Comparison of hydrogen- and halogen-bonding interactions in the complexes of the substituted carbonyl compounds with hypohalous acids and monohaloamines

Structural Chemistry - An ab initio study of the complexes formed by hypohalous acids and monohaloamines (designated as HAX where A = O or NH and X = Cl, Br, or I) with RCHO (R = H, CH3, OCH3, and...     

Competition of hydrogen bonds and halogen bonds in complexes of hypohalous acids with nitrogenated bases

A theoretical study of the complexes formed by hypohalous acids (HOX, X = F, Cl, Br, I, and At) with three nitrogenated bases (NH 3, N 2, and NCH) has been carried out by means of ab initio methods, up to MP2/aug-cc-pVTZ computational method. In general, two minima complexes are found, one with an OH...N hydrogen bond and the other one with a X...N halogen bond. While the first one is more stable for the smallest halogen derivatives, the two complexes present similar stabilities for the iodine case and the halogen-bonded structure is the most stable one for the hypoastatous acid complexes.     

Probing the weak interactions between amino acids and carbon monoxide

The relatively weak interactions between some non-charged amino acids with CO were investigated theoretically by using density functional theory （DFT） method. The stretching frequency of CO correlates well with its bond length followed the Badger＇s rule, and the correlation between binding energy and Mulliken charge partition of CO was also investigated for the first time. 2007 Ying Wu Lin. Published by Elsevier B.V. on behalf of Chinese Chemical Society. All rights reserved.     

Weak interactions between deposited metal overlayers and organic functional groups of self-assembled monolayers

The purpose of our research is to study the reactions, interactions or penetration between vacuum-deposited metals (M) and the organic functional end groups (OFGs) of self-assembled monolayers (SAMs) under controlled conditions. Metal/SAM systems are models for understanding bonding at M/organic interfaces and the concomitant adhesion between the different materials. In broad terms, the M/OFGs form interacting interfaces (e.g., Cr/COOH or Cu/COOH) in which the deposit resides on top of the OFGs or weakly interacting interfaces through which the overlayer penetrates and resides at the SAM/gold interface. We present a review of XPS results from weakly interacting systems (e.g., Cu/OH, Cu/CN, Ag/CH₃, Ag/COOH) and discuss in more depth the time-temperature dependence of the disappearance of the metal from the M/SAM interface following deposition. In this work, XPS and ISS were used to characterize octadecanethiol (ODT, HS(CH₂)₁₇CH₃), mercaptoundecanoic acid (MUA, HS(CH₂)₁₀COOH), and mercaptohexadecanoic acid (MHA, HS(CH₂)₁₅COOH) SAMs before and after depositing up to 1.0 nm Ag or Cu at ca. 10⁻⁷ torr. The SAMs were prepared by self-assembly onto gold films on <100> silicon substrates in an ethanolic thiol solution. XPS spectra indicate that no strong interaction occurs between the deposited Ag and the COOH organic functional group (OFG) of MUA or MHA, although a stronger interaction is evident for MHA, and a unidentate is formed for Cu on mercaptoundecanol (MUO). The Ag interaction with ODT is weak. ISS compositional depth profiles (CDPs) for Ag on MHA and MUA and ODT are compared over a temperature range of 113 to 293 K. The ISS results indicate that Ag remains on the surface of MUA for up to 1 h after deposition, whereas Ag penetrates ODT in less than 5 min at 295 K. The time for Ag to penetrate into MHA is several times longer than for MUA, depending on the SAM temperature. The time dependence of the slower Ag penetration through MUA and MHA is compared with that for ODT at temperatures below 295 K. Although Ag/OFGs are expected to have relatively weak interactions, the Ag/COOH system was anticipated to be more interactive than was found, so rapid penetration of Ag through the COOH SAM is an unexpected result.     

Weak interactions in furan dimers

Dimers of furan, 2,3-dihydrofuran, 2,5-dihydrofuran and tetrahydrofuran were investigated with the use of theoretical methods to determine the interactions that keep the molecules together. The QTAIM and NCI methods confirmed that for furan dimers the C–H?O hydrogen bond and stacking interactions can form the dimers with similar energy. For 2,3-dihydrofuran, 2,5-dihydrofuran and tetrahydrofuran, the decisive mechanism of dimer formation is the stacking interaction between the furan rings.     

Weak dihydrogen bond interactions in organic crystals

Database analysis on H ? H interactions of the type CH₂ ? H₂C and N-H ? H-N in organic crystals substantiate the occurrence of dihydrogen bonds in the absence of metal atoms.     

