Academic Year 2014

A priori selected configuration interaction (SCI) with truncation energy error [C.F.Bunge, J.Chem.Phys. 125,014107(2006)] and CI by parts [C.F.Bunge and R.Carbo-Dorca, J.Chem.Phys.125,014108(2006)] are used to approximate the total nonrelativistic electronic ground state energy of water at fixed experimental geometry with CI up to sextuple excitations. Correlation-consistent polarized core-valence basis sets (cc-pCVnZ) up to sextuple zeta and augmented correlation-consistent polarized core-valence basis sets (aug-cc-pCVnZ) up to quintuple zeta quality are employed. Truncation energy errors range bewtween less than one microH, and 160 microH (0.1 kcal/mol) for the largest orbital set. Coupled cluster CCSD and CCSD(T) calculations are also obtained for comparison. The upgrading of critical sections of the program will be discussed.

The global trend of looking for more ecologically friendly, 'green' techniques manifested itself in the chemistry of carbon nanomaterials. The main principles of green chemistry emphasize how important it is to avoid the use, or at least to reduce the consumption of organic solvents for a chemical process. And it is precisely this aspect which was systematically addressed and emphasized by our research group since the very beginning of our work on the chemistry of carbon nanomaterials in early 2000’s. In the present talk, we focus on the results obtained up to now on solvent-free techniques for (mainly covalent) functionalization of fullerene C60, single-walled and multi-walled carbon nanotubes (SWNTs and MWNTs, respectively), as well as nanodiamond (ND). We designed a series of simple and fast functionalization protocols based on thermally activated reactions with chemical compounds stable and volatile at 150-200 °C under reduced pressure, when not only the reactions take place at a high rate, but also excess reagents are spontaneously removed from the functionalized material, thus making unnecessary its purification. The main two classes of reagents are organic amines and thiols, including bifunctional ones, which can be used in conjunction with different forms of nanocarbons. The resulting chemical processes comprise nucleophilic addition of amines and thiols to fullerene C60 and to defect sites of pristine MWNTs, as well as direct amidation of carboxylic groups of oxidized nanotubes (mainly SWNTs) and ND. In the case of bifunctional amines and thiols, reactions of the second functional group can give rise to cross-linking effects, or be employed for further derivatization steps.

The recent developments of ab initio methodology [1,2] have been successful in yielding [3-6] the complete rotational-vibrational spectrum of near-spectroscopic accuracy for the diatomic molecules B2, F2 and O2. Most significantly, this theoretical work provided the spectroscopic data which, as yet, has been inaccessible to experimental spectroscopy for the boron [3] and oxygen molecules [4] in their ground states. In particular, for the ground state of O2, the theoretical studies yielded 15% of the full spectrum [4] which has eluded the spectroscopic measurements. For the ground state of B2, the theory [3] has yielded 85% of the full spectrum which could not be determined experimentally. Furthermore, the theoretical results led to the reassignment of the electronic transitions in B2 that are believed to be responsible for the observed spectrum reported by Bredohl and co-workers [7]. Ab initio potential for the ground state of F2 has yielded [5,6] the rotational-vibrational spectrum within 5 cm-1 of the experiment and predicted an additional vibrational energy level. The theoretical results are based on the ability of the newly developed ab initio method [1-6] (on the basis of intrinsic scaling) to approximate the full configuration interaction (FCI) and complete basis set (CBS) limit very closely. Furthermore, the effects that are due to the inner shell (core) electron correlation and relativity have been found to be significant. Finally, some new developments of ab initio methodology for application to larger systems are also discussed.
[1] L. Bytautas, K. Ruedenberg, J. Chem. Phys. 121, 10905 (2004).
[2] L. Bytautas, K. Ruedenberg, J. Chem. Phys. 122, 154110 (2005).
[3] L. Bytautas, N. Matsunaga, G. E. Scuseria, K. Ruedenberg, J. Phys. Chem. A 116, 1717 (2012).
[4] L. Bytautas, N. Matsunaga, K. Ruedenberg, J. Chem. Phys. 132, 074307 (2010).
[5] L. Bytautas, N. Matsunaga, T. Nagata, M. S. Gordon, K. Ruedenberg, J. Chem. Phys. 127, 204301 (2007).
[6] L. Bytautas, N. Matsunaga, T. Nagata, M. S. Gordon, K. Ruedenberg, J. Chem. Phys. 127, 204313 (2007).
[7] H. Bredohl, I. Dubois, F. Melen, J. Mol. Spectrosc. 121, 128 (1987).

