Solvent effects on the conformation and far UV CD spectra of gramicidin

Solvent effects on the far-uv CD spectra of the polypeptide gramicidin have been studied systematically in a series of alcohols of increasing chain length, ranging from methanol to dodecanol. The effects observed are of two types: primary, involving a change in the equilibrium mixture of conformers present, and secondary, involving a shift in the spectral peak positions as a function of solvent polarizability. To quantitate the primary effect, the ratio of the individual conformers present was estimated by deconvolution of the spectra into their component species. For short chain length alcohols, both parallel and antiparallel double helices are found in considerable abundance. As the solvent chain length is increased and its polarity is decreased, the left-handed antiparallel double helical species is favored. For all alcohols with chain lengths of four or more carbon atoms, the ratio of the conformers present remains relatively constant. To quantitatively examine the secondary effect, the magnitudes of the spectral shifts on the dominant conformer (species 3) have been correlated with the dielectric constants and refractive indices of the solvents, thereby indicating what underlying physical properties are responsible for these shifts. This work thus demonstrates that for gramicidin, a flexible polypeptide, the solvent effects on the CD spectra can be resolved into two types: changes due to the mixture of conformers present and shifts in the spectral characteristics. Both effects need to be considered when interpreting CD spectra in terms of secondary structure for this and other polypeptides in nonaqueous solutions.     

Solvation effects on the 31P-nmr chemical shifts and infrared spectra of phosphate diesters

The effects of organic solvents on the ³¹P-mr chemical shifts of various phosphate diesters have been investigated in water and mixed-organic solvent systems. The addition of organic solvents to cyclic phosphates and to diethyl phosphate causes large upfield shifts of the phosphorus resonance which are attributed to solvent-induced changes in the local hydration of the phosphodiester group. This is consistent with the fact that there is an inverse correlation between the hydrogen-bond-donating ability of the solvents and the magnitude of the shifts they induce. Other possible interpretations, such as solvent-induced ion pairing and solvent-induced conformational changes, appear to be eliminated. Fourier-transform ir study of the cyclic nucletides reveals that there are also large solvent-induced shifts in the frequency of the antisymmetric OPO stretching frequency, and a comparison of the two types of measurements indicates that there is a linear correlation between shifts observed in the ir and in the ³¹P-nmr spectra. With UpU, the solvent-induced ³¹P-nmr shifts are ～3 times smaller than those observed with the cyclic phosphates and the solvent-induced shift of the OPO band is reduced (factor of ～1.7) as compared with the cyclic phosphates. With the single-stranded polynuclotides, poly(C) and poly(U), the solvent-induced shifts in both the nmr and ir are quite small (～0.1 ppm and ～1 cm^?1). The very small solvent effects observed with poly(U) and poly(C) are attributed to a combination of steric effects and a polyelectrolyte effect which maintains a high density of counterions with waters of hydration in the vicinity of the charged backbone and makes the phosphates much less susceptible to solvent-induced changes in hydration.     

Axial pertubations on the electronic and magnetic properties of ferric porphyrins: II. Solvent effects on the proton NMR spectra of low-spin cyano complexes

The proton NMR spectra of a series of low-spin bis-cyano ferric complexes of tetraarylporphyrins and octaethylporphyrin in a variety of solvents have been recorded and analyzed. The hyperfine shifts are shown to be very sensitive to the solvent, experiencing an overall downfield bias as the solvent hydroge-bonding donor strength increased. The characteristic pattern of the contact and dipolar shifts for the meso-aryl group in tetraarylporphyrin complexes are shown to permit a quantitative separation of the dipolar and contact contributions to the hyperfine shift. The separated components indicate that increased solvent hydrogen bonding strength significantly decreases the magnetic anisotropy of the iron and diminishes porphyrin → iron π bonding. The changes in anisotropy with solvent are shown to be consistent with the coordinated cyanide acting as a proton acceptor. Although similar effects are found to be absent in bis-imidazole complexes, a downfield bias of half the magnitude of the bis-cyano complexes is observed in mixed cyano/imidazole complexes. Hence, the heme hyperfine shifts in cyano-metmyoglobins and -hemoglobins may serve as probes for the protonation of the distal histidyl imidazole.     

