Competition between Loss of H2 versus H+H in the Fragmentation of the Fluorene Cation.

The fluorene cation is a frequently studied molecule in the context of fragmentation experiments. This is because of its potential role in interstellar chemistry, notably as a precursor of PAH cages. In this paper, we analyze H, H+ , H2 and H 2 + ${{\rm{H}}_2^ + }$ losses from the fluorene cation using the SMF (Statistical Molecular Fragmentation) model. We calculate the probabilities of all the 534 possible fragmentation channels as a function of the excitation energy, up to the loss of three hydrogens. Four different types of hydrogen atom pairings (from the same carbon, from the same ring, from different rings and across-the-bay) have been tested in order to determine which types contribute to the actual production of hydrogen molecules. The simulated breakdown curves are in very good agreement with different experimental results when same ring pairing is taken into account. It was possible to deduce from the model the locations of the emitted H, H+ , H2 and H 2 + ${{\rm{H}}_2^ + }$ species.

Multiple dehydrogenation of fluorene cation and neutral fluorene using the statistical molecular fragmentation model.

The statistical molecular fragmentation (SMF) model was used to analyze the 306 fragmentation channels (containing 611 different species) that result from the fluorene (C13H10+) cation losing up to three hydrogen atoms (neutral radicals and/or a proton). Breakdown curves from such analysis permit one to extract experimentally inaccessible information about the fragmentation of the fluorene cation, such as the locations of the lost hydrogen atoms (or proton), yields of the neutral fragments, electronic states of the residues, and quantification of very low probability channels that would be difficult to detect. Charge localization during the fragmentation pathways was studied to provide a qualitative understanding of the fragmentation process. Breakdown curves for both the fluorene cation and neutral fluorene were compared. The SMF results match the rise and fall of the one hydrogen loss yield experimentally measured by imaging photoelectron-photoion coincidence spectroscopy using a VUV synchrotron.

Probing the structural properties of the water solvation shell around gold nanoparticles: A computational study.

While subjected to radiation, gold nanoparticles (GNPs) have been shown to enhance the production of radicals when added to aqueous solutions. It has been proposed that the arrangement of water solvation layers near the water-gold interface plays a significant role. As such, the structural and electronic properties of the first water solvation layer surrounding GNPs of varying sizes were compared to bulk water using classical molecular dynamics and quantum and semi-empirical methods. Classical molecular dynamics was used to understand the change in macroscopic properties of bulk water in the presence of different sizes of GNP, as well as by including salt ions. The analysis of these macroscopic properties has led to the conclusion that larger GNPs induce the rearrangement of water molecules to form a 2D hydrogen-bond network at the interface. Quantum methods were employed to understand the electronic nature of the interaction between water molecules and GNPs along with the change in the water orientation and the vibrational density of states. The stretching region of vibrational density of states was found to extend into the higher wavenumber region, as the size of the GNP increases. This extension represents the dangling water molecules at the interface, as a result of reorientation of the water molecules in the first solvation shell. This multi-level study suggests that in the presence of GNP of increasing sizes, the first water solvation shell undergoes a rearrangement to maximize the water-water interactions as well as the water-GNP interactions.

The statistical molecular fragmentation model compared to experimental plasma induced hydrocarbon decays.

We compare the predictions of our recently developed statistical molecular fragmentation (SMF) model with experimental results from plasma induced hydrocarbon decay. The SMF model is an exactly solvable statistical model, able to calculate the probabilities for all possible fragmentation channels as a function of the deposited excitation energy. The weights of the channels are calculated from the corresponding volume of the accessible phase space of the system, taking into account all relevant degeneracies, symmetries and density functions. An experiment designed to study the abatement of propene in N2 using a photo-triggered discharge producing a homogeneous plasma at sub-atmospheric pressure was also performed. Using a 0D model that simulates the complex chemical kinetics in the plasma, it was possible to assess the percentages of the original parent hydrocarbon's fragmentation channels based on the detected species. These results were compared to those obtained from the SMF model. Previous plasma induced hydrocarbon fragmentation experiments for ethene, ethane and propane, were also compared to the predictions of the SMF model. For energies below that of metastable dinitrogen (i.e. below 6.17 eV and 8.4 eV), the SMF model and the experimental fragmentation channels coincide. This study allows one to draw conclusions both on the range of excitation energies transferred to the parent hydrocarbon molecules during plasma discharge and on the probability of the dynamical coupling of two H atoms from neighbouring carbon atoms to form H2 molecules.

