Chain conformation and solvent partitioning in reversed-phase liquid chromatography: Monte Carlo simulations for various water/methanol concentrations

Many structural models for the stationary phase in reversed-phase liquid chromatography (RPLC) systems have been suggested from thermodynamic and spectroscopic measurements and theoretical considerations. To provide a molecular picture of chain conformation and solvent partitioning in a typical RPLC system, a particle-based Monte Carlo simulation study is undertaken for a dimethyl octadecyl (C(18)) bonded stationary phase on a model siliceous substrate in contact with mobile phases having different methanol/water concentrations. Following upon previous simulations for gas-liquid chromatography and liquid-liquid phase equilibria, the simulations are conducted using the configurational-bias Monte Carlo method in the Gibbs ensemble and the transferable potentials for phase equilibria force field. The simulations are performed for a chain surface density of 2.9 micromol/m(2), which is a typical bonded-phase coverage for mono-functional alkyl silanes. The solvent concentrations used here are pure water, approximately 33 and 67% mole fraction of methanol and pure methanol. The simulations show that the chain conformation depends only weakly on the solvent composition. Most chains are conformationally disordered and tilt away from the substrate normal. The interfacial width increases with increasing methanol content and, for mixtures, the solvent shows an enhancement of the methanol concentration in a 10 Angstrom region outside the Gibbs dividing surface. Residual surface silanol groups are found to provide hydrogen bonding sites that lead to the formation of substrate bound water and methanol clusters, including bridging clusters that penetrate from the solvent/chain interfacial region all the way to the silica surface.     

Structural modifications and adsorption capability of C18-silica/binary solvent interphases studied by EPR and RP-HPLC

The structure of the octadecyl (C18) chain layer attached to a silica surface in the presence of binary solvents (acetonitrile/water; methanol/water) was investigated by electron paramagnetic resonance (EPR) and reverse-phase high-performance liquid chromatography (RP-HPLC), using 4-hydroxy-2,2,6,6 tetramethylpiperidine-N-oxyl (Tempol) to mimic the behavior of pollutants with medium-low polarity. The computer-aided analysis of the EPR spectra provided structural and dynamical information of the probe and its environments which clarified the modifications of the chain conformations that occur at different solvent compositions. Capacity factors, k', were calculated as a function of the percentage of water/organic solvent (mobile phase), and the retention behavior of the C18-functionalized silica surface (stationary phase) was compared with the results obtained with EPR analysis under static conditions. In particular, EPR analysis showed that, at percentages of ACN equal or higher than 50%, the chain layer assume a quite ordered structure, whereas at percentages lower than 50% the chains tend to collapse and fold on the silica surface. In this latter situation, the hydrophobic net of the C18 chains strongly limits Tempol mobility. In methanol/water mixtures, both EPR and RP-HPLC analysis showed that the probe was adsorbed into a poorly ordered interphase. If the residual silanols at the silica surface were bonded to a sililating agent (endcapping), both EPR and RP-HPLC analysis showed a decreased adsorption of the probe with respect to the non-endcapped silica at the same mobile phase composition.     

Preferential solvation of some n-alkyl p-substituted benzoates in propylene glycol + water cosolvent mixtures

The preferential solvation parameters by propylene glycol (PG) of the homologous series of the n-alkyl esters of p-hydroxybenzoic and p-aminobenzoic acids, namely, methyl, ethyl, propyl and butyl derivatives, were derived from their thermodynamic properties of solution by means of the inverse Kirkwood–Buff integrals (IKBI) method. The preferential solvation parameters by the cosolvent, δx_1,3, are negative in water-rich mixtures, but positive in PG-rich mixtures, and the relative magnitudes of δx_1,3 are proportional to the alkyl chain length despite of the solvent involved in the preferential solvation, i.e. PG or water. It is possible that the hydrophobic hydration around aromatic ring and/or methylene groups plays a relevant role in the drugs solvation in water-rich mixtures. The more solvation by PG in PG-rich mixtures could be due mainly to polarity effects and acidic behaviour of the hydroxyl or amine groups of the compounds in front to the more basic solvent present in the mixtures, i.e. PG.     

