The nature of the C–As bonds in arsaalkynes: an atoms in molecules and electron localization function study

The nature of the C–As bonds present in a series of six neutral and anionic arsaalkynes was investigated. The optimized geometries, vibrational frequencies, and wavefunctions of all the studied species were computed using density functional theory (B3LYP/6-311++G(2d,2p)). To understand the bonding characteristics, Atoms in Molecules theory and topological analysis of the electron localization function were used. For comparison, natural bond orbital analysis was also performed. The results suggest that in five of the six studied compounds, the C–As bonds are essentially triple bonds, with similar characteristics to the C–P analogues in phosphaalkynes.     

Fluorine as a Lewis acid: A symmetry-adapted perturbation theory based on density functional theory and interacting quantum atoms study of noncovalent interactions in the NCF⋯NH3 complex

Different computational methods are used to investigate the nature of interaction in the NCF⋯NH₃ model complex, in which the fluorine atom acts as a Lewis acid and forms a noncovalent bond with the ammonia (Lewis base). Symmetry-adapted perturbation theory based on density functional theory (SAPT(DFT)) indicates that the noncovalent interaction in the NCF⋯NH₃ complex is mainly electrostatics. However, dispersion and induction terms also play important roles. Although fluorine noncovalent interactions are typically classified as halogen bonds, they are somewhat different from the well-known halogen bonds of iodine, bromine, and chlorine. The halogen bonds of NCCl⋯NH₃ and NCBr⋯NH₃ are directional and the C  X  N (X = Cl or Br) angle tends to be linear. In contrast, the fluorine interaction in NCF⋯NH₃ is not directional; the interaction energy shows no sensitivity to the angular (C  F  N ) distortions, and the energy profile is flat over a wide angular range (from 180° to about 140° ). However, for the angles less than 130° , the energy curve shows a clear angular dependence and the interaction between NCF and NH₃ becomes stronger as the C  F  N angle decreases. It seems that at the tighter angles, a tetrel-bonded NCF⋯NH₃ complex is preferred. Moreover, interacting quantum atoms (IQA) analysis shows that the competition between different intra-atomic and interatomic interactions determines the geometry of NCF⋯NH₃ complex.     

Congested molecules. Where is the steric repulsion? An analysis of the electron density by the method of interacting quantum atoms

The computed electron density of several congested saturated hydrocarbons and halogenated derivatives has been analyzed by the method of interacting quantum atoms (IQA). For all the molecules studied, the calculations show the existence of a bond path between the congested atoms and which, according to the Quantum Theory of Atoms in Molecules, indicates that there is a stabilizing interaction between these atoms. The bond path is found to exist up to interatomic distances well‐beyond the sum of the van der Waals radii. The IQA results indicate that steric hindrance is not a repulsive force between the congested atoms but that is the result of an increase in the intra‐atomic or self‐energy of the congested atoms. This increase in self‐energy is caused by the deformation of the atomic basin of the congested atoms. © 2013 Wiley Periodicals, Inc.     

Is spin-component scaled second-order Møller-Plesset perturbation theory an appropriate method for the study of noncovalent interactions in molecules?

Testing of the spin-component scaled second-order M?ller-Plesset (SCS-MP2) method for the computation of noncovalent interaction energies is done with a database of 165 biologically relevant complexes. The effects of the spin-scaling procedure (i.e., MP2 vs SCS-MP2), the basis set size, and the corrections for basis set superposition error (BSSE) are systematically examined. When using two-point basis set extrapolations for the correlation energy, augmentation of the atomic orbital basis with computationally costly diffuse functions is found to be obsolete. In general, SCS-MP2 also improves results for noncovalent interactions statistically on MP2, and significant outliers are removed. Moreover, it is shown that effects of BSSE and one-particle basis set incompleteness almost cancel each other in the case of triple-zeta sets (SCS-MP2/TZVPP or SCS-MP2/cc-pVTZ without counterpoise correction), which opens a practical route to efficient computations for large systems. We recommend SCS-MP2 as the preferred quantum chemical wave function based method for the noncovalent interactions in large biologically relevant systems when reasonable coupled-cluster with single and double and perturbative triple excitations (CCSD(T)) calculations cannot be performed anymore. A comparison to MP2 and CCSD(T) interaction energies for n-alkane dimers, however, indicates (and this also holds to a lesser extent for hydrogen-bonded systems) limitations of SCS-MP2 when treating chemically "saturated" interactions. The different behavior of second-order perturbation theory for saturated and for stacked pi-systems is discussed.     