Statistical molecular fragmentation: which parameters influence the branching ratios?

The fragmentation of molecules under conditions that result in yields of products that are thermodynamically controlled can be readily studied with statistical models. We explore which parameters influence the branching ratios using our recently developed Statistical Molecular Fragmentation model (SMF) and apply it to the decomposition of propane. We find that the fragmentation process has low sensitivity to the differences between the molecular descriptions given by commonly used ab initio methods (B3LYP, CCSD(T) and composite methods with different atom-centered basis sets). However, the branching ratios are most influenced by the vibrational frequencies of the molecules and radicals present in the decomposition pathways.

Influence of Water on the Oxidation of Dimethyl Sulfide by the ·OH Radical.

Oxidative stress of sulfur-containing biological molecules in aqueous environments may lead to the formation of adduct intermediates that are too short-lived to be experimentally detectable. In this study we have modeled the simplest of such oxidative reactions: the attack of dimethyl sulfide (DMS) by a hydroxyl radical (·OH) to form a radical adduct, whose subsequent heterolytic dissociation leads to a radical cation (DMS+) that is important for further reactions. We have modeled the aqueous environment with a limited number of discrete water molecules, selected after an original multistep procedure, and further embedded in a polarizable continuum model, to observe the impact of the water configuration on the heterolytic dissociation of the radical adduct. Molecular dynamics and quantum chemical methods (DFT, MP2, and CCSD) were used to elucidate the lowest energy structures resulting from the ·OH attack on DMS. Subsequent high level ab initio valence bond (BOVB) calculations revealed the possibility for the occurrence of subsequent heterolytic dissociation.

Coupled Valence-Bond State Molecular Dynamics Description of an Enzyme-Catalyzed Reaction in a Non-Aqueous Organic Solvent.

Enzymes are widely used in nonaqueous solvents to catalyze non-natural reactions. While experimental measurements showed that the solvent nature has a strong effect on the reaction kinetics, the molecular details of the catalytic mechanism in nonaqueous solvents have remained largely elusive. Here we study the transesterification reaction catalyzed by the paradigm subtilisin Carlsberg serine protease in an organic apolar solvent. The rate-limiting acylation step involves a proton transfer between active-site residues and the nucleophilic attack of the substrate to form a tetrahedral intermediate. We design the first coupled valence-bond state model that simultaneously describes both reactions in the enzymatic active site. We develop a new systematic procedure to parametrize this model on high-level ab initio QM/MM free energy calculations that account for the molecular details of the active site and for both substrate and protein conformational fluctuations. Our calculations show that the reaction energy barrier changes dramatically with the solvent and protein conformational fluctuations. We find that the mechanism of the tetrahedral intermediate formation during the acylation step is similar to that determined under aqueous conditions, and that the proton transfer and nucleophilic attack reactions occur concertedly. We identify the reaction coordinate to be mostly due to the rearrangement of some residual water molecules close to the active site.

Calculation of space localized properties in correlated quantum Monte Carlo methods with reweighting: the nonlocality of statistical uncertainties.

We study the efficiency of quantum Monte Carlo (QMC) methods in computing space localized ground state properties (properties which do not depend on distant degrees of freedom) as a function of the system size N. We prove that for the commonly used correlated sampling with reweighting method, the statistical fluctuations σ2(N) do not obey the locality property. σ2(N) grow at least linearly with N and with a slope that is related to the fluctuations of the reweighting factors. We provide numerical illustrations of these tendencies in the form of QMC calculations on linear chains of hydrogen atoms.

