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We present a computational study of the electronic structure and lattice dynamics of IrTe2 that sheds light on the debated mechanism of the temperature-induced phase transitions of this material. At ambient temperature, IrTe2 adopts a hexagonal crystal structure typical of metal chalcogenides. Upon cooling, some Ir–Ir distances shorten, thus inducing lattice modulations. We demonstrate that this is due to the formation of multicenter bonds involving both Ir and Te atoms. We show how the formation of these bonds is energetically favorable but lowers the vibrational entropy; therefore, they are destabilized by temperature. The obtained model is exploited to rationalize the effect of Se doping and other experimental results from the literature.

Here we present a colloidal approach to synthesize bismuth chalcohalide nanocrystals (BiEX NCs, in which E=S, Se and X=Cl, Br, I). Our method yields orthorhombic elongated BiEX NCs, with BiSCl crystallizing in a previously unknown polymorph. The BiEX NCs display a composition-dependent band gap spanning the visible spectral range and absorption coefficients exceeding 105 cm-1 . The BiEX NCs show chemical stability at standard laboratory conditions and form colloidal inks in different solvents. These features enable the solution processing of the NCs into robust solid films yielding stable photoelectrochemical current densities under solar-simulated irradiation. Overall, our versatile synthetic protocol may prove valuable in accessing colloidal metal chalcohalide nanomaterials at large and contributes to establish metal chalcohalides as a promising complement to metal chalcogenides and halides for applied nanotechnology.

The mechanism of silver-oxygen and silver-sulfur reactions is revealed by means of molecular dynamics simulations, performed with reactive force fields purposely built and extensively tested against quantum-chemical results. Different reaction mechanisms and rates for Ag-O and Ag-S emerge. This study solves the long-lasting question why silver exposed to the environment is strongly vulnerable to sulfur corrosion (tarnishing) but hardly reacts with O2 , despite the thermodynamic prediction that both oxide and sulfide should form. The reliability of the simulation results is confirmed by the agreement with a multitude of experimental results from the literature.

Methylammonium lead halide perovskites have emerged as ideal materials for photovoltaics and other optoelectronic applications. Their optimal properties stem from complex mechanisms at an atomic level. In these structures, methylammonium molecules undergo continuous temperature-induced reorientations. The underlying atomistic mechanism of this phenomenon and its effect on the material properties are unexplored in many aspects. Here, we address this issue through extensive first-principles and force-field calculations. We show that the interplay between thermal energy and the energetics of molecular orientations fully explains the orthorhombic–tetragonal–cubic phase transitions of the material. The close links among methylammonium orientations, electronic structures, and optical properties are identified. Hydrogen bonding between organic and inorganic sublattices is demonstrated to be the key player in these relationships. We validate our findings against temperature-dependent one-photon and two-photon photoluminescence spectra of CH3NH3PbBr3 and results from the literature. The gained insights can explain the diversity of spectral features observed in the experimental data., The authors acknowledge the CINECA award under the ISCRA initiative for high-performance computing resources and support.

The unique combination of organic and inorganic layers in 2D layered perovskites offers promise for the design of a variety of materials for mechatronics, flexoelectrics, energy conversion, and lighting. However, the potential tailoring of their properties through the organic building blocks is not yet well understood. Here, different classes of organoammonium molecules are exploited to engineer the optical emission and robustness of a new set of Ruddlesden-Popper metal-halide layered perovskites. It is shown that the type of molecule regulates the number of hydrogen bonds that it forms with the edge-sharing [PbBr6 ]4- octahedra layers, leading to strong differences in the material emission and tunability of the color coordinates, from deep-blue to pure-white. Also, the emission intensity strongly depends on the length of the molecules, thereby providing an additional parameter to optimize their emission efficiency. The combined experimental and computational study provides a detailed understanding of the impact of lattice distortions, compositional defects, and the anisotropic crystal structure on the emission of such layered materials. It is foreseen that this rational design can be extended to other types of organic linkers, providing a yet unexplored path to tailor the optical and mechanical properties of these materials and to unlock new functionalities.

