Crossed molecular beam experiments and theoretical simulations on the multichannel reaction of toluene with atomic oxygen.

Despite extensive experimental and theoretical studies on the kinetics of the O(3P) + C7H8 (toluene) reaction and a pioneering crossed molecular beam (CMB) investigation, the branching fractions (BFs) of the CH3C6H4O(methylphenoxy) + H, C6H5O(phenoxy) + CH3, and spin-forbidden C5H5CH3 (methylcyclopentadiene) + CO product channels remain an open question, which has hampered the proper inclusion of this important reaction in the chemical modelling of various chemical environments. We report a CMB study with universal soft electron-ionization mass-spectrometric detection of the reactions O(3P,1D) + toluene at the collision energy of 34.7 kJ mol-1. From CMB data we have inferred the reaction dynamics and quantified the BFs of the primary products and the role of intersystem crossing (ISC). The CH3-elimination channel dominates (BF = 0.69 ± 0.22) in the O(3P) reaction, while the H-displacement and CO-formation channels are minor (BF = 0.22 ± 0.07 and 0.09 ± 0.05, respectively), with ISC accounting for more than 50% of the reactive flux. Synergistic transition-state theory (TST)-based master equation simulations including nonadiabatic TST on ab initio coupled triplet/singlet potential energy surfaces were employed to compute the product BFs and assist in the interpretation of the CMB results. In the light of the good agreement between the theoretical predictions for the O(3P) + toluene reaction and the CMB results as well as the absolute rate constant as a function of temperature (T) (from literature), the so-validated computational methodology was used to predict channel-specific rate constants as a function of T at 1 atm.

Intersystem crossing in the entrance channel of the reaction of O(3P) with pyridine.

Two quantum effects can enable reactions to take place at energies below the barrier separating reactants from products: tunnelling and intersystem crossing between coupled potential energy surfaces. Here we show that intersystem crossing in the region between the pre-reactive complex and the reaction barrier can control the rate of bimolecular reactions for weakly coupled potential energy surfaces, even in the absence of heavy atoms. For O(3P) plus pyridine, a reaction relevant to combustion, astrochemistry and biochemistry, crossed-beam experiments indicate that the dominant products are pyrrole and CO, obtained through a spin-forbidden ring-contraction mechanism. The experimental findings are interpreted-by high-level quantum-chemical calculations and statistical non-adiabatic computations of branching fractions-in terms of an efficient intersystem crossing occurring before the high entrance barrier for O-atom addition to the N-atom lone pair. At low to moderate temperatures, the computed reaction rates prove to be dominated by intersystem crossing.

Crossed-Beam and Theoretical Studies of the O(3P, 1D) + Benzene Reactions: Primary Products, Branching Fractions, and Role of Intersystem Crossing.

Reliable modeling of hydrocarbon oxidation relies critically on knowledge of the branching fractions (BFs) as a function of temperature (T) and pressure (p) for the products of the reaction of the hydrocarbon with atomic oxygen in its ground state, O(3P). During the past decade, we have performed in-depth investigations of the reactions of O(3P) with a variety of small unsaturated hydrocarbons using the crossed molecular beam (CMB) technique with universal mass spectrometric (MS) detection and time-of-flight (TOF) analysis, combined with synergistic theoretical calculations of the relevant potential energy surfaces (PESs) and statistical computations of product BFs, including intersystem crossing (ISC). This has allowed us to determine the primary products, their BFs, and extent of ISC to ultimately provide theoretical channel-specific rate constants as a function of T and p. In this work, we have extended this approach to the oxidation of one of the most important species involved in the combustion of aromatics: the benzene (C6H6) molecule. Despite extensive experimental and theoretical studies on the kinetics and dynamics of the O(3P) + C6H6 reaction, the relative importance of the C6H5O (phenoxy) + H open-shell products and of the spin-forbidden C5H6 (cyclopentadiene) + CO and phenol adduct closed-shell products are still open issues, which have hampered the development of reliable benzene combustion models. With the CMB technique, we have investigated the reaction dynamics of O(3P) + benzene at a collision energy (Ec) of 8.2 kcal/mol, focusing on the occurrence of the phenoxy + H and spin-forbidden C5H6 + CO and phenol channels in order to shed further light on the dynamics of this complex and important reaction, including the role of ISC. Concurrently, we have also investigated the reaction dynamics of O(1D) + benzene at the same Ec. Synergistic high-level electronic structure calculations of the underlying triplet/singlet PESs, including nonadiabatic couplings, have been performed to complement and assist the interpretation of the experimental results. Statistical (RRKM)/master equation (ME) computations of the product distribution and BFs on these PESs, with inclusion of ISC, have been performed and compared to experiment. In light of the reasonable agreement between the CMB experiment, literature kinetic experimental results, and theoretical predictions for the O(3P) + benzene reaction, the so-validated computational methodology has been used to predict (i) the BF between the C6H5O + H and C5H6 + CO channels as a function of collision energy and temperature (at 0.1 and 1 bar), showing that their increase progressively favors radical (phenoxy + H)-forming over molecule (C5H6 + CO and phenol stabilization)-forming channels, and (ii) channel-specific rate constants as a function of T and p, which are expected to be useful for improved combustion models.

