Density functional theory calculations and classical molecular dynamics simulations have been use... more Density functional theory calculations and classical molecular dynamics simulations have been used to investigate the structure and dynamics of water molecules on kaolinite surfaces and confined in the interlayer of a halloysite model of nanometric dimension. The first technique allowed us to accurately describe the structure of the tetrahedral-octahedral slab of kaolinite in vacuum and in interaction with water molecules and to assess the performance of two widely employed empirical force fields to model water/clay interfaces. Classical molecular dynamics simulations were used to study the hydrogen bond network structure and dynamics of water adsorbed on kaolinite surfaces and confined in the halloysite interlayer. The results are in nice agreement with the few experimental data available in the literature, showing a pronounced ordering and reduced mobility of water molecules at the hydrophilic octahedral surfaces of kaolinite and confined in the halloysite interlayer, with respect to water interacting with the hydrophobic tetrahedral surfaces and in the bulk. Finally, this investigation provides new atomistic insights into the structural and dynamical properties of water-clay interfaces, which are of fundamental importance for both natural processes and industrial applications.
The journal of physical chemistry. A, Jan 10, 2015
The performance of a method is generally measured by an assessment of the errors between the meth... more The performance of a method is generally measured by an assessment of the errors between the method's results and a set of reference data. The prediction uncertainty is a measure of the confidence that can be attached to a method's prediction. Its estimation is based on the random part of the errors not explained by reference data uncertainty, which implies an evaluation of the systematic component(s) of the errors. As the predictions of most density functional approximations (DFA) present systematic errors, the standard performance statistics, such as the mean of the absolute errors (MAE or MUE), cannot be directly used to infer prediction uncertainty. We investigate here an a posteriori calibration method to estimate the prediction uncertainty of DFAs for properties of solids. A linear model is shown to be adequate to address the systematic trend in the errors. The applicability of this approach to modest-size reference sets (28 systems) is evaluated for the prediction of ...
A computational protocol that combines periodic and QM/QM&amp... more A computational protocol that combines periodic and QM/QM' calculations has been applied to investigate the structural (geometrical and electronic) and photophysical absorption properties of the salicylidene aniline (SA) thermochromic molecular crystal. The protocol consists of three different steps, namely (i) the description of the molecular crystal using a periodic approach taking into account dispersion interactions, (ii) the identification of reliable finite models (clusters), and (iii) the calculation of vertical transition energies including environmental effects through the use of an electronic embedding model (QM/QM' ONIOM approach). The encouraging results obtained in this work for the β polymorph of SA, both in terms of accuracy and computational cost, open the way to the simulation and the prediction of the photophysical behavior of other molecular crystals, especially those much less well characterized experimentally.
The structural and 13 C/ 1 H NMR parameters of the four crystal forms (1α, 1·H 2 O, 1β, and 1γ) o... more The structural and 13 C/ 1 H NMR parameters of the four crystal forms (1α, 1·H 2 O, 1β, and 1γ) of the solid wheel-and-axle (WAA) metal−organic compound [(p-cymene)-Ru(κN-INA)Cl 2 ] have been studied by means of periodic DFT calculations. The quality of the results obtained strongly depends on a correct description of long-range interactions; thus, in the geometry refinement protocol used, the pure DFT functionals need to be coupled with a dispersion-correction term (B3LYP-D2, B3LYP-D*). The solid-state 13 C/ 1 H NMR δ iso parameters and 13 C MAS NMR spectra, calculated by means of the PBE-GIPAW method, agree well with the experimental data for the four crystal forms (mean absolute deviations of the 13 C and 1 H δ iso data values lie in the ranges 1.3−2.9 and 0.3−1.0 ppm, respectively). In this context, some revisions in the experimental assignment of the 13 C/ 1 H NMR δ iso parameters of the 1·H 2 O, 1β, and 1γ crystal forms can be suggested. The mismatch in the assignment seems to be due to the rotation of the −COOH moiety, which occurs at the 1α−1·H 2 O transition and was not considered in the experiments. Finally, the results obtained suggest the presence of two COOH···Cl hydrogen bonds of comparable strength established by the two molecules in the asymmetric unit of the 1γ polymorph, in partial disagreement with previous findings.
The molecular crystal of oxalyl dihydrazide differentiates into five polymorphs that are governed... more The molecular crystal of oxalyl dihydrazide differentiates into five polymorphs that are governed by inter-and intramolecular hydrogen bonds. The complex mixture of such interactions with long range dispersive forces makes its computational characterization very challenging; thus it represents an ideal benchmark for ab initio methods when striving for a description of polymorphism in molecular crystals. Indeed, a complete experimental energetic profile of this system is still lacking, and it is here investigated by means of periodic dispersion-corrected DFT and Local second order Møller-Plesset Perturbation theory calculations. In this work, the empirical dispersion correction schemes proposed by Tkatchenko and Scheffler (TS) [Tkatchenko et al., Phys. Rev. Lett., 2009, 102, 073005] and Grimme (D2) [Grimme, J. Comput. Chem., 2006, 27, 1787] have been used in combination with the PBE semilocal functional for geometry optimizations. We observed that PBE-TS provides a remarkable improvement in predicting the crystal structure of oxalyl dihydrazide polymorphs with respect to commonly used DFT-D functionals. The relative stabilities of the five forms have then been computed at the PBE-TS/D2, PBE0-D2, B3LYP-D2 and B3LYP-D3(BJ)+gCP level on the PBE-TS hydrogen-optimized geometries and benchmarked against high level periodic LMP2 calculations. PBE-TS, B3LYP-D2 and B3LYP-D3(BJ)+E
Periodic DFT calculations employing the PBE, PBE0 and B3LYP functionals coupled with different di... more Periodic DFT calculations employing the PBE, PBE0 and B3LYP functionals coupled with different dispersion correction schemes have been applied to para-diiodobenzene molecular crystal in order to determine how they perform in reproducing the energetic and crystal geometry of its two well known polymorphs.
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Papers by Davide Presti