Chemistry

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Shiv Nadar University

Quantitative Structure-Retention Relationship (QSRR) models are developed for the prediction of protein retention times in anion-exchange chromatography systems. Topological, subdivided surface area, and TAE (Transferable Atom Equivalent) electron-density-based descriptors are computed directly for a set of proteins using molecular connectivity patterns and crystal structure geometries. A novel algorithm based on Support Vector Machine (SVM) regression has been employed to obtain predictive QSRR models using a two-step computational strategy. In the first step, a sparse linear SVM was utilized as a feature selection procedure to remove irrelevant or redundant information. Subsequently, the selected features were used to produce an ensemble of nonlinear SVM regression models that were combined using bootstrap aggregation (bagging) techniques, where various combinations of training and validation data sets were selected from the pool of available data. A visualization scheme (star plots) was used to display the relative importance of each selected descriptor in the final set of "bagged" models. Once these predictive models have been validated, they can be used as an automated prediction tool for virtual high-throughput screening (VHTS).

World University root node

(SoNS) School of Natural Sciences

Journal of Chemical Information and Computer Sciences

Prediction of protein retention times in anion-exchange chromatography systems using support vector regression

In this paper, a novel approach is described for the a priori prediction of protein retention in ion exchange systems. Quantitative structure retention relationship (QSRR) models based on a genetic algorithm/partial least squares approach were developed using experimental chromatographic data in concert with molecular descriptors computed using protein crystal structures. The resulting QSRR models were well-correlated, with cross-validated r2 values of 0.938 and 0.907, and the predictive power of these models was demonstrated using proteins not included in the derivation of the models. Importantly, these models were able to predict selectivity reversals observed with two different stationary phase materials. To our knowledge, this is the first published example of predictive QSRR models of protein retention based on crystal structure data.

Analytical Chemistry

Prediction of protein retention in ion-exchange systems using molecular descriptors obtained from crystal structure

First-principles calculations are carried out with the objective of assigning a chemical identity to the variety of forms of molecular oxygen which are known to exist on a TiO2(110) surface. Six different geometries and spin configurations of O2 are shown to be stable in the bridging oxygen defect site. The relationship of these results to experimental observations is discussed. © 1999 American Institute of Physics.

Fulltext

Journal of Chemical Physics

Adsorption of O2 on TiO2(110): A theoretical study

The 11A' and 21A' states of ozone are known to have a conical intersection near 83° in C2v, the intersection seam continuing into asymmetric geometries. We have calculated ab initio the symmetric stretch, antisymmetric stretch and bend components of the Born couplings between these states in the vicinity of the intersection seam, using MRD-CI wavefunctions and an analytical gradient formalism. All three components are significant and sharply peaked near the intersection seam. The non-adiabatic couplings in the vicinity of the energetically accessible conical intersection are expected to be important in understanding the spectroscopy of ozone in the region of the Huggins band. The conical nature of the intersection is illustrated. The singularity in the couplings is eliminated by constructing quasidiabatic states. Different diabatization schemes are discussed and compared. The quasidiabatic states are shown to have distinct characteristics. © 1998 Taylor & Francis Group, LLC.

Molecular Physics

Non-adiabatic coupling of the 11A' and 21A' states of ozone in the vicinity of their conical intersection and construction of diabatic states

Temperature dependence of the intensity of the phonon-assisted excitation probability (as a function of the intensity of the luminescence bands corresponding to the (Formula presented) transitions) of (Formula presented) ion in GdTb((Formula presented) (GTMO), above and below the ferroelectric phase transition temperature ((Formula presented)) is investigated in the present work. The experiments reveal a sharp change in the intensity near (Formula presented) . This change is attributed to a sharp change in the electron-phonon coupling near (Formula presented) . A phenomenological model is proposed to fit the experimental data, in broad accordance with the Ginzburg-Landau equations for critical behavior. The investigations also clearly indicate that phonon-assisted excitation probability can be used to probe structural phase transitions. © 1997 The American Physical Society.