Weak calcium-mediated interactions between Lewis X-related trisaccharides studied by NMR measurements of residual dipolar couplings

The Lewis X (LeX) determinant, a trisaccharide with the carbohydrate sequence Galbeta(1-->4)[Fucalpha(1-->3)]GlcNAcbeta, is believed to be responsible for Ca2+-mediated cell-cell interactions. In partly oriented phases composed of mixtures of penta(ethyleneglycol)monododecyl ether HO(CH2CH2O)5C12H25 and n-hexanol in the presence of Ca2+ ions, the variation of the residual dipolar couplings 1DCH of various CiHi vectors in LeX as a function of the concentration of the trisaccharide demonstrates the existence of very weak LeX-Ca2+-LeX complexes in solution. Synthetic 3-, 4-, and 6-deoxy-LeX variants were also shown to form complexes in the presence of calcium ions, despite the replacement of one of their hydroxyl groups by hydrogen atoms. This is the first direct observation in solution of a calcium-mediated interaction between LeX molecules.     

Weak attractive interactions between methylthio groups and electron-deficient alkenes in peri-naphthalenes: a competition with conjugative effects

The solid-state conformations of five peri-disubstituted naphthalenes bearing a methylthio group and an electron-deficient alkene indicate a weak attractive interaction between the functional groups in four cases in which out-of-plane displacements lead to a common orientation of the MeSsp(2)-C vector to the alkene bond. In some cases the interaction is not strong enough to outweigh the tendency of the alkene to conjugate with the aromatic ring, and in one case this optimisation of conjugation alone controls the molecular conformation. The methylthio group lies close to the aromatic plane in all but one example for which the plane of the sulfide group is presented to the alkene.     

Characterization of hydrogen bonds in the interactions between the hydroperoxyl radical and organic acids

The hydrogen bonds formed between the hydroperoxyl radical and formic, acetic, and trifluoroacetic acids were characterized using geometric, energetic, and electronic parameters through calculations done with the UB3LYP/6-311++G (3df,3pd) and UB3LYP/EPR-III methods. The wave functions were analyzed through the natural bond orbital, natural steric analysis, natural resonance theory, and atoms in molecules methods. The energy decomposition method proposed by Xantheas was used. The vibrational frequencies and the intensity of the O-H stretching bands, as well as the spin densities, were compared with experimental evidence. The results allowed the characterization of the hydrogen bonds formed in the complexation of the acids with the hydroperoxyl radical. Complexation led to significant alterations in the equilibrium geometry of the monomers. Energetic analysis proved that the studied complexes are stable and allowed the understanding of the effect of the electron-donating and electron-withdrawing groups in their stabilization. The alterations in the electronic structure of the monomers after complexation led to an increase in the resonance of the carboxyl group, which can be partially attributed to the hydrogen bond.     

Weak intermolecular interactions in gas-phase nuclear magnetic resonance

Gas-phase nuclear magnetic resonance (NMR) spectra demonstrating the effect of weak intermolecular forces on the NMR shielding constants of the interacting species are reported. We analyse the interaction of the molecular hydrogen isotopomers with He, Ne, and Ar, and the interaction in the He-CO(2) dimer. The same effects are studied for all these systems in the ab initio calculations. The comparison of the experimental and computed shielding constants is shown to depend strongly on the treatment of the bulk susceptibility effects, which determine in practice the pressure dependence of the experimental values. Best agreement of the results is obtained when the bulk susceptibility correction in rare gas solvents is evaluated from the analysis of the He-rare gas interactions, and when the shielding of deuterium in D(2)-rare gas systems is considered.     

Investigation of the interactions between ginsenosides and amino acids by mass spectrometry and theoretical chemistry

In order to evaluate the essence of the interactions of ginsenosides and proteins which are composed by α-amino acids, electrospray ionization mass spectrometry was employed to study the noncovalent interactions between ginsenosides (Rb₂, Rb₃, Re, Rg₁ and Rh₁) and 18 kinds of α-amino acids (Asp, Glu, Asn, Phe, Gln, Thr, Ser, Met, Trp, Val, Gly, Ile, Ala, Leu, Pro, His, Lys and Arg). The 1:1 and 2:1 noncovalent complexes of ginsenosides and amino acids were observed in the mass spectra. The dissociation constants for the noncovalent complexes were directly calculated based on peak intensities of ginsenosides and the noncovalent complexes in the mass spectra. Based on the dissociation constants, it can be concluded that the acidic and the basic amino acids, Asp, Glu, Lys and Arg, bound to ginsenosides more strongly than other amino acids. The experimental results were verified by theoretical calculations of parameters of noncovalent interaction between ginsenoside Re and Arg which served as a representative example. Two kinds of binding forms, “head–tail” (“H–T”) and “head–head” (“H–H”), were proposed to explain the interaction between ginsenosides and amino acids. And the interaction in “H–T” form was stronger than that in “H–H” form.     