A comparative study of the multicomponent Ugi reactions of an oxabicycloheptene-based β-amino acid in water and in methanol

Di-exo-3-amino-7-oxabicyclo[2.2.1]hept-5-ene-2-carboxylic acid 1, five aldehydes and two isocyanides were reacted both in methanol and in water to prepare a 10-membered β-lactam library via a Ugi-4-centre-3-component reaction. The yields were found to be similar in water and methanol. The diastereoselectivities of the aqueous reactions were similar, though in a few cases higher than those in methanol. The benefits of water are the facile isolation of the precipitated product and the shorter reaction time.     

Is it possible to predict the average surface hydrophobicity of a protein using only its amino acid composition?

Hydrophobicity is one of the most important physicochemical properties of proteins. Moreover, it plays a fundamental role in hydrophobic interaction chromatography, a separation technique that, at present time, is used in most industrial processes for protein purification as well as in laboratory scale applications. Although there are many ways of assessing the hydrophobicity value of a protein, recently, it has been shown that the average surface hydrophobicity (ASH) is an important tool in the area of protein separation and purification particularly in protein chromatography. The ASH is calculated based on the hydrophobic characteristics of each class of amino acid present on the protein surface. The hydrophobic characteristics of the amino acids are determined by a scale of aminoacidic hydrophobicity. In this work, the scales of Cowan-Whittaker and Berggren were studied. However, to calculate the ASH, it is necessary to have the three-dimensional protein structure. Frequently this data does not exist, and the only information available is the amino acid sequence. In these cases it would be desirable to estimate the ASH based only on properties extracted from the protein sequence. It was found that it is possible to predict the ASH from a protein to an acceptable level for many practical applications (correlation coefficient > 0.8) using only the aminoacidic composition. Two predictive tools were built: one based on a simple linear model and the other on a neural network. Both tools were constructed starting from the analysis of a set of 1982 non-redundant proteins. The linear model was able to predict the ASH for an independent subset with a correlation coefficient of 0.769 for the case of Cowan-Whittaker and 0.803 for the case of Berggren. On the other hand, the neural model improved the results shown by the linear model obtaining correlation coefficients of 0.831 and 0.836, respectively. The neural model was somewhat more robust than the linear model particularly as it gave similar correlation coefficients for both hydrophobicity scales tested, moreover, the observed variabilities did not overcome 6.1% of the mean square error. Finally, we tested our models in a set of nine proteins with known retention time in hydrophobic interaction chromatography. We found that both models can predict this retention time with correlation coefficients only slightly inferior (11.5% and 5.5% for the linear and the neural network models, respectively) than models that use the information about the three-dimensional structure of proteins.     

Regio- and stereochemistry in the aza-Diels–Alder reaction of an azoalkene with furan and 2,3-dihydrofuran: a molecular electron density theory study

Structural Chemistry - In the present work, a molecular electron density theory (MEDT) study is carried out to shed light on the regio- and stereochemistry in two Diels–Alder (DA) reactions...     

A study of anhydrocelluloses--is a cellulose structure with residues in a 1C4-conformation more prone to hydrolysis?

A study of the effect of introduction of 3,6-anhydroglucose residues in the cellulose structure on glycoside hydrolysis rate was performed. A cellotetrose with an 3,6-anhydroglucose as the third residue was synthesised. Acidic hydrolysis of this tetrasaccharide showed that hydrolysis of the 3,6-anhydro-β-D-glucoside linkage was 31.400 times faster than hydrolysis of cellobiose. A series of different 3,6-anhydrocelluloses with different degree of substitution were prepared by tosylation of cellulose with varying amounts of tosyl chloride in dimethylacetamide and subsequent treatment with sodium hydroxide. Anhydrocelluloses with degrees of substitution of 0.02, 0.07, 0.31 and 0.74 were obtained. The anhydrocelluloses were subjected to acidic hydrolysis in 2.0 M aqueous HCl and the rate of hydrolysis monitored by ion chromatography analysis of the amount of glucose and/or cellobiose formed. All 3,6-anhydrocelluloses hydrolyzed with a faster rate than cellulose, but the anhydrocellulose with a low degree of substitution (ds = 0.07) hydrolyzed fastest which was 90 times faster than cellulose.     

The spin-crossover phenomenon in the solid state: Do domains play a role? A micro-Raman study

In order to assess experimentally the extent to which the nucleation-growth mechanism influences the phenomenon of spin-state crossover in the solid state, variable temperature micro-Raman mapping experiments have been conducted for the first time on the spin-crossover complex Fe(pz)[Ni(CN)₄]·2H₂O. The results point to the absence of domains with dimensions greater than ∼1 micron.     