We consider series of defected graphitic hydrocarbon molecules with one 5,7-ring embedded dislocation and also different ones with two 5,7 defect pairs. In one series, two defects are contiguous (Stone-Wales: 5775) within the graphitic lattice, the other defected species have two 5,7-pairs separated by one or two pairs of carbon hexagons. Separated 5,7-pairs are oriented either anti to each other, or have one of two syn or "linear" orientations. Each series is constructed by circumscription of a defect with an integer (R) number of layers of sp2 carbon hexagons. Edges of molecules in each series terminate in a C-H bond (mostly with a zig-zag edge). In the infinite circumscription limit, energies and other properties of a series represent graphene with a single defect. Energies, structures and other properties of each member of a series are compared with its isomeric non-defected series (based on 6,6-pairs). Structures are optimized in B3LYP//3-21G and better model chemistries. For R=number of circumscriptions, defected molecules of sufficient R have disrupted quasi-planar geometries consistent with distortions expected for 5 and 7 membered rings. For isomeric pairs, ΔE's for distortion appear to converge as R-1. Patterns of ΔE convergence for the 57 dislocation and 5775 (Stone Wales) defect are similar in several model chemistries and converge to similar values, although geometry disruption becomes apparent for 5775 only at R=4 (C192H34). Via b3lyp//3-21G with R= 1 to 6, converged values are 5.5 ev (57) and 5.2 ev (5775). For separated-pair defects, ΔE values are larger (ca. 8 to 11 ev,). Values of ΔE increase with extent of pair separation for 57 pairs in an anti-orientation, but ΔE decreases slightly with separation, when pairs have linear orientations. Energies of anti-oriented 57 defect pairs may be related to "migration" of the Stone Wales defect over a graphene lattice.

In this talk we will discuss several basic molecular simulations that have lead to a curiosity in the application to real world problems in the area of carbon nanostructures. From these we have explored numerical simulations in the area of graphene from use in semiconductors to actual industrial production of graphene derivatives. Experience in the development of scientific strategies and industrial applications will be discussed through my experiences in both public and private sectors.

Carbon chemistry can be considered the Chemistry of Life, if we include water and light. With one electron less, boron chemistry has sometimes gone unnoticed and its role in biology is unknown. In this talk we will review similarities and differences of the boron and carbon worlds of chemistry.

Heterocyclic systems with a ring-junction nitrogen atom are of great importance because many of their derivatives exhibit a wide range of biological and pharmaceutical applications. Within this huge family of compounds, the unsaturated bicyclic system 4H-quinolizin-4-one is interesting in view of the potential biological activity and its applications as selective fluorescent indicator. However, despite the potential applications of the 4H-quinolizin-4-one derivatives, scarcely synthetic routes are available and in some cases, the use of drastic reaction conditions, multi-steps protocols to obtain adequated starting materials or the use of highly expensive metals (i.e., Pd or Rh) are required, even with the disadvantage of accomplishing poor global yields. Recently, we reported that the synthesis of a novel ferrocenyl vinyl ketene as a stable η⁴-[Fe(CO)₃] complex can be successfully accomplished through the reaction of η²-[Fe(CO)₄] complex with MeLi under mild carbonylation conditions. The reactivity of this η⁴-[Fe-(CO)η₃] ferrocenyl vinyl ketene complex under thermal conditions lead to the formation of a 3-ferrocenyl-4H-quinolizin-4-one. ¹ The pathway of this process, studied computationally within the DFT framework, revealed that the metal fragment [Fe(CO)₃] plays a central role in the stabilization of different intermediates generated during the reaction through steps of olefin isomerization, migration, and cyclization. In order to reveal the synthetic scope of this process, we decided to extend this methodology to other substrates including alkyl, aryl and heterocyclic groups. Thus, in this lecture it will be exposed a concise and general synthetic method for obtaining new fluorescent compounds using as key intermediate, vinyl ketenes stabilized by the Fe(CO)₃ fragment.² In addition, the fluorescent properties of these new compounds reveal their potential applications as chemical sensors.

¹ a) M. C. Ortega-Alfaro, A. Rosas-Sánchez, B. E. Zarate-Picazo, J. G. López-Cortés, R. A. Toscano, F. Cortés Organometallics, 2011, 30, 4830-4837;
² A. Rosas-Sánchez, J. G. López-Cortés, R. A. Toscano, P. Carreón-Castro, M. C. Ortega-Alfaro, Org. Lett. 2014, (enviado).

We propose a mechanism by which chloromethane and dichloromethane decomposition reaction occurs on the surfaces of graphene. To this end we have performed calculations on the graphene surface with metal adsorption on the sheet to reduce the formation of fre radical intermediates.

One of Douglas Klein's interest along his scientific career has been the concept of order in chemistry. In one of his papers on the subject he mentioned that the periodic table, which entails the concept, can be regarded as a multi-poset, i.e. a set with different order relations for its elements. In this lecture we show how the original Mendeleevian periodic table entails two basic concepts, ordering, as Klein early noticed, and classification. Delving into the mathematics of classification and ordering we derived a generalised formalism for periodic table, which solves the question of a formal definition of periodic table. The definition we propose meet the customary periodic tables of chemical elements and beyond, namely other sets of chemicals. We finally show how the formalised definition of periodic table meets Klein's ideas on multiposets.