Multicenter Bonding in Ditetracyanoethylene Dianion: A Simple Aromatic Picture in Terms of Three-Electron Bonds.

The nature of the multicenter, long bond in ditetracyanoethylene dianion complex [TCNE]2(2-) is elucidated using high level ab initio Valence Bond (VB) theory coupled with Quantum Monte Carlo (QMC) methods. This dimer is the prototype of the general family of pancake-bonded dimers with large interplanar separations. Quantitative results obtained with a compact wave function in terms of only six VB structures match the reference CCSD(T) bonding energies. Analysis of the VB wave function shows that the weights of the VB structures are not compatible with a covalent bond between the π* orbitals of the fragments. On the other hand, these weights are consistent with a simple picture in terms of two resonating bonding schemes, one displaying a pair of interfragment three-electron σ bonds and the other displaying intrafragment three-electron π bonds. This simple picture explains at once (1) the long interfragment bond length, which is independent of the countercations but typical of three-electron (3-e) CC σ bonds, (2) the interfragment orbital overlaps which are very close to the theoretical optimal overlap of 1/6 for a 3-e σ bond, and (3) the unusual importance of dynamic correlation, which is precisely the main bonding component of 3-e bonds. Moreover, it is shown that the [TCNE]2(2-) system is topologically equivalent to the square C4H4(2-) dianion, a well-established aromatic system. To better understand the role of the cyano substituents, the unsubstituted diethylenic Na(+)2[C2H4]2(2-) complex is studied and shown to be only metastable and topologically equivalent to a rectangular C4H4(2-) dianion, devoid of aromaticity.

Assessing spin-component-scaled second-order Møller-plesset theory using anharmonic frequencies.

Four common parametrisations of spin-component-scaled second-order Møller-Plesset (MP2) theory are benchmarked by calculating the anharmonic vibrational frequencies of a test suite consisting of eighteen diatomic and five small molecules. Of the four methods, the scaled opposite-spin MP2 (SOS-MP2), the variable-scaling opposite-spin MP2 (VOS-MP2) and the spin-component-scaled MP2 (SCS-MP2) methods perform statistically better than standard MP2 theory, while the spin-component scaled for nucleic bases MP2 (SCSN-MP2) performs worse. Vibrations of closed-shell diatomic molecules are slightly more accurately described by the SOS-MP2 method of Head-Gordon (ε(MAD) =51 cm(-1) ) than the SCS-MP2 method of Grimme (ε(MAD) =61 cm(-1)) or the size-consistent parametrisation of VOS-MP2 (ε(MAD) =54 cm(-1)). For open-shell diatomic molecules, the SOS-MP2 (ε(MAD) =83 cm(-1)) and SCS-MP2 (ε(MAD) =81 cm(-1)) methods are of similar accuracy, while VOS-MP2 is slightly better (ε(MAD) =77 cm(-1)). Since the VOS-MP2 and SOS-MP2 methods tend to have smaller deviations from experiment, and they can be made computationally more economical than the SCS-MP2 or MP2 methods, we suggest that they should be the preferred ab initio method for computing vibrational frequencies in large molecules.

A diffusion Monte Carlo study of the O-H bond dissociation of phenol.

The homolytic O-H bond dissociation energy (BDE) of phenol was determined from diffusion Monte Carlo (DMC) calculations using single determinant trial wave functions. DMC gives an O-H BDE of 87.0 +/- 0.3 kcal/mol when restricted Hartree-Fock orbitals are used and a BDE of 87.5 +/- 0.3 kcal/mol with restricted B3LYP Kohn-Sham orbitals. These results are in good agreement with the extrapolated B3P86 results of Costa Cabral and Canuto (88.3 kcal/mol), the recommended experimental value of Borges dos Santos and Martinho Simões (88.7 +/- 0.5 kcal/mol), and the G3 (88.2 kcal/mol), CBS-APNO (88.2 kcal/mol), CBS-QB3 (87.1 kcal/mol) results of Mulder.