Why substituting the asparagine at position 35 in Bacillus circulans xylanase with an aspartic acid remarkably improves the enzymatic catalytic activity? A quantum chemistry-based calculation study

Xylanases from Bacillus circulans (BCX) are known as configuration-retaining glycoside hydrolases, which hydrolyze xylans with two glutamic acid residues (Glu78 and Glu172) serving as catalytic active residues according to a double displacement mechanism. Existing experimental researches show that mutating the asparagines (Asn) to aspartic acid (Asp) at position 35 next to Glu172 can obviously improve the catalytic activity of BCX. To better understand the inherent mechanism for the experimental finding, we performed quantum chemistry calculations on two model systems to mimic the catalyses of wild-type and mutant BCXs. Geometrical structures and relative energies of intermediates and transition states involved in the hydrolysis reactions are given in detail. It is found that in the wild-type model system Asn35 interacts with Glu172 via a loose hydrogen bond, while in the mutant model system Asp35 forms a very tight hydrogen bond with Glu172. The glycosidic bond cleavage is proposed to be the rate-determining step for the hydrolysis reaction, whose barrier varies from 98 to 65 kJ mol⁻¹ when Asn35 is replaced by Asp35, showing the presence of Asp35 remarkably reduces the energy demand for the hydrolysis reaction. The present result provides a theoretical elucidation for why a single amino acid substitution can importantly influences catalytic activity of BCX.     

Inhibition of TRAF6-Ubc13 interaction in NFkB inflammatory pathway by analyzing the hotspot amino acid residues and protein–protein interactions using molecular docking simulations

Protein–protein interactions (PPIs) are important in most of the biochemical processes. Hotspot amino acid residues in proteins are the most important contributors for proper protein–protein interactions. Hotspot amino acid residues have been looked down upon as important therapeutic targets in inhibiting PPIs. Interaction between TRAF6 and Ubc13 is a crucial point in the NFkB inflammatory pathway. Dysfunction of the NFkB pathway is associated with numerous human diseases including cancer and neurodenegeration disorders. Ubc13 also interacts specifically to TRAF6 and not with other proteins of the TRAF family and this makes the TRAF6-Ubc13 complex an important target for specific inhibition. Hence, interfering with the TRAF6-Ubc13 association may prove effective in suppressing the NFkB disease pathway. In the present study, we searched the TRAF6-Ubc13 interaction interface to analyze their binding hotspot amino acid residues using various computational techniques. Heterocyclic compounds are known for their medicinal properties. We screened for heterocyclic analogues to the known TRAF6 inhibitor PDTC, to predict a better inhibitor using in silico protein–ligand and protein–protein interaction studies. Our in silico prediction results suggest that tetrahydro-2-thiophenecarbothioamide (Chemspider ID 36027528) binds one of the major hot-spot residues of TRAF6-Ubc13 interface and can be a better alternative in suppressing TRA6-Ubc13 complex formation in chronic inflammation than PDTC.     

Spectrofluorimetric determination of trace amounts of coenzyme A using a terbium ion–ciprofloxacin complex probe in the presence of periodic acid

A new spectrofluorimetric method was developed for the determination of trace amounts of coenzyme A (CoA). In the presence of periodic acid (H₅IO₆), CoA can remarkably enhance the fluorescence intensity of the Tb³⁺–ciprofloxacin (CIP) complex at 545 nm in a buffer solution at pH 5.4; the enhanced fluorescence intensity of the Tb³⁺ ion is proportional to the concentration of CoA. The optimal conditions for the determination of CoA were also investigated. The linear range and the detection limit for the determination of CoA were 6.08 × 10⁻⁶–1.64 × 10⁻⁵ and 2.1 × 10⁻⁸ mol L⁻¹, respectively. This method is simple, practical and relatively free of interference from coexisting substances, and can be successfully applied to assess CoA in injection and biological samples. Moreover, the enhancement mechanism of the fluorescence intensity of the CoA–Tb³⁺–CIP system in the presence of H₅IO₆ is also discussed.     

Spectrophotometric study of the incorporation of NBD probes in micelles: is a long alkyl chain on the fluorophore an advantage?