Differential Congo Red staining: The effects of pH, non-aqueous solvents and the substrate

Summary Congo Red is an acid-base indicator dye. In free solution the colour and absorption characteristics of Congo Red depend not only on the pH but are also governed by the nature of the solvent environment. In tissue sections stained by Congo Red, alteration of the pH and the use of non-aqueous solvents can effect differential colouring of the tissue components. Stained sections of unmodified and chemically substituted celluloses show that differential red or blue coloration reflects the acidic or basic character of the substrate. In stained tissue sections, secondary protein structure and porosity of the substrate may also influence their colour. The effect of non-aqueous solvents is probably to modify the ionization state of the dye- substrate complex, thus altering the colour of the Congo Red. Such solvents may also change the aggregation or solvation states of the dye, with consequent modification in the colour of tissue components.     

Effects of non-aqueous solvents on CO2 absorption in monoethanolamine: Ab initio calculations

Monoethanolamine (MEA) is the most typical alkanolamine and its aqueous solutions are widely used for CO₂ absorption with mature technology, but the regeneration process is energy consuming. To reduce the energy demand, non-aqueous solvents, such as methanol and ethanol are proposed to substitute water in amine solutions. To understand the influence of the aqueous and non-aqueous solvents on CO₂ capture process, the chemical reactions of MEA absorbing CO₂ were conducted via ab initio calculations. The non-aqueous solvents discussed in this paper are methanol, ethanol, 1-propanol and 2-propanol. The reaction patterns were investigated and energy barriers were observed. The results show that zwitterion formation and the followed intermolecular hydrogen transfer are proven to be the most possible reaction pattern in both aqueous and non-aqueous solvents. The energy analysis shows that the forward reaction energy barriers increase while the backward barriers decrease as the solvent changes from water to methanol, ethanol, 1-propanol and 2-propanol in turn. The decreases of the energy barriers for backward processes are much higher than the corresponding increases for forward processes. These results indicate that lower energies are required in non-aqueous solvents than in water during the desorption reactions and the non-aqueous solvents are very promising to reduce the regeneration energy consumption in MEA capturing CO₂ process. Moreover, the reaction energy gaps between different solvation effects were found to have linear relationship with the logarithm of the dielectric constant difference, which could provide an easy way to theoretically predict the reaction energies of monoethanolamine absorbing CO₂ in other solvation effect and can be used to screen appropriate CO₂ capture solvent.     

Solvent effects on the electrochemical properties of IrCl2(bpy)2+

To investigate the solvent dependence of the d-d contribution to the redox orbital of the cis-dichloro- bis-(s,2′-bipyridine) iridium(III) ion, the first reduction electron transfer has been studied in various non-aqueous and aqueous solvents by cyclic voltammetry and spectroelectrochemistry. Totally irreversible electrochemical processes and chloride release have been observed in water, methanol and formamide, which are consistent with the proposed pre-dominantly metallic nature of the redox orbital in these solvents. In other solvents the electron reduction sequence and the low chemical reaction rate of chloride release suggest a strong interaction between the ligand and metal-centered redox orbitals. Correlation of the reduction potential with the Gutmann's acceptor number and dielectric constant of the solvents indicates that chloride release depends strongly upon the dissociative properties of the solvent. The electrochemical behaviour and photochemical observations are compared.     

Protein design for non-aqueous solvents

Improving protein stability in unnatural and suboptimal environments is a promising application of protein engineering technology. Carefully designed amino acid alterations may lead to dramatic positive effects on the stability of proteins under highly perturbing conditions, such as in non-aqueous solvents. Applications of biocatalysts and proteins with specific binding capabilities in the chemical industry have been severely limited by constraints placed on the solvent environment. With the advent of convenient methods for altering the amino acid composition and even synthesizing entirely new protein molecules, it is worthwhile to consider engineering proteins for stability in non-aqueous solvents. In order to identify the features that a protein would need for stability in organic media, we have been studying the structure and properties of the hydrophobic protein crambin. Crambin is unique in that it is soluble and stable in very high concentrations of polar organic solvents. Crambin and its water-soluble homologs offer a powerful demonstration of protein engineering for non-aqueous solvents. This paper describes the structural features that contribute to crambin's special properties. Based on these observations and consideration of how non-aqueous solvents affect the interactions important in protein folding, a set of rules for designing non-aqueous solvent-stable proteins is proposed.     

Non-aqueous capillary electrophoresis of drugs: properties and application of selected solvents

The electrophoretic mobility of selected acidic and basic test solutes have been determined in non-aqueous media prepared by adding various combinations of ammonium acetate, sodium acetate, methane sulphonic acid and acetic acid to acetonitrile, propylene carbonate, methanol, formamide, N-methylformamide, N,N-dimethylformamide and dimethylsulphoxide, respectively. The apparent pH (pH*) of these non-aqueous media have been measured and it was found that pH* is an important factor for the separations in non-aqueous capillary electrophoresis. However, in some solvents the concentration of sodium acetate has a strong influence on the mobility despite very small changes in pH*. Due to the fact that a change in one parameter influences a number of other parameters it is very difficult to conduct systematic studies in non-aqueous media and to compare the migration of the species at fixed pH* values from one solvent to another. Thus pH* is only of value for comparison when used with a specific solvent or solvent mixture. The viscosity of the above-mentioned solvents were measured at various temperatures and means to adjust the viscosity of the non-aqueous media used for capillary electrophoresis are discussed and the separation of ibuprofen and its major metabolites in urine is used as an example.     