Thorough searches for more and more performing materials or for materials with novel properties and functions require a profound understanding of their structure-property relationships. While a detailed knowledge of the structure of a material, either through experimental and/or in silico ap- proaches, is a necessary and fundamental prerequisite for its study, it should not be overlooked that the geometrical and electronic (and magnetic) structure of a material is ultimately related to its chemical bonding features. And as an obvious consequence, the material's properties are in turn de- termined by those same features. The aim of this chapter is therefore to present an overview of theories, models and techniques which have found broad applications in the study of chemical bonding in materials. Rather than offering a comprehensive list of examples from literature, our main focus is on discussing the basic tenets of such tools, along with a discussion of their physical contents and limits, so as to favor their proper use. None- theless, the chapter concludes with a number of worked examples, illus- trating in some detail the synergic use of most of the outlined approaches.

Without new materials there would be no new technologies, just old bottlenecks. Until a few years ago, new materials could only be discovered experimentally. Now the situation is dramatically different: having solved the crystal structure prediction problem—the most formidable obstacle on the way to computational materials discovery—computational design of materials has become a reality. This ongoing scientific revolution has already led to the prediction of new materials with superior properties, with subsequent experimental confirmation.

The application of high pressure (hundreds of gigapascals) to materials, besides modifying their properties, changes dramatically their reactivity. Consequently, new compounds are formed, which violate the chemical paradigms known to date. In fact, it was recently discovered (Zhang et al., Science, 2013) that sodium subchlorides (NaxCl, x > 1) become stable at high pressure. In this work, we carry out a thorough study of these compounds as well as of other alkali subhalides by means of evolutionary crystal structure prediction calculations combined with an in-depth analysis of their crystal and electronic structures. The results of our investigation are threefold. We present an updated phase diagram of NaxCl, including one new compound (Na4Cl3) and two previously undiscovered phases of Na3Cl. We demonstrate the appearance of remarkable features in the electronic structure of sodium subchlorides, such as chlorine atoms acquiring a −2 oxidation state. Most importantly, we derive a model which enables one to rationalize the stability of alkali subhalides at high pressure. The predictive ability of our model was validated by the results of crystal structure prediction calculations we carried out on alkali subhalides A3Y (A = Li, Na, K; Y = F, Cl, Br). Moreover, we show how the stability of recently reported high-pressure compounds can be rationalized on the basis of the insights gained in the present study.

The accurate, experimental charge density distribution, ρ(r), of the potent antimalarial drug dihydroartemisinin (DHA) has been derived for the first time from single-crystal X-ray diffraction data at T=100(2) K. Gas-phase and solid-state DFT simulations have also been performed to provide a firm basis of comparison with experimental results. The quantum theory of atoms in molecules (QTAIM) has been employed to analyse the ρ(r) scalar field, with the aim of classifying and quantifying the key real-space elements responsible for the known pharmacophoric features of DHA. From the conformational perspective, the bicyclo[3.2.2]nonane system fixes the three-dimensional arrangement of the 1,2,4-trioxane bearing the active O-O redox centre. This is the most nucleophilic function in DHA and acts as an important CH×××O acceptor. On the contrary, the rest of the molecular backbone is almost neutral, in accordance with the lipophilic character of the compound. Another remarkable feature is the C-O bond length alternation along the O-C-O-C polyether chain, due to correlations between pairs of adjacent C-O bonds. These bonding features have been related with possible reactivity routes of the α- and β-DHA epimers, namely 1) the base-catalysed hemiacetal breakdown and 2) the peroxide reduction. As a general conclusion, the base-driven proton transfer has significant non-local effects on the whole polyether chain, whereas DHA reduction is thermodynamically favourable and invariably leads to a significant weakening (or even breaking) of the O-O bond. The influence of the hemiacetal stereochemistry on the electronic properties of the system has also been considered. Such findings are discussed in the context of the known chemical reactivity of this class of important antimalarial drugs. Disclosing an antimalarial pharmacophore: The pharmacophoric ability of the potent antimalarial drug dihydroartemisinin (DHA) resides on the interplay among the chemical features within the molecular backbone. These have been quantitatively rationalised at the molecular and sub-molecular level through an experimental and theoretical study of the DHA charge density and the electrostatic potential in real space (see figure).