Physical Review B - Condensed Matter and Materials Physics

Temperature dependence of phonon-assisted excitation probability in GdTb: Evidence for a change in electron-lattice coupling near a structural phase transition

One- and two-dimensional cellular automata (CA) simulations of neutral "atoms," viewed as "complex" distributions of electron density around a central nucleus, are performed in order to explore CA-based discretized and connectionist approaches to the synthesis and structure-dynamics problems of many-electron systems. A link between CA and the quantum mechanics of atoms is made by taking the Thomas-Fermi theory as an illustrative example. Starting from a nonstationary distribution, the stationary distribution of electron density around a nucleus arises out of a natural stability criterion described through CA rules. © 1996 John Wiley & Sons, Inc.

International Journal of Quantum Chemistry

"Atom" as a complex system: One- and two-dimensional cellular automata simulations

The dynamics of Jahn–Teller systems has recently been discussed in terms of generalized electronic charge and current densities in nuclear‐coordinate space. The introduction of the electronic phase as a function of both electronic and nuclear coordinates, in addition to the electronic density, was a crucial component of this formulation. Here, a densitybased treatment of Born couplings is derived from first‐principles quantum mechanics beyond the Born–Oppenheimer approximation. Because of the degenerate electronic configuration of a Jahn–Teller molecule, there are an infinite number of ways in which the charge distribution can be oriented for the same energy, leading to a vanishing bond hardness for the molecule in the symmetric nuclear configuration. Further, the moving nuclear framework serves as the perturbation necessary to define the orientation of the charge density, leading to unhindered rotation of the charge cloud. This leads to the dynamical Jahn–Teller problem, namely, the coupling of electronic and nuclear motions through the Born coupling terms. Applications to superconductivity theory are discussed. © 1995 John Wiley & Sons, Inc. Copyright © 1995 John Wiley & Sons, Inc.

Density functional theory of born couplings: Consequences for electron flow in Jahn–Teller molecules and superconductors

We report the results of ab initio calculations of the nonadiabatic Born coupling terms for the two lowest-lying singlet A″ excited states of ozone (1A2 and 1B1 in C2v symmetry) whose electronic potential energy surfaces exhibit a crossing at a bond angle near 120°. Since photoexcitation from the ground state to these A″ states is believed to be responsible for the Chappuis band of ozone, determination of the nonadiabatic coupling terms in the molecular Hamiltonian is therefore likely to be of importance in understanding the predissociative features of the spectrum. The nuclear derivative coupling matrix elements are computed between ab initio electronic wavefunctions obtained from multi-reference configuration interaction (MRD-CI) calculations in a basis of configuration state functions constructed from MCSCF orbitals. The first-derivative nonadiabatic coupling terms are calculated analytically in a manner similar to the calculation of analytic energy gradients, thereby avoiding the cumbersome numerical differentiation of CI and SCF coefficients. The calculated analytical derivative coupling matrix elements are used to determine a suitable transformation to a quasidiabatic basis. © 1995 Elsevier Science B.V. All rights reserved.

Chemical Physics

Nonadiabatic coupling of the 1 1A″ and 2 1A″ states of ozone

The Journal of Chemical Physics

Comment on "electron flow and electronegativity equalization in the process of bond formation" [J. Chem. Phys. 99, 5151 (1993)]

The first discussion of the dynamics of Jahn–Teller systems in terms of the electronic density as the fundamental variable was given by W.J. Clinton in 1960, where the degenerate electronic configuration of a Jahn–Teller molecule was interpreted in terms of the infinite number of ways in which the charge distribution can be oriented for the same energy. The moving nuclear framework serves as the perturbation necessary to define the orientation of the charge density, with no activation energy required to put the charge cloud into motion. Recently, this notion of the electronic charge cloud in a Jahn–Teller molecule sweeping out the potential surface over which the nuclei move has found mathematical expression in our work in terms of a generalized electronic current density in nuclear‐coordinate space [N. Sukumar and B.M. Deb, Int. J. Quantum Chem. 40, 501 (1991)]. The introduction of the electronic phase as a function of both electronic and nuclear coordinates, in addition to the electronic density, is a crucial component of this formulation. In the present work, the density‐based treatment is extended to the nonadiabatic situation, with the Born couplings interpreted as nonadiabatic currents in parameter space. Abelian and non‐Abelian gauge transformations of these currents are discussed. © John Wiley & Sons, Inc. Copyright © 1994 John Wiley & Sons, Inc.