L-alanine in a droplet of water: a density-functional molecular dynamics study

We report the results of a Born-Oppenheimer molecular dynamics study on an L-alanine amino acid in neutral aqueous solution. The whole system, the L-alanine zwitterion and 50 water molecules, was treated quantum mechanically. We found that the hydrophobic side chain (R = CH3) defines the trajectory path of the molecule. Initially fully hydrated in an isolated droplet of water, the amino acid moves to the droplet's surface, exposing its hydrophobic methyl group and alpha-hydrogen out of the water. The structure of an L-alanine with the methyl group exposed to the water surface was found to be energetically favorable compared to a fully hydrated molecule. The dynamic behavior of the system suggests that the first hydration shell of the amino acid is localized around carboxylate (CO2-) and ammonium (NH3+) functional groups; it is highly ordered and quite rigid. In contrast, the hydration shell around the side chain is much less structured, suggesting a modest influence of the methyl group on the structure of water. The number of water molecules in the first hydration shell of an alanine molecule is constantly changing; the average number was found to equal 7. The molecular dynamics results show that L-alanine in water does not have a preferred conformation, as all three of the molecule's functional sites (i.e., CH3, NH3+, CO2-) perform rotational movements around the C(alpha)-site bond.     

Computational Study on the Antifreeze Glycoproteins as Inhibitors of Clathrate‐Hydrate Formation

The ability of antifreeze glycoproteins to inhibit clathrate‐hydrate formation is studied using DFT. A 5¹² cavity, dodecahedral (H₂O)₂₀, and the AATA peptide are used to model the inhibitor–clathrate interaction. The presence of AATA in the vicinity of the water cavities not only leads to the formation of complexes, with different peptide/cavity ratios, but also to the deformation of the cavity and to the elongation of several of the hydrogen bonds responsible for keeping the dodecahedral (H₂O)₂₀ together. The complexes are formed through hydrogen bonding between the peptides and the water cavities. The glycoproteins are expected to anchor onto the clathrate surface, blocking the access of new water molecules and preventing the incipient crystals from growing. They are also expected to weaken the clathrate structure. Amide IR bands are associated with the complexes’ formation. They are significantly red‐shifted in the hydrogen‐bonded systems compared to isolated AATA. The amide A band is the most sensitive to hydrogen bonding. In addition a distinctive band around 3100 cm^?1 is proposed for the identification of clathrate–peptide hydrogen‐bonded complexes.     

Structure and dynamics of water surrounding the poly(methacrylic acid): a molecular dynamics study

All-atom molecular dynamics simulations are used to study a single chain of poly(methacrylic acid) in aqueous solutions at various degrees of charge density. Through a combination of analysis on the radial distribution functions of water and snapshots of the equilibrated structure, we observe that local arrangements of water molecules, surrounding the functional groups of COO- and COOH in the chain, behave differently and correlated well to the resulting chain conformation behavior. In general, due to strong attractive interactions between water and charged COO- via the formation of hydrogen bonds, water molecules tend to form shell-like layers around the COO- groups. Furthermore, water molecules often act as a bridging agent between two neighboring COO- groups. These bridged water molecules are observed to stabilize the rodlike chain conformation that the highly charged chain reveals, as they significantly limit torsional and bending degrees of the backbone monomers. In addition, they display different dynamic properties from the bulk water. Both the resulting oxygen and hydrogen spectra are greatly shifted due to the presence of strong H-bonded interactions.     

