A consensus has progressively developed that the path towards complex organic molecules could be favoured by the icy mantles of interstellar dust particles. However, the question of whether activation energy is required to promote those reactions is open. This work deals with the simplest process thought to increase complexity i.e. successive additions of a single atom (H). Two situations can be considered, the direct additions of H in the gas phase and the atomic hydrogenation processes on water ice surfaces available in the interstellar medium (ISM). The synthesis of methanol, largely discussed in the literature is revisited as a case study. Computational investigations of the reactions leading from CO to CH3OH show that, with [H...(H2O)(n)] complexes as hydrogenation vectors, all steps of the process are barrier-less, contrary to the gas phase process and this, whatever the level of theory considered. The key parameter is the position of the CO + [H...(H2O)(n)] initial system on the global energy scale. At the present level of theory, when H is pre-adsorbed on the ice, the system happens to be high enough above the reaction path, namely, above any intermediates and possible transition states. This is true whatever the dimension of the ice support, even for the simplest model of one H2O molecule. Application of such a simplified synthetic approach, here validated for the synthesis of methanol, could be generalized, providing a simple way to get a fair insight into the important class of atomic hydrogenations on ices in the ISM.

Context. Helium, the second most abundant element in the Universe, with a relative abundance of He/H ~ 1/10, has never been observed in any other form than that of a neutral atom (He) or an ion (He+) in the interstellar medium. Since He is a noble gas its non-observation as part of neutral molecular systems is understandable, but it is very surprising for a positively charged species such as HeH+ that is a stable diatomic ion whose spectral signatures are well known in the laboratory. Aims. This non-observation, even in hydrogen rich regions, could imply that HeH+ is not a proper target and that alternatives have to be considered, such as small HeHn+ clusters. The present study aims at finding whether the leading term HeH3+ fulfills the conditions required. Methods. We addressed the question with state-of-the-art numerical simulations. We determined a two-dimension ab initio potential energy surface (PES) of the HeH3+ cluster along the He...H3+ and HeH+...H2 reaction coordinates. The calculations rely on complete active space configuration interaction followed by a second order perturbation treatment (CAS-PT2). This surface was used for the evaluation of the two radiative associations rate constants by means of a quantum treatment of the collision between the interacting fragments. Results. These calculations show unambiguously that HeH3+ is the most stable point on the corresponding global PES. Then, we determined the rate constants of the radiative associations HeH+ + H2 and He + H3+ leading to HeH3+. Conclusions. Significative values were obtained that reach up to 2 × 10-18 cm3 s-1, which should stimulate new tentatives to detect molecular helium in astrophysical objects.

In this contribution, we propose a deeper understanding of the electronic effects affecting the nucleation of water around the Au+ and Hg2+ metal cations using quantum chemistry. To do so, and in order to go beyond usual energetical studies, we make extensive use of state of the art quantum interpretative techniques combining ELF/NCI/QTAIM/EDA computations to capture all ranges of interactions stabilizing the well characterized microhydrated structures. The Electron Localization Function (ELF) topological analysis reveals the peculiar role of the Au+ outer-shell core electrons (subvalence) that appear already spatially preorganized once the addition of the first water molecule occurs. Thus, despite the addition of other water molecules, the electronic structure of Au(H2O)(+) appears frozen due to relativistic effects leading to a maximal acceptation of only two waters in gold's first hydration shell. As the values of the QTAIM (Quantum Theory of Atoms in Molecules) cations's charge is discussed, the Non Covalent Interactions (NCI) analysis showed that Au+ appears still able to interact through longer range van der Waals interaction with the third or fourth hydration shell water molecules. As these types of interaction are not characteristic of either a hard or soft metal cation, we introduced the concept of a "pseudo-soft" cation to define Au+ behavior. Then, extending the study, we performed the same computations replacing Au+ with Hg2+, an isoelectronic cation. If Hg2+ behaves like Au+ for small water clusters, a topological, geometrical, and energetical transition appears when the number of water molecules increases. Regarding the HSAB theory, this transition is characteristic of a shift of Hg2+ from a pseudosoft form to a soft ion and appears to be due to a competition between the relativistic and correlation effects. Indeed, if relativistic effects are predominant, then mercury will behave like gold and have a similar subvalence/geometry; otherwise when correlation effects are predominant, Hg2+ behaves like a soft cation.

