Leonardo Baptista | UERJ - Universidade do Estado do Rio de Janeiro / Rio de Janeiro State University (original) (raw)

Papers by Leonardo Baptista

Journal of chemical physics online/The Journal of chemical physics/Journal of chemical physics, Mar 25, 2024

Theoretical study of three gas-phase reactions involving the production or loss of methane cations

Physical Chemistry Chemical Physics, 2014

Please note that technical editing may introduce minor changes to the text and/or graphics, which... more Please note that technical editing may introduce minor changes to the text and/or graphics, which may alter content. The journal's standard Terms & Conditions and the Ethical guidelines still apply. In no event shall the Royal Society of Chemistry be held responsible for any errors or omissions in this Accepted Manuscript or any consequences arising from the use of any information it contains.

Chemical Physics, 2013

Abstract A theoretical study on the molecular structure of C n H − clusters, where 1 ⩽ n ⩽ 6, a... more Abstract A theoretical study on the molecular structure of C n H − clusters, where 1 ⩽ n ⩽ 6, and C n H x + clusters, where 1 ⩽ n ⩽ 4 and 0 ⩽ x ⩽ 2 n + 2, has been performed at the DFT level. More than 300 configurations were examined and their total electronic energies ordered for each cluster mass. The D-plot methodology was employed for classifying different structures into cluster families and identifying the most stable structures. For each family, the binding energies of the analyzed cluster species have been determined and displayed as a function of the cluster mass. The fluctuations of these curves are then compared to experimental data, namely, to the dependence of relative ion desorption yields on cluster mass, obtained from Plasma Desorption Mass Spectroscopy (PDMS) of quite distinct types of organic samples: solid methane, cholesterol and pump oil vapor adsorbed on polycrystalline LiF. It is found that theoretical predictions and experimental data are in good agreement, showing that the abundance of the emitted small cluster ions is determined by their own structure and not by the structure of the original sample.

Carbohydrate Polymers, Oct 1, 2018

The formation of the SA/CS polyelectrolyte complex was evaluated.  The SA/CS complex occurs thro... more The formation of the SA/CS polyelectrolyte complex was evaluated.  The SA/CS complex occurs through coordination of Na+, formation of H bonds with covalent character and ionic interaction between the charged groups.  The presence of two water molecule increases the stability of SA/CS complex.  When the glyphosate molecule was added, it interacted preferentially with chitosan.

Nitro-aromatics compounds are more toxic and cancerous than their aromatics parents. Unfortunatel... more Nitro-aromatics compounds are more toxic and cancerous than their aromatics parents. Unfortunately, these compounds were identified in Diesel engines emissions and in particulate matter collected in urban areas. By these reasons, the present project aims to investigate the gas phase mechanism of the aromatic nitration following two proposals found in the literature. The proposed mechanisms have been studied by methods based on density functional theory: M06-2X, B3LYP and B2PLYP. Further, the electronic energy of all molecules that take part in the mechanism has been corrected by CCSD(T) method. All study was performed with cc-pVTZ basis set. The results showed that reactions between phenil radical and NO2 proceeds without a barrier forming a vibrational and rotational excited nitrobenzene. The evaluated Arrhenius parameters indicates that the formation of benzene nitrite is faster than the formation of nitrobenzene, while the reaction path initialized by OH addition to the aromatic ring, it is only important at high temperatures. The partial results indicate the formation of nitrophenol during the combustion, in agreement with experimental evidences.

Revista processos químicos, Jul 1, 2015

Journal of Chemical Physics, Sep 13, 2018

The size distributions of neutral and cationic Ba x (CH 3 CN) n (x = 0, +1; n ≤ 7) clusters, as p... more The size distributions of neutral and cationic Ba x (CH 3 CN) n (x = 0, +1; n ≤ 7) clusters, as produced by a standard laser vaporization-supersonic expansion pickup source, were determined from molecular beam experiments. The size distribution for cations is in the range of n = 1-7, whereas only the n = 1 complex is observed for neutral clusters, and these two features are unaffected by the variables controlling the performance of the cluster source. The distinct behavior is compatible with the expected charge-dipole interactions in the ionic species, which are stronger than the dipole induced-dipole interactions at play in neutral clusters, and it is corroborated by the relative magnitude of the theoretical successive binding energies (SBEs) for the lowest-lying isomers of cationic and neutral clusters with n = 1-5, as computed at the density functional theory level. The theoretical results also allow for the rationalization of the bimodal Ba + (CH 3 CN) 1-7 size distribution, featuring an apparent minimum at n = 3, in terms of chiefly 6s-5d σ hybridization of the Ba + ions, which ultimately leads to a relatively small third SBE for the Ba + (CH 3 CN) 3 complex, as compared to those for n = 1, 2, and 4. Additional Born-Oppenheimer molecular dynamics simulations on the Ba + (CH 3 CN) 2-4 clusters suggest that all of the ligands are coordinated to the Ba + ion and prevent considering completion of the first solvent shell as responsible for the bimodal size distribution.