The chemistry of the elements is heavily altered by high pressure, with stabilization of many new and often unexpected compounds, the emergence of which can profoundly change models of planetary interiors, where high pressure reigns. The C-H-O system is one of the most important planet-forming systems, but its high-pressure chemistry is not well known. Here, using state-of-the-art variable-composition evolutionary searches combined with quantum-mechanical calculations, we explore the C-H-O system at pressures up to 400 GPa. Besides uncovering new stable polymorphs of high-pressure elements and known molecules, we predicted the formation of new compounds. A 2CH4:3H2 inclusion compound forms at low pressure and remains stable up to 215 GPa. Carbonic acid (H2CO3), highly unstable at ambient conditions, was predicted to form exothermically at mild pressure (about 1 GPa). As pressure rises, it polymerizes and, above 314 GPa, reacts with water to form orthocarbonic acid (H4CO4). This unexpected high-pressure chemistry is rationalized by analyzing charge density and electron localization function distributions and implications for general chemistry and planetary science are also discussed.

Helium is generally understood to be chemically inert and this is due to its extremely stable closed-shell electronic configuration, zero electron affinity and an unsurpassed ionization potential. It is not known to form thermodynamically stable compounds, except a few inclusion compounds. Here, using the ab initio evolutionary algorithm USPEX and subsequent high-pressure synthesis in a diamond anvil cell, we report the discovery of a thermodynamically stable compound of helium and sodium, Na2He, which has a fluorite-type structure and is stable at pressures >113 GPa. We show that the presence of He atoms causes strong electron localization and makes this material insulating. This phase is an electride, with electron pairs localized in interstices, forming eight-centre two-electron bonds within empty Na8 cubes. We also predict the existence of Na2HeO with a similar structure at pressures above 15 GPa.

The Source Function (SF), introduced in 1998 by Richard Bader and Carlo Gatti, is succinctly reviewed and a number of paradigmatic applications to in vacuo and crystal systems are illustrated to exemplify how the SF may be used to discuss chemical bonding in both conventional and highly challenging cases. The SF enables the electron density to be seen at a point determined by source contributions from the atoms or a group of atoms of a system, and it is therefore well linked to the chemist's awareness that any local property and chemical behaviour is to some degree influenced by all the remaining parts of a system. The key and captivating feature of the SF is that its evaluation requires only knowledge of the electron density (ED) of a system, thereby enabling a comparison of ab initio and X-ray diffraction derived electron density properties on a common and rigorous basis. The capability of the SF to detect electron-delocalization effects and to quantify their degree of transferability is systematically explored in this paper through the analysis and comparison of experimentally X-ray derived Source Function patterns in benzene, naphthalene and (±)-8'-benzhydrylideneamino-1,1'-binaphthyl-2-ol (BAB) molecular crystals. It is shown that the SF tool recovers the characteristic SF percentage patterns caused by ?-electron conjugation in the first two paradigmatic aromatic molecules in almost perfect quantitative agreement with those obtained from ab initio periodic calculations. Moreover, the effect of chemical substitution on the degree of transferability of such patterns to the benzene- and naphthalene-like moieties of BAB is neatly shown and quantified by the observed systematic deviations, relative to benzene and naphthalene, of only those SF contributions from the substituted C atoms. Finally, the capability of the SF to reveal electron-delocalization effects is challenged by using a promolecule density, rather than the proper quantum mechanical density, to determine the changes in SF patterns along the cyclohexene, 1,3-cyclohexadiene and benzene molecule series. It is shown that, differently from the proper quantum density, the promolecular density is unable to reproduce the SF trends anticipated by the increase of electron delocalization along the series, therefore ruling out the geometrical effect as being the only cause for the observed SF patterns changes.The Source Function (SF), enabling the electron density to be viewed at a point as determined by source contributions from the various atoms or group of atoms of a system, is defined in terms of observables and it is amenable to experimental determination from accurate X-ray diffraction data. The use of the SF tool to discuss chemical bonding in molecules and crystals is reviewed, ahead of demonstrating that such a tool is also able to detect electron-delocalization effects and to assess their transferability properties in a series of paradigmatic molecular crystals, starting from knowledge of only the X-ray derived crystal electron densities.

