Infrared spectroscopic and DFT investigations of the vanadate–tellurate glasses structures

Vanadate–tellurate vitreous systems with composition (1 ? x)TeO₂·xV₂O₅ where x = 0.3 and 0.4 have been prepared by the conventional melt-quench method. The structural aspects have been investigated using FTIR spectroscopy and the density functional theory (DFT) calculations.The present study provides the interesting information concerning devitrification behavior of the vanadate–tellurate vitreous system which occur Te₂V₂O₉ crystalline phase. The structure of the heat-treated glasses was found to consist mainly of rings containing [TeO₃], [TeO₄], [VO₄] and some [VO₅] structural units.     

DFT study of chemical mechanism of pre-SERS spectra in Pyrazine–metal complex and metal–Pyrazine–metal junction

The chemical mechanism of Normal Raman Scattering (NRS) and pre-surface enhanced Raman scattering (pre-SERS) spectra for Pyrazine–Ag₂ complex, Ag₂–Pyrazine–Ag₂ junction and Ag₂–Pyrazine–Au₂ junction were investigated with density functional theory (DFT) and charge difference densities (CDDs) for the first time. The NRS intensities of the above three structures enhanced obviously relative to isolated Pyrazine and the enhancement mechanism was confirmed to be static chemical enhancement. The pre-SERS intensities of the above three structures enhanced evidently compared to corresponding NRS intensities, and the enhancement mechanism was confirmed to charge transfer (CT) resonance Raman enhancement. The largest enhanced orders of NRS and pre-SERS intensities among the three structures were up to 10³ and 10⁵, respectively. Compared the intensity of pre-SERS with corresponding intensity of NRS spectra, the enhancement effect of Pyrazine–Ag₂ complex was larger than the others. Intramolecular and intermolecular CT on resonant electronic transition were described by CDDs.     

DFT study of the electronic and charge transfer properties of perfluoroarene–thiophene oligomers

The ground state structures of 5,5″-diperfluorophenyl-2,2′:5′,2″:5″,2‴-quaterthiophene (1), 5,5′-bis{1-[4-(thien-2-yl)perfluorophenyl]}-2,2′-dithiophene (2), 4,4′-bis[5-(2,2′-dithiophenyl)]-perfluorobiphenyl (3), 5,5″-diperfluorophenyl-2,2′:5′,2″-tertthiophene (4), 5,5′-diperfluorophenyl-2,2′-dihiophene (5), and 5,5-diperfluorophenylthiophene (6) have been optimized at the B3LYP/6-31G(d), B3LYP/6-31G(d,p), PBE0/6-31G(d), and PBE0/6-31G(d,p) level of theories. The B3LYP/6-31+G(d) and PBE0/6-31+G(d) level of theories have been applied to investigate the absorption spectra. The PBE0 functional is good to predict the C–S bond lengths while the C–F bond lengths are good envisaged with B3LYP functional. The increment of thiophene rings between two perfluoroarene rings leads to red shift in absorption spectra. The electron affinities are energetically destabilized while energetic stabilization of the radical-cation increases by decreasing the thiophene rings from four to one. The perfluoroarene rings leads to enhance the electron injection.     

Protein–protein recognition: a computational mutagenesis study of the MDM2–P53 complex

Protein P53 is involved in more than 50% of the human cancers and the P53–MDM2 complex is a target for anticancer drug design. It is possible to engineer small P53 mimics that would be expected to disrupt the P53–MDM2 complex, and release P53 to initiate cell-cycle arrest or apoptosis. These small peptides should bind to the functional epitopes of the protein–protein interface, and prevent the interaction between P53 and MDM2. Here, we apply an improved computational alanine scanning mutagenesis method, which allows the determination of the hot spots present in both monomers, P53 and MDM2, of three protein complexes (the P53-binding domain of human MDM2, its analogue from Xenopus laevis, and the structure of human MDM2 in complex with an optimized P53 peptide). The importance of the hydrogen bonds formed by the protein backbone has been neglected due to the difficulty of measuring experimentally their contribution to the binding free energy. In this study we present a computational approach that allows the estimation of the contribution to the binding free energy of the C=O and N–H groups in the backbone of the P53 and MDM2 proteins. We have noticed that the hydrogen bond between the HE1 atom of the hot spot Trp23 and the O atom of the residue Leu54, as well as the NH-pi hydrogen bond between the Ile57 and Met58 were observed in the Molecular dynamics simulation, and their contribution to the binding free energy measured. This study not only shows the reliability of the computational mutagenesis method to detect hot spots but also demonstrates an excellent correlation between the quantitative calculated binding free energy contribution of the C=O and N–H backbone groups of the interfacial residues and the qualitative values expected for this kind of interaction. The study also increases our understanding of the P53–MDM2 interaction.     

