A molecular dynamics study of the dielectric properties of aqueous solutions of alanine and alanine dipeptide

Molecular dynamics simulations were used to compute the frequency-dependent dielectric susceptibility of aqueous solutions of alanine and alanine dipeptide. We studied four alanine solutions, ranging in concentration from 0.13-0.55 mol/liter, and two solutions of alanine dipeptide (0.13 and 0.27 mol/liter). In accord with experiment we find a strong dielectric increment for both solutes, whose molecular origin is shown to be the zwitterionic nature of the solutes. The dynamic properties were analyzed based on a dielectric component analysis into solute, a first hydration shell, and all remaining (bulk) waters. The results of this three component decomposition were interpreted directly, as well as by uniting the solute and hydration shell component to a "suprasolute" component. In both approaches three contributions to the frequency-dependent dielectric properties can be discerned. The quantitatively largest and fastest component arises from bulk water [i.e., water not influenced by the solute(s)]. The interaction between waters surrounding the solute(s) (the hydration shell) and bulk water molecules leads to a relaxation process occurring on an intermediate time scale. The slowest relaxation process originates from the solute(s) and the interaction of the solute(s) with the first hydration shell and bulk water. The primary importance of the hydration shell is the exchange of shell and bulk waters; the self-contribution from bound water molecules is comparatively small. While in the alanine solutions the solute-water cross-terms are more important than the solute self-term, the solute contribution is larger in the dipeptide solutions. In the latter systems a much clearer separation of time scales between water and alanine dipeptide related properties is observed. The similarities and differences of the dielectric properties of the amino acid/peptide solutions studied in this work and of solutions of mono- and disaccharides and of the protein ubiquitin are discussed.     

Identification of the molecular motions responsible for the slower secondary (beta) relaxation in sucrose

Broad-band isothermal dielectric relaxation measurements of anhydrous sucrose were made at ambient pressure in its liquid and glassy states. We found a new secondary relaxation that is slower than the one commonly observed in sugars. Additionally, we carried out the dielectric measurements of the equimolar mixture of D-glucose and D-fructose in wide ranges of temperature and frequency. Comparison of the behavior of these two systems allowed us to make suggestions on the origin of the slower beta-relaxation in sucrose. Computer simulations and coupling model calculations were performed to support our interpretation of the kind of molecular motions responsible for the slower secondary relaxation in the disaccharide considered.     

Two secondary modes in decahydroisoquinoline: which one is the true Johari Goldstein process?

Broadband dielectric measurements were carried out at isobaric and isothermal conditions up to 1.75 GPa for reconsidering the relaxation dynamics of decahydroisoquinoline, previously investigated by Richert et al. [R. Richert, K. Duvvuri, and L.-T. Duong, J. Chem. Phys. 118, 1828 (2003)] at atmospheric pressure. The relaxation time of the intense secondary relaxation tau(beta) seems to be insensitive to applied pressure, contrary to the alpha-relaxation times tau(alpha). Moreover, the separation of the alpha- and beta-relaxation times lacks correlation between shapes of the alpha-process and beta-relaxation times, predicted by the coupling model [see for example, K. L. Ngai, J. Phys.: Condens. Matter 15, S1107 (2003)], suggesting that the beta process is not a true Johari-Goldstein (JG) relaxation. From the other side, by performing measurements under favorable conditions, we are able to reveal a new secondary relaxation process, otherwise suppressed by the intense beta process, and to determine the temperature dependence of its relaxation times, which is in agreement with that of the JG relaxation.     

Study of dielectric relaxations of anhydrous trehalose and maltose glasses

We investigated the frequency dependent dielectric relaxation behaviors of anhydrous trehalose and maltose glasses in the temperature range which covers a supercooled and glassy states. In addition to the α-, Johari-Goldstein (JG) β-, and γ-relaxations in a typical glass forming system, we observed an extra relaxation process between JG β- and γ-relaxations in the dielectric loss spectra. We found that the unknown extra relaxation is a unique property of disaccharide which might originate from the intramolecular motion of flexible glycosidic bond. We also found that the temperature dependence of the JG β-relaxation time changes at 0.95T(g) and it might be universal.     