Molecular modeling of the short-side-chain perfluorosulfonic acid membrane

Presented here is a first principles based molecular modeling investigation of the possible role of the side chain in effecting proton transfer in the short-side-chain perfluorosulfonic acid fuel cell membrane under minimal hydration conditions. Extensive searches for the global minimum energy structures of fragments of the polymer having two pendant side chains of distinct separation (with chemical formula: CF(3)CF(O(CF(2))(2)SO(3)H)(CF(2))(n)CF(O(CF(2))(2)SO(3)H)CF(3), where n = 5, 7, and 9) with and without explicit water molecules have shown that the side chain separation influences both the extent and nature of the hydrogen bonding between the terminal sulfonic acid groups and the number of water molecules required to transfer the proton to the water molecules of the first hydration shell. Specifically, we have found that fully optimized structures at the B3LYP/6-311G** level revealed that the number of water molecules needed to connect the sulfonic acid groups scaled as a function of the number of fluoromethylene groups in the backbone, with one, two, and three water molecules required to connect the sulfonic acid groups in fragments with n = 5, 7, and 9, respectively. With the addition of explicit water molecules to each of the polymeric fragments, we found that the minimum number of water molecules required to effect proton transfer also increases as the number of separating tetrafluoroethylene units in the backbone is increased. Furthermore, calculation of water binding energies on CP-corrected potential energy surfaces showed that the water molecules bound more strongly after proton dissociation had occurred from the terminal sulfonic acid groups independent of the degree of separation of the side chains. Our calculations provide a baseline for molecular results that can be used to assess the impact of changes of polymer chemistry on proton conduction, including the side chain length and acidic functional group.     

Design,synthesis and structural analysis of mixed α/β-peptides that adopt stable cyclic hairpin-like conformations

The strategic replacement of four α-amino acid residues of a cyclo-(ααααα)₂ peptide by β-, β²- or β³-amino acids residues provided a series of novel 2:1 α/β-mixed peptides that were designed to adopt cyclic hairpin-like structures. It was shown that conformationally stable cyclo-(αβαβα)₂ isomers can be obtained using both enantiomers of the central two basic α-amino acid residues, a known α-amino acid turn sequence and several combinations of facing β-amino acid residues with no side chain or a hydrophobic side chain having specific regio- and stereochemistry. The X-ray analysis of two derivatives provides molecular details of the intra-molecular hydrogen bonding interaction, dihedral angles of the backbone and side chain positioning of the novel cyclic hairpin-like structures. One of these isomers forms an unprecedented hexagon-shaped nano-channel assembly in the crystal structure. Well-defined cyclic hairpin-like structures as described here and derivatives that can be readily designed based on this research can be used as scaffolds onto which functional groups can be grafted in a spatially controlled manner and as β-hairpin mimics with specific biological properties.     

α-氨基丁酸对映异构体在DMF+水混合溶剂中的焓对作用

利用等温滴定微量热法(ITC)分别测定了298.15K时L-α-氨基丁酸和D-α-氨基丁酸两种对映异构体在不同组成的二甲基甲酰胺(DMF)+水混合溶剂中的稀释焓.根据统计热力学的McMillan-Mayer理论计算各溶剂组成下的同系焓对作用系数(hxx).从溶质-溶质和溶质-溶剂相互作用的观点出发探讨了三元水溶液中疏水-疏水、疏水-亲水和亲水-亲水作用的竞争平衡.实验发现,在所研究的混合溶剂组成范围内(wDMF=0-0.3),α-氨基丁酸两种对映体的hxx都是较大的正值,且都随wDMF的增大而逐渐减小,而有趣的是L型对映体的hxx值普遍比D型的大(hLLhDD),说明ITC可以区分对映异构体的同手性焓对作用.结果表明:在α-氨基丁酸+水+DMF三元溶液体系中,疏水-疏水和疏水-亲水作用在分子对作用过程中占优势;在α-氨基丁酸的同种对映体发生分子对作用时,L-L分子对比D-D分子对在构型上更有利于α-碳上疏水侧链(CH3CH2-)的靠拢,疏水基团的水合壳层发生交盖,局部破坏而释放出部分结构化的水,过程自发、吸热且伴随显著熵增(ΔG0,ΔH0,ΔS=(ΔH-ΔG)/T0),因而在稀释时释放出更多热量,hxx具有较大的正值.     

