Interplay between halogen bonds and hydrogen bonds in OH/SH···HOX···HY (X = Cl, Br; Y = F, Cl, Br) complexes

The character of the cooperativity between the HOX···OH/SH halogen bond (XB) and the Y―H···(H)OX hydrogen bond (HB) in OH/SH···HOX···HY (X = Cl, Br; Y = F, Cl, Br) complexes has been investigated by means of second-order Møller?Plesset perturbation theory (MP2) calculations and “quantum theory of atoms in molecules” (QTAIM) studies. The geometries of the complexes have been determined from the most negative electrostatic potentials (V _S,min) and the most positive electrostatic potentials (V _S,max) on the electron density contours of the individual species. The greater the V _S,max values of HY, the larger the interaction energies of halogen-bonded HOX···OH/SH in the termolecular complexes, indicating that the ability of cooperative effect of hydrogen bond on halogen bond are determined by V _S,max of HY. The interaction energies, binding distances, infrared vibrational frequencies, and electron densities ρ at the BCPs of the hydrogen bonds and halogen bonds prove that there is positive cooperativity between these bonds. The potentiation of hydrogen bonds on halogen bonds is greater than that of halogen bonds on hydrogen bonds. QTAIM studies have shown that the halogen bonds and hydrogen bonds are closed-shell noncovalent interactions, and both have greater electrostatic character in the termolecular species compared with the bimolecular species.

Neural mechanisms of mother–infant bonding and pair bonding: Similarities,differences, and broader implications

This article is part of a Special Issue “Parental Care”.Mother–infant bonding is a characteristic of virtually all mammals. The maternal neural system may have provided the scaffold upon which other types of social bonds in mammals have been built. For example, most mammals exhibit a polygamous mating system, but monogamy and pair bonding between mating partners occur in ~ 5% of mammalian species. In mammals, it is plausible that the neural mechanisms that promote mother–infant bonding have been modified by natural selection to establish the capacity to develop a selective bond with a mate during the evolution of monogamous mating strategies. Here we compare the details of the neural mechanisms that promote mother–infant bonding in rats and other mammals with those that underpin pair bond formation in the monogamous prairie vole. Although details remain to be resolved, remarkable similarities and a few differences between the mechanisms underlying these two types of bond formation are revealed. For example, amygdala and nucleus accumbens–ventral pallidum (NA–VP) circuits are involved in both types of bond formation, and dopamine and oxytocin actions within NA appear to promote the synaptic plasticity that allows either infant or mating partner stimuli to persistently activate NA–VP attraction circuits, leading to an enduring social attraction and bonding. Further, although the medial preoptic area is essential for maternal behavior, its role in pair bonding remains to be determined. Our review concludes by examining the broader implications of this comparative analysis, and evidence is provided that the maternal care system may have also provided the basic neural foundation for other types of strong social relationships, beyond pair bonding, in mammals, including humans.     

Interplay between halogen and chalcogen bonding in the XCl∙∙∙OCS∙∙∙NH3 (X = F,OH, NC,CN, and FCC) complex

The interplay between halogen and chalcogen bonding in the XCl???OCS and XCl???OCS???NH₃ (X = F, OH, NC, CN, and FCC) complex was studied at the MP2/6-311++G(d,p) computational level. Cooperative effect is observed when halogen and chalcogen bonding coexist in the same complex. The effect is studied by means of binding distance, interaction energy, and cooperative energy. Molecular electrostatic potential calculation reveals the electrostatic nature of the interactions. Cooperative effect is explained by the difference of the electron density. Second-order stabilization energy was calculated to study the orbital interaction in the complex. Atoms in molecules analysis was performed to analyze the enhancement of the electron density in the bond critical point.     

DFT study on the reactions of ClO–/BrO– with RCl (R = CH3, C2H5, and C3H7) in gas phase

Gas-phase reactions of ClO^–/BrO^– with RCl (R = CH₃, C₂H₅, and C₃H₇) have been investigated in detail using the popular DFT functional BHandHLYP/aug-cc-pVDZ level of theory. As a result, our findings strongly suggest that the type of reaction is firstly initiated by a typical S_N2 fashion. Subsequently, two competitive substitution steps, named as S_N2-induced substitution and S_N2-induced elimination, respectively, would proceed before the initial S_N2 product ion-dipole complex separates, in which the former exhibits less reactivity than the latter. Those are consistent with relevant experimental results. Moreover, we have also explored reactivity difference for the title reactions in term of some factors derived from methyl group, p-π electronic conjugation, ionization energy (IE), as well as molecular orbital (MO) analysis.