Chain conformations and phase separation in polymer solutions with varying solvent quality

Molecular dynamics simulations are used to investigate the conformations of a single polymer chain, represented by the Kremer-Grest bead-spring model, in a solution with a Lennard-Jones liquid as the solvent when the interaction strength between the polymer and solvent is varied. Results show that when the polymer-solvent interaction is unfavorable, the chain collapses as one would expect in a poor solvent. For more attractive polymer-solvent interactions, the solvent quality improves and the chain is increasingly solvated and exhibits ideal and then swollen conformations. However, as the polymer-solvent interaction strength is increased further to be more than about twice the strength of the polymer-polymer and solvent-solvent interactions, the chain exhibits an unexpected collapsing behavior. Correspondingly, for strong polymer-solvent attractions, phase separation is observed in the solutions of multiple chains. These results indicate that the solvent becomes effectively poor again at very attractive polymer-solvent interactions. Nonetheless, the mechanism of chain collapsing and phase separation in this limit differs from the case with a poor solvent rendered by unfavorable polymer-solvent interactions. In the latter, the solvent is excluded from the domain of the collapsed chains while in the former, the solvent is still present in the pervaded volume of a collapsed chain or in the polymer-rich domain that phase separates from the pure solvent. In the limit of strong polymer-solvent attractions, the solvent behaves as a glue to stick monomers together, causing a single chain to collapse and multiple chains to aggregate and phase separate.     

Adsorption of interacting oligomers and polymers at an interface

We discuss in a qualitative way the physical background of a recently developed polymer adsorption theory, in which all the possible chain conformations for interacting chain molecules near an adsorbing interface are taken into account. Any conformation is described as a step-weighted random walk in a lattice. Each step is weighted according to a segmental weighting factor that contains the adsorption energy (for segments in contact with the surface), the entropy of mixing, and the attraction or repulsion between segments and solvent molecules. A suitable computing method is used to calculate the contribution of all chain conformations to the concentration profile, to the adsorbed amount, to the fraction of trains, loops and tails, to the layer thickness, etc. The theory is valid for any chain length and any concentration in the solution.Results for various chain lengths are given. Oligomers have a low affinity for the surface, whereas polymer adsorption isotherms are of the well known high affinity type. Three concentration regimes can be distinguished. In (extremely) dilute solutions the molecules on the surface adsorb as isolated chains (the Henry region).     

Influence of bonded-phase coverage in reversed-phase liquid chromatography via molecular simulation I. Effects on chain conformation and interfacial properties

Particle-based Monte Carlo simulations were employed to examine the effects of bonding density on molecular structure in reversed-phase liquid chromatography. Octadecylsilane stationary phases with five different bonding densities (1.6, 2.3, 2.9, 3.5, and 4.2 mumol/m(2)) in contact with a water/methanol (50/50 mol%) mobile phase were simulated at a temperature of 323 K. The simulations indicate that the alkyl chains become more aligned and form a more uniform alkyl layer as coverage is increased. However, this does not imply that the chains are highly ordered (e.g., all-trans conformation or uniform tilt angle), but rather exhibit a broad distribution of conformations and tilt angles at all bonding densities. At lower densities, significant amounts of the silica surface are exposed leading to an enhanced wetting of the stationary phase. At high densities, the solvent is nearly excluded from the bonded phase and persists only near the residual silanols. An enrichment in the methanol concentration and a disruption in the mobile phase's hydrogen bond network are observed at the interface as bonding density is increased.     

Importance of chirality and reduced flexibility of protein side chains: a study with square and tetrahedral lattice models

