热塑性淀粉中氢键及其对性能的影响

热塑性淀粉中的氢键对热塑性淀粉的性能有决定性的作用．本文利用红外光谱分析甘油或甲酰胺塑化热塑性淀粉中塑化剂和淀粉间的氢键形成情况，发现在淀粉中，与塑化剂形成氢键的主要是C-O-C基团中的氧原子和C-O-H基团中的氢原子；而且过量的塑化剂之间会形成氢键，减弱塑化剂与C-O-C中氧原子的氢键作用．与甘油相比，甲酰胺可以和淀粉形成更稳定的氢键．X-ray衍射研究了氢键对两种热塑性淀粉在不同湿度环境下的回生性能的影响．结果表明甲酰胺可以有效抑制淀粉回生．热动态力学分析(DMTA)研究发现，氢键使甲酰胺塑化热塑性淀粉的玻璃化转变温度更低．氢键使甲酰胺塑化热塑性淀粉强度和杨氏模量低，但伸长率和断裂能大．     

分子动力学模拟方法研究结构水在糖原合成酶激酶-3β中的作用

用分子动力学模拟的方法揭示了结构水分子在糖原合成酶激酶-3β(GSK-3β)中的作用.如果没有结构水,ATP嘌呤环的结合位置将发生偏移以填补结构水留下的空间;ATP结合口袋中的氢键网络将被破坏,保守残基Lys85与ATP的磷酸根侧链只能形成一个保守氢键,无法维持磷酸根转移所需的线性关系;由于失去了氢键网络的稳定作用,Glu97和Lys85会向远离ATP的方向移动,并导致Arg96的侧链发生偏转,使Arg96无法保持与Arg180和Lys205之间正常的相对位置,最终影响GSK-3β与底物的结合.     

分子动力学模拟方法研究结构水在糖原合成酶激酶-3β中的作用

用分子动力学模拟的方法揭示了结构水分子在糖原合成酶激酶-3β(GSK-3β)中的作用. 如果没有结构水, ATP嘌呤环的结合位置将发生偏移以填补结构水留下的空间; ATP结合口袋中的氢键网络将被破坏, 保守残基Lys85与ATP的磷酸根侧链只能形成一个保守氢键, 无法维持磷酸根转移所需的线性关系; 由于失去了氢键网络的稳定作用, Glu97和Lys85会向远离ATP的方向移动, 并导致Arg96的侧链发生偏转, 使Arg96无法保持与Arg180和Lys205之间正常的相对位置, 最终影响GSK-3β与底物的结合.     

膦系阻垢剂对碳酸钙阻垢机理的研究

在模拟循环水中,通过静态阻垢实验研究了HEDP,PBTCA,ATMP和EDTMP对碳酸钙的阻垢性能,在相同的加药浓度下(按物质的量浓度计)阻垢性能的强弱顺序为HEDPPBTCAATMPEDTMP;同时采用分子动力学方法,模拟计算了阻垢剂负二价离子与方解石(104),(102),(202)和(113)面的相互作用.结果表明:阻垢剂分子中的膦酸基团和羧酸基团与碳酸钙中的Ca2+形成的离子键对吸附起到了主要作用,同时阻垢剂与晶面间存在较弱的范德华力相互作用.阻垢剂与各晶面的结合能强弱顺序为(113)≥(102)≥(202)(104);分子中的羟基易与垢晶面形成氢键而加强阻垢效果;羧基的位置不同对阻垢作用的影响不同.将静态阻垢的实验结果与分子动力学模拟结果进行了相关性分析,发现阻垢剂在(104)面和(102)面上的吸附对阻垢作用的贡献较大.     

雪卡毒素毒性机理的分子对接及分子动力学研究

采用分子对接和分子动力学方法,研究了雪卡毒素与其毒性作用靶点之一钠通道的结合模式,并与钠通道阻滞剂奎尼丁比较.研究结果表明,雪卡毒素、奎尼丁与钠通道作用方式有所不同.分子动力学模拟表明,对接受体-配体复合物体系在2.5 ns的模拟过程中稳定.奎尼丁在钠通道中央与GLU1784,THR1858各形成1个稳定氢键,吡啶环与...     