Pb(2+) complexes can attain several different topologies, depending of the shape of the Pb 6s6p lone pair. In this paper, we study structures with a bisdirected Pb lone pair with quantum mechanics (DFT) and QM/MM calculations. We study small symmetric Pb(2+) models to see what factors are needed to get a bisdirected lone pair. Two important mechanisms have been found: First, the repulsion of the lone pair of Pb(2+) with other lone pairs in the equatorial plane leads to a bisdirected structure. Second, a bisdirected lone pair can also arise due to interactions with double bonds, lone pairs, or hydrogen atoms. Moreover, we have analyzed Pb(2+) sites in proteins and to see if a bisdirected lone pair can exist in an asymmetrical environment. Several instances of bisdirected lone pairs were discovered.

In Nature, the family of copper monooxygenases comprised of peptidylglycine α-hydroxylating monooxygenase (PHM), dopamine β-monooxygenase (DβM), and tyramine β-monooxygenase (TβM) is known to perform dioxygen-dependent hydroxylation of aliphatic C-H bonds by using two uncoupled metal sites. In spite of many investigations, including biochemical, chemical, and computational, details of the C-H bond oxygenation mechanism remain elusive. Herein we report an investigation of the mechanism of hydroxylation by PHM by using hybrid quantum/classical potentials (i.e., QM/MM). Although previous investigations using hybrid QM/MM techniques were restricted to geometry optimizations, we have carried out ab initio molecular dynamics simulations in order to include the intrinsic flexibility of the active sites in the modeling protocol. The major finding of this study is an extremely fast rebound step after the initial hydrogen-abstraction step promoted by the cupric-superoxide adduct. The hydrogen-abstraction/rebound sequence leads to the formation of an alkyl hydroperoxide intermediate. Long-range electron transfer from the remote copper site subsequently triggers its reduction to the hydroxylated substrate. We finally show two reactivity consequences inherent in the new mechanistic proposal, the investigation of which would provide a means to check its validity by experimental means.

From computational chemistry simulations, a ligand has emerged that could be selective of Pb2+ toward Zn2+ and Ca2+, an important point when designing new chelators usable in vivo as remediation agents against lead poisoning (saturnism). Some electronic properties of 1,4,7,10,13,16-hexaoxa-cyclooctadeca-2,5,8,11,14,17-hexaene (hoc-18) are examined here in details, together with those of some thio-analogs. Several interpretative ab initio methodologies that allow clarifying a number of characteristics of hoc-18 towards Zn2+, Ca2+ and Pb2+ are considered from the viewpoint of coordination chemistry.

In this contribution, following the results exposed at the Seventh International Conference of Computational Methods in Sciences and Engineering (ICCMSE 09), we present an overview of some available new techniques able to unravel interactions in large complex systems such as biomolecules, ions in solution, lanthanides and actinides complexes. We first focus our attention on Quantum Chemistry (QC) interpretative techniques introducing some Energy Decomposition Analysis (EDA) scheme such as the newly introduced fragment localized Single-CI DFT scheme. We then present the recently developed DEMEP analysis which is an extension of the topological analysis of the Electron Localization Function (ELF) to the computations of chemically intuitive local electrostatic moments. In a second part, we then discuss how such QC techniques can be used, following a "bottom-up" strategy in order to develop new generation polarizable force field based on distributed multipoles such as the AMOEBA and SIBFA (Sum of Interaction Between Fragments ab initio) procedure; or on electronic density as for the GEM (Gaussian electrostatic Model) method which is based on density fitting. Some applications are detailed.

From computational chemistry simulations, a ligand has emerged that could be selective of Pb 2+ toward

A simple quantum chemical approach to characterize low-barrier hydrogen bonds with the electron localization function topological analysis has been proposed. Various systems, from protonated water dimers to the full phosphorescent yellow protein, have been described. In both cases, a V(H) basin appears (see graphic).

Although potentially powerful, molecular oxygen is an inert oxidant due to the triplet nature of its ground state. Therefore, many enzymesse various metal cations (M) to produce singlet active species M(n) O(2) . In this communication we investigate the topology of the Electron Localization Function (ELF) within five biomimetic complexes which are representative of the strategies followed by metalloenzymes to activate O(2) . Thanks to its coupling to the constrained DFT methods the ELF analysis reveals the tight connection between the spin state of the adduct and the spatial organization of the oxygen lone pairs. We suggest that enzymes could resort to spin state control to tune the regioselectivity of substrate oxidations.

