneling propargyl alcohol. Assigned are also for α-fenchol the third – in contrast localized – torsional conformer and the most stable dimer, as well as for propargyl alcohol the two most stable dimers.

Infrared Spectrum and UV-Induced Photochemistry of Matrix-Isolated Phenyl 1-Hydroxy-2-Naphthoate

The conformational stability, infrared spectrum, and photochemistry of phenyl 1-hydroxy-2-naphthoate (PHN) were studied by matrix isolation infrared spectroscopy and theoretical computations performed at the DFT(B3LYP)/6-311++G(d,p) level of theory. The main intramolecular interactions determining the relative stability of seven conformers of the molecule were evaluated. According to the calculations, the twofold degenerated O–H···O=C intramolecularly hydrogen-bonded conformer with the phenyl ring ester group ±68.8° out of the plane of the substituted naphtyl moiety is the most stable conformer of the molecule. This conformer is considerably more stable than the second most stable form (by ~15 kJ mol−1), in which a weaker O–H···O–C intramolecular hydrogen bond exists. The compound was isolated in cryogenic argon and N2 matrices, and the conformational composition in the matrices was investigated by infrared spectroscopy. In agreement with the predicted relative energies of the conformers, the analysis of the spectra indicated that only the most stable conformer of PHN was present in the as-deposited matrices. The matrices were then irradiated at various wavelengths by narrowband tunable UV light within the 331.7–235.0 nm wavelength range. This resulted in the photodecarbonylation of PHN, yielding 2-phenoxynaphthalen-1-ol, together with CO. The extension of the decarbonylation was found to depend on the excitation wavelength.

Synthesis, Characterization and TheoreticalStudies of Nand#39;-(4-methoxybenzylidene)benzenesulfonohydrazide

Nand#39;-(4-methoxybenzylidene)benzenesulfonohydrazide was synthesized and elemental analysis was conducted; IR, Raman, 1H, and 13C NMR spectral data were recorded. The potential energy surfaces (PES) of the Nand#39;-(4-methoxybenzylidene)benzenesulfonohydrazide molecule were obtained by selected degree of torsional freedom, which varied from 0o to 360and#186; in 4and#186; increments. The conformers were optimized by using a (DFT/B3LYP/6-31G(d,p)) basis set in the gas phase. The eleven conformers in the gas phase of the obtained molecule were determined and the most stable conformer (conformer 1) was re-optimized by three different basis sets of 6-31G(d,p), 6-311G(d,p), and LanL2Dz. HOMO-LUMO analyses were performed. NBO analysis was performed to describe the around of intramolecular charge transfer. The vibrational spectra were measured in solid phase IR and detailed analysis of the vibrational spectra of conformer 1 was done; all the bands of the spectra were interpreted by the use of the potential energy distributions (PED) and the molecular electrostatic potential (MEP) was plotted.

Mesomorphic, Optical and DFT Aspects of Near to Room-Temperature Calamitic Liquid Crystal

A new liquid crystalline, optical material-based Schiff base core with a near to room-temperature mesophase, (4-methoxybenzylideneamino)phenyl oleate (I), was prepared from a natural fatty acid derivative, and its physical and chemical properties investigated by experimental and theoretical approaches. The molecular structure was confirmed by elemental analysis, FT-IR (Fourier-Transform-Infrared Spectroscopy) and NMR (nuclear magnetic resonance) spectroscopy. Optical and mesomorphic activities were characterized by differential scanning calorimetry (DSC) and polarized optical microscopy (POM). The results show that compound (I) exhibits an enantiotropic monomorphic phase comprising a smectic A phase within the near to room-temperature range. Ordinary and extraordinary refractive indices as well as birefringence with changeable temperatures were analyzed. Microscopic and macroscopic order parameters were also calculated. Theoretical density functional theory (DFT) calculations were carried out to estimate the geometrical molecular structures of the prepared compounds, and the DFT results were used to illustrate the mesomorphic results and optical characteristics in terms of their predicted data. Three geometrical isomers of the prepared compound were investigated to predict the most stable isomer. Many parameters were affected by the geometrical isomerism such as aspect ratio, planarity, and dipole moment. Thermal parameters of the theoretical calculations revealed that the highest co-planar aromatic core is the most stable conformer.