Structure and dynamics of methanol in water: a quantum mechanical charge field molecular dynamics study

An ab initio quantum mechanical charge field molecular dynamics simulation was carried out for one methanol molecule in water to analyze the structure and dynamics of hydrophobic and hydrophilic groups. It is found that water molecules around the methyl group form a cage-like structure whereas the hydroxyl group acts as both hydrogen bond donor and acceptor, thus forming several hydrogen bonds with water molecules. The dynamic analyses correlate well with the structural data, evaluated by means of radial distribution functions, angular distribution functions, and coordination number distributions. The overall ligand mean residence time, τ identifies the methanol molecule as structure maker. The relative dynamics data of hydrogen bonds between hydroxyl of methanol and water molecules prove the existence of both strong and weak hydrogen bonds. The results obtained from the simulation are in excellent agreement with the experimental results for dilute solution of CH(3)OH in water. The overall hydration shell of methanol consists in average of 18 water molecules out of which three are hydrogen bonded.     

High-pressure gas hydrates

It has long been known that crystalline hydrates are formed by many simple gases that do not interact strongly with water, and in most cases the gas molecules or atoms occupy 'cages' formed by a framework of water molecules. The majority of these gas hydrates adopt one of two cubic cage structures and are called clathrate hydrates. Notable exceptions are hydrogen and helium which form 'exotic' hydrates with structures based on ice structures, rather than clathrate hydrates, even at low pressures. Clathrate hydrates have been extensively studied because they occur widely in nature, have important industrial applications, and provide insight into water-guest hydrophobic interactions. Until recently, the expectation-based on calculations-had been that all clathrate hydrates were dissociated into ice and gas by the application of pressures of 1 GPa or so. However, over the past five years, studies have shown that this view is incorrect. Instead, all the systems so far studied undergo structural rearrangement to other, new types of hydrate structure that remain stable to much higher pressures than had been thought possible. In this paper we review work on gas hydrates at pressures above 0.5 GPa, identify common trends in transformations and structures, and note areas of uncertainty where further work is needed.     

Effect of Guest–Host Hydrogen Bonding on the Structures and Properties of Clathrate Hydrates

To provide improved understanding of guest–host interactions in clathrate hydrates, we present some correlations between guest chemical structures and observations on the corresponding hydrate properties. From these correlations it is clear that directional interactions such as hydrogen bonding between guest and host are likely, although these have been ignored to greater or lesser degrees because there has been no direct structural evidence for such interactions. For the first time, single‐crystal X‐ray crystallography has been used to detect guest–host hydrogen bonding in structure II (sII) and structure H (sH) clathrate hydrates. The clathrates studied are the tert‐butylamine (tBA) sII clathrate with H₂S/Xe help gases and the pinacolone + H₂S binary sH clathrate. X‐ray structural analysis shows that the tBA nitrogen atom lies at a distance of 2.64 Å from the closest clathrate hydrate water oxygen atom, whereas the pinacolone oxygen atom is determined to lie at a distance of 2.96 Å from the closest water oxygen atom. These distances are compatible with guest–water hydrogen bonding. Results of molecular dynamics simulations on these systems are consistent with the X‐ray crystallographic observations. The tBA guest shows long‐lived guest–host hydrogen bonding with the nitrogen atom tethered to a water HO group that rotates towards the cage center to face the guest nitrogen atom. Pinacolone forms thermally activated guest–host hydrogen bonds with the lattice water molecules; these have been studied for temperatures in the range of 100–250 K. Guest–host hydrogen bonding leads to the formation of Bjerrum L‐defects in the clathrate water lattice between two adjacent water molecules, and these are implicated in the stabilities of the hydrate lattices, the water dynamics, and the dielectric properties. The reported stable hydrogen‐bonded guest–host structures also tend to blur the longstanding distinction between true clathrates and semiclathrates.     

