Solvation of the Whelk-O1 chiral stationary phase: a molecular dynamics study

Density functional theory calculations and molecular dynamics simulations are employed to explore the solvation of the Whelk-O1 chiral stationary phase. First, a semi-flexible representation of the Whelk-O1 selective molecule is extracted from an extensive series of B3LYP/6-311+ G(2d,p) calculations. The resulting model is used to build a chiral surface, including end-caps, for molecular dynamics study of the interface between solvent and Whelk-O1. Three solvent environments in common use for Whelk-O1 HPLC have been examined: a normal-phase solvent of n-hexane/2-propanol; a reversed-phase solvent of water/methanol; and a supercritical solvent of CO(2) and methanol. In each case, we analyze the interface with an emphasis on solvent composition and solvent hydrogen bonding to the Whelk-O1 selector.     

水、甲醇和乙醇液体微结构性质的Car-Parrinello 分子动力学模拟

采用Car-Parrinello 分子动力学(CPMD)方法分别研究了水、甲醇和乙醇的液体微结构性质.研究结果显示:在水、甲醇和乙醇三个体系中O…O径向分布函数曲线的第一个峰位置分别为0.278、0.276 和0.275nm; O…H径向分布函数曲线的第一个峰位置分别为0.178、0.176和0.177 nm.表明基团(氢原子、甲基、乙基)的差异对O…O第一个峰的位置影响很小.但基团的差异对径向分布函数峰高的影响却很显著,由水到乙醇第一个峰的高度逐渐变高.空间分布函数表明氧原子和氢原子在溶剂分子周围有取向地分布,这与径向分布函数所表现出尖锐的第一个峰相一致.氢键分布分析显示,水、甲醇和乙醇的平均氢键数分别为3.62、1.99 和1.87,表明水形成了网状氢键结构,而甲醇、乙醇形成链状氢键结构.     

水和甲醇混合溶剂氢键相互作用及对高分子链溶解能力的理论研究

用密度泛函理论对水和甲醇混合溶剂体系的氢键结构进行了详细研究.通过构象和频率分析发现在水团簇中五聚体和六聚体环状结构最为稳定,同时发现一个全新的特征,即甲醇分子能与水五聚体和六聚体形成双氢键.根据各相互作用的稳定化能,分析了水和甲醇混合溶剂对PNIPAM溶解能力的影响,并对实验现象给予了合理解释.     

Elucidating Solvent Effects on Strong Intramolecular Hydrogen Bond: DFT-MD Study of Dibenzoylmethane in Methanol Solution

The dynamic aspect of solvation plays a crucial role in determining properties of strong intramolecular hydrogen bonds since solvent fluctuations modify instantaneous hydrogen-bonded proton transfer barriers. Previous studies pointed out that solvent-solute interactions in the first solvation shell govern the position of the proton but the ability of the electric field due to other solvent molecules to localize the proton remains an important issue. In this work, we examine the structure of the O−H⋅⋅⋅O intramolecular hydrogen bond of dibenzoylmethane in methanol solution by employing density functional theory-based molecular dynamics and quantum chemical calculations. Our computations showed that homogeneous electric fields with intensities corresponding to those found in polar solvents are able to considerably alter the proton transfer barrier height in the gas phase. In methanol solution, the proton position is correlated with the difference in electrostatic potentials on the oxygen atoms of dibenzoylmethane even when dibenzoylmethane-methanol hydrogen bonding is lacking. On a timescale of our simulation, the hydrogen bonding and solvent electrostatics tend to localize the proton on different oxygen atoms. These findings provide an insight into the importance of the solvent electric field on the structure of a strong intramolecular hydrogen bond.     

Solvation of the N-(1-Phenylethyl)-N'-[3-(triethoxysilyl)propyl]-urea chiral stationary phase in mixed alcohol/water solvents

A theoretical and experimental study of alcohol/water and alcohol/alcohol solvent mixtures near a surface of N-(1-phenylethyl)-N'-[3-(triethoxysilyl)propyl]-urea (PEPU), a Pirkle-type chiral stationary phase, is presented. Molecular dynamics simulations are performed at room temperature for water/methanol, water/1-propanol, water/2-propanol, and methanol/1-propanol solvent mixtures confined between two PEPU surfaces. The interface was also prepared experimentally by attaching the PEPU molecules to atomic force microscopy tips and oxidized Si(111) substrates. Chemical force spectrometric measurements between such PEPU-terminated tips and samples were taken in the solvent mixtures, and the results are compared to the molecular dynamics study. We find that the extent of hydrogen bonding at the surface is the dominant contributor to the measured forces.     