部分水解的预交联凝胶型聚丙烯酰胺的水化层结构

部分水解的预交联凝胶型聚丙烯酰胺在水溶液中的吸水溶胀能对油藏高渗透区域产生有效封堵,有利于提高驱油效率.分子模拟结果表明,凝胶颗粒的溶胀主要归因于侧链亲水基团在水溶液中的水化作用,这些带负电的亲水基团中心原子通过氢键和静电作用在其周围极化出一层排列规整、有序而紧密的水化层,并将水分子束缚其中;同时水化层内的水分子之间依赖氢键网络促进水化层的稳定.本文从微观结构、动力学和氢键等方面比较了各亲水基团中心原子的水化能力,发现—COO-官能团具有较强的束缚水分子的能力,对水化层的稳定有重要影响.     

膦系阻垢剂阻碳酸钙垢机理的研究

在模拟循环水中, 通过静态阻垢实验研究了HEDP, PBTCA, ATMP和EDTMP对碳酸钙的阻垢性能, 在相同的加药浓度下(按物质的量浓度计)阻垢性能的强弱顺序为HEDP＞PBTCA＞ATMP＞EDTMP; 同时采用分子动力学方法, 模拟计算了阻垢剂负二价离子与方解石(104), (102), (202)和(113)面的相互作用. 结果表明: 阻垢剂分子中的膦酸基团和羧酸基团与碳酸钙中的Ca^2＋形成的离子键对吸附起到了主要作用, 同时阻垢剂与晶面间存在较弱的范德华力相互作用. 阻垢剂与各晶面的结合能强弱顺序为(113)≥(102)≥(202)＞(104); 分子中的羟基易与垢晶面形成氢键而加强阻垢效果; 羧基的位置不同对阻垢作用的影响不同. 将静态阻垢的实验结果与分子动力学模拟结果进行了相关性分析, 发现阻垢剂在(104)面和(102)面上的吸附对阻垢作用的贡献较大.     

_f-A_aD_d型氢键体系的网络结构参数

利用溶胶-凝胶分配理论对氢键溶液的模型体系进行研究,给出了凝胶点后氢键网络中各结构参数的计算方案,并进行相应的数值计算.结果表明,因受体基团本身的性质及两类质子受体基团的数量比不同,受体基团的竞争作用对网络结构有明显影响,这提供了控制氢键网络结构特征的可能方法.     

Af-AaDd型氢键体系的网络结构参数

利用溶胶-凝胶分配理论对氢键溶液的模型体系进行研究, 给出了凝胶点后氢键网络中各结构参数的计算方案, 并进行相应的数值计算. 结果表明, 因受体基团本身的性质及两类质子受体基团的数量比不同, 受体基团的竞争作用对网络结构有明显影响, 这提供了控制氢键网络结构特征的可能方法.     

Af-AaDd型氢键体系的网络结构参数

利用溶胶-凝胶分配理论对氢键溶液的模型体系进行研究, 给出了凝胶点后氢键网络中各结构参数的计算方案, 并进行相应的数值计算. 结果表明, 因受体基团本身的性质及两类质子受体基团的数量比不同, 受体基团的竞争作用对网络结构有明显影响, 这提供了控制氢键网络结构特征的可能方法.     

1H NMR detection of immobilized water molecules within a strong distal hydrogen-bonding network of substrate-bound human heme oxygenase-1

Solution 1H NMR is used to probe the environments of the donor protons of eight strong hydrogen bonds on the distal side of the heme substrate in the cyanide-inhibited, substrate-bound complex of human heme oxygenase, hHO. It is demonstrated that significant magnetization transfer from the bulk water signal to the eight labile protons does not result from chemical exchange, but from direct nuclear Overhauser effect due to the dipolar interaction of these labile protons with "ordered" water molecules. The enzyme labile proton to water proton distances are estimated at approximately 3 A. It is proposed that the role of the strong hydrogen-bonding network is to immobilize numerous water molecules which both stabilize the activated hydroperoxy species and funnel protons to the active site.     

Regulating the Coordination State of a Heme Protein by a Designed Distal Hydrogen-Bonding Network

Heme coordination state determines the functional diversity of heme proteins. Using myoglobin as a model protein, we designed a distal hydrogen-bonding network by introducing both distal glutamic acid (Glu29) and histidine (His43) residues and regulated the heme into a bis-His coordination state with native ligands His64 and His93. This resembles the heme site in natural bis-His coordinated heme proteins such as cytoglobin and neuroglobin. A single mutation of L29E or F43H was found to form a distinct hydrogen-bonding network involving distal water molecules, instead of the bis-His heme coordination, which highlights the importance of the combination of multiple hydrogen-bonding interactions to regulate the heme coordination state. Kinetic studies further revealed that direct coordination of distal His64 to the heme iron negatively regulates fluoride binding and hydrogen peroxide activation by competing with the exogenous ligands. The new approach developed in this study can be generally applicable for fine-tuning the structure and function of heme proteins.     

