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1.
Dithiothreitol (DTT) is the standard reagent for reducing disulfide bonds between and within biological molecules. At neutral pH, however, >99% of DTT thiol groups are protonated and thus unreactive. Herein, we report on (2S)-2-amino-1,4-dimercaptobutane (dithiobutylamine or DTBA), a dithiol that can be synthesized from l-aspartic acid in a few high-yielding steps that are amenable to a large-scale process. DTBA has thiol pK(a) values that are ~1 unit lower than those of DTT and forms a disulfide with a similar E°' value. DTBA reduces disulfide bonds in both small molecules and proteins faster than does DTT. The amino group of DTBA enables its isolation by cation-exchange and facilitates its conjugation. These attributes indicate that DTBA is a superior reagent for reducing disulfide bonds in aqueous solution.  相似文献   

2.
Aqueous acid dissociation free energies for a diverse set of 57 monoprotic acids have been calculated using a combination of experimental and calculated gas and liquid-phase free energies. For ionic species, aqueous solvation free energies were calculated using the recently developed SM6 continuum solvation model. This model combines a dielectric continuum with atomic surface tensions to account for bulk solvent effects. For some of the acids studied, a combined approach that involves attaching a single explicit water molecule to the conjugate base (anion), and then surrounding the resulting anion-water cluster by a dielectric continuum, significantly improves the agreement between the calculated pK(a) value and experiment. This suggests that for some anions, particularly those concentrating charge on a single exposed heteroatom, augmenting implicit solvent calculations with a single explicit water molecule is required, and adequate, to account for strong short-range hydrogen bonding interactions between the anion and the solvent. We also demonstrate the effect of adding several explicit waters by calculating the pK(a) of bicarbonate (HCO(3)(-)) using as the conjugate base carbonate (CO(3)(2-)) bound by up to three explicit water molecules.  相似文献   

3.
随机产生单笼形水分子簇(H2O)n(n=8~36),经分类统计后发现,在笼形水分子簇中,其1221,1212,2121和2112四类氢键的个数与水分子和氢键总数之间有定量关系,且1212类氢键的个数与2121类的氢键始终相等.如果笼形水分子簇中某一类氢键数已知,则它的其余三类氢键的个数也随即确定.  相似文献   

4.
Prolonged hydrogenation of C(60) molecules by reaction with H(2) at elevated temperature and pressure results in fragmentation and collapse of the fullerene cage structure. However, fragments can be preserved by immediate termination of dangling bonds by hydrogen. Here we demonstrate that not only fullerene fragments but also hydrogenated fragmented fullerenes (e.g., C(58)H(40) and C(59)H(40)) can be synthesized in bulk amount by high-temperature hydrogenation of C(60). We confirm successful synthesis of these species by matrix-assisted laser desorption ionization time-of-flight mass spectrometry and complete speciation of the resultant complex fullerene mixtures by high-resolution field desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry.  相似文献   

5.
The overlapping pK(a) values of 5,7-dihydroxyflavone (chrysin) in EtOH-water solutions were determined by means of a UV-vis spectroscopic method that uses absorbance diagrams, at constant ionic strength (0.050 M) and temperature (25.0+/-0.1 degrees C). It was observed that the pK(a) values increase when the polarity-polarizability and solvation abilities of the reaction medium decrease. In order to calculate the pK(a1) and pK(a2) of chrysin in pure water, various relationships between the determined pK(a) and properties of solvents (relative permittivity, alpha-parameter of Taft and parameter Acity), are proposed. Moreover, with the aim of explaining the first pK(a1) value obtained, the molecular conformations and solute-solvent interactions of the 7(O(-))chrysinate monoanion were also investigated, using ab initio methods. Several ionization reactions and equilibria in water, which possesses a high hydrogen-bond-donor ability, are proposed. These reactions and equilibria constituted the necessary theoretical basis to calculate the first acidity constant of chrysin. The HF/6-31G(d) and HF/6-31+G(d) methods were used for calculations. Tomasi's method was used to analyze the formation of intermolecular hydrogen bonds between the 7(O(-))chrysinate monoanion and water molecules. It was proposed that in alkaline aqueous solutions the monoanion of chrysin is solvated with one water molecule. The agreement between the experimental and theoretical pK(a1) values provides good support for the acid-base reactions proposed in this paper.  相似文献   

