Alejandro López-Castillo

Experimental and theoretical investigations on photoabsorption and photoionization of trimethylphosphate in the vacuum-ultraviolet energy range

In this work, we report a joint experimental-theoretical investigation on interaction of vacuum-ultraviolet radiation with trimethylphosphate (TMP) molecule (C(3)H(9)O(4)P) in gas phase. This species together with tetrahydrofuran (THF) are model compounds of deoxyribose nucleic acids (DNA)/ribose nucleic acids (RNA) backbone. Absolute photoabsorption cross sections (σ(a)) and ionization yields (η) are measured using the double-ion-chamber technique in the 11.0-21.45 eV energy range. Photoionization (σ(i)) and neutral-decay (σ(n)) cross sections in absolute scale are also derived. Moreover, theoretical photoabsorption cross sections are calculated using the time-dependent density functional theory from the excitation threshold up to 16 eV. Good agreement between the present calculated and experimental photoabsorption cross sections in the 11.0-14.5 eV range is encouraging. Also, the present measured data of σ(a) and σ(i) for TMP are about 1.3 and 1.5 times of those of THF, respectively. Thus, the experimental evidences that the majority of strand breaks being located at sugar rings in the irradiated DNA/RNA backbone moiety may be induced by a possible migration of the hole, initially created at phosphate group, to the linked sugar groups. Finally, absolute partial photoionization cross sections are derived from the experimental time-of-flight mass spectra.

Stability and molecular properties of the boron-nitrogen alternating analogs of azulene and naphthalene: a computational study

AbstractIn this work, the spectroscopic information, stability and aromaticity of the boron-nitrogen azulene and naphthalene molecules are provided by the use of CC2 (geometry optimization, dipole moment, UV–vis spectrum calculations) and DFT (vibrational spectrum and NMR calculations) methodologies. One isomer of the investigated boron-nitrogen naphthalene (boroazanaphthalene) and two isomers of boron-nitrogen azulene, 1,3,4,6,8-pentaaza-2,3a,5,7,8a-pentaboraazulene (BN-azulene) and 2,3a,5,7,8a-pentaaza-1,3,4,6,8- pentaboraazulene (NB-azulene), are stable systems. However, these molecules have different properties, i.e., different stability, dipole moment, and aromaticity based on the NICS approach. BN-naphthalene has a high dipole moment magnitude showing high polar character, while naphthalene is apolar. BN- and NB-azulene are weakly polar, while ordinary azulene is highly polar in character. Also, substitution of C atoms by B and N atoms decreases the aromaticity. In the case of NB-azulene, the seven-membered ring has anti-aromaticity behavior while both rings of BN-azulene exhibit aromaticity. We expect that the new theoretical data provided in this work will be useful in identifying and characterizing experimentally the compounds investigated, and in helping our understanding of the chemistry of boron-nitrogen molecules. Graphical abstractBoron-nitrogen alternating analogs of azulene. Spectral distinction between isomers

Spurious Phosphorus Pyramidalization Induced by Some DFT Functionals

The molecular geometries of boraphosphabenzene (BP-benzene) and boron phosphorus coronene (BP-coronene) can be misinterpreted when they are obtained from density functional theory (DFT) calculations. In this study, we found that some exchange-correlation (XC) functionals yielded a distorted geometry of the above molecules when P atoms are present in their resonance structures. This phosphorus pyramidalization may be due to spurious errors caused by using these functionals. To verify this behavior, the electronic structures of BP-benzene and BP-coronene were studied using sixteen functionals (B3LYP, B97D, BHLYP, BP96, PBE, PBE0, PWLDA, Slater-Dirac-exchange, TPSS, M05, M06, M062X, M08HX, M11, wB97 and wB97X-D) with the SVP or TZVPP basis sets. The calculations were carried out using the TURBOMOLE and GAMESS programs. The geometry optimization calculations were carried out for each functional using both of the basis sets. Two different initial geometries, plane (D3h symmetry) and distorted (C1 symmetry) were considered. The optimized geometries of the BP-systems obtained at the MP2/TZVPP and CC2/TZVPP levels of theory exhibited D3h symmetry. These calculations were used as a reference and compared with those obtained from DFT. The optimized geometries obtained from DFT were found to exhibit C1 symmetry for the majority of the XC functionals.

Theoretical characterization of the BN and BP coronenes by IR, Raman, and UV-VIS spectra

Boron-nitrogen coronene (BNC) and boron-phosphorous coronene (BPC), not yet synthesized molecules and of possible interest for material science, are composed of six condensed rings of borazine and boraphosphabenzene molecules, respectively. They are similar to the carbon coronene molecule (CC). Moreover, CC and BNC are isoelectronic and the BPC is formally isoelectronic with respect to other coronenes, if only the valence electrons are considered. In this work, the BNC and BPC were theoretically characterized using IR, Raman, and UV-VIS spectroscopies. The coronenes studied have D(6h) and D(3h) symmetries for carbon and boron compounds, respectively. The calculated vibrational and electronic spectra for the CC are in good agreement with the experimental data, indicating that the calculations for BNC and BPC will be useful to identify these compounds, when synthesized. The main vibrational modes of the CC, BNC, and BPC are correlated. However, the BPC vibrational frequencies are substantially lower than the CC and BNC ones. The electronic ground state studies showed that the BPC has intermediate characteristics between the CC and BNC.