Ultraviolet resonance Raman evidence for utilization of the heme 6-propionate hydrogen-bond network in signal transmission from heme to protein in Ec DOS protein

The direct oxygen sensor protein from Escherichia coli (Ec DOS) is a heme-based signal transducer protein responsible for phosphodiesterase (PDE) activity. Binding of either O2 or CO molecule to a reduced heme enhances the PDE activity toward 3',5'-cyclic diguanylic acid. We report ultraviolet resonance Raman (UVRR) spectroscopic investigations of the reduced, O2- and CO-bound forms of heme-bound PAS domain of Ec DOS. The UVRR results show that heme discriminates different ligands, resulting in altered conformations in the protein moiety. Specifically, the environment around Trp53 that contacts the 2-vinyl group of heme, is changed to a more hydrophobic environment by O2 binding, whereas it is changed to a more hydrophilic environment by CO-binding. In addition, the PDE activity of the O2- and CO-bound forms for the Trp53Phe mutant is significantly decreased compared with that of the wild type (WT), demonstrating the importance of Trp53 for the catalytic reaction. On the other hand, the binding of O2 or CO to the heme produces drastic changes in the Tyr126 of Ibeta-strand at the surface of the sensor domain. Furthermore, we found that Asn84 forms a hydrogen bond with Tyr126 either in the O2- or CO-bound forms but not in the reduced form. Finally, the PDE activities of the ligand-bound forms for Asn84Val and Tyr126Phe mutants are significantly reduced as compared with that of WT, suggesting the importance of the hydrogen-bonding network from heme 6-propionate to Tyr126 through Asn84 in signal transmission.     

The hydrogen-bonding network in heme oxygenase also functions as a modulator of enzyme dynamics: chaotic motions upon disrupting the H-bond network in heme oxygenase from Pseudomonas aeruginosa

Relaxation compensated Carr-Purcell-Meiboom-Gill (rc-CPMG) NMR experiments have been used to investigate micros-ms motions in heme oxygenase from Pseudomonas aeruginosa (pa-HO) in its ferric state, inhibited by CN- (pa-HO-CN) and N3- (pa-HO-N3), and in its ferrous state, inhibited by CO (pa-HO-CO). Comparative analysis of the data from the three forms indicates that the nature of the coordinated distal ligand affects the micros-ms conformational freedom of the polypeptide in regions of the enzyme far removed from the heme iron and distal ligand. Interpretation of the dynamical information in the context of the crystal structure of resting state pa-HO shows that residues involved in the network of structural hydrogen-bonded waters characteristic of HOs undergo micros-ms motions in pa-HO-CN, which was studied as a model of the highly paramagnetic S = 5/2 resting state form. In comparison, similar motions are suppressed in the pa-HO-CO and pa-HO-N3 complexes, which were studied as mimics of the obligatory oxyferrous and ferric hydroperoxide intermediates, respectively, in the catalytic cycle of heme degradation. These findings suggest that in addition to proton delivery to the nascent Fe(III)-OO(-) intermediate during catalysis, the hydrogen-bonding network serves two additional roles: (i) propagate the electronic state (reactive state) in each of the distinct steps of the catalytic cycle to key but remote sections of the polypeptide via small rearrangements in the network of hydrogen bonds and (ii) modulate the conformational freedom of the enzyme, thus allowing it to adapt to the demanding changes in axial coordination state and substrate transformations that take place during the catalytic cycle. This idea was probed by disrupting the hydrogen-bonding network in pa-HO by replacing R80 with L. NMR spectroscopic studies conducted with R80L-pa-HO-N3 and R80L-pa-HO-CO revealed that the mutant exhibits nearly global conformational disorder, which is absent in the equivalent complexes of the wild type enzyme. The "chaotic" disorder in the R80L mutant is likely related to its significantly lower efficiency to hydroxylate heme in the presence of H2O2, relative to the wild type enzyme.     

