James D. Petke

STEREOELECTRONIC PROPERTIES OF PHOTOSYNTHETIC AND RELATED SYSTEMS — V. AB INITIO CONFIGURATION INTERACTION CALCULATIONS ON THE GROUND AND LOWER EXCITED SINGLET AND TRIPLET STATES OF ETHYL CHLOROPHYLLIDE a AND ETHYL PHEOPHORBIDE a

Abstract— Ab initio configuration interaction wavefunctions and energies are reported for the ground state and many low‐lying excited singlet and triplet states of ethyl pheophorbide a (Et‐Pheo a) and ethyl chlorophyllide a (Et‐Chl a), and are employed in an analysis of the electronic absorption spectra of these systems.

Stereoelectronic properties of photosynthetic and related systems: Ab initio configuration interaction calculations on the ground and lower excited singlet and triplet states of magnesium porphine and porphine

Abstract Ab initio configuration interaction wavefunctions and energies are reported for the ground state and many low-lying singlet and triplet states of magnesium chlorin and chlorin, and are employed in an analysis of the electronic absorption spectra of these systems. In chlorin, the calculated visible spectrum consists of two 1 (π, π ∗ ) states, the lower energy, y-polarized state exhibiting moderate absorption intensity in contrast to the very weak absorption of the higher energy x-polarized state. The configurational composition of both states is well described by the four-orbital model. Five 1 (π, π ∗ ) states are responsible for the Soret band envelope. A moderately intense y-state lies under the low energy edge of the band envelope, while two x-polarized states of moderate and strong intensity, respectively, are responsible for the band maximum. The final two 1 (π, π ∗ ) states lie at the high energy edge of the Soret band and introduce a measure of asymmetry into the band envelope. Two 1 (n, π ∗ ) states of very weak oscillator strength are also found in this region of the spectrum. All the Soret states are of complex configurational composition, and several of the higher lying states contain contributions from doubly excited configurations. The calculated visible spectrum of magnesium chlorin also consists of two 1 (π, π ∗ ) states, with the weakly absorbing x-polarized state lying approximately 200 cm−1 lower in energy than the moderately intense y-polarized state. The configurational composition of both states is well described by the four-orbital model. Four 1 (π, π ∗ ) states constitute the bulk of the intensity in the Soret band envelope. In distinction to chlorin, the moderately intense 1 (π, π ∗ ) state at the low energy edge of the band envelope is x-polarized. Two intense 1 (π, π ∗ ) states of y- and x-polarization, respectively, constitute the band maximum region, and a single x-polarized state of moderately strong intensity can be assigned to the high energy shoulder of the band envelope. Two other weakly absorbing 1 (π, π ∗ ) states are also found in this region, along with another weakly absorbing state of mixed in-plane and out-of-plane polarization. No clearly defined 1 (n, π ∗ ) states are observed. As was the case for chlorin, all the Soret states are of complex configurational composition, and some of the higher energy states contain significant contributions from doubly excited configurations. Chlorin and magnesium chlorin both possess three 3 (π, π ∗ ) states which lie below S1 and a single 3 (π, π ∗ ) which lies slightly above S2. All four of the low-lying 3 (π, π ∗ ) states in each molecule are well described by the four-orbital model, with T1 being essentially a single configuration in each case. The remainder of the 3 (π, π ∗ ) states are clustered in the same energetic region as the comparable 1 (π, π ∗ ) Soret states, with comparably complex configurational compositions. Dipole moments and charge distributions for low-lying singlet and triplet states are also reported, and are used to rationalize chemical reactivity characteristics.

STEREOELECTRONIC PROPERTIES OF PHOTOSYNTHETIC AND RELATED SYSTEMS—VII. AB INITIO QUANTUM MECHANICAL CHARACTERIZATION OF THE ELECTRONIC STRUCTURE AND SPECTRA OF CHLOROPHYLLIDE a AND BACTERIOCHLOROPHYLLIDE a CATION RADICALS

Abstract— Ab initio configuration interaction wavefunctions and energies are reported for 29 doublet states and three quartet states of the cation radicals of ethyl chlorophyllide a (Et‐Chl a+) and ethyl bacteriochlorophyllide a (Et‐BChl a+).

Experimental and theoretical studies of Schiff base chlorophylls

Abstract— A protonated Schiff base of Ni (II)‐pyrochlorophyll a has been synthesized which exhibits a reversible bathochromic shift of 504 cm‐1 relative to Ni (II)‐pyrochlorophyll a. The magnitude of this shift lies between those observed for P700 and P680, the photoactive pigments of photosystems I and II in plants. Cyclic voltammetric measurements show that the protonated Schiff base is about 0.2 V more difficult to oxidize than its unprotonated form. These results suggest that a protonated Schiff base may be a better model for P680 than, as was originally assumed, for P700. In addition, the results of solvent and counterion effect studies show that microenvironmental perturbations in the neighborhood of the protonated Schiff base moiety are unlikely to induce further spectral shifts. Ab initio quantum mechanical calculations show a small hypsochromic shift rather than the observed bathochromic one, and the reasons for this discrepancy are discussed.