Microbial aldolases as C–C bonding enzymes—unknown treasures and new developments

Aldolases are a specific group of lyases that catalyze the reversible stereoselective addition of a donor compound (nucleophile) onto an acceptor compound (electrophile). Whereas most aldolases are specific for their donor compound in the aldolization reaction, they often tolerate a wide range of aldehydes as acceptor compounds. C–C bonding by aldolases creates stereocenters in the resulting aldol products. This makes aldolases interesting tools for asymmetric syntheses of rare sugars or sugar-derived compounds as iminocyclitols, statins, epothilones, and sialic acids. Besides the well-known fructose 1,6-bisphosphate aldolase, other aldolases of microbial origin have attracted the interest of synthetic bio-organic chemists in recent years. These are either other dihydroxyacetone phosphate aldolases or aldolases depending on pyruvate/phosphoenolpyruvate, glycine, or acetaldehyde as donor substrate. Recently, an aldolase that accepts dihydroxyacetone or hydroxyacetone as a donor was described. A further enlargement of the arsenal of available chemoenzymatic tools can be achieved through screening for novel aldolase activities and directed evolution of existing aldolases to alter their substrate- or stereospecifities. We give an update of work on aldolases, with an emphasis on microbial aldolases.     

Molecular properties of phosphoenolpyruvate carboxylase from C3, C3−C4 intermediate,and C4 Flaveria species

Phosphoenolpyruvate carboxylase (PEPCase; EC 4.1.1.31) from Flaveria trinervia Mohr (C₄), F. floridana Johnston (C₃–C₄), and F. cronquistii Powell (C₃) leaves were compared by electrotransfer blotting/enzyme-linked immunoassay (Western-blot analysis), mobility of the native enzyme in polyacrylamide gels and in isoelectric focusing (IEF) gels, peptide mapping, and in-vitro translation of RNA isolated from each plant. The PEPCases from the C₃ and C₃–C₄ plants were very similar to each other in terms of electrophoretic mobilities on gels and isoenzyme patterns on IEF gels, and identical in peptide mapping. Quantitative differences were noted, however, in that the C₃–C₄ intermediate plant contained more PEPCase overall and that the relative activity of individual isoenzymes shifted between the C₃ and C₃–C₄ intermediate PEPCases. The PEPCase from the C₄ plant had a different isoenzyme pattern, a different peptide map, and was far more abundant than the other two enzymes. Western blot analysis demonstrated the cross-reactivity of PEPCases from all three Flaveria species with antibody raised against maize PEPCase. The results provide evidence, at the molecular level, that supports the view of C₃–C₄ intermediate species as C₃-like plants with some C₄-like photosynthetic characteristics, but there are differences from the C₃ plant in the quantity and properties of the PEPCase from the C₃–C₄ intermediate plant.Abbreviations IEF isoelectric focusing - kDa kilodalton - PEPCase phosphoenolpyruvate carboxylase - Rubisco Ribulose-1,5-bisphosphate carboxylase/oxygenase     

Structures and aromaticity of X2Y 2 − (X = C, Si, Ge and Y = N, P, As) anions

The equilibrium geometries, total energies, and vibrational frequencies of anions X₂Y₂ ⁻ (X = C, Si, Ge and Y = N, P, As) are theoretically investigated with density functional theory (DFT) method. Our calculation shows that for C₂N₂ ⁻ species, the D _2h isomer is the most stable four-membered structure, and for other species the C _2v isomer in which two X atoms are contrapuntal is the most stable structure at the B3LYP/6-311 +G_* level. Wiberg bond index (WBI) and negative nucleus-independent chemical shift (NICS) value indicate the existence of delocalization in stable X₂Y₂ ⁻ structures. A detailed molecular orbital (MO) analysis further reveals that stable isomers of these species have strongly aromatic character, which strengthens the structural stability and makes them closely connected with the concept of aromaticity.     

