The CRYSTAL code, 1976-2020 and beyond, a long story.

CRYSTAL is a periodic ab initio code that uses a Gaussian-type basis set to express crystalline orbitals (i.e., Bloch functions). The use of atom-centered basis functions allows treating 3D (crystals), 2D (slabs), 1D (polymers), and 0D (molecules) systems on the same grounds. In turn, all-electron calculations are inherently permitted along with pseudopotential strategies. A variety of density functionals are implemented, including global and range-separated hybrids of various natures and, as an extreme case, Hartree-Fock (HF). The cost for HF or hybrids is only about 3-5 times higher than when using the local density approximation or the generalized gradient approximation. Symmetry is fully exploited at all steps of the calculation. Many tools are available to modify the structure as given in input and simplify the construction of complicated objects, such as slabs, nanotubes, molecules, and clusters. Many tensorial properties can be evaluated by using a single input keyword: elastic, piezoelectric, photoelastic, dielectric, first and second hyperpolarizabilities, etc. The calculation of infrared and Raman spectra is available, and the intensities are computed analytically. Automated tools are available for the generation of the relevant configurations of solid solutions and/or disordered systems. Three versions of the code exist: serial, parallel, and massive-parallel. In the second one, the most relevant matrices are duplicated on each core, whereas in the third one, the Fock matrix is distributed for diagonalization. All the relevant vectors are dynamically allocated and deallocated after use, making the code very agile. CRYSTAL can be used efficiently on high performance computing machines up to thousands of cores.

The VN3H defect in diamond: a quantum-mechanical characterization.

The VN3H defect in diamond (a vacancy surrounded by three nitrogen and one carbon atoms, the latter being saturated by a hydrogen atom) is investigated quantum-mechanically by use of a periodic supercell approach, an all-electron Gaussian-type basis set, "hybrid" functionals of density functional theory, and the Crystal program. Three fully optimized structural models (supercells containing 32, 64, and 128 atoms) are considered to investigate the effect of defect concentration. The electronic configuration of the defect is reported along with a description of its structural features. In particular, the influence of the lone-pair electrons of the three nitrogen atoms on the C-H bond is discussed. A thorough characterization of the vibrational spectroscopic features of the VN3H defect is also presented, where the anharmonicity of the most relevant normal modes is discussed. The infrared and Raman spectra show specific peaks, which allow for the identification of this particular defect among the many defects that are commonly present in both natural and irradiation-damaged diamonds. In particular, the main feature of the spectral fingerprint of the defect (i.e. the C-H stretching mode), experimentally observed at 3107 cm-1, is here computed at 3094 cm-1 with the B3LYP "hybrid" functional (with an anharmonic redshift of 157 cm-1 with respect to its harmonic value). The role played by the three nitrogen atoms on the spectral features of the defect is clearly identified through the redshift due to the 14N → 15N isotopic substitution.

Strong and Anomalous Thermal Expansion Precedes the Thermosalient Effect in Dynamic Molecular Crystals.

The ability of thermosalient solids, organic analogues of inorganic martensites, to move by rapid mechanical reconfiguration or ballistic event remains visually appealing and potentially useful, yet mechanistically elusive phenomenon. Here, with a material that undergoes both thermosalient and non-thermosalient phase transitions, we demonstrate that the thermosalient effect is preceded by anomalous thermal expansion of the unit cell. The crystal explosion occurs as sudden release of the latent strain accumulated during the anisotropic, exceedingly strong expansion of the unit cell with αa = 225.9 × 10(-6) K(-1), αb = 238.8 × 10(-6) K(-1) and αc = -290.0 × 10(-6) K(-1), the latter being the largest negative thermal expansivity observed for an organic compound thus far. The results point out to the occurence of the thermosalient effect in phase transitions as means to identify new molecular materials with strong positive and/or negative thermal expansion which prior to this work could only be discovered serendipitously.

Communication: A combined periodic density functional and incremental wave-function-based approach for the dispersion-accounting time-resolved dynamics of 4He nanodroplets on surfaces: 4He/graphene.

