Conformational landscape of (R,R)-pterocarpans with biological activity in vacuo and in aqueous solution (PCM and/or water clusters)

All possible combinations of stable dihedral values have been considered in vacuo at the B3LYP/6-31G level for 3,9-dihydroxy-4,8-diprenylpterocarpan (erybraedin C), whose hydroxy out-out conformation had been examined earlier together with the conformational preferences of 3,9-dimethoxy-4-prenylpterocarpan (bitucarpin A) at the same level (Phys. Chem. Chem. Phys. 2004, 6, 2849). The structure with O5 trans with respect to H6a (O(t)) is about 2 kcal/mol less stable in vacuo than that with one of the H6 trans to it (H(t)); in aqueous solution its energy gap is nearly conserved. The in-in arrangement of the hydroxyl groups of erybraedin turns out to be preferred in vacuo (even considering zero point and thermal effects), where pseudo H-bonds are formed between hydroxy hydrogens and pi electron distributions of prenyl groups. The continuum solvent effect (water) at the IEF-PCM/B3LYP/6-31G level on the relative stability of the various rotamers is very limited both on bitucarpin and erybraedin. Considering the dihydrated derivatives, significant differences in the solvation energy are found between the distinct hydration sites, increasing in the order: methoxy O, ring O, hydroxy O, and hydroxy H. In hydroxy-water interactions, in fact, water prefers to behave as an H-bond acceptor unless nearby bulky groups prevent its approach. Interestingly enough, a bridging water molecule between the hydroxy H of erybraedin and the prenyl group can be found. The inclusion of BSSE corrections in hydroxy-water interactions decidedly favors out-out hydrated arrangements, followed by out-in and in-out ones. Bulk solvent effects with IEF-PCM about the dihydrated systems almost invert the stability order found in vacuo. When a four-water cluster is considered using QM methods, waters gather in H-bonded pairs around the solute OH groups. MD simulations, carried out on a pterocarpan solute (J. Phys. Chem. B 2005, 109, 16918), supply water adducts consistent with a liquid state that have also been embedded in the continuum solvent.     

Dipolarity, hydrogen-bond basicity and hydrogen-bond acidity of aqueous poly(ethylene glycol) solutions.

Poly(ethylene glycol) (PEG) in water is known to alter the structure and/or state of water to give a different polarity from that of pure water. We determined using the solvatochromic comparison method the dipolarity/polarizability (pi*), hydrogen bond (HB) accepting basicity (beta) and HB donating acidity (alpha) of aqueous solutions of PEGs of variegated molecular weights at different concentrations in order to understand the influence of the polymer on these properties of water. It was observed that PEG decreases alpha for water while it does not change pi* and beta appreciably in the range of the molecular weight and compositions studied.     

Structural and atoms-in-molecules analysis of hydrogen-bond network around nitroxides in liquid water

In this study, we investigated the hydrogen-bond network patterns involving the NO moieties of five small nitroxides in liquid water by analyzing nanosecond scale molecular dynamics trajectories. To this end, we implemented two types of hydrogen-bond definitions, based on electronic structure, using Bader's atoms-in-molecules analysis and based on geometric criteria. In each definition framework, the nitroxide/water hydrogen-bond networks appear very variable from a nitroxide to another. Moreover, each definition clearly leads to a different picture of nitroxide hydration. For instance, the electronic structure-based definition predicts a number of hydrogen bonds around the nitroxide NO moiety usually larger than geometric structure-based ones. One particularly interesting result is that the strength of a nitroxide/water hydrogen bond does not depend on its linearity, leading us to question the relevance of geometric definition based on angular cutoffs to study this type of hydrogen bond. Moreover, none of the hydrogen-bond definitions we consider in the present study is able to quantitatively correlate the strength of nitroxide/water hydrogen-bond networks with the aqueous nitroxide spin properties. This clearly exhibits that the hydrogen-bonding concept is not reliable enough to draw quantitative conclusions concerning such properties.     

天花粉蛋白溶液构象与稳定性及生物活性的关系

用圆二色性研究了天花粉蛋白在不同PH,不同温度和不同的时间条件下的溶液构象变化.阐明了天花粉蛋白溶液的外部环境,并研究了天花粉蛋白的溶液构象与抗生育活性的关系,结果表明随着溶液中a-helix含量的增加,抗生育活性也相应增加,当a-helix含量减少到15%以下,其抗生育活性也就丧失.     

