Annik Vivier Bunge

OH hydrogen abstraction reactions from alanine and glycine: A quantum mechanical approach

Density functional theory (B3LYP and BHandHLYP) and unrestricted second‐order Møller–Plesset (MP2) calculations have been performed using 3‐21G, 6‐31G(d,p), and 6‐311 G(2d,2p) basis sets, to study the OH hydrogen abstraction reaction from alanine and glycine. The structures of the different stationary points are discussed. Ring‐like structures are found for all the transition states. Reaction profiles are modeled including the formation of prereactive complexes, and very low or negative net energy barriers are obtained depending on the method and on the reacting site. ZPE and thermal corrections to the energy for all the species, and BSSE corrections for B3LYP activation energies are included. A complex mechanism involving the formation of a prereactive complex is proposed, and the rate coefficients for the overall reactions are calculated using classical transition state theory. The predicted values of the rate coefficients are 3.54×108 L⋅mol−1⋅s−1 for glycine and 1.38×109 L⋅mol−1⋅s−1 for alanine.

Symmetry-eigenfunctions for many-electron atoms and molecules: A unified and friendly approach for frontier research and student training

Abstract Atomic and molecular many-electron symmetry-eigenfunctions are obtained by means of a FORTRAN program based on projection operators and ordered Slater determinants. When degeneracies exist, Schmidt orthonormalization of a conveniently ordered manifold allows for the construction of a hierarchy of interacting spaces, unattainable through Racah algebra or group-theoretical methods, but necessary for compact many-electron theories and calculations beyond Hartree-Fock. Through a strict modular organization, this program offers a variety of concurrent evolution pathways covering all kinds of symmetry-eigenfunctions. Also, the results it generates can be fed into other modules for the general and efficient calculation of many-electron wave functions, or for symbolic evaluation of selected many-electron matrix elements of symmetry-operators such as the Hamiltonian. The program may be run interactively or in batch form to produce lists of configuration state functions for actual electronic structure calculations. In tutorial and interactive modes, help, status and overview commands can be invoked as an aid to gain working knowledge on many-electron symmetry-eigenfunctions. Standard FORTRAN 77 and full validation of array dimensions expressed in terms of parameters ensure widespread portability.

Spin eigenfunctions for many-electron calculations

Abstract We discuss a modular and efficient FORTRAN program which operating on a given linear combination of Slater determinants generates a spin eigenfunction by means of a symmetric, idempotent and hermtitian projection operator. In combination with other modules described in two previous and three further papers it may be used to generate all symmetry eigenfunctions needed in atomic and molecular electronic structure calculations. In particular, first-order and second-order interacting spaces are discussed.

Angular momentum eigenfunctions for many-electron calculations

Abstract We discuss a modular and efficient FORTRAN program to generate many-particle jj-JM and L 2 eigenfunctions obtained as projections of a single ordered Slater determinant built up from symmetry-adapted one-electron functions. Interacting spaces useful in calculations beyond Hartree-Fock are considered. In combination with other modules described in the previous and in four further papers this program can be used to generate all symmetry-eigenfunctions needed in atomic electronic structure calculations.

Eigenfunctions of spin and orbital angular momentum by the projection operator technique

A computer program has been written in Fortran IV to produce eigenfunctions of spin and orbital angular momentum (LS functions) by the projection operator technique. The projection operator acts on a Slater determinant built up from symmetry-adapted spinorbitals. When degeneracies exist, it is easy to provide a set of determinants whose projections span the whole degenerate space. In such cases, the LS functions are Schmidt orthonormalized. These functions provide natural partitions of degenerate LS spaces which are useful in the simplification and systematization of atomic calculations. Some representative examples are discussed.

Systematic search of excited states of negative ions lying above the ground state of the neutral atom

Abstract Nonrelativistic fixed-core valence-shell configuration interaction calculations are carried out for excited states of atomic negative ions in the range H through Ca, in an effort to identify the ones which are metastable against autoionization. Approximate relativistic corrections are included in some cases. From Be onwards, all (Core)n(n+1)sq(n+1)pr neutrals appear to bind an extra electron into a bound ( Core ) n (n+1) s q (n+1) p r+1 2S+1 L negative ion, in all cases where the 2S+1L continuum starts at the corresponding neutral atom state. Similarly as in the recently discussed case of Li−, alkali-earths (Be−, Mg−, Ca−), Zn−, B−, Al−, C−, Si−, Ar−, and possibly S−, have two bound excited states connected by an E1 transition in regions extending from infrared to vacuum ultraviolet. Negative neon is found to decay by E1 radiation into a continuum, thus Ne− beams are unlikely to be made in the future. However, there exists a metastable [Ne]3p54s4p 4S state of negative argon, making possible the production of Ar− beams.