Complexes pairing hypohalous acids with nitrosyl hydride. blue shift of a NH bond that is uninvolved in a H-bond

Correlated calculations are used to analyze the interaction between nitrosyl hydride (HNO) and hypohalous acids (HOF, HOCl, and HOBr). Two minima are located on the potential energy surface of each complex, in both of which HOX acts as proton donor. Donation to the N atom of HNO makes for a more strongly bound complex, as compared to the OH..O bond in the secondary minimum. Binding energies of the global minimum are about 22 kJ/mol, as compared to 18 kJ/mol for the secondary structure; there is little sensitivity to the identity of the halogen atom. Whereas the covalent OH bond of HOX stretches and shifts to the red upon complexation, the NH bond of HNO, whether involved in a H-bond or not, behaves in the opposite manner.     

Cation interactions with polyamic acids

Polyamic acid films interact as ion-exchange substrates for dilute aqueous cation solutions. Three conditions were evaluated: basic solutions which form soluble amic acid salts and dissolve the film, weakly acidic solutions which encourage classical weak acid cation exchange, and strongly acidic solutions which discourage exchange. Thermal treatment of the generated cationamate salts generally causes degradation of the polymer backbone. Furthermore, lead and copper react directly with the polyamic acid to yield surface-bound salts, but tin and aluminum seem unreactive.     

Weak interactions in the assembly of strongly chemisorbed molecules

The intermolecular structure of bimolecular complexes formed on Pt(111) at room temperature through CH···O interactions between 1-methylnaphthalene or 1-ethylnaphthalene and 2,2,2-trifluoroacetophenone is directed by the partial dehydrogenation of the alkyl groups.     

Weak interactions and molecular recognition in systems involving electron transfer proteins

Electrostatic interactions and other weak interactions between amino acid side chains on protein surfaces play important roles in molecular recognition, and the mechanism of their intermolecular interactions has gained much interest. We established that charged peptides are useful for investigating the molecular recognition character of proteins and their molecular interaction induced structural changes. Positively charged lysine peptides competitively inhibited electron transfer from reduced cytochrome f (cyt f or cytochrome c (cyt c) to oxidized plastocyanin (PC), due to neutralization of the negatively charged site of PC by formation of PC-lysine peptide complexes. Lysine peptides also inhibited electron transfer from cyt c to cytochrome c peroxidase. Likewise, negatively charged aspartic acid peptides interacted with the positively charged sites of cytfand cyt c, and competitively inhibited electron transfer from reduced cytfor cyt c to oxidized PC and from [Fe(CN)6]4- to oxidized cyt c. Changes in the geometry and a shift to a higher redox potential of the active site Cu of PC on oligolysine binding were detected by spectroscopic and electrochemical measurements, owing to the absence of absorption in the visible region for lysine peptides. Structural and redox potential changes were also observed for cyt f and cyt c by interaction with aspartic acid peptides.     

金属配合物与DNA的弱相互作用

介绍了金属配合物与DNA相互作用的嵌入、沟槽和静电3种主要模式,并介绍了目前常用的研究方法,包括紫外-可见吸收光谱法、荧光光谱、黏度法、循环伏安法。     

Weak acids enhance halogen activation on atmospheric water's surfaces

We report that rates of I(2)(g) emissions, measured via cavity ring-down spectroscopy, during the heterogeneous ozonation of interfacial iodide: I(-)(surface, s) + O(3)(g) + H(+)(s) →→ I(2)(g), are enhanced several-fold, whereas those of IO·(g) are unaffected, by the presence of undissociated alkanoic acids on water. The amphiphilic weak carboxylic acids appear to promote I(2)(g) emissions by supplying the requisite interfacial protons H(+)(s) more efficiently than water itself, at pH values representative of submicrometer marine aerosol particles. We infer that the organic acids coating aerosol particles ejected from ocean's topmost films should enhance I(2)(g) production in marine boundary layers.