Quantitative characteristics of qualitative localized bonding patterns.

Patterns of localized and delocalized chemical bonding obtained using the recently proposed adaptive natural density partitioning (AdNDP) provide a qualitative description of electronic structure but miss any quantitative information. Descriptors, such as the electron localization function (ELF), provide quantitative characteristics of bonding and can enhance the usefulness of qualitative patterns. In the present study, we used ELF and a related construct, charge-density-weighted ELF (ELF rho), to characterize localized and delocalized bonding in a variety of systems. It is demonstrated that ELF rho yields a more detailed description than ELF when used to analyze bonding in aromatic, conflicting aromatic, and antiaromatic systems. Both canonical molecular orbitals (CMOs) and localized multicenter two-electron (nc-2e) bonds obtained in the latter case by AdNDP localization are used to calculate ELF rho.

Breathing orbital valence bond method in diffusion Monte Carlo: C-H bond dissociation of acetylene.

This study explores the use of breathing orbital valence bond (BOVB) trial wave functions for diffusion Monte Carlo (DMC). The approach is applied to the computation of the carbon-hydrogen (C-H) bond dissociation energy (BDE) of acetylene. DMC with BOVB trial wave functions yields a C-H BDE of 132.4 +/- 0.9 kcal/mol, which is in excellent accord with the recommended experimental value of 132.8 +/- 0.7 kcal/mol. These values are to be compared with DMC results obtained with single determinant trial wave functions, using Hartree-Fock orbitals (137.5 +/- 0.5 kcal/mol) and local spin density (LDA) Kohn-Sham orbitals (135.6 +/- 0.5 kcal/mol).

Isomer energy differences for the C4H3 and C4H5 isomers using diffusion Monte Carlo.

A new diffusion Monte Carlo study is performed on the isomers of C4H3 and C4H5 emulating the methodology of a previous study (Int. J. Chem. Kinet. 2001, 33, 808). Using the same trial wave function form of the previous study, substantially different isomerization energies were found owing to the use of larger walker populations in the present work. The energy differences between the E and i isomers of C4H3 were found to be 10.5 +/- 0.5 kcal/mol and for C4H5, 9.7 +/- 0.6 kcal/mol. These results are in reasonable accord with recent MRCI and CCSD(T) findings.

Graphene layer growth chemistry: five- and six-member ring flip reaction.

Reaction pathways are presented for hydrogen-mediated isomerization of a five- and six-member carbon ring complex on the zigzag edge of a graphene layer. A new reaction sequence that reverses the orientation of the ring complex, or "flips" it, was identified. Competition between the flip reaction and the "ring separation" was examined. Ring separation is the reverse of the five- and six-member ring complex formation reaction, previously reported as "ring collision". The elementary steps of the pathways were analyzed using density functional theory (DFT). Rate coefficients were obtained by solution of the energy master equation and classical transition-state-theory utilizing the DFT energies, frequencies, and geometries. The results indicate that the flip reaction pathway dominates the separation reaction and should be competitive with other pathways important to the graphene zigzag edge growth in high-temperature environments.

Quantum Monte Carlo study of first-row atoms using transcorrelated variational Monte Carlo trial functions.

The effect of using the transcorrelated variational Monte Carlo (TC-VMC) approach to construct a trial function for fixed node diffusion Monte Carlo (DMC) energy calculations has been investigated for the first-row atoms, Li to Ne. The computed energies are compared with fixed node DMC energies obtained using trial functions constructed from Hartree-Fock and density functional levels of theory. Despite major VMC energy improvement with TC-VMC trial functions, no improvement in DMC energy was observed using these trial functions for the first-row atoms studied. The implications of these results on the nodes of the trial wave functions are discussed.

Zori 1.0: a parallel quantum Monte Carlo electronic structure package.

The Zori 1.0 package for electronic structure computations is described. Zori performs variational and diffusion Monte Carlo computations as well as correlated wave function optimization. This article presents an overview of the implemented methods and code capabilities.