A General Analysis of Field-Based Molecular Similarity Indices

A formalism is presented that incorporates the entirety of all field-based molecular similarity indices of general form Sij=Ωij/h(Ωii,Ωjj), where the numerator is given by the inner product or “overlap” of field functions Fi and Fj corresponding to the ith and jth molecules, respectively, and the denominator is given by a suitable mean function of the self-similarities Ωii and Ωjj. This family of similarity indices includes the index initially introduced by Carbó nearly twenty years ago, where h(Ωii,Ωjj) is taken to be the geometric mean of Ωii and Ωjj, and the well-known indices due to Hodgkin and Richards, and Petke, where h(Ωii,Ωjj) is taken to be the arithmetic mean and maximum of Ωii and Ωjj, respectively. Two new indices based upon the harmonic mean and minimum of Ωii and Ωjj are also defined, and it is demonstrated that the entire set of field-based similarity indices can be generated from a one-parameter family of functions, called generalized means, through proper choice of the parameter value and suitable limiting procedures. Ordering and rigorous bounds for all of the indices are described as well as a number of inter-relationships among the indices. The generalization of field-based similarity indices, coupled with the relationships among indices that have been developed in the present work, place the basic theory of these indices on a more unified and mathematically rigorous footing that provides a foundation for a better understanding of the quantitative aspects of field-based molecular similarity.

Application of the shape group method to conformational processes: Shape and conjugation changes in the conformers of 2‐phenyl pyrimidine

The shape group method (SGM) and the associated (a,b)‐parameter maps provide a detailed shape characterization of molecular charge distributions. This method is applied to the study of the variations of shape and conjugation of conformers of 2‐phenyl pyrimidine in their electronic ground state. Within the SGM framework, the method of (a,b)‐parameter maps provides a concise, nonvisual, algorithmic technique for shape characterization of molecules with fixed nuclear geometries. Moreover, shape codes derived from the (a,b)‐parameter maps afford a practical means for efficiently storing the shape properties of molecules in an electronic database. The shape codes of two or more charge distributions can be compared directly, and numerical measures of molecular shape similarity can be computed using a technique that is simple, fast, and inexpensive, especially in relation to direct, pairwise comparisons of electronic charge densities. The quantitative and automated nature of the method suggests applications in the field of computer‐aided molecular design. In this study, the method is used for the first time to determine detailed numerical shape codes and shape similarity measures for a nontrivial conformational problem involving changes in energy and in conjugation. Numerical shape similarity measures of eight conformers of 2‐phenyl pyrimidine are determined and correlated with variations in conformational energy and conjugation. The competing effects of steric repulsion and conjugation lead to important correlations between conformational energy and shape.

STEREOELECTRONIC PROPERTIES OF PHOTOSYNTHETIC AND RELATED SYSTEMS—IX. AB INITIO QUANTUM MECHANICAL CHARACTERIZATION OF THE ELECTRONIC STRUCTURE AND SPECTRUM OF THE BACTERIOCHLOROPHYLLIDE a ANION RADICAL

Ab initio configuration interaction wavefunctions and energies are reported for 16 doublet states of the anion radical of ethyl bacteriopheophorbide a (Et‐BPheo a‐˙), and are employed in an analysis of the electronic absorption spectrum.

DEVELOPMENT OF THEORETICAL METHODOLOGY FOR LARGE MOLECULES

A major advantage of the use of floating spherical Gaussian or vitals (FSGO) is the extreme rapidity with which the necessary quantum mechanical integrals can be evaluated. This advantage has been exploited in several quantum mechanical procedures for molecular electronic structure calculations, as described below. Several other properties of these functions have also been exploited, and have led to the development of semiclassical point charge and harmonic oscillator models capable of describing first and second order electromagnetic properties and intermolecular forces with reasonable accuracy in all cases and with considerably better accuracy than much more elaborate theoretical procedures in some cases. These applications are also described below. The primary intent of the current paper is to present an overview of some of the uses of FSGOs in the study of molecular electronic structure and properties and to indicate possible directions for future applications. No attempt will be made to include all possible applications. Rather, those applications of interest to the authors have been stressed. Hopefully, this paper will further stimulate the development of additional uses of these remarkable functions.

Electronic Excited States of Biomolecular Systems: Ab Initio FSGO-based Quantum Mechanical Methods with Applications to Photosynthetic and Related Systems

The accelerating rate with which new computer hardware is being introduced has spurred development of a wide variety of sophisticated scientific software for the simulation of chemical and biological systems. Molecular mechanics and dynamics methods, which are based on potential energy functions derived from empirical and quantum mechanically calculated data, are now widely employed in investigations of the conformations and interactions of molecules in their ground electronic states. Applications to systems as complex as proteins and nucleic acids have made significant contributions to our understanding, especially as regards the molecular basis of structure and function. Direct application of quantum mechanical methods to such studies of large biomolecules have been sparse, and have not, in general had the impact that molecular mechanical and dynamical methods have had in shaping our understanding of these systems. When dealing with electronic excited states, however, quantum mechanical methods are required. And knowledge of the electronic structure and properties of these states is important for a detailed understanding of a number of photobiological processes (such as photosynthesis and vision), and for analyzing and interpreting the results obtained from applications of absorption, emission, and circular dichroism spectroscopy to the study of individual and interacting biomolecules.