Chemical potentials of water and organic solutes in imidazolium ionic liquids: a simulation study

The excess chemical potentials of a series of molecules dissolved in the ionic liquid dimethyl imidazolium chloride have been determined by a series of transformations. The molecules are water, methanol, dimethyl ether, acetone and propane. Water and methanol have large negative values of the excess chemical potential (-29kJmol^?1 and — 14kJ mol^?1 respectively); the polar molecules dimethyl ether and acetone have positive values of about 7kJmol^?1 while the value for propane is +26 kJ mol^?1. Hydrogen bonding to the anion plays an important part in the stabilization of water and methanol.     

Conductometric and fluorometric studies of sodium dodecyl sulphate in aqueous solution and in the presence of amino acids

The critical micelle concentration (CMC) of sodium dodecyl sulphate (SDS) in pure water and in the presence of amino acids (0.01, 0.02 and 0.03 mol kg^?1), L-valine (Val) and L-leucine (Leu) was determined from conductometric and fluorometric methods using pyrene as luminescence probe. Depression in the CMC at low concentration of amino acids is attributed to the increased hydrophobic–hydrophobic interaction between the non-polar groups of the surfactant, while, at high concentration, amino acids bind strongly with the anion, DS^?, head groups of SDS, thereby, delaying the micelle formation, resulting in increased CMC. A pronounced decrease in the CMC, while a marked increase in λ⁰₊, with decrease in the solvated radius (rather than crystal radius) of the counterions is observed. Negative values of ΔG⁰_m and ΔH⁰_m indicate that micellisation of SDS in the presence of amino acids is thermodynamically spontaneous and exothermic. Highest negative value of ΔH⁰_m in 0.01 m Val, with lowest CMC value, shows that 0.01 m aqueous Val is the most suitable medium favouring the micellisation of SDS. Decrease in I₁/I₃ from Val to Leu confirms the relative hydrophobicity of two amino acids. The observed values of the packing parameter, P, of SDS in water and in aqueous amino acids suggest that micelles formed are spherical in nature.     

Infrared Spectra Interpretations of Clay-Adsorbed Water in Relation to the “Anomalous” Water Controversy

Abstract

The nature of surface adsorbed water has been the subject of countless investigations. Much of the discussion has centered around the degree and strength of H-bonding to surface groups and between adjacent water molecules.^1,2 Water condensed into glass or quartz capillaries sometimes has unusual properties. This unusual water has been referred to as “orthowater,”³ “anomalous water,”^4,5,6 and “polywater”^7,8 and was thought by some to be polymers of water formed by specific surface catalysis.^1–3 Several possible structures of “polywater” have been suggested which require formation of symmetrical or very strong H-bonds between water molecules.^4,6,7 Infrared spectra of polywater have been presented^7,8 and the strongest absorption band which appeared at 1595 cm^?1 was assigned to the symmetric O-H-O bond. However, more recent investigations suggest that the observed polywater bands may actually be SO₄ ^2-, -COOH^?, or HCO₃ ^? bands, impurities collected by surface diffusion,⁹ or bands of a HNO₃ solution formed by corona discharge.¹⁰ Other observers^11,12 suggest that polywater may be a hydrosol formed by surface contaminates.     

Selective Fluorescent Detection of Aspartic Acid and Glutamic Acid Employing Dansyl Hydrazine Dextran Conjugate

Highly water soluble polymer (DD) was prepared and evaluated for its fluorescence response towards various amino acids. The polymer consists of dansyl hydrazine unit conjugated into dextran template. The conjugation enhances higher water solubility of dansyl hydrazine moiety. Of screened amino acids, DD exhibited selective fluorescence quenching in the presence of aspartic acid (Asp) and glutamic acid (Glu). A plot of fluorescence intensity change of DD against the concentration of corresponding amino acids gave a good linear relationship in the range of 1?×?10^?4 M to 25?×?10^?3 M. This establishes DD as a potential polymeric sensor for selective sensing of Asp and Glu.

Singlet-singlet energy transfer in liquid solution between Rhodamine 6G and benzophenone in presence of non-linear absorption

Results are presented on non-linear absorption of benzophenone in a methanol solution. Using a mixture of Rhodamine 6G and benzophenone, we show the possibility of singlet-singlet energy transfer between these two molecules.The experimental data give a value for the energy transfer probability of 10¹² M^?1 sec^?1.     

