Marco Antonio Chaer Nascimento

This issue of Theoretical Chemistry Accounts is dedicated to Professor Marco Antonio Chaer Nascimento on the occasion of his 65th birthday. Professor Chaer played a pioneering and active role in the early stages and latter developments of research activities in theoretical chemistry in Brazil. As part of this commemoration, an international scientific meeting also took place in Rio de Janeiro, Brazil, in the week of June 11–13, 2012. This special volume contains a selected sample of contributions from his former students, colleagues, and collaborators.

Photoelectrochemical cells with TiO₂ electrodes to convert sunlight and water into gaseous hydrogen and oxygen are a source of clean and renewable fuel. Despite their great potential, far-from-ideal performance and poor utilization of the solar spectrum have prevented them from becoming a widespread and practical technology. We review recent experimental work that uses dynamics measurements to study limitations of photoelectrochemical cells from a fundamental level and the use of TiO₂ nanotube arrays as a superior alternative to TiO₂ nanoparticles. Through a combination of nanoscale size control, doping, composite materials, and the incorporation of noble-metal nanoparticles, improved performance and light harvesting are demonstrated.

The adsorption and dissociation of water on CeO₃(111), CeO₃(221), CeO₃(331), and CeO₃(110) has been studied by means of periodic density functional theory using slab models. The presence of step sites moderately affects the adsorption energy of the water molecule but in some cases as in CeO₃(331) is able to change the sign of the energy reaction from endo- to exothermic which has important consequences for the catalytic activity of this surface. Finally, no stable molecular state has been found for water on CeO₃(110) where the reaction products lead to a very stable hydroxylated surface which will rapidly become inactive.

An extensive theoretical study has been carried out to determine barriers for the proton exchange reactions of C2–C4 alkanes in ZSM-5. It was found that cluster size and cavity structure are very important for predicting this barrier. A decrement of up to 20 kcal/mol was observed when employing the periodic model instead of using the small cluster model. Effects of basis set quality and electron correlation to the activation energy are positive and in combination could contribute up to 8 kcal/mol. An extrapolation scheme for estimating the reaction barrier that takes into account effects of cluster size, basis set quality, and electron correlation has been proposed. The regioselectivity and the chain length were discussed.

The ground and excited state properties of copper proteins are studied and analyzed using hybrid quantum mechanics/molecular mechanics technique. Wildtype plastocyanin, characterized by an intense blue color, and wild-type nitrosocyanin, a red protein, are considered. These proteins differ from some ligands of the copper containing chromophore; we also studied the effects of selective mutations of one of the active site residue in plastocyanin. It is shown that this mutation is able to strongly modify the UV/VIS spectrum continuously modifying the absorption spectrum of the protein that from blue becomes red. Electrostatic and polarization effects of the macromolecular environment on the chromophore are taken into account using original techniques. Principal transitions are analyzed by mean of natural transition orbitals.

The hydration of mesityl oxide (MOx) was investigated through a sequential quantum mechanics/ molecular mechanics approach. Emphasis was placed on the analysis of the role played by water in the MOx syn–anti equilibrium and the electronic absorption spectrum. Results for the structure of the MOx–water solution, free energy of solvation and polarization effects are also reported. Our main conclusion was that in gas-phase and in low-polarity solvents, the MOx exists dominantly in synform and in aqueous solution in anti-form. This conclusion was supported by Gibbs free energy calculations in gas phase and in-water by quantum mechanical calculations with polarizable continuum model and thermodynamic perturbation theory in Monte Carlo simulations using a polarized MOx model. The consideration of the in-water polarization of the MOx is very important to correctly describe the solute–solvent electrostatic interaction. Our best estimate for the shift of the π–π^* transition energy of MOx, when it changes from gas-phase to water solvent, shows a red-shift of -2,520 ± 90 cm^-1, which is only 110 cm^-1 (0.014 eV) below the experimental extrapolation of -2,410 ± 90 cm^-1. This red-shift of around -2,500 cm^-1 can be divided in two distinct and opposite contributions. One contribution is related to the syn → anti conformational change leading to a blue-shift of ~ 1,700 cm^-1. Other contribution is the solvent effect on the electronic structure of the MOx leading to a red-shift of around -4,200 cm^-1. Additionally, this red-shift caused by the solvent effect on the electronic structure can by composed by approximately 60 % due to the electrostatic bulk effect, 10 % due to the explicit inclusion of the hydrogen-bonded water molecules and 30 % due to the explicit inclusion of the nearest water molecules.

