Interaction of a tripeptide with cesium perfluorooctanoate micelles

The interaction of alanyl-phenylalanyl-alanine (Ala-Phe-Ala) with the micelles formed by cesium perfluorooctanoate (CsPFO) in water was studied in the isotropic phase by means of 1H NMR and by molecular dynamics (MD) simulations. Information on the location of the peptide was experimentally obtained from selective variations in Ala-Phe-Ala chemical shifts and from differential line broadening in the presence of the paramagnetic ion Mn2+. The peptide-micelle association constant was estimated analyzing the chemical shift variations of the most sensitive Ala-Phe-Ala resonances with the peptide concentration. MD simulations of Ala-Phe-Ala in the micellar environment confirmed the experimental observations, identifying the hydrogen bonding interactions of the different peptide moieties with the micelle, yielding a binding constant close to the experimental one. NOESY experiments suggest that the peptide in the micellar environment does not adopt a preferred conformation but is mainly unstructured. Details on the conformational behavior of the peptide in the micellar solution observed through MD were consistent with a different conformational equilibrium in the proximity of the micelle. Information on Ala-Phe-Ala dynamics was obtained from 1H T1 data and compared to MD simulation results on the overall tumbling motion.     

All-atom Molecular Dynamics Simulationsand NMR Spectroscopy Study on Interactions and Structures in N-Glycylglycine Aqueous Solution

All-atom molecular dynamics (MD) simulation and the NMR spectra are used to investi-gate the interactions in N-glycylglycine aqueous solution. Different types of atoms exhibit different capability in forming hydrogen bonds by the radial distribution function analysis. Some typical dominant aggregates are found in different types of hydrogen bonds by the statistical hydrogen-bonding network. Moreover, temperature-dependent NMR are used to compare with the results of the MD simulations. The chemical shifts of the three hydrogen atoms all decrease with the temperature increasing which reveals that the hydrogen bonds are dominant in the glycylglycine aqueous solution. And the NMR results show agreement with the MD simulations. All-atom MD simulations and NMR spectra are successful in revealing the structures and interactions in the N-glycylglycine-water mixtures.     

Hydrogen bonded dimers of triurea derivatives of triphenylmethanes

Tri-(2-alkoxy-5-ureido-phenyl)methanes represent a novel self-complementary motif forming hydrogen bonded homo- and heterodimers in nonpolar, aprotic solvents as evidenced by 1H NMR and ESI-mass spectra and by the formation of heterodimers. MD simulations suggest the formation of hydrogen bonds of different strength in agreement with NMR data. The dimerization does not interfere with that of tetraurea calix[4]arenes. A combination of both motifs may be used therefore to build up larger structures via self-assembly processes. [structure: see text]     

All-atom molecular dynamic simulations and relative NMR spectra study of weak C-H...O contacts in amide-water systems

Amide-water mixtures are studied by all-atom molecular dynamics (MD) simulations and the relative temperature-dependent NMR experiment. The weak C-H...O contacts are found in the amide-water systems theoretically and experimentally. The statistical results of the average numbers of hydrogen bonds indicate that the methyl groups in amide molecules represent different capabilities in forming the weak C-H...O contacts. The statistics also imply that the C-H...O contacts are more obvious in the amide-rich region than those in the water-rich region. The temperature-dependent NMR spectra are also adopted to investigate the weak C-H...O contacts in the amide-water systems. The relative chemical shifts of the methyl groups are in good agreement with the MD simulations.     

Studies on the Structures and Hydrogen-bonding Interactions in Aqueous Glycine Solutions Using All-atom Molecular Dynamics Simulations and NMR Spectroscopy

All-atom molecular dynamics （MD） simulations and chemical shifts were used to study interactions and structures in the glycine-water system. Radial distribution functions and the hydrogen-bond network were applied in MD simulations. Aggregates in the aqueous glycine solution could be classified into different regions by analysis of the hydrogen-bonding network. Temperature-dependent NMR spectra and the viscosity of glycine in aqueous solutions were measured to compare with the results of MD simulations. The variation tendencies of the hydrogen atom chemical shifts and viscosity with concentration of glycine agree with the statistical results of hydrogen bonds in the MD simulations.     

