Knowledge on the binding behaviour of proteins, polypeptides or amino acids at liquid–solid interfaces provides valuable insight into the molecular mechanisms of protein– protein or protein–membrane interactions in a biological context. Application of this knowledge is also germane to the purification of proteins or other classes of biomacromolecules. Therefore, extraction of data associated with amino acid, peptide or protein adsorption to chemically modified surfaces is a highly desirable prelude to more detailed biophysical studies on the mechanistic basis of molecular recognition phenomena associated with peptide–or protein– ligand interactions per se. The magnitude of the interaction of a protein or polypeptide with a chemically or biologically defined surface is governed by the system free energy before and after the interaction and can attributed to the changes in the corresponding enthalpy and entropy of the system. In view of these dependencies, the use of experimental approaches that are capable of delineating and evaluating thermodynamic and extra-thermodynamic parameters and linear or non-linear free energy relationships associated with the binding behaviour and molecular properties of polypeptides and proteins should thus form an essential and integral part of any serious effort to understand the origin of molecular recognition phenomena in biology. In this mini-review, a thermodynamic framework is developed, based on an analysis of the van’t Hoff plot dependencies as well as data derived from micro-calorimetric measurements, in order to further illustrate the molecular nature of the interactions that occur between polypeptides or proteins and solid surfaces in the various modes of liquid chromatography. In developing the framework of this mini-review, and in the interests of conciseness and space, emphasis has been specifically focused on interactions mediated by the ‘hydrophobic effect’, an aptly called but incompletely understood phenomenon that is central to: hydrophobic interaction (HIC) and reversedphase chromatography (RPC), protein folding and polypeptide coiled coil formation; protein and polypeptide aggregation and fibril formation as well as many other aspects of molecular biorecognition involving protein or polypeptide docking to chemically modified surfaces, lipid bilayers or cellular organelle structures, protein–and polypeptide–drug interactions; intraand extra-cellular protein and polypeptide trafficking and protein or polypeptide bait-prey biointeraction phenomena, including receptor cognate recognition and immune complex formation. As is evident from this mini-review, similar treatments as elaborated for proteins and polypeptides have (surprising) commonality in terms of the thermodynamic and extra-thermodynamic origins of the dissolution of non-polar compounds in water, the extraction or partition of biomolecules in heterogeneous two-phase solvent systems and the ‘salting in’ or ‘salting out’ of proteins from aqueous solution with various salts, solvents and co-solvents. Extension and application of this knowledge in the broader context of biological supra-molecular interactions within living cells is readily apparent. To highlight the approach, examples derived from recent investigations reported from this laboratory have been employed to illustrate the power of the experimental methods used and the utility of the derived information. Consequently, analyses of experimental data acquired in such studies not only provides versatile approaches to probing the interaction mechanisms associated with protein–ligand binding processes in hydrophobic interaction or reversed-phase liquid chromatography at the molecular level per se, but also have the potential to facilitate mechanistically and thermodynamically the interpretation of biorecognition processes in vitro, in vivo and in silico.

Thermodynamic analysis of the interaction between proteins and solid surfaces: application to liquid chromatography.

The molecular geometries and harmonic vibrational frequencies of the ground and the lowest triplet state of dibenzothiophene have been calculated using the Becke-3-Lee−Yang−Parr (B3LYP) density functional methods with the 6-31G* basis set. A structural change occurs from a benzene-like to a planar, quinone-like form upon the excitation to the first excited state. Scaled vibrational frequencies for the ground state obtained from the B3LYP calculation show good agreement with experiment. On the basis of the calculated and experimental vibrational frequencies, a few vibrational fundamentals for both states are newly assigned and the spectral position of some missing lines are predicted.

Density Functional Theory Calculation of Molecular Structure and Vibrational Spectra of Dibenzothiophene in the Ground and the Lowest Triplet State

Fragmentation of molecules by collision-induced dissociation (CID) is not well-understood, making interpretation of MS/MS spectra difficult and limiting the effectiveness of software tools intended to aid mass spectral interpretation. An approach is required which is tailored to each individual molecule and improves the ‘chemical sense’ of the software.

It was hypothesised that the bonds which break during CID of protonated molecules are the bonds which are elongated, and hence weakened, as a result of conformational changes induced by protonation. Bond length changes for a test set of molecules were calculated using quantum chemistry software. Density Functional Theory (DFT) or Austin Model 1 (AM1) or both were used to energy minimise the structures of the neutral molecules and their corresponding protonated molecules (protonated at all possible sites). Bonds which elongated to the greatest extent after protonation were compared to the bonds which were found to cleave to give the product ions in the CID spectra of these compounds. Quantum chemistry modelling was also applied to the deprotonated molecules.

AM1 calculated bond lengths were found to be similar to those generated by DFT and have the advantage of being rapidly obtained. All the polarised bonds which cleaved were calculated to elongate significantly, thus achieving a 100% success rate in the prediction of bond cleavage as a result of protonation on a heteroatom. The proton is mobile across the molecule, leading to fragmentation when the proton reaches a site where it causes significant bond elongation, provided the molecule has sufficient internal energy. Cleavage of carbon-carbon bonds was not predicted. The success rate for predicting bond cleavage in deprotonated molecules was 48%, suggesting this approach cannot be applied reliably for these anions.

AM1 calculated bond length change acts as a descriptor for predicting polarised bond cleavage in protonated pseudo-molecular ions having the potential to be incorporated in mass spectral interpretive software to increase the accuracy of prediction of CID spectra.

Understanding MS/MS fragmentation pathways of small molecular weight molecules

The thermal treatment of abietane skeleton diterpenoids yields a number of mono-, di- and tri-aromatic hydrocarbons. The aromatization process follows the thermal constraint and the degree of aromatization is higher with higher operating temperature. It seems possible to correlate the composition pitches with the thermal treatments specially those, which were used in Antic production sites. During the aromatization process, the retene, which is formed, is demethylated to give the 7-ethyl-1-methylphenanthrene and then the 1,7-dimethylphenanthrene. In the mean time, the retene is also methylated and gives methylretenes (MR) and dimethylretenes (DMR). The semi-empirical AM1/RHF method has been used to calculate local minimum structures of ∼60 retene-like molecules together with their relative enthalpies of formation. This study allows to correlate the calculated geometries and the stabilities and to link the thermodynamic properties and shapes of individual isomers with their relative abundance during thermal degradation.

Molecular characterization of retene derivatives obtained by thermal treatment of abietane skeleton diterpenoids

Quantum Mechanics Calculations on PASH: Attempts to Correlate Thermodynamic Properties to Chromatographic Behaviour and/or Relative Abundance or Presence in Petroleum Samples

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Quantum Mechanics Calculations on PASH: Attempts to Correlate Thermodynamic Properties to Chromatographic Behaviour and/or Relative Abundance or Presence in Petroleum Samples