Photophysical properties of 2-amino-9,10-anthraquinone: evidence for structural changes in the molecule with solvent polarity.

The photophysical properties of 2-amino-9,10-anthraquinone (2AAQ) have been investigated in different solvents and solvent mixtures and correlated with the Lippert-Mataga solvent polarity parameter, Deltaf. In the low solvent polarity region with Deltaf < ca. 0.1, the dye shows unusually high fluorescence quantum yields (Phif) and lifetimes (tauf) in comparison to those in other solvents of medium to high polarities. Similarly, the radiative rate constants (kf) are relatively lower and the non-radiative rate constants (knr) are relatively higher in the low polarity solvents in comparison to those in the medium to high polarity solvents. The current results have been rationalized assuming that the dye adopts different structural forms below and above the Deltaf value of approximately 0.1. It is inferred that in the low solvent polarity region the dye exists in a non-planar structure, with its 2-NH2 plane away from that of the 9,10-anthraquinone moiety in the ground state. In solvents of medium to high polarities, the dye exists in a polar intramolecular charge transfer (ICT) structure, where the amino lone pair of the 2-NH2 group is in strong resonance with the anthraquinone pi-cloud in the ground state. In all the solvents, however the dye is inferred to exist in the ICT structure in its excited (S1) state. Supportive evidence for the above hypothesis has been obtained from the solvent polarity effect on the Stokes' shifts for the dye. Quantum chemical studies on the structures of 2AAQ dye in the gas phase also give qualitative support for the inferences drawn from the photophysical properties of the dye in different solvents.     

To keep or not to keep? the question of crystallographic waters for enzyme simulations in organic solvent

The use of enzymes in non-aqueous solvents expands the use of biocatalysts to hydrophobic substrates, with the ability to tune selectivity of reactions through solvent selection. Non-aqueous enzymology also allows for fundamental studies on the role of water and other solvents in enzyme structure, dynamics, and function. Molecular dynamics simulations serve as a powerful tool in this area, providing detailed atomic information about the effect of solvents on enzyme properties. However, a common protocol for non-aqueous enzyme simulations does not exist. If you want to simulate enzymes in non-aqueous solutions, how many and which crystallographic waters do you keep? In the present work, this question is addressed by determining which crystallographic water molecules lead most quickly to an equilibrated protein structure. Five different methods of selecting and keeping crystallographic waters are used in order to discover which crystallographic waters lead the protein structure to reach an equilibrated structure more rapidly in organic solutions. It is found that buried waters contribute most to rapid equilibration in organic solvent, with slow-diffusing waters giving similar results.     

Engineering enzymes for non-aqueous solvents.

Enzymes may be redesigned to permit catalysis in non-aqueous solvents by engineering their amino acid sequences, thereby altering their physical and chemical properties to suit the new solvent environment. The interactions that contribute to protein stability in non-aqueous solvents are discussed in the context of attempting to identify possible approaches to constructing enzymes which exhibit enhanced stability in non-aqueous media. These approaches are illustrated by several examples where protein engineering has resulted in enzymes that are better suited for catalysis in organic solvents.     

Effect of selected anions and solvents on the electron absorption, nuclear magnetic resonance, and infrared spectra of the N-retinylidene-n-butylammonium cation.

The specific conteranion and the solvent have been shown to regulate the electronic excitation energy of the N-retinylidene-n-butylammonium cation. Halogenated hydrocarbon solvents which can hydrogen bond with the anion shift the lambda-max to longer wavelengths, whereas the solvent dipole, acting as a bulk effect, shifts the wavelength-max to shorter wavelength. Here solvents which can donate two hydrogens for hydrogen bonding, such as cis- and trans-1,2-dichloroethylene and cis- and trans-1,2-dichlorocyclohexane, are used as solvents for the Cl-, Br-, and I- salts. As expected the cis solvents allow longer wavelengths than do the trans solvents. Results of nuclear magnetic resonance spectroscopy are shown to be in agreement with electronic absorption spectroscopy. The C-11 proton and the C-13 and C-9 methyl protons show a considerable downfield shift in the salts with respect to the Schiff base. Furthermore the same protons show a continuing downfield shift as the anions are exchanged from Cl-, Br- to I-. This is an agreement with the interpretation of greater positive charge delocalization as the anions are changed in the above manner. The infrared absorptions of the C - N group in the Schiff base and the protonated form are shown to be almost similar. This is rationalized by showing that the force constant can remain constant as the highly related factors bond order, bond distance, and the effective electronegativity are changed in a self-compensating manner.     