Ab‐initio study of initial atmospheric oxidation reactions of C3 and C4 alkanes

Second‐order, Møller–Plesset (MP2)‐unrestricted Hartree–Fock calculations with full geometry optimization in the 6‐31G(d, p) basis set were carried out to study the initial atmospheric oxidation reactions of alkanes. All structures in the initial hydrogen abstraction reaction by an OH radical and the subsequent addition of molecular oxygen to the alkyl radical were characterized for alkanes with three and four carbon atoms. The reaction paths for the formation of the peroxyl radicals were obtained and discussed in the light of similarities along series involving primary, secondary, and tertiary hydrogens. A 0.999 correlation was found between the height of our barriers for the OH abstraction of a primary hydrogen atom from alkanes containing one to four carbon atoms and the optimally estimated activation energies for this reaction recently presented. From the slope and the intersection at zero activation energy an equation was obtained that yields scaled values of the activation energies to account for the tunnel effect and for the error due to the basis set and the method employed. We present new results for the abstraction of the less favored primary hydrogens in propane, butane, and isobutane, which should be important at high temperatures. Negative net activation energies were obtained for the addition of molecular oxygen to all the alkyl radicals formed in the first reaction. The structure of the peroxyl radicals is discussed; and very good correlations are observed for similar compounds, regardless of the length of the carbon chain. A revision of some experimental values is suggested. Single point density functional calculations at the MP2 geometries were also performed with the B3LYP functional for comparison. The observed trends are exactly the same for the two methods. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 845–856, 1999

Molecular symmetry eigenfunctions for many-electron calculations

Abstract We discuss a modular FORTRAN program which operating on an ordered Slater determinant generates an eigenfunction spanning an irreducible representation of a given molecular symmetry group. The program is supported by a database of point group representation matrices. In combination with other modules described in two previous and two further papers it may be used to acquire a working knowledge about molecular symmetry eigenfunctions and to generate lists of many-electron symmetry-adapted configurations suitable for electronic structure calculations beyond Hartree-Fock.

HQRII1: An accurate, portable and fast diagonalization routine

Abstract Drawing upon subroutines HQRII and SHQRII, the most efficient FORTRAN codes available to solve the eigenproblem for dense real symmetric matrices, we developed a new FORTRAN program, named HQRII1. It is considerably more accurate than the above mentioned programs and runs on a VAX-11/780 computer 16, 19 and 23 percent faster than SHQRII for matrices of order 100, 150 and 200, respectively.

New algorithm and FORTRAN module to carry out the four-index transformation of atomic and molecular physics wholly in central memory

Abstract This is the first of three companion papers describing a complete and modular library to carry out the four-index transformation of a block [( pq/mrs )] of two-electron integrals involving symmetry-adapted primitive orbitals p, q, r, s and a symmetry-related index m into a block [( ij/klm )] of integrals over symmetry-adapted orthonormal (orbitals i, j, k, l . The index m allows for the unified treatment of atomic and molecular, relativistic and nonrelativistic calculations. A new algorithm based on a generalization of a method by Saunders & van Lenthe [ Mol. Phys. 48, 923 (1983)] for non-symmetry orbitals has been developed. It is here implemented by means of a FORTRAN code, controlled by subroutine C4ITD, requiring all computed quantities to be held in central memory. A non-redundant set of integrals is used throughout. All pertinent sums run only over a limited range determined by a given symmetry. The rate determining steps may be carried out in parallel and are vectorizable within each possible concurrent processor. For 20 non-symmetry orbitals and with 64-bit precision on a VAX-11/780 computer, using a working set of 200 kbytes, subroutine C4ITD takes 48 CPU s. Ninety percent of this time is spent in steps dominated by vector-scalar-multiply-and-add (VSMA) operations carried out at 0.170 mega floating point operations per second, which is 91% of the performance achieved on the same computer by an equivalent mix of pure VSMA operations and vector sizes. C4ITD will be useful in atomic and molecular electronic structure calculations beyond Hartree-Fock.