Microscopic dynamics in water and ionic aqueous solutions: velocity cross-correlations

The microscopic momentum transfer between distinct particles in water and ionic aqueous solutions has been investigated by molecular dynamics simulation. The time correlation functions between the initial velocity of a central molecule and later velocities of molecules within different coordination shells were calculated for liquid water. Special attention was paid to the influence of the intermolecular hydrogen bonds on the exchange of momentum among water molecules and on the power spectra of the velocity autocorrelation functions. The velocity cross-correlations between ions in an aqueous NaCl solution also were calculated. It was observed that the difference between the results for the Na⁺ and Cl^? ions are associated mainly with the different sizes of the ions.     

Effect of water–methanol content on the structure of Nafion in the sandwich model and solvent dynamics in nano-channels; a molecular dynamics study

Continuing an ongoing study, molecular dynamics (MD) simulations were performed to investigate the effects of methanol concentration on Nafion morphology, such as the size of solvent cluster, solvent location, and polymer structure via the sandwich model. Our survey shows that high methanol concentrations resulted in increment of solvent cluster size in Nafion membrane. The sulfonic acid clusters also befall much in order as subsequent layers of such ionic clusters are formed. The number of neighbouring hydronium ions around a sulfur atom is independent of methanol concentration, but the first shell of hydronium and water around sulfonic acid clusters is broader. Although methanol would prefer to interact with water molecules rather than sulfonic acid groups, gathering of methanol molecules via hydrophobic self-aggregation is preferred. Methanol is located closer to the hydrophobic part of the polymer than water, while water is located closer to the hydrophilic part of the polymer. It was found that methanol distributes specifically more than water in nano-channels. Investigation of solvent dynamics in nano-channels shows that diffusion coefficients (D) of water, methanol, and hydronium decrease with increasing methanol concentration and they may be ordered as follows: D _Water?>?D _Methanol?>?D _Hydronium (D _Water?≈?1.6–2.0D _Methanol and D _Methanol?≈?2.1–3.0D _Hydronium).     

A study of water vapour adsorption on the (110) surface of copper

The adsorption of water vapour on the (110)Cu face has been studied by AES and Δφ measurements in the 5 × 10^?9 to 3 × 10^?7 Torr range between 75 and 500°C. At lower temperatures, an initial physisorption of oriented water dipoles produces a fast initial Δφ decrease. Further adsorption causes no important changes of the Cu surface potential. At higher temperatures (above 100°C) a partial dissociation of the water molecules leads to a dissociative chemisorption producing a Δφ increase after the initial Δφ decrease due to water physisorption.     

Isosteres of peptides: boron analogs as dipolar forms of α‐amino acids – a theoretical study

Modification of peptides to produce peptidomimetics is of great interest, with the aim of designing potent, selective, and metabolically stable analogs having certain conformational properties. Organoboranes have been reported in the literature with a wide range of therapeutic applications. One of the therapeutically important class of molecules is amine‐carboxyboranes derived from amino acids by replacement of the Cα atom of an amino acid/peptide by boron. The conformational preferences of these peptides, with respect to backbone ω, ?, and ψ torsion angles, have been investigated by theoretical calculations. The amide bond in these molecules has the same geometry in the ground and transition states as the natural peptides. However, the boron isosteres of glycine and alanine peptides are less structured than their natural derivatives, but are distinguished by structures with a positive value for the ? angle, which is normally disfavored for natural peptides. This property could be used to build peptides with a geometry not usually seen in natural peptides. Copyright © 2007 John Wiley & Sons, Ltd.     

Investigation of ionization equilibria of L-aspartic and L-glutamic acids in water at a microscopic level by DFT method

The pK_a values of different dissociable groups of L-Aspartic and L-Glutamic acids in vacuo and in aqueous medium over a wide pH range have been estimated by DFT/B3LYP/6-31G(d) and 6-31G++(d,p) methods. For both the amino acids discrete water molecules (n?=?0, 3 and 6) have been used to get the first hydration sphere. Starting from a low pH, all possible tautomers resulting from each dissociation step are assumed to exist in a cyclic equilibrium. The structures of the species involved in the dissociation and tautomerization processes have been optimized in vacuo and also in aqueous medium considering H-bonded water molecules under the PCM formalism. For obtaining pK_a in aqueous medium the difference in Gibbs energy of the clusters H₃O⁺.mH₂O and (H₂O) _m+1 (m?=?an integer) is necessary and has been evaluated from computed literature data. Calculations reveal that in vacuo the neutral or less charged species predominate but in aqueous medium the zwitterionic or more chargeable forms contribute appreciably. The Gibbs energy changes for the microscopic cyclic equilibria have been estimated theoretically. These lead to overall (macroscopic) pK_a values for the ionization steps which are in good agreement with available experimental data for both the amino acids.     

