Spectroscopic investigations (FTIR,UV-VIS,NMR) and DFT calculations on the molecular structure of Nω-Nitro-L-arginine

The spectroscopic properties of N_ω-nitro-l-arginine were investigated by FT-IR, UV-VIS, and ¹H NMR spectra. Geometrical parameters and energies were calculated using the density functional theory (DFT) B3LYP method with the 6-311G basis set. Geometrical optimization of the molecule has been performed, vibrational spectra have been calculated, and fundamental vibrations have been determined from the total energy distribution (TED) of the vibrational modes. The HOMO-LUMO analysis is carried out for various electric fields (0.0–0.025 A^?1). The HOMO-LUMO gap is decreased while increasing the electric field. The calculated quantum chemical parameters are calculated and correlated to the inhibition efficiency, A Mullliken population was also important for determining local reactivity by indicating reactive centers and identifying potential nucleophilic and electrophilic attack sites. Charge transfer occurs inside the compound based on the HOMO LUMO gap. Calculations of DFT were evaluated in their ability to predict inhibition efficiency.     

Molecular docking studies,structural and spectroscopic properties of monomeric and dimeric species of benzofuran-carboxylic acids derivatives: DFT calculations and biological activities

Structural optimization, molecular docking analysis, electronic and vibrational properties have been investigated for the 1-benzofuran-2-carboxylic acid (2BF) and 1-benzofuran-3-carboxylic acid (3BF) using DFT/B3LYP/6-311++G(d,p) level of theory. The theoretical parameters have a very good consistency with the experimental ones. The weak intermolecular interactions were analyzed by different tool such as: Hirshfeld surfaces, topological analysis and natural bond orbital studies. The nonlinear optical properties have been investigated. Molecular electrostatic potential and frontier molecular orbitals (FMOs) analysis have been carried out to understand the reactivity of the molecule. In addition, TD-DFT calculation is initiated to simulate the UV–vis absorption spectrum and to determine several important electronic properties like HOMO-LUMO gap energy and electronic transitions. The complete vibrational assignments and the force constants were reported for monomer and dimers of both acids. The biological activities of the tow acids have been studied via molecular docking analysis. The later calculations prove that the studied acids have an inhibitor effect against cancer and microbial diseases.     

Size-expanded yDNA bases: an ab initio study

xDNA and yDNA are new classes of synthetic nucleic acids characterized by having base-pairs with one of the bases larger than the natural congeners. Here these larger bases are called x- and y-bases. We recently investigated and reported the structural and electronic properties of the x-bases (Fuentes-Cabrera et al. J. Phys. Chem. B 2005, 109, 21135-21139). Here we extend this study by investigating the structure and electronic properties of the y-bases. These studies are framed within our interest that xDNA and yDNA could function as nanowires, for they could have smaller HOMO-LUMO gaps than natural DNA. The limited amount of experimental structural data in these synthetic duplexes makes it necessary to first understand smaller models and, subsequently, to use that information to build larger models. In this paper, we report the results on the chemical and electronic structure of the y-bases. In particular, we predict that the y-bases have smaller HOMO-LUMO gaps than their natural congeners, which is an encouraging result for it indicates that yDNA could have a smaller HOMO-LUMO gap than natural DNA. Also, we predict that the y-bases are less planar than the natural ones. Particularly interesting are our results corresponding to yG. Our studies show that yG is unstable because it is less aromatic and has a Coulombic repulsion that involves the amino group, as compared with a more stable tautomer. However, yG has a very small HOMO-LUMO gap, the smallest of all the size-expanded bases we have considered. The results of this study provide useful information that may allow the synthesis of an yG-mimic that is stable and has a small HOMO-LUMO gap.     

Cyclic oligothiophenes: novel organic materials and models for polythiophene. A theoretical study

Cyclic oligothiophenes (CnT, n = 6-30, even only) in syn- and anti-conformations are studied theoretically at the B3LYP/6-31G(d) level of theory. Strain energies, ionization potentials, HOMO-LUMO gaps, bond length alternations, NICS values, and IR and Raman spectra have been studied. The properties of anti-conformers change systematically with increasing ring size and were studied in detail in neutral, radical cation, and dication forms. In syn-conformation, the oligomers lose their nearly planar ring shape and bend significantly for n > 14, and thus properties cannot be related to ring size. The HOMO-LUMO gap in C14T-syn is even lower than polythiopehene. IR and Raman spectra calculated at the B3LYP/6-31G(d) level are used to differentiate syn- from anti-conformations. The properties of cyclic oligomers are compared to those of the linear system, and cyclic oligothiophenes are revealed as good models for polythiophene. To assist the experimental study of known cyclic oligomers having dibutyl substituents on alternate thiophene rings, the corresponding dimethyl-substituted oligomers are also studied. The experimentally evaluated HOMO-LUMO gaps for alternately dibutyl-substituted cyclic oligomers match the calculated values; however, they are significantly higher than those of the unsubstituted analogues.     

