A Multiconformational Transition State Theory Approach to OH Tropospheric Degradation of Fluorotelomer Aldehydes.

Experimental work on the OH-initiated oxidation reactions of fluorotelomer aldehydes (FTALs) strongly suggests that the respective rate coefficients do not depend on the size of the Cx F2x+1 fluoroalkyl chain. FTALs hence represent a challenging test to our multiconformer transition state theory (MC-TST) protocol based on constrained transition state randomization (CTSR), since the calculated rate coefficients should not show significant variations with increasing values of x ${x}$ . In this work we apply the MC-TST/CTSR protocol to the x = 2 , 3 ${x={\rm 2,3}}$ cases and calculate both rate coefficients at 298.15 K with a value of k = ( 2 . 4 ± 1 . 4 ) × 10 - 12 ${k=(2.4\pm 1.4)\times {10}^{-12}}$  cm3  molecule-1 s-1 , practically coincident with the recommended experimental value of kexp = ( 2 . 8 ± 1 . 4 ) × 10 - 12 ${(2.8\pm 1.4)\times {10}^{-12}}$  cm3  molecule-1 s-1 . We also show that the use of tunneling corrections based on improved semiclassical TST is critical in obtaining Arrhenius-Kooij curves with a correct behavior at lower temperatures.

Switching on H-Tunneling through Conformational Control.

H-tunneling is a ubiquitous phenomenon, relevant to fields from biochemistry to materials science, but harnessing it for mastering the manipulation of chemical structures still remains nearly illusory. Here, we demonstrate how to switch on H-tunneling by conformational control using external radiation. This is outlined with a triplet 2-hydroxyphenylnitrene generated in an N2 matrix at 10 K by UV-irradiation of an azide precursor. The anti-orientation of the nitrene's OH moiety was converted to syn by selective vibrational excitation at the 2ν(OH) frequency, thereby moving the H atom closer to the vicinal nitrene center. This triggers spontaneous H-tunneling to a singlet 6-imino-2,4-cyclohexadienone. Computations reveal that such fast H-tunneling occurs through crossing the triplet-to-singlet potential energy surfaces. Our experimental realization provides an exciting novel strategy to attain control over tunneling, opening new avenues for directing chemical transformations.

Spin-forbidden heavy-atom tunneling in the ring-closure of triplet cyclopentane-1,3-diyl.

In 1975, Buchwalter and Closs reported one of the first examples of heavy-atom quantum mechanical tunneling (QMT) by studying the ring closure of triplet cyclopentane-1,3-diyl to singlet bicyclo[2.1.0]pentane in cryogenic glasses. Since then, no clear theoretical evidence has been provided to elucidate how the intersystem crossing (ISC) and QMT are related in the reaction mechanism. In this work, we unequivocally show that at cryogenic temperatures, the ISC occurs solely in the quantum tunneling regime, with weak coupling non-adiabatic transition state theory rate constants predicting a spontaneous reaction in fair agreement with experimental observations. Despite its limitations, such an approach can be used to help unlock a comprehensive understanding of a variety of spin-forbidden chemical reactions in the low temperature regime.

Simplified Protocol for the Calculation of Multiconformer Transition State Theory Rate Constants Applied to Tropospheric OH-Initiated Oxidation Reactions.

Chemical kinetics plays a fundamental role in the understanding and modeling of tropospheric chemical processes, one of the most important being the atmospheric degradation of volatile organic compounds. These potentially harmful molecules are emitted into the troposphere by natural and anthropogenic sources and are chemically removed by undergoing oxidation processes, most frequently initiated by reaction with OH radicals, the atmosphere's "detergent". Obtaining the respective rate constants is therefore of critical importance, with calculations based on transition state theory (TST) often being the preferred choice. However, for molecules with rich conformational variety, a single-conformer method such as lowest-conformer TST is unsuitable while state-of-the-art TST-based methodologies easily become unmanageable. In this Feature Article, the author reviews his own cost-effective protocol for the calculation of bimolecular rate constants of OH-initiated reactions in the high-pressure limit based on multiconformer transition state theory. The protocol, which is easily extendable to other oxidation reactions involving saturated organic molecules, is based on a variety of freeware and open-source software and tested against a series of oxidation reactions of hydrofluoropolyethers, computationally very challenging molecules with potential environmental relevance. The main features, advantages and disadvantages of the protocol are presented, along with an assessment of its predictive utility based on a comparison with experimental rate constants.

Heavy-Atom Tunneling Through Crossing Potential Energy Surfaces: Cyclization of a Triplet 2-Formylarylnitrene to a Singlet 2,1-Benzisoxazole.