6.
In this paper we determine the overlapping pK(a) values of resorcinol in water, applying a UV-Vis spectroscopic method that uses absorbance diagrams. On the other hand, in order to explain the pK(a) values obtained, we also investigate the molecular conformations and solute-solvent interactions of the resorcinate anions, using ab initio and density functional theory methods. Several ionization reactions and equilibria in protic solvents, which possess a high hydrogen-bond-donor capability, are proposed. The mentioned reactions and equilibria constituted the indispensable theoretical basis to calculate the acidity constants of resorcinol. Basis sets at the HF/6-31 + G(d) and B3LYP/6-31 + G(d) levels of theory were used for calculations. Tomasi's method was used to analyze the formation of intermolecular hydrogen bonds between the resorcinate anions and water molecules. In this way, it was determined that in alkaline aqueous solutions the monoanion and dianion of resorcinol are solvated with two and four molecules of water, respectively. The agreement between the experimentally determined pK(a) values and those reported in the literature demonstrates the applicability and accurateness of the spectroscopic method here used. On the other hand, the agreement between the experimental and theoretically calculated pK(a) values provides solid support for the acid-base reactions proposed in this work.  相似文献   

7.
彭昌盛 《化学学报》2009,67(16):1936-1942
水的一些奇特性质主要源于水分子之间存在的氢键, 但在分子尺度上的氢键结构和数据仍是目前研究和争论的焦点. 统计分析了目前文献中普遍采用的水分子和氢键结构数据, 并在此基础上应用AutoCAD图形软件模拟出(H2O)10结构的最小冰聚体结构单元(Minimum Ice Structural Unit, MISU)模型, 以及由MISU聚合而成的冰晶体三维模型. 根据MISU模型, 可以计算得到冰在0 ℃融化为水、水由0 ℃加热至100 ℃、水在100 ℃汽化为水蒸气的三相转化过程中分别需要吸收5.86, 4.40和24.94 kJ•mol-1的能量以断裂16.7%, 12.5%和70.8%的氢键. 如若不考虑氢键的影响, 那么计算得到水的融化热和汽化热分别为0.15和15.73 kJ•mol-1, 与VIA族氢化物H2S, H2Se, H2Te的融化热和汽化热基本呈线性关系. 另外, 由MISU模型计算得到冰在0 ℃融化为水时, 密度由923.17 kg•m-3增至999.89 kg•m-3, 亦与实际测量数据基本一致.  相似文献   

8.
Metal‐ion accumulation on protein surfaces is a crucial step in the initiation of small‐metal clusters and the formation of inorganic materials in nature. This event is expected to control the nucleation, growth, and position of the materials. There remain many unknowns, as to how proteins affect the initial process at the atomic level, although multistep assembly processes of the materials formation by both native and model systems have been clarified at the macroscopic level. Herein the cooperative effects of amino acids and hydrogen bonds promoting metal accumulation reactions are clarified by using porous hen egg white lysozyme (HEWL) crystals containing RhIII ions, as model protein surfaces for the reactions. The experimental results reveal noteworthy implications for initiation of metal accumulation, which involve highly cooperative dynamics of amino acids and hydrogen bonds: i) Disruption of hydrogen bonds can induce conformational changes of amino‐acid residues to capture RhIII ions. ii) Water molecules pre‐organized by hydrogen bonds can stabilize RhIII coordination as aqua ligands. iii) Water molecules participating in hydrogen bonds with amino‐acid residues can be replaced by RhIII ions to form polynuclear structures with the residues. iv) RhIII aqua complexes are retained on amino‐acid residues through stabilizing hydrogen bonds even at low pH (≈2). These metal–protein interactions including hydrogen bonds may promote native metal accumulation reactions and also may be useful in the preparation of new inorganic materials that incorporate proteins.  相似文献   