POTENTIAL ENERGY SURFACES OF α-(1→3)-LINKED DISACCHARIDES CALCULATED WITH THE MM3 FORCE-FIELD

The adiabatic conformational surfaces of sixteen 4′,6′,6-trideoxy-α-d-(1→3)-linked disaccharides were obtained using the MM3 force-field at two different dielectric constants. Calculations were carried out on disaccharides with different configurations at C2, C4 and C2′, which are neighbors to the glycosidic linkage, as well as that of the linked carbon (C3). The resulting maps were similar, indicating that the substituents do not play a major role in the conformational features of these disaccharides. However, the preferred minimum conformation and the flexibility were found to be slightly dependant on the configurations of the carbons. Although equatorial bonds and vicinal axial substituents tend to increase the overall flexibility, it was found that these factors can have a cross over effect; i.e., an axial hydroxyl group on C2 may decrease the flexibility if the glycosyl group on C3 is also axial. The relative stabilities of the minimal energy conformations of the 16 compounds also show deviations of the predicted increased stabilities of equatorially substituted compounds over axially substituted ones: these deviations occur mainly for the C2 substituent.     

Characterization of the glycosidic linkage of underivatized disaccharides by interaction with Pb(2+) ions

Electrospray ionization in combination with tandem mass spectrometry and lead cationization is used to characterize the linkage position of underivatized disaccharides. Lead(II) ions react mainly with disaccharides by proton abstraction to generate [Pb(disaccharide)(m)-H](+) ions (m = 1-2). At low cone voltages, an intense series of doubly charged ions of general formula [Pb(disaccharide)(n)](2+) are also observed. Our study shows that MS/MS experiments have to be performed to differentiate Pb(2+)-coordinated disaccharides. Upon collision, [Pb(disaccharide)-H](+) species mainly dissociate according to glycosidic bond cleavage and cross-ring cleavages, leading to the elimination of C(n)H(2n)O(n) neutrals (n = 2-4). The various fragmentation processes allow the position of the glycosidic bond to be unambiguously located. Distinction between glc-glc and glc-fru disaccharides also appears straightforward. Furthermore, for homodimers of D-glucose our data demonstrate that the anomericity of the glycosidic bond can be characterized for the 1 --> n linkages (n = 2, 4, 6). Consequently, Pb(2+) cationization combined with tandem mass spectrometry appears particularly useful to identify underivatized disaccharides.     

Dynamical behavior of highly concentrated trehalose water solutions: a dielectric spectroscopy study

Trehalose solutions were investigated by means of broadband dielectric spectroscopy at different water contents, ranging from an anhydrous sample to w(C) = 40%. While the structural α-relaxation was detectable only in the low hydration and dry samples, and in a quite limited range of temperatures, two secondary processes were presented and characterized in all the solutions investigated. In particular, the fastest secondary process displayed a characteristic behavior widely observed in other small organic glass formers. It had an Arrhenius-like temperature dependence, it sped up and increased the dielectric strength when adding water and finally it possessed an activation energy compatible with the breaking/formation of two hydrogen bonds. From all these indications it was plausible to attribute it to water dipole reorientation dynamics. The slower secondary process was again well described by an Arrhenius-like function, now the relaxation time at high temperature was only slightly dependent on the exact water amount but the activation energy was markedly dependent on it. The molecular origin of this process was tentatively attributed to the motion of the entire molecule involving rotation of the two monosugar rings around the glycosidic bond.     

Determining anomericity of the glycosidic bond in Zn(II)-diethylenetriamine-disaccharide complexes using MS n in a quadrupole ion trap

Zinc-diethylenetriamine (Zn-dien) N-glycoside complexes of four 1,4 and four 1,6 linked disaccharides are prepared. Each reaction mixture is ionized by electrospray and the resulting species [Zn(dien)(disaccharide)-H]+ is allowed to undergo collision-induced dissociation in a quadrupole ion trap. An MS3 analysis is used to differentiate alpha versus beta anomericity of the glycosidic bond in the disaccharide moiety. In addition, the MS2 and MS3 spectra can be used together to determine the linkage position of this glycosidic bond.     