Dynamical and structural properties of adsorbed water molecules at the TiO2 rutile-(110) surface: interfacial hydrogen bonding probed by ab-initio molecular dynamics

ABSTRACT

Ab-initio molecular dynamics (AIMD) simulations have been carried out to study a range of different and energetically-accessible adsorbed-water configurations and motifs for their vibrational and structural characteristics, in contact with rutile-(110) interfaces at 100?K. The radial pair distribution function between the titanium atoms at the interface and the hydrogen and oxygen atoms in the water monolayer show an orientation of the water molecules parallel to the surface of titania, and with hydrogen atoms pointed in the opposite direction to the surface. In some cases, a distinctive vibrational frequency region between 2500 and 3000?cm^?1 has also been observed, due to a strong dispersion interaction between water molecules. This behaviour is also seen in experimental studies of thin-film water coverage on TiO₂ surfaces.     

Die Eigenschwingungen des Metall-Hydratkomplexes in BeSO4·4H2O und BeSO4·4D2O

Infrared reflection spectra of single crystals of BeSO₄·4H₂O and BeSO₄·4D₂O have been obtained in polarized light at 300°K and at 14°K in the region between 4000 cm^?1 and 300 cm^?1. By a Kronig-Kramers analysis, the frequencies of the infrared active transitions have been calculated. These transitions are attributed to internal vibrations of the water molecules and sulfate ions and, in the region between 1000 cm^?1 and 300 cm^?1, especially to internal and external vibrations of the tetrahedral Be⁺⁺·4aqu-complexes. The vibrational modes of these complexes consist of a superposition of translational and librational modes of the water molecules and translational modes of the central Be⁺⁺-ion. The vibrational frequencies and normal modes of this complex have been calculated in a central-force model, and force-constants have been determined by fitting the calculated frequencies to the observed spectra. The calculations have shown that the modes, which comprise mainly translational motions of the water molecules, are strongly coupled with librational motions of the water molecules. On the other hand, there exist pure librational modes with practically no admixture of translational motions. The optimum sets of force constants for the BeSO₄·4H₂O crystal and the BeSO₄·4D₂O crystal differ in a manner which can be understood under the assumption that the dimensions of the Be(D₂O)₄ complex are about 0.1 Å larger than those of the Be(H₂O)₄ complex. Some arguments supporting this conclusion will be discussed.     

The internal coordinate path Hamiltonian; application to methanol and malonaldehyde

The internal coordinate path Hamiltonian is introduced for the study of the vibrations of molecules which have one large amplitude motion. The Hamiltonian is represented in terms of a one path coordinate and 3N—7 normal coordinates. The variational method is used to solve the Schrödinger equation. The molecules studied are methanol and malonaldehyde. For methanol the internal coordinate is a dihedral angle, for malonaldehyde it is the difference in the distances between the migrating hydrogen and the neighbouring oxygen atoms. For methanol there is little coupling between the path and the normal coordinates and so no complications were encountered in the calculations which used harmonic surfaces generated by density functional and M?ller—Plesset theory. Fundamental frequencies were predicted. Malonaldehyde is a different story. There is substantial coupling between the path coordinate and several of the normal coordinates. This introduces many complications: an anharmonic surface is essential and large variational configuration interaction calculations are essential for convergence. Furthermore, because the Coriolis terms require the evaluation of derivatives of both the nuclear coordinates and the normal coordinate eigenvectors along the path, great care must be taken with these numerical procedures. B3LYP predicts too low a transition state which overemphasizes the large Coriolis terms near the transition state. This may be one of the reasons why our fundamental vibrations are in poor agreement with observation. It is most encouraging that the tunnelling splitting is 58 cm^?1 (obs. 21.56 cm^?1), obtained with our quartic density functional surface.     

