Ruth I.J. Amos

Towards a chromatographic similarity index to establish localized quantitative structure-retention models for retention prediction: Use of retention factor ratio

Quantitative Structure-Retention Relationships (QSRR) have the potential to speed up the screening phase of chromatographic method development as the initial exploratory experiments are replaced by prediction of analyte retention based solely on the structure of the molecule. The present study offers further proof-of-concept of localized QSRR modelling, in which the retention of any given compound is predicted using only the most chromatographically similar compounds in the available dataset. To this end, each compound in the dataset was sequentially removed from the database and individually utilized as a test analyte. In this study, we propose the retention factor k as the most relevant chromatographic similarity measure and compare it with the Tanimoto index, the most popular similarity measure based on chemical structure. Prediction error was reduced by up to 8 fold when QSRR was based only on chromatographically similar compounds rather than using the entire dataset. The study therefore shows that the design of a practically useful structural similarity index should select the same compounds in the dataset as does the k-similarity filter in order to establish accurate predictive localized QSRR models. While low average prediction errors (Mean Absolute Error (MAE)<0.5min) and slopes of the regression lines through the origin close to 1.00 were obtained using k-similarity searching, the use of the structural Tanimoto similarity index, considered as the gold standard in Quantitative Structure-Activity Relationships (QSAR) studies, generally resulted in much higher prediction errors (MAE>1min) and significant deviations from the reference slope of 1.0. The Tanomoto similarity index therefore appears to have limited general utility in QSRR studies. Future studies therefore aim at designing a more appropriate chromatographic similarity index that can then be applied for unknown compounds (that is, compounds which have not been tested previously on the chromatographic system used, but for which the chemical structures are known).

Prediction of retention in hydrophilic interaction liquid chromatography using solute molecular descriptors based on chemical structures

Quantitative structure-retention relationship (QSRR) models are developed to predict the retention times of analytes on five hydrophilic interaction liquid chromatography (HILIC) stationary phases (bare silica, amine, amide, diol and zwitterionic), with a view to selecting the most suitable stationary phase(s) for the separation of these analytes. The study was conducted using six β-adrenergic agonists as target analytes. Molecular descriptors were calculated based only on chemical structures optimized using density functional theory. A genetic algorithm (GA) was then used to select the most relevant molecular descriptors and these were used to build a retention model for each stationary phase using partial least squares (PLS) regression. This model was then used to predict the retention of the test set of target analytes. This process created an optimized descriptor set which enhanced the reliability of the developed QSRR models. Finally, the QSRR models developed in the work were utilized to provide some insight into the separation mechanisms operating in the HILIC mode. Three performance criteria - mean absolute error (MAE), root mean square error of prediction scaled to retention time (RMSEP), and the number of selected descriptors, were used to evaluate the developed models when applied to an external test set of six β-adrenergic agonists and showed highly predictive abilities. MAE values ranged from 13 to 25s on four of the stationary phases, with a somewhat higher error (50s) being observed for the zwitterionic phase. RMSEP values of 4.88-11.12% were recorded. Validation was performed through Y-randomization and chemical domain applicability, from which it was evident that the developed optimized GA-PLS models were robust. The high levels of accuracy, reliability and applicability of the models were to a large extent due to the optimization of the GA descriptor set and the presence of relevant structural and geometric molecular descriptors, together with descriptors based on important physicochemical properties, which establish a strong connection between retention time and meaningful chemical properties. The present strategy, while it is a pilot study, holds great promise for broader screening of HILIC stationary phases for desired separation, as well as for acquisition of information about molecular mechanisms of separation under chromatographic conditions.

