Hydrogen Bonds in GlcNAc( β1,3)Gal( β)OMe in DMSO Studied by NMR Spectroscopy and Molecular Dynamics Simulations

Shim, Gyu-Chang,Shin, Jae-Min,Kim, Yang-Mee Korean Chemical Society 2004 Bulletin of the Korean Chemical Society Vol.25 No.2

Hydrogen bond is an important factor in the structures of carbohydrates. Because of great strength, short range, and strong angular dependence, hydrogen bonding is an important factor stabilizing the structure of carbohydrate. In this study, conformational properties and the hydrogen bonds in GlcNAc( ${\beta}$1,3)Gal(${\beta}$)OMe in DMSO are investigated through NMR spectroscopy and molecular dynamics simulation. Lowest energy structure in the adiabatic energy map was utilized as an initial structure for the molecular dynamics simulations in DMSO. NOEs, temperature coefficients, SIMPLE NMR data, and molecular dynamics simulations proved that there is a strong intramolecular hydrogen bond between O7' and HO3' in GlcNAc( ${\beta}$1,3)Gal(${\beta}$)OMe in DMSO. In aqueous solution, water molecule makes intermolecular hydrogen bonds with the disaccharides and there was no intramolecular hydrogen bonds in water. Since DMSO molecule is too big to be inserted deep into GlcNAc(${\beta}$1,3)Gal(${\beta}$)OMe, DMSO can not make strong intermolecular hydrogen bonding with carbohydrate and increases the ability of O7' in GlcNAc(${\beta}$1,3)Gal(${\beta}$)OMe to participate in intramolecular hydrogen bonding. Molecular dynamics simulation in conjunction with NMR experiments proves to be efficient way to investigate the intramolecular hydrogen bonding existed in carbohydrate.

Quantum Mechanical Study on Hydrogen Bonds between 3-Aminophenol and CHxCl4 − x (x = 1, 2, 3): Effect of the Number of Halogen Atoms

이소영,강혁 대한화학회 2015 Bulletin of the Korean Chemical Society Vol.36 No.3

Hydrogen bonds between 3-aminophenol and three chlorine-substituted methanes (CHCl3, CH2Cl2, and CH3Cl) were quantum mechanically studied at MP2/aug-cc-pVDZ level. Several low-energy structures with a hydrogen bond were identified for all chlorinated methanes, and the properties of their CH stretching vibrations were investigated. When it is hydrogen-bonded to 3-aminophenol (3AP), the CH stretching frequency of CHCl3 is blue-shifted by 18–54 cm−1, and its IR absorption intensity is 48–74 times increased, depending on the isomer. The symmetric and antisymmetric CH stretches of CH2Cl2 and CH3Cl are shifted in either direction by a few cm−1 upon hydrogen-bonding to 3AP, and their IR intensity was increased by a few times. It is concluded that all chlorinated methanes can make a π-hydrogen bond to 3AP but only CHCl3, the one with the most chlorine atoms, makes a blue-shifting hydrogen bond, or an “antihydrogen bond”.

2-Pyridone을 이용한 Nucleic Acid Bases간의 Multiple Hydrogen Bonding에 관한 연구

황정숙 대전대학교 기초과학연구소 2000 自然科學 Vol.11 No.2

핵산 염기간의 multiple hydrogen bonding model로서 2-pyridone의 N-methyl-2-pyrrolidone 에 대한 hydrogen bonding association을 25℃ 사염화 탄소 용액에서 측정하여 94 M^(?)의 값을 얻었다. Complexation constant 값을 고정한 후, pK_(a) of N-H acids와 bases의 log K 간의 Bronsted relationship을 이용하여, 2-Pyridone의 dimerization constant 값 k_(d)를 계산한 결과 1.2×10^(5) M^(-1)로 나왔다. 2-pyridone의 oxygen bases에 대한 hydrogen bonding equilbrium constant는 다른 N-H acid의 같은 bases에 대한 예상처보다 큰 것으로 보였다. Hydrogen bonding association of 2-pyridone to N-methyl-2-pyrrolidone in carbon tetrachloride at 25° was measured( 94N^(-l)). After fixing the complaxation constant, the dunerization constant of 2-pyridone was also calculated from the relationship between the pK_(a), of N-H acids and log K for bases and got the value of kd as 12x10^(5) with the standard deviation of 0.002. it seems that the hydrogen bonding equilibrium constant for 2-pyridone to the oxygen bases is larger than the expected from the other N-H acid to the same base.

