Roles of electrostatic interaction and dispersion in CH···CH,CH···π, and π···π ethylene dimers

The structural, mechanical, electronic, and optical properties of orthorhombic Bi₂S₃ and Bi₂Se₃ compounds have been investigated by means of first principles calculations. The calculated lattice parameters and internal coordinates are in very good agreement with the experimental findings. The elastic constants are obtained, then the secondary results such as bulk modulus, shear modulus, Young’s modulus, Poisson’s ratio, anisotropy factor, and Debye temperature of polycrystalline aggregates are derived, and the relevant mechanical properties are also discussed. Furthermore, the band structures and optical properties such as real and imaginary parts of dielectric functions, energy-loss function, the effective number of valance electrons, and the effective optical dielectric constant have been computed. We also calculated some nonlinearities for Bi₂S₃ and Bi₂Se₃ (tensors of elasto-optical coefficients) under pressure.

Effect of stepwise microhydration on the methylammonium···phenol and ammonium···phenol interaction

A computational study has been performed for studying the characteristics of the interaction of phenol with ammonium and methylammonium cations. The effect of the presence of water molecules has also been considered by microhydrating the clusters with up to three water molecules. Clusters of phenol with ammonium and methylammonium cations present similar characteristics, though ammonium complexes have been found to be more stable than the methylammonium ones. The first water molecule included in the complexes interacts with a N-H group of ammoniun cations and simultaneously with the hydroxyl oxygen atom of phenol (or the aromatic ring). This first water molecule is more tightly bound in the complex, so the stability gain as more water molecules are included drops significantly by 2-3 kcal?mol^?1 with respect to the first one. As more water molecules are included, the differences between favorable coordination sites (the cation, the hydroxyl group or a previous water molecule) decrease. As a consequence, several of the most stable complexes located including three water molecules already exhibit hydrogen bonds between the hydroxyl group and one water molecule. The results indicate that a cyclic pattern formed by a series of hydrogen bonds: π···H-N-H···O-H···O-?, is characteristic of the most stable minima, being kept as more water molecules are included in the system. Therefore, this pattern can be expected to be crucial in ammonium cations···phenol interaction if exposed to the solvent to any degree.     

Competition and interplay between the lithium bonding and hydrogen bonding: R3C···HY···LiY and R3C···LiY···HY triads as a working model (R=H, CH3; Y=CN, NC)

UMP2 calculations with aug-cc-pVDZ basis set were used to analyze intermolecular interactions in R₃C···HY···LiY and R₃C···LiY···HY triads (R=H, CH₃; Y=CN, NC), which are connected via lithium and hydrogen bonds. To better understand the properties of these systems, the corresponding dyads were also studied. Molecular geometries and binding energies of dyads, and triads were investigated at the UMP2/aug-cc-pVDZ computational level. Particular attention was paid to parameters such as cooperative energies, and many-body interaction energies. All studied complexes, with the simultaneous presence of a lithium bond and a hydrogen bond, showed cooperativity with energy values ranging between ?1.71 and ?9.03 kJ mol^?1. The electronic properties of the complexes were analyzed using parameters derived from atoms in molecules (AIM) methodology. Energy decomposition analysis revealed that the electrostatic interactions are the major source of the attraction in the title complexes.     

Co-localization of CD9 and GPIIb-IIIa (·IIb ·3 integrin) on activated platelet pseudopods and ·-granule membranes

Summary CD9 is a 24-kDa membrane glycoprotein expressed on the surface of human platelets and potentially involved in cellular activation and adhesion functions. This protein belongs to a recently delineated family of cell-surface antigens that span the membrane four times, called tetraspans, and found mainly in leucocytes and tumour cells. As a first approach to clarify the function of CD9, we used immunoelectron microscopy to determine the localization of this antigen in human platelets, and compared its distribution with that of the GPIIb-IIIa integrin, the platelet receptor for fibrinogen. Monoclonal antibodies against CD9 (MAb7) and GPIIb-IIIa (HP1-1D) coupled to colloidal gold of different sizes (5 and 15 nm) were incubated with intact platelets in suspension or on ultrathin sections of platelets embedded in LR white. CD9 was found in association with GPIIb-IIIa on the inner face of ·-granule membranes. These two antigens also co-localized on pseudopods of activated platelets and in contact regions between adjacent platelets. CD63, another member of the tetraspan family, was absent from ·-granules but was associated with lysosomal structures. Flow cytometric analysis of platelet CD9 with a series of monoclonal antibodies revealed an increased expression upon thrombin stimulation, confirming the presence of an intracellular granular pool. The observation that CD9 and GPIIb-IIIa are stored in the same intracellular structures and migrate to the same activation zones after platelet stimulation lends support to previous suggestions of a close association between CD9 and GPIIb-IIIa in human platelets and of a possible involvement of CD9 in adhesive functions of platelets. This revised version was published online in November 2006 with corrections to the Cover Date.     