Rapid method development in hydrophilic interaction liquid chromatography for pharmaceutical analysis using a combination of quantitative structure-retention relationships and design of experiments

A design-of-experiment (DoE) model was developed, able to describe the retention times of a mixture of pharmaceutical compounds in hydrophilic interaction liquid chromatography (HILIC) under all possible combinations of acetonitrile content, salt concentration, and mobile-phase pH with R2 > 0.95. Further, a quantitative structure-retention relationship (QSRR) model was developed to predict retention times for new analytes, based only on their chemical structures, with a root-mean-square error of prediction (RMSEP) as low as 0.81%. A compound classification based on the concept of similarity was applied prior to QSRR modeling. Finally, we utilized a combined QSRR-DoE approach to propose an optimal design space in a quality-by-design (QbD) workflow to facilitate the HILIC method development. The mathematical QSRR-DoE model was shown to be highly predictive when applied to an independent test set of unseen compounds in unseen conditions with a RMSEP value of 5.83%. The QSRR-DoE computed retention time of pharmaceutical test analytes and subsequently calculated separation selectivity was used to optimize the chromatographic conditions for efficient separation of targets. A Monte Carlo simulation was performed to evaluate the risk of uncertainty in the models prediction, and to define the design space where the desired quality criterion was met. Experimental realization of peak selectivity between targets under the selected optimal working conditions confirmed the theoretical predictions. These results demonstrate how discovery of optimal conditions for the separation of new analytes can be accelerated by the use of appropriate theoretical tools.

Hydrogen-atom abstraction from a model amino acid: dependence on the attacking radical

We have used computational chemistry to examine the reactivity of a model amino acid toward hydrogen abstraction by HO•, HOO•, and Br•. The trends in the calculated condensed-phase (acetic acid) free energy barriers are in accord with experimental relative reactivities. Our calculations suggest that HO• is likely to be the abstracting species for reactions with hydrogen peroxide. For HO• abstractions, the barriers decrease as the site of reaction becomes more remote from the electron-withdrawing α-substituents, in accord with a diminishing polar deactivating effect. We find that the transition structures for α- and β-abstractions have additional hydrogen-bonding interactions, which lead to lower gas-phase vibrationless electronic barriers at these positions. Such favorable interactions become less important in a polar solvent such as acetic acid, and this leads to larger calculated barriers when the effect of solvation is taken into account. For Br• abstractions, the α-barrier is the smallest while the β-barrier is the largest, with the barrier gradually becoming smaller further along the side chain. We attribute the low barrier for the α-abstraction in this case to the partial reflection of the thermodynamic effect of the captodatively stabilized α-radical product in the more product-like transition structure, while the trend of decreasing barriers in the order β > γ > δ ∼ ε is explained by the diminishing polar deactivating effect. More generally, the favorable influence of thermodynamic effects on the α-abstraction barrier is found to be smaller when the transition structure for hydrogen abstraction is earlier.

Use of dual-filtering to create training sets leading to improved accuracy in quantitative structure-retention relationships modelling for hydrophilic interaction liquid chromatographic systems

The development of quantitative structure retention relationships (QSRR) having sufficient accuracy to support high performance liquid chromatography (HPLC) method development is still a major issue. To tackle this challenge, this study presents a novel QSRR methodology to select a training set of compounds for QSRR modelling (i.e. to filter the database to identify the most appropriate compounds for the training set). This selection is based on a dual filtering strategy which combines Tanimoto similarity (TS) searching as the primary filter and retention time (tR) similarity clustering as the secondary filter, using a database of pharmaceutical compound retention times collected over a wide range of hydrophilic interaction liquid chromatography (HILIC) systems. To employ tR similarity filtering, correlation to a molecular descriptor is used as a measure of retention time. For the retention time of a compound to be modelled a relationship between experimental chromatographic data and various molecular descriptors is calculated using a genetic algorithm-partial least squares (GA-PLS) regression. The proposed dual-filtering-based QSRR model significantly improves the retention time predictability compared to the diverse, global, and TS-based QSRR models, with an average root mean square error in prediction (RMSEP) of 11.01% over five different HILIC stationary phases. The average CPU time for implementing the proposed approach is less than 10min, which makes it quite favorable for rapid method development in HILIC. In addition, interpretation of the molecular descriptors selected by this novel approach provided some insight into the HILIC mechanism.

