Thaciana Malaspina

Ab initio calculation of hydrogen bonds in liquids: A sequential Monte Carlo quantum mechanics study of pyridine in water

A systematic procedure based on the sequential Monte Carlo quantum mechanics (S-MC/QM) methodology has been used to obtain hydrogen bond strength and structures in liquids. The system considered is pyridine in water. The structures are generated by NVT Monte Carlo simulation, of one pyridine molecule and 400 water molecules. The hydrogen bonds are obtained using a geometric and energetic procedure. Detailed analysis shows that 62% of the configurations have one hydrogen bond. In the average, pyridine in liquid water makes 1.1 hydrogen bonds. The sampling of the structures for the quantum mechanical calculations is made using the interval of statistical correlation obtained by the autocorrelation function of the energy. A detailed statistical analysis is presented and converged results are obtained. The QM calculations are performed at the ab initio MP2/6-31+G(d) level and the results are compared with the optimized 1:1 cluster. Our results using QM calculations on 155 structures making one hydrogen bond gives an average binding energy of 3.7 kcal/mol, after correcting for basis set superposition error, indicating that in the liquid the binding energy is about 2/3 of the corresponding binding in the optimized cluster.

Effects of hydroxyl group distribution on the reactivity, stability and optical properties of fullerenols.

We investigate the impact of hydroxyl groups on the properties of C(60)(OH)(n) systems, with n = 1, 2, 3, 4, 8, 10, 16, 18, 24, 32 and 36 by means of first-principles density functional theory calculations. A detailed analysis from the local density of states has shown that adsorbed OH groups can induce dangling bonds in specific carbon atoms around the adsorption site. This increases the tendency to form polyhydroxylated fullerenes (fullerenols). The structural stability is analyzed in terms of the calculated formation enthalpy of each species. Also, a careful examination of the electron density of states for different fullerenols shows the possibility of synthesizing single molecules with tunable optical properties.

Analyzing the n ®p * electronic transition of formaldehyde in water: a sequential Monte Carlo/time-dependent density functional theory

The n®p* absorption transition of formaldehyde in water is analyzed using combined and sequential classical Monte Carlo (MC) simulations and quantum mechanics (QM) calculations. MC simulations generate the liquid solute-solvent structures for subsequent QM calculations. Using time-dependent density functional theory in a localized set of gaussian basis functions (TD-DFT/6-311++G(d,p)) calculations are made on statistically relevant configurations to obtain the average solvatochromic shift. All results presented here use the electrostatic embedding of the solvent. The statistically converged average result obtained of 2300 cm-1 is compared to previous theoretical results available. Analysis is made of the effective dipole moment of the hydrogen-bonded shell and how it could be held responsible for the polarization of the solvent molecules in the outer solvation shells.

Prediction of the hydration properties of diamondoids from free energy and potential of mean force calculations.

Molecular dynamics simulations were used to predict the thermodynamical properties of the hydration process of the adamantane, diamantane, and trimantane, the first three members of the series of diamondoids. Free-energy results suggest that the water solubility of these molecules is low. The hydration free energy increases with size of the diamondoid. As for the alkane hydrocarbons, hydration free energy correlates linearly with the surface accessible solvent area; however, here it has been shown that small diamondoids present hydration free energy significantly lower than the n-alkanes of similar molecular weights. The decomposition of the hydration free energy in enthalpic and entropic terms revealed that the hydration process of the small diamondoids is entropic driven. The potential of mean-force calculations indicates that the aggregation of these species in the aqueous medium should occur spontaneously and that the contribution of the solvent is greater the larger the diamondoid.

The gas-phase alcoholysis of protonated homoleptic alkoxysilanes

Tetra-alkoxysilanes are common and useful reagents in sol–gel processes and understanding their reactivity is important in the design of new materials. The mechanism of gas-phase reactions that mimic alcoholyis of Si(OMe)4 (usually known as TMOS) under acidic conditions have been studied by Fourier transform ion cyclotron resonance techniques and density functional calculations at the B3LYP/6-311+G(d,p) level. The proton affinity of TMOS has been estimated at 836.4 kJ mol−1 and protonation of TMOS gives rise to an ionic species that is best represented as trimethoxysilyl cations associated with a methanol molecule. Protonated TMOS undergoes rapid and sequential substitution of the methoxy groups in the gas-phase upon reaction with alcohols. The calculated energy profile of the reaction indicates that the substitution reaction through an SN2 type mechanism may be more favorable than frontal attack at silicon. Furthermore, the sequential substitution reactions are promoted by a mechanism that involves proton shuttle from the most favorable protonation site to the oxygen of the departing group mediated by the neutral reagent molecule.

Peculiar Aqueous Solubility Trend in Cucurbiturils Unraveled by Atomistic Simulations

Cucurbiturils (CBs) compose a family of macrocycles whose elementary unit is glycouril (GLYC). CBs are of high interest in chemistry and biology due to their versatile applications, ranging from sensors to advanced drug-delivery systems. Here, we report a systematic hydration study of all currently known CBs by classical molecular dynamics simulations to understand their different aqueous solubilities, as revealed in the experiments. Water readily penetrates CBs, including the smallest CB, that is, CB[5]. The number of CB[n]-water hydrogen bonds can be assessed as 2 × n. The hydration enthalpies of the CBs were found to be significantly favorable, due to a number of strong hydrogen bonds with water. However, these enthalpy gains are not enough to compensate for an even larger entropic penalty due to modifying a genuine bulk arrangement of water molecules. We found that the free energy of hydration moderately but uniformly increases with the number of GLYCs. Therefore, the better solubility of odd-numbered CBs is independent of the CB-water interactions, either an enthalpic or entropic contribution. The higher solubilities of CB[n]s with n = 5, 7, or 9 occur exclusively because of their amorphous solid states. Our results allow the prognosis of the aqueous solubilities of not-yet-synthesized CBs.