All-atom Molecular Dynamic Simulations and NMR Spectra Study on Intermolecular Interactionsof N,N-dimethylacetamide-Water System

N,N-dimethylacetamide (DMA) has been investigated extensively in studying models of peptide bonds. An all-atom MD simulation and the NMR spectra were performed to investigate the interactions in the DMA-water system. The radial distribution functions (RDFs) and the hydrogen-bonding network were used in MD simulations. There are strong hydrogen bonds and weak C-H￠ ￠ ￠O contacts in the mixtures, as shown by the analysis of the RDFs. The insight structures in the DMA-water mixtures can be classified into different regions by the analysis of the hydrogen-bonding network. Chemical shifts of the hydrogen atom of water molecule with concentration and temperatures are adopted to study the interactions in the mixtures. The results of NMR spectra show good agreement with the statistical results of hydrogen bonds in MD simulations.     

特殊缔合体系TFE水溶液分子动力学模拟

三氟乙醇(TFE)水溶液是一类特殊的缔合体系. 采用分子动力学模拟方法结合核磁共振化学位移研究了TFE水溶液体系全浓度范围的氢键网络, 并对动力学模拟结果和核磁共振化学位移进行了比较. 从径向分布函数(RDF)发现, TFE水溶液中存在着强氢键, 而体系中的C—H…O弱相互作用较为明显, 也不能忽略. 氢键网络分析发现TFE 水溶液体系的氢键大致分为以下三个区域: 在水富集区域, 水分子倾向于自身缔合形成稳定的簇结构, 随着TFE 浓度的增加, 水的有序结构受到破坏, 水分子和TFE分子发生交叉缔合作用形成氢键; 在TFE富集区域, 水分子较少, TFE分子自身通过氢键形成多缔体结构. 此外, 分子动力学统计的平均氢键数的变化和文献报导的核磁共振化学位移变化趋势相同, 实验和理论的结果吻合较好.     

Comprehensive Characterization of the Self-Folding Cavitand Dynamics

The conformational equilibria and guest exchange process of a resorcin[4]arene derived self-folding cavitand receptor have been characterized in detail by molecular dynamics simulations (MD) and ¹H EXSY NMR experiments. A multi-timescale strategy for exploring the fluxional behaviour of this system has been constructed, exploiting conventional MD and accelerated MD (aMD) techniques. The use of aMD allows the reconstruction of the folding/unfolding process of the receptor by sampling high-energy barrier processes unattainable by conventional MD simulations. We obtained MD trajectories sampling events occurring at different timescales from ns to s: 1) rearrangement of the directional hydrogen bond seam stabilizing the receptor, 2) folding/unfolding of the structure transiting partially open intermediates, and 3) guest departure from different folding stages. Most remarkably, reweighing of the biased aMD simulations provided kinetic barriers that are in very good agreement with those determined experimentally by ¹H NMR. These results constitute the first comprehensive characterization of the complex dynamic features of cavitand receptors. Our approach emerges as a valuable rational design tool for synthetic host-guest systems     

Molecular Dynamics Simulations and NMR Experimental Study of Oxidized Glutathione in Aqueous Solution

All-atom molecular simulations and NMR experiments have been used to study the conformations and interactions of oxidized glutathione (GSSG) in aqueous solution. The simulations are characterized by the radius of gyration, intramolecular distance, root-mean-square deviation and solvent-accessible surface area. The variations in these properties show time dependences. Interestingly, the two chains connected by the disulfide linkage in GSSG show different flexibilities in aqueous solution. The conformations of GSSG can convert from ??extended?? to ??folded?? states. Also, the two different kinds of amide hydrogen atoms in cysteine (Cys) and glycin (Gly) show different capabilities in forming N?CH?O hydrogen bonds with water molecules. Temperature-dependent NMR results show agreements with the MD simulations.     