9.
In investigations of the proteins which are responsible for the surface adhesion of the blue mussel Mytilus edulis, an unusually frequent appearance of the otherwise rare amino acid 3-(3,4-dihydroxyphenyl)-L-alanine (L-DOPA) has been observed. This amino acid is thought to play a major role in the mechanism of mussel adhesion. Here we report a detailed structural and spectroscopic investigation of the interface between L-DOPA and a single-crystalline Au(110) model surface, with the aim of understanding fundamentals about the surface bonding of this amino acid and its role in mussel adhesion. Molecular layers are deposited by organic molecular beam deposition (OMBD) in an ultrahigh-vacuum environment. The following experimental techniques have been applied: ex situ Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), low-energy electron diffraction (LEED), high-resolution electron energy loss spectroscopy (HREELS), and scanning tunneling microscopy (STM). Vibrational spectra of isolated L-DOPA molecules and the zwitterionic bulk have been calculated using density functional theory (DFT). The predicted modes are assigned to observed spectra, allowing conclusions regarding the molecule-substrate and molecule-molecule interactions at the L-DOPA/Au(110) interface. We find that zwitterionic L-DOPA forms a monochiral, one-domain commensurate monolayer on Au(110), with the catechol rings on top of [110] gold rows, oriented parallel to the surface. The (2 x 1)-Au(110) surface reconstruction is not lifted. The carboxylate group is found in a bidentate or bridging configuration, the amino group is tilted out of the surface plane, and the hydroxyl groups do not dehydrogenate on Au(110). Similar to the case for the bulk, molecules form dimers on Au(110). However, the number of hydrogen bridge bonds between L-DOPA molecules is reduced as compared to the bulk. Thicker layers which are deposited onto the commensurate interface do not order in the bulk structure. In conclusion, our study shows that the aromatic ring system of L-DOPA functions as a surface anchor. Since it is also known that the hydroxyl groups support cross-link reactions between L-DOPA residues in the mussel glue protein, we can conclude that the catechol ring supports surface adhesion of mussel proteins via two independent functions.  相似文献   

10.
Various amino acid-carrying amphiphiles were synthesized, and the pK values of the attached amino acid residues were investigated at the air-water interface and in aqueous vesicles using pi-A isotherm measurements, (1)H NMR titration, and IR spectroscopy in reflection-adsorption mode. The epsilon-amino group of the Lys residue embedded at the air-water interface displays a significant pK shift (4 or 5 unit) compared with that observed in bulk water, while the pK shift in aqueous vesicles was not prominent (ca. 1 unit). Moreover, pK values of the amino acids at the air-water interface can be tuned simply by control of the subphase ionic strength as well as by molecular design of the amphiphiles. A simple equation based on the dominant contribution by the electrostatic energy to the pK shift reproduces well the surface pressure difference between protonated and unprotonated species, suggesting a reduction in the apparent dielectric constant at the air-water interface. Hydrolysis of a p-nitrophenyl ester derivative was used as a model reaction to demonstrate the use of the Lys-functionalized monolayer. Efficient hydrolysis was observed, even at neutral pH, after tuning of pK for the Lys residue in the monolayer, which is a similar case to that occurring in biological catalysis.  相似文献   

11.
Tryptophan is an essential amino acid, and understanding the conformational preferences of monomer and dimer is a subject of outstanding relevance in biological systems. An exhaustive first principles investigation of tryptophan ( W ) and its ionized counterparts cations (WC) , anions (WA) , and zwitterions (WZ) has been carried out. A comprehensive and systematic study of tryptophan dimer (WD) conformations resulted in about 62 distinct minima on the potential energy surface. The hydrogen bonds and a variety of noncovalent interactions such as OH‐π, NH‐π, CH‐π, CH‐O, and π‐π interactions stabilized different forms of tryptophan and its dimers. Over all in monomeric conformers which have NH‐O, hydrogen bonds showed higher stability than other conformers. A cursory analysis reveal that the most stable dimers stabilized by hydrogen bonding interactions while the less stable dimers showed aromatic side chain interactions. Protein Data Bank analysis of tryptophan dimers reveals that at a larger distance greater than 5 Å, T‐shaped orientations (CH‐π interactions) are more prevalent, while stacked orientations (π‐π interactions) are predominant at a smaller distance. © 2013 Wiley Periodicals, Inc.  相似文献   