Solvation of perfluorooctane and octane in water, methanol, acetonitrile, and aqueous mixtures of methanol and acetonitrile

Molecular dynamics simulations are used to examine the local solvation structure of single octane and perfluorooctane molecules in liquid water, methanol, acetonitrile, and aqueous mixtures of methanol and acetonitrile. The motivation is to obtain baseline information about the solvation of perfluorooctane by liquids used as the mobile phase in liquid chromatography and how it differs from the solvation of octane. While octane is uniformly solvated by both water and the second component, perfluorooctane is solvated by methanol and acetonitrile with the exclusion of water from the first solvation layer when the solvent is a mixture.     

Theoretical study of the relative stability of rotational conformers of alpha and beta-D-glucopyranose in gas phase and aqueous solution

The alpha-beta anomer energy difference and the stability of 10 rotamers of counterclockwise D-glucopyranose were studied in vacuo and in aqueous solution at the B3LYP/6-31+G(d,p) level. To obtain the solute charge distribution and the solvent structure around it, we used the averaged solvent electrostatic potential from molecular dynamics method, ASEP/MD, which alternates molecular dynamics and quantum mechanics calculations in an iterative procedure. The main characteristics of the anomeric equilibrium, both in vacuo and in solution, are well reproduced. The relative stability of the different anomers is related to the availability of the free pairs of electrons in the anomeric oxygen to interact with the water molecules. The influence of solvation in the conformer equilibrium is also analyzed.     

The effect of solvent polarity on the molecular surface properties and adhesion of Escherichia coli

The elasticity and molecular surface characteristics of Escherichia coli JM109 were investigated via atomic force microscopy (AFM) in solvents expressing different polarities. The nature of bacterial adhesion and surface characteristics was probed in formamide, water, and methanol, with dielectric constants of 111, 80, and 33, respectively. Solvent polarity affected the elasticity of the bacterium, the conformation of the cell surface biopolymers, the height of the surface biopolymers, and measured adhesion forces between the bacterium and silicon nitride. By applying the Hertz model to force-indentation data, we determined that the Young's modulus was greatest in the least polar solvent, with values of 182 +/- 34.6, 12.8 +/- 0.1, and 0.8 +/- 0.3 MPa in methanol, water, and formamide, respectively. The thickness of the biopolymer brush layer on the bacterial surface was quantified using a steric model, and these values increased as polarity increased, with values of 27, 93, and 257 nm in methanol, water, and formamide, respectively. The latter results suggest that highly polar conditions favor extension of the biopolymer brush layer. Cross-sectional analysis performed on tapping mode images of the bacterial cells in methanol, water, and formamide further supported this hypothesis. The image height values are larger, since the image analysis measures the height of the bacterium and the polymer layer, but the trend with respect to solvent polarity was the same as was obtained from the steric model of the brush length. Measured adhesion forces scaled inversely with solvent polarity, with greatest adhesion observed in the least polar solvent, methanol. The combined conformational changes to the bacterial surface and biopolymer layer result in different presentations of macromolecules to a substrate surface, and therefore affect the adhesion forces between the bacterial molecules and the substrate. These results suggest that polarity of the solvent environment can be manipulated as a design parameter to control or modify the bacterial adhesion process.     

Relation between solvent and protein dynamics as studied by dielectric spectroscopy

