Found in translation: Quantum chemical tools for grasping non-covalent interactions

Today's quantum chemistry methods are extremely powerful but rely upon complex quantities such as the massively multidimensional wave function or even the simpler electron density. Consequently, chemical insight and a chemist's intuition are often lost in this complexity leaving the results obtained difficult to rationalize. To handle this overabundance of information, computational chemists have developed tools and methodologies that assist in composing a more intuitive picture that permits better understanding of the intricacies of chemical behavior. In particular, the fundamental comprehension of phenomena governed by non-covalent interactions is not easily achieved in terms of either the total wave function or the total electron density, but can be accomplished using more informative quantities. This perspective provides an overview of these tools and methods that have been specifically developed or used to analyze, identify, quantify, and visualize non-covalent interactions. These include the quantitative energy decomposition analysis schemes and the more qualitative class of approaches such as the Non-covalent Interaction index, the Density Overlap Region Indicator, or quantum theory of atoms in molecules. Aside from the enhanced knowledge gained from these schemes, their strengths, limitations, as well as a roadmap for expanding their capabilities are emphasized. (C) 2017 Author (s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license

Computational Quantum Chemical Studies on Radicals

Peter Rudolf Tentscher

Radicals play an important role in many areas of chemistry, such as atmospheric, aquatic, polymer, and biological, to name a few. Radicals are often highly reactive species which are short-lived and therefore harder to study by experimental techniques. In principle, computational quantum chemistry enables the study of arbitrary chemical species, including elusive radicals. However, the approximate quantum chemical methods which are used for production simulations need to be validated for the type of problem in question. First, it is necessary to validate that highly accurate reference methods commonly applied to closed-shell systems are equally applicable to radicals. I show that the “gold standard” for closed-shell systems (coupled cluster with singles, doubles, and perturbative triples excitations (CCSD(T))) can produce molecular geometries and vibrational frequencies suitable for (sub-)kJ/mol thermochemistry for radical species as well. However, additional diagnosis is necessary, especially for vibrational frequency calculations. Coupled cluster methods are then used to compute benchmark binding energies between small radicals and water or hydrogen fluoride as a proxy to the aqueous condensed phase. I find that many common density functional theory (DFT) methods cannot reproduce these binding energies to within chemical accuracy (1 kcal/mol). However, some functionals, for example MPW1K and BHandHLYP, perform better than others. If more accurate ab initio methods are computationally too demanding for the system of interest, these DFT methods should be used for (micro-)solvated radicals. Complexes of radicals with polar solvent are found to be more strongly bound than expected. This can not be explained by dispersive and electrostatic interactions alone. Using natural bond orbitals, I show that additional donor-acceptor interactions may be responsible for the strong intermolecular binding observed. One of the most fundamental processes involving aqueous organic radicals is the one-electron oxidation of closed-shell organics. I study the vertical ionization of neutral organics. That is, the ionization is faster than the reorganization of the solvent (and solute), and the conformation is assumed to be unchanged during the ionization process. I find that the difference between the gas-phase and aqueous-phase vertical ionization energy, ∆VIE = VIEaq − VIEgas, ranges from ≈ 0 to -1.0 eV for small aromatic compounds. The differences in ∆VIE between different compounds seem to be caused by the solvent structures of the ≈ 70 water molecules closest to the solute. In natural surface waters, oxidized organics arise through the reaction of photochemically created radicals with organic molecules already present in the water column. One example for such a reaction is the oxidation of sulfonamide antibiotics. I show that upon oxidation of sulfadiazine and related compounds, an aniline radical cation is formed. The reactivity of this oxidized species is strikingly different from its reduced counterpart: the barrier for a nucleophilic attack on the aniline ring is drastically lowered, and a fast rearrangement reaction can take place. I demonstrate that current quantum chemical protocols are suitable for mechanistic studies of solvated radicals, and I successfully apply them to such problems. To achieve chemical accuracy for quantum computational protocols, further developments are necessary. To validate novel approaches, the benchmark data presented in this thesis may be used.