Force‐field parameters of the Ψ and Φ around glycosidic bonds to oxygen and sulfur atoms

The Ψ and Φ torsion angles around glycosidic bonds in a glycoside chain are the most important determinants of the conformation of a glycoside chain. We determined force‐field parameters for Ψ and Φ torsion angles around a glycosidic bond bridged by a sulfur atom, as well as a bond bridged by an oxygen atom as a preparation for the next study, i.e., molecular dynamics free energy calculations for protein‐sugar and protein‐inhibitor complexes. First, we extracted the Ψ or Φ torsion energy component from a quantum mechanics (QM) total energy by subtracting all the molecular mechanics (MM) force‐field components except for the Ψ or Φ torsion angle. The Ψ and Φ energy components extracted (hereafter called “the remaining energy components”) were calculated for simple sugar models and plotted as functions of the Ψ and Φ angles. The remaining energy component curves of Ψ and Φ were well represented by the torsion force‐field functions consisting of four and three cosine functions, respectively. To confirm the reliability of the force‐field parameters and to confirm its compatibility with other force‐fields, we calculated adiabatic potential curves as functions of Ψ and Φ for the model glycosides by adopting the Ψ and Φ force‐field parameters obtained and by energetically optimizing other degrees of freedom. The MM potential energy curves obtained for Ψ and Φ well represented the QM adiabatic curves and also these curves' differences with regard to the glycosidic oxygen and sulfur atoms. Our Ψ and Φ force‐fields of glycosidic oxygen gave MM potential energy curves that more closely represented the respective QM curves than did those of the recently developed GLYCAM force‐field. © 2009 Wiley Periodicals, Inc., J Comput Chem, 2009     

Sugar pucker modulates the cross-correlated relaxation rates across the glycosidic bond in DNA

The dependence of N1/9 and C1' chemical shielding (CS) tensors on the glycosidic bond orientation (chi) and sugar pucker (P) in the DNA nucleosides 2'-deoxyadenosine, 2'-deoxyguanosine, 2'-deoxycytidine, and 2'-deoxythymidine was studied using the calculation methods of quantum chemistry. The results indicate that these CS-tensors exhibit a significant degree of conformational dependence on chi and P structural parameters. The presented data test underlying assumptions of currently established methods for interpretation of cross-correlated relaxation rates between the N1/9 chemical shielding tensor and C1'-H1' dipole-dipole (Ravindranathan et al. J. Biomol. NMR 2003, 27, 365-75. Duchardt et al. J. Am. Chem. Soc. 2004, 126, 1962-70) and highlight possible limitations of these methods when applied to DNA.     

Computational study of the dynamics of mannose disaccharides free in solution and bound to the potent anti-HIV virucidal protein cyanovirin

In this paper, we present a computational study of the dynamics of the potent anti-HIV virucidal protein cyanovirin in complex with mannose disaccharides. Recently, it has been experimentally demonstrated that cyanovirin binds mannose oligomers on the surface of glycoprotein gp120. gp120, a protein on the surface of the HIV virus, is key in the process of viral docking and transfer of genetic material into human cells. Cyanovirin prevents the transfer of viral RNA into human cells. In this study, we found that, among all residues that show nuclear Overhauser effects in the solution NMR experiments, residues Glu41 and Arg76 appear to interact with the sugar at the high-affinity binding site through stronger Coulombic interactions. In particular, Arg76 participates in a dynamical mechanism that caps and locks the sugar once it is bound to the protein. We also studied the distribution of glycosidic torsional angles of mannose disaccharides in solution and compared it with those when bound at the high- and low-affinity sites of the protein. Throughout our 20 ns simulations, we find that the sugar bound to the high-affinity site preserves the most favorable conformation in solution while the sugar bound at the low-affinity site does not. The sugar at the low-affinity site can adopt both conformations, but we find it most predominantly on the one that is least probable for the free sugar in solution. We also carried out a detailed study of the interactions between the disaccharides and different amino acids as well as between the disaccharide and the solvent at both binding locations.     

