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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.

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Chemistry

(SoNS) School of Natural Sciences

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.

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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.

Density functional theory for Jahn–Teller systems

Some consequences of the quantum fluid dynamics formulation are discussed for excited states of atoms and molecules and for time-dependent processes. It is shown that the conservation of electronic current density j(r) j). Our numerical results are presented elsewhere and further development is in progress. © 1993, Walter de Gruyter. All rights reserved.

Zeitschrift fur Naturforschung - Section A Journal of Physical Sciences

Electron Charge and Current Densities, the Geometrie Phase and Cellular Automata

On the basis of an improved Thomas-Fermi-Dirac (TFD)-type method, a characteristic radius rD is defined for a free atom or ion, where the electron density acquires the universal value of 0.008714. This value is obtained from the ratio of the Dirac exchange constant to the TF kinetic energy constant. Among vertical groups in the Periodic Table, rD calculated from near-Hartree-Fock densities shows striking linear relationships with the empirical covalent radius, the van der Waals radius, the Wigner-Seitz radius, the ionic radius, the first ionization potential, the electronegativity, the softness, the dipole polarizability and the London dispersion coefficient. The potential at rD due to the net charge inside a sphere of radius rd also varies linearly as Mulliken's electronegativity, among vertical groups. On the average, a sphere of radius rd contains more than 95% of the total electronic charge. The horizontal variations in rd among non-transition, transition, and inner transition atoms are sensitive to the changes in electronic configuration, identifying half-filled and completely filled Subshells and also reflecting the lanthanide contraction. © 1992.

Journal of Molecular Structure: THEOCHEM

A universal density criterion for correlating the radii and other properties of atoms and ions

In excited states of atoms and molecules, as well as in time‐dependent situations, the one‐electron density no longer suffices to completely characterize the electronic state; in addition, one now requires information about the electronic phase or the current density. We show that, for a stationary electronic state, the continuity equation of quantum fluid dynamics represents a differential equation for the electronic phase, which must be solved subject to certain periodicity conditions. These periodicity conditions arise from the nodal topology of the wave function and give rise to quantized vortices of current. The consequences of writing an electronic “wave function” for a many‐electron system directly in terms of the single‐particle density and phase have been investigated. We have shown that such a procedure leads to the appearance of an “internal magnetic vector potential.” We also establish the connection between the electronic phase and the geometrical (“Berry”) phase accompanying the adiabatic transport of a quantal system around a closed loop in parameter space. This leads to a generalization of the current density concept and allows us to discuss the geometrical phase in terms of the circulation of this current in parameter space. Copyright © 1991 John Wiley & Sons, Inc.

Phase associated with the single‐particle density of many‐electron systems

We have carried out a computational study of hydrazine and five of its 1,1‐dimethyl derivatives, focusing on their electrostatic potentials and relative bond strengths. Our approach has involved the calculation of ab initio self‐consistent‐field molecular orbital wave functions and molecular properties using the GAUSSIAN 82 system of programs. The electrostatic potentials of the hydrazines possess negative regions of varying sizes and strengths associated with the nitrogens of the α‐diamino linkages. Through an analysis of the positions of the most negative potentials of these regions, we have obtained directly the dihedral angles between the nitrogen lone pairs in these systems. Our use of the electrostatic potential to obtain these angles is a direct and general approach, in contrast to indirect procedures used in the past. We find this dihedral angle to be close to 90° in hydrazine, with variations in the substituted hydrazines that depend on the nature of the substituents. A highly polar structure is found for 1‐chloromethyl‐1‐methylhydrazine, which involves a delocalization of electronic charge from the substituted nitrogen towards the CH2Cl group. We find that substituents able to withdraw significant amounts of electronic density from the central nitrogen lone pair regions, either through resonance or by induction, have a slight bond strengthening effect on the central N‐N bond. This is attributed to a decrease in the repulsion between the weakened nitrogen lone pair regions. The difficulties encountered in seeking the controlled oxidation of hydrazine to nitro derivatives may be due, in part, to the fact that two factors which would favor this, highly negative nitrogen potentials and strong N‐N bonds, are opposing in nature. Copyright © 1990 John Wiley &amp; Sons, Inc.

A computational analysis of the electrostatic potentials and relative bond strengths of hydrazine and some of its 1,1‐dimethyl derivatives

Formulation of the expectations of eight operators required for the evaluation of the Born corrections, the Born couplings, and higher derivatives of the Born-Oppenheimer wave functions are derived for the case of a Gaussian-lobe orbital (GLO) basis. The relative simplicity of these analytical formulas is a special advantage of GLO and reduces the computer time in these calculations. Some operators treated here require a modification of the Slater rules. As examples of applications of these techniques, ab initio calculations of the orbital stresses and the Born corrections for the ground state X 1Sg+ and excited states 1Σ g+ (II), C, C′ 3Πu, and 3Πu (Π) of N2 are reported. The obtained results show that the Born correction near the avoided crossing region strongly depends upon the nuclear separation; in this region configuration interaction makes an important contribution. © 1988 American Institute of Physics.

Ab initio evaluation of the Born correction, Born couplings, and higher derivative matrix elements with Gaussian-lobe orbitals

A computational study of six nitramines, RiR2NNO2, has been carried out with the objective of gaining a better understanding of how the properties of the NNO2 group are affected by the natures of R1 and R2. An ab initio SCF procedure was used, with the initial step being the determination of each molecule's optimized geometry. This was subsequently used to compute its bond orders, dipole moment, and electrostatic potential. In most instances, the NNO2 portions of the molecules are planar, due to the strong electron-withdrawing effect of the nitro group; the amino-type nitrogen can better respond to this when in a planar configuration. One consequence is that the N-NO2 bonds possess some degrees of double bond character; their bond orders range from 1.36 to 1.63, with the weaker bonds corresponding to the more electron-withdrawing and R1 R2 groups. The strong negative electrostatic potentials normally associated with the lone pairs of amino-type nitrogens are greatly weakened or eliminated in most of these molecules; several of them show evidence of significant hyperconjugation, resulting in enhanced acidic character. © 1988, American Chemical Society. All rights reserved.

Journal of the American Chemical Society

Computational evaluation and comparison of some nitramine properties

A computational analysis of phenol and p-nitrophenol has been carried out with the objective of determining the extent to which the conjugation between the -OH group and the aromatic ring is affected by a 90° rotation of the former. The ab initio SCF-MO GAUSSIAN 82 procedure was used to compute optimized geometries, electronic densities and electrostatic potentials. The effect of rotation upon the structures and distributions of π electronic charge are rather small. However, the electrostatic potential reveals that as a consequence of rotation around the COH bond, there should be an overall preference for the ortho positions as the initial sites for electrophilic attack. The -NO2 group deactivates the aromatic ring toward electrophiles and increases the positive character of the hydroxyl hydrogen. © 1988.

An examination of some effects of OH rotation in phenol and p-nitrophenol

Ab initio configuration interaction calculations have been carried out for the lower electronic states of the glycine zwitterion in both the gas phase and in dilute aqueous solution. The solution calculations employ a fractional charge model for the water molecules. The calculated gas phase and solution spectra differ sharply. While excited electronic states of marked Rydberg character are more strongly affected than are valence states, all transitions are shifted to higher energy in solution. We find good agreement with experimentally observed optical absorption spectrum of the glycine zwitterion in thin films. © 1986, American Chemical Society. All rights reserved.