Molecular docking,quantum chemical computational and vibrational studies on bicyclic heterocycle “6-nitro-2,3-dihydro-1,4-benzodioxine”: Anti-cancer agent

The heterocyclic aromatic compounds are primarily used to make pharmaceutical and agrochemicals. In addition, these compounds can be chosen as antioxidants, corrosion inhibitors, electro and opto-electronic devices, polymer material, dye stuff, developers, etc. On the account of this, the heterocyclic aromatic 6-nitro-2,3-dihydro-1,4-benzodioxine (6N3DB) was chosen and the structure is optimized to predict the important properties of it. The structural parameters such as bond length and bond angle have been obtained by DFT/B3LYP/6-311++G(d,p) basis set to know the geometry and orientation of 6N3DB. The molecule has been characterized by FT-IR and FT-Raman spectroscopic techniques to predict the functional groups, vibrational modes and aromatic nature of 6N3DB. The chemical shifts of ¹H and ¹³C have been obtained experimentally and compared with the theoretical data. The parameters such as the band gap between HOMO-LUMO orbitals, λ_max, and electron transition probability in frontier orbitals have been estimated to know the NLO and corrosion inhibition activity. HOMO-LUMO orbital diagram has been obtained for different energy levels and their band gap energies have been compared with UV–vis band gap values. The chemical significance of the molecule has been explained using ELF, LOL, and RDG. The binding energy and intermolecular energy values indicate that the title compound possesses anti-cancer property through hydrolase inhibition activity.     

Reduction of benzylidene dibenzo[a,d]cycloheptenes: over-reduction of antiaromatic dianions to aromatic tetraanions

The antiaromaticity of a series of dianions of p-substituted benzylidene dibenzo[a,d]cycloheptenes was examined through calculated measures of antiaromaticity. The nucleus-independent chemical shifts (NICS) and magnetic susceptibility exaltation both showed substantial antiaromatic character in the benzannulated tropylium anion. When the antiaromaticity was normalized for the area of the ring, these tropylium anions were shown to be among the most antiaromatic anions in the chemical literature. Attempts to make the dianion through reduction with lithium or potassium gave the tetraanion as the only species observable in the (1)H NMR spectrum. Quench of the reaction mixture with trimethylsilyl chloride or D(2)O confirmed the presence of the tetraanion, but only as a small portion of the reaction mixture, with the major product being unreacted starting material. The failure to observe starting material was attributed to similarities in the structures of the starting material and anion radical (first reduction), allowing rapid electron transfer between them. The inability to see the dianion (second reduction) could be the result of the very small HOMO-LUMO gap anticipated for highly antiaromatic species, which would allow access to diradical species. The magnitude of the HOMO-LUMO gap was determined by the difference between the HOMO and LUMO energies from geometry optimization and the lowest energy transition from TD-DFT calculations. The HOMO-LUMO gap for the benzylidene dibenzocycloheptatriene dianions was shown to be much smaller than the HOMO-LUMO gap of species for which (1)H NMR spectra had been observed.     

Compound-Specific Isotope Analysis of Amino Acid Labeling with Stable Isotope Nitrogen (15N) in Higher Plants

Individual free amino acid δ¹⁵N values in plant tissue reflect the metabolic pathways involved in their biosynthesis and catabolism and could thus aid understanding of environmental stress and anthropogenic effects on plant metabolism. In this study, compound-specific nitrogen isotope analysis of amino acid by gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS) was carried out to determine individual free amino acid δ¹⁵N values. High correlations were observed between the δ¹⁵N values obtained by GC-C-IRMS and elemental analyzer-isotope ratio mass spectrometry (EA-IRMS) determinations, and the mean precision measured was better than 1 ‰. Cation-exchange chromatography was employed to purify the sample, and the difference between prior to and following passage through the resin was within 1 ‰. The amino acid δ¹⁵N values of plant leave samples following incubation in ¹⁵N-nitrate at different time points were determined. A typical foliar free amino acid ¹⁵N-enrichment pattern was found, and glutamine was the most rapidly labeled amino acid; other amino acids derived from the GS-GOGAT cycle were also enriched. The pyruvate family amino acids were labeled less quickly followed by the aromatic amino acids. This study highlighted that amino acid metabolism pathways had a major effect on the δ¹⁵N values. With the known amino acid metabolism pathways and δ¹⁵N values determined by the presented method, the influence of various external factors on the metabolic cycling of amino acid can be understood well.