Theoretical investigations of the H···π and X (X = F,Cl, Br,I)···π complexes between hypohalous acids and benzene

The H···π and X (X = F, Cl, Br, I)···π interactions between hypohalous acids and benzene are investigated at the MP2/6-311++G(2d,2p) level. Four hydrogen-bonded and three halogen-bonded complexes were obtained. Ab initio calculations indicate that the X···π interaction between HOX and C₆H₆ is mainly electrostatically driven, and there is nearly an equal contribution from both electrostatic and dispersive energies in the case of XOH–C₆H₆ complexes. Natural bond orbital (NBO) analysis reveals that there exists charge transfer from benzene to hypohalous acids. Atom in molecules (AIM) analysis locates bond critical points (BCP) linking the hydrogen or halogen atom and carbon atom in benzene.     

A comprehensive analysis of P···π pnicogen bonds: substitution effects and comparison with Br···π halogen bonds

Journal of Molecular Modeling - Ab initio calculations were carried out in a systematic investigation of P···π pnicogen-bonded complexes XH2P···C2H2/C2H4 and...     

Hydrogen bonds determine the structures of the ternary heterocyclic complexes C₂H₄O···2HF, C₂H₅N···2HF and C₂H₄S···2HF: density functional theory and topological calculations

A theoretical study of structural, electronic, topological and vibrational parameters of the ternary hydrogen-bonded complexes C₂H₄O···2HF, C₂H₅N···2HF and C₂H₄S···2HF is presented here. Different from binary systems with a single proton donor, the tricomplexes have the property of forming multiple hydrogen bonds, which are analyzed from a structural and vibrational point of view, but verified only by means of the quantum theory of atoms in molecules (QTAIM). As traditionally done in the hydrogen bond theory, the charge transfer between proton donors and acceptors was computed using the CHELPG calculations, which also revealed agreement with dipole moment variation and a cooperative effect on the tricomplexes. Furthermore, redshift events on proton donor bonds were satisfactorily identified, although, in this case, an absence of experimental data led to the use of a theoretical argument to interpret these spectroscopic shifts. It was therefore the use of the QTAIM parameters that enabled all intermolecular vibrational modes to be validated. The most stable tricomplex in terms of energy was identified via the strength of the hydrogen bonds, which were modeled as directional and bifurcated.     

Combined DFT and NBO study on the electronic basis of Si···N-β-donor bond

Two groups of isoelectronic molecules with different SiXN (X=C, N, O ) units are analyzed by a combined DFT and NBO study to investigate the electronic basis of Si···N-β-donor bond. The influence of various energy components on the formation of Si···N-β-donor bond is explored. The importance of the electron delocalization from the lone pair of nitrogen atom into the acceptor-orbitals connected with Si atom is elicited by our calculations. The electron delocalization from the lone pair of nitrogen atom into the antibonding orbital of Si-X bond is quite different among the isoelectronic molecules with various types of SiXN units.     

Insights into the strength and nature of carbene···halogen bond interactions: a theoretical perspective

Halogen-bonding, a noncovalent interaction between a halogen atom X in one molecule and a negative site in another, plays critical roles in fields as diverse as molecular biology, drug design and material engineering. In this work, we have examined the strength and origin of halogen bonds between carbene CH₂ and XCCY molecules, where X?=?Cl, Br, I, and Y?=?H, F, COF, COOH, CF₃, NO₂, CN, NH₂, CH₃, OH. These calculations have been carried out using M06-2X, MP2 and CCSD(T) methods, through analyses of surface electrostatic potentials V _S(r) and intermolecular interaction energies. Not surprisingly, the strength of the halogen bonds in the CH₂···XCCY complexes depend on the polarizability of the halogen X and the electron-withdrawing power of the Y group. It is revealed that for a given carbene···X interaction, the electrostatic term is slightly larger (i.e., more negative) than the dispersion term. Comparing the data for the chlorine, bromine and iodine substituted CH₂···XCCY systems, it can be seen that both the polarization and dispersion components of the interaction energy increase with increasing halogen size. One can see that increasing the size and positive nature of a halogen’s σ-hole markedly enhances the electrostatic contribution of the halogen-bonding interaction.

