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We study the static and dynamic properties of the water-density fluctuations in the interface of large nonpolar solutes. With the help of extensive molecular dynamics simulations of TIP4P water near smooth spherical solutes, we show that for large solutes, the interfacial density profile is broadened by capillary waves. For purely repulsive solutes, the squared width of the interface increases linearly with the logarithm of the solute size, as predicted by capillary-wave theory. The apparent interfacial tension extracted from the slope agrees with that of a free liquid--vapor interface. The characteristic length of local density fluctuations is [approximately equal to]0.5 nm, measured along the arc, again consistent with that of a free liquid--vapor interface. Probed locally, the interfacial density fluctuations exhibit large variances that exceed those expected for an ideal gas. Qualitatively consistent with theories of the free liquid--vapor interface, we find that the water interface near large and strongly nonpolar solutes is flickering, broadened by capillary-wave fluctuations. These fluctuations result in transitions between locally wet and dry regions that are slow on a molecular time scale. capillary waves | drying transition | hydrophobic effect | surface tension

Ab initio molecular dynamics simulations of hydroxide and hydronium ions are described near a hydrophobic interface, which has shown that both ions behave like amphiphilic surfactants that stick to a hydrophobic hydrocarbon surface with their hydrophobic side. The results have shown why hydrophobic surfaces in contact with water acquire a net negative charge, a phenomenon that has important implications for biology and polymer science.

The adsorption behavior of amino acids on mesoporous materials (SBA-15) in relation to amino acid concentration, ion strength and pH is investigated. The results show that for acidic and basic amino acid, the adsorption on SBA-15 depends on the electrostatic interaction with the adsorbents and for neutral amino acids the adsorption depends on hydrophobic interactions with the mesoporous material.

Off-lattice self-consistent-field theory is used to study the phase behavior of both saturated and unsaturated lipid molecules at air-water interfaces. In saturated lipids, the micellar and lamellar phases show first-order phase transitions, which are sensitive to the hydrophilicity and hydrophobicity of lipid molecules.

An innovative sample introduction method that facilitates extreme simplification of the layout of a capillary array electrophoresis (CAE) chip is described. Multiple samples were directly injected onto CAE channels from sample loaders using hydrophilic sample bridges, thus obviating auxiliary components of sample wells and sampling channels of a typical CAE chip. Hydrophilic sample bridges were spontaneously formed in hydrophobic surroundings to connect sample loaders to corresponding CAE channels, through which electrosample injections were effectively made. Sample dispersion was intrinsically avoided due to the 'sticky' nature of the bridges. Utilizing hydrophilic interactions, target spots for formation of sample bridges can be expanded from the actual openings of CAE channels, which reduces the burden of precise positioning of samples toward CAE channels. In this work, simultaneous introduction of multiple samples onto well-less CAE channels arranged with 1-mm gaps was successfully demonstrated. Well-less CAE chips, feasible now due to the hydrophilic sample bridges, would bring unprecedented advantages in both production and operation because of their extreme simplicity.

Detailed structural analysis of glycoproteins requires methods capable of isolating glycopepfides from tryptic digests of purified glycoproteins and complex protein mixtures. Here, we describe the selective and reproducible isolation of glycopeptides from a peptide mixture using ion-pairing normal-phase chromatography (IPNPLC). The addition of inorganic monovalent ions in normal-phase chromatography appears to increase the hydrophobicity difference between peptides and glycopeptides, allowing for more efficient separation. Our data show that IP-NPLC effectively enriches glycopeptides from a tryptic digest of ribonuclease B, bovine fetuin, and a complex mixture of glycoproteins, when compared with normal-phase chromatography alone. The results of the IP-NPLC experiments can be explained using the Wimley-White water/octanol free energy scale to illustrate the hydrophobicity difference of nonglycosylated peptides with and without ion-pairing. We believe that IP-NPLC will be an important tool in glycoprotein characterization and glycoproteomic studies.

A deep, water-soluble cavitand has extracted a variety of neutral hydrophobic species into its cavity. The dynamics have shown that self-exchange of neutral guests is independent of guest concentration and has occurred through rate-determining unfolding of the cavitand.

Report is presented on the binary complex structures of enzyme PrnB with D and L-tryptophan and D and L-7-chloro-tryptophan. The structures identify a common hydrophobic pocket for the indole ring but exhibit unusual heme ligation and substrate binding when compared with the tryptophan 2,3-dioxygenase crystal structures.