Side chains of amino acid residues are the determining factor that distinguishes proteins from other unstable chain polymers. In simple models they are often represented implicitly (e.g., by spin states) or simplified as one atom. Here we study side chain effects using two-dimensional square lattice and three-dimensional tetrahedral lattice models, with explicitly constructed side chains formed by two atoms of different chirality and flexibility. We distinguish effects due to chirality and effects due to side chain flexibilities, since residues in proteins are L residues, and their side chains adopt different rotameric states. For short chains, we enumerate exhaustively all possible conformations. For long chains, we sample effectively rare events such as compact conformations and obtain complete pictures of ensemble properties of conformations of these models at all compactness region. This is made possible by using sequential Monte Carlo techniques based on chain growth method. Our results show that both chirality and reduced side chain flexibility lower the folding entropy significantly for globally compact conformations, suggesting that they are important properties of residues to ensure fast folding and stable native structure. This corresponds well with our finding that natural amino acid residues have reduced effective flexibility, as evidenced by statistical analysis of rotamer libraries and side chain rotatable bonds. We further develop a method calculating the exact side chain entropy for a given backbone structure. We show that simple rotamer counting underestimates side chain entropy significantly for both extended and near maximally compact conformations. We find that side chain entropy does not always correlate well with main chain packing. With explicit side chains, extended backbones do not have the largest side chain entropy. Among compact backbones with maximum side chain entropy, helical structures emerge as the dominating configurations. Our results suggest that side chain entropy may be an important factor contributing to the formation of alpha helices for compact conformations.     

Solubility and preferential solvation of some non-steroidal anti-inflammatory drugs in methanol + water mixtures at 298.15 K

The equilibrium solubilities of naproxen (NAP), ketoprofen (KTP), and ibuprofen (IBP) in methanol + water binary mixtures at 298.15 K were determined and the preferential solvation parameters were derived by means of the inverse Kirkwood–Buff integrals (IKBI) method. These drugs are very sensitive to specific solvation effects. The preferential solvation parameters by methanol δx_1,3 are negative in water-rich mixtures but positive in compositions from 0.32 in mole fraction of methanol to pure methanol. It is conjecturable that in the former case the hydrophobic hydration around aromatic rings and/or methyl groups plays a relevant role in the solvation. The higher solvation by methanol in mixtures of similar co-solvent compositions and in methanol-rich mixtures could be explained in terms of the higher basic behaviour of this co-solvent interacting with the hydroxyl group of the drugs. Moreover, drug solubilities were correlated by using the modified nearly ideal binary solvent/Redlich–Kister model obtaining average percentage deviations (APDs) lower than 9.0%.     

Structure of triplex DNA in the gas phase

Extensive (more than 90 microseconds) molecular dynamics simulations complemented with ion-mobility mass spectrometry experiments have been used to characterize the conformational ensemble of DNA triplexes in the gas phase. Our results suggest that the ensemble of DNA triplex structures in the gas phase is well-defined over the experimental time scale, with the three strands tightly bound, and for the most abundant charge states it samples conformations only slightly more compact than the solution structure. The degree of structural alteration is however very significant, mimicking that found in duplex and much larger than that suggested for G-quadruplexes. Our data strongly supports that the gas phase triplex maintains an excellent memory of the solution structure, well-preserved helicity, and a significant number of native contacts. Once again, a linear, flexible, and charged polymer as DNA surprises us for its ability to retain three-dimensional structure in the absence of solvent. Results argue against the generally assumed roles of the different physical interactions (solvent screening of phosphate repulsion, hydrophobic effect, and solvation of accessible polar groups) in modulating the stability of DNA structures.     

Computational study on the properties and structure of methyl lactate

A theoretical study on the properties and molecular level structure of the very important green solvent methyl lactate is carried out in the gas phase and methanol and water solutions, with the solvent treated both explicitly and as a continuum. Torsional barriers giving rise to different conformers by rotation of the hydroxyl and methyl groups were analyzed using density functional theory (DFT) to establish the most stable conformer both in gas phase and solution. DFT computations on lactate dimers were also done to study short-range features, and the effect of the surrounding solvent on intra- and intermolecular hydrogen bonding was analyzed according to the polarizable continuum model approach. We have also studied lactate/water and lactate/methanol small clusters together with the corresponding binding energies. Moreover, classical molecular dynamics simulations (MD) were carried out to study medium- and large-range effects at lower computational cost. MD simulations at different pressure and temperature conditions on pure lactate were carried out, and mixtures with water and methanol of different compositions were also studied. Structural information, analyzed through the radial distribution functions, together with dynamic aspects of pure and mixed fluids were considered. The intramolecular hydrogen bonding ability of methyl lactate together with the possibility of homo- and hetero-intermolecular association determines the behavior of this molecule in pure fluids or in mixed.     