In this work we propose a general strategy to calculate accurate He-surface interaction potentials. It extends the dispersionless density functional approach recently developed by Pernal et al. [Phys. Rev. Lett. 103, 263201 (2009)] to adsorbate-surface interactions by including periodic boundary conditions. We also introduce a scheme to parametrize the dispersion interaction by calculating two- and three-body dispersion terms at coupled cluster singles and doubles and perturbative triples (CCSD(T)) level via the method of increments [H. Stoll, J. Chem. Phys. 97, 8449 (1992)]. The performance of the composite approach is tested on (4)He/graphene by determining the energies of the low-lying selective adsorption states, finding an excellent agreement with the best available theoretical data. Second, the capability of the approach to describe dispersionless correlation effects realistically is used to extract dispersion effects in time-dependent density functional simulations on the collision of (4)He droplets with a single graphene sheet. It is found that dispersion effects play a key role in the fast spreading of the (4)He nanodroplet, the evaporation-like process of helium atoms, and the formation of solid-like helium structures. These characteristics are expected to be quite general and highly relevant to explain experimental measurements with the newly developed helium droplet mediated deposition technique.

Density functional theory study of the interaction of vinyl radical, ethyne, and ethene with benzene, aimed to define an affordable computational level to investigate stability trends in large van der Waals complexes.

Our purpose is to identify a computational level sufficiently dependable and affordable to assess trends in the interaction of a variety of radical or closed shell unsaturated hydro-carbons A adsorbed on soot platelet models B. These systems, of environmental interest, would unavoidably have rather large sizes, thus prompting to explore in this paper the performances of relatively low-level computational methods and compare them with higher-level reference results. To this end, the interaction of three complexes between non-polar species, vinyl radical, ethyne, or ethene (A) with benzene (B) is studied, since these species, involved themselves in growth processes of polycyclic aromatic hydrocarbons (PAHs) and soot particles, are small enough to allow high-level reference calculations of the interaction energy ΔEAB. Counterpoise-corrected interaction energies ΔEAB are used at all stages. (1) Density Functional Theory (DFT) unconstrained optimizations of the A-B complexes are carried out, using the B3LYP-D, ωB97X-D, and M06-2X functionals, with six basis sets: 6-31G(d), 6-311 (2d,p), and 6-311++G(3df,3pd); aug-cc-pVDZ and aug-cc-pVTZ; N07T. (2) Then, unconstrained optimizations by Møller-Plesset second order Perturbation Theory (MP2), with each basis set, allow subsequent single point Coupled Cluster Singles Doubles and perturbative estimate of the Triples energy computations with the same basis sets [CCSD(T)//MP2]. (3) Based on an additivity assumption of (i) the estimated MP2 energy at the complete basis set limit [EMP2/CBS] and (ii) the higher-order correlation energy effects in passing from MP2 to CCSD(T) at the aug-cc-pVTZ basis set, ΔECC-MP, a CCSD(T)/CBS estimate is obtained and taken as a computational energy reference. At DFT, variations in ΔEAB with basis set are not large for the title molecules, and the three functionals perform rather satisfactorily even with rather small basis sets [6-31G(d) and N07T], exhibiting deviation from the computational reference of less than 1 kcal mol(-1). The zero-point vibrational energy corrected estimates Δ(EAB+ZPE), obtained with the three functionals and the 6-31G(d) and N07T basis sets, are compared with experimental D0 measures, when available. In particular, this comparison is finally extended to the naphthalene and coronene dimers and to three π-π associations of different PAHs (R, made by 10, 16, or 24 C atoms) and P (80 C atoms).

Maximum probability domains in crystals: the rock-salt structure.

The present paper studies MX crystals in rock-salt structure (M: Li, Na, K; X: F, Cl, Br, I). They are often described as being formed by ions. Pictures based on quantum mechanical calculations sustain and quantify it. The tools used are (i) the Quantum Theory of Atoms in Molecules, (ii) the Electron Localization Function, and (iii) the maximization of the probability to find in a spatial domain a number of electrons equal to that of the ion under consideration. The present paper shows that the images provided by these three different tools to analyze the quantum mechanical calculations yield, for these systems, very similar results, in the sense that the spatial domains and probability distributions are close. While results for the first two methods are already present in the literature, the last of the methods is applied for the first time to these systems, and details about the method of calculation and program are also given.

Border reactivity of polycyclic aromatic hydrocarbons and soot platelets toward ozone. A theoretical study.