The effect of electrolyte concentration on the dynamic surface tension and dilational viscoelasticity of adsorption layers of chitosan and dodecyl chitosan was investigated. It was found that for both polymers salt addition results in a decrease of the lag time of adsorption corresponding to the beginning of the formation of a gel-like network inside the adsorption layer via formation of hydrophobic cross-links between nonpolar groups.

The hairpin formation between a polyproline type-II helix and an [alpha]-helix as present in the natural miniprotein peptide YY (PYY) is examined. The results have indicated that helical hairpin formation in pancreatic peptide (PP)-fold is both reversible and cooperative and that specific N- and C-terminal tertiary hydrophobic contacts between the polyproline and the [alpha]-helix provide the driving force for folding.

S100B is a calcium-binding protein, which binds calcium and also undergoes certain changes, exposing the hydrophobic surface residues. Such conformational changes help the protein to interact with various biological target molecules, also maintaining a balance between the amide exchange rates.

The study explains the phenomenon of protein nitration, which is found to play a very critical role in the onset and progression of several neurodegenerative diseases. The analysis shows that nitration modifies protein function by altering the hydrophobicity, hydrogen bonding and electrostatic properties of the targeted protein.

The study of the interactions between the hydrophobic and ionic solutes in aqueous guanidinium (Gdm) chloride and urea solutions provides a better understanding of the protein denaturation mechanism. The results show that the primary mechanism of denaturation involves a direct electrostatic interaction between the denaturant molecules and proteins.

The equation of state and salvation of small apolar solutes are studied by performing the molecular dynamics simulations of aqueous mixtures of methanol and sorbitol over a range of binary compositions, density and temperature. The results show the increasing sorbitol concentration under isthermal, isobaric conditions resulting in monotonic increases in apolar solute excess chemical potential over the range of experimentally relevant temperatures.

A novel strategy is developed to prepare various micro/nanostructured polyanilines (PANI) on polymer substrates. The poly acrylate acid (PAA) brushes have acted as templates and dopants of PANI and the surface of the polypropylene (PP) films grafted with polyaniline nanowires and nanoribbons have displayed superhydrophobicity with contact angles for water of approximately 145 and 151 [degree], respectively.

The self-assembly reactions between the fluorinated ditopic ligand 1,4-bis(4-pyridyl)tetrafluorobenzene and different nitrogen-protected palladium(II) and platinum(II) complexes are examined. The results have indicated the predominance of hydrophobic over electrostatic interactions in these systems and have shown that palladium ethylenediamine square is capable of establishing intermolecular interaction exclusively in aqueous media.

Physics-based analytical forms are proposed to express the cavity component of the free energy of hydrophobic association of spherical and spheroidal solute particles. These expressions are derived on the basis of an analysis of the change of the number and free energy of water molecules upon the formation of a hydrophobic dimmer and a Gaussian model of the density of the solute.

The study employs the umbrella-sampling molecular dynamics simulations in explicit water as functions of distance and orientation to calculate and parameterize the potentials of mean force of identical hydrophobic side chains of amino acid. The analysis of the positions and depths of the contact minima and the positions and heights of the desolvation maxima proves and confirms the application of such potentials in coarse-grain protein-folding simulations.

Numerical results from self-consistent field calculations on the micellization of telechelic associate polymers and their non-functional analogues are presented. The results are confronted with simple scaling concepts and it is found that there is a good agreement between the numerical dependence of the aggregation number upon both backbone and terminal hydrophobe length.

Although ion exchange is often depicted as a process driven by electrostatic forces, ionic solvation or hydrophobic forces contribute greatly to ion exchange selectivity and is often the dominant factor. On a variety of commercial anion exchange columns, monovalent Cl[O.sub.4.sup.-] elutes after doubly charged S[O.sub.4.sup.2-] and even triply charged P[O.sub.4.sup.3-]. For identically charged alkali metal ions, electrostatic charge densities based on crystal radii would suggest [Li.sup.+] to be the most strongly retained on a cation exchanger. In practice, it is typically the least strongly held cation on most cation exchangers, because of its very high hydration energy and with most eluents its capacity factor approaches zero. Even when the ion is very poorly solvated, as with tetraalkylammonium ([NR.sub.4.sup.+]) cations, there has never been a report on a polymeric ion exchanger of an ideal electrostatic selectivity order where [NR.sub.4.sup.+] cations elute in their increasing charge density order: R = n-butyl first, followed by n-propyl, ethyl, and last, methyl. We show that this selectivity order is easily achieved on recently described methracrylate-based monolithic capillary cation exchange columns (Ueki, Y.; Umemura, T.; Li, J. X.; Odake, T; Tsunoda, K. Anal. Chem. 2004, 76, 7007-7012) with minor amounts of hydroorganic modifiers. Indeed, under such conditions, [Li.sup.+] (and other alkali cations) elutes after N[Me.sub.4.sup.+].