Phase separation in binary mixtures containing polymers: A quantitative comparison of single-chain-in-mean-field simulations and computer simulations of the corresponding multichain systems

We discuss a phenomenological, coarse-grained simulation scheme, single-chain-in-mean-field (SCMF) simulation, for investigating the kinetics of phase separation in dense polymer blends and mixtures of polymers and solvents. In the spirit of self-consistent-field calculations, we approximate the interacting multichain problem by that of a single chain in an external field, which, in turn, depends on the local densities of the components. To study the time evolution of the mixture, we perform an explicit Monte Carlo (MC) simulation of an ensemble of independent chains in the external field and periodically calculate the average densities and update the external field. Unlike dynamic self-consistent-field theory, these SCMF simulations do not assume that the chain conformations relax much more quickly than the density and incorporate the single-chain dynamics explicitly rather than via an Onsager coefficient. This allows us to study systems with large spatial inhomogeneities and dynamic asymmetries. To assess the accuracy and limitations of the simulation scheme, we compare the results of SCMF simulations using a discretized Edwards Hamiltonian with computer simulations of the corresponding multichain system for (1) the early stages of spinodal decomposition of a symmetric binary polymer blend in response to a quench from χN = 0.314 to χN = 5 (where χ is the Flory–Huggins parameter and N is the number of segments), for which the growth rate of composition fluctuations is compared with MC simulations of the bond fluctuation model and alternative dynamic self-consistent-field calculations, and (2) the evaporation of a solvent from a low-molecular-weight thin polymer film, for which a comparison is made with molecular dynamics (MD) simulations of a bead-necklace model with a monomeric solvent. In the latter case, the polymer conformations are extracted from MD simulations and modeled in the SCMF simulations by a discretized Edwards Hamiltonian augmented by a chain-bending potential. From the MD simulations of thin polymer films in equilibrium with its vapor, phase coexistence has been determined, and the second- and third-order virial coefficients in the SCMF simulations have been adjusted accordingly. Finally, MD simulations of bulk solutions of a polymer and a solvent over a range of compositions, as well as the pure solvent at various densities, have been performed to determine self-diffusion coefficients that enter the SCMF simulations in the form of density-dependent segmental mobilities. A comparison of the polymer and solvent profiles in a thin film as a function of time and the fraction of the solvent evaporating from a solvent-swollen film, as obtained from MD simulations and parameterized SCMF simulations, shows satisfactory agreement for this simple mapping procedure. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 934–958, 2005     

Conformational preferences of proline oligopeptides

A conformational study on the terminally blocked proline oligopeptides, Ac-(Pro)(n)()-NMe(2) (n = 2-5), is carried out using the ab initio Hartree-Fock level of theory with the self-consistent reaction field method in the gas phase and in solutions (chloroform, 1-propanol, and water) to explore the preference and transition between polyproline II (PPII) and polyproline I (PPI) conformations depending on the chain length, the puckering, and the solvent. The mean differences in the free energy per proline of the up-puckered conformations relative to the down-puckered conformations for both diproline and triproline increases for the PPII-like conformations and decreases for the PPI-like conformations as the solvent polarity increases. These calculated results indicate that the PPII-like structures have preferentially all-down puckerings in solutions, whereas the PPI-like structures have partially mixed puckerings. The free energy difference per proline residue between the PPII- and PPI-like structures decreases as the proline chain becomes longer in the gas phase but increases as the proline chain becomes longer in solutions and the solvent polarity increases. In particular, our calculated results indicate that each of the proline oligopeptides can exist as an ensemble of conformations with the trans and cis peptide bonds in solutions, although the PPII-like structure with all-trans peptide bonds is dominantly preferred, which is reasonably consistent with the previously observed results. In diproline Ac-(Pro)(2)-NMe(2), the rotational barrier to the cis-to-trans isomerization for the first prolyl peptide bond increases as the solvent polarity increases, whereas the rotational barrier for the second prolyl peptide bond does not show the monotonic increase as the solvent polarity increases. When the rotational barriers for these two prolyl peptide bonds were compared, it could be deduced that the conformational transition from PPI with the cis peptide bond to PPII with the trans peptide bond is initiated at the C-terminus and proceeds to the N-terminus in water. This is consistent with the results from NMR experiments on polyproline in D(2)O but opposite to the results from enzymatic hydrolysis kinetics experiments on polyproline.     