Hydrogen-bonded networks of 2,2′-substituted 4,4′-biimidazoles: New ligands for the assembled metal complexes

4,4′-Biimidazole derivatives having alkyl-substituents at 2- and 2′-positions were synthesized as new component molecules of supramolecular assemblies based on hydrogen-bonding interaction. The crystal structure analyses of methyl and ethyl derivatives revealed intriguing three-dimensional structures constructed by hydrogen-bonded networks. Furthermore, the methyl derivative formed a six-membered cyclic motif of hydrogen-bonded network to build up a channel structure. The ethyl derivative gave the two polymorphous, anhydrate and dihydrate, depending on conditions of the crystallization. The anhydrate constructed three-dimensional hydrogen-bonded networks by direct N–H⋯N hydrogen-bondings. In the crystal structure of the dihydrate of ethyl derivative, three-dimensional hydrogen-bonding interaction through water molecules formed a channel structure.     

An atomistic level description of guest molecule effect on the formation of hydrate crystal nuclei by <Emphasis Type="Italic">ab initio</Emphasis> calculations

In the present study, we report the results of a systematic investigation of cage-like water structures using the first-principles calculations. These results show that, in the case of methane hydrate, the following nucleation mechanism can be revealed. The formation of small water cavities filled with methane is the first step of the formation of methane hydrate. It is not necessary to occupy all dodecahedral cages by guest molecules. After that small cavities start to form the H-bonding network with surrounding water molecules and a small number of water molecules is enough for the formation of a stable hydrogen-bonding network. The structural information contained in such nuclei is conserved in the forming crystal. Moreover, the presence of a methane molecule between small cages is also important to prevent the adhesion of cavities. It found that the ozone molecule can also stabilize the small cage since the value of the interaction energy between the ozone guest and the water host framework is very close to that obtained for the methane case. However, ozone affects the structure of large cavities and hence, the second guest is necessary to stabilize the hydrate structure.     

An approach to helical tubular self-aggregation using C2-symmetric self-complementary hydrogen-bonding cavity molecules

In an approach to helical self-aggregation, C2-symmetric cavity compounds based on the fusion of the bicyclo[3.3.1]nonane and indole framework and incorporating two 2-pyridone hydrogen-bonding motifs, compounds (-)-4 (pyrrole N-butyl) and (-)-5 (pyrrole N-decyl), have been synthesized. The 2-pyridone AD-DA hydrogen-bonding motif failed to operate in the solid state as demonstrated by X-ray diffraction analysis of (-)-4. Instead, the hydrogen-bonded (D-A) chains ...O=C-N-H...O=C-N-H...O=C-N-H..., interconnecting columnar stacks, comprise helices of the right-handed (P) chirality motif. In solution, the aggregation of (-)-5 was studied by NMR, electronic, and CD spectroscopies, and VPO measurements. These investigations strongly suggest that (-)-5 associates to oligomers in CHCl3 and CH2Cl2 using the 2-pyridone motif, fitting the equal K model, and that pi-stacking can be ruled out as a mode of aggregation. We conclude that the so formed aggregates of (-)-5 have a helical structure, based on the fact that only helical tubular structures can result when enantiomerically pure 5 uses its 2-pyridone AD-DA hydrogen-bonding motifs for aggregation.     

Solvent-induced polymorphism of three-dimensional hydrogen-bonded networks of hexakis(4-carbamoylphenyl)benzene

The crystal structures for three types of three-dimensional (3-D) hydrogen-bonded networks of hexakis(4-carbamoylphenyl)benzene (1), the network morphologies of which depend greatly on crystallization conditions, have been determined. When this compound is crystallized from hot DMSO, the resulting crystals, 1.12DMSO (orthorhombic, Pca2(1)), showed a 3-D hydrogen-bonded porous network (type A) via 1-D catemer chains as a hydrogen-bonding motif of six primary amide groups. The type A network creates chambers surrounded by six molecules of 1 and channels along the c axis to give the highest porosity among the network polymorphs of 1 investigated here. Crystallization from a boiling mixture of n-PrOH and water gave 1.6n-PrOH (monoclinic, P2(1)/c), which exhibits another type of 3-D hydrogen-bonded porous network (type B) via cyclic dimers as another hydrogen-bonding motif of six primary amide groups. The type B network leads to triangle-like channels along the a axis having a cross section of ca. 9.2 x 9.7 x 9.7 A (including van der Waals radii). The crystal structure of 1.H(2)O (monoclinic, P2(1)/c), which was produced under hydrothermal conditions, showed a nonporous 3-D hydrogen-bonded network chain of amide groups (type C) composed of a mixed hydrogen bonding motif of helical catemer chains/cyclic dimer/catemer. Solvent-induced topological isomerism of these 3-D hydrogen-bonded networks of 1 arises from (i) the guest inclusion ability based on a radially functionalized hexagonal structure of 1, (ii) the correlation between the hydrogen bond donor ability of the syn and anti protons of the primary amide group in host 1 and the hydrogen bond acceptor ability of the oxygen atoms of 1 and guest solvents, and (iii) the polarity of the bulk crystallization solvents.     