Fluorescence spectroscopy is widely used as a tool for elucidating the structure and dynamics of the micellar medium. A prerequisite commonly encountered for quantitative approaches is that the fluorophore resides exclusively in the micellar phase. Providing the fluorophore with a long alkyl chain may appear advantageous with regard to fixing the probe into the micelle. The present work was aimed at determining which are the consequences of this process from a spectroscopic viewpoint. The nitrobenzoxadiazolyl (NBD) moiety, which leads to well known fluorescent probes, was directly grafted on three fatty amines, the chain length of which varied from 8 to 18 carbon atoms. The spectroscopic properties of these NBD derivatives were investigated in three different micellar media: SDS, CTAB and TX100. The dyes were incorporated into micelles, where they were located in the interfacial region, whatever the chain length. When the dyes were previously dissolved in ethanol, and subsequently placed in the presence of the surfactant solution, complete solubilization was obtained. However, when the surfactant solution was used to dissolve directly a thin film of dye, a certain amount of dye remained non-incorporated and formed microcrystals, whose quantity and size increased with chain length. These microcrystals were mainly detected by UV/Vis-absorption and fluorescence microscopy. They induced drastic errors in the determination of fluorescence quantum yields, although they hardly interfered with other steady-state measurements and with dynamical fluorescence measurements. In conclusion, it appeared that for a small, non-ionic fluorophore such as NBD, the presence of a long alkyl chain is not an advantage. It slows down the incorporation process, unless some alcohol is introduced in the medium. Short-chain probes are therefore best suited for the study of the micellar medium.     

<Superscript>119</Superscript>Sn Mössbauer study of the influence of a gas atmosphere on the valence state and distribution of tin atoms in the MgO structure

Analysis of the Mössbauer spectra of dopant ¹¹⁹Sn in cubic MgO has demonstrated that the Sn²⁺ ions can be stabilized on the surface of crystallites of an oxide with a structure differing from the corundum structure. The Mössbauer parameters (at 100 K, the isomer shift is δ = 2.50 ± 0.01 mm/s and the quadrupole splitting is Δ = 2.30 ± 0.02 mm/s) point to the stereochemical activity of the lone pair of Sn²⁺. Being in contact with oxygen at 295 K, tin is rapidly converted to the tetravalent state (δ = 0.08 ± 0.01 mms, Δ = 0.58 ± 0.01 mm/s). The lack of formation of Sn²⁺ on the surface of another cubic oxide (MnO) can be explained by rapid segregation of tin from the bulk of crystallites as stannate clusters.     

What makes for a good catalytic cycle? A theoretical study of the SPhos ligand in the Suzuki-Miyaura reaction

The Suzuki-Miyaura cross-coupling reaction with the SPhos ligand was studied with DFT and analyzed within the energetic span model. With this information, we designed a modification to the SPhos (the "InPhos"), which theoretically corrects the deficiencies of the prior ligand.     

Can the replacement of a single atom in the enzyme horseradish peroxidase convert it into a monoxygenase? A density functional study

Density functional calculations on horseradish peroxidase mutants are presented, whereby one or two of the nitrogen atoms of the axial histidine ligand have been replaced by phosphorus atoms. Our calculations show that phosphorus entices a push effect on the oxoiron group, whereas a histidine side chain withdraws electrons. As a result, we predict that a phosphorus-substituted histidine ligand will convert the active form of a peroxidase into a monoxygenase. This subsitution may be useful for the bioengineering of commercially exploitable enzymes.     

How many electrons form chemical bonds in the NgBeS (Ng = Ar,Kr, Xe) molecules? Topological study using the electron localisation function (ELF) and electron localisability indicator (ELI-D)

Nature of bonding in the NgBeS (Ng = Ar, Kr, Xe) molecules has been studied using topological analysis of ELF, ELI-D functions with the wave function approximated at the DFT (M062X, B3LYP + ZORA), MP2, CCSD and CASSCF level of calculations. Both Xe–Be and Be=S bonds display topological features typical for the covalent-dative bonding. The V₂(Xe) attractor characterising electron density, involved in interaction with the beryllium atom, is closer to the C(Be) core than to C(Xe). The population of the respective basin ranges between 1.59e (B3LYP + ZORA) and 1.83e (CCSD). The beryllium–sulphur bond is described by the bonding disynaptic basin V(Be,S) with the population between 3.22e (CASSCF) and 3.48e (M062X). The approximate weights for the Be–S and Be=S resonance forms are 0.3 and 0.7, respectively, in all molecules. Both the NgBe and BeS bonds are highly polarised with the values of the p _SBe and p _NgBe polarity indices (CCSD) of 0.8 and 0.9–1.0 for all studied molecules.