Combined study of vibrational spectra of α-carboline by theoretical and experimental IR methods

This paper reports the application of a scaled ab initio density-functional theory (DFT) at B3LYP/ccpvtz level to calculate the vibrational spectrum of α-carboline (9H-pyrido[2,3-b]indole), αCB, as well as the comparison of theoretical results with the experimental spectra. They have been recorded in Cl₃CD solution and in solid KBr pellets in the 4000-700 cm⁻¹ range. To test the adequacy of the computational method to reproduce the experimental vibrational spectra of αCB, this computational method has also been applied to the related and simpler molecules indole, Ind, and α-azaindole, αAInd. Previously reported assignments for the last compounds have been taken as reference for the subsequent assignments of the αCB vibrational bands. The results show that the hydrogen bonding interactions mainly affect the high frequency region while the skeletal vibration region keeps rather unchanged with the physical state of the sample. Moreover, apart from the vibrations involving the whole carboline nucleus, most of the experimental bands retain their original Ind and/or αAInd frequencies, thus allowing an easy assignment of the computed modes to the αCB vibrational bands.     

Crystal and molecular structure of N-(4-nitrophenyl)-β-alanine--its vibrational spectra and theoretical calculations

The N-(4-nitrophenyl)-β-alanine in crystalline form directly by the addition of 4-nitroaniline to the acrylic acid in aqueous solution has been obtained. The title β-alanine derivative crystallizes in the P2(1)/c space group of monoclinic system with four molecules per unit cell. The X-ray geometry of β-alanine derivative molecule has been compared with those obtained by molecular orbital calculations corresponding to the gas phase. In the crystal the molecules related by an inversion center interact via symmetrically equivalent O-H···O hydrogen bonds with O···O distance of 2.656(2) ? forming a dimeric structure. The dimers of β-alanine derivative weakly interact via N-H···O hydrogen bonds between the H atom of β-amine groups and one of O atom of nitro groups. The room temperature powder vibrational (infrared and Raman) measurements are in accordance with the X-ray analysis. In aqueous solution of 4-nitroaniline and acrylic acid, the double CC bond of vinyl group of acrylic acid breaks as result of 4-nitroaniline addition.     

Experimental and theoretical thermochemistry of β-tetralone

The standard (p^° = 0.1 MPa) molar enthalpy of formation β-tetralone was measured, at T = 298.15 K, by static bomb calorimetry and the standard molar enthalpy of vaporization, at T = 298.15 K, was obtained using Calvet microcalorimetry.These values were used to derive the standard molar enthalpy of formation of the compound in the gaseous phase, at T = 298.15 K, ?(75.2 ± 2.5) kJ · mol^?1.Additionally, high-level density functional theory calculations using the B3LYP hybrid exchange-correlation energy function with extended basis sets and more accurate correlated computational techniques of the MCCM/3 suite have been performed.     

Complexes of α-, β-, and γ-cyclodextrins with nitrophenols: A theoretical study of the structure and energy

Detailed quantum mechanical calculations of the interaction of cyclodextrin (α-, β-, and γ-CD) with 4-nitrophenol (I), 4-nitro-2,6-dimethylphenol (II), 4-nitro-3,5-dimethylphenol (III), and their anions (IVVI) with the formation of intercalation complexes are carried out for the first time. The calculations of the compounds are performed within the density functional theory by the hybrid Becke–Lee–Yang–Parr (B3LYP) method with LanL2DZ basis sets. For the α-CD+III and α-CD+VI complexes it is shown that a nitrophenol molecule of III and a nitrophenolate anion of VI are not contained in the α-CD torus, which agrees with the experimental equilibrium constants. It is found that the calculated equilibrium constants of the formation of guest–host complexes with phenolate anions are much larger than those of neutral molecules. The most stable CD complexes with nitrophenols and their anions should be expected for γ-CD. The β-CD complexes when the guest enters into the host cavity are formed only with compounds I, V, and VI.     

Experimental and theoretical study of S-benzyl β-N-(-2-methyl-3-phenylallylidene)dithiocarbazate as anti-bacterial agent

Research on Chemical Intermediates - The NS based S-benzyl β-(N-2-methyl-3-phenylallylidene)dithiocarbazate (L) Schiff base was synthesized by 1:1 condensation method between S-benzyl...     

A comparative study of the structure and properties of β-galactosidases

A comparative study of β-galactosidase amino acid sequences of E. coli and another four out of 11 microorganisms selected at the first stage was performed. It was shown that the functional amino acid residues in the catalytic domain and the ligand environment of the magnesium cation for all five sequences are identical. The mechanism of the catalytic action of E. coli and K. lactis β-galactosidases was investigated by the method of nucleophilic competition. It was shown that the mechanism of the effects of nucleophilic agents is kinetically identical both enzymes: the presence of methanol or butanediols affects the stage of degalactosylation; the presence of magnesium cations promotes the activity of both β-galactosidases; and the mechanisms of the thermal inactivation of E. coli and K. lactis β-galactosidases are different.     