Continued development of a new sequence--specific algorithm for peptide retention prediction in RP HPLC is reported. Our discovery of the large effect on the apparent hydrophobicity of N-terminal amino acids produced by the ion-pairing retention mechanism has led to the development of sequence-specific retention calculator (SSRCalc) algorithms. These were optimized for a set of ~2000 tryptic peptides confidently identified by off-line micro-HPLC-MALDI MS (MS/MS) (300-[Angstrom] pore size C18 sorbent, linear water/acetonitrile gradient, and trifluoroacetic acid as ion-pairing modifier). The latest version of the algorithm takes into account amino acid composition, position of the amino acid residues (N- and C-terminal), peptide length, overall hydrophobicity, pI, nearest-neighbor effect of charged side chains (K, R, H), and propensity to form helical structures. A correlation with [R.sup.2]~0.98 was obtained for the 2000-peptide optimization set. A flexible structure for the SSRC programming code allows easy adaptation to different chromatographic conditions. This was demonstrated by adapting the algorithm (~0.98 [R.sup.2] value) for a set of ~2500 peptides separated on a 100-[Angstrom] pore size C18 column. The SSRCalc algorithm has also been extensively tested for a number of real samples, providing solid support for protein identification and characterization; correlations in the range of 0.95-0.97 [R.sup.2] value have normally been observed.

The results of fully atomistic molecular dynamics (MD) simulations of a series of Gemini surfactants, C5H25-[alpha],[omega]-bis([C12H25N.sup.+](CH3)2[Cl.sup.-]), at the air/water interface with s=3,4,6,12,14, and 16, at values of the initial surface area per surfactant [A.sub.s]= 70 [angstrom.sup.2], 77 [angstrom.sup.2], 95 [angstrom.sup.2], 151 [angstrom.sup.2], 151 [angstrom.sup.2], 133 [angstrom.sup.2], and 103 [angstrom.sup.2], respectively, are reported. The MD simulations are found to confirm the bending of the spacer toward the hydrophobic chains as the spacer length is increased and the spacer becomes more hydrophobic.

The effects of the turn, the hydrophobic cluster, and a disulfide cross-linker on the folding kinetics of a designed alpha-helical hairpin, Z34C, are examined using an infrared temperature-jump method in conjunction with site-specific mutagenesis. Results reveal that Z34C folds with an ultrafast rate and support a folding mechanism in which the rate-limiting step corresponds to the formation of the reverse turn.

The tertiary interactions between amide-I vibrators on the separate helices of transmembrane helix dimers were probed by ultrafast 2D vibrational photon echo spectroscopy. The 2D IR approach proves to be a useful structural method for the study of membrane-bound structures. The 27-residue human erythrocyte protein Glycophorin A transmembrane peptide sequence: [KKITLIIFG.sub.79][VMAGVIGTILLISWG.sub.94]IKK was labeled at [G.sub.79] and [G.sub.94] with [sup.13]C = [sup.16]O or [sup.13]C = [sup.18]O. The isotopomers and their 50:50 mixtures formed helical dimers in SDS micelles whose 2D IR spectra showed components from homodimers when both helices had either [sup.13]C = [sup.16]O or [sup.13]C = [sup.18]O substitution and a heterodimer when one had [sup.13]C = [sup.16]O substitution and the other had [sup.13]C = [sup.18]O substitution. The cross-peaks in the pure heterodimer 2D IR difference spectrum and the splitting of the homodimer peaks in the linear IR spectrum show that the amide-I mode is delocalized across a pair of helices. The excitation exchange coupling in the range 4.3-6.3 [cm.sup.-1] arises from through-space interactions between amide units on different helices. The angle between the two [Gly.sub.79] amide-I transition dipoles, estimated at 103[degrees] from linear IR spectroscopy and 110[degrees] from 2D IR spectroscopy, combined with the coupling led to a structural picture of the hydrophobic interface that is remarkably consistent with results from NMR on helix dimers. The helix crossing angle in SDS is estimated at 45[degrees]. Two-dimensional IR spectroscopy also sets limits on the range of geometrical parameters for the helix dimers from an analysis of the coupling constant distribution. tertiary interaction | vibrational spectra | multidimensional spectroscopy

A study on the phase behavior of a series of carbohydrate-based gemini surfactants with varying spacer lengths is conducted using static and dynamic light scattering between pH 2 and 12. Upon increasing the pH to slightly basic values, flocculation followed by redispersion upon charge reversal is observed up to a spacer length of eight methylene units.