We have quantified the extent of the nonadditivity of the short-range exchange-repulsion energy, E(exch-rep), in several polycoordinated complexes of alkali, alkaline-earth, transition, and metal cations. This was done by performing ab initio energy decomposition analyses of interaction energies in these complexes. The magnitude of E(exch-rep(n-body, n > 2)) was found to be strongly cation-dependent, ranging from close to zero for some alkali metal complexes to about 6 kcal/mol for the hexahydrated Zn(2+) complex. In all cases, the cation-water molecules, E(exch-rep(three-body)), has been found to be the dominant contribution to many-body exchange-repulsion effects, higher order terms being negligible. As the physical basis of this effect is discussed, a three-center exponential term was introduced in the SIBFA (Sum of Interactions Between Fragments Ab initio computed) polarizable molecular mechanics procedure to model such effects. The three-body correction is added to the two-center (two-body) overlap-like formulation of the short-range repulsion contribution, E(rep), which is grounded on simplified integrals obtained from localized molecular orbital theory. The present term is computed on using mostly precomputed two-body terms and, therefore, does not increase significantly the computational cost of the method. It was shown to match closely E(three-body) in a series of test cases bearing on the complexes of Ca(2+), Zn(2+), and Hg(2+). For example, its introduction enabled to restore the correct tetrahedral versus square planar preference found from quantum chemistry calculations on the tetrahydrate of Hg(2+) and [Hg(H(2)O)(4)](2+).

Reduced Variational Space (RVS) calculations are reported that afford insight into the energetic origins of the hemi- and holo-directing behavior of [Pb(H2O)n](2+) complexes. It is shown that the distribution of ligands around the Pb(2+) center arises from a delicate balance between the first-order Coulomb plus exchange-repulsion energy that favors holo-directionality, and the second-order charge transfer plus polarization term that favors hemi-directionality. It is additionally demonstrated that the pseudopotential/basis set combination used to study such complexes should be carefully selected, as artifacts can arise when using large-core pseudopotentials. Finally, based on these findings, we introduce a new SIBFA force field parametrization for Pb(2+). Results yield close agreement with ab initio complexation energies in a series of [Pb(H2O)n](2+) complexes and successfully encapsulate the hemi- and holo-directing properties. SIBFA thus appears to be the first classical force field to be able to model the holo-/hemi-directed transition within Pb complexes, avoiding the need for explicit wave function treatment and consequently providing the opportunity to deal with large leaded systems of biological interest.

The competition between coordination of an incoming ligand (CO, CH3CN, PH3, H2O, MeOH, PhOH and O2 in its triplet state) and decoordination of one arm of the tripod is examined in the case of the [Cu(TMPA)]+ and [Cu(tren)]+ complexes from a theoretical point of view. It is shown that in the case of strong ligand (CO, CH3CN and PH3), arm and ligand coordination are competitive but that coordination of both is the most favored structure. In the case of ROH ligands, a structure with one arm decoordinated and interacting through H-bond with the hydroxyl hydrogen is found. This structure is of special interest as it allows liberation of one bonding site, which can be used for further dioxygen coordination. The consequences of these results on the oxidation of alcohols by dioxygen catalyzed by these classes of complexes are discussed.

Using DFT and ELF topological analysis, we study the directionality of the Pb2+ lone pair in the presence of neutral and anionic ligands. Archetypal [PbLn(HL)m]2−n complexes (n=1–3, m=1–7, L=Cl− or SH−) are investigated in the gas phase or using a solvation continuum. We show that the presence of only one anion within the coordination sphere of Pb2+ induces hemidirectionality for all complexes. Such a finding is important for future toxicology studies if one wants to stabilize Pb2+ valence shell in a hemidirected structure, a key issue in the search for specific chelators of lead.

In this article, we resort to first-principles molecular dynamic simulations to examine the thermal effects on the structure of [Pb(CO)(n)](2+) complexes. Values of n are chosen to sample structures where hemidirected (n = 2, 4 and 6) or holodirected (n = 7 and 8) structures are found when using static approaches. In all cases, highly flexible structures are observed. In particular, hemidirectional distortions are characterized using geometrical and topological analysis. The octacarbonyl complex exhibits the decoordination of one of its carbonyl ligands at 300 K.

Following our previous study (Piquemal et al. , 2003), we present here a DFT study of the inhibition of the Tyrosinase enzyme. Broken-symmetry DFT computations are supplemented with Spin-Flip TD-DFT calculations, which, for the first time, are applied to such a dicopper enzyme. The chosen biomimetic model encompasses a dioxygen molecule, two Cu(II) cations, and six imidazole rings. The docking energy of a natural substrate, namely phenolate, together with those of several inhibitor and non-inhibitor compounds, are reported and show the ability of the model to rank the most potent inhibitors in agreement with experimental data. With respect to broken-symmetry calculations, the Spin-Flip TD-DFT approach reinforces the possibility for theory to point out potent inhibitors: the need for the deprotonation of the substrates, natural or inhibitors, is now clearly established. Moreover, Electron Localization Function (ELF) topological analysis computations are used to deeply track the particular electronic distribution of the Cu-O-Cu three-center bonds involved in the enzymatic Cu 2 O 2 metallic core (Piquemal and Pilmé, 2006). It is shown that such bonds exhibit very resilient out-of-plane density expansions that play a key role in docking interactions: their 3D-orientation could be the topological electronic signature of oxygen activation within such systems.