     

Potentiometric determination of the dissociation constants of L-histidine, proline and tryptophane in various hydroorganic media

The dissociation constant values of L-histidine, proline and tryptophane were determined at 25 +/- 0.1 degrees C by potentiometric pH titration in pure water and different hydroorganic solvent media. The organic solvents used were methanol, ethanol, N,N-dimethylformamide, dimethyl sulfoxide, acetone and dioxane. Initial estimates of the dissociation constant values of the different amino acids studied have been refined with ESAP2M computer program. It was observed that changing the medium permittivity as the solvent is enriched in methanol or ethanol has little influence on the pK*(a) values of the amino acids studied. The results obtained are discussed in terms of average macroscopic properties of the mixed solvents and the possible variation in microheterogeneity of the salvation shells around the solute.     

过渡金属-双硫分子配合物的理论研究

采用密度泛函方法, 对一系列过渡金属-双硫分子配合物的结构和相关性质进行了理论计算研究, 讨论了中心金属原子、配体等结构修饰对分子性质的影响. 计算结果表明, 过渡金属双硫分子配合物的HOMO和LUMO轨道主要由其配体轨道组成, 且其能隙很小; 中心金属原子和配体中一些基团的改变对分子配合物构型的影响很小, 而且HOMO-LUMO能隙变化不大. 配合物的氧化主要表现在配体部分, 氧化过程对调控HOMO-LUMO能隙具有十分重要的作用.     

Disiline-doped boron nitride nanotubes: A computational study

The properties of the electronic structure of the Disiline-doped boron nitride nanotubes (Disiline-BNNTs) are investigated by a density functional theory (DFT) calculation. The structural forms are firstly optimized and the CS tensors calculated. Subsequently, the chemical-shielding isotropic (CS^I) and chemical shielding anisotropic (CS^A) parameters are found. The shielding values of boron (B) and nitrogen (N) atoms were calculated by Gauge-Including Atomic Orbital (GIAO), Continuous Set of Gauge Transformations (CSGT) and Individual Gauges for Atoms in Molecules (IGAIM) methods, using B3LYP/6-311+G*. The B3LYP level of theory with IGAIM was the best method to evaluate the theoretical chemical shifts for studied models. The results reveal a significant effect of Disiline doping on the chemical shielding tensors at the sites of those ¹¹B and ¹⁵N nuclei located in the nearest neighborhood of the Disiline-doped ring. Furthermore, the values of dipole moments and HOMO-LUMO gaps change in the Disiline-doped models in comparison with the original pristine model.     

Computational design and characterization of new thieno-expanded tricyclic purine analogs

Unnatural nucleobases are under intense research due to their widespread applications in nucleic acids research. In this work, four new thieno-expanded purine analogs comprising ^ttzA, ^tthA, ^ttzG, and ^tthG were computationally designed based on the isomorphic tz- and th-bases. These base analogs can also be seen as modified derivatives of the previously reported tricyclic purine analogs (^ttA and ^ttG). The structural, electronic, and photophysical properties are studied by means of DFT and TDDFT calculations. We find out that these new bases can form stable Watson-Crick base pairs with natural counterparts, thus potentially mimicking natural nucleobases in DNA/RNA duplexes. Calculations reveal that these bases have smaller AIPs and HOMO-LUMO gaps than natural ones, suggesting that they are candidates for applications in nanowire technology. Particularly, the photophysical properties were explored, and the results are compared with those for tz-, th-, and tt-bases. The nature of the low-lying excited states is discussed, and analyses reveal that the thiophene-homologation would not change excitation maxima of ^thA and ^tzA, while it will result in large red-shifts of those of ^thG and ^tzG. Meanwhile, thiophene insertion has relatively larger influences on the emissions ^thA and ^tzG, for which the fluorescence was 37 nm blue-shifted and 19 nm red-shifted, respectively. Taking these new bases as derivatives of ^ttA and ^ttG, it was found that the modifications would result in large red-shifts of both the excitation maxima and the fluorescence. The effects of water solution and base paring on the phtotophysical properties were also considered.     