PAH-based models, with an even or odd number of unsaturated carbon atoms and π electrons (even and odd PAHs for short), are selected to investigate, by molecular and periodic methods, their electron distribution and border reactivity toward ozone, and also to represent local features and edge reactivity of even or odd soot platelets. These results will contrast those previously collected for the internal positions of similar even (J. Phys. Chem. A 2005, 109, 10929.) or odd systems (J. Phys. Chem. A 2008, 112, 973.). Topologically different peripheral positions, representative of armchair and zigzag borders, exhibit different reactivity right from the beginning. Ozone attacks start off either to give primary ozonides by concerted addition or, nonconcertedly, to first produce trioxyl intermediates. Then, a variety of pathways are described, whose viability depends on both model and position. They can open the way to the possible formation of epoxide, aldehyde, and phenol groups (all entailing O(2) production) or ether (+CO(2)), lactone (+H(2)CO), and ketone functionalities. To sum up, functionalization, regardless of how achieved, can give a number of groups, most of which actually observed in PAH ozonization experimental studies. This picture can be matched up to the results on internal sites of our preceding papers, for which epoxidation was the only outcome. Most interestingly, formation of a ketone group may turn an even system into an odd one (and conversely) while involving production of HOO(•).

Periodic DFT modeling of bulk and surface properties of MgCl2.

MgCl(2) is the preferred support for the industrial Ziegler-Natta catalysts, and is believed to act as a template for the epitactic chemisorption of the active Ti species. As the first step of a thorough computational modeling of these systems, we studied the bulk and surface structure of the ordered alpha and beta phases of MgCl(2) by means of periodic DFT (B3LYP) methods using localized basis sets. The layer structure of both phases was reproduced satisfactorily with the inclusion of a (small) empirical dispersion correction ("DFT-D") as a practical method to describe the attraction between the layers. Surface models were studied on slabs with adequate thickness. It appears that various surfaces exposing 5-coordinated Mg are very similar in energy and are the lowest non-trivial surfaces. Cuts exposing 4-coordinated Mg are significantly less stable; both kinetic and equilibrium models of crystal growth indicate that they should normally not be formed to a significant extent. "Nano-ribbons" of single, flat chains of MgCl(2), sometimes proposed as components of the disordered delta phase, were also evaluated, but are predicted to be unstable to rearrangement. Implications for the role of MgCl(2) as catalyst support are discussed.

Soot platelets and PAHs with an odd number of unsaturated carbon atoms and pi electrons: theoretical study of their spin properties and interaction with ozone.

PAHs made from an odd number of unsaturated carbon atoms and pi electrons (odd PAHs) have been detected in flames and flank the more familiar even PAHs, having approximately the same quantitative importance, particularly for PAHs containing more than 25 carbon atoms. Similarly, soot platelets containing an odd number of carbon atoms can be reasonably assumed to form during combustion. PAHs are intended here as small models for the investigation of some of their local features. To this end, quantum mechanical calculations were also carried out on periodic models. The spin density patterns were found to be highly dependent on the PAH size and shape. PAHs and soot, once released in the environment, can undergo several oxidation processes. Ozone is then taken as a probe of the reactivity properties of some internal exposed portions of a platelet. A primary ozonide (PO) corresponds to an energy minimum, but the relevant concerted addition pathway does not exist, because a PO-like saddle point is second-order. The reaction begins with a nonconcerted attack that produces a trioxyl radical (TR). Subsequent O2 loss from the TR leaves either an epoxide with a pi-delocalized electron or a pi-delocalized oxepine, by cleavage of the ring carbon-carbon bond. The initial doublet spin multiplicity thus provides a description of the reaction surface unlike that for the internal reactivity of the closed-shell even systems investigated in a previous work, even though the final functionalization is the same.

Aromatic hydrocarbon nitration under tropospheric and combustion conditions. A theoretical mechanistic study.

The viability of some nitration pathways is explored for benzene (B), naphthalene (N), and in part pyrene (P). In principle, functionalization can either take place by direct nitration (NO2 or N2O5 attack) or be initiated by more reactive species, as the nitrate and hydroxyl radicals. The direct attack of the NO2 radical on B and N, followed by abstraction of the H geminal to the nitro group (most likely accomplished by 3O2) could yield the final nitro-derivatives. Nevertheless, the initial step (NO2 attack) involves significant free energy barriers. N2O5 proves to be an even worst nitrating agent. These results rule out direct nitration at room temperature. Instead, NO3 and, even more easily, HO can form pi-delocalized nitroxy- or hydroxycyclohexadienyl radicals. A subsequent NO2 attack can produce several regio- and diastereoisomers of nitroxy-nitro or hydroxy-nitro cyclohexadienes. In this respect, the competition between NO2 and O2 is considered: the rate ratios are such to indicate that the NO3 and HO initiated pathways are the major source of nitroarenes. Finally, if the two substituents are 1,2-trans, either a HNO3 or a H2O concerted elimination can give the nitro-derivatives. Whereas HNO3 elimination is feasible, H2O elimination presents, by contrast, a high barrier. Under combustion conditions the NO2 direct nitration pathway is more feasible, but remains a minor channel.

