Ralph E. Christoffersen

Ab Initio Calculations on Large Molecules

Publisher Summary This chapter illustrates the efforts that have been made to develop procedures for treating large molecules in a practical manner. It considers an arbitrary and myopic definition of a large molecule as one in which there are ≥ 36 electrons and containing atoms including hydrogen and others from the first row of the periodic table. The chapter is limited to the procedures that are based upon an ab initio formalism. While several of these approaches such as CNDO (complete neglect of differential overlap), INDO (intermediate neglect of differential overlap), MCZDO (multi-center zero differential overlap), and NEMO (nonempirical molecular orbital theory) have provided useful and informative results, it seems clear that an ab initio approach is desired for several reasons. First, the identification and improvement of inadequacies is more straightforward in an ab initio approach, since only a model plus a basis set need to be examined. Second, the parametrization techniques are developed typically for the determination of the total energy and are not applicable in general to other properties. Third, the evaluation of integrals over Slater-type orbitals for properties other than the energy presents formidable problems, which are solved usually by invoking additional parameterization procedures. Consequently, these and other theoretical and practical difficulties associated with the use of semiempirical techniques have led to the search for alternative formulations of an ab initio nature.

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.

A model for the ab initio calculation of some solvent effects

Abstract A theory of solvent-solute interactions is presented, in which a classical model due to Kirkwood is used to derive an expression for the potential affecting a molecule due to a solvent. From this the quantum mechanical hamiltonian for the molecule in the presence of the solvent can be deduced, and a variational minimization of the total energy of the system leads to an ab initio scheme which includes solvent effects. The solvation energy of He in CCl 4 is reported as an illustration of the method.

Electron population analysis. Gross atomic charges in molecules

Abstract A definition of “gross atomic population” is proposed in which the arbitrary division of individual overlap terms is not needed. The proposed definition is applied to LiH, BH, HF, and H 2 O.

Ab Initio Calculations on Large Molecules Using Molecular Fragments. Hydrocarbon Characterizations

An ab initio procedure for investigation of large molecules is described. The procedure involves two steps, the first of which is the determination of a set of orbitals by the examination of molecular fragments. These molecular fragments and associated orbitals are then combined to form large molecules of interest, using an ordinary LCAO MO SCF‐type procedure. The molecular fragment investigations employed are designed to obtain nonlinear parameters for use in large molecules, and are not used in this study to obtain “small molecules” from which “large molecules” can be formed. Several descriptions of molecular fragments are explored, in which floating spherical Gaussian orbitals are employed, and applications of the method to ethane, propane, ethylene, and benzene are given. Comparisons are made with other methods, and several general characteristics of the method are also discussed.

Ab initio calculations on large molecules using molecular fragments. Preliminary investigations

Abstract The preliminary characterization of an ab initio SCF procedure for investigations of large molecules is given. The method is based upon the use of floating spherical Gaussian orbitals, which are obtained by a prior study of molecular fragments.

Application of computational technologies to ribozyme biotechnology products

Abstract Ribozymes are RNA molecules that act enzymatically to cleave other RNA molecules. The cleavage reaction requires the binding of ribozyme to specific sites on the target RNA through (mostly) Watson-Crick base-pairing interactions. Association of ribozyme with target completes a three-dimensional ribozyme/target complex which results in cleavage of the target RNA. We are employing both computational and experimental approaches to identify sites on target RNA molecules that are open to ribozyme attack and to determine which ribozymes are most active against those sites. Two types of computational technologies are available for aiding in the identification of target sites and design of active ribozymes. First, DNA/RNA sequence analysis software is employed to identify sequence motifs necessary for ribozyme cleavage and to look for sequence conservation between different sources of the target organism so that ribozymes with the broadest possible target range can be designed. Second, RNA folding algorithms are employed to predict the secondary structure of both ribozyme and target RNA in an attempt to identify combinations of ribozyme and target site that will successfully associate prior to ribozyme cleavage. The RNA folding algorithms utilize a set of thermodynamic parameters obtained from measurements on short RNA duplexes; while these rules give reasonable predictions of secondary structure for a small set of highly structured RNAs, they remain largely untested for predicting the structure of messenger RNAs. This paper outlines the current status of designing ribozymes that fold correctly and of locating target sites that are sufficiently unfolded to allow ribozyme cleavage.

Ab initio calculations on large molecules using molecular fragments. Preliminary investigation of ethyl chlorophyllide a and related molecules

Abstract Ab initio SCF calculations using the molecular fragment method are reported for four molecules related to chlorophyll a, i.e., free-base porphine, magnesium porphine, magnesium chlorin, and ethyl chlorophyllide a. Molecular orbital structure, the “four-orbital model”, reactivity sites, and Mg···N interactions are discussed.

Ab Initio Calculations on Large Molecules Using Molecular Fragments. Oxygen‐Containing Molecules

An ab initio procedure for the investigation of large molecules is applied to a series of oxygen‐containing molecules. Prototype molecules used to characterize the procedure include H2O, H2O2, CH3OH, CH3OCH3, furan, H2CO, CH3CHO, (CH3)2CO, HCOOH, CH3COOH, and HCOOCH3. The method is found to provide interesting and useful information concerning electronic structure and molecular geometry in spite of the restricted sets of basis orbitals employed. When possible, comparisions are made with other theoretical results as well as experimental values.