Jose M. Hermida-Ramón

Ultrafast Ring-Opening/Closing and Deactivation Channels for a Model Spiropyran–Merocyanine System

The photochemistry of a model merocyanine-spiropyran system was analyzed theoretically at the MS-CASPT2//SA-CASSCF(14,12) level. Several excited singlet states were studied in both the closed spiropyran and open merocyanine forms, and the paths to the different S(1)/S(0) conical intersections found were analyzed. After absorption of UV light from the spiropyran form, there are two possible ultrafast routes to efficient conversion to the ground state; one involves the rupture of the C(spiro)-O bond leading to the open form and the other involves the lengthening of the C(spiro)-N bond with no photoreaction. From the merocyanine side the excited state can reach a very broad S(1)/S(0) conical intersection region that leads the system to the closed form after rotation of the central methine bond. Alternatively, rotation of the other methine bonds connects the system through different S(1)/S(0) conical intersections to several merocyanine isomers. The present work provides a theoretical framework for the recent experimental results (Buback , J. J. Am. Chem. Soc. 2010, 132, 1610-1619) and sheds light on the complex photochemistry of these kinds of compounds.

SERS Chiral Recognition and Quantification of Enantiomers through Cyclodextrin Supramolecular Complexation

We introduce here a simple approach in which a cyclodextrin, functionalized with thiols in the narrower rim, is assembled onto the silver surface of a SERS platform composed of polystyrene beads coated with silver nanoparticles. Trapping properties of the fabricated sensor are demonstrated through the retention of different enantiomers (R,R or/and S,S) of hydrobenzoin (HBZ), a molecule that has not been reported before in SERS because it has no affinity for coinage metal surfaces. Further, selective recognition of each enantiomer and semiquantification of its proportion in a racemic mixture are provided by the analysis of the SERS spectra of the HBZ-cyclodextrin complex, in full agreement with the surface selection rules.

Theoretical characterization of structures and energies of benzene–(H2S)n and (H2S)n (n=1–4) clusters

An ab initio study was performed in clusters up to four H(2)S molecules and benzene using calculations at MP26-31+G(*) and MP2/aug-cc-pVDZ levels. Differences between both sets of calculations show the importance of using large basis sets to describe the intermolecular interactions in this system. The obtained binding energies reflect that benzene has not the same behavior in H(2)S as in water, pointing to a higher solubility of this molecule in H(2)S than in water. The Bz-cluster binding energy was fitted to an asymptotic representation with a maximum value of the energy of -8.00 kcal/mol that converges in a cluster with 12 H(2)S molecules. The obtained intermolecular distance in the Bz-H(2)S dimer is similar to the experimental value; however, the difference is much larger for the angles defining the orientation. The influence of benzene produces a distortion of the (H(2)S)(n) clusters, so the intermolecular distances change with regard to the (H(2)S)(n) isolated clusters. Frequency shifts are larger in clusters with benzene than without it. In the smallest clusters the shift associated to the stretching of the S-H bonded to benzene is the largest one, but for the cluster with three H(2)S molecules this stretching is combined with the other S-H stretching of the molecule so the resulting shift is not the largest one.

Inter- and intramolecular potential for the N-formylglycinamide-water system. A comparison between theoretical modeling and empirical force fields

An intramolecular NEMO potential is presented for the N‐formylglycinamide molecule together with an intermolecular potential for the N‐formylglycinamide‐water system. The intramolecular N‐formylglycinamide potential can be used as a building block for the backbone of polypeptides and proteins. Two intramolecular minima have been obtained. One, denoted as C5, is stabilized by a hydrogen bonded five member ring, and the other, denoted as C7, corresponds to a seven membered ring. The interaction between one water molecule and the N‐formylglycinamide system is also studied and compared with Hartree‐Fock SCF calculations and with the results obtained for some of the more commonly used force fields. The agreement between the NEMO and SCF energies for the complexes is in general superior to that of the other force fields. In the C7 region the surfaces obtained from the intramolecular part of the commonly used force fields are too flat compared to the NEMO potential and the ab initio calculations. We further analyze the possibility of using a charge distribution obtained from one conformation to describe the charge distribution of other conformations. We have found that the use of polarizabilities and generic dipoles can model most of the changes in charge density due to the different geometry of the new conformations, but that one can expect additional errors in the interaction energies that are of the order of 1 kcal/mol.

Blue‐shifting hydrogen bond in the benzene–benzene and benzene–naphthalene complexes

Ab initio complete optimizations at MP2/6‐31++G** level have been performed in the T‐shaped geometry of the benzene–benzene and benzene–naphthalene complexes. To check the effect of the basis set superposition error (BSSE), optimizations have been done in the BSSE corrected and BSSE uncorrected potential energy surfaces. The BSSE effect in the calculation of the Hessian has also been evaluated to check its influence in the frequency values. Quantum theory atoms in molecules (QTAIM) calculations have also been performed on both dimers. Intermolecular energies differ around a 25% when the optimization is performed with or without counterpoise corrected gradients. The influence of BSSE is also noticeable in the distances. Frequency shifts show big changes because of the BSSE. Thus, uncorrected values are up 350% larger than corrected ones. The hypotheses given in the literature to explain the origin of the blue‐shifting hydrogen bond do not seem to give a suitable explanation for all characteristics of the behavior found in the studied systems.

Electron Density Based Partitioning Scheme of Interaction Energies.