Chalcogen Bonds in Selenocysteine Seleninic Acid, a Functional GPx Constituent, and in Other Seleninic or Sulfinic Acid Derivatives.

The controlled oxidation reaction of L-selenocystine under neutral pH conditions affords selenocysteine seleninic acid (3-selenino-L-alanine) which is characterized also by means of single-crystal X-ray diffraction. This technique shows that selenium forms three chalcogen bonds (ChBs), one of them being outstandingly short. A survey of seleninic acid derivatives in the Cambridge Structural Database (CSD) confirms that the C-Se(=O)O- functionality tends to act as a ChB donor robust enough to systematically influence the interactional landscape in the solid. Quantum Theory of Atom in Molecules (QTAIM) analysis proves the attractive nature of the short contacts observed in crystals containing the seleninic functionality and calculation of surface molecular electrostatic potential (MEP) reveals that remarkably positive σ-holes can frequently be found opposite to the covalent bonds at selenium. Both CSD searches and QTAIM and MEP approaches show that also the sulfinic acid moiety can function as a ChB donor, albeit less frequently than the seleninic acid one. These findings may contribute to a better understanding, at the atomic level, of the mechanism of action of the enzymes that control oxidative stress and ROS deactivation and that contain selenocysteine seleninic acid and cysteine sulfinic acid in the active site.

Structural properties of the chelating agent 2,6-bis(1-(3-hydroxypropyl)-1,2,3-triazol-4-yl)pyridine: a combined XRD and DFT structural study.

The conformational isomerism of the chelating agent 2,6-bis(1-(3-hydroxypropyl)-1,2,3-triazol-4-yl)pyridine (PTD), exploited in fuel reprocessing in spent nuclear waste, has been studied by single crystal X-ray diffraction analysis in combination with an extensive DFT conformational investigation. In the solid-state, the elucidated crystal structure (i.e., not yet published) shows that by thermal treatment (DSC) no other phases are observed upon crystallization from the melt, indicating that the conformation observed by X-ray data is rather stable. Mapping of intermolecular and intramolecular noncovalent interactions has been used to elucidate the unusual arrangement of the asymmetric unit. Considerations relating to the stability of different conformational isomers in aqueous and non-aqueous solutions are also presented. The accurate structural description reported here might open various research topics such as the potential of PTD to act as an outer sphere ligand in the formation of second sphere coordination complexes and their interconversion by mechanochemical means.

Thermodynamics of aqueous perfluorooctanoic acid (PFOA) and 4,8-dioxa-3H-perfluorononanoic acid (DONA) from DFT calculations: Insights into degradation initiation.

Modern fluorosurfactants introduced during and after perfluoroalkyl carboxylates/sulfonates phase-out present chemical features designed to facilitate abatement, hence reducing persistence. However, the implications of such features on environmental partitioning and stability are yet to be fully appreciated, partly due to experimental difficulties inherent to the handling of their (diluted) aqueous solutions. In this work, rigorous quantum chemistry calculations were carried out in order to provide theoretical insights into the thermodynamics of hydroperfluorosurfactants in aqueous medium. Estimates of acid dissociation constant (pKa), standard reduction potential (E0), and bond dissociation enthalpy (BDE) and free energy (BDFE) were computed for perfluorooctanoic acid (PFOA), 4,8-dioxa-3H-perfluorononanoic acid (DONA) and their anionic forms via ensemble averaging at density functional theory level with implicit solvent models. A a> in the neighborhood of zero and a E0 of about 2.2 V were obtained for PFOA. Predictions for the acidic function of DONA compare well with PFOA's, with a pKa of 0.8-1.5 and a E0 of 2.07-2.15 V. Deprotonation thus represents the dominant phenomenon at environmental conditions. Calculations indicate that H-abstraction of the aliphatic proton of DONA by a hydroxyl radical is the thermodynamically favored reaction path in oxidative media, whereas hydrolysis is not a realistic scenario due to the high dissociation constant. Short intramolecular interactions available to the peculiar hydrophobic tail of DONA were also reviewed, and the relevance of the full conformational space of the fluorinated side chain discussed.

