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”.

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.

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.

X-선 회절로 얻은 수소결합의 결합거리 보정 방법 : 중성자 회절결과와 결합원자가 방법 이용 Use of Neutron Data and Bond Valence Method

김신애 한국광물학회 2003 광물과 암석 (J.Miner.Soc.Korea) Vol.16 No.1

이 연구에서는 X-선 회절법으로 측정한 수소결합의 거리를 보정하는 두 가지 방법을 제시하였다. O…O 거리가 2.5 Å 이상인 수소결합의 경우는 저온에서 측정한 중성자 회절에 의한 수소결합 데이터를 이용하여 얻은 최적화 곡선 식 d(O-H)=exp((2.173-d(O…O))/0.138)+0.958을 이용하여 수소결합 거리를 보정한다. O…O 거리가 2.5 Å 이하의 짧은 수소결합의 경우는 결합원자가 최적화 방법(valence-least-squares)을 이용하는 것이 효과적이다. X-선 회절분석으로 얻은 긴 O…O 거리를 갖는 분자간 수소결합의 경우는 수소결합의 거리보정을 해주어야 한다. In this study we have derived the two correction methods of hydrogen bonding distance. In case of the intermediate or long hydrogen bond(>2.5 A), hydrogen bonding distances can be corrected by using the function d(O-H)=exp((2.173-d(O…0))/0.138)+0.958 obtained by least-squares fit to the data from the neutron diffraction at low temperatures. The valence-least-squares method is effective for the distance correction of very short hydrogen bond(<2.5 A). The distance correction is necessary for the long intermolecular hydrogen bond obtained from X-ray diffraction analysis.

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.

X-ray Diffraction and Infrared Spectroscopy Studies on Crystal and Lamellar Structure and CHO Hydrogen Bonding of Biodegradable Poly(hydroxyalkanoate)

Sato Harumi,Murakami Rumi,Zhang Jianming,Ozaki Yukihiro,Mori Katsuhito,Takahashi Isao,Terauchi Hikaru,Noda Isao The Polymer Society of Korea 2006 Macromolecular Research Vol.14 No.4

Temperature-dependent, wide-angle, x-ray diffraction (WAXD) patterns and infrared (IR) spectra were measured for biodegradable poly(3-hydroxybutyrate) (PHB) and its copolymers, poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) P(HB-co-HHx) (HHx=2.5, 3.4, 10.5, and 12 mol%), in order to explore their crystal and lamellar structure and their pattern of C-H...O=C hydrogen bonding. The WAXD patterns showed that the P(HB-co-HHx) copolymers have the same orthorhombic system as PHB. It was found from the temperature-dependent WAXD measurements of PHB and P(HB-co-HHx) that the a lattice parameter is more enlarged than the b lattice parameter during heating and that only the a lattice parameter shows reversibility during both heating and cooling processes. These observations suggest that an interaction occurs along the a axis in PHB and P(HB-co-HHx). This interaction seems to be due to an intermolecular C-H...O=C hydrogen bonding between the C=O group in one helical structure and the $CH_3$ group in the other helical structure. The x-ray crystallographic data of PHB showed that the distance between the O atom of the C=O group in one helical structure and the H atom of one of the three C-H bonds of the $CH_3$ group in the other helix structure is $2.63{\AA}$, which is significantly shorter than the sum of the van der Waals separation ($2.72{\AA}$). This result and the appearance of the $CH_3$ asymmetric stretching band at $3009 cm^{-1}$ suggest that there is a C-H...O=C hydrogen bond between the C=O group and the $CH_3$ group in PHB and P(HB-co-HHx). The temperature-dependent WAXD and IR measurements revealed that the crystallinity of P(HB-co-HHx) (HHx =10.5 and 12 mol%) decreases gradually from a fairly low temperature, while that of PHB and P(HB-co-HHx) (HHx = 2.5 and 3.5 mol%) remains almost unchanged until just below their melting temperatures. It was also shown from our studies that the weakening of the C-H...O = C interaction starts from just above room temperature and proceeds gradually increasing temperature. It seems that the C-H...O=C hydrogen bonding stabilizes the chain holding in the lamellar structure and affects the thermal behaviour of PHB and its copolymers.

Anion Receptor with Xylene Bridged Two Imidazolium Rings

In, Sungjae,Cho, Seung Joo,Kang, Jongmin Taylor Francis 2005 Supramolecular chemistry Vol.17 No.6

<P>A m-xylene bridged imidazolium receptor 1 has been designed and synthesized. The receptor 1 utilizes two imidazole (C–H) + —anion hydrogen bonds and one aromatic hydrogen—anion hydrogen bond. The major driving force of complexation between the receptor 1 and anions comes from two imidazole (C–H) + —anion hydrogen bonding. However, some hydrogen bonding energy between aromatic hydrogen and anion exists, although it is expected to be much smaller than that of imidazole (C–H) + —anion hydrogen bonds.</P>