A Study of the Solvation Structure of l‐Leucine in Alcohol–Water Binary Solvents through Molecular Dynamics Simulations and FTIR and NMR Spectroscopy

The solvation structures of l ‐leucine (Leu) in aliphatic‐alcohol–water and fluorinated‐alcohol–water solvents are elucidated for various alcohol contents by using molecular dynamics (MD) simulations and IR, and ¹H and ¹³C NMR spectroscopy. The aliphatic alcohols included methanol, ethanol, and 2‐propanol, whereas the fluorinated alcohols were 2,2,2‐trifluoroethanol and 1,1,1,3,3,3‐hexafluoro‐2‐propanol. The MD results show that the hydrophobic alkyl moiety of Leu is surrounded by the alkyl or fluoroalkyl groups of the alcohol molecules. In particular, TFE and HFIP significantly solvate the alkyl group of Leu. IR spectra reveal that the Leu C?H stretching vibration blueshifts in fluorinated alcohol solutions with increasing alcohol content, whereas the vibration redshifts in aliphatic alcohol solutions. When the C?H stretching vibration blueshifts in the fluorinated alcohol solutions, the hydrogen and carbon atoms of the Leu alkyl group are magnetically shielded. Consequently, TFE and HFIP molecules may solvate the Leu alkyl group through the blue‐shifting hydrogen bonds.     

不同氢化度氢化丁腈橡胶的结构表征与分子模拟

通过核磁共振波谱(¹H NMR)、 红外光谱(IR)及热分析等方法研究了不同氢化度氢化丁腈橡胶(HNBR)分子结构之间的差异, 结果表明, 在丁腈橡胶(NBR)加氢过程中, 聚丁二烯上的乙烯基加氢速率最快, 其次是反式1,4结构, 顺式1,4结构的加氢速率最慢, 而腈基基本不发生氢化反应. 采用核磁共振谱法对不同氢化度HNBR中不同链段的含量进行定量分析, 依据此结果建模并进行分子模拟计算, 得到不同氢化丁腈橡胶的密度、 内聚能密度(CED)和玻璃化转变温度(T_g)等参数, 模拟值与实验结果吻合. 实验结果表明, 随着氢化度的增加, HNBR的热氧化稳定性逐渐增加, 这主要是由于氢化度增加后分子链中双键含量逐渐减少而CED增加的缘故. 分子模拟可以有效地计算出多种结构参数, 为共聚橡胶材料的制备与加工提供基础数据及理论指导.     

Hydrogen Bonding Between Ions of Like Charge in Ionic Liquids Characterized by NMR Deuteron Quadrupole Coupling Constants—Comparison with Salt Bridges and Molecular Systems

We present deuteron quadrupole coupling constants (DQCC) for hydroxyl‐functionalized ionic liquids (ILs) in the crystalline or glassy states characterizing two types of hydrogen bonding: The regular Coulomb‐enhanced hydrogen bonds between cation and anion (c–a), and the unusual hydrogen bonds between cation and cation (c–c), which are present despite repulsive Coulomb forces. We measure these sensitive probes of hydrogen bonding by means of solid‐state NMR spectroscopy. The DQCCs of (c–a) ion pairs and (c–c) H‐bonds are compared to those of salt bridges in supramolecular complexes and those present in molecular liquids. At low temperatures, the (c–c) species successfully compete with the (c–a) ion pairs and dominate the cluster populations. Equilibrium constants obtained from molecular‐dynamics (MD) simulations show van't Hoff behavior with small transition enthalpies between the differently H‐bonded species. We show that cationic‐cluster formation prevents these ILs from crystallizing. With cooling, the (c–c) hydrogen bonds persist, resulting in supercooling and glass formation.     

All‐atom Molecular Dynamic Simulations Combined with the Chemical Shifts Study on the Weak Interactions of Ethanol‐water System

All‐atom molecular dynamics (MD) simulation combined with chemical shifts was performed to investigate the interactions over the entire concentration range of the ethanol (EtOH)‐water system. The results of the simulation were adopted to explain the NMR experiments by hydrogen bonding analysis. The strong hydrogen bonds and weak C–H···O contacts coexist in the mixtures through the analysis of the radial distribution functions. And the liquid structures in the whole concentration of EtOH‐water mixtures can be classified into three regions by the statistic analysis of the hydrogen‐bonding network in the MD simulations. Moreover, the chemical shifts of the hydrogen atom are in agreement with the statistical results of the average number hydrogen bonds in the MD simulations. Interestingly, the excess relative extent of η_rel^E calculated by the MD simulations and chemical shifts in the EtOH aqueous solutions shows the largest deviation at x_EtOH≈0.18. The excess properties present good agreement with the excess enthalpy in the concentration dependence.     