Structural and Thermodynamic Characterization of Cadherin·β-Catenin·α-Catenin Complex Formation

The classical cadherin·β-catenin·α-catenin complex mediates homophilic cell-cell adhesion and mechanically couples the actin cytoskeletons of adjacent cells. Although α-catenin binds to β-catenin and to F-actin, β-catenin significantly weakens the affinity of α-catenin for F-actin. Moreover, α-catenin self-associates into homodimers that block β-catenin binding. We investigated quantitatively and structurally αE- and αN-catenin dimer formation, their interaction with β-catenin and the cadherin·β-catenin complex, and the effect of the α-catenin actin-binding domain on β-catenin association. The two α-catenin variants differ in their self-association properties: at physiological temperatures, αE-catenin homodimerizes 10× more weakly than does αN-catenin but is kinetically trapped in its oligomeric state. Both αE- and αN-catenin bind to β-catenin with a K_d of 20 nm, and this affinity is increased by an order of magnitude when cadherin is bound to β-catenin. We describe the crystal structure of a complex representing the full β-catenin·αN-catenin interface. A three-dimensional model of the cadherin·β-catenin·α-catenin complex based on these new structural data suggests mechanisms for the enhanced stability of the ternary complex. The C-terminal actin-binding domain of α-catenin has no influence on the interactions with β-catenin, arguing against models in which β-catenin weakens actin binding by stabilizing inhibitory intramolecular interactions between the actin-binding domain and the rest of α-catenin.     

The interaction of spectrin · actin and synthetic phospholipids

Using differential scanning calorimetry and freeze fracture electron microscopy interactions were studied between lipids and a spectrin · action complex isolated from human erythrocyte membranes. With dispersions of $\text{1,2-}\text{dimyristoyl}\text{-sn-}\text{glycero}\text{-3-}\text{phosphocholine}$, $\text{1,2-}\text{dimyristoyl}\text{-sn-}\text{glycero}\text{-3-}\text{phosphoglycerol}$ and mixtures of these two compounds, which for experimental reasons were chosen as the lipid counterpart, such an interaction could clearly be deduced from changes in the temperature and the enthalpy of the phase transition. Furthermore it was demonstrated that the interaction with this membrane protein protects the bilayer against the action of Ca²⁺ and Mg²⁺ and prevents fusion of lipid vesicles which easily occurs in some of the systems when divalent ions were added to the pure lipid vesicles.     

The cooperativity between hydrogen and halogen bond in the XY···HNC···XY (X,Y = F,Cl, Br) complexes

The cooperativity between hydrogen and halogen bonds in XY···HNC···XY (X, Y = F, Cl, Br) complexes was studied at the MP2/aug-cc-pVTZ level. Two hydrogen-bonded dimers, five hydrogen-bonded dimers, and ten trimers were obtained. The hydrogen- and halogen-bonded interaction energies in the trimers were larger than those in the dimers, indicating that both the hydrogen bonding interaction and the halogen bonding interaction are enhanced. The binary halogen bonding interaction plays the most important role in the ternary system. The hydrogen donor molecule influences the magnitude of the halogen bonding interaction much more than the hydrogen bonding interaction in the trimers with respect to the dimers. Our calculations are consistent with the conclusion that the stronger noncovalent interaction has a bigger effect on the weaker one. The variation in the vibrational frequency in the HNC molecule was considered. The NH antisymmetry vibration frequency has a blue shift, whereas the symmetry vibration frequency has a red shift. A dipole moment enhancement is observed upon formation of the trimers. The variation in topological properties at bond critical points was obtained using the atoms in molecules method, and was consistent with the results of the interaction energy analysis.     

PHY·FI: fast and easy online creation and manipulation of phylogeny color figures

Background  

The need to depict a phylogeny, or some other kind of abstract tree, is very frequently experienced by researchers from a broad range of biological and computational disciplines. Thousands of papers and talks include phylogeny figures, and often during everyday work, one would like to quickly get a graphical display of, e.g., the phylogenetic relationship between a set of sequences as calculated by an alignment program such as ClustalW or the phylogenetic package Phylip. A wealth of software tools capable of tree drawing exists; most are comprehensive packages that also perform various types of analysis, and hence they are available only for download and installing. Some online tools exist, too.     