In this work, we study the competence between the reactions of hydrogen and methyl scission during thermal cracking and combustion of propane, the emergence of the two isomers of the propyl radical, n-propyl and i-propyl, and their subsequent β-scission reaction to ethene and methyl radical. The purpose of the study was to analyze the accuracy of density functional (DFT) methods as applied on this relatively well-known subset of the reactions implied in the production of propylene oxide from propane and propene. Conventional (B3LYP, B3PW91) and state-of-the-art (PBE0, M06, BMK) DFT methods were employed, and their accuracy checked against experimental data and calculations performed using model chemistries (complete basis set CBS-4M, QB3, and APNO, and G4 methods) and ab initio methods (MP2, CCSD(T) with a large 6-311 ++G(3df,2pd) basis set). The results obtained at the BMK level for the thermodynamics of the reactions are closer to experimental data than those afforded by any other DFT method and very similar actually to CBS or CCSD(T) results, even if a medium size basis set is used. Activation energies determined using twoand three-parameter Arrhenius equations are also very good, but the preexponential factors are incorrect. Tunneling and internal rotation corrections must be applied to obtain semiquantitative results.

Alanine scanning mutagenesis (ASM) of protein–protein interfacial residues is a popular means to understand the structural and energetic characteristics of hot spots in protein complexes. In this work, we present a computational approach that allows performing such type of analysis based on the molecular mechanics/Poisson– Boltzmann surface area method. This computational approach has been used largely in the past and has proven to give reliable results in a wide range of complexes. However, the sequential preparation and manual submission of dozens of files has been often a major obstacle in using it. To overcome these limitations and turn this approach user-friendly, we have designed the plug-in CompASM (computational alanine scanning mutagenesis). This software has an easy-to-use graphical interface to prepare the input files, run the calculations, and analyze the final results. CompASM was built in TCL/TK programming language to be included in VMD as a plug-in. The CompASM package is distributed as an independent platform, with script code under the GNU Public License from http://compbiochem.org/Software/compasm/Home.html.

A formal derivation of the nuclear-ensemble method for absorption and emission spectrum simulations is presented. It includes discussions of the main approximations employed in the method and derivations of new features aiming at further developments. Additionally, a method for spectrum decomposition is proposed and implemented. The method is designed to provide absolute contributions of different classes of states (localized, diffuse, charge-transfer, delocalized) to each spectral band. The methods for spectrum simulation and decomposition are applied to the investigation of UV absorption of benzene, furan, and 2-phenylfuran, and of fluorescence of 2-phenylfuran.

Approaches to the calculation of magnetizability and nuclear magnetic shieldings in a molecule, based on continuous translation of the origin of the magnetic fieldinduced electronic current density, are reviewed. The connections among apparently unrelated philosophies (Geertsen propagator methods, Keith-Bader continuous set of gauge transformations, and analytical reformulation by Lazzeretti, Malagoli, and Zanasi) are emphasized, and a unitary theoretical scheme is given.

Electronic polarization induced by the interaction of a reference molecule with a liquid environment is expected to affect the magnetic shielding constants. Understanding this effect using realistic theoretical models is important for proper use of nuclear magnetic resonance in molecular characterization. In this work, we consider the pyridine molecule in water as a model system to briefly investigate this aspect. Thus, Monte Carlo simulations and quantum mechanics calculations based on the B3LYP/ 6-311++G (d,p) are used to analyze different aspects of the solvent effects on the ¹⁵N magnetic shielding constant of pyridine in water. This includes in special the geometry relaxation and the electronic polarization of the solute by the solvent. The polarization effect is found to be very important, but, as expected for pyridine, the geometry relaxation contribution is essentially negligible. Using an average electrostatic model of the solvent, the magnetic shielding constant is calculated as -58.7 ppm, in good agreement with the experimental value of -56.3 ppm. The explicit inclusion of hydrogen-bonded water molecules embedded in the electrostatic field of the remaining solvent molecules gives the value of -61.8 ppm.

In the present study, the effect of the potential energy surface representation on the infrared spectra features of the H⁺ ₅ and D⁺ ₅ clusters is investigated. For the spectral simulations, we adopted a recently proposed (Sanz-Sanz et al. in Phys Rev A 84:060502-1–4, 2011) two-dimensional adiabatic quantum model to describe the proton-transfer motion between the two H₂ or D₂ units. The reported calculations make use of a reliable “on the fly” DFT-based potential surface and the corresponding new dipole moment surface. The results of the vibrational predissociation dynamics are compared with earlier and recent experimental data available from mass-selected photodissociation spectroscopy, as well as with previous theoretical calculations based on an analytical ab initio parameterized surfaces. The role of the potential topology on the spectral features is studied, and general trends are discussed.