Hydrogen-bonding interactions in peptide nucleic acid and deoxyribonucleic acid: a comparative study

Peptide nucleic acid (PNA) is a synthetic analogue of deoxyribonucleic acid (DNA) capable of tightly binding to itself and DNA with high specificity. Using hybrid density functional methods, hydrogen-bond (H-bond) strengths have been evaluated for isolated Watson-Crick base pairs, PNA base pairs, and charged as well as neutral DNA base pairs. Heterogeneous base pairs of PNA with charged and neutral DNA have also been investigated. The competing effects of short-range H-bonding and long-range Coulombic repulsions in charged DNA base pairs have been analyzed. Polarizable continuum models have been employed to evaluate solvation effects on the binding energies.     

Hydrogen-bonding interactions in cinchonidine-2-methyl-2-hexenoic acid complexes: a combined spectroscopic and theoretical study

Molecular interactions between cinchonidine (CD) and 2-methyl-2-hexenoic acid (MHA) have been studied by means of NMR, ATR-IR MES, DFT, and ab initio molecular dynamics. These interactions are of particular interest due to their pivotal role in the chiral induction occurring in the heterogeneous catalytic asymmetric hydrogenation of alpha,beta-unsaturated acids. The population density of the Open(3) conformer of CD, the most populated one at room temperature in apolar solvents, considerably increased to a maximum by addition of MHA to CD in toluene. The CD-MHA complex showed prominent symmetric and asymmetric carboxylate stretching vibrations in the regions of 1350-1410 and 1520-1580 cm(-1), respectively. DFT calculations revealed that these vibrational frequencies are expected to significantly shift depending on the chemical surrounding of MHA, that is, the hydrogen bond network. Earlier postulated 1:1 binding between CD and MHA was considered unlikely; instead, a dynamic equilibrium involving the MHA monomer and dimer, the 1:3 and possibly 1:2 CD-MHA complexes, were rationalized. Stable CD-MHA structures suggested by DFT calculations are the "1:3, halfN, cyclic" and the "1:3, halfN, cyclic tilted" complexes, where three MHA molecules are connected in wire by hydrogen bonding, two having direct interaction with CD. The confinement of CD's torsional motions in the complexes, leading to a slightly distorted Open(3) conformer via specific hydrogen-bonding interactions, was clearly reproduced by ab initio molecular dynamics, and the stable and flexible nature of the interaction was verified. Theoretical IR spectra of the complexes reproduced the characteristic vibrational frequencies of the complexes observed experimentally, supporting the stability of the 1:3 and implying the possibility of even higher molecular weight CD-MHA complexes.     

Hydrogen-bonding interactions in acetic acid monohydrates and dihydrates by density-functional theory calculations

Equilibrium structures and the respective binding energies of acetic acid monohydrates and dihydrates have been determined by density-functional theory calculations with different basis sets, including 6-31+G(3d,p), 6-311++G(d,p), and 6-311++G(3df,3pd). Given that the C=O and OH groups in acetic acid provide the predominant hydrogen-bonding interactions with water, six stable conformer structures have been found each for the monohydrate and syn-dihydrate. Of the three syn- and three anti-conformers of acetic acid with water, the most stable monohydrate structure is found to be that of the syn-conformer bonding with water in a cyclic double H-bonded geometry. Similarly, the syn-conformer bonding with two water molecules in a cyclic double H-bonded geometry has also been determined to be the most stable among the six plausible structures for the syn-dihydrate. Frequency analysis of the stable conformers has been performed and the vibrational spectra of the most stable monohydrate and dihydrate structures are compared with the experimental gas-phase and matrix data. Furthermore, the calculated binding energies between an acetic acid and a water molecule for both monohydrate and dihydrate are larger than that between two water molecules, which supports our recent experimental observation of coevaporation of acetic acid with water upon annealing acetic acid on ice.     

Hydrogen-bonding interactions in ferrocene-peptide conjugates containing valine

The synthesis and characterization of a series of ferrocene (Fc) peptide conjugates containing the amino acid valine is reported, where the peptide substituents are part of the hydrophobic sequence of the amyloid β-peptide. The hydrogen-bonding (H-bonding) interaction in these compounds is studied by variable temperature ¹H NMR spectroscopy. The solid-state structures, determined by single crystal X-ray crystallography, of two of the conjugates (Fc[CO-Leu-Val-OMe]₂1 and Fc[CO-Gly-Val-OH]₂6) are reported. Both structures are stabilized by intramolecular H-bonds exhibiting the familiar “Herrick motif” involving the proximal amide NH and the amide CO of the adjacent amino acid. This motif is sufficiently rigid and is maintained in solution as suggested by CD studies. However, the intermolecular H-bonding patterns observed on conjugates 1 and 6 are significantly different resulting in very different supramolecular architectures. For conjugate 1, a more conventional set of head-to-tail stacking interactions which is stabilized by β-sheet-like H-bonding interactions between the individual molecules is observed. However, for conjugate 6, the presence of the C-terminal acid group and presumably the flexibility of the Gly linker enables the formation of a more open structure that contains hydrophobic channels occupied by solvent molecules.     