Journal of Physical Chemistry A, Apr 13, 2010

A combined density functional theory and transition state theory study of the gas-phase addition ... more A combined density functional theory and transition state theory study of the gas-phase addition of OH to 3,7-dimethylocta-2,6-dien-1-ol (trans-geraniol), 6-methyl-5-hepten-2-one, and 6-hydroxy-4-methyl-4-hexenal is presented. In this study, all different possibilities for the addition of the OH radical to the CC double bonds in trans-geraniol, 6-methyl-5-hepten-2-one, and 6-hydroxy-4-methyl-4-hexenal were considered. The geometries, energies, and harmonic vibrational frequencies at each stationary point were determined at the MPW1K/cc-pVDZ and BH&HLYP/cc-pVDZ levels. Global rate coefficients of 0.94 × 10-10 and 3.1 × 10-10 cm 3 molecule-1 s-1 , 2.11 × 10-11 and 7.53 × 10-11 cm 3 molecule-1 s-1 , and 2.70 × 10-13 , and 4.37 × 10-12 cm 3 molecule-1 s-1 were calculated using data obtained at the BH&HLYP/cc-pVDZ and MPW1K/cc-pVDZ levels of theory. These coefficients correspond to the sum of the rate coefficients of the individual paths for trans-geraniol, 6-hydroxy-4-methyl-4-hexenal, and 6-methyl-5-hepten-2-one, when reacting with OH radicals. The calculated rate coefficients are in good agreement with the available experimental data.

Journal of Physical Chemistry A, Feb 24, 2020

Monthly Notices of the Royal Astronomical Society, Apr 4, 2019

Glycine is the smallest amino acid, frequently found in meteorites samples and interstellar ices.... more Glycine is the smallest amino acid, frequently found in meteorites samples and interstellar ices. Studies about its formation and survival on the hostile interstellar medium (ISM) have been reported. In this work, the hypothesis that high-energy collision phenomena promote desorption of a fraction of the icy glycine to the gas phase, possibly assisted by molecular ionization, is assumed. In order to simulate the chemical behaviour of glycine and its radical cation under interstellar environments, a decomposition kinetics scheme is proposed. Calculations have been performed at the CCSD(T)/6-311++G(2d,2p)//B3LYP/6-311++G(2d,2p) level. Rate coefficients have been calculated at different temperatures (50-300 K), adopting the canonical variational transition state theory. In order to mitigate the ISM non-thermalized conditions, microcanonical variational rate coefficients have also been predicted. Eight stationary points, characterized as minimum energy points, have been located for neutral glycine, while four have been found for the glycine radical cation. The lowest energy conformer of neutral form accounts for 75 per cent of the population, whereas the radical cation global minimum accounts for approximately 100 per cent, at 300 K. The most favourable decomposition channel for neutral glycine is the deamination, with a barrier height of 44.76 kcal mol −1. The most favourable reaction channel for glycine radical cation is the dissociation forming H, CO 2 , and CH 2 NH + 2 with the dissociation limit of 18.03 kcal mol −1 , with respect to the lowest energy conformer.

Journal of Biomolecular Structure & Dynamics, Nov 23, 2017

Components of ginger (Zingiber officinale) extracts have been described as potential new drug can... more Components of ginger (Zingiber officinale) extracts have been described as potential new drug candidates against Alzheimer disease (AD), able to interact with several molecular targets related to the AD treatment. However, there are very few theoretical studies in the literature on the possible mechanisms of action by which these compounds can work as potential anti-AD drugs. For this reason, we performed here docking, molecular dynamic simulations and mmpbsa calculations on four components of ginger extracts former reported as active inhibitors of human acetylcholinesterase (HssAChE), and compared our results to the known HssAChE inhibitor and commercial drug in use against AD, donepezil (DNP). Our findings points to two among the compounds studied: (E)-1,7-bis(4-hydroxy-3-methoxyphenyl)hept-4-en-3-on and 1-(3,4-dihydroxy-5-methoxyphenyl)-7-(4-hydroxy-3- ethoxyphenyl) heptane-3,5-diyl diacetate, as promising new HssAChE inhibitors that could be as effective as DNP. We also mapped the binding of the studied compounds in the different binding pockets inside HssAChE and established the preferred interactions to be favored in the design of new and more efficient inhibitors.