Transitions of tethered polymer chains: a simulation study with the bond fluctuation lattice model

A polymer chain tethered to a surface may be compact or extended, adsorbed or desorbed, depending on interactions with the surface and the surrounding solvent. This leads to a rich phase diagram with a variety of transitions. To investigate these transitions we have performed Monte Carlo simulations of a bond fluctuation model with Wang-Landau and umbrella sampling algorithms in a two-dimensional state space. The simulations' density-of-states results have been evaluated for interaction parameters spanning the range from good- to poor-solvent conditions and from repulsive to strongly attractive surfaces. In this work, we describe the simulation method and present results for the overall phase behavior and for some of the transitions. For adsorption in good solvent, we compare with Metropolis Monte Carlo data for the same model and find good agreement between the results. For the collapse transition, which occurs when the solvent quality changes from good to poor, we consider two situations corresponding to three-dimensional (hard surface) and two-dimensional (very attractive surface) chain conformations, respectively. For the hard surface, we compare tethered chains with free chains and find very similar behavior for both types of chains. For the very attractive surface, we find the two-dimensional chain collapse to be a two-step transition with the same sequence of transitions that is observed for three-dimensional chains: a coil-globule transition that changes the overall chain size is followed by a local rearrangement of chain segments.     

The effects of chain length,embedded polar groups,pressure, and pore shape on structure and retention in reversed-phase liquid chromatography: Molecular-level insights from Monte Carlo simulations

Particle-based simulations using the configurational-bias and Gibbs ensemble Monte Carlo techniques are carried out to probe the effects of various chromatographic parameters on bonded-phase chain conformation, solvent penetration, and retention in reversed-phase liquid chromatography (RPLC). Specifically, we investigate the effects due to the length of the bonded-phase chains (C₁₈, C₈, and C₁), the inclusion of embedded polar groups (amide and ether) near the base of the bonded-phase chains, the column pressure (1, 400, and 1000 atm), and the pore shape (planar slit pore versus cylindrical pore with a 60 Å diameter). These simulations utilize a bonded-phase coverage of 2.9 μ$\mu$mol/m²and a mobile phase containing methanol at a molfraction of 33% (about 50% by volume). The simulations show that chain length, embedded polar groups, and pore shape significantly alter structural and retentive properties of the model RPLC system, whereas the column pressure has a relatively small effect. The simulation results are extensively compared to retention measurements. A molecular view of the RPLC retention mechanism emerges that is more complex than can be inferred from thermodynamic measurements.     

Cages, baskets, ladders, and tubes: conformational studies of polyhedral oligomeric silsesquioxanes

The conformational flexibility of a series of cage, basket, ladder, and tube polyhedral oligomeric silsesquioxanes (POSS) has been examined using the Low Mode:Monte Carlo conformational search method in conjunction with the MM3/GBSA(CHCl3) surface. An ensemble of low energy structures was generated and used to explore the molecular shape and flexibility of each system. The results indicate that, except for the ladder molecule, the incompletely condensed systems that are studied are relatively rigid. Even in cases where the molecule is able to adopt numerous low energy conformations, the overall shape remains cage-like and the conformations differ only by small angles or substituent orientations. The ladder molecule is the most flexible and this ensemble clusters into two families: one that is cage-like and the other that is more open and ladder-like. The conformational flexibilities in the gas and solvent phases, as approximated using the GBSA continuum solvent model, are very similar.     