Not long ago, the occurrence of quantum mechanical tunneling (QMT) chemistry involving atoms heavier than hydrogen was considered unreasonable. Contributing to the shift of this paradigm, we present here the discovery of a new and distinct heavy-atom QMT reaction. Triplet syn-2-formyl-3-fluorophenylnitrene, generated in argon matrices by UV-irradiation of an azide precursor, was found to spontaneously cyclize to singlet 4-fluoro-2,1-benzisoxazole. Monitoring the transformation by IR spectroscopy, temperature-independent rate constants (k≈1.4×10-3  s-1 ; half-life of ≈8 min) were measured from 10 to 20 K. Computational estimated rate constants are in fair agreement with experimental values, providing evidence for a mechanism involving heavy-atom QMT through crossing triplet to singlet potential energy surfaces. Moreover, the heavy-atom QMT takes place with considerable displacement of the oxygen atom, which establishes a new limit for the heavier atom involved in a QMT reaction in cryogenic matrices.

What Electronic Structure Method Can Be Used in the Global Optimization of Nanoclusters?

The problem of obtaining the spatial structure of nanoclusters is known to be very difficult due to the large number of local minima associated with their potential energy surfaces (isomers). In global optimization approaches, such as basin hopping and genetic algorithms, the problem is normally tackled by first using a low-level and affordable method to evaluate the energy. Afterward, the putative global minimum (and often a few others) is refined with calculations using higher level methods and larger basis sets. There is no guarantee, however, that the structure obtained at the lower level method will be the global minimum at the refined one. In this work, we have performed benchmark coupled cluster calculations at the complete basis set limit for a large number of different isomers of representative clusters of third row elements. Such calculations are then employed to check the hypothesis that lower level methods can be used in the global optimization with reliable results. For this, we have developed a methodology that allows us to compare a large number of minima obtained at different calculation levels. The results indicate that, if the global optimization is capable of reaching not only the global minimum but also a reduced number of low lying structures, most of the tested density functional theory (DFT) functionals are good choices, with emphasis on TPSSh. Besides giving a more solid ground to this commonly used approach, this work helps guiding such global optimizations. The use of the MP2 method and several scaled variants is also assessed, from where it is concluded that the scaled variants yield better results than standard MP2 or DFT approaches, except for one system where a large number of van der Waals structures exist.

Exploring the Reactivity of Hydrofluoropolyethers toward OH through a Cost-Effective Protocol for Calculating Multiconformer Transition State Theory Rate Constants.

In this work, we propose a cost-effective protocol for the calculation of rate constants within the framework of multiconformer transition state theory. We have developed this methodology while calculating for the first time on a theoretical level rate constants for a series of six reactions between the OH radical and hydrofluoropolyethers: the latter are promising third-generation CFC replacements whose atmospheric impact is still widely unknown. Our investigation, which is based on computationally accessible M08-HX/apcseg-2//M08-HX/pcseg-1 calculations, shows that two of our rate constants are within a factor of 0.6 and 1.4 of experimental data, a good result that probably benefits from some error cancellation. It also exhibits a reactivity trend, for which we provide detailed insights that could be used to shed new light on the general reactivity of ethers toward OH. Finally, because the studied reactions share a ubiquitous mechanism in atmospheric chemistry, we hope that our protocol can be routinely applied to explore the reactivity of computationally challenging reactions and to pave new ways in the development of greener CFC replacements.

Coupled-cluster reaction barriers of HO2+H2O+O3: An application of the coupled-cluster//Kohn-Sham density functional theory model chemistry.

In this work, we report a theoretical investigation concerning the use of the popular coupled-cluster//Kohn-Sham density functional theory (CC//KS-DFT) model chemistry, here applied to study the entrance channel of the HO2+H2O+O3 reaction, namely by comparing CC//KS-DFT calculations with KS-DFT, MRPT2//CASSCF, and CC//CASSCF results from our previous investigations. This was done by performing single point energy calculations employing several coupled cluster methods and using KS-DFT geometries optimized with six different functionals, while conducting a detailed analysis of the barrier heights and topological features of the curves and surfaces here obtained. The quality of this model chemistry is critically discussed in the context of the title reaction and also in a wider context.

Semi-quantitative chemometric models for characterization of mixtures of sugars using infrared spectral data.