12.
We utilized X-ray absorption spectroscopy (XAS) and X-ray Raman scattering (XRS) in order to study the ion solvation effect on the bulk hydrogen bonding structure of water. The fine structures in the X-ray absorption spectra are sensitive to the local environment of the probed water molecule related to the hydrogen bond length and angles. By varying the concentration of ions, we can distinguish between contributions from water in the bulk and in the first solvation sphere. We show that the hydrogen bond network in bulk water, in terms of forming and breaking hydrogen bonds as detected by XAS/XRS, remains unchanged, and only the water molecules in the close vicinity to the ions are affected.  相似文献   

13.
Alkyl-N-iminodiacetic acids with varying alkyl chain lengths have been prepared and characterized with respect to structure, acidic properties, and ability to form aggregates in water. The alkyl-N-iminodiacetic acids are the group of ligands with the lowest molecule weight which can be characterized as chelating surfactants, compounds with surface chemical properties which at the same time have a high ability to bind metal ions. The solid alkyl-N-iminodiacetic acids have a unique structure with neutral zwitterionic units linked together to polymer chains through a short strong hydrogen bond, d(O(-H)...O) approximately 2.46 A, and where the nu(O-H) stretching vibration at ca. 720 cm(-1) supports the presence of such a hydrogen bond. The polymer chains are cross-linked together to bilayers through relatively strong hydrogen bonds between ammonium and carboxylate groups, and where the parallel alkyl groups are interdigitating each other; the bilayer surface consists of hydrophilic iminodiacetic acid groups. The acidic properties of monomeric alkyl-N-iminodiacetic acids in water are in the expected ranges with pK(a) values of about 1.7, 2.3, and 10.3. n-Octadecyl-N-iminodiacetic acid, present as aggregates in water, displays very acidic properties of the first proton, and a substantially weakened acidity of the second proton, pK(a2) = 5.5-7.5, depending on ionic strength, and pK(a3) = 9.5-10.5. This pattern of the acidic constants strongly indicates that the polymer structure with short strong hydrogen bonds is maintained in the aggregates and that such bonds can exist in aqueous systems if they are supported by a strong and rigid backbone structure, as the bilayers of well-organized long interdigitating alkyl chains in the studied systems. Hydrogenbis(methyl-N-iminodiacetic acid) perchlorate precipitates from perchloric acidic solutions of methyl-N-iminodiacetic acid. The structure is built up of dimers of zwitterionic methyl-N-iminodiacetic acid units linked together by an extra proton in a short strong hydrogen bond, d(O(-H)...O) approximately 2.456(6) A, and nu(O-H) = 789 cm(-1).  相似文献   

14.
The synthesis of novel ortho-coumaric acid derivatives, with an amide group linked with an olefin moiety, which introduced photoinduced switching of the intramolecular hydrogen bonds is presented. An intramolecular OH...O=C hydrogen bond formed in a Z-phenol compound was switched to an intramolecular NH...O hydrogen bond in Z phenolate state via deprotonation. The pK(a) value of the Z-phenol derivative was lower than that of E-phenol, and a novel photocycle system involving protonation and deprotonation processes was achieved.  相似文献   

