Setting up the HyDRA blind challenge for the microhydration of organic molecules

The procedure leading to the first HyDRA blind challenge for the prediction of water donor stretching vibrations in monohydrates of organic molecules is described. A training set of 10 monohydrates with experimentally known and published water donor vibrations is presented and a test set of 10 monohydrates with unknown or unpublished water donor vibrational wavenumbers is described together with relevant background literature. The rules for data submissions from computational chemistry groups are outlined and the planned publication procedure after the end of the blind challenge is discussed.

Vibrational Frequencies of Dichlorine Monoxide: A Mathematical Model

Determinedstretching vibrational frequencies of a triatomic molecule, i.e..Dichlorine Monoxide (Cl2O) upto third overtone by Lie algebraic method.Fundamental vibrational wavenumbers calculated by Lie algebraic model are compared with available experimental values.

Formation of C4H4 from photolysis of icy C2H2 with 175 nm at 60 K

ABSTRACT The absorption spectrum of solid acetylene (C2H2) at 10 K was measured in wavelength range 107–250 nm with UV light from a synchrotron source. Based on the absorption spectrum, we irradiated at 175 nm the icy acetylene at 60 K; the results yielded a new set of IR absorption lines with similar temporal profiles of production during the photolysis periods. From icy 12C2H2, these new features were recorded at 3276.8, 1598.7, 963.0, 936.3, and 671.3 cm−1, which are assigned to modes ν1, ν6, ν14, ν15, and ν11 (mixing with ν17), respectively, of vinylacetylene (C4H4) based on the results of 13C- and D-isotopic experiments and quantum-chemical calculations. These calculations using density-functional theory (B3LYP/6–311++G**) predict vibrational wavenumbers and IR intensities of vinylacetylene that agree satisfactorily with our experimental results. This work enhances our understanding of the photochemistry of icy acetylene in cold astronomical environments; for instance, the present result can be applied directly to the photochemical processes on Titan's surface.

Theoretical Study on Molecular Structure and Electronic Properties of New 1,3-Diaza-adamantan-6-ones Derivatives

In this study, the structural geometry and vibrational frequencies (IR) of 1,3-Diaza-adamantane-6-ones derivatives including Adamantane (A), 1,3-Diaza-adamantan (D), 1,3-Diaza-adamantan-6-one (DO), 5-Benzyl-1,3-diaza-adamantan-6-one (BD), 5-(4-Hydroxybenzyl)-1,3-diaza-adamantan-6-one (HBD), 5-(4-Methoxybenzyl)-1,3-diaza-adamantan-6-one (MBD), and 5-(4-Hydroxy-3-methoxybenzyl)-1,3-diaza-adamantan-6-one (HMBD) were theoretically studied. In addition, molecular orbital energies, including the highest occupied molecular orbitals (HOMOs), and lowest unoccupied molecular orbitals (LUMOs), and electronic properties of the titled molecules were theoretically studied using the computational method. Optimized molecular structures were obtained by DFT method with the hybrid B3LYP functional at a relatively small basis set of 6-31G. The calculated vibrational wavenumbers were obtained using the same level of the theory mentioned above. The contributions to the molecular orbitals of adamantane and substituted-phenyl groups in the title compounds were determined. Moving from A to HMBD, a decrease in the value of LUMO and total energy are noticed, while an increase in the value of HOMO is noted. These findings are supported by the decreasing in the EHOMO-LUMO gap values. Furthermore, a decrease in the value of ionization potential (IP) is obtained, while an increase in the electronegativity (EA) is observed.

Computational Design, Spectral, NBO, DOS, Bioactivity Evaluation, ADMET Analysis, Third-Order non-linear Optical and Quantum Chemical Investigations on Hydrogen Bonded Novel Organic Molecular Complex of 4-[Bis[2-(acetyloxy)ethyl]amino]benzaldehyde (4B2AEAB) Derivatives for Opto-Electronic Applications

In this paper, the authors reported a theoretical investigation on molecular structure, geometry optimization, global and local chemical reactivity descriptors calculations, NBO study, DOS, non-linear optical behaviour and vibrational wavenumbers of the novel 4-[bis[2- (acetyloxy)ethyl]amino]benzaldehyde (4B2AEAB) were carried out by DFT (B3LYP and B3PW91) methods with 6-31+G (d, p) basis set in water solvent. The calculated vibrational wavenumbers are found to be in good agreement with experimental FT-IR spectra and PED analysis using GaussView 5.0 and VEDA 4 program. The UV-Vis absorption spectrum of 4B2AEAB was calculated by using TD-DFT/B3LYP/6-31+G(d,p) in gas phase, water, CHCl3, DMSO and CH2Cl2 solvents using CPCM model and λmax in range of 354.16, 341.35, 343.74, 342.18 and 342.64 nm, respectively. The density of state (DOS spectrum) of the compound in term of HOMOs and LUMOs and MESP were calculated and analyzed. The temperature effects on the thermodynamic properties are also discussed. The calculated 1H NMR and 13C NMR chemical shift using GIAO method and solvent effect are investigated by B3LYP/6-31+G(d,p) in gas phase, chloroform, water, DMSO and CH2Cl2 solvents and correlate with experimental chemical shifts. The dipole moment, polarizability and the first static hyperpolarizability values show that the 4B2AEAB molecule is active non-linear optical (NLO) material. The nucleophilic and electrophilic reactive sites in the 4B2AEAB and its derivatives were analyzed by Fukui function analysis using Mulliken charge. The charge transfer, conjugative interactions and delocalization of electron density are analyzed by natural bond orbital (NBO) analysis. The biological properties and ADMET study of 4B2AEAB and its derivatives are also discussed.