Developing a Library of Mannose-Based Mono- and Disaccharides: A General Chemoenzymatic Approach to Monohydroxylated Building Blocks

Regioselective deprotection of acetylated mannose-based mono- and disaccharides differently functionalized in anomeric position was achieved by enzymatic hydrolysis. Candida rugosa lipase (CRL) and Bacillus pumilus acetyl xylan esterase (AXE) were immobilized on octyl-Sepharose and glyoxyl-agarose, respectively. The regioselectivity of the biocatalysts was affected by the sugar structure and functionalization in anomeric position. Generally, CRL was able to catalyze regioselective deprotection of acetylated monosaccharides in C6 position. When acetylated disaccharides were used as substrates, AXE exhibited a marked preference for the C2, or C6 position when C2 was involved in the glycosidic bond. By selecting the best enzyme for each substrate in terms of activity and regioselectivity, we prepared a small library of differently monohydroxylated building blocks that could be used as intermediates for the synthesis of mannosylated glycoconjugate vaccines targeting mannose receptors of antigen presenting cells.     

Assignment of the Stereochemistry and Anomeric Configuration of Sugars within Oligosaccharides Via Overlapping Disaccharide Ladders Using MSn

A systematic approach is described that can pinpoint the stereo-structures (sugar identity, anomeric configuration, and location) of individual sugar units within linear oligosaccharides. Using a highly modified mass spectrometer, dissociation of linear oligosaccharides in the gas phase was optimized along multiple-stage tandem dissociation pathways (MSⁿ, n = 4 or 5). The instrument was a hybrid triple quadrupole/linear ion trap mass spectrometer capable of high-efficiency bidirectional ion transfer between quadrupole arrays. Different types of collision-induced dissociation (CID), either on-resonance ion trap or beam-type CID could be utilized at any given stage of dissociation, enabling either glycosidic bond cleavages or cross-ring cleavages to be maximized when wanted. The approach first involves optimizing the isolation of disaccharide units as an ordered set of overlapping substructures via glycosidic bond cleavages during early stages of MSⁿ, with explicit intent to minimize cross-ring cleavages. Subsequently, cross-ring cleavages were optimized for individual disaccharides to yield key diagnostic product ions (m/z 221). Finally, fingerprint patterns that establish stereochemistry and anomeric configuration were obtained from the diagnostic ions via CID. Model linear oligosaccharides were derivatized at the reducing end, allowing overlapping ladders of disaccharides to be isolated from MSⁿ. High confidence stereo-structural determination was achieved by matching MSⁿ CID of the diagnostic ions to synthetic standards via a spectral matching algorithm. Using this MSⁿ (n = 4 or 5) approach, the stereo-structures, anomeric configurations, and locations of three individual sugar units within two pentasaccharides were successfully determined.

Electrostatic interactions between a protein and oppositely charged micelles

Micellar solutions made of a fully fluorinated surfactant, LiPFN, form water-soluble complexes with lysozyme in a wide concentration range. Such complexes are stabilized by electrostatic and, very presumably, double-layer interactions. The mixtures were investigated by combining electrophoretic mobility, DLS, and dielectric relaxation methods. The former gives information on the surface charge density of protein-micelle complexes and indicates that the resulting adducts retain a negative charge (i.e., charge neutralization is incomplete). The double-layer thickness of proteins, micelles, and protein-micelle complexes is also connected to the dielectric relaxation frequency. Changes in particle size (inferred by DLS), charge density, and double-layer thickness are closely interrelated to each other. A model was developed to quantify such properties.     

Field desorption mass spectrometry of natural products—II: Physiologically active pennogenin—and hederagenin-glycosides

Field desorption mass spectra of underivatized saponios, naturel oligoglycosides of physiological activity, showed intense ions formed by attachment of alkali cations to the neutral molecule and to structurally highly significant subunits. This cationization was generated by small amounts of alkali salts which were present in samples after isolation from biological material. When the mass spectre were produced by laser-supported desorption and were recorded at high resolution on vapor-deposited AgBr plates unambiguous determination of the molecular weghts (in the mass range from 700 to 1400) was performed. Moreover, ions formed by direct bond cleavages in the oligosaccharide moiety of the natural saponins clearly gave information about the sequence of the sugar units in the molecule and their individual chemical structures. The formation of these fragments in FD-MS is discussed in relation to the well established mechanism of glycosidic bond cleavage by acidic solvolysis. In principle this comparison showed the usefulness of this approach for the interpretation of FD mass spectra of substances containing heteroatom linkages e.g., glycosides, esters, amides, imines, mercaptans, etc.     

