Molecular Mechanics and SCF MO Conformational Analysis of Indol-3-ylacetic Acid Phytohormone (Auxin)

Conformational analysis of indol-3-ylacetic acid (IAA)-plant growth hormone has been performed using molecular mechanics and the ab initio SCF MO theory. The equilibrium geometry of IAA has been determined. Relative energies of alternative conformations, their charge distribution, dipole moment and energy barriers between them have been calculated. The position of the carboxyl group relative to the indole ring depends on two torsion angles, Tl(C2-C3-C8-C9) and T2(C3-C8-C9=02). Rotational barriers for these two angles were explored and it emerged that both rotations (about the C3-C8and C8-C9 bonds) can be accomplished in a reasonable time period at room temperature (the barrier height is about 4.6-10.9 (TI) and 1.7-3.8 (T2) kJ/mol respectively, according to ab initio calculations. Ab initio (GAMESS)and molecular mechanics (DISCOVER (CVFF and cff91), SYBYL(TRIPOS) and MM2(87), calculations revealed qualitatively the same shape of potential energy surface (E =f(Tl, T2)). However, energy differences between various conformations depend on the basis set (ab initio calculations) and force field (molecular mechanics) used

Hydrogen bonding in infinite hydrogen fluoride and hydrogen chloride chains

Hydrogen bonding in infinite HF and HCl bent (zigzag) chains is studied using the ab initio coupled-cluster singles and doubles (CCSD) correlation method. The correlation contribution to the binding energy is decomposed in terms of nonadditive many-body interactions between the monomers in the chains, the so-called energy increments. Van der Waals constants for the two-body dispersion interaction between distant monomers in the infinite chains are extracted from this decomposition. They allow a partitioning of the correlation contribution to the binding energy into short- and long-range terms. This finding affords a significant reduction in the computational effort of ab initio calculations for solids as only the short-range part requires a sophisticated treatment whereas the long-range part can be summed immediately to infinite distances.Comment: 9 pages, 4 figures, 3 tables, RevTeX4, corrected typo

Ab initio Green's function formalism for band structures

Using the Green's function formalism, an ab initio theory for band structures of crystals is derived starting from the Hartree-Fock approximation. It is based on the algebraic diagrammatic construction scheme for the self-energy which is formulated for crystal orbitals (CO-ADC). In this approach, the poles of the Green's function are determined by solving a suitable Hermitian eigenvalue problem. The method is not only applicable to the outer valence and conduction bands, it is also stable for inner valence bands where strong electron correlations are effective. The key to the proposed scheme is to evaluate the self-energy in terms of Wannier orbitals before transforming it to a crystal momentum representation. Exploiting the fact that electron correlations are mainly local, one can truncate the lattice summations by an appropriate configuration selection scheme. This yields a flat configuration space; i.e., its size scales only linearly with the number of atoms per unit cell for large systems and, under certain conditions, the computational effort to determine band structures also scales linearly. As a first application of the new formalism, a lithium fluoride crystal has been chosen. A minimal basis set description is studied, and a satisfactory agreement with previous theoretical and experimental results for the fundamental band gap and the width of the F 2p valence band complex is obtained.Comment: 20 pages, 3 figures, 1 table, RevTeX4, new section on lithium fluorid

The low temperature interface between the gas and solid phases of hard spheres with a short-ranged attraction

At low temperature, spheres with a very short-ranged attraction exist as a close-packed solid coexisting with an infinitely dilute gas. We find that the ratio of the interfacial tension between these two phases to the thermal energy diverges as the range of the attraction goes to zero. The large tensions when the interparticle attractions are short-ranged may be why globular proteins only crystallise over a narrow range of conditions.Comment: 6 pages, no figures (v2 has change of notation to agree with that of Stell

Methane adsorption in metal-organic frameworks containing nanographene linkers: a computational study

Metal-organic framework (MOF) materials are known to be amenable to expansion through elongation of the parent organic linker. For a family of model (3,24)-connected MOFs with the rht topology, in which the central part of organic linker comprises a hexabenzocoronene unit, the effect of the linker type and length on their structural and gas adsorption properties is studied computationally. The obtained results compare favourably with known MOF materials of similar structure and topology. We find that the presence of a flat nanographene-like central core increases the geometric surface area of the frameworks, sustains additional benzene rings, promotes linker elongation and the efficient occupation of the void space by guest molecules. This provides a viable linker modification method with potential for enhancement of uptake for methane and other gas molecules