Quantum Mechanical Study on the Blue-Shifting Hydrogen-Bond between 3-Aminophenol and CHX3 (X=F, Cl)

이소영,강혁 대한화학회 2015 Bulletin of the Korean Chemical Society Vol.36 No.1

Intermolecular bonding between 3-aminophenol and two halomethanes, namely fluoroform and chloroform, was quantum mechanically investigated. Several low-energy structures are found, and all geometries within 1 kcal/mol show π-hydrogen bonds between the aromatic ring and the hydrogen atom of the halomethane. The C H stretching frequency of halomethane involved in the π-hydrogen bond is blue-shifted, and the amount of blue shift is the largest with the most stable isomer and decreases with decreasing stability. Binding energy, infrared intensity, and dipole moment as a function of relative stability are also reported. This study forms another example of a blue-shifting hydrogen bond, or an anti-hydrogen bond.

Cooperative Effect of the Two Hydrogen Bonding Types on 11/9-Helical Folding of α/β-Peptides

장근혁,이미혜,이재연,심지현,강필재,최문근,최수혁 대한화학회 2018 Bulletin of the Korean Chemical Society Vol.39 No.2

α/β-Peptide 11/9-helix is an unconventional helical structure in which 11- and 9-membered ring hydrogen bonds alternate along the helical axis. We have examined the interplay and the relative strength of these two hydrogen bonding types by IR, NMR, and X-ray crystallographic methods. A pair of two adjacent hydrogen bonds with opposite directionality cooperatively stabilized each other in non-hydrogen-bonding solvents. In contrast, an unpaired hydrogen bond was unstable to promote helical folding. The IR and the NMR data of α/β-depsipeptides suggested that a 9-membered ring hydrogen bond is favored over an 11-membered ring hydrogen bond.

Vapor-liquid equilibrium correlations for systems containing amines using a lattice fluid equation of state with hydrogen bonding

Alexander Breitholz,유기풍,임종성,Chul Soo Lee,강정원 한국화학공학회 2008 Korean Journal of Chemical Engineering Vol.25 No.4

The nonrandom lattice equation of state with hydrogen bonding (NLF-HB EOS) was examined for the correlation of vapor-liquid equilibria (VLE) for binary amine and hydrocarbon mixture at various temperatures. For these mixtures, the consideration of hydrogen bondings in the lattice equation of state clearly improves the prediction for VLE. The amines were divided into four groups due to the different strength of the hydrogen bonding. For all groups, different hydrogen bonding parameters were obtained and evaluated. The effects of varying hydrogen bonding energies for NLF-HB EOS are discussed. For systems containing lower amines, the NLF-HB EOS showed excellent agreement with the experimental data. For the correlation of systems containing tertiary amine molecules, binary interaction parameter had to be involved instead of hydrogen bonding parameters.

Ab Initio Studies of Hydrogen Bihalide Anions: Anharmonic Frequencies and Hydrogen-Bond Energies

Cheong, Byeong-Seo Korean Chemical Society 2019 대한화학회지 Vol.63 No.4

Hydrogen bihalide anions, $XHX^-$ (X = F, Cl, and Br) have been studied by high level ab initio methods to determine the molecular structure, vibrational frequencies, and energetics of the anions. All bihalide anions are found to be of linear and symmetric structures, and the calculated bond lengths are consistent with experimental data. The harmonic frequencies exhibit large deviations from the experimental frequencies, suggesting the vibrations of these anions are very anharmonic. Two different approaches, the VSCF and VPT2 methods, are employed to calculate the anharmonic frequencies, and the results are compared with the experimental frequencies. While the ${\nu}_1$ and ${\nu}_2$ frequencies are in reasonable agreement with the experimental values, the ${\nu}_3$ and ${\nu}_1+{\nu}_3$ frequencies still exhibit large deviations. The hydrogen-bond energies and enthalpies are calculated at various levels including the W1BD and G4 composite methods. The hydrogen-bond enthalpies calculated are in good agreement with the experimental values.

Hydrogen-bonded supramolecular manganese(II) complexes with network and sheet structures bridged by terephthalate unit

Hong, Chang Seop,Yoon, Jung Hee,You, Young Sin Elsevier 2005 Inorganica chimica acta Vol.358 No.12

