Judith Millán

Ab initio ground potential energy surface, VTST and QCT study of the O(3P)+CH4(X 1A1)→OH(X 2Π)+CH3(X 2A2″) reaction

An ab initio study of the ground potential energy surface (PES) of the O(3P)+CH4→OH+CH3 reaction has been performed using the second- and fourth-order Mo/ller–Plesset methods with a large basis set. A triatomic analytical ground PES with the methyl group treated as an atom of 15.0 a.m.u. has been derived. This PES has been employed to study the kinetics [variational transition state theory (VTST) and quasiclassical trajectory (QCT) rate constants] and dynamics (QCT method) of the reaction. The ab initio points have also been used directly to calculate the VTST rate constant considering all atoms of the system. The best VTST methods used lead to a good agreement with the experimental rate constant for 1000–2500 K, but QCT rate constant values are about one-third the experimental ones for 1500–2500 K. The cold QCT OH(v=0) rotational distribution arising from the simulation of the reaction with O(3P) atoms produced in the photodissociation of NO2 at 248 nm is in good agreement with experiment, while the very...

Ab initio potential energy surface, variational transition state theory, and quasiclassical trajectory studies of the F+CH4→HF+CH3 reaction

In this work we present a study of the F+CH(4)-->HF+CH(3) reaction (DeltaHdegrees(298 K)=-32.0 kcal mol(-1)) using different methods of the chemical reaction theory. The ground potential energy surface (PES) is characterized using several ab initio methods. Full-dimensional rate constants have been calculated employing the variational transition state theory and using directly ab initio data. A triatomic analytical representation of the ground PES was derived from ab initio points calculated at the second- and fourth-order Møller-Plesset levels with the 6-311+G(2df,2pd) basis set, assuming the CH(3) fragment to be a 15 a.m.u. pseudoatom in the fitting process. This is suggested from experiments that indicate that the methyl group is uncoupled to the reaction coordinate. A dynamics study by means of the quasiclassical trajectory (QCT) method and employing this analytical surface was also carried out. The experimental data available on the HF internal states distributions are reproduced by the QCT results. Very recent experimental information about the reaction stereodynamics is also borne out by our QCT calculations. Comparisons with the benchmark F+H(2) and analogous Cl+CH(4) reactions are established throughout.

Ab initio, kinetics, and dynamics study of Cl+CH4→HCl+CH3

The Cl+CH4→HCl+CH3 reaction has been studied using different levels of the chemical reaction theory. Ab initio calculations at the fourth-order Moller–Plesset perturbation theory//second-order Moller–Plesset perturbation theory level, employing the 6-311G(2df,2pd) basis set, satisfactorily describe the system stationary points. A kinetics study using variational transition state theory has been accomplished, using ab initio information along the minimum energy reaction path. The agreement with experimental rate constants in the 200–500 K range is the best reported up to date. Reduced-dimensionality quasiclassical trajectory (QCT) calculations of the reaction dynamics have been performed on an analytical many-body potential energy surface, which is fitted to ab initio calculations of the system. The various experiments showing the absence of energy release to the CH3 group has led us to invoke a pseudotriatomic approximation, in which the CH3 moiety is treated as a single particle, so as to carry out dynam...

Ab initio analytical potential energy surface and quasiclassical trajectory study of the O+(4S)+H2(X 1Σg+)→OH+(X 3Σ−)+H(2S) reaction and isotopic variants

An analytical potential energy surface (PES) representation of the O+(4S)+H2(X 1Σg+) system was developed by fitting around 600 CCSD(T)/cc-pVQZ ab initio points. Rate constant calculations for this reaction and its isotopic variants (D2 and HD) were performed using the quasiclassical trajectory (QCT) method, obtaining a good agreement with experimental data. Calculations conducted to determine the cross section of the title reaction, considering collision energies (ET) below 0.3 eV, also led to good accord with experiments. This PES appears to be suitable for kinetics and dynamics studies. Moreover, the QCT results show that, although the hypotheses of a widely used capture model are not satisfied, the resulting expression for the cross section can be applied within a suitable ET interval, due to errors cancellation. This could be a general situation regarding the application of this simple model to ion–molecule processes.

Shaping Micelles: The Interplay Between Hydrogen Bonds and Dispersive Interactions†

A subtle interplay: In the formation of a 1.6 nm micelle containing up to six molecules of propofol, a hydrogen-bond network is shown to influence the structure of the micelle, whereas the nonpolar groups arrange in such a way that the remaining noncovalent interactions are maximized. Such globular structures present a characteristic signature in the IR spectrum that will allow their identification in more complex media.