Simulação do equilíbrio: o método de Monte Carlo

We make several simulations using the Monte Carlo method in order to obtain the chemical equilibrium for several first-order reactions and one second-order reaction. We study several direct, reverse and consecutive reactions. These simulations show the fluctuations and relaxation time and help to understand the solution of the corresponding differential equations of chemical kinetics. This work was done in an undergraduate physical chemistry course at UNIFIEO.

PRACTICAL STOCHASTIC MODEL FOR CHEMICAL KINETICS

The Practical Stochastic Model is a simple and robust method to describe coupled chemical reactions. The connection between this stochastic method and a deterministic method was initially established to understand how the parameters and variables that describe the concentration in both methods were related. It was necessary to define two main concepts to make this connection: the filling of compartments or dilutions and the rate of reaction enhancement. The parameters, variables, and the time of the stochastic methods were scaled with the size of the compartment and were compared with a deterministic method. The deterministic approach was employed as an initial reference to achieve a consistent stochastic result. Finally, an independent robust stochastic method was obtained. This method could be compared with the Stochastic Simulation Algorithm developed by Gillespie, 1977. The Practical Stochastic Model produced absolute values that were essential to describe non-linear chemical reactions with a simple structure, and allowed for a correct description of the chemical kinetics.

Spontaneous Chiral Symmetry Breaking for Finite Systems

Theoretical clues are desirable to help uncover the origin of bio-homochirality in life, as well as the mechanisms for the asymmetric production of functional chiral substances. Here, an open-to-matter reaction network based on a model proposed by Plasson et al. is studied. In the extended model, the statistical fluctuations lead the system to break chiral symmetry autonomously, that is, without any initial enantiomeric excess or external influence. In the stability diagrams, we observe regions of parameter space that correspond to racemic, homochiral, chiral oscillatory, and, to our knowledge, for the first time in a chiral model, chaotic regimes. The dependencies of the final concentrations of chiral substances on the parameters are determined analytically and discussed for both the racemic and homochiral regimes.

A previously undescribed hexapeptide His-Arg-Phe-Leu-Arg-His-NH 2 from amphibian skin secretion shows CO 2 and metal biding affinities

HIGHLIGHTSIdentification of a HRFLRH peptide from Phyllomedusa centralis skin secretion.Evidences of interaction of the peptide with CO2, Zn and Cd by Mass Spectroscopy.NMR structural investigations of the peptide in the presence of CO2 and the metals. ABSTRACT A previously undescribed six residues long peptide His‐Arg‐Phe‐Leu‐Arg‐His was identified and purified from the skin secretion of the amphibian Phyllomedusa centralis. A synthetic analogue carboxyamidated HRFLRH‐NH2 showed structural changes induced by CO2 and metal ions in aqueous solution when analyzed by NMR. The present work reports NMR structures for the carboxyamidated hexapeptide in the presence CO2, Zn2+ and Cd2+, suggesting possible affinity regions on the polypeptide chain for each ligand. The NMR structures were optimized by DFT to identify probable biding sites of these species in the polypeptide structure. To our best knowledge, this is the first time that a putative CO2 binding site is described on a peptide structure obtained in aqueous conditions, at room temperature.

Boron–nitrogen dative bond

AbstractThis study consists of the theoretical analysis of some organic molecules and their inorganic similar compounds, through substitution of two carbon atoms by boron and nitrogen atoms. The methods DFT/B3-LYP/TZVPP and CC2/TZVPP were considered. Firstly, ethane, ethene, and ethyne molecules (based on C atoms and their BN/NB analogs) were studied. These molecules were considered as a reference for the analysis of other molecules with functional groups. These molecules with functional groups are: ethanol, ethanal (and its isomer ethenol), ethanoic acid (and its isomer ethenediol), ethylamine, ethylbenzene, propane, and fluoroethane. We studied the energies, bond length, population analysis, and bond order. The dative bonds (BN) are bigger and weaker than that covalent based on C atoms. The dative bond has π character when the BN bond is double and triple. It is possible to distinguish two different behaviors for BN bonds, one when the functional group is bounded to the B atom, and the other to the N atom. When the functional group is bounded to the B atom, the BN bond is weaker and lengthier than that when the same group is bounded to the N atom. However, the isomer with weaker BN bond is the most stable one. Graphical abstractComparative studies of dative bonds among substituted inorganic molecules, e.g., BN-ethanol, show important differences in terms of length and energy in comparison to organic analogous. There is also a difference when comparing BN or NB molecules (according to witch atom the functional group is bonded to, B or N); bond length, for example, is bigger for BN molecules.

Probing the (empirical) quantum structure embedded in the periodic table with an effective Bohr model

The atomic shell structure can be observed by inspecting the experimental periodic properties of the Periodic Table. The (quantum) shell structure emerges from these properties and in this way quantum mechanics can be explicitly shown considering the (semi-) quantitative periodic properties. These periodic properties can be obtained with a simple effective Bohr model. An effective Bohr model with an effective quantum defect (u) was considered as a probe in order to show the quantum structure embedded in the Periodic Table. u(Z) shows a quasi-smoothed dependence of Z, i.e., u(Z) ≈ Z2/5 – 1.