Tuning the electronic structures and optical properties of fluorene-based donor–acceptor copolymers by changing the acceptors: a theoretical study

Five fluorene-based conjugated copolymers were studied to explore the effect of acceptor on the electronic and optical properties. Their ground-state, excited-state electronic structures and the tunable optical properties were theoretically investigated using density functional theory (DFT) and time-dependent density functional theory (TDDFT) methods. The acceptors including quinoxaline (Q), 2,1,3-benzothiadiazole (BT), thieno[3,4-b]pyrazine (TP), 2,1,3-benzooxadiazole (BO), and pyridopyrazine (PP) can significantly influence the copolymers’ electronic structures, molecular orbitals, geometric conformations, and optical properties. Calculations were made on systems containing one, two, three, and four oligomers in the neutral, cationic, and anionic structures, which can be extrapolated to infinite chain length polymers. The result indicated that the sequence of the band gap was on the reverse trend of emission wavelength. The strong electron-withdrawing strength of TP unit and coplanar backbone in poly[2,7-(9,9′-dihexylfluorene)-alt-2,3-dimethyl-5,7-dithien-2-yl-thieno[3,4-b] pyrazine] resulted in the enhanced degree of intramolecular charge transfer (ICT) and lowest band gap. The contribution of acceptors to IP was also found to follow the sequence of TP < Q < PP < BT < BO. The absorption and emission spectra exhibited red-shift with increasing the conjugation lengths. The present study suggested that the electronic and optical properties of donor–acceptor conjugated copolymers were affected by the acceptor structure.     

N–H stretching frequencies and the conformation of substituted ureas: an ab initio MO study

The dependence of N–H stretching-mode frequencies in representative di- and trialkyl ureas on the conformational state of the ureido group has been studied by ab initio MO calculations using HF/3-21G and HF/6-31G** basis sets. The molecules studied were 1,3-dimethylurea, 1-methyl-3,3-dimethylurea and 1-methyl-3,3-di-iso-propylurea. The principal conclusions from the ab initio results are:

• 1.the trans–trans conformer (N–H bonds trans to the CO bond) has N–H stretching bands with about 20–30 cm⁻¹ higher frequency than the respective cis–cis structure, in accord with earlier literature assignments based on experimental data;
• 2.the N–H stretching frequency interval in tri-substituted ureas is 15–20 cm⁻¹ higher than the N–H band position in the 1,3-disubstituted molecule studied, the effect being determined mostly by the higher N–H stretching force constant;
• 3.in the absence of the steric hindrance the stable rotameric forms of the ureido grouping are almost planar at HF/3-21G level of calculations, while HF/6-31G** calculations predict a slightly pyramidal structure at the nitrogen atoms in the trans–trans conformer;
• 4.in 1-methyl-3,3-di-iso-propylurea the steric influence of the two bulky iso-propyl groups cause a deviation from planarity of the N–H bond. The non-planar conformation is accompanied by a shift of the N–H stretching mode frequency towards higher values; and
• 5.the variations of the theoretically estimated N–H stretching-mode frequencies appear to be principally determined by changes in the N–H stretching force constants in the different molecules.

© 1997 Elsevier Science B.V.     

The bridged effect on the geometric,optoelectronic and charge transfer properties of the triphenylamine–bithiophene-based dyes: a DFT study

Research on Chemical Intermediates - The dye-sensitized solar cells containing a triphenylamine unit as the electron donor connected with a terminal cyanoacrylic acid electron acceptor by...     

A DFT study on the effect of hydrogen bonding on the reaction of a μ-benzoquinone diruthenium complex with acetylene

A DFT study was carried out to investigate the reaction mechanisms of a model μ-benzoquinone diruthenium complex {CpRu(μ-H)}₂(μ-η²:η²-C₆H₄O₂), derived from the experimental compound {Cp*Ru(μ-H)}₂(μ-η²:η²-C₆H₃RO₂) (R = H or R = Me, Cp* = η⁵-C₅Me₅), with acetylene both in aprotic and protic solvents. Results of calculations show that the influence of the solvent methanol on the reaction is mainly on the step of acetylene coordination. Enhanced hydrogen bonding is the reason for acceleration of the reaction in protic solvent, which is supported by NBO charge analysis.     