Sugars (saccharides) are sweet-tasting carbohydrates that are abundant in foods and play very important roles in living organisms, particularly as sources and stores of energy, and as structural elements in cellular membranes. They are desirable therapeutic targets, as they participate in multiple metabolic processes as fundamental elements. However, the physicochemical characterization of sugars is a challenging task, mostly due to the structural similarity shared by the large diversity of compounds of this family. The need for fast, accurate enough, and cost-effective analytical methods for these substances is of extreme relevance, in particular because of the recently increasing importance of carbohydrates in Medicine and food industry. With this in view, this work focused on the development of chemometric models for semi-quantitative analysis of samples of different types of sugars (glucose, galactose, mannitol, sorbose and fructose) using infrared spectra as data, as an example of application of a novel approach, where the Principal Component Analysis (PCA) score plots are used to estimate the composition (weight-%) of the mixtures of the sugars. In these plots, polygonal geometric shapes emerge in the vectorial space of the most significant principal components, that allow grouping different types of samples on the vertices, edges, faces and interior of the polygons according to the composition of the samples. This approach was applied successfully to mixtures of up to 5 sugars and shown to appropriately extract the compositional information from the hyper-redundant complex spectral data. Thought the method has been applied here to a specific problem, it shall be considered as a general procedure for the semi-quantitative analysis of other types of mixtures and applicable to other types of data reflecting their composition. In fact, the methodology appears as an efficient tool to solve three main general problems: (i) use hyper-redundant (in variables) data, as spectral information, directly and with minimum pre-treatment, to evaluate semi-quantitatively the composition of mixtures; (ii) do this for systems which produce data that can be considered rather similar; and (iii) do it for a number of substances present in the mixtures that might be greater than that usually considered in chemistry, which in general is limited to 3 components. In addition, this work also demonstrates that, similarly to the developed analysis based on the PCA score plots, the Multivariate Curve Resolution with Alternating Least Squares (MCR-ALS) chemometric method can also be used successfully for the qualitative (when used without any previous knowledge of the components present in the samples) or semi-quantitative (when the pure components spectral profiles are provided as references) analyses of mixtures of (at least) up to 5 distinct sugars.

A detailed test study of barrier heights for the HO2 + H2O + O3 reaction with various forms of multireference perturbation theory.

We report an ab initio multireference perturbation theory investigation of the HO(2) + H(2)O + O(3) reaction, with particular emphasis on the barrier heights for two possible reaction mechanisms: oxygen abstraction and hydrogen abstraction, which are identified by two distinct saddle points. These saddle points and the corresponding pre-reactive complexes were optimized at the CASSCF(11,11) level while the single point energies were calculated with three different MRPT2 theories: MRMP, CASPT2, and SC-NEVPT2. Special attention has been drawn on the "intruder state" problem and the effect of its corrections on the relative energies. The results were then compared with single reference coupled-cluster methods and also with our recently obtained Kohn-Sham density functional theory (KS-DFT) calculations [L. P. Viegas and A. J. C. Varandas, Chem. Phys., (2011)]. It is found that the relative energies of the pre-reactive complexes have a very good agreement while the MRPT2 classical barrier heights are considerably higher than the KS-DFT ones, with the SC-NEVPT2 calculations having the highest energies between the MRPT2 methods. Possible explanations have been given to account for these differences.

Inducing molecular reactions by selective vibrational excitation of a remote antenna with near-infrared light.

We demonstrate here that selective vibrational excitation of a moiety, remotely attached in relation to the molecular reaction site, might offer a generalized strategy for inducing bond-breaking/bond-forming reactions with exquisite precision. As a proof-of-principle, the electrocyclic ring-expansion of a benzazirine to a ketenimine was induced, in a cryogenic matrix, by near-IR light tuned at the overtone stretching frequency of its OH remote antenna. This accomplishment paves the way for harnessing IR vibrational excitation as a tool to guide a variety of molecular structure manipulations in an exceptional highly-selective manner.

Reliability of semiempirical and DFTB methods for the global optimization of the structures of nanoclusters.

In this work, we explore the possibility of using computationally inexpensive electronic structure methods, such as semiempirical and DFTB calculations, for the search of the global minimum (GM) structure of chemical systems. The basic prerequisite that these inexpensive methods will need to fulfill is that their lowest energy structures can be used as starting point for a subsequent local optimization at a benchmark level that will yield its GM. If this is possible, one could bypass the global optimization at the expensive method, which is currently impossible except for very small molecules. Specifically, we test our methods with clusters of second row elements including systems of several bonding types, such as alkali, metal, and covalent clusters. The results reveal that the DFTB3 method yields reasonable results and is a potential candidate for this type of applications. Even though the DFTB2 approach using standard parameters is proven to yield poor results, we show that a re-parametrization of only its repulsive part is enough to achieve excellent results, even when applied to larger systems outside the training set.

Glucuronidation of Methylated Quercetin Derivatives: Chemical and Biochemical Approaches.