Hydrogen-bonding interactions of the trifluoromethyl group: 2-Trifluoromethylvinyl alcohol

As part of our investigation of intramolecular hydrogen bonding and its geometrical consequences, ab initio molecular orbital calculations on 2-trifluoromethylphenol and 2-trifluoromethylvinyl alcohol and their parent structures were performed at the MP2/6–31+G^** level of theory. The intramolecular hydrogen bonding in 2-trifluoromethylvinyl alcohol appears stronger than that in 2-trifluoromethylphenol as witnessed by the shorter F...H interaction (1.96 Å) and the greater bond length changes in the rest of the molecule, as compared with the respective parent molecules. Beyond the geometrical characteristics, the energetics of hypothetical isodesmic reactions and the small shift of the O(SINGLE BOND)H stretching frequency indicate that these C(SINGLE BOND)F...H(SINGLE BOND)O interactions are rather weak. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 62: 645–652, 1997     

Immobilization of Tyrosinase in Poly(2-thiophen-3-yl-alkyl ester) Derivatives

In this study, construction of novel biosensors for the determination of phenolic compound was performed via immobilization of tyrosinase during the electrochemical synthesis of conducting block copolymers of 2-thiophen-3-yl-alkyl ester derivatives with 3,4-ethylenedioxythiophene and synthesis of poly(3,4-ethylenedioxythiophene) (PEDOT). The resultant biosensors were characterized in terms of their maximum reaction rates, Michaelis–Menten constants (K_m), temperature and pH stabilities. All the copolymer matrices represented higher reaction rates and higher K_m values in comparison to both polypyrrole and PEDOT matrices and a relation between the morphology of the matrice and the kinetic parameters was observed. Biosensors maintained their activity even at temperatures as high as 80°C and could be used at pHs higher than 8 with high precision. The amount of phenolics in actual samples (red wines) was investigated using electrodes, and results were compared with those found from Folin–Ciocalteau method. Hence, the present study has proven the suitability of these copolymers to be used as polymer matrices for enzyme immobilization.     

Hydrogen-bonding interactions in gas-phase polyether/ammonium ion complexes

Hydrogen bonds are among the most important interactions involved in selective complexation in host-guest chemistry. In this study a variety of hydrogen-bonded crown ether/ammonium ion complexes are generated in the gas phase by association reactions between an amine substrate and a polyether, one of which is initially protonated, and stabilized by many collisions in the chemical ionlzation source of a triple quadrupole mass spectrometer or in a quadrupole ion trap. The nature of the hydrogen-bonding interactions of the ion complexes are evaluated by comparison of their collision-activated dissociation spectra. After collisional activation, those complexes that are weakly bound dissociate to form intact protonated polyether molecules and/or ammonium ions by simple cleavages of the hydrogen-bond association interactions. In contrast, those complexes strongly bound by multiple hydrogen bonds dissociate not only to the protonated polyether and/or ammonium ions but also by extensive covalent bond cleavage of the protonated ether skeleton.This latter type of dissociation behavior suggests that the polyether/ammonium ion complexes may be sufficiently strongly bound that surpassing the high barrier to decomposition results in formation of internally excited polyether molecules that may then undergo subsequent fragmentation by skeletal cleavages. Moreover, complexes involving multiple hydrogen bonds may have slower dissociation kinetics, allowing competition from fast dissociation processes that have substantial energy barriers.     

Hydrogen-bonding interactions in acetonitrile oligomers using density functional theory method

Hydrogen-bonding interaction in acetonitrile oligomers is studied using density functional theory method. Two types of hydrogen-bonded oligomers are considered viz. cyclic and ladder. Different levels are used to optimize the geometry of acetonitrile monomer and found that at B3LYP/aug-cc-pvtz level the geometrical parameters and vibrational frequencies are in agreement with the experimental determinations. The BSSE corrected total energies of acetonitrile oligomers show that the cyclic structures are more stable than the ladder and the hydrogen bonds in former are stronger than those in the latter. Many-body analysis approach was used to study the nature of interactions between different molecules in these oligomers. It is found that the contribution from many-body energies to the binding energy of a complex is different in cyclic and ladder structures. An increase and decrease in the energy per hydrogen bond with cluster size for the cyclic and ladder structures, respectively, indicates the positive and negative hydrogen-bond cooperativity, respectively.     