FTIR study of the sol–gel synthesis of cementitious gels: C–S–H and N–A–S–H

The study explored the compatibility between the main product of Portland cement hydration and the main product of the alkali activation of fly ash: C–S–H and N–A–S–H gels, respectively. Both gels were synthesized with laboratory reagents at different pH values. Blends of the two were synthesized as well, using the sol–gel procedure. All the gels were characterized with Fourier transform IR spectroscopy (FTIR). The gels synthesized with this procedure were shown to precipitate together with a silica-rich gel. In addition, the pH level was found to play a determinant role in both C–S–H and N–A–S–H gel synthesis. The C–S–H gel is the major phase formed at pH > 11 and N–A–S–H gel for pH > 12. The results relating to the joint synthesis of the two (C–S–H and N–A–S–H) gels were not conclusive. Technique used for the characterization failed to differentiate between them in the blended material.

Intramolecular hydrogen bond in the push–pull CF3-aminoenones: DFT and FTIR study,NBO analysis

Postulated conformers of trifluoromethylated β-aminoenones stabilized by intramolecular NH?O and N?HO bonds were studied by IR and NMR spectroscopy and evaluated with quantum chemical calculations (B3LYP/6-311+G(d,p), MP2/6-311+G(d,p)//B3LYP/6-311+G(d,p) and MP2/6-31G(d,p)) and NBO analysis. The influence of the nature of EWG, substituents at the nitrogen atom and double bond, and of orbital interactions of heteroatoms and double bonds in these structures on the proton affinity of basic and acid centers, strength of hydrogen bonds, and the energy of tautomeric transfers is discussed. The theoretical results agree satisfactorily with the experimental observations.     

Calorimetric investigation of the complex formation reaction of 18-crown-6 ether with d,l-alanine in water–ethanol mixtures

The standard thermodynamic parameters (Δ_r G°, Δ_r H°, and TΔ_r S°) of the reaction of molecular complex formation of 18-crown-6 ether (18C6) with d,l-alanine (Ala), [Ala18C6], have been obtained from calorimetric titration experiments carried out using the microcalorimetric system TAM III (TA Instruments, USA) at T = 298.15 K in water–ethanol (H₂O–EtOH) solvents at X _EtOH = 0 ÷ 0.6 mol fractions. Results show that the increase of the EtOH concentration in solvent brings about an increase of the [Ala18C6] complex stability and of the exothermicity of the reaction of complex formation. The solvation contributions of 18C6, Ala, [Ala18C6] to Δ_r G° and Δ_r H° at various X _EtOH values are also analyzed.     

Host–guest inclusion complex of β-cyclodextrin and benzoic acid in water–ethanol solvents: spectroscopic and thermodynamic characterization of complex formation

Journal of Thermal Analysis and Calorimetry - In this study, an inclusion complex of benzoic acid with β-cyclodextrin (BA-βCD) was obtained from water–ethanol solvents. The yield of...     

Structure and property of the hydrogen bonding complex between triazines and water

The study of the intermolecular interactions that drive the solvation of six-membered nitrogenated aromatic rings is of particular importance since they are known to constitute key building blocks of pro- teins and nucleotides[1―5]. The investigation of the 1:1 adduct of these molecules with water will be the first step in the understanding of such interactions. These molecules possess two different proton-acceptor sites: the ring π cloud and the lone pairs of electrons on the nitrogen atoms…     

Density functional efficiency in the calculations of vibrational frequencies and molecular structures of β-diketones

Density functional theory (DFT) levels are employed to calculate the vibrational frequencies and geometrical data of β-diketones. We evaluate the relative performance of the different levels by comparing theoretical results to experimental values. The applied DFT levels in this work are B3LYP, BLYP, B3P86, B3PW91, BPW91, G96LYP, BP86, and G96PW91 with the standard 6-31G, 6-31G*, 6-31G**, 6-31+G**, 6-31++G**, 6-311G**, 6-311++G** basis sets. The best results are obtained at the B3LYP, B3PW91, and B3P86 levels.     

Investigations of the hydrophobic and hydrophilic interactions in polymer–water systems by ATR FTIR and Raman spectroscopy

ATR FTIR and Raman spectra of polymers containing amide groups in the main chain and in the side chain and of the amide low-molecular-weight model compounds in water media were measured. The hydrophobic and hydrophilic interactions of the dissolved compounds with the neighboring water molecules are reflected in the wavenumbers of the CH₃ stretching and of the Amide I and II vibrations. The possibility of the existence of β-sheet-like structures in polypeptides surrounded by water molecules is also discussed.     