Solvent effects on the spectroscopic properties of aflatoxin B1

1. Solvent-induced changes in the spectral properties of aflatoxin B1 were investigated using protic and aprotic solvents. 2. The absorption data were less sensitive to solvent effects than the fluorescence emission data. 3. Stokes shifts in protic solvents were greater than those in aprotic solvents indicating hydrogen bond formation between solvent and the excited state of aflatoxin B1. 4. From the Stokes shift data for aprotic solvents, the dipole moment of aflatoxin B1 was estimated to increase by 15.7 Debye units upon excitation to the excited singlet state.     

A histological comparison of phase-partition fixation with fixation in aqueous solutions

In phase-partition fixation, tissue is immersed in a non-aqueous solvent at equilibrium with an aqueous solution of a fixing agent to minimize osmotic effects. Preservation of morphology afforded by phase-partition fixation using formalin and glutaraldehyde and several organic solvents was compared to aqueous 10% neutral buffered formalin fixation for five tissues. It was shown that phase-partition fixation can provide excellent fixation for light microscopy if the proper combinations of fixatives and solvents are used.     

Effect of water activity on the lipase catalyzed esterification of geraniol in ionic liquid [bmim]PF6

Enzymatic reactions in non-aqueous media have been shown to be effective in carrying out chemical transformation where the reactants are insoluble in water or water is a byproduct limiting conversion. Ionic liquids, liquid organic salts with infinitesimal vapor pressure, are potentially useful alternatives to organic solvents. It is known that the thermodynamic water activity is an important variable affecting the activity of enzymes in non-aqueous solvents. This study investigated the influence of water activity on the esterification of geraniol with acetic acid in ionic liquid [bmim]PF6 catalyzed by immobilized Candida antarctica lipase B. The conversion of geraniol in [bmim]PF6 was significant although the reaction rate was slower than in organic solvents. The profile of initial reaction rate-water activity was determined experimentally, and differed from the data reported for other non-aqueous solvents. A maximum in the initial reaction rate was found at aw = 0.6. The pseudo reaction equilibrium constant, Kx, was measured experimentally for the reaction. The average value of Kx in [bmim]PF6 was 12, 20-fold lower than the value reported for the same system in hexane.     

Isotopic effects in the electronic spectra of tryptophan

Summary. No influence of isotopic substitution in deuterium-substituted tryptophan on the florescence excitation spectrum has previously been found out. Here, the isotopic effects of electronic excitation of deuterium-substituted tryptophan were experimentally and theoretically analyzed for first time. It was shown a short-wave shift of the UV-absorption maximum at 220 nm corresponding to the 360 cal/mol and short-wave shift for fluorescence spectrum corresponding to the 210 cal/mol. To account for this effect, the quantum chemical calculations of the geometric and electron structure, frequencies of normal vibrations and transition energies have been performed. The isotopic effects originate from the zero-point energies of ground and excited states. It was found that isotopic shifts depend on the position of isotope in the molecule and kind of transition. So, it can be utilized in the analysis of proteins structure and complexation.     

Enzymes in non-aqueous solvents

For a variety of reasons including increased recognition of the large degree of association, by non-polar interaction, of enzymes with other cellular components such as membranes, enzymes are increasingly being investigated in mixed solvents less polar than water. Such solvents may be quite relevant because their polarity more nearly resembles the natural cellular microenvironment than does pure water. The single most important criterion in selecting a non-aqueous solvent is its compatibility with the maintenance of the enzyme's catalytic activity, which must be determined experimentally for each enzyme. Non-aqueous solvents have a variety of effects on enzymes: they may bind specifically, compete with substrate binding, dissociate multimers, shift an equilibrium between two enzyme conformations, alter the amount of helix, react with the enzyme, stabilize or destabilize the enzyme, and affect the rate of the catalytic reaction in several different ways. Typically, modest concentrations of hydroxylic solvents have little effect on rates, and may even enhance the rate significantly. Higher concentrations give lower rates, in a solvent-specific and enzyme-specific manner. Hydroxylic solvents may replace water as acceptor of a phosphoryl, glycosyl, or acyl group produced by a hydrolytic enzyme. Non-aqueous solvents also make it possible to run hydrolytic reactions in the reverse direction, forming a condensation product and water as a by-product. Non-aqueous solvents are being extensively used in cryoenzymology as antifreeze agents, in solubilizing and purifying enzymes, and to a lesser degree in two-phase systems in which the non-polar substrate is dissolved in the non-aqueous phase. Liquefied aqueous phenol is an extraordinary solvent for enzymes and other proteins. It is a powerful denaturant which rapidly and irreversibly extracts the enzyme into the phenol-rich phase of a phenol-water system. This property makes phenol useful for removing protein contaminants, and for detecting labile enzyme-substrate intermediates, by extracting substrate covalently bound to enzyme into the phenol-rich phase away from all other substrate, which generally remains in the aqueous phase.     