We present results obtained by dielectric spectroscopy in wide frequency (10(-2)-10(9) Hz) and temperature ranges on human hemoglobin in the three different solvents water, glycerol, and methanol, at a solvent level of 0.8 g of solvent/g of protein. In this broad frequency region, there are motions on several time-scales in the measured temperature range (110-370 K for water, 170-410 K for glycerol, and 110-310 K for methanol). For all samples, the dielectric data shows at least four relaxation processes, with frequency dependences that are well described by the Havriliak-Negami or Cole-Cole functions. The fastest and most pronounced process in the dielectric spectra of hemoglobin in glycerol and methanol solutions is similar to the alpha-relaxation of the corresponding bulk solvent (but shifted to slower dynamics due to surface interactions). For water solutions, however, this process corresponds to earlier results obtained for water confined in various systems and it is most likely due to a local beta-relaxation. The slowing down of the glycerol and methanol relaxations and the good agreement with earlier results on confined water show that this process is affected by the interaction with the protein surface. The second fastest process is attributed to motions of polar side groups on the protein, with a possible contribution from tightly bound solvent molecules. This process is shifted to slower dynamics with increasing solvent viscosity, and it shows a crossover in its temperature dependence from Arrhenius behavior at low temperatures to non-Arrhenius behavior at higher temperatures where there seems to be an onset of cooperativity effects. The origins of the two slowest relaxation processes (visible at high temperatures and low frequencies), which show saddlelike temperature dependences for the solvents water and methanol, are most likely due to motions of the polypeptide backbone and an even more global motion in the protein molecule.     

The Solvent‐Dependent Shift of the Amide I Band of a Fully Solvated Peptide as a Local Probe for the Solvent Composition in the Peptide/Solvent Interface

We determine the shift and line shape of the amide I band of a model AK peptide from molecular dynamics (MD) simulations of the peptide dissolved in methanol/water mixtures with varying composition. The IR spectra are determined from a transition dipole coupling exciton model. A simplified empirical model Hamiltonian is employed, which takes into account both the effect of hydrogen bonding and the intramolecular vibrational coupling. We consider a single isolated AK peptide in a mostly helical conformation, while the solvent is represented by 2600 methanol or water molecules, simulated for a pressure of 1 bar and a temperature of 300 K. Over the course of the simulations, minor reversible conformational changes at the termini are observed, which are found to only slightly affect the calculated spectral properties. Over the entire composition range, which varies from pure water to the pure methanol solvent, a monotonous shift towards higher frequency of the IR amide I band of about 8 wavenumbers is observed. This shift towards higher frequency is comparable to the shift found in preliminary experimental data also presented here on the amide I′ band. The shift is found to be caused by two counter‐compensating effects. An intramolecular red shift of about 1.2 wavenumbers occurs, due to stronger intramolecular hydrogen bonding in a methanol‐rich environment. Dominating, however, is the intermolecular solvent‐dependent shift towards higher frequency of about 10 wavenumbers, which is attributed to the less effective hydrogen‐bond‐donor capabilities of methanol compared to water. The importance of the solvent contribution to the IR shift, as well as the significantly different hydrogen formation capabilities of water and methanol, makes the amide I band sensitive to composition changes in the local environment close to the peptide/solvent interface. This allows, in principle, an experimental determination of the composition of the solvent in close proximity to the peptide surface. For the AK peptide case, we observe at low methanol concentrations a significantly enhanced methanol concentration at the peptide/solvent interface, supposedly promoted by the partially hydrophobic character of the AK peptide’s solvent‐accessible surface.     

The Solvent Quality of Water for Poly(N-isopropylacrylamide) in the Collapsed State: Implications from Single-molecule Studies

Both of temperature(in water) and composition(in the water/methanol mixed solvent) can induce the coil-toglobule transition of poly(N-isopropylacrylamide)(PNIPAM). The atomic force microscope(AFM) based single molecule force spectroscopy(SMFS) has been exploited to investigate the interactions between the polymer chain and solvent at the single-molecule level. It is found that the single-chain mechanics of PNIPAM show a remarkable dependence on the two external stimuli. A confusing experimental result is that all the force-extension(F-E) curves of unfolding an individual PNIPAM globule present a feature of elastic(monotonically increasing force) stretching but not plateau(constant force) stretching predicted by theory. In this article, we clarify that the presence of the interior solvent molecules in the single-chain globule is the origin of the discrepancy between the F-E curves obtained from theory and experiment. Although both of the external stimuli do tend to lower the solvent quality for PNIPAM, water and the water/methanol mixed solvent will never be the strongly poor solvent for PNIPAM, even at the worst condition.     

