Freddy Fernandes Guimarães

Global optimization analysis of water clusters (H2O)n (11⩽n⩽13) through a genetic evolutionary approach

The structures and stabilities of water clusters (H2O)n with 11⩽n⩽13 are determined by a genetic algorithm approach with two new evolutionary operators—namely annihilator and history operators. These studies show that the modified genetic algorithm provides an efficient procedure for calculating global minima with an especial attention to molecular water clusters. The actual results are in quantitative agreement with previous calculations using the basin hopping Monte Carlo method.

The principles of infrared-x-ray pump-probe spectroscopy. Applications on proton transfer in core-ionized water dimers

In this paper we derive the basic physics underlying infrared-x-ray pump-probe spectroscopy (IR, infrared). Particular features of the spectroscopy are highlighted and discussed, such as dependence on phase of the infrared pulse, duration and delay time of the x-ray pulse, and molecular orientation. Numerical applications are carried out for the water dimer using wave packet techniques. It is shown that core ionization of the donor oxygen of the water dimer results in a drastic change of the potential with the global minimum placed in the proton transfer region. The results of the modeling indicate that IR-x-ray pump-probe spectroscopy can be used to study the dynamics of proton transfer in this core-ionized state, and that, contrary to conventional core level photoelectron spectroscopy, x-ray core-ionization driven by an IR field is a proper method to explore the proton transfer in a system like the water dimer. We observe that the trajectory of the nuclear wave packet in the ground state potential well is strongly affected by the absolute phase of the IR pulse.

Selective gating to vibrational modes through resonant X-ray scattering

The dynamics of fragmentation and vibration of molecular systems with a large number of coupled degrees of freedom are key aspects for understanding chemical reactivity and properties. Here we present a resonant inelastic X-ray scattering (RIXS) study to show how it is possible to break down such a complex multidimensional problem into elementary components. Local multimode nuclear wave packets created by X-ray excitation to different core-excited potential energy surfaces (PESs) will act as spatial gates to selectively probe the particular ground-state vibrational modes and, hence, the PES along these modes. We demonstrate this principle by combining ultra-high resolution RIXS measurements for gas-phase water with state-of-the-art simulations.

Gradual collapse of nuclear wave functions regulated by frequency tuned X-ray scattering

As is well established, the symmetry breaking by isotope substitution in the water molecule results in localisation of the vibrations along one of the two bonds in the ground state. In this study we find that this localisation may be broken in excited electronic states. Contrary to the ground state, the stretching vibrations of HDO are delocalised in the bound core-excited state in spite of the mass difference between hydrogen and deuterium. The reason for this effect can be traced to the narrow “canyon-like” shape of the potential of the state along the symmetric stretching mode, which dominates over the localisation mass-difference effect. In contrast, the localisation of nuclear motion to one of the HDO bonds is preserved in the dissociative core-excited state . The dynamics of the delocalisation of nuclear motion in these core-excited states is studied using resonant inelastic X-ray scattering of the vibrationally excited HDO molecule. The results shed light on the process of a wave function collapse. After core-excitation into the state of HDO the initial wave packet collapses gradually, rather than instantaneously, to a single vibrational eigenstate.

Salt or cocrystal of salt? Probing the nature of multicomponent crystal forms with infrared spectroscopy.

Abstract The recognition of the nature of a multicomponent crystal form (solvate, salt, cocrystal or cocrystal of salt) is of great importance for pharmaceutical industry because it is directly related to the performance of a pharmaceutical ingredient, since there is interdependence between the structure, its energy and its physical properties. In this context, here we have identified the nature of multicomponent crystal forms of the anti-HIV drug lamivudine with mandelic acid through infrared spectroscopy. These investigated crystal forms were the known S-mandelic acid cocrystal of lamivudine R-mandelate trihydrate (1), a cocrystal of salt, and lamivudine R-mandelate (2), a salt. This approach also supports the identification and distinction of both ionized and unionized forms of mandelic acid in the infrared spectrum of 1. In this way, infrared spectroscopy can be useful to distinguish a cocrystal of salt from either salt or cocrystal forms. In the course of this study, for the first time we have also characterized and determined the crystal structure of R-mandelic acid cocrystal of sodium R-mandelate (3).

