Piero Ugliengo

B3LYP augmented with an empirical dispersion term (B3LYP-D*) as applied to molecular crystals

The B3LYP method augmented with a damped empirical dispersion term (−f(R)C6/R6) is shown to yield structures and cohesive energies, for a representative set of molecular crystals, in excellent agreement with experimental data. Vibrational lattice modes of crystalline urea are also reported to be very close to experiment. The role of the damping function in scaling the dispersion contribution has been analyzed as well as the relevance of the BSSE in the prediction of structure and cohesive energy.

Intermolecular interaction energies in molecular crystals: comparison and agreement of localized Møller-Plesset 2, dispersion-corrected density functional, and classical empirical two-body calculations.

A comparative analysis of the intermolecular energy for a data set including 60 molecular crystals with a large variety of functional groups has been carried out using three different computational approaches: (i) a method based on a physically meaningful empirical partition of the interaction energy (PIXEL), (ii) density functional methods with a posteriori empirical correction for the dispersion interactions (DFT-D), and (iii) a full periodic ab initio quantum mechanical method based on Møller-Plesset perturbation theory for the electron correlation using localized crystal orbitals (LMP2). Due to the large computational cost, LMP2 calculations have been restricted to a subset of seven molecular crystal comprising benzene, formic acid, formamide, succinic anhydride, urea, oxalic acid, and nitroguanidine, and the results compared with PIXEL and DFT-D data as well as with the experimental data show excellent agreement among all adopted methods. This shows that both DFT-D and PIXEL approaches are robust predictive tools for studying molecular crystals. A detailed analysis shows a very similar dispersion contribution of the two methods across the 60 considered molecular crystals. The study also confirms that pure DFT shows serious deficiencies in properly handling molecular crystals in which the dispersive contribution is large. Due to the negligible requested computational resources, PIXEL is the method of choice in screening of a large number of molecular crystals, an essential step to predict crystal polymorphism or to study crystal growth processes. DFT-D can then be used to refine the ranking emerged from PIXEL calculations due to its general applicability and robustness in properly handling short-range interactions.

Hydroxyls nests in defective silicalites and strained structures derived upon dehydroxylation: vibrational properties and theoretical modelling

Defective silicalite, an efficient and selective catalyst in the gas phase Beckmann rearrangement reaction, has been characterised by infrared spectroscopy and by molecular modelling techniques. We report a detailed IR study on the effect of outgassing treatments at increasing temperature on silanols bands and on framework modes. The effect of a temperature decrease up to 100 K (during the IR measurement) on the H-bonding interactions has also been investigated. The interaction of silanols with mesitylene, a probe molecule which cannot penetrate the channels, has been studied in order to distinguish between internal and external OH groups. Molecular mechanics and ab initio methods have also been used to model the structure and the vibrational features of a properly designed nest in order to support the assignments of the IR spectrum.

Ab initio study of the adducts of carbon monoxide with alkaline cations

The interaction between CO (either via the C or the O end) and the alkaline cations (Li+, Na+, K+, Rb+, and Cs+) has been studied by means of six ab initio methods, featuring the classical Hartree–Fock, the second order Mo/ller–Plesset treatment of electron correlation, one local density functional and two gradient‐corrected methods as well as a quadratic configuration interaction inclusive of single and double substitutions with a noniterative triples contribution to the energy. Basis sets adopted for CO, Li+, Na+, and K+ and the corresponding adducts are of triple‐ζ valence quality augmented with a double set of polarization functions (d on C and O; p on the cations). For Rb+ and Cs+, Hay–Wadt effective core potential basis sets have been adopted. Calculated features are the binding energy, the frequency and intensity of the CO stretch, the bending mode, the cation‐carbon (or oxygen) stretch, and the equilibrium geometry. Gradient‐corrected density functional methods yield results nearly as good as the ...

Ab Initio Modeling of Protein/Biomaterial Interactions : Glycine Adsorption at Hydroxyapatite Surfaces

How does glycine adsorb at hydroxyapatite surfaces? Ab initio simulations based on periodic B3LYP GTO calculations reveal the detailed mechanism of binding to the (001) and (010) surfaces by shedding light on how acid and basic amino acid residues of proteins interact with hydroxyapatite based biomaterials.