Mapping of the SecA·SecY and SecA·SecG interfaces by site-directed in vivo photocross-linking

The two major components of the Eubacteria Sec-dependent protein translocation system are the heterotrimeric channel-forming component SecYEG and its binding partner, the SecA ATPase nanomotor. Once bound to SecYEG, the preprotein substrate, and ATP, SecA undergoes ATP-hydrolytic cycles that drive the stepwise translocation of proteins. Although a previous site-directed in vivo photocross-linking study (Mori, H., and Ito, K. (2006) Proc. Natl. Acad. Sci. U.S.A. 103, 16159-16164) elucidated residues of SecY needed for interaction with SecA, no reciprocal study for SecA protein has been reported to date. In the present study we mapped residues of SecA that interact with SecY or SecG utilizing this approach. Our results show that distinct domains of SecA on two halves of the molecule interact with two corresponding SecY partners as well as with the central cytoplasmic domain of SecG. Our data support the in vivo relevance of the Thermotoga maritima SecA·SecYEG crystal structure that visualized SecYEG interaction for only one-half of SecA as well as previous studies indicating that SecA normally binds two molecules of SecYEG.     

Reactivity of essential histidine residues in EF-Tu · GDP and EF-Tu · GTP from Escherichia coli

The microenvironment of histidine residues located in the binding site of elongation factor EF-Tu from Escherichia coli for the 3′ terminus of aminoacyl-tRNA is altered during transition of EF-Tu · GDP to EF-Tu · GTP.     

Thermodynamic contributions of single internal rA·dA, rC·dC, rG·dG and rU·dT mismatches in RNA/DNA duplexes

The thermodynamic contributions of rA·dA, rC·dC, rG·dG and rU·dT single internal mismatches were measured for 54 RNA/DNA duplexes in a 1 M NaCl buffer using UV absorbance thermal denaturation. Thermodynamic parameters were obtained by fitting absorbance versus temperature profiles using the curve-fitting program Meltwin. The weighted average thermodynamic data were fit using singular value decomposition to determine the eight non-unique nearest-neighbor parameters for each internal mismatch. The new parameters predict the ΔG°₃₇, ΔH° and melting temperature (T_m) of duplexes containing these single mismatches within an average of 0.33 kcal/mol, 4.5 kcal/mol and 1.4°C, respectively. The general trend in decreasing stability for the single internal mismatches is rG·dG > rU·dT > rA·dA > rC·dC. The stability trend for the base pairs 5′ of the single internal mismatch is rG·dC > rC·dG > rA·dT > rU·dA. The stability trend for the base pairs 3′ of the single internal mismatch is rC·dG > rG·dC >> rA·dT > rU·dA. These nearest-neighbor values are now a part of a complete set of single internal mismatch thermodynamic parameters for RNA/DNA duplexes that are incorporated into the nucleic acid assay development software programs Visual oligonucleotide modeling platform (OMP) and ThermoBLAST.     

Effects of urea and guanidine · HCl on the folding and unfolding of pancreatic trypsin inhibitor

Concentrated solutions of urea and of guanidine · HCl produced a random spectrum of single-disulphide forms of the polypeptide chain of the pancreatic trypsin inhibitor. Guanidine · HCl also unfolded completely, with accompanying interchange of disulphide bonds, the two-disulphide form of this protein in the native-like conformation; urea produced an equilibrium mixture in which one-quarter of the molecules had the native-like conformation and disulphide bonds. The unfolded forms of the protein in the denaturants were very flexible polypeptide chains. The observations suggest that urea and guanidine · HCl are denaturants because they produce essentially equally favourable solvation of all portions of a polypeptide.The energetics of the conformational transitions involved in folding and unfolding of the inhibitor were determined in urea and compared with those observed in its absence. The denaturant lowers the stability of the native, folded inhibitor relative to that of the reduced, unfolded state by 6.5 kilocalories per mole; the greatest part of this apparent free-energy difference was expressed at the two-disulphide stage of folding. The results are consistent with other indications that most of the favourable interactions stabilizing the native conformation of this protein are not encountered until the final stage of folding, when all may occur simultaneously.The unfolded one- and two-disulphide species produced in guanidine · HCl were trapped, and their rearrangement to the normal intermediates followed after removal of the denaturant. The random single-disulphide species, with one exception, reverted very rapidly to the non-random spectrum of intermediates normally observed during folding; this confirms that these species are normally rapidly interconverted and that normal refolding of the reduced protein is not dependent kinetically upon residual stable conformation in the reduced protein. The unfolded two-disulphide species refolded to the native-like conformation more slowly, but appeared to pass through the same intermediates normally observed during refolding from the fully reduced state.