Effect of temperature on pH measurements and acid-base equilibria in methanol-water mixtures

The knowledge of the acid-base equilibria in water-solvent mixtures of both common buffers and analytes is necessary in order to predict their retention as function of pH, solvent composition and temperature. This paper describes the effect of temperature on acid-base equilibria in methanol-water solvent mixtures commonly used as HPLC mobile phases. We measured the delta-correction parameter (delta = sw pH - ss pH = Ej - log sw(gamma)oh) between two pH scales: pH measured in the solvent concerned and referred to the same standard state, ss pH, and the pH measured in that solvent mixture but referred to water as standard state, sw pH, for several methanol compositions in the temperature range of 20-50 degrees C. These determinations suggest that the delta-term depends only on composition of the mixture and on temperature. In water-rich mixtures, for which methanol is below 40% (w/w), delta-term seems to be independent of temperature, within the experimental uncertainties, whereas for methanol content larger than 50% (w/w) the delta-correction decreases as temperature increases. We have attributed this decrease to a large increase in the medium effect when mixtures have more than 50% methanol. The pKa of five weak electrolytes of different chemical nature in 50% methanol-water at 20-50 degrees C are presented: the effect of temperature on pKa was large for amines, pyridine and phenol, but almost no dependence was found for benzoic acid. This indicates that buffers can play a critical role in affecting retention and selectivity in HPLC at temperatures far from 25 degrees C, particularlyfor co-eluted solutes.     

Radical processes induced in poly(siloxaneurethaneureas) by ionising radiation

The effect of ionizing radiation on poly(siloxaneurethaneureas), comprising the soft phase of poly(dimethylsiloxane) chains and hard urethane segments, was examined by electron paramagnetic resonance (EPR) spectroscopy and gas chromatography (GC). It was found that radical processes in the investigated polymers were determined predominantly by polysiloxane segments. Dehydrogenation proceeded mainly in the terminal groups of dimethylsiloxane sequences, forming methylene radicals, whereas abstraction of methyl group dominated in inner fragments of the polysiloxane chain. However, upon irradiation no change in glass transition temperature of polysiloxane segments was detected by DSC.     

Computer simulation study of the global phase behavior of linear rigid Lennard-Jones chain molecules: comparison with flexible models

The global phase behavior (i.e., vapor-liquid and fluid-solid equilibria) of rigid linear Lennard-Jones (LJ) chain molecules is studied. The phase diagrams for three-center and five-center rigid model molecules are obtained by computer simulation. The segment-segment bond lengths are L = sigma, so that models of tangent monomers are considered in this study. The vapor-liquid equilibrium conditions are obtained using the Gibbs ensemble Monte Carlo method and by performing isobaric-isothermal NPT calculations at zero pressure. The phase envelopes and critical conditions are compared with those of flexible LJ molecules of tangent segments. An increase in the critical temperature of linear rigid chains with respect to their flexible counterparts is observed. In the limit of infinitely long chains the critical temperature of linear rigid LJ chains of tangent segments seems to be higher than that of flexible LJ chains. The solid-fluid equilibrium is obtained by Gibbs-Duhem integration, and by performing NPT simulations at zero pressure. A stabilization of the solid phase, an increase in the triple-point temperature, and a widening of the transition region are observed for linear rigid chains when compared to flexible chains with the same number of segments. The triple-point temperature of linear rigid LJ chains increases dramatically with chain length. The results of this work suggest that the fluid-vapor transition could be metastable with respect to the fluid-solid transition for chains with more than six LJ monomer units.     

Properties of Star-Branched Polymer Chains Near a Surface

We considered two model systems of star-branched polymers near an impenetrable surface. The model chains were constructed on a simple cubic lattice. Each star polymer consisted of f = 3 arms of equal length and the total number of segments was up to 799. The excluded volume effect was included into these models only and therefore the system was studied at good solvent conditions. In the first model system polymer chain was terminally attached with one arm to the surface. The grafted arm could slide along the surface. In the second system the star-branched chain was adsorbed on the surface and the strength of adsorption was were varied. The simulations were performed using the dynamic Monte Carlo method with local changes of chain conformations. The internal and local structures of a polymer layer were determined. The lateral diffusion and internal mobility of star-branched chains were studied as a function of strength of adsorption and the chain length. The lateral diffusion and internal mobility of star-branched chains were studied as a function of strength of adsorption and the chain length. It was shown that the behavior of grafted and weakly adsorbed chains was similar to that of a free three-dimensional polymer, while the strongly adsorbed chains behave as a two-dimensional system.