Water exchange dynamics of lithium(I) ion in aqueous solution

The water exchange dynamics of the fourfold coordinated first hydration shell of the lithium(I) ion was studied by both direct and umbrella sampling QM/MM-MD and classical MD simulations. The structural changes and energetics accompanying the activation process are discussed. The overall exchange rate constant was found to be k(ex) = 5.8 x 10(9) s(-1) from classical MD simulations. QM/MM-MD umbrella sampling simulations predict an exchange rate constant of k(TST) = 1.01 x 10(10) s(-1) as obtained from classical transition-state theory. First-shell ligands exchange preferably via an associatively activated mode.     

Structure and dynamics at the surface of a concentrated aqueous solution of CsF

A molecular dynamics simulation of a liquid layer of a concentrated CsF solution in water has been performed in order to compare the results with those obtained in an experimental study of our group. The main result of the experiment was the existence of a monolayer of nearly pure water constituting the surface and a homogeneous mixture constituting the bulk of the system. The simulation reveals the same phenomena which can be explained by the circumstance that the ions near the surface mostly keep their first solvation shell intact. The water molecules belonging to these shells and being placed on the vapor side constitute this monolayer. The density profiles of the ions indicate that the Cs ions penetrate further into the surface than the F ions. The orientational structure of the first shell of water molecules around an ion is the same for ions in the surface and ions in the bulk in contrast to the dynamics which is altered. The spectra of the librational motion are shifted to lower frequencies. In addition to that the spectra belonging to libration which involves motion of the dipole moment develop a peak in the low frequency range irrespective of whether the water molecules are bonded to Cs or to F ions. This can be correlated with an overall preferred orientation of the water molecules in the surface which is most pronounced for the dipole moment. The calculation of the diffusion coefficients shows that the top surface layer of nearly pure water is a region of enhanced and extremely anisotropic mobility. The mean residence time of water molecules in the surface in the first shell of an ion is reduced according to the enhanced mobility.     

Structure and dynamics of beta-cyclodextrin in aqueous solution at the density-functional tight binding level

Structure and dynamics of beta-cyclodextrin (beta-CyD), a prototype host for inclusion compounds of biological interest, is investigated by means of density-functional based tight-binding molecular dynamics (MD) simulations. The computational protocol is benchmarked against available experimental data and first-principles calculations. Solvent-solute interactions, including the diffusion into and dwell time of the solvent in the cavity of beta-CyD, are studied with a hybrid QM/MM method. Comparison of MD simulations of beta-CyD in the gas phase and in water shows that the solvent reduces the flexibility of the structure framework, while the terminal hydroxyl groups become more flexible and are embedded in a network of hydrogen bonds. Our 160 ps MD simulations, provide enough sampling to discuss the dynamics of the water inside the cavity. The dwell time of the encapsulated water molecule has a wide distribution with a peak at 70 fs. Surprisingly, despite only the 17% difference between the "top" and "bottom" opening area of the beta-CyD cone, 64% of the water molecules enter the cavity through the slightly bigger "bottom" aperture.     

Structure and dynamics of La(III) in aqueous solution – An ab initio QM/MM MD approach

Ab initio QM/MM MD simulations have allowed to clarify some of the ambiguities arising from various studies on the hydrated La(III) ion. Both nine- and ten-coordinated hydrates co-exist and interchange in a dissociative process on the nano- or even subnanosecond scale, and thus much faster than any other trivalent main group or transition metal ions. The weak ion–ligand bond (53 N/m) supplies a reasonable explanation for it. The simulation results for La(III) are also compared to those for the isoelectronic ions Cs(I) and Ba(II) obtained by the same ab initio MD procedure, leading to conclusions on the influence of central ion charge on structural and dynamic properties of hydrate complexes.     

Stability of a novel hexapeptide, (Me)Arg-Lys-Pro-Trp-tert-Leu-Leu-OEt, with neurotensin activity, in aqueous solution and in the solid state

The stability and some physicochemical properties of a novel hexapeptide, (Me)Arg-Lys-Pro-Trp-tert-Leu-Leu-OEt (I), with neurotensin activity, were investigated. The degradation of I in aqueous solution was observed as a pseudo-first order reaction. By determining the degradation rate of I at various pH values, it was found that I was most stable at around pH 4. The activation energies of the degradation in aqueous solutions at pH 2.2, 6.1, 7.0 and 8.0 were 16.3, 22.2, 23.9 and 24.2 kcal/mol, respectively. The enzymatic hydrolysis of I was studied in vitro with a porcine liver esterase at 37 degrees C. The degradation of I in this system was observed as a pseudo-first order reaction. The degradation rate of I in the presence of the esterase was about 10000 times larger than the rate in a buffer solution. I in the solid state was stable under 65 degrees C and labilized by strong light and/or high humidity. The pKa1, pKa2 and pKa3 of I were 7.1, 10.0 and 11.3, respectively. The partition coefficients between n-octanol and the buffer solution at pH values ranging from 2 to 11 were measured. The partition coefficient increased with the increase of the pH value. But the value at pH 7.0 was 2.10 x 10(-2), which was very low. The solubility of I in aqueous solution was more than 10 mg/ml. From the results of the powder X-ray diffraction pattern, I in the solid state was found to be amorphous. The dissolution rates in the 1st and 2nd fluid of JPXI at 37 degrees C and 100 rpm were 19.4 and 9.0 mg/cm2.min, respectively.     