Pharmacology and structures of the free base of the anaesthetic kazcaine and its complex with β-cyclodextrin

The base form of the local anaesthetic kazcaine (BFK, [1-(2-ethoxyethyl)-4-ethynyl-4-benzoyloxypiperidine, C₁₈H₂₃NO₃]) and β-cyclodextrin (β-CD) co-crystallized as BFK:β-CD inclusion complex in 1:2 M ratio from a mixture of water and ethanol while the filtered mother liquor yielded crystals of free BFK. X-ray diffraction showed that the crystals of BFK and its inclusion complex with β-CD belong to monoclinic (P2₁/c) and triclinic (P1) space groups, respectively. The crystals of free BFK are stabilized by pairs of C–H?O, C–H?π and ≡C–H?O type interactions and van der Waals contacts. In the 1:2 BFK:β-CD complex the two β-CD molecules are in hydrogen-bonding contact with their primary hydroxyl groups, the 1-(2-ethoxyethyl)-4-ethynyl-piperidine moiety being located in one and the benzoyloxy group of BFK in the other β-CD. This crystal structure is of the channel-type, the β-CD molecules of the 1:2 BFK:β-CD complex interacting with their secondary hydroxyl groups. The pharmacological activities of the 1:2 BFK/β-CD inclusion complex have been determined in mice, rats, porpoises and rabbits and compare favourably with those of kazcaine, procaine, dicaine, lidocaine and trimecaine. The methods used include terminal (superficial), infiltration, conduction anaesthesia, and acute toxicity.     

Physical–chemical study of water in contact with a hydrophilic polymer: Nafion

The study detailed in this paper is about the determination of the physical–chemical parameters of water, after keeping it in prolonged contact with the Nafion polymer. The parameters under study are: electrical conductivity, χ (μS cm^?1); heat of mixing with acid (HCl), ΔQ _mix ^HCl (J kg^?1) or basic (NaOH) solutions, ΔQ _mix ^NaOH  (J kg^?1), and pH. χ increases of up to two orders of magnitude, ΔQ _mix ^NaOH  (J kg^?1) is exothermic and increases as the electrical conductivity increases, with a roughly linear trend, up to one order of magnitude. The analogous ΔQ _mix ^HCl  (J kg^?1), on the contrary, is found to be null. The pH is quite acid and shows a very good linear correlation with log χ. The linear correlations hint at a single cause for the variation of the three very different physical–chemical parameters. This complex and hard to rationalize phenomenology, finds a good theoretical support in the work hypothesis of the formation of dissipative structures within the liquid. These are far-from-equilibrium systems outside the paradigm of classical thermodynamics. The work hypothesis of the formation of molecular aggregates of water molecules (dissipative structures, aqueous nanostructures, clusters, coherence domains, etc.) is shared with two other aqueous systems obtained with different preparation protocols, so we briefly recall them here: (1) EDS (extremely diluted solutions): obtained through an iterative process of successive dilutions and agitations. (2) IFW (iteratively filtered water): obtained through an iterative process of successive filtrations through sintered glass filters. (3) INW (iteratively nafionized water): obtained through an iterative process of successive drying and wetting of the Nafion polymer. Each protocol produces water exhibiting its own peculiarities, to the point that they can be considered different, albeit with the common element of a variation of the super-molecular structure of the water solvent. The physical–chemical properties of these perturbed waters cannot be framed by the paradigm of classical thermodynamics, but rather require the use of the thermodynamics of systems far from the equilibrium and of irreversible processes.     

A virtual screening study of the acetylcholine binding protein using a relaxed–complex approach

The nicotinic acetylcholine receptor (nAChR) is a member of the ligand-gated ion channel family and is implicated in many neurological events. Yet, the receptor is difficult to target without high-resolution structures. In contrast, the structure of the acetylcholine binding protein (AChBP) has been solved to high resolution, and it serves as a surrogate structure of the extra-cellular domain in nAChR. Here we conduct a virtual screening study of the AChBP using the relaxed–complex method, which involves a combination of molecular dynamics simulations (to achieve receptor structures) and ligand docking. The library screened through comes from the National Cancer Institute, and its ligands show great potential for binding AChBP in various manners. These ligands mimic the known binders of AChBP; a significant subset docks well against all species of the protein and some distinguish between the various structures. These novel ligands could serve as potential pharmaceuticals in the AChBP/nAChR systems.