EPFL2013

Quantum chemical studies of reactive species in water

Daniela Trogolo

In this thesis, quantum chemical methods have been applied to elucidate the thermodynamics and the kinetics of reactions involving reactive species in water. Due to their high reactivity in water, many transient species are difficult to study by experimental means only. Here, quantum chemical models are used to provide a deeper insight into the chemical nature and aqueous behaviors of such species. In the first chapter, I investigate the gas phase electronic structure and the thermodynamics of inorganic chloramines, bromamines, and bromochloramines, collectively termed halamines. The halamines are halogen oxidants that arise from reactions between ammonia and hypohalous acids during water disinfection processes, and these reactive species are implicated in the formation of disinfection byproducts that are harmful to human health. Despite their relevance in both drinking water chemistry and in biochemistry, the stabilities and speciation of these molecules are difficult to investigate by experimental means. To accurately predict the electronic structures and gas phase thermodynamic properties of halamines, I design a computational protocol, TA14, based on the high-quality Weizmann and Feller-Peterson-Dixon composite methods. TA14 combines a systematic sequence of wave function theory calculations, including the evaluations of dynamical and static electron correlation (CCSDTQ), core/valence electron correlation contributions, scalar and spin-orbit relativistic contributions, and VPT2 anharmonic vibrations. Using TA14, I successfully assess the gas phase total atomization energies, free enthalpies of formation, and Gibbs free energies of formation of halamines within uncertainty bounds of 1-3 kJ/mol. Analysis of the energy components contributing to total atomization energies of halamines reveals that N-Cl and N-Br bonds are held together mostly or entirely by electron correlation forces, with small or even negative Hartree Fock contributions. For example, the Hartree Fock component of the total atomization energy is negative for both NBr3 and NBr2Cl, implying that these molecules would be predicted as unstable without accounting for dynamical electron correlation. Reported thermochemical data enable the determination of equilibrium constants for reactions involving halamines, opening possibilities for more quantitative studies of the chemistry of these poorly understood compounds. In the second chapter, I evaluate the aqueous equilibria and speciation of halamines. I combine theoretical benchmark-quality gas phase Gibbs free energies of formation (chapter 2) with the computed Gibbs free energies of solvation, thereby obtaining aqueous phase Gibbs free energies of formation for halamines. The 'half-and-half' solvation approach, based on averaging the estimates of SMD implicit solvent model and the cluster-continuum solvent model, produces an average error of 3.3 kJ/mol in the free energies of solvation for a set of structurally related molecules containing H, N, O, and Cl. Taking into consideration the combined uncertainties of the computed gas free energy of formation values and the computed free energy of solvation values, we assign an uncertainty of 6-7 kJ/mol to the theoretical standard Gibbs free energies of formation in aqueous phase of halamines. Aqueous Gibbs free energies of formation values are key thermodynamic properties for investigating chemical processes involving halamines during drinking water treatment. The newly reported thermodynamic data can be used to determine the stabilities (reaction equilibria) of halamines in water. Based on our estimated uncertainties of 6-7 kJ/mol in the computed aqueous free energy of formation values of halamines, we expect roughly 1 order-of-magnitude uncertainty in the aqueous equilibrium constants for the reactions leading to the production of halamines in water. ...

EPFL2016

Libraries of Extremely Localized Molecular Orbitals. 3. Construction and Preliminary Assessment of the New Databanks

Benjamin André René Meyer

The fast and reliable determination of wave functions and electron densities of macromolecules has been one of the goals of theoretical chemistry for a long time, and in this context, several linear scaling techniques have been successfully devised over the years. Different approaches have been adopted to tackle this problem, and one of them exploits the fact that, according to the traditional chemical perception, molecules can be seen as constituted of recurring units (e.g., functional groups) with well-defined chemical features. This has led to the development of methods in which the global wave functions or electron densities of macromolecules are obtained by simply transferring density matrices or fuzzy electron densities associated with molecular fragments. In this context, we propose an alternative strategy that aims at quickly reconstructing wave functions and electron densities of proteins through the transfer of extremely localized molecular orbitals (ELMOs), which are orbitals strictly localized on small molecular units and, for this reason, easily transferable from molecule to molecule. To accomplish this task we have constructed original libraries of ELMOs that cover all the possible elementary fragments of the 20 natural amino acids in all their possible protonation states and forms. Our preliminary test calculations have shown that, compared to more traditional methods of quantum chemistry, the transfers from the novel ELMO databanks allow to obtain wave function and electron densities of large polypeptides and proteins at a significantly reduced computational cost. Furthermore, notwithstanding expected discrepancies, the obtained electron distributions and electrostatic potentials are in very good agreement with those obtained at Hartree-Fock and density functional theory (DFT) levels. Therefore, the results encourage to use the new libraries as alternatives to the popular pseudoatom-databases of crystallography in the refinement of crystallographic structures of macromolecules. In particular, in this context, we have already envisaged the coupling of the ELMO databanks with the promising Hirshfeld atom refinement technique to extend the applicability of the latter to very large systems.

AMER CHEMICAL SOC2018