Correlation of protein structure and dynamics to scalar couplings across hydrogen bonds

NMR-observable scalar couplings across hydrogen bonds in nucleic acids and proteins present a quantitative measure for the geometry and--by the implicit experimental time averaging--dynamics of hydrogen bonds. We have carried out in-depth molecular dynamics (MD) simulations with various force fields on three proteins: ubiquitin, the GB1 domain of protein G, and the SMN Tudor domain, for which experimental h3JNC' scalar couplings of backbone hydrogen bonds and various high-resolution X-ray structures are available. Theoretical average values for h3JNC' were calculated from the snapshots of these MD simulations either by density functional theory or by a geometric parametrization (Barfield, M. J. Am. Chem. Soc. 2002, 124, 4158-4168). No significant difference was found between the two methods. The results indicate that time-averaging using explicit water solvation in the MD simulations improves significantly the agreement between experimental and theoretical values for the lower resolution structures ubiquitin (1.8 A), Tudor domain (1.8 A), and protein G (2.1 A). Only marginal improvement is found for the high-resolution structure (1.1 A) of protein G. Hence, experimental h3JNC' values are compatible with a static, high-resolution structural model. The MD averaging of the low-resolution structures moves the averages of the rHO distance and the H...O=C angle theta closer to their respective values in the high-resolution structures, thereby improving the agreement using experimental h3JNC' data. In contrast, MD averaging with implicit water models deteriorates the agreement with experiment for all proteins. The differing behavior can be explained by an artifactual lengthening of H-bonds caused by the implicit water models.     

Thermal and solvent effects on NMR indirect spin-spin coupling constants of a prototypical Chagas disease drug

NMR J-couplings across hydrogen bonds reflect the static and dynamic character of hydrogen bonding. They are affected by thermal and solvent effects and can therefore be used to probe such effects. We have applied density functional theory (DFT) to compute the NMR (n)J(N,H) scalar couplings of a prototypical Chagas disease drug (metronidazole). The calculations were done for the molecule in vacuo, in microsolvated cluster models with one or few water molecules, in snapshots obtained from molecular dynamics simulations with explicit water solvent, and in a polarizable dielectric continuum. Hyperconjugative and electrostatic effects on spin-spin coupling constants were assessed through DFT calculations using natural bond orbital (NBO) analysis and atoms in molecules (AIM) theory. In the calculations with explicit solvent molecules, special attention was given to the nature of the hydrogen bonds formed with the solvent molecules. The results highlight the importance of properly incorporating thermal and solvent effects into NMR calculations in the condensed phase.     

Solution and solid-state models of peptide CH...O hydrogen bonds

Fumaramide derivatives were analyzed in solution by (1)H NMR spectroscopy and in the solid state by X-ray crystallography in order to characterize the formation of CH...O interactions under each condition and to thereby serve as models for these interactions in peptide and protein structure. Solutions of fumaramides at 10 mM in CDCl(3) were titrated with DMSO-d(6), resulting in chemical shifts that moved downfield for the CH groups thought to participate in CH...O=S(CD(3))(2) hydrogen bonds concurrent with NH...O=S(CD(3))(2) hydrogen bonding. In this model, nonparticipating CH groups under the same conditions showed no significant change in chemical shifts between 0.0 and 1.0 M DMSO-d(6) and then moved upfield at higher DMSO-d(6) concentrations. At concentrations above 1.0 M DMSO-d(6), the directed CH...O=S(CD(3))(2) hydrogen bonds provide protection from random DMSO-d(6) contact and prevent the chemical shifts for participating CH groups from moving upfield beyond the original value observed in CDCl(3). X-ray crystal structures identified CH...O=C hydrogen bonds alongside intermolecular NH...O=C hydrogen bonding, a result that supports the solution (1)H NMR spectroscopy results. The solution and solid-state data therefore both provide evidence for the presence of CH...O hydrogen bonds formed concurrent with NH...O hydrogen bonding in these structures. The CH...O=C hydrogen bonds in the X-ray crystal structures are similar to those described for antiparallel beta-sheet structure observed in protein X-ray crystal structures.     