In this paper, a new partitioning of the complex interaction energy is proposed. This new partitioning is based on the decomposition of the one-electron and exchange-correlation densities into unperturbed and deformation densities. Thus, the proposed energy fragmentation can be applied at the SCF level and post-SCF levels as long as the corresponding density matrices have been evaluated previously. It provides the typical description of the complex interaction as a summation of electrostatic, exchange-repulsion, and polarization terms. However, the new method allows splitting up the exchange-repulsion into exchange and Pauli-repulsion energies. A full theoretical description of the method is presented, and some examples of its application to small complexes are discussed. A comparison with results obtained using perturbation methods is also carried out, showing that the first order terms obtained from symmetry adapted perturbation theories are perfectly reproduced with the new method. A clear bridge between qualitative deformation density plots and quantitative measures of the interaction energy components can be established within the framework of this new partitioning scheme, giving rise to a graphical and very intuitive interpretation of the complex formation.

Anion-π Aromatic Neutral Tweezers Complexes: Are They Stable in Polar Solvents?

The impact of the solvent environment on the stabilization of the complexes formed by fluorine (T-F) and cyanide (T-CN) substituted tweezers with halide anions has been investigated theoretically. The study was carried out using computational methodologies based on density functional theory (DFT) and symmetry adapted perturbation theory (SAPT). Interaction energies were obtained at the M05-2X/6-31+G* level. The obtained results show a large stability of the complexes in solvents with large dielectric constant and prove the suitability of these molecular tweezers as potential hosts for anion recognition in solution. A detailed analysis of the effects of the solvent on the electron withdrawing ability of the substituents and its influence on the complex stability has been performed. In particular, the interaction energy in solution was split up into intermonomer and solvent-complex terms. In turn, the intermonomer interaction energy was partitioned into electrostatic, exchange, and polarization terms. Polar resonance structures in T-CN complexes are favored by polar solvents, giving rise to a stabilization of the intermonomer interaction, the opposite is found for T-F complexes. The solvent-complex energy increases with the polarity of the solvent in T-CN complexes, nonetheless the energy reaches a maximum and then decreases slowly in T-F complexes. An electron density analysis was also performed before and after complexation, providing an explanation to the trends followed by the interaction energies and their different components in solution.

Analysis of the SERS Spectrum by Theoretical Methodology: Evaluating a Classical Dipole Model and the Detuning of the Excitation Frequency

Surface-enhanced Raman scattering (SERS) spectroscopy is gaining prominence as one of the most powerful ultradetection techniques. The SERS outcome is essentially a complicated pattern of vibrational bands that allows multiplex analysis but, at the same time, makes difficult the interpretation of unknown analytes or known substances in the presence of complex unknown chemical environments. Herein, we show two computational methods to reproduce the spectral shape of the SERS spectra. The first, based in the modification of the classical dipole model, reproduces with a notable similarity the experimental spectrum excited far to the red of the localized surface plasmon resonance (LSPR). This light and time-efficient model is of great interest to elucidate the orientation of the target on the plasmonic surface or even to accurately identify suspected unknown targets in real samples. However, the experimental SERS spectrum in resonance with the LSPR is also modeled by using a more classical CPHF approach. This method provides also good agreement with the experiment but at the expense of much more computational time.

A computational study of the protonation of simple amines in water clusters.

The microsolvation study of a group of amines with a variable number of water molecules was performed by conducting a theoretical analysis of the properties of the clusters formed by the amines with up to seven molecules of water. We describe the microsolvation of several amines focusing on the dissociation of a water molecule that transfers a proton to the amine and forms a hydroxide ion. Ab initio calculations were performed on these clusters employing the DFT/B3LYP and MP2 methods with the 6-311++G(2d,p) basis set. Several stationary points for each cluster were thus located and characterized as minima from frequency calculations. Intermolecular BSSE corrected interaction energies were obtained. The protonation mechanism of the amines was examined in terms of some parameters that include the lengths of the bonds involved in the process of proton transfer and the frequencies associated with certain O-H and N-H stretching modes. On the basis of the calculations, all studied amines present similar behavior but trimethylamine, whose limitations to be integrated in the water hydrogen bond network cause the instability of some of their complexes. The cyclic configurations are the most stable structures up to five water molecules due to the presence of cooperative effects associated with the hydrogen bonds of water molecules. However, when the number of water molecules increases the spatial forms become the most stable configurations. The dissociated forms were not found to have the most stable configuration in any of the studied systems but energetic differences between the dissociated and non-dissociated forms decrease with the number of water molecules.

Method for Slater-Type Density Fitting for Intermolecular Electrostatic Interactions with Charge Overlap. I. The Model

The effects of charge overlap, or charge penetration, are neglected in most force fields and interaction terms in QM/MM methods. The effects are however significant at intermolecular distances near the van der Waals minimum. In the present study, we propose a method to evaluate the intermolecular Coloumb interaction using Slater-type functions, thus explicitly modeling the charge overlap. The computational cost of the method is low, which allows it to be used in large systems with most force fields as well as in QM/MM schemes. The charge distribution is modeled as a distributed multipole expansion up to quadrupole and Slater-type functions of angular momentum up to L = 1. The exponents of the Slater-type functions are obtained using a divide-and-conquer method to avoid the curse of dimensionality that otherwise is present for large nonlinear optimizations. A Levenberg-Marquardt algorithm is applied in the fitting process. A set of parameters is obtained for each molecule, and the process is fully automated. Calculations have been performed in the carbon monoxide and the water dimers to illustrate the model. Results show a very good accuracy of the model with relative errors in the electrostatic potential lower than 3% over all reasonable separations. At very short distances where the charge overlaps is the most significant, errors are lower than 8% and lower than 3.5% at distances near the van der Waals minimum.