Hydrogen-bonding network in the organic salts of 4-nitrobenzoic acid

The crystal structures of six novel salts of 4-nitrobenzoic acid — namely, 2-hydroxyethylammonium 4-nitrobenzoate (I), 2-hydroxypropylammonium 4-nitrobenzoate (II), 1-(hydroxymethyl)propylammonium 4-nitrobenzoate (III), 3-hydroxypropylammonium 4-nitrobenzoate (IV), bis-(2-hydroxyethylammonium) 4-nitrobenzoate (V), morpholinium 4-nitrobenzoate (VI) — containing the same anion but different cations have been studied. The ionic forms of I-VI serve as building blocks of the supramolecular architecture, and in crystals they are held together via ionic N-H···O and O-H···O hydrogen bonds. In the crystal packing the building blocks of I-III are self-assembled via N-H...O, O-H···O and C-H...O hydrogen bonds to form the chains which are further consolidated into two-dimensional layers by the same type of interactions. In IV-VI the chain-like structures have been generated by building blocks.     

Configuration and conformational equilibrium of (±)-trans-1-oxo-3-thiophen-2-yl-isochroman-4-carboxylic acid methyl ester

The X-ray analysis of 1-oxo-3-thiophen-2-yl-isochroman-4-carboxylic acid methyl ester 1 confirmed its trans-configuration and a conformation with diaxial H-3 and H-4 atoms in solid state. NMR experiments indicated that trans-1 exists in solution in both expected conformers. In CDCl₃ and especially in CD₃OD or DMSO, the conformational equilibrium is shifted towards the conformer with diequatorial H-3 and H-4, which was also determined by 2D NOESY experiments. The shift is due to the greater polarity of that conformer deduced by ab initio calculations.     

Hydrogen-bonding versus van der Waals interactions in self-assembled monolayers of substituted isophthalic acids

Self-assembled monolayers of a series of isophthalic acids (5-octadecyloxyisophthalic acid, 5-decyloxyisophthalic acid, 5-hexyloxyisophthalic acid, and 5-pentyloxyisophthalic acid) formed on highly ordered pyrolytic graphite (HOPG) at the solid-liquid interface were studied using scanning tunneling microscopy (STM). Although these molecules have the same dicarboxyl headgroup, their hydrocarbon tails are of different lengths. Hydrogen-bonding between headgroups and van der Waals interactions between the hydrocarbon tails control the final morphology of the monolayer. The STM images show that both van der Waals interactions (vdWs) and hydrogen-bonding (H-B) compete to control the structure, but the final structure of the monolayer is determined by balance between the two interactions.     

Hydrogen-bonding effects in calix

The synthesis and spectroscopic characterization of self-assembling calix[4]arene based capsules 1a.1a and 1b.1b are described. These compounds feature four urea substituents at the upper rims and four secondary amide fragments at the lower rims that can participate in inter- and intramolecular hydrogen bonding in apolar solution. Communication between the calixarene rims in 1a, b influences the self-assembled cavity's size and shape. Specifically. dimerization results in a perfect cone conformation of the calixarene skeleton in 1a, b and stabilizes a seam of intramolecular amide C=O...H-N hydrogen bonds at the lower rim. This seam is cycloenantiomeric, with either clockwise or counterclockwise arrangements of the head-to-tail amides. Complexation of Na+-cation breaks hydrogen bonds at the lower rim but maintains the capsular assembly. Encapsulation properties of 1a.1a and 1b.1b were studied in nonpolar solvents and their binary mixtures as well as through heterodimerization experiments. The presence of amide groups at the lower rim causes notable differences in the capsule's binding affinities when compared to the corresponding tetraester capsules 1c.1c and 1d.1d. In the monomeric state calixarenes 1a, b are in a pinched cone conformation. The solid state X-ray crystallographic studies with monomeric 1a reveal only two intramolecular C=O...H-N hydrogen bonds between the adjacent amides at the lower rim, and an extensive network of intermolecular hydrogen bonds between urea groups at the upper rim.     

Hydrogen-bonding interactions in the binding of loop 1 of fasciculin 2 to Torpedo californica acetylcholinesterase: a density functional theory study

In the present study, the interactions of model complexes at the interface between loop1 of fasciculin 2 (Fas2) and acetylcholinesterase (AChE) are theoretically explored. Three interaction models based upon the crystal structure of the complex of Fas2 with AChE from Torpedo californica (PDB code ) were fully optimized at the B3LYP/6-311G(d,p) level of theory. The atoms-in-molecules (AIM) approach was employed to characterize the corresponding noncovalent hydrogen bonds through the densities and the Laplacians of electron densities at the bond critical points. The total interaction energy of loop 1 (Fas2) with AChE is predicted to be -99.4 kcal/mol. It is concluded that the Fas2 residue Thr8, which contributes more than half of the total binding energy, plays the most important role among the three binding sites. The energy decomposition results through the Kitaura-Morokuma scheme suggest that the electrostatic term is the major component of the entire interaction energy. The positive cooperativity effect revealed in the Thr8(F)-related models was confirmed through the geometry characteristics, AIM results, and the energy decomposition analysis.     