A series of amphiphilic lipopeptides (ALPs), consisting of an alternating hydrophilic and hydrophobic amino acid residue sequence coupled to a phospholipids tail, was designed to form supramolecular assemblies composed of beta-sheet monolayers decorated by lipid tails at the air-water interface. In situ grazing-incidence X-ray diffraction (GIXD) revealed that lipopeptides six to eight amino acids in length form a new type of 2-dimensional (2D) self-organized monolayers that exhibit beta-sheet ribbons segregated by lipid tails.

A study reports the first comprehensive investigation of the molecular dynamics of the C-terminus of membrane-associated full-length lapidated Ras protein determined by solid-state nuclear molecular resonance. The C-terminus of Ras shows a versatile dynamics with segmental fluctuations and axially symmetric overall motions on the membrane surface.

The solvation of methane and methane decorated with charges in spherically confined water droplets are examined as an illustration of the profound effects of confinement on hydrophobic and ionic interactions. Reflecting the charge asymmetry of the water molecule, negative ions have a stronger preference for the surface compared to positive ions of the same charge magnitude.

Abstract -- Using the standard addition method as an example, several versions of it recommended for the determination of volatile components in complex hydrophobic matrices additionally containing compounds with sorption [...]

Osmotic vapor pressure and density measurements were made for aqueous alpha-cyclodextrin (alpha-CD) solutions in the temperature range between 293.15 and 313.15 K, with a view to examining the effects due to size, interacting sites, and hydrophobicity. Further analysis was made by applying two exact theories of solutions, namely McMillan-Mayer and Kirkwood-Buff, to obtain the solute virial coefficient.

A method to calculate the hydration of hydrophobic solutes by the fundamental measure theory, which permits calculations of the density profile and the hydration energy for hydrophobic molecules, is presented. The method is used to calculate hydration of spherical solutes of various sizes from one angstrom up to several nanometers, and the free energies, the enthalpies, and the entropies of hydrated rare gases and hydrocarbons are evaluated.

X-ray diffraction is used to map systematic changes in preferred orientation and phase observed throughout the Ti[O.sub.2] thin films. The results have shown that the photocatalytic activity and hydrophobicity are dependent on the rutile:anatase ratio at any given location on the film.

Thermophile Hydrogenobacter thermophilus cytochrome c552 (HT) is a stable protein, which has a denaturation temperature [T.sub.m)) of 109.8 and 129.7 degree Celsius for the oxidized and reduced forms, respectively. The removal of a single hydroxyl group from the hydrophobic core of HT, through the replacement of a Tyr by Phe, was found to result in further elevation of the [T.sub. m) value of the oxidized form by approximately 6 degree Celsius, the [T.sub. m) value of the reduced one remaining essentially unaltered.

An acoustic sensing technique using multiresonance thickness-shear mode (MTSM) sensors was used to characterize various superhydrophobic (SH) with enhanced superhydrophobicity achieved by the use of nanoparticles. The MTSM sensors were capable of differentiating SH properties created by nano-scale features for film, demonstrating similar macroscopic contact angles.

A new method that allows fast and quantitative recovery of hydrophobic or amphipathic peptides, or both, after their intimate incorporation into lipid membranes, is proposed. It relies on the use of small Sep-Pak cartridges and simple chromatographic handling. Peptides selected for this study are the 35 amino acid transmembrane domain of the Neu/erbB-2 protein and its point mutated (V664E) analogue expressed in some cancers, the 25 amino acid BH4 domain from the Bcl-2 antiapoptotic protein and the 15 amino acid Catestatin segment from chromogranin A found to have antimicrobial capabilities. Incorporation of peptides into membranes is accomplished using organic solvent cosolubilization and several cycles of freeze-drying/hydration from aqueous solution. For the hydrophobic peptides, separation from the membrane is performed on Sep-Pak [C.sub.2] columns in two steps: (i) water/methanol elution of lipids and (ii) peptide elution using aprotic solvents (acetonitrile, 2-propanol). For amphipathic peptides, separation is performed on Sep-Pak [C.sub.l8] columns using selective elution in one single step: water/methanol elution to recover first the peptide and then the lipids. Peptide and lipid recovery after all purification steps range from 60 to 80%, with peptide purity above 96%. This new method is simple, inexpensive, and very fast: a 10-mg membranous mixture containing 10% (w/w) peptide may be separated in 20-30 man.

The performance of a given membrane in gas separation, nanofiltration and pervaporation is found to be interplay between the thickness of the top layer, steric hindrance during transport and is indirectly determined by effects of hydrophobicity/hydrophilicity. The results have shown that multifunctional membranes would rapidly gain importance in view of the flexibility of processes and the robustness of the separation.