Effect of non aqueous solvent on structural stability of α-amylase: A cost-effective prospective for protein stabilization

The aim of the present study is to assess the effect of non-aqueous organic solvent on structural stability, molecular integrity and structure of α-amylase. The activity and thermal stability of the enzyme was measured before and after treatment with non polar solvent (i.e. hexane). The activity was found to be marginally affected and thermal stability was found to be significantly increased after treatment with hexane. The enzyme was found to be more resistant to thermal inactivation in hexane compared to in an aqueous buffer. The fluorescence measurement indicated a blue shift of 3 nm in the emission maximum (λ_max) probably due to a minor change in the polarity of aromatic amino acid residues after treatment with a non-aqueous solvent. Assessment of thermal denaturation profile, 1-anilino-8-naphthalene-sulfonate (ANS) binding and acrylamide quenching of the enzyme suggested an increase in the molecular integrity and overall stability of the enzyme after treatment with hexane. However, these entire molecular events were not accompanied by any major change in the secondary structure. Our findings suggest that treatment of proteins or enzymes in non-aqueous solvents could be an attractive and cost-effective strategy to improve their structural stability without compromising their biological functions.     

Substitution effects on the optical spectra of diarylethene photochroms: ab initio insights

Using a time-dependent density functional approach and taking into account the bulk solvent effects, we study the modification of the optical properties of maleic anhydride diarylethenes induced by structural changes. Our results reproduce the auxochromic shifts described by experiments. We show that the closed forms of diarylethene molecules are much more sensitive to heteroatom substitution of the cyclopentadienyl rings than the open forms. The addition of electro-active groups to the reactive carbon atoms is also investigated. The major effect on the UV/visible spectra originates from the resonance effect as measured by the Hammett's factor.     

A light-harvesting antenna protein retains its folded conformation in the absence of protein-lipid and protein-pigment interactions

The first study by nmr of the integral membrane protein, the bacterial light-harvesting (LH) antenna protein LH1 beta, is reported. The photosynthetic apparatus of purple bacteria contains two different kinds of antenna complexes (LH1 and LH2), which consist of two small integral membrane proteins alpha and beta, each of approximately 6 kDa, and bacteriochlorophyll and carotenoid pigments. We have purified the antenna polypeptide LH1 beta from Rhodobacter sphaeroides, and have recorded CD spectra and a series of two-dimensional nmr spectra. A comparison of CD spectra of LH1 beta observed in organic solvents and detergent micelles shows that the helical character of the peptide does not change appreciably between the two milieus. A significantly high-field shifted methyl signal was observed both in organic solvents and in detergent micelles, implying that a similar three-dimensional structure is present in each case. However, the 1H-nmr signals observed in organic solvents had a narrower line width and better resolution, and it is shown that in this case organic solvents provide a better medium for nmr studies than detergent micelles. A sequential assignment has been carried out on the C-terminal transmembrane region, which is the region in which the pigment is bound. The region is shown to have a helical structure by the chemical shift values of the alpha-CH protons and the presence of nuclear Overhauser effects characteristic of helices. An analysis of the amide proton chemical shifts of the residues surrounding the histidine chlorophyll ligand suggests that the local structure is well ordered even in the absence of protein-lipid and protein-pigment interactions. Its structure was determined from 348 nmr-derived constraints by using distance geometry calculations. The polypeptide contains an alpha-helix extending from Leu19 (position of cytoplasmic surface) to Trp44 (position of periplasmic surface). The helix is bent, as expected from the amide proton chemical shifts, and it is similar to the polypeptide fold of the previously determined crystal structure of Rhodopseudomonas acidophila Ac10050 LH2 beta (S. M. Prince et al., Journal of Molecular Biology, 1997, Vol. 268, pp. 412-423). It is concluded that the polypeptide conformation of this region may facilitate assembly of the LH complex.