Atomistic Details of Peptide Reversed-Phase Liquid Chromatography from Molecular Dynamics Simulations

Peptide separations by reversed-phase liquid chromatography (RPLC) are an integral part of bottom-up proteomics. These separations typically employ C18 columns with water/acetonitrile gradient elution in the presence of formic acid. Despite the widespread use of such workflows, the exact nature of peptide interactions with the stationary and mobile phases is poorly understood. Here, we employ microsecond molecular dynamics (MD) simulations to uncover details of peptide RPLC. We examined two tryptic peptides, a hydrophobic and a hydrophilic species, in a slit pore lined with C18 chains that were grafted onto SiO₂ support. Our simulations explored peptide trapping, followed by desorption and elution. Trapping in an aqueous mobile phase was initiated by C18 contacts with Lys butyl moieties. This was followed by extensive anchoring of nonpolar side chains (Leu/Ile/Val) in the C18 layer. Exposure to water/acetonitrile triggered peptide desorption in a stepwise fashion; charged sites close to the termini were the first to lift off, followed by the other residues. During water/acetonitrile elution, both peptides preferentially resided close to the pore center. The hydrophilic peptide exhibited no contacts with the stationary phase under these conditions. In contrast, the hydrophobic species underwent multiple transient Leu/Ile/Val binding interactions with C18 chains. These nonpolar interactions represent the foundation of differential peptide retention, in agreement with the experimental elution behavior of the two peptides. Extensive peptide/formate ion pairing was observed in water/acetonitrile, particularly at N-terminal sites. Overall, this work uncovers an unprecedented level of RPLC molecular details, paving the way for MD simulations as a future tool for improving retention prediction algorithms and for the design of novel column materials.

Application of a modified linear solvation energy relationship (LSER) model to retention on a butylimidazolium-based column for high performance liquid chromatography

Previously, a new HPLC stationary phase based on n-butylimidazolium bromide was investigated using a linear solvation energy relationship (LSER) to systematically evaluate the intermolecular interactions between 32 test solutes and the stationary phase. The results and further comparisons with conventional reversed phase systems revealed that retention properties are similar to phenyl phases in both methanol/water and acetonitrile/water mixtures. In this work, the LSER model is extended by including the degree of ionization molecular descriptor, D, which takes into account the pK(a) of ionizable analytes and the pH of the mobile phase. The D molecular descriptor has been further divided into D(+) and D(-) components that separately account for the ionization of basic and acidic solutes, respectively. This is the first study where the ionization terms for weakly acidic solutes and weakly basic solutes have been separated. LSER results obtained with the expanded solute set with and without the inclusion of the D(+) and D(-) solute descriptors were compared. The improved correlation and standard error obtained for the expanded test set in the presence and absence of the D(+) and D(-) descriptors (R(2): 0.987 vs 0.846; SE: 0.051 vs 0.163 for 60% MeOH) support inclusion of these additional terms. Further, the coefficients obtained from the multiple linear regression for the expanded test set with the D(+) and D(-) descriptors were more consistent with the coefficients obtained when the test set included just neutral analytes. In addition, the expanded LSER model did a better job of predicting elution order for the ionizable analytes. This work provides further supporting evidence for the multimodal nature of the butylimidazolium stationary phase.

A visual approach to stationary phase selectivity classification based on the Snyder-Dolan Hydrophobic-Subtraction Model

A novel type of stationary phase selectivity classification "triangle" has been developed based on the Snyder-Dolan (S-D) Hydrophobic-Subtraction Model, wherein the apices of a set of four triangles represent the relative contributions of steric hindrance (chi(S)), hydrogen-bonding acidity (chi(A)), hydrogen-bonding basicity (chi(B)), cation-exchange capacity (chi(C)) to selectivity. We found that "effective selectivity" of a stationary phase is mathematically given by the ratio of system dependent interaction coefficients but not their absolute values. Thus by normalizing the S*, A, B and C terms of the S-D model by H, we were able to obtain four parameters which fully define the chromatographic selectivity of the stationary phases. By examining the parameters in groups of three, we can represent all the result in a set of four "selectivity triangles". The distinctive feature of this approach compared to the S-D phase classification scheme is that it allows the visualization of column selectivity by plotting three-dimensional data in a two-dimensional space. Moreover, it very clearly shows that the RPLC columns thus far characterized cover only a small fraction of separation selectivity space leaving a great deal of room for researchers to develop novel RPC materials. Various applications of these "selectivity triangles" will be discussed in this paper.

Stationary phase characterization and method development

The properties of stationary phases and their characterization methods are reviewed. New and significant developments have occurred in the last few years, and new methods for stationary phase characterization have become available. The characterization methods are discussed, and the differences between the different methods are pointed out. In addition, method development approaches are reviewed, with special emphasis on recent developments that employ multiple parameters in parallel. Also, the renewed interest of temperature as a tool in method development is surveyed.