Polymorphism and conformerism in chalcones

Herein two solid state phenomena have been observed in two chalcones. Firstly, polymorphism has been found in (E)-1-(2-aminophenyl)-3-(3,4,5-trimethoxyphenyl)prop-2-en-1-one (1). This compound crystallizes with only one conformer rather than three in the known reported structure. In the polymorphs, the conformation of the phenyl ring bonded to carbonyl differs slightly. The intermolecular hydrogen bonding from NH2 is the main interaction responsible for polymorphism. Our polymorph is assembled only with weak N–H⋯π interactions instead of strong N–H⋯O and N–H⋯N ones observed in the known structure. DFT calculations reveal that the three conformers of the known polymorph deviate from the minimum energy conformation which is adopted in our crystal form to compensate for the absence of strong intermolecular contacts. Second, conformerism is reported for (E)-1-(3-hydroxyphenyl)-3-(4-nitrophenyl)prop-2-en-1-one (2). Three crystallographically independent molecules are found in the structure of 2: two of them are similarly planar with an anti conformation around the single bond between the carbonyl and α carbons while the third one is twisted, with its phenyl ring bonded to carbonyl rotated by ca. 60° besides presenting a syn conformation around the corresponding rotatable bond. Both conformational features are related to the crystal packing, allowing accommodation of twisted molecules onto the layers made up of hydrogen bonded planar molecules. Furthermore, our potential energy surface scans indicate that the planar and twisted conformations of the phenyl ring bonded to carbonyl are not compatible with the syn and anti conformations of the chalcone skeleton.

Isostructurality and the conformational role of the 2′,3′-moieties in the diversity of lamivudine crystal forms probed in halide salts

Crystal engineering of the anti-HIV drug lamivudine has currently provided improvement in its pharmaceutical performance besides getting insights into several branches of nucleoside structural chemistry. Here, we demonstrated the synthon robustness and the role of the five-membered ring conformation in the diversity of lamivudine crystal forms even with supramolecular isomerism. Oxathiolane conformation defines the ability of lamivudine to assemble into different multicomponent molecular crystal forms. This was observed in a polymorph of lamivudine hydrochloride, which is related to the previously reported lamivudine hydrochloride monohydrate. The absence of water molecules has little effect on their supramolecular organization. If water is not present, just one conformational change from C3′-endo puckering in the monohydrate form to the C2′-endo one in the anhydrate form reported here is enough to cause a hydrogen bonding reorganization involving the 5′-OH group. DFT calculations reveal a low energy gap for this change in the oxathiolane conformation. Therefore, lamivudine can variably forward its 5′-OH group through changing oxathiolane conformations of similar energies. In addition, the isostructurality and robustness of the supramolecular synthons were illustrated in two halide salts of lamivudine with hydrobromic and hydrofluoric acids. While the previously reported lamivudine hydrochloride is strictly isostructural to the hydrobromide salt, the lamivudine hydrofluoride crystallized as a hydrofluoric acid cocrystal. HF cocrystallization appears to be primarily related to further stabilization between sheets rather than a major size effect.

Aplicação de técnicas multivariadas e inteligência artificial na análise de espectros de infravermelho para determinação de matéria orgânica em amostras de solos

APPLICATION OF MULTIVARIATE CALIBRATION AND ARTIFICIAL INTELLIGENCE IN THE ANALYSIS OF INFRARED SPECTRA TO QUANTIFY ORGANIC MATTER IN SOIL SAMPLES. In this paper studies based on Multilayer Perception Artificial Neural Network and Least Square Support Vector Machine (LS-SVM) techniques are applied to determine of the concentration of Soil Organic Matter (SOM). Performances of the techniques are compared. SOM concentrations and spectral data from Mid-Infrared are used as input parameters for both techniques. Multivariate regressions were performed for a set of 1117 spectra of soil samples, with concentrations ranging from 2 to 400 g kg-1. The LS-SVM resulted in a Root Mean Square Error of Prediction of 3.26 g kg-1 that is comparable to the deviation of the Walkley-Black method (2.80 g kg-1).

Pump-probe spectroscopy of molecules driven by infrared field in both ground and excited electronic states.

Pump-probe spectra of molecules driven by strong infrared (IR) field in both ground and excited states are studied theoretically. The role of the final state interaction becomes important when pump and probe pulses overlap, and the Rabi frequency is comparable with the lifetime broadening of the excited state and the duration of the pump pulse. Our theoretical approach is applied to x-ray absorption of nitrogen molecule and valence photoionization of carbon monoxide. It is shown that IR-x-ray pump-probe spectroscopy can directly evidence the delocalization of core hole.

Anomalously strong two-electron one-photon X-ray decay transitions in CO caused by avoided crossing.

The unique opportunity to study and control electron-nuclear quantum dynamics in coupled potentials offered by the resonant inelastic X-ray scattering (RIXS) technique is utilized to unravel an anomalously strong two-electron one-photon transition from core-excited to Rydberg final states in the CO molecule. High-resolution RIXS measurements of CO in the energy region of 12–14 eV are presented and analyzed by means of quantum simulations using the wave packet propagation formalism and ab initio calculations of potential energy curves and transition dipole moments. The very good overall agreement between the experimental results and the theoretical predictions allows an in-depth interpretation of the salient spectral features in terms of Coulomb mixing of “dark” with “bright” final states leading to an effective two-electron one-photon transition. The present work illustrates that the improved spectral resolution of RIXS spectra achievable today may call for more advanced theories than what has been used in the past.