Static normal coordinate deformations of the heme group in mutants of ferrocytochrome c from Saccharomyces cerevisiae probed by resonance Raman spectroscopy

The function of heme proteins is, to a significant extent, influenced by the ligand field probed by the heme iron, which itself can be affected by deformations of the heme macrocycle. The exploration of this field is difficult because the heme structure obtained from X-ray crystallography is not resolved enough to unambiguously identify structural changes on the scale of 10(-2) A. However, asymmetric deformations in this order of magnitude affect the depolarization ratio of the resonance Raman lines assignable to normal vibrations of the heme group. We have measured the dispersion of the depolarization ratios of four structure sensitive Raman bands (i.e., nu4, nu11, nu21, and nu28) in yeast iso-1-ferrocytochrome c and its mutants N52V, Y67F, and N52VY67F with B- and Q-band excitation. The DPR dispersion of all bands indicates the presence of asymmetric in-plane and out-of-plane deformations. The replacement of the polar tyrosine residue at position 67 by phenylalanine significantly increases the triclinic B2g deformation, which involves a distortion of the pyrrole symmetry. We relate this deformation to changes of the electronic structure of pyrrole A, which modulates the interaction between its propionate substituents and the protein environment. This specific heme deformation is eliminated in the double mutant N52VY67F. The additional substitution of N52 by valine induces a tetragonal B1g deformation which involves asymmetric changes of the Fe-N distances and increases the rhombicity of the ligand field probed by the heme iron. This heme deformation might be caused by the elimination of the water-protein hydrogen-bonding network in the heme cavity. The single mutation N52V does not significantly perturb the heme symmetry, but a small B1g deformation is consistent with our data and the heme structure obtained from a 1 ns molecular dynamics simulation of the protein.     

Role of heme types in heme-copper oxidases: effects of replacing a heme b with a heme o mimic in an engineered heme-copper center in myoglobin

To address the role of the secondary hydroxyl group of heme a/o in heme-copper oxidases, we incorporated Fe(III)-2,4 (4,2) hydroxyethyl vinyl deuterioporphyrin IX, as a heme o mimic, into the engineered heme-copper center in myoglobin (sperm whale myoglobin L29H/F43H, called Cu(B)Mb). The only difference between the heme b of myoglobin and the heme o mimic is the substitution of one of the vinyl side chains of the former with a hydroxyethyl group of the latter. This substitution resulted in an approximately 4 nm blue shift in the Soret band and approximately 20 mV decrease in the heme reduction potential. In a control experiment, the heme b in Cu(B)Mb was also replaced with a mesoheme, which resulted in an approximately 13 nm blue shift and approximately 30 mV decrease in the heme reduction potential. Kinetic studies of the heme o mimic-substituted Cu(B)Mb showed significantly different reactivity toward copper-dependent oxygen reduction from that of the b-type Cu(B)Mb. In reaction with O2, Cu(B)Mb with a native heme b showed heme oxygenase activity by generating verdoheme in the presence of Cu(I). This heme degradation reaction was slowed by approximately 19-fold in the heme o mimic-substituted Cu(B)Mb (from 0.028 s(-1) to 0.0015 s(-1)), while the mesoheme-substituted Cu(B)Mb shared a similar heme degradation rate with that of Cu(B)Mb (0.023 s(-1)). No correlation was found between the heme reduction potential and its O2 reactivity. These results strongly suggest the critical role of the hydroxyl group of heme o in modulating heme-copper oxidase activity through participation in an extra hydrogen-bonding network.