热分析技术研究疏水缔合微区对含氟丙烯酸酯共聚物凝胶中水状态的影响

丙烯酸 (AA)与不同含量的 2 (N 乙基全氟辛烷基磺酰胺 )乙基甲基丙烯酸酯 (FMA)在叔丁醇中进行自由基共聚 ,合成了一系列疏水改性共聚物凝胶 .用示差扫描量热法 (DSC) ,热失重分析 (TGA)研究了含氟疏水改性凝胶中水的状态 ,证明FMA改性凝胶中存在 3种状态的水 ,即不可冻结水 ,可冻结结合水和自由水 .对于未改性凝胶和FMA含量为 1mol%的疏水改性凝胶 ,在凝胶中水含量分别低于 0 60 9mol%和 0 698mol%时 ,DSC升温曲线上观察不到熔融峰 ,说明凝胶中存在不可冻结水 .提出计算凝胶中 3种状态的水含量和熔融焓的理论假设 .计算出FMA含量为 1mol%的疏水改性凝胶中自由水和可冻结结合水的摩尔熔融焓分别为75 89 0 3和 6864 0 6J mol.计算结果表明疏水改性后 ,单位聚合物单元上结合的可冻结水数目 (n1 )和非冻结水的数目 (n0 )都增加     

Fluoroalkyl and alkyl chains have similar hydrophobicities in binding to the "hydrophobic wall" of carbonic anhydrase

The hydrophobic effect, the free-energetically favorable association of nonpolar solutes in water, makes a dominant contribution to binding of many systems of ligands and proteins. The objective of this study was to examine the hydrophobic effect in biomolecular recognition using two chemically different but structurally similar hydrophobic groups, aliphatic hydrocarbons and aliphatic fluorocarbons, and to determine whether the hydrophobicity of the two groups could be distinguished by thermodynamic and biostructural analysis. This paper uses isothermal titration calorimetry (ITC) to examine the thermodynamics of binding of benzenesulfonamides substituted in the para position with alkyl and fluoroalkyl chains (H(2)NSO(2)C(6)H(4)-CONHCH(2)(CX(2))(n)CX(3), n = 0-4, X = H, F) to human carbonic anhydrase II (HCA II). Both alkyl and fluoroalkyl substituents contribute favorably to the enthalpy and the entropy of binding; these contributions increase as the length of chain of the hydrophobic substituent increases. Crystallography of the protein-ligand complexes indicates that the benzenesulfonamide groups of all ligands examined bind with similar geometry, that the tail groups associate with the hydrophobic wall of HCA II (which is made up of the side chains of residues Phe131, Val135, Pro202, and Leu204), and that the structure of the protein is indistinguishable for all but one of the complexes (the longest member of the fluoroalkyl series). Analysis of the thermodynamics of binding as a function of structure is compatible with the hypothesis that hydrophobic binding of both alkyl and fluoroalkyl chains to hydrophobic surface of carbonic anhydrase is due primarily to the release of nonoptimally hydrogen-bonded water molecules that hydrate the binding cavity (including the hydrophobic wall) of HCA II and to the release of water molecules that surround the hydrophobic chain of the ligands. This study defines the balance of enthalpic and entropic contributions to the hydrophobic effect in this representative system of protein and ligand: hydrophobic interactions, here, seem to comprise approximately equal contributions from enthalpy (plausibly from strengthening networks of hydrogen bonds among molecules of water) and entropy (from release of water from configurationally restricted positions).     

Hidden Isolated OH at the Charged Hydrophobic Interface Revealed by Two‐Dimensional Heterodyne‐Detected VSFG Spectroscopy

Water around hydrophobic groups mediates hydrophobic interactions that play key roles in many chemical and biological processes. Thus, the molecular‐level elucidation of the properties of water in the vicinity of hydrophobic groups is important. We report on the structure and dynamics of water at two oppositely charged hydrophobic ion/water interfaces, that is, the tetraphenylborate‐ion (TPB^?)/water and tetraphenylarsonium‐ion (TPA⁺)/water interfaces, which are clarified by two‐dimensional heterodyne‐detected vibrational sum‐frequency generation (2D HD‐VSFG) spectroscopy. The obtained 2D HD‐VSFG spectra of the anionic TPB^? interface reveal the existence of distinct π‐hydrogen bonded OH groups in addition to the usual hydrogen‐bonded OH groups, which are hidden in the steady‐state spectrum. In contrast, 2D HD‐VSFG spectra of the cationic TPA⁺ interface only show the presence of usual hydrogen‐bonded OH groups. The present study demonstrates that the sign of the interfacial charge governs the structure and dynamics of water molecules that face the hydrophobic region.     