The vibrational spectra and structure of diiminosuccinonitrile and N,N′-dichlorodiiminosuccinonitrile

The i.r. spectra of diiminosuccinonitrile and N,N′-dichlorodiiminosuccinonitrile were recorded as Nujol mulls, as pellets in KBr and polyethylene matrices and as solutions in CH₃CN in the region 4000-30 cm⁻¹. Raman spectra of the pure solids were obtained and polarization data were recorded from saturated solutions in CH₃CN.The mutual exclusion of i.r. and Raman lines revealed that both compounds existed in the trans conformation and no additional conformers (gauche or cis) were detected in solution.The fundamental frequencies for both molecules were assigned on basis of i.r. and Raman activities, Raman polarization data and the results of normal coordinate analyses.     

A theoretical study on the molecular structure and vibrational (FT-IR and Raman) spectra of a new organic–inorganic compound of 2[N(C3H7)4]SbCl4

The salt bis-tetrapropylammonium tetrachloroantimonate (III) is crystallized in the monoclinic system with the P2₁/c space group. The unit cell dimensions are: a = 18.1973(5) Å, b = 15.7225(4) Å, c = 13.6491(3) Å, β = 91.65(1)° and Z = 4. The vibrational spectra have been measured at room temperature by FT-infrared spectroscopy (4000–400 cm⁻¹) on polycrystalline samples, and by FT-Raman spectroscopy (3500–30 cm⁻¹) on monocrystals. The structure of the 2[N(C₃H₇)₄]SbCl₄ formed by two types of cations (C₃H₇)₄N⁺ and two types of anions [SbCl₄]⁻ was optimized by density functional theory (DFT) using the B3LYP method. Actually the values obtained by the B3LYP/LanL2MB basis with the aid of a calculation of the potential energy distribution (PED) are in good agreement with the experimental data. A root mean square (rms) difference value was calculated and the small differences between experimental and calculated modes have been interpreted by intermolecular interactions with-in the crystal. A comparison between the results of the 2[N(C₃H₇)₄]SbCl₄ compound and the simulated compounds based on the (CH₃)₄N⁺) and (C₂H₅)₄N⁺ fragments, shows an increase in the wavenumber of the bands assigned to the stretching vibration of the (NC) group for the 2[N(C₃H₇)₄]SbCl₄ compound. The comparison between the [N(C₃H₇)₄]Cl ligand and the 2[N(C₃H₇)₄]SbCl₄ compound of the infrared and Raman spectrum shows an increase in the wavenumber for the bands assigned to the stretching vibration of (CH₃) and the bending vibration of (NC₄) groups in the 2[N(C₃H₇)₄]SbCl₄ compound.     

Quantum-chemical modeling of the effect of microhydration and media on the vibrational spectra of 2-(2′-pyridyl)-benzimidazole and its 1-methylsubstituted analogue

Quantum-chemical calculations of the optimized structures, harmonic force fields, and frequencies of 1 : 1 and 1 : 2 complexes of 2-(2′-pyridyl)-benzimidazole and 1-methyl-2-pyridine-2-yl-1H-benzimidazole are performed by means of DFT (B3LYP/6-31+G**). The shifts in the frequencies of the vibrational spectra of the investigated complexes are considered with allowance for the conformational structure and effect of the medium. Analytical bands (spectral marks) are proposed that can be used to identify complexes of 2-(2′-pyridyl)-benzimidazole and 1-methyl-2-pyridine-2-yl-1H-benzimidazole with water. It is concluded that considering the environment within a model of a polarized continuum allows the forecasting of possible shifts in the frequencies in the vibrational spectra of the studied compounds in aqueous media and DMF.     

Some anomalies in the vibrational spectra of α, β-unsaturated ketones

Summary Some anomalies in the intensities of the bands of the C=C and C=O bonds in the vibrational spectra of , -unsaturated ketones have been explained by a difference in the sequence of the frequencies of the in-phase (_s) and out-of-phase (_as) vibrations of the multiple bonds in their cis (_s<_as) and trans (_s>_as) arrangements.     