In-situ immunofluorescent localization of phosphoenolpyruvate and ribulose 1,5-bisphosphate carboxylases in leaves of C3, C4, and C3−C4 intermediatePanicum species

The in-situ inter- and intracellular localization patterns of phosphoenolpyruvate (PEP) and ribulose 1,5-bisphosphate (RuBP) carboxylases in green leaves of severalPanicum species were investigated using an indirect immunofluorescence technique. Four species were examined and compared:P. miliaceum (C₄),P. bisulcatum (C₃), andP. decipiens andP. milioides (C₃–C₄ intermediates which have Kranz-like leaf anatomy and reduced photorespiration). In the C₄ Panicum, PEP carboxylase was located in the cytosol of the mesophyll cells and RuBP carboxylase was restricted to the bundle-sheath chloroplasts. In contrast, in the C₃ Panicum species, PEP carboxylase was found throughout the leaf chlorenchyma, in both the cytosol and chloroplasts, and RuBP carboxylase was located in the chloroplasts. For the C₃–C₄ intermediate plants, the patterns depended on the species examined. ForP. decipiens, the in-situ localization of both carboxylases was similar to that described forP. bisulcatum and other C₃ plants. However, inP. milioides, PEP carboxylase was found exclusively in the cytosol of the mesophyll cells, as inP. miliaceum and other C₄ species, whereas RuBP carboxylase was distributed in both the mesophyll and bundle-sheath chloroplasts.Abbreviations PEP phosphoenolpyruvate - RuBP ribulose 1,5-bisphosphate     

Theoretical study of X- · 1 · YF (1 = triazine,X = Cl,Br and I,Y = H,Cl, Br,I, PH2 and AsH2): noncovalently electron-withdrawing effects on anion-arene interactions

The ternary complexes X^- · 1 · YF (1 = triazine, X = Cl, Br and I, Y = H, Cl, Br, I, PH₂ and AsH₂) have been investigated by MP2 calculations to understand the noncovalently electron-withdrawing effects on anion-arene interactions. The results indicate that in binary complexes (1 · X^-), both weak σ-type and anion-π complexes can be formed for Cl^- and Br^-, but only anion-π complex can be formed for I^-. Moreover, the hydrogen-bonding complex is the global minimum for all three halides in binary complexes. However, in ternary complexes, anion-π complex become unstable and only σ complex can retain in many cases for Cl^- and Br^-. Anion-π complex keeps stable only when YF = HF. In contrast with binary complexes, σ complex become the global minimum for Cl^- and Br^- in ternary complexes. These changes in binding mode and strength are consistent with the results of covalently electron-withdrawing effects. However, in contrast with the covalently electron-withdrawing substituents, Cl^- and Br^- can attack the aromatic carbon atom to form a strong σ complex when the noncovalently electron-withdrawing effect is induced by halogen bonding. The binding behavior for I^- is different from that for Cl^- and Br^- in two aspects. First, the anion-π complex for I^- can also keep stable when the noncovalent interaction is halogen bonding. Second, the anion-π complex for I^- is the global minimum when it can retain as a stable structure.     

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.     

Efficient Preparation of Cyclic 3′,5′-Phosphoramidites and -Amidates of Antiviral and Antitumor 5-X-2′-Deoxyuridines (X = H,CH3, I,F, CF3, trans-CH=CHBr)

Abstract

Direct cyclization of the title nucleosides with (Me₂N)₃P followed by oxidation with N₂O₄ or t-BuOOH affords the individual cyclic 3′,5′-phosphoramidate diastereomers shown to be isolable in 45-77% yields.     

Cα-H···O=C hydrogen bonds contribute to the specificity of RGD cell-adhesion interactions

Background  

The Arg-Gly-Asp (RGD) cell adhesion sequence occurs in several extracellular matrix molecules known to interact with integrin cell-surface receptors. Recently published crystal structures of the extracellular regions of two integrins in complex with peptides containing or mimicking the RGD sequence have identified the Arg and Asp residues as key specificity determinants for integrin recognition, through hydrogen bonding and metal coordination interactions. The central Gly residue also appears to be in close contact with the integrin surface in these structures.     

Ecotypic differences in the C3 and C4 photosynthetic activity in Mollugo verticillata,a C3−C4 intermediate

Four populations of Mollugo verticillata L. were compared on the basis of their photosynthetic products, photosynthetic rates, enhancement under low oxygen concentration, and CO₂ compensation points. In addition, pulse-chase labeling experiments were conducted using one of the four populations. Depending on the plant population, C₄ acids ranged from 40% to 11% of the primary products under short-term exposure to ¹⁴CO₂. These compounds were also metabolized during pulse-chase experiments. All four populations had significantly different photosynthetic rates and those rates were correlated with the amounts of labelled C₄ acids produced and C₄-acid turnover. Three populations of M. verticillata had similar compensation points (40 l/l) and degrees of photosynthetic enhancement under low [O₂] (20%), the fourth population was much lower in both characteristics (CO₂ compensation, 25 l/l; low-O₂ enhancement, 12%). The results verify the intermediate nature of photosynthesis in this species, and illustrate populational differences in its photosynthetic and photorespiratory carbon metabolism.Abbreviations PGA 3-phosphoglyceric acid - Kan Kansas - Mass Massachusetts - Mex Mexico     