On the thermodynamic stability of hydrogen clathrate hydrates

The cage occupancy of hydrogen clathrate hydrate has been examined by grand canonical Monte Carlo (GCMC) simulations for wide ranges of temperature and pressure. The simulations are carried out with a fixed number of water molecules and a fixed chemical potential of the guest species so that hydrogen molecules can be created or annihilated in the clathrate. Two types of the GCMC simulations are performed; in one the volume of the clathrate is fixed and in the other it is allowed to adjust itself under a preset pressure so as to take account of compression by a hydrostatic pressure and expansion due to multiple cage occupancy. It is found that the smaller cage in structure II is practically incapable of accommodating more than a single guest molecule even at pressures as high as 500 MPa, which agrees with the recent experimental investigations. The larger cage is found to encapsulate at most 4 hydrogen molecules, but its occupancy is dependent significantly on the pressure of hydrogen.     

Molecular Dynamics Study of N-Dodecyl-N,N-Dimethyl-3-Ammonio-1-Propanesulfonate Mono-Layer Adsorbed at the Air/Water Interface

Molecular dynamics (MD) simulation has been carried out to investigate the properties of a mono-layer of N-dodecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate (SB12-3) adsorbed at the air/water interface. The simulation results show that SB12-3 can form a closely packed mono-layer at the air/water interface, the anionic sulfonic groups of the hydrophilic head group have stronger interactions with the water molecules by comparison with the cationic quaternary nitrogen of the hydrophilic head group, and water molecules can gather more easily and aggregate around the sulfonic groups. With the addition of the Ca²⁺ ions, the number of hydrogen bonds between the SB12-3 surfactant molecules and water molecules remains almost unchanged, which may explain the salt resistance behavior for SB12-3 especially for di-valent ions. The hydrophobic tail in SB12-3 is more ordered in the beginning of the chain.     

Communication: On the locality of hydrogen bond networks at hydrophobic interfaces

The formation of structured hydrogen bond networks in the solvation shells immediate to hydrophobic solutes is crucial for a large number of water mediated processes. A long lasting debate in this context regards the mutual influence of the hydrophobic solute into the bulk water and the role of the hydrogen bond network of the bulk in supporting the solvation structure around a hydrophobic molecule. In this context we present a molecular dynamics study of the solvation of various hydrophobic molecules where the effect of different regions around the solvent can be analyzed by employing an adaptive resolution method, which can systematically separate local and nonlocal factors in the structure of water around a hydrophobic molecule. A number of hydrophobic solutes of different sizes and two different model potential interactions between the water and the solute are investigated.     

Spectroscopic observation of critical guest concentration appearing in tert-butyl alcohol clathrate hydrate

The tert-butyl alcohol (TBA) is the most hydrophobic of the simple alcohol and by itself does not form a clathrate hydrate with water. A genuine clathrate hydrate is synthesized by exposing a gaseous guest to solid TBA + H2O powders. Here, we examine three consecutive spectroscopic approaches of (1) the occurrence of a "free" OH stretching band (nu(OH)) signal of TBA molecules representing an absence of hydrogen bonding between the host water and guest TBA, (2) a tuning effect for creating fresh cages via the rearrangement of the host-water lattice, and finally (3) the existence of a critical guest concentration (CGC) that appears only when the TBA concentration is dilute. The present findings from this simple three-step approach can be extended to other alcoholic guest species with the specific modifications to provide the new insights into inclusion chemistry.     