Quantum mechanical calculation of the OH vibrational frequency in crystalline solids

The OH vibrational frequency of four crystalline compounds ranging from ionic (brucite, Mg(OH)2, and portlandite, Ca(OH)2) to semi-covalent (edingtonite, as representative of free surface OH groups in silica, and acid chabazite, as representative of acid zeolites) has been investigated at quantum mechanical level with the CRYSTAL program using the B3LYP hybrid functional. The OH vibration is calculated in two ways: (i) in the harmonic approximation, by diagonalizing the fully coupled dynamical matrix to yield the harmonic frequency ω h . (ii) at the anharmonic level, by decoupling the OH stretching mode from the bulk phonons and by numerically solving the one-dimensional Schrödinger equation associated with the OH potential energy to yield the fundamental ω01 and the first overtone ω02 frequencies. The harmonic and anharmonic frequencies differ by more than 150 cm−1. In the cases where direct comparison is possible (brucite, portlandite and edingtonite), the experimental and calculated frequencies differ by less than 10 cm−1; the calculated anharmonicity constant, ω e x e  = (2ω01 − ω02)/2, is systematically smaller than the experimental value by about 10 cm−1. The effect of the computational parameters on the computed frequencies is explored, with particular attention to the grid used for the construction of the DFT exchange and correlation contribution to the Hamiltonian and the accuracy in the geometry optimisation.

Performance of six functionals (LDA, PBE, PBESOL, B3LYP, PBE0, and WC1LYP) in the simulation of vibrational and dielectric properties of crystalline compounds. The case of forsterite Mg2SiO4

The performance of six different density functionals (LDA, PBE, PBESOL, B3LYP, PBE0, and WC1LYP) in describing the infrared spectrum of forsterite, a crystalline periodic system with orthorhombic unit cell (28 atoms in the primitive cell, Pbmn space group), is investigated by using the periodic ab initio CRYSTAL09 code and an all‐electron Gaussian‐type basis set. The transverse optical (TO) branches of the 35 IR active modes are evaluated at the equilibrium geometry together with the oscillator strengths and the high‐frequency dielectric tensor ϵ∞. These quantities are essential to compute the dielectric function ϵ(ν), and then the reflectance spectrum R(ν), which is compared with experiment. It turns out that hybrid functionals perform better than LDA and GGA, in general; that B3LYP overperforms WC1LYP and, in turn, PBE0; that PBESOL is better than PBE; that LDA is the worst performing functional among the six under study.

J-ICE: a new Jmol interface for handling and visualizing crystallographic and electronic properties

The growth in complexity of quantum mechanical software packages for modelling the physicochemical properties of crystalline materials may hinder their usability by the vast majority of non-specialized users. Consequently, a free operating-system-independent graphical user interface (GUI) has been developed to drive the most common simulation packages for treating both molecules and solids. In order to maintain maximum portability and graphical efficiency, the popular molecular graphics engine Jmol, written in the portable Java language, has been combined with a specialized GUI encoded in HTML and JavaScript. This framework, called J-ICE, allows users to visualize, build and manipulate complex input or output results (derived from modelling) entirely via a web server, i.e. without the burden of installing complex packages. This solution also dramatically speeds up both the development procedure and bug fixing. Among the range of software appropriate for modelling condensed matter, the focus of J-ICE is currently only on CRYSTAL09 and VASP.

A periodic ab initio study of the structure and relative stability of silica polymorphs

Abstract The equilibrium geometry and total energy of four all-silica zeolite frameworks, sodalite, chabazite, faujasite and edingtonite, have been obtained at a periodic ab initio all-electron level (CRYSTAL code) and compared with the corresponding quantities for α - and β -quartz. The dependence of the results on the adopted basis set and hamiltonian (Hartree–Fock, or with an a posteriori correlation correction; various local and gradient-corrected density functional methods and Beckes hybrid scheme) is discussed. The various methods provide a similar order in the relative stabilities; large quantitative differences are however observed, Hartree–Fock and LDA results being at the extremes. The combined use of force-field and ab initio schemes in the geometry optimization is discussed.

Role of dispersive interactions in layered materials: a periodic B3LYP and B3LYP-D* study of Mg(OH)2, Ca(OH)2 and kaolinite

The role of dispersive interactions on the structure, energetic and vibrational features of brucite [Mg(OH)2], portlandite [Ca(OH)2] and kaolinite [Al2Si2O5(OH)4] layered materials has been addressed for the first time. Dispersion contribution is included with a −C6/R6 empirical correction to the B3LYP functional (B3LYP-D* recipe) which has recently been employed to study molecular crystals. To decrease the spurious effect of the basis set superposition error, Gaussian basis sets of triple-zeta plus polarization functions were adopted. Comparing B3LYP and B3LYP-D* results shows the latter to provide significant improvement as far as structure and energetic data are concerned. For the treated systems the cell parameter controlling the inter-layer distance, usually overestimated by the pure B3LYP, is in good agreement with experiment. The inter-layer interaction energy is dramatically increased by the dispersion contribution which, for kaolinite, fully justifies the request of strong Lewis basic molecules needed to swell the material. In general, B3LYP harmonic frequencies are scarcely changed by the dispersive correction albeit some modes sensitive to the inter-layer separation may be significantly perturbed at B3LYP-D*. The present results are encouraging although fine tuning of the proposed empirical correction for inorganic systems might be needed.