Structure and dynamics of solvated Sn(II) in aqueous solution: an ab initio QM/MM MD approach

Structural and dynamical properties of the hydrated Sn(II) ion have been investigated by ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations at double-zeta HF quantum mechanical level. The results indicate Sn(II)aq to be a rather peculiar, if not unique, case of a hydrated ion: four of its eight first-shell ligands do not take place in the otherwise frequent ligand-exchange processes, forming an approximately tetrahedral cage around the ion. The remaining ligands, however, exchange at a rate that is rather comparable to monovalent than divalent ions. This very surprising behavior of ligand exchange not yet observed in any previous simulation of over 30 hydrated metal ions is consistently confirmed by vibrational spectra, bond lengths, and a detailed analysis of the trajectories of the simulation.     

Structure and dynamics of the CrIII ion in aqueous solution: Ab initio QM/MM molecular dynamics simulation

Structural and dynamical properties of the Cr(III) ion in aqueous solution have been investigated using a combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation. The hydration structure of Cr(III) was determined in terms of radial distribution functions, coordination numbers, and angular distributions. The QM/MM simulation gives coordination numbers of 6 and 15.4 for the first and second hydration shell, respectively. The first hydration shell is kinetically very inert but by no means rigid and variations of the first hydration shell geometry lead to distinct splitting in the vibrational spectra of Cr(H(2)O)(6) (3+). A mean residence time of 22 ps was obtained for water ligands residing in the second hydration shell, which is remarkably shorter than the experimentally estimated value. The hydration energy of -1108 +/- 7 kcal/mol, obtained from the QM/MM simulation, corresponds well to the experimental hydration enthalpy value.     

Structure of small associates of glycyrrhizic acid with cholesterol in aqueous solution: Molecular dynamics simulation

In a recent work by Zelikman et al.(J. Struct. Chem., 2015, 56(1)), the molecular dynamics simulation of dimers of glycyrrhizic acid (GA) arising from the spontaneous collision of two GA molecules in water is performed. Several relatively stable dimer structures are found, and when a cholesterol molecule is inserted, associates are observed constituting a GA dimer with a cholesterol molecule “stuck” to it. Here, we simulate the associates consisting of three and four GA molecules and a cholesterol molecule. It appears that the cholesterol molecule, as a rule, also locates at the surface of the GA associate. Therewith, the trimers do not form any clear characteristic structures, as dimers do, and the tetramers can be two stuck dimers.     

Structure and excitation relaxation dynamics of dimethylanthracene dimer in a gamma-cyclodextrin nanocavity in aqueous solution

Dimethylanthracene (DMA), which exhibits almost no self-association in bulk organic solvents, forms a dimer and emits excimer-like fluorescence in a gamma-cyclodextrin nanocavity in a dilute aqueous solution. The 1Bb and 1La electronic transitions of the DMA dimer split by 2230 and 344 cm(-1), respectively, in a fluorescence excitation spectrum obtained with the excimer-like emission. From these energy splits, the structure of dimer in relation to a dielectric constant inside gamma-CD was discussed on the basis of atom-atom Lennard-Jones potential calculations including Coulombic interactions. Excitation relaxations of DMA in the presence of alpha-, beta-, and gamma-CDs in aqueous solutions were investigated by time-resolved fluorescence. The results suggest that both the hydrated and anhydrated species exist in the alpha- and gamma-CD complexes, while only the anhydrated species exists in the beta-CD complex.     

Conformational analysis of hydroxymatairesinol in aqueous solution with molecular dynamics

Molecular dynamics simulations were performed on the naturally occuring lignan hydroxymatairesinol (HMR) using the GROMACS software. The aim of this study was to explore the conformational behavior of HMR in aqueous solution adopting the TIP4P model. The topology of HMR was constructed by hand and HMR was modeled with the OPLS‐AA force field implemented in GROMACS. The five torsional angles in HMR were properly analyzed during the simulations. Correlations through certain patterns were observed between the angles. The determining property for the conformation preferred in aqueous solution was found to be the dipole moment and not the lowest energy in gas phase. The solvation effects on HMR was also studied by quantum chemical calculations applying the COnductorlike Screening MOdel (COSMO), the results of which were compared with results from a previous study using the Polarized Continuum Model (PCM). In the present work, COSMO was found to give more credible relative energies than PCM. © 2009 Wiley Periodicals, Inc., J Comput Chem, 2009     