Noncovalent Interactions Descriptor Based on the Source Function of Individual Localized Molecular Orbitals in Whole Space.

The partitioning of total electron density into localized molecular orbitals (LMOs) within the source function framework is presented as an exploit useful to the characterization of noncovalent interactions. The resulting approach uses only a converged LMO base as input and does not require grid data handling or numerical integration, making it viable for the study of large systems. Tests conducted on a series of prototypical hydrogen and halogen bonds demonstrate that this descriptor retrieves chemically intuitive interaction motifs beyond the classical two-center picture. Advantages and disadvantages of different localization schemes are discussed in terms of their peculiar description of σ-π mixing and in terms of their inherent basis set dependence.

Nucleophilicity and electrophilicity of the C(sp3)-H bond: methane and ethane binary complexes with iodine.

The occurrence of stable van der Waals complexes of small saturated hydrocarbons with molecular iodine is assessed in order to investigate the ability of sp3-hybridized carbon atoms to act as either electron donors or electron acceptors depending on the ligand orientation. Systematic ab initio potential energy surface exploration of methane-I2 and ethane-I2 model dimers was followed by thorough characterization. Despite modest evidence of whole-adduct polarization, the resulting interactions feature a dominant dispersive character. The noncovalent interaction descriptors employed comprise NBO, AIM, NCI, and source function analyses. The relevance of bonding C-H orbitals in donor-acceptor interactions involving saturated hydrocarbons is highlighted. The results here presented corroborate existing literature regarding the electrophilicity of the aliphatic C-H group, and also indicate that the nucleophilic character of C(sp3) shares a dependence on electron withdrawing/donating substituents similar to that extensively documented for σ-holes. Indeed, the sole difference between the two, aside from the nucleophilicity/electrophilicity switch, seems to lie in their directionality. Nucleophilic sites on C(sp3) are not limited to the outermost region of C along a covalent bond axis, but can also engage electrophiles via the bifurcation plane of a CH2 unit. Since valence electrons on these carbon atoms are engaged in covalent bonds, they can only interact with polarizing ligands via the electron density accumulation/depletion in the four corresponding σ orbitals. These, however, do not seem to interact individually with the accompanying electrophile. Source function and NCI results suggest instead that nucleophilic carbon centres participate in the noncovalent bond themselves by drawing electron density from their shared electron pairs.

Exploring short intramolecular interactions in alkylaromatic substrates.

From proteins and peptides to semiconducting polymers, aliphatic chains on aromatic groups are recurring motifs in macromolecules from very diverse application fields. Fields in which molecular folding and packing determine the macroscopic physical properties that make such advanced materials appealing in the first place. Within each macromolecule, the intrinsic structure of each unit defines how it interacts with its neighbours, ultimately opening up or denying certain backbone conformations. This eventually also determines how macromolecules interact with each other. This account deals specifically with the conformational problem of many common alkylaromatic units, examining the features of an intramolecular interaction involving a side chain with as few as three methylene groups. A set of 23 model compounds featuring an intramolecular interaction between an aliphatic X-H (X = C, N, O, and S) bond and an aromatic ring was considered. Quantitative computational analysis was made possible, thanks to complete basis set extrapolated CCSD(T) calculations and NCI topological analysis, the latter of which revealed an elaborate network of dispersive and steric interactions leading to somewhat unintuitive and unexpected results, such as the higher energetic stability of certain twisted conformational isomers over those with extended side chains. Vicinal covalent effects from polarizing groups and various heteroatoms, along with the occurrence of non-dispersive phenomena, were also investigated. The conclusions drawn from the investigation include a comprehensive set of guidelines intended to aid in the prediction of the most stable conformation for this class of building blocks. Our findings affect a variety of different research fields, including the tailoring of functional materials for organic electronics and photovoltaics, with insights into a rational treatment of conformational disorder, and the study of protein- and peptide-folding preferences, putting an emphasis on peculiar interactions between the backbone and aromatic residues.