三氟乙酸溶液中尼龙6链凝聚缠结的NMR弛豫研究

采用1D和2DNMR技术,归属了三氟乙酸(TFA)溶液中尼龙6链上的主要¹HNMR共振信号.不同温度下测定的自旋-自旋弛豫时间(t2)提供了大分子主链间凝聚缠结及TFA溶液中尼龙6链随温度变化的动力学信息.结果表明,尼龙6主链上亚甲基基团有不同程度的凝聚缠结,距离CO和NH基团越远,凝聚缠结越明显.与CO和NH基团相连的亚甲基基团的缠结不很明显,主要是因为尼龙6链间氢键的存在.升高温度,热运动加快,这些凝聚缠结逐渐减弱.NH质子的t2H值几乎不随温度变化,TFA质子的t2H值随温度升高而快速下降,表明尼龙6链间氢键随温度升高而破坏,TFA质子又与因温度升高而从尼龙6中释放出来的自由NH和CO基团形成新的氢键.     

Synthesis of cyclic bis- and trismelamine derivatives and their complexation properties with barbiturates

Cyclic bis- and trismelamine derivatives were prepared from cyanuric chloride by stepwise substitutions with appropriate amines. The complexation abilities of these melamine derivatives with barbituric acid derivatives were evaluated by UV-vis spectroscopy and (1)H NMR. The structure was also confirmed by X-ray crystallography. Both the acyclic and the cyclic bismelamine derivatives formed a 1 : 1 complex via six hydrogen bonds with barbituric acid derivatives. van't Hoff analyses on the complexation of the bismelamines with the barbituric acid derivative revealed that the complexation of the cyclic bismelamine was entropically favored and enthalpically less favored process than those of the acyclic bismelamine. X-Ray crystallographic analysis and (1)H NMR studies revealed that the cyclic trismelamine bound one barbituric acid derivative into the cavity via six hydrogen bonds by two melamine moieties and another barbituric acid via three hydrogen bonds by the residual melamine moiety.     

CHARMM36 all‐atom additive protein force field: Validation based on comparison to NMR data

Protein structure and dynamics can be characterized on the atomistic level with both nuclear magnetic resonance (NMR) experiments and molecular dynamics (MD) simulations. Here, we quantify the ability of the recently presented CHARMM36 (C36) force field (FF) to reproduce various NMR observables using MD simulations. The studied NMR properties include backbone scalar couplings across hydrogen bonds, residual dipolar couplings (RDCs) and relaxation order parameter, as well as scalar couplings, RDCs, and order parameters for side‐chain amino‐ and methyl‐containing groups. It is shown that the C36 FF leads to better correlation with experimental data compared to the CHARMM22/CMAP FF and suggest using C36 in protein simulations. Although both CHARMM FFs contains the same nonbond parameters, our results show how the changes in the internal parameters associated with the peptide backbone via CMAP and the χ₁ and χ₂ dihedral parameters leads to improved treatment of the analyzed nonbond interactions. This highlights the importance of proper treatment of the internal covalent components in modeling nonbond interactions with molecular mechanics FFs. © 2013 Wiley Periodicals, Inc.     

The Double‐Faced Nature of Hydrogen Bonding in Hydroxy‐Functionalized Ionic Liquids Shown by Neutron Diffraction and Molecular Dynamics Simulations

We characterize the double‐faced nature of hydrogen bonding in hydroxy‐functionalized ionic liquids by means of neutron diffraction with isotopic substitution (NDIS), molecular dynamics (MD) simulations, and quantum chemical calculations. NDIS data are fit using the empirical potential structure refinement technique (EPSR) to elucidate the nearest neighbor H???O and O???O pair distribution functions for hydrogen bonds between ions of opposite charge and the same charge. Despite the presence of repulsive Coulomb forces, the cation–cation interaction is stronger than the cation–anion interaction. We compare the hydrogen‐bond geometries of both “doubly charged hydrogen bonds” with those reported for molecular liquids, such as water and alcohols. In combination, the NDIS measurements and MD simulations reveal the subtle balance between the two types of hydrogen bonds: The small transition enthalpy suggests that the elusive like‐charge attraction is almost competitive with conventional ion‐pair formation.