15.
A set of linear free energy models are presented for determining the pK(a) values of amines, alcohols, and carboxylic acids. Models are determined from a series of pK(a) predictors, taken both from traditional natural atomic orbital analysis (NAO) and from a novel approach introduced here of using a reference molecule: an ammonium ion for amines and a hydrogen sulfide molecule for alcohols and carboxylic acids. Using these reference molecules, we calculate the barrier to proton transfer and show that a number of properties associated with the transition state are correlated with the pK(a). By considering 38 predictors, we obtain a four-variable model for amines and a three-variable model for oxygen-containing compounds. The model for amines is based on 145 compounds and has a root mean squared error (RMSE) of 0.45 and R(2) = 0.98. The oxygen set has 48 molecules: RMSE = 0.26, and R(2) = 0.993. Similar, linear, and multilinear models are constructed after separating the sets into chemically similar categories: alcohols, carboxylic acids, and primary, secondary, tertiary, and aromatic amines. This separation gives simpler models with relatively low RMSE values, where the most important predictor of the pK(a) is the difference in energy between transferring the proton from the reference molecular base to the conjugate acid from the data set.  相似文献   

16.
The structure and geometry of hydrogen-bonded complexes formed between heterocyclic bases, namely, pyridine and 2,4,6-trimethylpyridine (collidine), and water were experimentally studied by NMR spectroscopy in frozen phase and in highly polar aprotic liquefied freon mixtures and theoretically modeled for gas phase. Hydrogen-bonded species in frozen heterocycle-water mixtures were characterized experimentally using 15N NMR. When base was in excess, one water molecule was symmetrically bonded to two heterocyclic molecules. This complex was characterized by the rHN distances of 1.82 Angstrom for pyridine and 1.92 Angstrom for collidine. The proton-donating ability of water in such complexes was affected by an anticooperative interaction between the two coupled hydrogen bonds and exhibited an apparent pK(a) value of about 6.0. When water was in excess, it formed water clusters hydrogen bonded to base. Theoretical analysis of binding energies of small model heterocycle-water clusters indicated that water in such clusters was oriented as a chain. The NMR estimated rHN distances in these species were 1.69 Angstrom for pyridine and 1.64 Angstrom for collidine. Here, the proton-donating ability of the hydroxyl group bonded to the heterocycle was affected by a mutual cooperative interaction with other water molecules in the chain and became comparable to the proton-donating ability of a fictitious acid, exhibiting an apparent pK(a) value of about 4.9. This value seems to depend only slightly on the length of the water chain and on the presence of another base at the other end of the chain if more than two water molecules are involved. Thus, the proton-donating ability of the outer hydroxyl groups of biologically relevant water bridges should be comparable to the proton-donating ability of a fictitious acid exhibiting a pK(a) value of about 4.9 in water. Driven by the mixing entropy, monomeric water presented in the aprotic freonic mixtures above 170 K but completely precipitated upon further cooling. Traces of water could be suspended in the mixtures down to 130 K in the presence of about 20-fold excess of heterocyclic bases. The obtained experimental data indicated that at these conditions water trended to form the symmetric 2:1 heterocycle-water complexes, whose bridge protons resonated around 6.7 ppm.  相似文献   

17.
Ab initio quantum mechanical calculations were used in studying the origin of the exceptionally high basicities of four diamines (13-16) with pK(a1) values ranging from 12.1 to 25. The computational approach involved the calculation of the gas-phase proton affinities of the molecules studied at the MP2/6-31G//HF/6-31G level and the solvation energies with the polarizable continuum model at the HF/6-31G level. The calculated gas-phase and aqueous-phase proton affinities of a structurally diverse series of amines were compared with the corresponding experimental gas-phase proton affinities and pK(a1) values. The calculated values were found to be in reasonable agreement with the experimental ones. The high basicities of the studied diamines were found to originate from the nitrogen lone-pair repulsion, solvation effects, and strong intramolecular hydrogen bonds. Each of these factors were found to be able to increase the pK(a1) values of the high-basicity diamines by 2-6 pK(a) units. The relative contributions of the factors varied between the compounds. The nitrogen lone-pair repulsion was estimated to be the most important factor in increasing the pK(a1) values. In addition, barriers for proton transfers between the nitrogens of selected diamines were calculated, and comparison was made between the barrier heights and the geometries of the diamines.  相似文献   