Kinetics of the thermal reactions of some disaccharides

The kinetics of the early stages of pyrolysis of several disaccharides have been examined thermogravimetrically. Cleavage of the glycosidic bond has been postulated as the rate-determining step for these thermal reactions. This step is followed primarily by the formation of anhydrohexopyranoses with the elimination of water. The kinetic parameters for these disaccharides have been compared with the literature values for aqueous acid hydrolyses of these same compounds.     

Cationic host-guest polymerization of N-vinylcarbazole and vinyl ethers in MCM-41, MCM-48, and nanoporous glasses

The synthesis of poly(vinyl ether)s or polyvinylcarbazole under the conditions of constricted geometry can be achieved by means of cationic host-guest polymerisation of the corresponding monomers in the pores of MCM-41 (pore diameter 3.6 nm), MCM-48 (pore diameter 2.4 nm) and in nanoporous glasses (Gelsil with a pore diameter of 5 nm) with bis(4-methoxyphenyl)methyl chloride (BMCC) or triphenylmethyl chloride as the internal surface initiator. The reaction products are new polymer/ MCM-41, polymer/MCM-48 etc., host-guest hybrid materials. The molecular mass of the enclosed polymer and the degree of loading of the host compounds can be adjusted within certain limits. The molecular dynamics were investigated by using broad-band dielectric spectroscopy. Under the conditions of constricted geometry, molecular fluctuation is observed as well as a secondary beta-relaxation, which is hardly affected (in comparison with the free melt) and which corresponds to the relaxation between structural substates (dynamic glass transition). This process is several orders of magnitude faster in its relaxation rate than in the free melt and thus follows a confinement effect. This is already well known in lower molecular weight systems with constricted geometry.     

Differentiation of the Stereochemistry and Anomeric Configuration for 1-3 Linked Disaccharides Via Tandem Mass Spectrometry and <Superscript>18</Superscript>O-labeling

Collision-induced dissociation (CID) of deprotonated hexose-containing disaccharides (m/z 341) with 1–2, 1–4, and 1–6 linkages yields product ions at m/z 221, which have been identified as glycosyl-glycolaldehyde anions. From disaccharides with these linkages, CID of m/z 221 ions produces distinct fragmentation patterns that enable the stereochemistries and anomeric configurations of the non-reducing sugar units to be determined. However, only trace quantities of m/z 221 ions can be generated for 1–3 linkages in Paul or linear ion traps, preventing further CID analysis. Here we demonstrate that high intensities of m/z 221 ions can be built up in the linear ion trap (Q3) from beam-type CID of a series of 1–3 linked disaccharides conducted on a triple quadrupole/linear ion trap mass spectrometer. ¹⁸O-labeling at the carbonyl position of the reducing sugar allowed mass-discrimination of the “sidedness” of dissociation events to either side of the glycosidic linkage. Under relatively low energy beam-type CID and ion trap CID, an m/z 223 product ion containing ¹⁸O predominated. It was a structural isomer that fragmented quite differently than the glycosyl-glycolaldehydes and did not provide structural information about the non-reducing sugar. Under higher collision energy beam-type CID conditions, the formation of m/z 221 ions, which have the glycosyl-glycolaldehyde structures, were favored. Characteristic fragmentation patterns were observed for each m/z 221 ion from higher energy beam-type CID of 1–3 linked disaccharides and the stereochemistry of the non-reducing sugar, together with the anomeric configuration, were successfully identified both with and without ¹⁸O-labeling of the reducing sugar carbonyl group.     

Concise synthesis of 5-methoxy-6-hydroxy-2-methylchromone-7-O- and 5-hydroxy-2-methylchromone-7-O-rutinosides. Investigation of their cytotoxic activities against several human tumor cell lines

The synthesis of two novel 2-methylchromone-7-O-rutinosides is reported, and the in vitro biological activities of these compounds and their synthetic precursors have been investigated on the basis of their cytotoxicity against several human tumor cell lines. The synthesis features early stage assembly of the acidic labile glycosidic bond between sugar and 2-methylchromone aglycon under phase transfer catalyzed glycosidation conditions, whereas all the other standard glycosylation conditions specific to a wide array of rutinosyl donors bearing different anomeric leaving groups (e.g., SPh, OC(NH)CCl(3), Br, OH groups) failed to furnish any detectable products.