<P><B>Graphical abstract</B></P><P>Two hydrogen-bonded supramolecular assemblies, [Mn(4-methylpyrazole)<SUB>3</SUB>(H<SUB>2</SUB>O)(tp)]<SUB><I>n</I></SUB> with a 3D framework and [Mn(4-methylpyrazole)<SUB>4</SUB>(tp)]<SUB><I>n</I></SUB> (tp=terephthalate) exhibiting a 2D sheet structure, have been prepared and characterized by X-ray crystallography and magnetic measurements.</P><ce:figure></ce:figure> <P><B>Abstract</B></P><P>Two 1D complexes [Mn(4- methylpyrazole)<SUB>3</SUB>(H<SUB>2</SUB>O)(tp)]<SUB><I>n</I></SUB> (<B>2</B>) and [Mn(4-methylpyrazole)<SUB>4</SUB>(tp)]<SUB><I>n</I></SUB> (<B>3</B>) (tp=terephthalate) were synthesized and characterized by means of X-ray analysis and magnetic studies. The molecular structure of <B>2</B> reveals that Mn(II) centers with asymmetric coordination surroundings are bridged by crystallographically different tp ligands, forming a 1D chain. The 1D coordination chains are interconnected by hydrogen bonds between free carboxylate oxygen atoms in a chain and hydrogens of pyrazole nitrogen atoms in neighboring chains, leading to a 3D framework. Compound <B>3</B> also exhibits a 1D coordination chain which is hydrogen-bonded to adjacent chains, providing a 2D sheet structure. Interestingly, the structures include intra- and interchain hydrogen bonds contributed from N–H groups of the capping 4-methylpyrazole ligands. Magnetic measurements show weak antiferromagnetic interactions with exchange coupling parameters of <I>J</I>=−0.018cm<SUP>−1</SUP> for <B>2</B> and <I>J</I>=−0.062cm<SUP>−1</SUP> for <B>3</B> through the extended tp ligand on the basis of an infinite chain model (<I>H</I>=−<I>J</I>∑<I>S</I><SUB><I>i</I></SUB>·<I>S</I><SUB>i+1</SUB>).</P>

Hydrogen-Bonding Induced Alternating Thin Films of Dendrimer and Block Copolymer Micelle

Park, Chi-Young,Rhue, Mi-Kyo,Im, Min-Ju,Kim, Chul-Hee The Polymer Society of Korea 2007 Macromolecular Research Vol.15 No.7

The hydrogen-bonding induced alternating multilayer thin films of dendrimers and block copolymer micelles were demonstrated. The block copolymer micelles derived from amphiphilic poly(2-ethyl-2-oxazoline)block-$poly({\varepsilon}-carprolactone)$ (PEtOz-PCL) in aqueous phase have a core-shell structure with a mean hydrodynamic diameter of 26 nm. The hydrogen bonding between the PEtOz outer shell of micelle and the carboxyl unit of poly(amidoamine) dendrimer of generation 4.5 (PAMAM-4.5G) at pH 3 was utilized as a driving force for the layerby-layer alternating deposition. The multilayer thin film was fabricated on the poly(methyl methacrylate) (PMMA) thin film spin-coated on silicon wafer or glass substrate by the alternate dipping of PEtOz-PCL micelles and PAMAM dendrimers in aqueous solution at pH 3. The formation of multilayer thin film was characterized by using ellipsometry, UV-vis spectroscopy, and atomic force microscopy. The PEtOz outer shell of PEtOz-PCL micelle provided the pH-responsive hydrogen bonding sites with peripheral carboxylic acids of PAM AM dendrimer. The multilayer thin film was reversibly removed after dipping in aqueous solution at $pH{\geq}5.6$ due to dissociation of the hydrogen bonding between PEtOz shell of PEtOz-PCL micelle and peripheral carboxyl units of PAMAM dendrimer.

MP2 Basis Set Limit Binding Energy Estimates of Hydrogen-bonded Complexes from Extrapolation-oriented Basis Sets

Park, Young-Choon,Lee, Jae-Shin Korean Chemical Society 2007 Bulletin of the Korean Chemical Society Vol.28 No.3

By use of a simple two-point extrapolation scheme estimating the correlation energies of the molecules along with the basis sets specifically targeted for extrapolation, we have shown that the MP2 basis set limit binding energies of large hydrogen-bonded complexes can be accurately predicted with relatively small amount of computational cost. The basis sets employed for computation and extrapolation consist of the smallest correlation consistent basis set cc-pVDZ and another basis set made of the cc-pVDZ set plus highest angular momentum polarization functions from the cc-pVTZ set, both of which were then augmented by diffuse functions centered on the heavy atoms except hydrogen in the complex. The correlation energy extrapolation formula takes the (X+1)-3 form with X corresponding to 2.0 for the cc-pVDZ set and 2.3 for the other basis set. The estimated MP2 basis set limit binding energies for water hexamer, hydrogen fluoride pentamer, alaninewater, phenol-water, and guanine-cytosine base pair complexes of nucleic acid by this method are 45.2(45.9), 36.1(37.5), 10.9(10.7), 7.1(6.9), and 27.6(27.7) kcal/mol, respectively, with the values in parentheses representing the reference basis set limit values. A comparison with the DFT results by B3LYP method clearly manifests the effectiveness and accuracy of this method in the study of large hydrogen-bonded complexes.