Computational, Experimental Structural Characterization and Molecular Docking Studies of 5,7-Dihydroxy-4-methoxyflavone against Cytochrome P450 Enzymes

In this work, the geometry optimization and harmonic vibrational wavenumbers of kaempferide (5,7-dihydroxy-4-methoxyflavone) were computed by density functional theory (DFT) method. Theoretically computed vibrational wavenumbers were compared with experimental values and the interpretation of the vibrational spectra has been studied. Frontier molecular orbitals (FMO) and molecular electrostatic potential (MEP) analysis of the title compound have been carried out. The 1H & 13C NMR, UV visible and electronic properties of the compound were investigated theoretically and compared with the experimental values. Molecular docking study of the compound against cytochrome P450 family enzymes (CYPs 1A1, 1A2, 3A4, 2C8, 2C9 and 2D6) were also studied and the results revealed that the title compound interact with human CYP2C8 enzymes with minimum binding energy of -9.43 kcal/mol. The compound forms hydrogen bond with the residues of Thr302, Thr305, Leu361, Val362, Cys435, Gln356 and Ala297. Thus, these studies assist to understand the inhibitory mechanism of kaempferide with CYP450 enzymes and may facilitate significant clinical implications in the prevention and treatment of various therapeutic diseases.

Design and Synthesis of the Candesartan Key Intermediate

This paper presents experimental data regarding the synthesis and structural characterization by: 1H-NMR, 13C-NMR, IR spectral analysis, melting point and thin layer chromatography of the candesartan key intermediate: methyl 2-[(tert-butoxycarbonyl)amino]-3-nitrobenzoate. In addition, a computational study of predicted molecular parameters, vibrational wavenumbers, frontier molecular orbitals energy diagram, molecular electrostatic potential map and other electronic distributions maps using restricted hybrid HF-DFT SCF calculation has been performed for obtaining the most stable conformer. For the most Stable conformer has been made a series of DFT calculations using the B3LYP levels using the 6-31G * basis set.

New bis 1,3,4-oxadiazole derivatives: syntheses, characterizations, computational studies, and antioxidant activities

In this study, two new bis oxadiazole derivatives (2a and 2b) were synthesized. The new compounds were characterized by elemental analyses, IR, 1H NMR, 13C NMR, and mass spectral studies and were tested for their antioxidant activity. According to the results, it was observed that the synthesized compounds (2a and 2b) had a very high activity in both 2,2-diphenyl-1-picrylhydrazyl (DPPH) and ferric reducing ability of plasma (FRAP) tests. The approximate geometries of the compounds 2a and 2b were prepared with GaussView5 visualization program. The optimized molecular geometric parameters, vibrational wavenumbers, UV–vis parameters, and HOMO–LUMO simulations were computed using Gaussian 09W program. The computations were performed at 6-311++G(d,p) basis set using the B3LYP functional in density functional theory (DFT) method. The harmonic vibrational wavenumbers computed in gas phase were scaled with 0.958 (1700–4000 cm−1) and 0.983 (0–1700 cm−1) for the B3LYP/6-311++G(d,p) level. To calculated the UV–vis spectroscopic parameters with TD-DFT method, the compounds 2a and 2b were optimized in DMF and DMSO solvents using the integral equation formalism polarizable continuum model (IEFPCM) method at the B3LYP/6-311++G(d,p) level. The HOMO, LUMO, and UV–vis analyses were studied to interpret intramolecular charge transfers.

DFT computations on vibrational spectra: Scaling procedures to improve the wavenumbers

The performance of ab initio and density functional theory (DFT) methods in calculating the vibrational wavenumbers in the isolated state was analyzed. To correct the calculated values, several scaling procedures were described in detail. The two linear scaling equation (TLSE) procedure leads to the lowest error and it is recommended for scaling. A comprehensive compendium of the main scale factors and scaling equations available to date for a good accurate prediction of the wavenumbers was also shown. Examples of each case were presented, with special attention to the benzene and uracil molecules and to some of their derivatives. Several DFT methods and basis sets were used. After scaling, the X3LYP/DFT method leads to the lowest error in these molecules. The B3LYP method appears closely in accuracy, and it is also recommended to be used. The accuracy of the results in the solid state was shown and several additional corrections are presented.