Description and comparison of chromatographic tests and chemometric methods for packed column classification

The main tests developed in last 20 years to investigate the chromatographic behaviour and the stationary phase properties are described in this paper. These properties are the hydrophobicity, depending on the surface area and the bonding density, the number of accessible residual silanol groups having sometimes different acidity, which can interact with neutral solutes by hydrogen bonds or with the ionic form of basic compounds and the shape or steric selectivity, depending on both the functionality of the silanising agent and the bonding density. Two types of tests are performed, either based on key solutes having well defined properties such as phenol, caffeine, amitriptyline, benzylamine, acenaphtene, o-terphenyl, triphenylene, p-ethylaniline, carotenoid pigments, or on retention models (solvation parameter, hydrophobic subtraction) obtained from the analyses of numerous and varied compounds. Thus, the chromatographic properties are either related to selectivities or retention factors calculated from key solutes, or they are described by interaction coefficients provided by multilinear regression from retention models. Three types of comparison methods are used based on these data. First, simple plots allow the study of differences between the columns as regards to one or two properties. Columns located in the same area of the plot display close properties. Second, chemometric methods such as principal component analysis (PCA) or hierarchical cluster analysis (HCA) can be performed to compare columns. In this case, all the studied properties are included in the comparison, done either by data projection to reduce the space in which the information is located (PCA) or by distance calculation and comparison for drawing a classification (HCA). Neighbouring columns are expected to provide identical chromatographic performances. These two chemometric methods can be used together, PCA before HCA. The third way is to calculate a discrimination factor from a reference column, through calculation methods based on the Pythagorean Theorem: the lower this factor, the closer the column properties. Following the presentation of the analytical conditions, the compounds and the data treatments used by the teams working in this field, the pertinence of the different selectivities, i.e. of the different probe solute couples or of the different interaction coefficients, are discussed as regards their discrimination capacity. The accuracy of chemometric treatments in the discrimination of stationary phases having different functionalities (octadecylsiloxane (ODS), cyano, fluorinated, phenyl, polar embedded group or "aqua" type) will be discussed, as well as their performances in the finer ODS discrimination. New two-dimensional plots, from data gained by different studies will be suggested, to improve the classification of stationary phases having different nature of bonded chains.

Combined supercritical fluid chromatographic methods for the characterization of octadecylsiloxane-bonded stationary phases

In this paper, we present a combination of a key-solute test based on retention and separation factors of large probe solutes (carotenoid pigments) and a quantitative structure-retention relationship analysis based on the retention factors of small probe solutes (aromatic compounds) to investigate the different chromatographic behavior of octadecylsiloxane-bonded stationary phases of all sorts: classical, protected against silanophilic interactions or not, containing polar groups (endcapping groups or embedded groups). Varied chemometric methods are used to enlighten the differences between the 27 phases tested. The results indicate that the two approaches chosen (carotenoid test and solvation parameter model) are complementary and provide precise information on the chromatographic behavior of ODS phases.

Selectivity in reversed-phase separations

The selectivity difference between 15 different stationary phases was measured using a large number of analytes at 2 or 3 different pH values (3, 7 and 10) with acetonitrile and methanol as the mobile phase modifiers. The packings discussed include standard C(8) and C(18) packings, packings with embedded polar groups, a phenyl packing, a pentafluoro-phenyl packing, an adamantylethyl packing and others. The major selectivity differences observed are discussed in detail. Specific effects such as pi-pi interactions on phenyl packings or hydrogen-bond interactions on phases with embedded polar groups are confirmed.

The chemical interpretation and practice of linear solvation energy relationships in chromatography

This review focuses on the use of linear solvation energy relationships (LSERs) to understand the types and relative strength of the chemical interactions that control retention and selectivity in the various modes of chromatography ranging from gas chromatography to reversed phase and micellar electrokinetic capillary chromatography. The most recent, widely accepted symbolic representation of the LSER model, as proposed by Abraham, is given by the equation: SP=c + eE + sS + aA + bB + vV, in which, SP can be any free energy related property. In chromatography, SP is most often taken as logk' where k' is the retention factor. The letters E, S, A, B, and V denote solute dependent input parameters that come from scales related to a solute's polarizability, dipolarity (with some contribution from polarizability), hydrogen bond donating ability, hydrogen bond accepting ability, and molecular size, respectively. The e-, s-, a-, b-, and v-coefficients and the constant, c, are determined via multiparameter linear least squares regression analysis of a data set comprised of solutes with known E, S, A, B, and V values and which span a reasonably wide range in interaction abilities. Thus, LSERs are designed to probe the type and relative importance of the interactions that govern solute retention. In this review, we include a synopsis of the various solvent and solute scales in common use in chromatography. More importantly, we emphasize the development and physico-chemical basis of - and thus meaning of - the solute parameters. After establishing the meaning of the parameters, we discuss their use in LSERs as applied to understanding the intermolecular interactions governing various gas-liquid and liquid-liquid phase equilibria. The gas-liquid partition process is modeled as the sum of an endoergic cavity formation/solvent reorganization process and exoergic solute-solvent attractive forces, whereas the partitioning of a solute between two solvents is thermodynamically equivalent to the difference in two gas/liquid solution processes. We end with a set of recommendations and advisories for conducting LSER studies, stressing the proper chemical and statistical application of the methodology. We intend that these recommendations serve as a guide for future studies involving the execution, statistical evaluation, and chemical interpretation of LSERs.