Charge transfer reactions from tryptophan and tyrosine to sulfur‐centered dimer radical cation in aqueous –sulfuric acid medium: a pulse radiolysis study

Kinetics and mechanism of one‐electron oxidation of N‐acetyl methionine (NAM), tryptophan (TrpH), tyrosine (TyrOH), and phenylalanine (Phe) have been studied in 33% v/v H₂SO₄ solution. The solvent radical (SO₄^?¯) oxidized NAM, TrpH, TyrOH, and Phe to produce NAM₂^?+ (480 nm), TrpH^?+ (330, 580 nm), TyrO^? (350, 410 nm), and Phe(?H)^? (320 nm), with rate constants (10⁹ M^?1 s^?1) 0.6, 2.7, 3.9, 1.6, respectively. Time resolved radical transformation from NAM₂^?+ to TrpH^?+ and TyrO^? have been observed to occur with k(10⁸ M^?1 s^?1) = 3.60 and 0.35, respectively. However, NAM₂^?+ to Phe(?H)^? and TrpH^?+ to TyrO^? radical transformations have not been observed in this medium. The study shows the kinetics and mechanism of oxidation of some amino acids in strong acidic solutions. To the best of our knowledge, radical cations of amino acids and electron transfer reactions between them could be studied in strong acidic solutions for the first time. Copyright © 2016 John Wiley & Sons, Ltd.     

Adsorption of nitrogen on platinum

The adsorption and desorption of nitrogen on a platinum filament have been studied by thermal desorption techniques. Nitrogen adsorption becomes significant only after any carbon contamination is removed from the surface by heating the platinum filament in oxygen, and after the CO content in the background gas is reduced substantially. At room temperature nitrogen populates an atomic tightly bound β-state, E^≠ = 19 kcal mole^?1. The saturation coverage of the (3-state is 4.5 × 10¹⁴ atoms cm^?2. Formation of the (β-state is a zero order process in the pressure range studied. At 90 K two additional α₁- and α₂-desorption peaks are observed. The activation energy for desorption for the α₂-state is 7.4 kcal mole^?1 at low coverage decreasing to 3 kcal mole^?1 at saturation of this state, 6 × 10 molecules cm^?2. The maximum total coverage in the α-states was 1.2 × 10¹⁵ molecules cm^?2. A replacement process between the β- and α-states has been observed where each atom in the (β-state excludes two molecules from the α-state.     

Amphiphilic p‐tert‐butylthiacalix[4]arenes containing quaternary ammonium groups: from small molecules toward water‐soluble nanoscale associates

The formation of supramolecular associates based on water‐soluble p‐tert‐butylthiacalix[4]arenes with amino acids has been studied. It was shown that amphiphilic p‐tert‐butylthiacalix[4]arenes preferably formed supramolecular associates with aromatic α‐amino acids (tyrosine and tryptophan). Increasing size of the substituents of p‐tert‐butylthiacalix[4]arenes led to increase molecular weight of supramolecular associates based on the macrocycles and “guest” molecules. The spatial structures of p‐tert‐butylthiacalix[4]arenes and their associates with phenylalanine were studied by two‐dimensional ¹H‐¹H nuclear Overhauser effect NMR spectroscopy. The ability of aggregates based on p‐tert‐butylthiacalix[4]arenes and amino acids to effectively interact with bovine serum albumin with the formation of 7‐ to 8‐nm nanoparticles was shown. Copyright © 2015 John Wiley & Sons, Ltd.     

Computational studies on nonenzymatic pyroglutamylation mechanism of N-terminal glutamic acid residues in aqueous conditions*

Spontaneous cyclisation of glutamic acid (Glu) residues located at N-termini in peptides and proteins is called ‘pyroglutamylation’ and is assumed to be involved in several neurodegenerative diseases. Although it has long been believed that N-terminal Glu residues undergo pyroglutamylation enzymatically, it has recently been experimentally confirmed that nonenzymatic pyroglutamylation can proceed in some types of aqueous buffer. However, the detailed mechanism has not been proposed or investigated, and even whether some small-molecule catalysts are required for pyroglutamylation has not been clarified. Therefore, we investigated three types of pyroglutamylation mechanism of N-terminal Glu residues using quantum chemical calculations: in the absence of any catalysts, catalysed by one water molecule, and catalysed by two water molecules. All calculations were performed using N-terminal Glu residues capped with a methylamino group on the C-terminal as a model compound. Optimised energy minima and transition state geometries were obtained using the B3LYP density functional method. The pyroglutamylation mechanism is roughly divided into two steps: cyclisation and dehydration, and the calculated activation barrier was 108 and 107?kJ mol^?1 in the two- and three-water-assisted pathways, respectively. The results of computational analysis suggest that water molecules can act as catalysts for pyroglutamylation.