Hydrogen-bonding interaction between acetic acid and pyridine 1:1 complex

Acetic acid (CH₃COOH) and pyridine (C₅H₅N) 1:1 complex was subjected to Density Functional Theory (DFT) calculations using 6-311G(d,p) basis set. Five equilibrium isomers were located, and the most stable structure has a strong NH–O hydrogen-bonding interaction. A normal-mode analysis of the vibrations of the five isomers was carried out and compared with the experimental values. The calculations indicate that solvents enhance significantly the strength of hydrogen bond as shown by the decrease of the N–H distance and appreciable red shift of the H–O vibration mode and blue shift of NH–O vibration mode.     

Perfluorobutane sulfonic acid hydration and interactions with O2 adsorbed on Pt3

The side chain of NAFION, a proton conductive membrane used as electrolyte in low-temperature fuel cells, is modeled with perfluorobutane sulfonic acid. Density functional theory is used to characterize structures and energetics of hydration of the model system interacting with a proton solvated with up to 24 water molecules and analyze interactions of some of these hydrated complexes with O(2) adsorbed on Pt(3). It is found that at least three water molecules are needed to ionize the sulfonic acid, and higher degrees of hydration induce the formation of cages where the water molecules are held together via complex hydrogen-bond networks. The interaction between the complex formed by the ionized acid and the hydrated proton, in contact with a bridge-adsorbed O(2)-Pt(3), promotes the protonation of the adsorbed O(2). Upon protonation, the O(2)-Pt(3) system evolves from hydrophobic to hydrophilic behavior, which may facilitate further interfacial contact.     

Hydrogen-bonding motifs in fullerene chemistry

The combination of fullerenes and hydrogen-bonding motifs is a new interdisciplinary field in which weak intermolecular forces allow modulation of one-, two-, and three-dimensional fullerene-based architectures and control of their function. This Minireview aims to extend the scope of fullerene chemistry to a truly supramolecular level from which unprecedented architectures may evolve. It is shown that electronic communication in C(60)-based hydrogen-bonded donor-acceptor ensembles is at least as strong as that found in covalently connected systems and that hydrogen-bonding fullerene chemistry is a versatile concept for the construction of functional ensembles.     

Molecular interactions in 3-carboxy-2-diphenylphosphinoylcyclopentanone

The results of the X-ray structure analysis of the title compound (I) have been reported in [Synthesis (1997) 356]. Now we continue our efforts to understand the energy situation and the arrangements in the crystal, which will be strongly influenced by the formation of hydrogen bonds with the help of the results of theoretical calculations. Furthermore, the IR spectroscopic measurements will be discussed in comparison to the X-ray data. The IR experiments elucidate the molecular arrangement in solution. Using different solvents, equilibrium states with coexisting conformational and associative arrangements were observed. Unexpectedly, the alternative use of the solvents CHCl(3) or CDCl(3) has different influence on the equilibrium arrangement of I in solution.     

刚性配体3-噻吩-5-三氟甲基-2,3-二氢-1-H吡唑合成的2个Keggin型超分子化合物

选用新颖的有机配体3-噻吩-5-三氟甲基-2,3-二氢-1-H吡唑（L）,在水热条件下成功得到2个新的基于Keggin多酸的超分子化合物,{[Ag（L）_2]_3[PMo_（12）O_（40）]}·3H_2O（1）和{[Ag（L）_2]_3[HSiMo_（12）O_（40）]}·3H_2O（2）.通过红外光谱、元素分析和单晶X-射线对化合物1和2的结构进行了表征.化合物1和2同构,包含1个孤立的Keggin多阴离子和3个金属-有机亚单元[Ag（L）2]＋.其中多酸阴离子和[Ag（L）2]＋片段通过氢键作用力交替连接形成1个一维超分子链.相邻一维链进一步通过氢键连接成二维超分子层状结构.光催化和电化学性质表明,化合物1和2具有相同的电化学性能.     

Synthesis and Antinociceptive Activity of N -Substituted 4-Aryl-4-oxo-2-[(3-thiophen-2-yl)amino]but-2-enamides

2-{[5-Aryl-2-oxofuran-3(2H)-ylidene]amino}thiophene-3-carboxylic acid derivatives reacted with substituted amines to give new N-substituted 4-aryl-4-oxo-2-[(3-thiophen-2-yl)amino]but-2-enamides. Antinociceptive activity of the synthesized compounds was studied.