Interstellar glycolamide: A comprehensive rotational study and an astronomical search in Sgr B2(N)

Context. Glycolamide is a glycine isomer and also one of the simplest derivatives of acetamide (e.g., one hydrogen atom is replaced with a hydroxyl group), which is a known interstellar molecule. Aims. In this context, the aim of our work is to provide direct experimental frequencies of the ground vibrational state of glycolamide in the centimeter-, millimeter- and submillimeter-wavelength regions in order to enable its identification in the interstellar medium. Methods. We employed a battery of state-of-the-art rotational spectroscopic techniques in the frequency and time domain to measure the frequencies of glycolamide. We used the spectral line survey named Exploring Molecular Complexity with ALMA (EMoCA), which was performed toward the star forming region Sgr B2(N) with ALMA to search for glycolamide in space. We also searched for glycolamide toward Sgr B2(N) with the Effelsberg radio telescope. The astronomical spectra were analyzed under the local thermodynamic equilibrium approximation. We used the gas-grain chemical kinetics model MAGICKAL to interpret the results of the astronomical observations. Results. About 1500 transitions have been newly assigned up to 460 GHz to the most stable conformer, and a precise set of spectroscopic constants was determined. Spectral features of glycolamide were then searched for in the prominent hot molecular core Sgr B2(N2). We report the nondetection of glycolamide toward this source with an abundance at least six and five times lower than that of acetamide and glycolaldehyde, respectively. Our astrochemical model suggests that glycolamide may be present in this source at a level just below the upper limit, which was derived from the EMoCA survey. We could also not detect the molecule in the region’s extended molecular envelope, which was probed with the Effelsberg telescope. We find an upper limit to its column density that is similar to the column densities obtained earlier for acetamide and glycolaldehyde with the Green Bank Telescope.

The smell of coffee: the carbon atom microwave structure of coffee furanone validated by quantum chemistry

The rotational spectra of coffee furanone (2-methyltetrahydrofuran-3-one) have been measured in the frequency range from 2.0 to 26.5 GHz using a molecular jet Fourier transform microwave spectrometer. Quantum chemical calculations used for the conformational analysis yielded two stable twist conformers, which were described using the Cremer–Pople notation for five-membered rings. The experimental spectrum of the more stable conformer with the methyl group in equatorial position was assigned and fitted using a rigid rotor model with centrifugal distortion corrections. The spectra of all five 13C-isotopologues could be observed in natural abundance. The carbon atom structure was experimentally deduced using Kraitchman’s equations and compared with the structure calculated by quantum chemistry.

Reply to the ‘Comment on “Polymorphism of levofloxacin: structure, properties and phase transformation”’ by Tejender S. Thakur, CrystEngComm, 2020, 22, DOI: 10.1039/C9CE01400D

Minor structural differences in molecular conformation were found where the levofloxacin molecule takes a less stable conformer in energy rather than the stable conformer as previously expected.

Synthesis of malonyldi(1,2,4-triazole), the study of the kinetic and thermodynamic features of its hydrolysis and prediction of biological activity

This article describes a two-step method for the synthesis of malondyl (1,2,4-triazole) (1,3-di (1H-1,2,4-triazol-1-yl)propane-1,3-dione) of 1,2,4-triazole through 1-trimethylsilyl-1,2,4-triazole, followed by reaction with malonyl chloride; the yield of the final product is 85%. The kinetics of hydrolysis of malonyldi(1,2,4-triazole) in the acetonitrile – water system (9:1) at 25 °C and 35 °C was studied, and the activation energy of the hydrolysis of malonyldi(1,2,4-triazole). To study the thermodynamic features of the reactions of obtaining this compound in the Spartan’14 1.1.4 program, a number of thermodynamic characteristics were calculated, which determine the spontaneous and exothermic nature of the process. For the molecule malonyldi(1,2,4-triazole), the most and least stable conformers were found in the program Molecular Operating Environment 2009.10, for which the surfaces of nucleophilic susceptibility were calculated in the program SCIGRESS Modeling 3.1.4. It was shown that the most stable conformer of the malonyldi(1,2,4-triazole) molecule should have the highest reactivity in reactions with different nucleophiles and the lowest value of the heat of formation. In this case, the nucleophilic susceptibility of carbonyl carbon atoms is different, despite the symmetry of the structure of the molecules malonyldi(1,2,4-triazole), which suggests a stepwise interaction of malonyldi(1,2,4-triazole) with nucleophiles. The structure of malonyldi(1,2,4-triazole) was confirmed by IR, 1H NMR spectroscopy, individuality – by thin-layer chromatography. The proposed mechanism for the hydrolysis of malonyldi(1,2,4-triazole) is described. The program PASS Professional 2007 predicted the most likely types of biological activity of the studied compounds. The most significant types of biological activity are anti-diabetic, anti-ulcer, anti-ischemic, anti-oxidant. The obtained data allow us to choose the optimal conditions for the synthesis of malonyldi(1,2,4-triazole) and to conclude that it is highly hydrolytically stable in an aqueous acetonitrile medium.

Molecular Docking Studies of Some Novel Fluoroquinolone Derivatives

An important parameter in the development of a new drug is the drug's affinity to the identified target (protein/enzyme). Predicting the ligand binding to the target (protein/enzyme) by molecular simulation would allow the synthesis to be restricted to the most promising compounds.A restricted hybrid HF-DFT calculation was performed in order to obtain the most stable conformer of each ligand and a series of DFT calculations using the B3LYP levels with 6-31G* basis set has been conducted. The docking studies of the quinolone compounds will be performed with the CLC Drug Discovery Workbench to identify and visualize the ligand-receptor interaction mode.