The calculated activation barrier of two-water-assisted pyroglutamylation was 108?kJ mol^?1, and the results of computational analysis indicate that water molecules can act as catalysts for pyroglutamylation.     

Understanding the complexation of aliphatic and aromatic acids guests with octa acid

In this study, inclusion of 10 guest molecules, adamantyl and naphthyl carboxylic acids with different structural and electronic properties, within a synthetic cavitand octa acid was probed by isothermal calorimetry, 1D and 2D ¹H nuclear magnetic resonance spectroscopy, and molecular dynamic simulations. Under the condition of the experiments (pH ~ 8.7), the guests were included as carboxylate anions with the polar anionic head group facing water and hydrophobic carbon skeleton buried within the cavitand, forming 1:1 host to guest complexes. Importance of weak interactions between the guest and the cavitand interior is reflected in the measured negative ΔH values. Although ΔH was negative for all guests, ΔS was positive for adamantyl guests and negative for naphthyl guests. Quite likely the difference in hydrophobicity between the 2 sets of molecules and the strength of interaction between the guest and the host are responsible for the sign difference in ΔS between the 2 series. The importance of steric factor during inclusion of naphthyl carboxylic acids within octa acid cavity is brought out by the difference in thermodynamic parameters between the 1‐ and 2‐substituted naphthyl carboxylic acids; 2‐naphthyl carboxylic acids that can penetrate deeply have larger ?ΔH and 1‐naphthyl carboxylic acids that can only enter the cavity in an angle have smaller ?ΔH. As expected, based on the well‐known concept of “enthalpy‐entropy compensation,” the molecules that have large ?ΔH are accompanied by large ?ΔS.     

Novel cross-linked membrane for direct methanol fuel cell application: sulfonated poly(ether ether nitrile)s

In order to reduce water uptake, swelling ratio, and methanol permeability in sulfonated proton exchange membranes (PEM), novel-sulfonated aromatic poly(ether ether nitrile)s-bearing pendant propenyl groups had been synthesized by direct copolymerization method. All the results showed that the propenyl groups were suitable cross-linkable groups, and that this method was an effective way to overcome the drawbacks of sulfonated polymers at high ion exchange capacity (IEC) values. By cross-linking, the water uptake, swelling ratio, and methanol diffusion could be restricted owing to the formation of compact network structure. For example, CSPEN-60 membranes showed the proton conductivity of 0.072 S cm^?1 at 80 °C, while the swelling ratios and water uptake (17.9 and 60.7 %) were much lower than that of the SPEN-60 membrane (60.8 and 295.2 %). Meanwhile, a 1.1 × 10^?7 cm² s^?1 of methanol diffusion was obtained which was much lower than that of Nafion 117 (14.1 × 10^?7 cm² s^?1). Although the proton conductivity of the CSPEN-60 membranes is lower than that of the SPEN-60 membrane, the selectivity is much higher. The CSPEN-60 membrane exhibited the highest selectivity among the tested membranes, about 5.8 times higher compared with that of Nafion117.     

Raman scattering in dried DNA and crystalline amino acids

Raman spectrum characteristics of dried deoxyribonucleic acid (DNA) and two types of crystalline amino acids (L-lysine, D-asparagine) are compared in a wide range of frequencies, including the regions of lattice (7 to 200 cm^?1) and intramolecular (200 to 4000 cm^?1) vibrations. It is found that the spectral position of the low-frequency band in the Raman spectrum of DNA with a peak near 26 cm^?1 correlates with the Raman spectrum of high-Q low-frequency modes that manifest themselves in the crystalline amino acids under investigation. The low-frequency band of DNA refers to a twist-like vibrational mode of nucleobases. The intensities of this DNA mode and the high-Q lattice modes of the crystalline amino acids L-lysine and D-asparagine are several times as high as those of the Raman lines corresponding to the intramolecular modes. Resonant coupling of low-frequency modes of DNA and amino acid molecular chains is analyzed.