The oxidized soot surface: theoretical study of desorption mechanisms involving oxygenated functionalities and comparison with temperature programed desorption experiments.

The desorption mechanism for oxygenated functionalities on soot is investigated by quantum mechanical calculations on functionalized polycyclic aromatic hydrocarbon (PAH) models and compared with recently published temperature programed desorption-mass spectrometry results. Substituents on PAHs of increasing size (up to 46 carbon atoms in the parent PAH) are chosen to reproduce the local features of an oxidized graphenic soot platelet. Initially, the study is carried out on unimolecular fragmentation (extrusion, in some cases) processes producing HO, CO, or CO2, in model ketones, carboxylic acids, lactones, anhydrides, in one aldehyde, one peroxyacid, one hydroperoxide, one secondary alcohol, and one phenol. Then, a bimolecular process is considered for one of the carboxylic acids. Furthermore, some cooperative effect which can take place by involving two vicinal carboxylic groups (derived from anhydride hydrolysis) is investigated for other four bifunctionalized models. The comparison between the computed fragmentation (desorption) barriers for the assessed mechanisms and the temperature at which maxima occur in TPD spectra (for HO, CO, or CO2 desorption) offers a suggestion for the assignment of these maxima to specific functional groups, i.e., a key to the description of the oxidized surface. Notably, the computations suggest that (1) the desorption mode from a portion of a graphenic platelet functionalized by a carboxylic or lactone groups is significantly dependent from the chemical and geometric local environment. Consequently, we propose that (2) not all carboxylic groups go lost at the relatively low temperatures generally stated, and (3) lactone groups can be identified as producing not only CO2 but also CO.

Ozone interaction with polycyclic aromatic hydrocarbons and soot in atmospheric processes: theoretical density functional study by molecular and periodic methodologies.

The ozonization mechanism for polycyclic aromatic hydrocarbons (PAHs) and soot is investigated by quantum mechanical calculations carried out on molecular and periodic systems. PAHs, interesting per se, serve also to model the local features of the graphenic soot platelets, for which another model is provided by a periodic representation of one graphenic layer. A concerted addition leads to a primary ozonide, while a nonconcerted attack produces a trioxyl diradical (in which one of the two unpaired electrons is pi-delocalized). Easy loss of (i) (1)O(2) or (ii) (3)O(2) from either intermediate, with spin conservation, would yield stable (i) singlet or (ii) triplet pi-delocalized species which carry an epoxide group. The trioxyl diradical pathway is estimated to be preferred, in these systems. An intersystem crossing, taking place in the trioxyl diradicals, can be invoked to allow the even easier loss of a ground-state oxygen molecule with the formation of a ground-state epoxide in a more exoergic and less demanding step. We propose that soot ozonization can take place by such a process, with ultimate functionalization of the graphenic platelets by epoxide groups.

Structural characterization of siliceous spicules from marine sponges.

Siliceous sponges, one of the few animal groups involved in a biosilicification process, deposit hydrated silica in discrete skeletal elements called spicules. A multidisciplinary analysis of the structural features of the protein axial filaments inside the spicules of a number of marine sponges, belonging to two different classes (Demospongiae and Hexactinellida), is presented, together with a preliminary analysis of the biosilicification process. The study was carried out by a unique combination of techniques: fiber diffraction using synchrotron radiation, scanning electron microscopy (SEM), thermogravimetric analysis (TGA), differential scanning calorimetric (DSC), Fourier transform infrared spectroscopy (FTIR), and molecular modeling. From a phylogenetic point of view, the main result is the structural difference between the dimension and packing of the protein units in the spicule filaments of the Demospongiae and the Hexactinellida species. Models of the protein organization in the spicule axial filaments, consistent with the various experimental evidences, are given. The three different species of demosponges analyzed have similar general structural features, but they differ in the degree of order. The structural information on the spicule axial filaments can help shed some light on the still unknown molecular mechanisms controlling biosilicification.