On the inter-ring torsion potential of regioregular P3HT: a first principles reexamination with explicit side chains.

Poly(3-alkylthiophene) is a family of conjugated semicrystalline polymers for organic electronic applications. Crucial for the fine-tuning of such systems is a detailed understanding of the correlation between molecular structure/morphology and electronic properties. However, a series of a priori assumptions is commonly made in order to deduce macromolecular-scale geometric and energetic features from those of rather small homologous molecular systems. Alkyl side chains are routinely shortened (if not systematically removed) during such high-accuracy ab initio calculations in order to reduce their conformational space. We will show through first principles calculations on a monosubstituted bithiophene molecule how a full-length alkyl fragment can influence both side chain energetics and backbone flexibility in alkylthiophene-based polymers and copolymers. Folded side chains, characterized by a gauche arrangement of the second torsion angle from the ring, are found to be substantially favoured over extended ones, thanks to a network of CH-π hydrogen-bond-like interactions with both aromatic rings. Trans-planar (conjugated) arrangements of limit-ordered crystalline models, and cisoid sequences suitable for the investigation of chain-folding phenomena, are also discussed in detail.

Computational 17O-NMR spectroscopy of organic acids and peracids: comparison of solvation models.

We examine several computational strategies for the prediction of the (17)O-NMR shielding constants for a selection of organic acids and peracids in aqueous solution. In particular, we consider water (the solvent and reference for the chemical shifts), hydrogen peroxide, acetic acid, lactic acid and peracetic acid. First of all, we demonstrate that the PBE0 density functional in combination with the 6-311+G(d,p) basis set provides an excellent compromise between computational cost and accuracy in the calculation of the shielding constants. Next, we move on to the problem of the solvent representation. Our results confirm the shortcomings of the Polarizable Continuum Model (PCM) in the description of systems susceptible to strong hydrogen bonding interactions, while at the same time they demonstrate its usefulness within a molecular-continuum approach, whereby PCM is applied to describe the solvation of the solute surrounded by some explicit solvent molecules. We examine different models of the solvation shells, sampling their configurations using both energy minimizations of finite clusters and molecular dynamics simulations of bulk systems. Hybrid molecular dynamics simulations, in which the solute is described at the PM6 semiempirical level and the solvent by the TIP3P model, prove to be a promising sampling method for medium-to-large sized systems. The roles of solvent shell size and structure are also briefly discussed.

A solid state density functional study of crystalline thiophene-based oligomers and polymers.

We present the results of a molecular modeling study of several thiophene-based oligomers and polymers by solid state density functional theory (DFT) calculations. In particular, we consider two polymers for which limit-ordered crystal structures have been reported by our group, on the basis of powder X-ray data analysis: poly(3-(S)-2-methylbutylthiophene) (P3MBT) and forms I' and II of poly(3-butylthiophene) (P3BT). The calculations employing the functional by Perdew and Wang (PWC) in conjunction with the double-ζ polarized numerical basis set (DNP) demonstrate that a standard quantum mechanical (QM) approach for solid phases can provide a balanced description of the overall structure and energetics of thiophene-based oligomers and polymers maintaining a moderate computational cost. In addition, the results compare well with those provided by specific force field parametrization developed by our group. In many cases, PWC/DNP models show even closer agreement with experimental crystal structures, making it the method of choice for computationally accessible problems. Finally, solid state DFT minimizations confirm that the reported crystal structures of P3MBT and P3BT correspond to well-defined energy minima.

Organic peracids: a structural puzzle for 17O NMR and ab initio chemical shift calculations.

We have applied (17)O NMR spectroscopy to investigate the structure of the organic peracids formed by reaction of acetic acid (AA) or lactic acid (LA) with aqueous hydrogen peroxide (HP), which are used in several "green chemistry" applications. The interpretation of the experimental spectra has been supported by ab initio calculations of the (17)O chemical shifts for several possible species, using a continuum representation of the solvent. The combined use of these tools has also allowed us to discuss the decomposition mechanism of LA/HP solutions. The calculated electric field gradients for water, HP, and CO(2) (a decomposition product of LA) correlate well with the experimental (17)O line widths.