Role of hydration in determining the structure and vibrational spectra of L-alanine and N-acetyl L-alanine N′-methylamide in aqueous solution: a combined theoretical and experimental approach

In this work we have utilized recent density functional theory Born-Oppenheimer molecular dynamics simulations to determine the first principles locations of the water molecules in the first solvation shell which are responsible for stabilizing the zwitterionic structure of L-alanine. Previous works have used chemical intuition or classical molecular dynamics simulations to position the water molecules. In addition, a complete shell of water molecules was not previously used, only the water molecules which were thought to be strongly interacting (H-bonded) with the zwitterionic species. In a previous work by Tajkhorshid et al. (J Phys Chem B 102:5899) the L-alanine zwitterion was stabilized by 4 water molecules, and a subsequent work by Frimand et al. (Chem Phys 255:165) the number was increased to 9 water molecules. Here we found that 20 water molecules are necessary to fully encapsulate the zwitterionic species when the molecule is embedded within a droplet of water, while 11 water molecules are necessary to encapsulate the polar region with the methyl group exposed to the surface, where it migrates during the MD simulation. Here we present our vibrational absorption, vibrational circular dichroism and Raman and Raman optical activity simulations, which we compare to the previous simulations and experimental results. In addition, we report new VA, VCD, Raman and ROA measurements for L-alanine in aqueous solution with the latest commercially available FTIR VA/VCD instrument (Biotools, Jupiter, FL, USA) and Raman/ROA instrument (Biotools). The signal to noise of the spectra of L-alanine measured with these new instruments is significantly better than the previously reported spectra. Finally we reinvestigate the causes for the stability of the P_π structure of the alanine dipeptide, also called N-acetyl-L-alanine N′-methylamide, in aqueous solution. Previously we utilized the B3LYP/6-31G* + Onsager continuum level of theory to investigate the stability of the NALANMA4WC Han et al. (J Phys Chem B 102:2587) Here we use the B3PW91 and B3LYP hybrid exchange correlation functionals, the aug-cc-pVDZ basis set and the PCM and CPCM (COSMO) continuum solvent models, in addition to the Onsager and no continuum solvent model. Here by the comparison of the VA, VCD, Raman and ROA spectra we can confirm the stability of the NALANMA4WC due to the strong hydrogen bonding between the four water molecules and the peptide polar groups. Hence we advocate the use of explicit water molecules and continuum solvent treatment for all future spectral simulations of amino acids, peptides and proteins in aqueous solution, as even the structure (conformer) present cannot always be found without this level of theory. Festschift in Honor of Philip J. Stephens’ 65th Birthday. During the proof stage of this article a very relevant article has been published by M. Losada and Y. Xu titled “Chirality transfer through hydrogen-bonding: Experimental and ab initio analyses of vibrational circular dichroism spectra of methyl lactate in water” in Phys Chem Chem Phys 2007, 9: 3127–3135. In that work they confirm that the effects of water are seen in the VCD spectra and hence it is fundamental to include explicit water molecules in modeling studies of the vibrational spectra of biomolecules in aqueous solution.     

Experimental and theoretical study of the dissociation enthalpy of the N–O bond on 2-hydroxypyridine N-oxide: theoretical analysis of the energetics of the N–O bond for hydroxypyrydine N-oxide isomers

The standard (p^∘=0.1 MPa) molar enthalpy of formation of crystalline 2-hydroxypyridine N-oxide was measured, at T=298.15 K, by static bomb calorimetry and the standard molar enthalpy of sublimation, at T=298.15 K, was obtained using Calvet microcalorimetry. These values were used to derive the standard molar enthalpy of formation of 2-hydroxypyridine N-oxide in gaseous phase, and to evaluate the dissociation enthalpy of the N–O bond. Additionally, high-level density functional theory calculations using the B3LYP hybrid exchange-correlation energy functional have been performed for the three isomers of hydroxypyridine N-oxide in order to confirm the experimental trend for the dissociation enthalpy of the (N–O) bond.     

Experimental and theoretical study of N-hexylcytosine and N-hexylcytosinium nitrate: the crucial role of hydrophobic and anion–π interactions

We report the synthesis and X-ray characterization of N¹-hexylcytosine (1) and N¹-hexylcytosinium nitrate (2). N¹-hexylcytosine (1) does not follow the same behaviour previously described for N¹-hexylthymine and N¹-hexyluracil in the solid state. This different behavior has been analyzed by means of density functional theory (DFT) calculations including the latest available correction for dispersion (D3). In addition hydrophobic and anion–π noncovalent interactions play a key role in stabilizing the 3D architectures of the compounds, which have been energetically studied using theoretical calculations and compared with similar structures retrieved from the Cambridge Structural Database (CSD). The anion–π–anion binding mode observed for nitrate in compound 2 is also observed in several crystal structures involving cytosine ring coordinated to transition metals.     