Investigations of the hydrophobic and hydrophilic interactions in polymer–water systems by ATR FTIR and Raman spectroscopy

ATR FTIR and Raman spectra of polymers containing amide groups in the main chain and in the side chain and of the amide low-molecular-weight model compounds in water media were measured. The hydrophobic and hydrophilic interactions of the dissolved compounds with the neighboring water molecules are reflected in the wavenumbers of the CH₃ stretching and of the Amide I and II vibrations. The possibility of the existence of β-sheet-like structures in polypeptides surrounded by water molecules is also discussed.     

Molecular mechanisms of ion-specific effects on proteins

The specific binding sites of Hofmeister ions with an uncharged 600-residue elastin-like polypeptide, (VPGVG)(120), were elucidated using a combination of NMR and thermodynamic measurements along with molecular dynamics simulations. It was found that the large soft anions such as SCN(-) and I(-) interact with the polypeptide backbone via a hybrid binding site that consists of the amide nitrogen and the adjacent α-carbon. The hydrocarbon groups at these sites bear a slight positive charge, which enhances anion binding without disrupting specific hydrogen bonds to water molecules. The hydrophobic side chains do not contribute significantly to anion binding or the corresponding salting-in behavior of the biopolymer. Cl(-) binds far more weakly to the amide nitrogen/α-carbon binding site, while SO(4)(2-) is repelled from both the backbone and hydrophobic side chains of the polypeptide. The Na(+) counterions are also repelled from the polypeptide. The identification of these molecular-level binding sites provides new insights into the mechanism of peptide-anion interactions.     

Effect of small cage guests on hydrogen bonding of tetrahydrofuran in binary structure II clathrate hydrates

Molecular dynamics simulations of the pure structure II tetrahydrofuran clathrate hydrate and binary structure II tetrahydrofuran clathrate hydrate with CO(2), CH(4), H(2)S, and Xe small cage guests are performed to study the effect of the shape, size, and intermolecular forces of the small cages guests on the structure and dynamics of the hydrate. The simulations show that the number and nature of the guest in the small cage affects the probability of hydrogen bonding of the tetrahydrofuran guest with the large cage water molecules. The effect on hydrogen bonding of tetrahydrofuran occurs despite the fact that the guests in the small cage do not themselves form hydrogen bonds with water. These results indicate that nearest neighbour guest-guest interactions (mediated through the water lattice framework) can affect the clathrate structure and stability. The implications of these subtle small guest effects on clathrate hydrate stability are discussed.     

Molecular dynamics study of the solvation of an alpha-helical transmembrane peptide by DMSO

A 10-ns molecular dynamics study of the solvation of a hydrophobic transmembrane helical peptide in dimethyl sulfoxide (DMSO) is presented. The objective is to analyze how this aprotic polar solvent is able to solvate three groups of amino acid residues (i.e., polar, apolar, and charged) that are located in a stable helical region of a transmembrane peptide. The 25-residue peptide (sMTM7) used mimics the cytoplasmic proton hemichannel domain of the seventh transmembrane segment (TM7) from subunit a of H(+)-V-ATPase from Saccharomyces cerevisiae. The three-dimensional structure of peptide sMTM7 in DMSO has been previously solved by NMR spectroscopy. The radial and spatial distributions of the DMSO molecules surrounding the peptide as well as the number of hydrogen bonds between DMSO and the side chains of the amino acid residues involved are extracted from the molecular dynamics simulations. Analysis of the molecular dynamics trajectories shows that the amino acid side chains are fully embedded in DMSO. Polar and positively charged amino acid side chains have dipole-dipole interactions with the oxygen atom of DMSO and form hydrogen bonds. Apolar residues become solvated by DMSO through the formation of a hydrophobic pocket in which the methyl groups of DMSO are pointing toward the hydrophobic side chains of the residues involved. The dual solvation properties of DMSO cause it to be a good membrane-mimicking solvent for transmembrane peptides that do not unfold due to the presence of DMSO.