Physical Chemistry Chemical Physics, 2017

This work presents the outcomes of broadband X-ray irradiation on an SO2(s) sample, with ΔH calcu... more This work presents the outcomes of broadband X-ray irradiation on an SO2(s) sample, with ΔH calculations for evaluating the most favorable reactions.

Química Nova, 2020

PREPARATION AND VALIDATION OF INPUT FILES FOR USE IN THE AIR QUALITY SIMULATOR (CMAQ). According ... more PREPARATION AND VALIDATION OF INPUT FILES FOR USE IN THE AIR QUALITY SIMULATOR (CMAQ). According to the inventories carried out by the air pollution control agencies, vehicle emissions are responsible for more than 70% of air pollutants in metropolitan regions. Proper handling of CMAQ input data is an important step in the formation of a database for the model. Thus, it is necessary to insert the meteorological data using the Weather Research and Forecasting (WRF) version 3.9 in the period of the 31 days of January 2013. Four domains with resolutions of 27, 9, 3 and 1 kilometers were used and 21 vertical layers. Spatial Allocator (SA) was used to format the maps and extract the data necessary for the construction of the SMOKE emissions inventory files. WRF was validated comparing the simulation results with data from two weather stations (Jardim Primavera and Nova Iguaçu), using the statistical methods MB, MAGE, RMSE and IOA. SMOKE presented a constant time profile, this occurred because the established hourly function only contemplated daily results without taking into account the variations over the week.

Physical Chemistry Chemical Physics, 2008

The thermodynamics of the oxidation mechanism of dimethyl sulfoxide (DMSO) by OH radical in the l... more The thermodynamics of the oxidation mechanism of dimethyl sulfoxide (DMSO) by OH radical in the liquid phase was investigated at the ab initio uPMP2/6-311G(d,p) level. Three distinct approaches to describing the solvent effect in the mechanism were considered: (1) a liquid phase mechanism considering the solvent as a continuum and polarizable medium; (2) a water-assisted gas phase reaction; (3) a combination of models 1 and 2, where the clusters containing the reactants and water molecules were studied in the polarizable continuum medium. The specific interactions and the bulk solvent effects were analyzed, the changes in the thermodynamic profile relative to the gas phase mechanism were determined and the overall rate coefficient for the oxidation of DMSO was evaluated.

Journal of Chemical Physics, Apr 30, 2020

This paper was selected as Featured ARTICLES YOU MAY BE INTERESTED IN Probabilistic performance e... more This paper was selected as Featured ARTICLES YOU MAY BE INTERESTED IN Probabilistic performance estimators for computational chemistry methods: Systematic improvement probability and ranking probability matrix. I. Theory

Journal of Physical Chemistry A, Sep 21, 2011

Using density functional methods, the initial reaction steps of limonene ozonolysis have been inv... more Using density functional methods, the initial reaction steps of limonene ozonolysis have been investigated with a focus on primary ozonide formation and its decomposition to Criegee intermediates and carbonyl compounds. The ozonide formation is highly exothermic, and the decomposition channels have similar free energies of activation, ΔG ‡ , indicating that there is no primary pathway for ozonide decomposition. Assuming that ozonide formation is the rate limiting step, the theoretical rate coefficient, k = 1.6 Â 10 À16 molecule À1 cm 3 s À1 , evaluated at the CCSD(T)/6-31G(d,p)//BHandHLYP/cc-pvdz level and 298.15 K for d-limonene is in good agreement with the experimental value, k exp = 3.3 Â 10 À16 molecule À1 cm 3 s À1. The theoretical Arrhenius expression is also in good agreement with experimental results.

Journal of Chemical Physics, Jan 7, 2018

Communication: An improved linear scaling perturbative triples correction for the domain based lo... more Communication: An improved linear scaling perturbative triples correction for the domain based local pairnatural orbital based singles and doubles coupled cluster method [DLPNO-CCSD(T)]