18.
Accurate calculation of pK(a) values and free energies for acid/base reactions in the condensed phase has been a long-standing goal of theoretical chemistry. We present a novel application of the Car-Parrinello molecular dynamics method to the problem of relative pK(a) determination. As a particular example, we focus on the second stage in the dissociation of histidine, a process that holds special importance for biology. Using constrained molecular dynamics, we have analyzed the structural, electronic, and dynamical transformations taking place along a preselected, intuitive reaction coordinate. By integrating the potentials of mean force for the deprotonation of histidine and for a reference reaction, autodissociation of water, we obtain a pK(a) value of 6.8, which appears to be in good agreement with the experimental estimate of 6.1. Detailed analysis was undertaken to determine the value of the constraint, which transformed the N*-H* from a covalent to a hydrogen bond. This helped to identify a number of properties that could be successfully used in monitoring the dissociation process. Additional analysis in terms of electron localization functions provided valuable insight into the nature of the deprotonation reaction.  相似文献   

19.
Aqueous solvolyses of acyl derivatives of hydrates (water adducts) of anthracene and benzofuran yield carbocations which undergo competitive deprotonation to form the aromatic molecules and nucleophilic reaction with water to give the aromatic hydrates. Trapping experiments with azide ions yield rate constants k(p) for the deprotonation and k(H2O) for the nucleophilic reaction based on the "azide clock". Combining these with rate constants for (a) the H(+)-catalyzed reaction of the hydrate to form the carbocation and (b) hydrogen isotope exchange of the aromatic molecule (from the literature) yields pK(R) = -6.0 and -9.4 and pK(a) = -13.5 and -16.3 for the protonated anthracene and protonated benzofuran, respectively. These pK values may be compared with pK(R) = -6.7 for naphthalene hydrate (1-hydroxy-1,2-dihydronaphthalene), extrapolated to water from measurements by Pirinccioglu and Thibblin for acetonitrile-water mixtures, and pK(a) = -20.4 for the 2-protonated naphthalene from combining k(p) with an exchange rate constant. The differences between pK(R) and pK(a) correspond to pK(H2O), the equilibrium constant for hydration of the aromatic molecule (pK(H2O) = pK(R) - pK(a)). For naphthalene and anthracene values of pK(H2O) = +13.7 and +7.5 compare with independent estimates of +14.2 and +7.4. For benzene, pK(a) = -24.3 is derived from an exchange rate constant and an assigned value for the reverse rate constant close to the limit for solvent relaxation. Combining this pK(a) with calculated values of pK(H2O) gives pK(R) = -2.4 and -2.1 for protonated benzenes forming 1,2- and 1,4-hydrates, respectively. Coincidentally, the rate constant for protonation of benzene is similar to those for protonation of ethylene and acetylene (Lucchini, V.; Modena, G. J. Am. Chem Soc. 1990, 112, 6291). Values of pK(a) for the ethyl and vinyl cations (-24.8) may thus be derived in the same way as that for the benzenonium ion. Combining these with appropriate values of pK(H2O) then yields pK(R) = -39.8 and -29.6 for the vinyl and ethyl cations, respectively.  相似文献   

20.
We have carried out ab initio molecular dynamics simulations of a liquid-vapor interfacial system consisting of a mixture of water and ammonia molecules. We have made a detailed analysis of the structural and dynamical properties of the bulk and interfacial regions of the mixture. Among structural properties, we have looked at the inhomogeneous density profiles of water and ammonia molecules, hydrogen bond distributions, orientational profiles, and also vibrational frequency distributions of bulk and interfacial molecules. It is found that the interfacial molecules show preference for specific orientations so as to form water-ammonia hydrogen bonds at the interface with ammonia as the acceptor. The structure of the system is also investigated in terms of inter-atomic voids present in the system. Among the dynamical properties, we have calculated the diffusion, orientational relaxation, hydrogen bond dynamics, and vibrational spectral diffusion in bulk and interfacial regions. It is found that the diffusion and orientation relaxation of the interfacial molecules are faster than those of the bulk. However, the hydrogen bond lifetimes are longer at the interface which can be correlated with the time scales found from the decay of frequency time correlations.  相似文献   

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