Effect of pH on the reactivity of dipeptides and α-amino acids in the N-acylation

The reaction kinetics of Gly, L-??-Ala, Gly-Gly, L-??-Ala-L-??-Ala and ??-Ala-??-Ala with picryl benzoate in water (40 wt %)-2-propanol was investigated. At pH = 4?C8 the rate constants of N-acylation of the anionic form of dipeptides are less than those of the corresponding amino acid anions, in agreement with their basicity, whereas the relative effective rate constants of reactions depend on pH: in acidic, neutral and slightly alkaline media the k _ef values are higher for the dipeptides, and in a strongly alkaline medium, for the amino acids. These differences are due to the changes in the concentrations of reactive forms of amino acids and dipeptides in the system at varying the medium pH.     

Structural and electronic properties of a Benzoin monomer

In the present work, we report structural and electronic properties of a benzoin monomer named as 2-oxo-1,2-diphenylethyl-2-bromopropanoate (C₁₇H₁₄BrO₃). The previously synthesized compound is characterized by single crystal X-ray diffraction. The optimized molecular geometry (bond lengths, and bond angles), HOMO-LUMO analysis and molecular electrostatic potential (MEP) are calculated by density functional theory (DFT) and Hartree-Fock (HF) methods with 6-311G(d) basis set in the neutral ground state and using DFT methods for singly oxidized doublet, singly reduced doublet, and neutral triplet state for the benzoin compound. The X-ray structure determination of the compound is compatible with the geometric parameters calculated at B3LYP/6-311G(d). In the triplet state the HOMO-LUMO energy gap of 2.39?eV which indicates semi-conductor property is recommended for the photovoltaic devices.     

A laser flash photolysis study of amino acids and dipeptides using 4-nitroquinoline 1-oxide as a photosensitizer: The pH dependence

The pH effects on the photochemical reaction of amino acids and related dipeptides with 4-nitroquinoline 1-oxide (4NQO) as a photosensitizer have been investigated by laser flash photolysis. The obtained kinetic parameters show that the electron transfer from Tryptophan (Trp), Tyrosine (Tyr) as well as dipeptides containing Trp and/or Tyr residue to triplet 4NQO (^T4NQO) are efficient, but inefficient from methionine (Met) and dipeptides containing neither Trp nor Tyr. The result was supported by the calculated values of the free energy change from measured oxidation potentials for the electron transfer. It was demonstrated that Trp and Tyr residues are initial reaction sites with ^T4NQO, while Tyr/O^? radical may be final species for Trp-Tyr dipeptide. In acidic aqueous solutions, the self-quenching rate constants of ^T4NQO and the rate constants of electron transfer from amino acids to ^T4NQO decrease with decreasing pH. In alkaline solutions, amino acids are easily oxidized by 4NQO under irradiation of laser pulse, and no transient absorption signal was observed.     

Synthesis,spectrophotometric, voltammetric,and density functional theory studies of tetrahydro[3,2-b]indolocarbazoles for sensing small molecules

Absorption spectra of tetrahydro[3,2-b]indolocarbazoles (THICZs) with respective molecular property and alkyl substituents have been prerecorded in diverse solvents in the scope between 200 and 600 nm for very fewer times in the literary study. The photo-physical behavior of liquified THICZs belonging to the existence surroundings. The solvatochromic behaviors of THICZs and solvent substance physical phenomenon can be analyzed by implementation of linear solvating energy state conception. Compound 4 shows excellent properties for sensing small molecules. The electrochemical behavior of some THICZs was investigated at carbon paste electrode where two electrode reactions were involved, irreversible oxidation-one electron transfer and quasi-reversible redox reactions forming phenolic followed by quinolone moiety electro active species. The density functional theory which means calculated molecular orbital energies (B3LYP/6-31G) and HOMO-LUMO gap/space for some presented indolocarbazoles have been performed.     