Hydrogen from Formic Acid through Its Selective Disproportionation over Sodium Germanate—A Non‐Transition‐Metal Catalysis System

A robust catalyst for the selective dehydrogenation of formic acid to liberate hydrogen gas has been designed computationally, and also successfully demonstrated experimentally. This is the first such catalyst not based on transition metals, and it exhibits very encouraging performance. It represents an important step towards the use of renewable formic acid as a hydrogen-storage and transport vector in fuel and energy applications.

Chemometric-assisted method development in hydrophilic interaction liquid chromatography: a review

With an enormous growth in the application of hydrophilic interaction liquid chromatography (HILIC), there has also been significant progress in HILIC method development. HILIC is a chromatographic method that utilises hydro-organic mobile phases with a high organic content, and a hydrophilic stationary phase. It has been applied predominantly in the determination of small polar compounds. Theoretical studies in computer-aided modelling tools, most importantly the predictive, quantitative structure retention relationship (QSRR) modelling methods, have attracted the attention of researchers and these approaches greatly assist the method development process. This review focuses on the application of computer-aided modelling tools in understanding the retention mechanism, the classification of HILIC stationary phases, prediction of retention times in HILIC systems, optimisation of chromatographic conditions, and description of the interaction effects of the chromatographic factors in HILIC separations. Additionally, what has been achieved in the potential application of QSRR methodology in combination with experimental design philosophy in the optimisation of chromatographic separation conditions in the HILIC method development process is communicated. Developing robust predictive QSRR models will undoubtedly facilitate more application of this chromatographic mode in a broader variety of research areas, significantly minimising cost and time of the experimental work.

Error measures in quantitative structure-retention relationships studies

An analysis and comparison of the use of four commonly used error measures (mean absolute error, percentage mean absolute error, root mean square error, and percentage root mean square error) for evaluating the predictive ability of quantitative structure-retention relationships (QSRR) models is reported. These error measures are used for reporting errors in the prediction of retention time of external test analytes, that is, analytes not employed during model development. The error-based validation metrics were compared using a simple descriptive statistic, the sum of squared residuals (SSR) of outliers to the edge of an error window. The comparisons demonstrate that Percentage Root Mean Squared Error of Prediction (RMSEP) provides the best estimate of the predictive ability of a QSRR model, having the lowest SSR value of 20.43.

Benchmarking of Computational Methods for Creation of Retention Models in Quantitative Structure–Retention Relationships Studies

Quantitative structure-retention relationship (QSRR) models are powerful techniques for the prediction of retention times of analytes, where chromatographic retention parameters are correlated with molecular descriptors encoding chemical structures of analytes. Many QSRR models contain geometrical descriptors derived from the three-dimensional (3D) spatial coordinates of computationally predicted structures for the analytes. Therefore, it is sensible to calculate these structures correctly, as any error is likely to carry over to the resulting QSRR models. This study compares molecular modeling, semiempirical, and density functional methods (both B3LYP and M06) for structure optimization. Each of the calculations was performed in a vacuum, then repeated with solvent corrections for both acetonitrile and water. We also compared Natural Bond Orbital analysis with the Mulliken charge calculation method. The comparison of the examined computational methods for structure calculation shows that, possibly due to the error inherent in descriptor creation methods, a quick and inexpensive molecular modeling method of structure determination gives similar results to experiments where structures are optimized using an expensive and time-consuming level of computational theory. Also, for structures with low flexibility, vacuum or gas phase calculations are found to be as effective as those calculations with solvent corrections added.

Nucleophilic Acyl Substitution of Acyl Diimides

The nucleophilic acyl substitution of the acyl diimide intermediate formed by the oxidation of isoniazid was found to involve two methanol molecules in a six-membered cyclic transition state. Calculations were performed in the gas phase at the B3LYP/6-311+G(d,p)//B3LYP/6-31G(d) level of theory and solvation effects were included both explicitly and implicitly by using CPCM. The effect of electron withdrawing and donating groups on the aryl ring was also explored. The results obtained are in good agreement with experimental observations for the oxidation of isoniazid.