If a molecule is viewed at zero order as a collection of atoms and at first order as a collection of bonds between some of those atoms, a cluster expansion provides a systematic way to express a property of the molecule exactly in terms of (successively smaller) contributions from successively larger molecular fragments. Cluster expansions for a variety of properties of several classes of molecules will be discussed, and attention will be paid to some of the questions which much be addressed in constructing such expansions. It will be shown that many empirical schemes found in the literature can be re-expressed as cluster expansions. For molecules containing conjugated or aromatic pi bonds it becomes convenient to invoke sigma-pi separation to allow different cluster expansions to be used for the relatively rapidly convergent sigma part and the relatively slowly convergent pi part of the molecular energy. This allows contact to be made with other methods of treating pi electron systems, such as Hess and Schaad’s treatment of conjugated molecules and Quantitative Resonance Theory (Herndon) or Conjugated Circuits Theory (Randic and Trinajstic) for aromatic rings. Particularly for aromatic systems, a number of questions of how best to construct the cluster expansion remain open.

Genes consist of sets of codons, with each codon having three nucleic acids. The mixing character of the codon set that comprises a gene is dened. Mixing character and its representation by Young Diagrams (YD) is reviewed. It is well known that that YDs are partially ordered by so-called majorization and comprise nodes in the Young Diagram Graph or Lattice. Young Diagrams also correspond to irreducible representations of the symmetric group a topic of much of Doug Klein's early work in spin-free quantum chemistry and his ongoing work in group theory; though, here, that is not further discussed. We examine the mixing character for 15 genes in the Rainbow Trout. Each mixing character is a partition of the integer 64, where 64 is the number of possible codons. We determine the comparability or incomparability of the 15 sample genes. The comparability or incomparability number of a gene is discussed in the context of gene complexity.

Double adsorption of alkalines on aromatic molecules, polyacenes and similar structures is shown to be locally stable if it happens on both sides of the same ring. In the case of light alkalines such as Li we see a surprising phenomenon: The distortion of the adsorbent becomes much stronger for such a double adsorption then for single adsorption, making a mirror symmetric configuration quite unstable. We shall discuss this phenomenon, exclude the option of a Jahn Teller effect, and relate it to a Peierls instability. The main purpose of this talk is to get the birthday child and the entire the audience to contribute to the understanding of this phenomenon.

We study theoretically how electrons, coherently injected at one point on the boundary of a 2D electron system, are focused by a perpendicular magnetic field onto another point on the boundary. We will start with the non-relativistic case but discuss also graphene's relativistic electron system. In weak magnetic fields, the four-point Hall resistance shows the characteristic equidistant peaks, which can be explained by classical cyclotron motion along the boundary. In strong fields, the Hall resistance shows a single extended plateau reflecting the quantum Hall effect. In intermediate fields, we find superimposed upon the lower Hall plateaus anomalous oscillations, which are explained by the interference between the occupied eigenstates.

We will discuss the role of sp2-carbon edge, its energy and growth [1], the similarities and contrasts between nanotubes and graphene, including the dynamics of defect healing [2]. Comprehensive DFT computations allow one to build a "nanoreactor" diagram of all important energy states, and then to predict the rate of carbon addition, the growth speed in different directions, and thus the shape of growing or shrinking graphene islands. Further, the nanoreactor approach helps understanding the role of auxiliary species, like hydrogen [3] or oxygen [4]. References:
[1] V. Artyukhov et al. Proc. Natl. Acad. Sci. 109, 15136 (2012); Y. Liu, et al. PRL 105, 235502 (2010).
[2] R. Rao et al. Nature Mater. 11, 213 (2012); Q. Yuan, et al. Phys. Rev. Lett. 108, 245505 (2012).
[3] Z. Yan et al. J. Amer. Chem. Soc., 135, 10755 (2013).
[4] Y. Hao et al. Science, 342, 720 (2013).

Electron atom/molecule resonances are temporarily bound states which lie in the continuum part of the electronic Hamiltonian. They are important in many physical and chemical processes. If the electronic coordinates of the Hamiltonian are scaled ("dilated") by a complex parameter, η = αe^iθ (&alpha, &theta real), then its complex eigenvalues represent the scattering states (resonant and non-resonant) while the eigenvalues corresponding to the bound states and the ionization thresholds remain real and unmodified. These make the study of these transient species position and widths amenable to complex scaled bound state methods. We have recently initially theoretically developed complex scaled muticonfigurational self consistent field (CMCSCF) and M₁ methods and applied them to "relatively" simple shape resonances in Be and N₂. Preliminary work has been done by us on complex scaled multiconfigurational time dependent Hartree Fock (CMCTDHF). In real space MCTDHF gives good excitation energies and linear response properties. The multiconfiguration spin-tensor electron propagator method gives accurate and reliable electron affinities and ionization potentials. We are complex scaling this method (CMCSTEP) and want to test its applicability. Finally, we have initially complex scaled a simple multireference configuration interaction method (CMRCI). Both CMCSTEP and our CMRCI use CMCSCF initial or reference states. We are further developing all five methods. Initial calculations with CMCSCF, M₁, CMCTDHF and CMRCI have been promising so far for relatively simple atoms and molecules. We then plan additional studies for shape and more complictaed resonances for atoms and molecules of chemical and physical interest including eventually C₆₀ and DNA and RNA nucleobases.