Influence of conjugated nitrogenous bases on the spectra and structure of mixed-ligand nickel(II) chelates containing β-diones

The infrared and electronic excitation spectra of a series of new nickel(II) chelates containing an-diimine (or nitrogenous base, enR) and the anion of a-dione (1,3-ketoenol or 1,3-ketoester,H) were obtained in the solid state and in solution. The composition and the overall structure of the new chelates in the solid state depends on ligand concentration, the substituents within the-dionato moiety and the counterion present. The IR and electronic excitation spectra of [Ni(enR)₂ ]NO₃ and [Ni(enR)(O₂NO)] indicate, in conjunction with other physicochemical measurements, bidentate coordination of the ligands, while the spectral shifts reveal replacement of the (O,O)nitrato group by basic solvents. The existence of the nickel(II) in an octahedral environment is confirmed by an X-ray structure analysis of [Ni(dpamH)₂acac]NO₃ · CH₃OH (monoclinic, space groupP2_l/n, a=17.296(1),b=7.462(1),c=21.604(3) å,=95.65(1),Z=4, R=0.0534,Rw=0.0600), where dpamH denotes the 2,2-dipyridylamine.     

The effects of substituents and solvents on the ground-state π-electronic structure and electronic absorption spectra of a series of model merocyanine dyes and their theoretical interpretation

Two series of new merocyanine dyes have been synthesised and the dependence of their electronic structure on substituents and solvents has been studied by NMR spectroscopy, by using both the NMR (13)C chemical shifts between adjacent C atoms in the polymethine chain and the (3)J(H,H) coupling constants for trans-vicinal protons. The widely used valence bond (VB) model based on two contributing structures cannot account theoretically for the observed alternating π-electron density in the polymethine chain. In addition, the prediction of zero-π-bond order alternation (or zero-bond length alternation) by this model is also incorrect. However, the results are consistent with the predictions of a qualitative VB model which considers the resonance of a positive charge throughout the whole polymethine chain. Based on this model and the Franck-Condon principle the effect of substituents and solvents on the fine structure of the electronic spectra of these dyes can be explained as vibronic transitions from the vibrational state v = 0 to v', where v is the vibrational quantum number of the totally symmetric C=C valence vibration of the polymethine chain in the electronic ground state and v' is that in the electronic excited state. In contrast, neither the effects of substituents or solvents on the electronic structure of merocyanines and their electronic spectra can be accounted for by the simple two state VB model.     

The spectra and structure of sulphur-containing organic compounds—V. The vibrational spectra and conformations of p-RC6H4SO2CH2X sulphones

The i.r. and Raman spectra of p-RC₆H₄SO₂CH₂X (R = H, CH₃, Cl, Br; X = Cl, Br) sulphone liquid solutions and crystals have been investigated. The existence of a mixture of trans and gauche conformations in liquid and solution phases has been established. The temperature dependences of the i.r. spectra have been studied and the values of ΔH = H (gauche) - H(trans) determined. The molecular conformations in the crystal have been determined by the dichroism of polarized i.r. spectral bands. In the case of CH₃C₆H₄SO₂CH₂Br polymorphic crystal modifications, differing in molecular conformations, have been found. An interpretation of the vibrational spectra is given. See Part IV, A. B. REMizov, F. S. BILALOV and 1. S. POMINOV, Spectrochim Acta, in press.     

Experimental and theoretical study of the charge transport property of 4,4′-N,N′-dicarbazole-biphenyl

The hole and electron mobilities of the amorphous films of the organic semiconductor 4,4′-N,N′-dicarbazole-biphenyl (CBP) at different electric fields were measured through the time of flight (TOF) method. Based on its crystalline structure, the hole and electron mobilities of CBP were calculated. A detailed comparison between experimental and theoretical results is necessary for further understanding its charge transport properties. In order to do this, charge mobilities at zero electric field, μ(0), were deduced from experimental data as a link between experimental and theoretical data. It was found that the electron transport of CBP is less affected by traps compared with its hole transport. This unusual phenomenon can be understood through the distributions of frontier molecular orbitals. We showed that designing materials with frontier molecular orbitals localized at the center of the molecule has the potency to reduce the influence of traps on charge transport and provide new insights into designing high mobility charge transport materials.     

Molecular structure,vibrational spectra and nonlinear optical properties of orthoarsenic acid–tris-(hydroxymethyl)-aminomethane DFT study

In this work, we report a theoretical study on molecular structure, vibrational spectra and nonlinear optical properties of orthoarsenic acid–tris-(hydroxymethyl)-aminomethane (OATA). The theoretical geometrical parameters in the ground state have been investigated by density functional method (B3LYP and BLYP) with 6-311G(d,p) basis set. The influence of intermolecular interactions effects on molecular properties has been considered by calculation performed on (OATA) dimer. The optimized geometric bond lengths and bond angles are in well agreement with the experimental data. As compared to theoretical frequencies of the monomer, the calculated values obtained for (OATA) dimer are in much better agreement with the experiment. All experimental vibrational bands have been discussed and assigned to normal modes on the basis of our theoretical calculations. B3LYP method has shown better fit to experimental ones than BLYP in calculation vibrational frequencies. To investigate nonlinear optical behaviour, the electric dipole moment μ, the polarizability α and the hyperpolarizability β were computed using DFT//B3LYP/6-311G(d,p) method.