Photon requirement for O2-Revolution in red (λ= 680 nm) light for some C3 and C4 plants and a C3–C4 intermediate species*

Photon requirements for O₂-evolution in red (λ=680nm) light (Ф_r) were measured for six C₃ species, one C₃-like, C₃–C₄ intermediate species, and three C₄ species, including examples of NADP-malic enzyme and PEP-carboxykinase C₄ sub-groups. Variation in Ф_r within the C₃ species was small with a mean value of 7.96 ±0.12 mol photon mol⁻¹ O₂, whereas the mean value for the C₄ species was 12.27± 1.53 mol photon mol⁻¹ O₂, with the lowest value, 9.24 ±0.13 mol photon mol⁻¹ O₂, for the PEP-carboxykinase C₄ species Spartina townsendii. The C₃–C₄ intermediate species Panicum milioides had a value of 9.05 ±0.29 mol photon mol⁻¹ O₂, approximately 1 mol photon mol⁻¹ O₂ greater than the C₃ species. The possibility that this extra cost is due to PEP-carboxylase-dependent recycling of CO₂ is discussed. No correlation was found between Ф_r and chlorophyll content or leaf absorptance. Based on white (Ф_W) and red light measurements of the photon requirement, values in red light were approximately 20% higher than white-light estimates. These results are discussed with reference to accepted mechanisms of energy transduction in thylakoid membranes (Z-scheme), expected inefficiencies and losses during light-harvesting and electron transport reactions, and the influence of respiratory processes.     

Immunofluorescent localization of phosphoenolpyruvate carboxylase and ribulose 1,5-bisphosphate carboxylase/oxygenase proteins in leaves of C3, C4 and C3−C4 intermediate Flaveria species

The concentrations of 17 nucleotides and three nucleosides have been determined in a batch suspension culture of Datura innoxia using a new procedure for extraction, purification and high-performance liquid chromatography separation of these compounds. The nucleotide pools change appreciably in the different phases of growth. These changes indicate the preparation for and initiation of cell proliferation, and reflect metabolic events during cell division, cell elongation and starvation. The main components of the nucleotide pool are uracil nucleotides, with uridine 5-diphosphate sugars as the predominant fraction, and the adenine nucleotides. Although their concentrations vary by a factor of more than 6 the ratio of the uracil to adenine nucleotides is kept fairly constant during growth. The energy charge is maintained at a rather high value. The correlation of these events with nutrient uptake and macromolecular synthesis by the batch culture is presented in the following paper.Abbreviations Glc glucose - GlcNAc 2-acetamido-2-deoxy-d-glucose - HPLC high performance liquid chromatography - UDP uridine 5-diphosphate     

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.

Specific Fragmentation of DNA of Adenovirus Serotypes 3, 5, 7, and 12, and Adeno-Simian Virus 40 Hybrid Virus Ad2+ND1 by Restriction Endonuclease R· EcoRI

The products of complete digestion of duplex DNA of each of seven human adenoviruses with restriction endonuclease R. EcoRI ranged from two fragments for adenovirus 7 DNA (Ad7) to six fragments for Ad12 and Ad2 DNA. Viral serotypes from the same subgroups appeared to have related cleavage sites; Ad3 DNA and Ad7 (cl E46-LL) DNA were each cleaved into three fragments, and Ad7 (cl 19) DNA lacked one of the cleavage sites present in Ad3 and Ad7 (cl E46-LL) DNA. One of the cleavage sites in Ad2 DNA was deleted in the DNA' of adeno-SV40 hybrid virus Ad2(+)ND1, and three of the cleavage sites in Ad2 DNA were missing in Ad5 DNA. Thus, Ad2(+)ND1 DNA was cleaved into five and Ad5 DNA into three fragments. Each fragment represented a unique segment of viral DNA since each fragment was obtained in equimolar amounts and since the sum of the molecular weights of the fragments equaled the molecular weight of the homologous intact adenovirus DNA.