Coordination-chemistry control of proton conductivity in the iconic metal-organic framework material HKUST-1

HKUST-1, a metal-organic framework (MOF) material containing Cu(II)-paddlewheel-type nodes and 1,3,5-benzenetricarboxylate struts, features accessible Cu(II) sites to which solvent or other desired molecules can be intentionally coordinated. As part of a broader investigation of ionic conductivity in MOFs, we unexpectedly observed substantial proton conductivity with the "as synthesized" version of this material following sorption of methanol. Although HKUST-1 is neutral, coordinated water molecules are rendered sufficiently acidic by Cu(II) to contribute protons to pore-filling methanol molecules and thereby enhance the alternating-current conductivity. At ambient temperature, the chemical identities of the node-coordinated and pore-filling molecules can be independently varied, thus enabling the proton conductivity to be reversibly modulated. The proton conductivity of HKUST-1 was observed to increase by ~75-fold, for example, when node-coordinated acetonitrile molecules were replaced by water molecules. In contrast, the conductivity became almost immeasurably small when methanol was replaced by hexane as the pore-filling solvent.     

Multinuclear NMR investigations of the oxygen, water, and hydroxyl environments in sodium hexaniobate

Solid-state (1)H, (17)O MAS NMR, (1)H-(93)Nb TRAPDOR NMR, and (1)H double quantum 2D MAS NMR experiments were used to characterize the oxygen, water, and hydroxyl environments in the monoprotonated hexaniobate material, Na(7)[HNb(6)O(19)].15H(2)O. These solid-state NMR experiments demonstrate that the proton is located on the bridging oxygen of the [Nb(6)O(19)](8-) cluster. The solid-state NMR results also show that the NbOH protons are spatially isolated from similar protons, but undergo proton exchange with the water species located in the crystal lattice. On the basis of double quantum (1)H MAS NMR measurements, it was determined that the water species in the crystal lattice have restricted motional dynamics. Two-dimensional (1)H-(17)O MAS NMR correlation experiments show that these restricted waters are preferentially associated with the bridging oxygen. Solution (17)O NMR experiments show that the hydroxyl proton is also attached to the bridging oxygen for the compound in solution. In addition, solution (17)O NMR kinetic studies for the hexaniobate allowed the measurement of relative oxygen exchange rates between the bridging, terminal, and hydroxyl oxygen and the oxygen of the solvent as a function of pH and temperature. These NMR experiments are some of the first investigations into the proton location, oxygen and proton exchange processes, and water dynamics for a base stable polyoxoniobate material, and they provide insight into the chemistry and reactivity of these materials.     

The solvent quality of water for poly(<Emphasis Type="Italic">N</Emphasis>-isopropylacrylamide) in the collapsed state: Implications from single-molecule studies

Both of temperature (in water) and composition (in the water/methanol mixed solvent) can induce the coil-to-globule transition of poly(N-isopropylacrylamide) (PNIPAM). The atomic force microscope (AFM) based single molecule force spectroscopy (SMFS) has been exploited to investigate the interactions between the polymer chain and solvent at the single-molecule level. It is found that the single-chain mechanics of PNIPAM show a remarkable dependence on the two external stimuli. A confusing experimental result is that all the force-extension (F-E) curves of unfolding an individual PNIPAM globule present a feature of elastic (monotonically increasing force) stretching but not plateau (constant force) stretching predicted by theory. In this article, we clarify that the presence of the interior solvent molecules in the single-chain globule is the origin of the discrepancy between the F-E curves obtained from theory and experiment. Although both of the external stimuli do tend to lower the solvent quality for PNIPAM, water and the water/methanol mixed solvent will never be the strongly poor solvent for PNIPAM, even at the worst condition.     

An in-situ multiple internal reflection Fourier transform infrared spectroscopic (MIRFTIRS) investigation of the growth mechanism of polyphenylene during electrooxidation of biphenyl in methylene dichloride

The MIRFTIRS method has been applied to study in-situ the growth mechanism of polyphenylene films during electrooxidation of biphenyl in methylene dichloride on platinum. When the electrode is polarized at 1.5 V vs. Ag/AgCl, a band at 1600 cm⁻¹ is observed, indicating a quinoid structure characteristic of the bipolaron state. The band disappears at potentials of 0 or −1 V. The polymer is in a neutral state but a residual concentration of NBu₄BF₄ salt remains in the film matrix.An important structural difference is observed between inner layers detected by MIRFTIRS (thickness from the electrode surface <1 μm) and outer layers of films analysed by ex-situ IR spectroscopy. The inner layers are formed by short and crosslinked chains, while the outer layers consist of longer and more linear chains.The solvent and residual water adsorb reversibly on the polymer, by Lewis acid-base interactions. When the polymer is in the oxidized state, the solvent of acidic character is removed from the polymer surface while adsorption of the more basic residual water is observed. The opposite is observed when the polymer is in the neutral state: the solvent enters again into the polymer and the adsorbed water is expelled from the surface.     

Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water

In this article, we analyze the folding dynamics of an all-atom model of a polyphenylacetylene (pPA) 12-mer in explicit solvent for four common organic and aqueous solvents: acetonitrile, chloroform, methanol, and water. The solvent quality has a dramatic effect on the time scales in which pPA 12-mers fold. Acetonitrile was found to manifest ideal folding conditions as suggested by optimal folding times on the order of approximately 100-200 ns, depending on temperature. In contrast, chloroform and water were observed to hinder the folding of the pPA 12-mer due to extreme solvation conditions relative to acetonitrile; chloroform denatures the oligomer, whereas water promotes aggregation and traps. The pPA 12-mer in a pure methanol solution folded in approximately 400 ns at 300 K, compared relative to the experimental 12-mer folding time of approximately 160 ns measured in a 1:1 v/v THF/methanol solution. Requisite in drawing the aforementioned conclusions, analysis techniques based on Markov state models are applied to multiple short independent trajectories to extrapolate the long-time scale dynamics of the 12-mer in each respective solvent. We review the theory of Markov chains and derive a method to impose detailed balance on a transition-probability matrix computed from simulation data.     

Nanocharacterization and nanofabrication of a Nafion thin film in liquids by atomic force microscopy

We demonstrated the nanocharacterization and nanofabrication of a Nafion thin film using atomic force microscopy (AFM). AFM images showed that the Nafion molecules form nanoclusters in water, in 5% methanol, and in acetic acid. Young's modulus E of a Nafion film was estimated by sequential force curve measurements in water and in 5% methanol on one sample surface. Ewater/E5% methanol was 1.75 +/- 0.40, so the film was much softer in 5% methanol than in water. Even when solvent was replaced from 5% methanol to water, Young's modulus was not recovered soon. We showed the first example of the mechanical properties of a Nafion film on the nanoscale. Furthermore, we succeeded in fabricating 3D nanostructures on a Nafion surface by AFM nanolithography in liquids. Our results showed the new potential of the AFM nanolithography of a polymer film by softening the molecules in liquids.     

Effect of the environment on the stability of surfactant–polypeptide self‐assembled complexes: Molecular dynamics simulations of stoichiometric complexes formed by N‐dodecyltrimethylammonium and poly(α,L‐glutamate) in chloroform,methanol, and water

A series of molecular dynamics simulations have been performed to study the supramolecular structure of self‐assembled complexes formed by N‐dodecyltrimethylammonium cations and the synthetic polypeptide poly(α,L ‐glutamate). The influence of the type of solvent has been investigated, considering explicit environments of chloroform, water, and methanol on a stoichiometric complex containing 15 residues. In chloroform, the complex stabilizes in a regular structure: the polypeptide adopts an α‐helix conformation that is regularly surrounded by surfactant molecules to form electrostatic interactions through a multiple interaction pattern. However, this structure destabilizes in methanol and water: (a) the α‐helix unfolds in the two solvents and (b) the electrostatic links between the surfactant molecules and the polyanion are disrupted in aqueous solution, although these interactions are still preserved in methanol. The role of the solvent environment in stabilizing or destabilizing the polypeptide secondary structure, the organization of the surfactant molecules, and predominantly the surfactant–polypeptide supramolecular organization is discussed in detail. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 1122–1133, 2006     

Mesoscopic description of solvent effects on polymer dynamics

Solvent effects on polymer dynamics and structure are investigated using a mesoscopic solvent model that accounts for hydrodynamic interactions among the polymer beads. The simulation method combines molecular dynamics of the polymer chain, interacting with the solvent molecules through intermolecular forces, with mesoscopic multiparticle collision dynamics for the solvent molecules. Changes in the intermolecular forces between the polymer beads and mesoscopic solvent molecules are used to vary the solvent conditions from those for good to poor solvents. Polymer collapse and expansion dynamics following changes in solvent conditions are studied for homopolymer and block copolymer solutions. The frictional properties of polymers are also investigated.