PM3 SCF Research Articles

Quantum-Chemical Investigation of the Mechanism of Transfer of Fluorine in the Reaction of F‐TEDA‐BF4 with Dimethylenebicyclo[3.3.1]nonane

The mechanism of the reaction of the N-fluoro reagent F‐TEDA‐BF4 with dimethylenebicyclo[3.3.1]nonane was investigated by the semiempirical PM3 SCF MO method using the Cramer–Truhlar SM5.42R solvation model. It was shown that the mechanism of addition of the fluorine corresponds to classical SN2 nucleophilic substitution involving single-electron transfer synchronous with the cleavage–formation of C—F and N—F bonds.

The use of PM3 SCF MO quantum mechanical calculations to refine NMR-determined structures of complexes of antifolate drugs with dihydrofolate reductase in solution

PM3 SCF MO calculations were carried out on model compounds related to trimethoprim and an interacting aspartic acid in its binding site in the enzyme Lactobacillus casei dihydrofolate reductase. The systems examined included 2,4-diaminopyrimidine/acetic acid and trimethoprim/propionic acid. The calculations provided the geometric parameters describing the interaction of the trimethoprim N1 and 2-amino group protons with the carboxylate oxygen atoms of the conserved aspartic acid 26 residue in the enzyme. In the calculations where water molecules or protein fragments were included, the calculated ionisation states agreed with the experimentally observed results. Calculated structures obtained from docking trimethoprim with dihydrofolate reductase using constraints based on the results of the PM3 calculations together with the NMR-based distance constraints were compared with previous results obtained from calculations using only the NMR constraints.

PM3 study of organometallic radicals formed by elements in periodic Groups 13–16

Calculations have been made by the PM3 SCF method of the molecular and electronic structures of a range of neutral, cationic and anionic organometallic radicals derived from permethyl derivatives of elements from Groups 13–16. In Group 13, the planar methyls M(CH 3) 3 all yield pyramidal mononuclear radical-anions [M(CH 3) 3] −, but only for M = Al was a stable dinuclear radical-anion [Al 2(CH 3) 6] − found; this is a weak complex of [Al(CH 3) 2] . and [Al(CH 3) 4] −.In Group 14, dinuclear σ radical-cations [M 2(CH 3) 6] + of D 3 d symmetry are found for M = SiPb, and analogous * radical-cations are found for M = PBi in Group 15. The dinuclear [M 2(CH 3) 4] + formed by sulphur and selenium both have C 2 h symmetry.

Isomerisation of decatetraenes and dimethyldecatetraenes via pentadienyl and 3-methylpentadienyl radicals

The thermal isomerisations of E,E-deca-l,3,7,9-tetraene and E,E-3,7-dimethyldeca-l,3,7,9-tetraene take place via the intermediacy of pentadienyl and 3-methylpentadienyl radicals, respectively, rather than by concerted Cope type rearrangements. The pentadienyl radicals isomerise to pairs of E- and Z-pentadienyl radicals which recombine by end to end and end to centre, but not centre to centre, coupling to give mixtures of isomeric decatetraenes. The relative free energies of formation of these decatetraenes were derived from their equilibrium proportions and compared with relative enthalpies of formation calculated by the empirical MM2(87) method and the semiempirical AM1 and PM3 SCF MO methods. None of these theories was successful at predicting and rationalizing the experimentally observed enthalpy changes. However, they all were somewhat better in dealing with branching than with cis/trans isomerisation. Frontal strain in the decatetraene plays an important part in influencing their stability.

Transition state structure in cycloaddition reactions as a function of ring size and geometry

The relative energies of the stepwise one-bond and synchronous two-bond reaction pathways are compared at the semi-empirical AM1 and PM3 SCF and ab initio MP2 levels for the closed shell π2s+π4s cycloaddition reaction between the NO2+ ion and ethyne. The intrinsic bias towards the stepwise route for this reaction is estimated at 11 kcal mol–1 for PM3 and rather more for AM1. There is reasonable agreement between the AM1 and PM3 geometries and those obtained using ab initio MCSCF methods for the π2s+π4s reaction between ethene and butadiene, the π2s+π2a cyclodimerisation of ethene, and the π2s+π2a reaction between ethene and ketene. The location of two second-order saddle points for the latter reaction, where the antarafacial component is located on either the ethene or the ketene, allows the antarafacial stabilisation via the carbonyl group to be estimated as 27 kcal mol–1. The effect of E/Z isomerism and of antarafacial components on the geometries and energies of the synchronous stationary points for a range of larger ring cycloadditions is established at the AM1 and PM3 levels. The prediction by Mclver that such reactions will become increasingly asynchronous as the ring size increases is only weakly manifested at the closed shell RHF SCF level, but is more prominent at the spin unrestricted UHF level. The crossover between synchronous and asynchronous bond formation probably occurs for ten-membered rings.

Molecular orbital studies of molecular exciplexes. Part 1: AM1 and PM3 calculations of the ammonia–oxygen complex and its solvation by water

Ground- and excited-state calculations of the triplet O2·NH3·nH2O complex as a model for solution photo-oxygenation of amines by triplet oxygen are reported at the AM1 and PM3 SCF–MO levels. For n < 3, the first excited AM1 triplet state corresponds to local excitation on the ammonia (TN), whereas the polar excited state (TP) corresponding to NH3+·O2–· becomes the lowest excited triplet state when n≥ 3. In contrast, the lowest excited PM3 triplet state is ionic even for n= 0, and the TP and ground-state (T0) triplet surfaces intersect at an N–O distance of 1.95 A for n= 5, with TP becoming a local minimum on ground triplet state surface at shorter N–O distances. The reliability of these models are discussed in terms of known errors and properties of the AM1 and PM3 methods, and by a comparison of the solvation enthalpies and structures of systems such as NH4+·nH2O, NH4+·nNH3, and HO–·nH2O (n= 1–4) with known experimental values.