Ab initio study of the O(1D)+CH4(X 1A1)→OH(X 2Π)+CH3(X 2A2″) reaction: Ground and excited potential energy surfaces

The two potential energy surfaces (1 1A and 2 1A PESs) adiabatically correlating the reactants and products asymptotes of the title reaction were studied by means of the CASSCF and CASPT2 ab initio methods. The minimum energy path determined for the ground PES evolved through the barrierless insertion of the O(1D) atom into a C–H bond. The OH+CH3 products result from the dissociation of the CH3OH methanol intermediate formed. Reactivity on the excited 2 1A PES was found to proceed via an abstraction pathway. The energy barrier involved is low enough to expect the 2 1A PES to play a non-negligible role in the title reaction, even at the usual conditions attained in the experiments. The crossing between the 1 1A and 3 1A PESs was also investigated, the latter surface correlating with the excited OH(A 2Σ+) product.

A Spectroscopic and Computational Study of Propofol Dimers and Their Hydrated Clusters

Propofol (2,6-diisopropylphenol, PPF) homodimers and their complexes with one water molecule are analyzed by means of mass-resolved excitation spectroscopy. Using two-color resonance-enhanced multiphoton ionization (REMPI) the S(1) electronic spectra of these systems are obtained, avoiding fragmentation. Due to the large size of these species, the spectra present a large abundance of lines. Using UV/UV hole-burning spectroscopy, two isomers of PPF(2) are found and the existence of at least three isomers for propofol(2)(H(2)O)(1) (PPF(2)W(1)) is demonstrated. Comparison with the structures calculated at the M06-2X/6-311++G(d,p) and M06-2X/6-31+G(d) levels of theory shows that the main driving forces in PPF(2) are several C-H···π interactions accompanied by dipole-dipole interaction between the OH moieties. On the other hand, there is evidence for the formation of cyclic hydrogen-bond structures in the heterotrimers. A comparison of the results obtained herein with those of similar systems from previously published studies follows.

Unravelling Protein–DNA Interactions at Molecular Level: A DFT and NCI Study

Histone-DNA interactions were probed computationally at a molecular level, by characterizing the bimolecular clusters constituted by selected amino acid derivatives with polar (asparagine and glutamine), nonpolar (alanine, valine, and isoleucine), and charged (arginine) side chains and methylated pyrimidinic (1-methylcytosine and 1-methylthymine) and puric (9-methyladenine and 9-methylguanine) DNA bases. The computational approach combined different methodologies: a molecular mechanics (MMFFs forced field) conformational search and structural and vibrational density-functional calculations (M06-2X with double and triple-ζ Poples basis sets). To dissect the interactions, intermolecular forces were analyzed with the Non-Covalent Interactions (NCI) analysis. The results for the 24 different clusters studied show a noticeable correlation between the calculated binding energies and the propensities for protein-DNA base interactions found in the literature. Such correlation holded even for the interaction of the selected amino acid derivatives with Watson and Crick pairs. Therefore, the balance between hydrogen bonds and van der Waals interactions (specially stacking) in the control of the final shape of the investigated amino acid-DNA base pairs seems to be well reproduced in dispersion-corrected DFT molecular models, reinforcing the idea that the specificity between the amino acids and the DNA bases play an important role in the regulation of DNA.

Water Encapsulation by Nanomicelles

Reported is the hydration of nanomicelles in the gas-phase using spectroscopic methods and quantum chemical calculations. A fine-tuning of the experimental conditions allowed formation of a propofol trimer and tetramer with a water molecule and to determine the structure of the aggregates. Their electronic and IR spectra were obtained using mass-resolved laser spectroscopy, together with the number of conformational isomers for each stoichiometry. Interpretation of the spectra in the light of high-level calculations allowed determination of the clusters structure and demonstration that the trimer of propofol with a water molecule forms cyclic hydrogen-bond networks but, on the other hand, the tetramer is big enough to encapsulate the water molecule inside its hydrophilic core. Furthermore, these hydrated nanomicelles present an unusually high binding energy, thus reflecting their high stability and their capability to trap water inside.

A combined spectroscopic and theoretical study of propofol·(H2O)3

Propofol (2,6-di-isopropylphenol) is probably the most widely used general anesthetic. Previous studies focused on its complexes containing 1 and 2 water molecules. In this work, propofol clusters containing three water molecules were formed using supersonic expansions and probed by means of a number of mass-resolved laser spectroscopic techniques. The 2-color REMPI spectrum of propofol[middle dot](H(2)O)(3) contains contributions from at least two conformational isomers, as demonstrated by UV/UV hole burning. Using the infrared IR/UV double resonance technique, the IR spectrum of each isomer was obtained both in ground and first excited electronic states and interpreted in the light of density functional theory (DFT) calculations at M06-2X/6-311++G(d,p) and B3LYP/6-311++G(d,p) levels. The spectral analysis reveals that in both isomers the water molecules are forming cyclic hydrogen bond networks around propofols OH moiety. Furthermore, some evidences point to the existence of isomerization processes, due to a complicated conformational landscape and the existence of multiple paths with low energy barriers connecting the different conformers. Such processes are discussed with the aid of DFT calculations.