A novel approach for the controlled delivery of an anti-inflammatory, chemopreventive drug by an enzyme-triggered drug release mechanism through the degradation of encapsulated hydrogels is reported. The hydro-and organogelators are synthesized in high yields from renewable resources by using regioselective enzyme catalysis.

Chemical etching and fluoroalkysilane self-assembly are used as the means to fabricate highly antireflective porous silicon surfaces with superhydrophobicity. The morphology had enabled the porous silicon surface to own a very low reflectance value that is averaged to be about 3% over the whole experimental photon wavelength spanning 300-800 nm.

The fabrication of single-walled carbon nanotube (SWNT) networks by using the evaporation of sodium dodecyl sulfate (SDS)-SWNT sessile drops on a hydrophobized silicon substrate is described. The sessile drops are analyzed by contact analysis and video microscopy and their evaporation are characterized by microscopic, spectroscopic and topographical methods.

Butane monooxygenase (BMO) from Pseudomonas butanovora has high homology to soluble methane monooxygenase (sMMO), and both oxidize a wide range of hydrocarbons; yet previous studies have not demonstrated methane oxidation by BMO. Studies to understand the basis for this difference were initiated by making single-amino-acid substitutions in the hydroxylase [alpha] subunit of butane monooxygenase (BMOH-[alpha]) in P. butanovora. Residues likely to be within hydrophobic cavities, adjacent to the diiron center, and on the surface of BMOH-[alpha] were altered to the corresponding residues from the o~ subunit of sMMO. In vivo studies of five site-directed mutants were carried out to initiate mechanistic investigations of BMO. Growth rates of mutant strains GI13N and L279F on butane were dramatically slower than the rate seen with the control P. butanovora wild-type strain (Rev WT). The specific activities of BMO in these strains were sevenfold lower than those of Rev WT. Strains G 113N and L279F also showed 277- and 5.5-fold increases in the ratio of the rates of 2-butanol production to l-butanol production compared to Rev WT. Propane oxidation by strain G113N was exclusively subterminal and led to accumulation of acetone, which P. butanovora could not further metabolize. Methane oxidation was measurable for all strains, although accumulation of 23 [micro]M methanol led to complete inhibition of methane oxidation in strain Rev WT. In contrast, methane oxidation by strain G113N was not completely inhibited until the methanol concentration reached 83 [micro]M. The structural significance of the results obtained in this study is discussed using a three-dimensional model of BMOH-[alpha]

Adsorption and desorption of fibronectin (FN) were investigated at thin films of alternating maleic acid copolymers with octadecene (POMA) and with propene (PPMA). The results reveal that the interfacial mode of adsorbed FN depends on the predominant interactions and large amounts of FN were tightly bound to POMA by hydrophobic interactions whereas FN adsorbed on PPMA was concluded to attain an unfolded structure allowing for the electrostatic matching of positively charged residues on FN with the maleic acid groups.

The properties of interfacial water on Cl- and H-terminated Si(111) surfaces was investigated using a first principle approach and characterized by means of energetic analysis combined with hydrogen bond counting. The interaction of water with both substrates was found to be significantly weak, although bonding with the Cl-terminated Si(111) surface was relatively stronger because of the electrostatic contribution.

With the advent of electrospray ionization mass spectrometry, the world was given a new way to look at complex peptide mixtures. Identification of proteins via their signature peptides requires ionization of a representative portion of the peptides derived from proteins by proteolysis. Unfortunately, matrix effects prohibited electrospray ionization of many peptides. This paper describes the development of a new labeling reagent that simultaneously adds a permanent positive charge to peptides and increases their hydrophobicity to enhance their ionization efficiency. The labeling agent is preactivated with N-hydroxysuccinimide to react with primary amines to form a peptide bond. In the most dramatic case, ionization efficiency of the peptide ADRDQYELLCLDNTRKPVDEYK increased 500-fold after derivatization as opposed to other peptides where ionization efficiency was impacted little. Ionization efficiency of peptides was enhanced roughly 10-fold in general by derivatization. Peptides of less than 500 Da experienced the greatest increase in ionization efficiency by derivatization. Poor ionization efficiency of native peptides was found to be due more to their inherent structural properties than the matrix in which ionization occurs.

The contribution of hydrophobic interactions to the dimerization of the prolyl dipepetidase DPP-IV was investigated. Results revealed that hydrophobic residues F713, W734 and Y735 were essential for DPP-IV dimerization and the enzymatic activity of DPP-IV was correlated with its quaternary structure.