Complex Formation Reactions of Divinyltin(IV) Complexes with Amino Acids,Peptides, Dicarboxylic acids and Related Compounds

Complex formation equilibria of divinyltin(IV) with amino acids, peptides, and dicarboxylic acids have been investigated. Stoichiometry and stability constants for the complexes formed were determined at 25°C and ionic strength 0.1 M NaNO₃. The results showed the formation of ML, MLH, and ML₂ (organotin : ligand : hydrogen) complexes with amino acids. Peptides form ML complexes and the corresponding deprotonated amide species MLH_?1. In the latter species the binding with divinyltin(IV) occurs through the terminal amino group, carboxylate oxygen, and the amide nitrogen atoms (CO^? ₂, N^? _amide, NH₂). The results showed the formation of ML and ML₂ complexes with dicarboxylic acids. The concentration distribution of the complexes in solution was evaluated. The bonding sites of the divinyltin(IV) complex in solid state with oxalic acid was investigated by means of elemental analyses, FTIR, and mass spectra. Non-isothermal decomposition of the above complex has been studied and the result was statistically analyzed. The main steps were identified for the thermal decomposition reaction and each step proved to be a first order reaction. The kinetic parameters E _a and A were calculated for each step in the reaction. The thermodynamic functions H, G, and S* were calculated for each step of the reaction.     

Effect of acids and bases on the solubility of amino acids

The effect of acids and bases on the solubility of amino acids at 298.2 K, within the pH range, (pH from 2 to 10) and out of the pH range, was determined. The amino acids considered were glycine, dl-alanine, dl-valine and dl-serine. The acids used were HCl and HNO₃ and the bases NaOH and KOH. It was observed that in the pH range (pH from 2 to 10) there is no significant difference in the solubility of dl-alanine in the presence of different ions such as Na⁺ or K⁺ at high pH, and Cl⁻ or NO₃⁻ at low pH values. However, at higher concentrations of the acids or the bases, there is an effect of the counterions in solubilities. For all the amino acids considered here the solubility was higher in nitric acid, as compared to hydrochloric acid, and higher in potassium hydroxide than in sodium hydroxide.     

Vibrational energies,bonding nature,electronic properties,spectroscopic investigations and analysis of 3-bromo-4-Chlorobenzophenone

In this present study, we investigated pharmaceutically active of 3-Bromo-4-chlorobenzophenone. Structural, electronic properties (HOMO-LUMO, MEP) are investigated using DFT tool. Vibrational spectral analysis for FT-IR and FT-Raman are made of headline molecule. Electronic transition properties are discussed with the help of UV–Vis spectral analysis. Biologically active sites are found from MEP analysis. Electron delocalization properties are studied explored from HOMO-LUMO band gap energy. Moreover, intra molecular interactions are explained from NBO method. Molecular docking studies are performed to find the interactions various pathologies. The topological properties of the electron density have been analyzed.     

Kinetic Screening for the Acid‐Catalyzed Hydrolysis of Some Hydrophobic Fe(II) Schiff Base Amino Acid Chelates and Reactivity Trends in the Presence of Alkali Halide and Surfactant

Kinetics of acid‐catalyzed hydrolysis of some high‐spin Fe(II) Schiff base amino acid complexes were followed spectrophotometrically at 298 K under pseudo–first‐order conditions. The studied ligands were derived from the condensation of 5‐bromosalicylaldehyde with different four amino acids (phenylalanine, aspartic acid, histidine, and arginine). The acid hydrolysis reaction was studied in aqueous media and in the presence of different concentrations of the alkali halide (KBr) and cationic surfactant (cetyl‐trimethyl ammonium bromide, CTAB). The general rate equation was suggested to be rate = k_obs[complex], where k_obs = k₂[H⁺]. The increase in [KBr] enhances the reactivity of the reaction, and the addition of CTAB to the reaction mixture accelerates the reaction reactivity. The obtained kinetic data were used to determine the values of δ_mΔG^# (the change in the activation barrier) for the studied complexes when transferred from “water to water containing different [KBr]” and from “water to water containing altered [CTAB].”     

Investigation of ion-pairing phenomenon in BaF2 aqueous solution: Experimental and theoretical studies

The ion-pair association constant values, related to the reaction Ba²⁺ + F⁻ ? [BaF]⁺, are determined by means of NMR spectroscopy. The values for thermodynamic functions of the ion-pairing process are calculated on the basis of the NMR results. In addition, the association entropy has been found to be dependent on temperature. Comparing the experimental data and Fuoss theory, it is found that [BaF]⁺ contact ion-pair is formed in the BaF₂ aqueous solution. Also, hydration of barium-fluoride ion-pair is investigated by the DFT method. The hydration number of barium-fluoride ion-pair is determined by comparing the experimental and theoretical results. The effect of number of water molecules on the properties of ion-pairs is investigated by determining NQR and NMR parameters. Also, the relation between the chemical shifts and the energy gap between the highest occupied molecular orbital (HOMO) and low-lying virtual molecular orbital (LUMO) is investigated.