The Huckel theory, with an extended basis set consisting of 2s and 2p carbon and 1s hydrogen orbitals, with inclusion of overlap and all interactions, yields a good qualitative solution of most hydrocarbon conformational problems. Calculations have been performed within the same parametrization for nearly all simple saturated and unsaturated compounds, testing a variety of geometries for each. Barriers to internal rotation, ring conformations, and geometrical isomerism are among the topics treated. Consistent σ and π charge distributions and overlap populations are obtained for aromatics and their relative roles discussed. For alkanes and alkenes charge distributions are also presented. Failures include overemphasis on steric factors, which leads to some incorrect isomerization energies; also the failure to predict strain energies. It is stressed that the geometry of a molecule appears to be its most predictable quality.

An Extended Hückel Theory. I. Hydrocarbons

An inductive method for a systematic selection of energy functions of interatomic interactions in large families of molecules is suggested and is applied to the family of cycloalkane and n‐alkane molecules. Equilibrium conformations, vibrational frequencies, and excess enthalpies, including strain energies and vibrational enthalpies, are all derived from the same set of energy functions. The energy‐function parameters are optimized by a least‐squares algorithm to give the best possible agreement with a large amount and variety of observed data. Analytical derivatives of the various calculated quantities with respect to the energy parameters help to facilitate the computational procedures. The resulting agreement with experiment is used as a measure of success of the energy functions with optimized parameters, referred to as “consistent force field” (CFF). Different CFF's are compared and selected according to their relative success. Energy functions commonly used in conformational analysis are examined in...

Consistent Force Field for Calculations of Conformations, Vibrational Spectra, and Enthalpies of Cycloalkane and n‐Alkane Molecules

A uniform notation and convention is suggested to describe the torsional angles in nucleic acids and their derivatives. The torsional angle χ, relating the stereochemistry of the base with respect to the sugar, shows more variation for the β-purine glycosides than for the β-pyrimidine glycosides. This variation is attributed to the fact that the β-purine derivatives may form intramolecular O(5′)-H…N(3) hydrogen bonding. The χ values for the α-purine and α-pyrimidine glycosides show preference for the –syn-clinal (or anti) conformation. The mode of puckering of the sugar also influences the χ value. The various possible conformations for the furanose ring are described by the torsional angles τ0 τ1, τ2, τ3, τ4, about the five ring bonds. From an analysis of the torsional angles (ω, ϕ, ψ, ψ′, ϕ′, ω′) about the sugar phosphate bonds in the x-ray structures of the known nucleosides, nucleotides, phosphodiesters, nucleic acids, and related compounds, and from a consideration of molecular models, it is found that the possible conformations for the backbone of helical nucleic acids is strikingly limited. Most importantly, the preferred conformation of the nucleotide unit in poly nucleotides and nucleic acids turns out to be the same as that found for the nucleotide in the crystal structure. It is observed that base “stacking” is a consequence of the restricted backbone conformation. The torsional angles are illustrated in the form of conformational “wheels”. Interrelation between the torsion angles about successive pairs of sugar-phosphate bonds are presented in the form of conformational maps: ω,ϕ; ϕ,ψ; ψ.ψ′; ψ′,ϕ′; ϕ′,ω′; ω′,ω. The ω′,ω map shows the perferred conformations about the inter-nucleotide bonds of right- and left-handed helices and the possible conformations of phosphodiesters. The preferred conformation of the pyrophosphate and triphosphate is that in which the phosphate oxygens display a staggered arrangement when viewed along the P–P axis. A plausible structure and conformation for the ATPM2− backbound complex is presented. This structure differs from that proposed by SzentGyorgi in that the metal (only transition metals are considered here) is not bound to the NH2 nitrogen of adenine, but rather is simultaneously bound to N(7) of the ring and three phosphates (α, β, γ), or N(7) of the ring and two phosphates (β, γ). The remaining metal coordination may be satisfied by solvent–metal or enzyme–metal bonds.

Stereochemistry of nucleic acids and their constituents.† IV. Allowed and preferred conformations of nucleosides, nucleoside mono-, di-, tri-, tetraphosphates, nucleic acids and polynucleotides‡

Wilm E. Donath

Papers

Conformations and Strain Energy of Cyclopentane and its Derivatives

Electronic Correlation in Molecules. I. Hydrogen in the Triplet State1