Zwitterionic and anionic multinuclear pentacoordinate silicon(IV) complexes with bridging (R,R)-tartrato(4-) ligands and SiO5 skeletons: synthesis and reactivity in aqueous solution

Two nutrients in one molecule: A zwitterionic λ(5)Si,λ(5)Si'-disilicate (1) was synthesized and characterized. It contains ligands that exclusively derive from natural products ((R,R)-tartaric acid, choline). Hydrolysis of 1 yields 2, which shows a remarkable kinetic stability in water. Upon dissolution of 1 and 2 in water, the nutrients choline and orthosilicic acid are formed by hydrolysis.     

Structure,conformation in aqueous solution and antimicrobial activity of ulvan extracted from green seaweed Ulva reticulata

The aim of this study is to elucidate the structure and investigate the antimicrobial activity of an ulvan obtained by water extraction from green seaweed Ulva reticulata collected at Nha Trang sea of Vietnam by using IR, NMR, SEC-MALLS and SAXS methods. The ulvan is composed of rhamnose, galactose, xylose, manose and glucose (mole ratio Rha: Gal: Xyl: Man: Glu = 1:0.12:0.1:0.06:0.03), uronic acid (22.5%) and sulphate groups (17.6%). Chemically structural determination showed that the ulvan mainly composed of disaccharide [→4)β-D-GlcA(1→4)α-L-Rha3S-(1→]. The results from SAXS indicated that ulvan under study has a rod-like bulky chain conformation. Ulvan from U. reticulata showed high antimicrobial activity, with inhibition zone diameter of 20 mm against Enterobacter cloace and 18 mm against Escherichia coli.     

Long-range hydrogen-bond structure in aqueous solutions and the vapor-water interface

There is a considerable disagreement about the extent to which solutes perturb water structure. On the one hand, studies that analyse structure directly only show local structuring in a solute's first and possibly second hydration shells. On the other hand, thermodynamic and kinetic data imply indirectly that structuring occurs much further away. Here, the hydrogen-bond structure of water around halide anions, alkali cations, noble-gas solutes, and at the vapor-water interface is examined using molecular dynamics simulations. In addition to the expected perturbation in the first hydration shell, deviations from bulk behavior are observed at longer range in the rest of the simulation box. In particular, at the longer range, there is an excess of acceptors around halide anions, an excess of donors around alkali cations, weakly enhanced tetrahedrality and an oscillating excess and deficiency of donors and acceptors around noble-gas solutes, and enhanced tetrahedrality at the vapor-water interface. The structuring compensates for the short-range perturbation in water-water hydrogen bonds induced by the solute. Rather than being confined close to the solute, it is spread over as many water molecules as possible, presumably to minimize the perturbation to each water molecule.     

Structure of gum arabic in aqueous solution

Gum arabic, a natural polysaccharide derived from exudates of Acacia senegal and Acacia seyal trees, is a commonly used food hydrocolloid. The complex chemical structure of the gum has been widely studied revealing a multifraction material consisting mainly of a highly branched polysaccharide and a protein–polysaccharide complex (GAGP) as a minor component. This work investigates its mesoscopic structure in aqueous solution by small‐angle X‐ray and neutron scattering combined with cryotransmission electrons microscopy. Scattering measurements reveal an intricate shape composed of many spheroidal aggregates assigned to the polysaccharide with a small amount of larger coils. A scattering peak is observed at moderate to high concentrations, the spacing of which exhibits a c^?1/3 power law relation to polymer concentration (c). Upon addition of salt, this peak disappears, indicating its electrostatic nature. The large coils contribute a q^?2 power law at the low scattering vector (q) range. However, at low concentration in which the interaggregate peak is not observed, a q^?1 power law at the low q range indicates the possible existence of a fraction with a locally extended conformation. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 3265–3271, 2006     

Structure and dynamics of phosphate ion in aqueous solution: an ab initio QMCF MD study

A simulation of phosphate in aqueous solution was carried out employing the new QMCF MD approach which offers the possibility to investigate composite systems with the accuracy of a QMMM method but without the time consuming creation of solute-solvent potential functions. The data of the simulations give a clear picture of the hydration shells of the phosphate anion. The first shell consists of 13 water molecules and each oxygen of the phosphate forms in average three hydrogens bonds to different solvent molecules. Several structural parameters such as radial distribution functions and coordination number distributions allow to fully characterize the embedding of the highly charged phosphate ion in the solvent water. The dynamics of the hydration structure of phosphate are described by mean residence times of the solvent molecules in the first hydration shell and the water exchange rate.