Botanical supplements derived from grapes are functional in animal model systems for the amelioration of neurological conditions, including cognitive impairment. Rats fed with grape extracts accumulate 3'-O-methyl-quercetin-3-O-ß-d-glucuronide (3) in their brains, suggesting 3 as a potential therapeutic agent. To develop methods for the synthesis of 3 and the related 4'-O-methyl-quercetin-7-O-ß-d-glucuronide (4), 3-O-methyl-quercetin-3'-O-ß-d-glucuronide (5), and 4'-O-methyl-quercetin-3'-O-ß-d-glucuronide (6), which are not found in the brain, we have evaluated both enzymatic semisynthesis and full chemical synthetic approaches. Biocatalysis by mammalian UDP-glucuronosyltransferases generated multiple glucuronidated products from 4'-O-methylquercetin, and is not cost-effective. Chemical synthetic methods, on the other hand, provided good results; 3, 5, and 6 were obtained in six steps at 12, 18, and 30% overall yield, respectively, while 4 was synthesized in five steps at 34% overall yield. A mechanistic study on the unexpected regioselectivity observed in the quercetin glucuronide synthetic steps is also presented.

Role of (H2O)(n) (n = 2-3) Clusters on the HO2 + O3 Reaction: A Theoretical Study.

We report a theoretical investigation on the role of the water dimer and trimer in the reaction between the hydroperoxyl radical and ozone. This study is part of an ongoing series of research endeavors that intend to deliver a comprehensive understanding on the role of water on this reaction. Due to the complexity of the potential energy surface, and to be able to make comparisons with our previous works, our calculations have employed model chemistries based on the Kohn-Sham DFT formalism. It is found that the calculated reaction paths share a common scheme, not only in the context of this work, but also in consideration of our previous studies. Also, oxygen-abstraction barriers are always submerged, with the relative energy between the hydrogen- and oxygen-abstraction saddle-points increasing with the number of water molecules, which maintain an apparent spectator role. Finally, we report novel HO2···(H2O)3 and HO3···(H2O)n complexes originating from our reaction schemes.

How Well Can Kohn-Sham DFT Describe the HO2 + O3 Reaction?

In a previous work (J. Chem. Theory Comput. 2010, 6, 412) we reported an ab initio investigation of the reaction between ozone and the hydroperoxyl radical. The studies on this atmospheric reaction are here continued with an evaluation of different exchange-correlation functionals (all rungs of "Jacob's ladder" of density functional approximations are represented) in Kohn-Sham DFT calculations. We focus on the comparison between the barrier heights of the oxygen- and hydrogen-abstraction mechanisms here calculated with the ones previously obtained at the CASPT2(11,11)/AVTZ level. The comparison is also extended to the remaining stationary points. Additionally, a relation between the fraction of exact exchange of one-parameter hybrid functionals and the imaginary frequency of a saddle point is developed, originating three new functionals that are also used in the present benchmark calculations.

HO2 + O3 Reaction: Ab Initio Study and Implications in Atmospheric Chemistry.

We report a theoretical investigation on the reaction between ozone and the hydroperoxyl radical, which is part of the ozone depletion cycle. This reaction represents a great challenge to the state of the art ab initio methods, while its mechanism remains unclear to both experimentalists and theoreticians. In this work we calculated the relative energies of the stationary points along the reaction coordinate of the oxygen- and hydrogen-abstraction mechanisms using different levels of theory and extrapolating some of the results to the complete one-electron basis set limit. Oxygen abstraction is shown to be preceded by formation of hydrogen-bonded complexes, while hydrogen abstraction shows a lower energy barrier than oxygen abstraction. Both mechanisms lead to formation of HO3 + O2 in a very troublesome region of the potential-energy surface that is not correctly described by single-reference methods. The implications of the results on reaction dynamics are discussed.

Accurate ab initio based multisheeted double many-body expansion potential energy surface for the three lowest electronic singlet states of H3+.

The authors present diabatic and adiabatic potential energy surfaces for the three lowest electronic singlet states of H3+. The modeling of the surfaces is based on the multi-sheeted double many-body expansion method which consists of dressing the various matrix elements of the diatomics-in-molecules potential matrix with three-body terms. The avoided crossing between the two lowest states and the conical intersection between the second and the third state are accurately represented by construction.

Symmetry analysis of the vibronic States in the upper conical potential (2(3)A') of triplet.

The symmetry properties of the rovibronic resonance states (Slonczewski resonances) supported by an upright conical potential are investigated. These symmetry properties lead to a useful correlation between states calculated with and without consideration of the geometrical phase, which can assist in the assignment of those states. The vibronic resonance states of triplet H3(+) (2(3)A'), which had been studied by us before, have now been assigned to spectroscopic quantum numbers.

Accurate double many-body expansion potential energy surface for triplet H3+. II. The upper adiabatic sheet (2(3)A').

We report on a global potential energy hypersurface for the upper sheet of the lowest triplet state of H3+. The analytic representation is based on the double many-body expansion theory. The ab initio data points, calculated with a large cc-pV5Z basis, are represented with a root mean square deviation of only 5.54 cm(-1) in the energy region below the H(+)+2H(2S) dissociation threshold. The quasi-bound vibronic states supported by this surface have also been calculated.