Characterisation of stationary phases in subcritical fluid chromatography by the solvation parameter model

This study is an investigation of numerical and graphical tools for the comparison of the chromatographic stationary phases previously characterized with the solvation parameter model [C. West, E. Lesellier, J. Chromatogr. A, in press]. Numerous methods are presented and discussed: the coefficient ratio comparison, principal component analysis (PCA) and calculation of the distance. The coefficient ratio comparison allows to estimate the weight of a particular type of interaction relative to dispersive interactions, but is not practical when a lot of chromatographic systems need to be compared. The principal component analysis is mainly used to reduce the set of correlated variables, but is not useful for non correlated variables such as the solvation parameters. The distance calculation is an interesting tool to measure the differences between two systems but suffers from a confusion between two notions: the difference in the type of interactions involved in the chromatographic system and the intensity of these interactions. Finally, we chose to associate each stationary phase to a vector in a five-dimensional space, according to a method proposed by Ishihama and Asakawa [Y. Ishihama, N. Asakawa, J. Pharm. Sci., 88(12) (1999) 1305] for the comparison of lipophilicity scales. Thus, the angles between the different vectors are used to compare the selectivities of the stationary phases, and the lengths of the vectors are used to compare the relative intensities of the interactions. This method was applied to different alkyl phases characterized in subcritical fluid chromatography (SubFC). The angle values are well suited to the description of the differences in chromatographic behaviour. As expected, a small angle value is obtained between C8, C12 and C18, when a greater one is noticed between C4 and the longer chain length alkyl bonded phases, showing the different acidity and basicity of the C4 phase. Moreover, a satisfactory correlation is obtained between the length of the vectors and the carbon number of the alkyl chain. The differences between classical alkyl-bonded silica phases and polar-embedded alkyl-bonded phases or fluorinated phases are also conveniently evidenced. Finally, graphical tools are investigated and a new type of representation, based in part on a radar plot, is proposed. This plot allows the comparison of stationary phases without reducing the number of studied variables. The comparisons based on this method are consistent with the observed chromatographic behaviour of the phases compared.

Characterization of stationary phases in subcritical fluid chromatography by the solvation parameter model

Varied types of alkylsiloxane-bonded and fluoroalkylsiloxane-bonded stationary phases, all commercially available, were investigated with subcritical fluid mobile phase. The effect of the alkyl chain length (from C4 to C18) and of the nature of the bonding (fluorodecylsiloxane, phenyl-C18 and polar-embedded-C18) on the chromatographic behaviour was investigated by the use of a linear solvation energy relationship (LSER), the solvation parameter model. A large set of test compounds provides precise and reliable information on the intermolecular interactions responsible for retention on these stationary phases used with a subcritical mobile phase. First of all, the results underline the close properties between subcritical fluid and organic liquid. The use of non aqueous mobile phases reduces the cavity energy and the mobile phase acidity generally encountered with aqueous liquid phases, allowing other interactions to take a part in retention. As expected, an increase in the alkyl chain length favours the dispersive interactions between the solutes and the stationary phases. Changes in basicity and acidity of the stationary phases are also related to the chain length, but, in this case, mobile phase adsorption onto the stationary phase is supposed to explain these behaviours. The addition of a phenyl group at the bottom of the C18 chain, near the silica, does not induce great modifications in the retentive properties. The fluorodecylsiloxane and the polar-embedded alkylsiloxane phases display very different properties, and can be complementary to the classical alkylsiloxane-bonded phases. In particular, the fluorinated phase does not favour the dispersive interactions, in comparison to hydrogenated stationary phases, when the basicity of the polar-embedded phase is obviously greater than the one of classical alkylsiloxane-bonded phases, due to the amide function. Finally, logk-logk curves plotted between the different phases illustrate the effect of the interaction properties on the retention of different classes of compounds.