Following a previous study by de Courcy et al. ((2009) Interdiscip. Sci. Comput. Life Sci. 1, 55-60), we demonstrate in this contribution, using quantum chemistry, that metal cations exhibit a specific topological signature in the electron localization of their density interacting with ligands according to its "soft" or "hard" character. Introducing the concept of metal cation subvalence, we show that a metal cation can split its outer-shell density (the so-called subvalent domains or basins) according to it capability to form a partly covalent bond involving charge transfer. Such behaviour is investigated by means of several quantum chemical interpretative methods encompasing the topological analysis of the Electron Localization Function (ELF) and Bader's Quantum Theory of Atoms in Molecules (QTAIM) and two energy decomposition analyses (EDA), namely the Restricted Variational Space (RVS) and Constrained Space Orbital Variations (CSOV) approaches. Further rationalization is performed by computing ELF and QTAIM local properties such as electrostatic distributed moments and local chemical descriptors such as condensed Fukui Functions and dual descriptors. These reactivity indexes are computed within the ELF topological analysis in addition to QTAIM offering access to non atomic reactivity local index, for example on lone pairs. We apply this "subvalence" concept to study the cation selectivity in enzymes involved in blood coagulation (GLA domains of three coagulation factors). We show that the calcium ions are clearly able to form partially covalent charge transfer networks between the subdomain of the metal ion and the carboxylate oxygen lone pairs whereas magnesium does not have such ability. Our analysis also explains the different role of two groups (high affinity and low affinity cation binding sites) present in GLA domains. If the presence of Ca(II) is mandatory in the central "high affinity" region to conserve a proper folding and a charge transfer network, external sites are better stabilised by Mg(II), rather than Ca(II), in agreement with experiment. The central role of discrete water molecules is also discussed in order to understand the stabilities of the observed X-rays structures of the Gla domain. Indeed, the presence of explicit water molecules generating indirect cation-protein interactions through water networks is shown to be able to reverse the observed electronic selectivity occuring when cations directly interact with the Gla domain without the need of water.

In this contribution, we study several monocarbonyl-metal complexes in order to unravel the contribution of relativistic effects to the metal-ligand bond length and complexation energy. Using scalar density functional theory (DFT) constrained space orbital variation (CSOV) energy decomposition analysis supplemented by all-electron four-component DFT computations, we describe the dependency of relativistic effects on the orbitals involved in the complexation for the Au+ isoelectronic series, namely, the fully occupied 5d orbitals and the empty 6s orbitals. We retrieve the well-known sensitivity of gold toward relativity. For platinum and gold, the four-component results illustrate the simultaneous relativistic expansion of the 5d orbitals and the contraction of the 6s orbitals. The consequences of such modifications are evidenced by CSOV computations, which show the importance of both donation and backdonation within such complexes. This peculiar synergy fades away with mercury and thallium for which coordination becomes driven by the accepting 6s orbitals only, which makes the corresponding complexes less sensitive toward the relativistic effects.

In order to assess the ability of theory to describe properly the dispersive interactions that are ubiquitous in peptide and protein systems, an isolated short peptide chain has been studied using both gas-phase laser spectroscopy and quantum chemistry. The experimentally observed coexistence of an extended form and a folded form in the supersonic expansion was found to result from comparable Gibbs free energies for the two species under the high-temperature conditions (< or = 320 K) resulting from the laser desorption technique used to vaporize the molecules. These data have been compared to results obtained using a series of quantum chemistry methods, including DFT, DFT-D, and post-Hartree-Fock methods, which give rise to a wide range of relative stabilities predicted for these two forms. The experimental observation was best reproduced by an empirically dispersion-corrected functional (B97-D) and a hybrid functional with a significant Hartree-Fock exchange term (M06-2X). In contrast, the popular post-Hartree-Fock method MP2, which is often used for benchmarking these systems, had to be discarded because of a very large basis-set superposition error. The applicability of the atomic counterpoise correction (ACP) is also discussed. This work also introduces the mandatory theoretical examination of experimental abundances. DeltaH(0 K) predictions are clearly not sufficient for discussion of folding, as the conformation inversion temperature is crucial to the conformation determination and requires taking into account thermodynamical corrections (DeltaG) in order to computationally isolate the most stable conformation.