Non-covalent interactions dictate how molecules interact with their surroundings. Enhancing their knowledge is crucial to explain phenomena of utmost importance like self-assembly, chemical reactivity and crystallization. In this work, the possibility of investigating Non-Covalent Interactions (NCIs) by using the Reduced Density Gradient (RDG) in tandem with energy densities descriptors is explored. A sample of 30 molecular adducts, spanning dispersive, hydrogen bonds and X H⋯π interactions was considered. Potential relationships among molecule⋯molecule stabilization energies and energy densities were sought for. Adducts characterized by NCIs having similar physical origins exhibit an excellent linear correlation between stabilization energies and kinetic energy densities integrated over the volume enclosed by low-value RDG isosurfaces. Estimating stabilization energies this way is computationally unexpensive and applicable also to electron densities derived from experiment, where a reliable approximation to the kinetic energy density in the intermolecular regions is afforded through Abramov’s functional. Potential energy densities, when averaged over the basins enclosed by low-value RDG isosurfaces, assume different values according to the kind of interaction class (dispersive, HBs, X H···π, and so on). This observation provides a new recipe to disentangle how the various NCIs contribute to the total stabilization energy. Implications on the possibility of retrieving quantitative thermodynamic information from the topology of suitable scalar fields are discussed.

Helium (He) is, on par with Neon, the most inert element in the Periodic Table. Indeed, no conclusive proofs about stable compounds containing chemical bonds with He at ambient conditions have been reported so far. However, pressure significantly affects chemical properties of elements. By using USPEX [1], a software which has been successfully used in the past to predict unexpected high pressure crystal structure [1], we found that above 160 GPa He and Sodium exothermically combine to form the compound Na2He, whose structure is reported in Fig. 1. Quasiharmonic free energy calculations based on computed phonon spectra indicate that the free energy of formation of Na2He is negative and that the latter is barely affected by the temperature (0-800 K range was considered). In order to understand the cause of stability of Na2He, we carried out a thorough study of its electronic structure at various pressures by means of several different approaches including the examination of the band structure and the analysis of real-space descriptors such as the electron density in the framework of the Quantum Theory of Atoms in Molecules [2], the Electron Localization Function [3] and the deformation density. By examining the band structure, we found that such compound is an insulator whose band-gap increases with pressure. Regarding real-space descriptors, two remarkable features of Na2He are the negative charge on He (obtained both using Mulliken and Bader partitioning) and the presence of interstitially localized electrons (i.e. Non-Nuclear Attractors), the latter being detectable in all the analyses above mentioned. In the range 160-350 GPa, the exothermicity associated to the formation of Na2He is mainly due to the volume reduction, while at higher pressures the electronic energy plays a prominent role in the stabilization of this compound. In this contribution we present the results of our study with particular emphasis on the role played by He in the stabilization of Na2He.

NCImilano, a Fortran90 code for applying the reduced density gradient (RDG) descriptor to a real-space study of noncovalent interactions, is presented. This code has been specifically designed for the X-ray charge density community, as it can deal with both gas-phase and solid-state electron densities as evaluated by popular multipolar (XD2006) and Gaussian-based quantum mechanical (Gaussian03/09,CRYSTAL) computational platforms. Moreover, it implements for the first time the possibility of plotting energy densities over RDG isosurfaces.

Malaria, an infection caused by the Plasmodium Falciparum protozoa, is nowadays one of the most lethal parasitic disease. As the Plasmodium protozoon is becoming resistant to quinoline-based molecules, the development of new drugs and the understanding of the key chemical features for their activity and of their mechanism of action is of great importance. In this context, we carried out a thorough analysis on the antimalarial drug dihydroartemisinin (DHA, Figure 1), through the study of its experimental and theoretical charge density (CD) distributions.[1] The experimental CD has been obtained by a single-crystal X-ray diffraction experiment at T = 100 K on a Bruker SMART APEX II diffractometer equipped with a CCD area detector, while the corresponding theoretical CD has been derived through fully periodic single point DFT calculations at the experimental geometry. We have identified nucleophilic as well as electrophilic regions of the molecule by analyzing its electrostatic potential and investigated the crystal packing and the change in the CD distribution moving from the isolated molecule to the crystal. Several CD analysis tools, with special emphasis on the Quantum Theory of Atoms in Molecules (QTAIM) [2], have been adopted, with the aim of fully characterize the chemical nature of specific functional groups, such as the peroxide group and the polyether chain. We have also performed geometry optimizations on deprotonated and radical anion of DHA, the latter being the intermediate species in most of the proposed antimalarial modes of action of the drug. Figure 1. Left: ORTEP plot of DHA at 100 K. Right: Map of the Laplacian of the experimental CD in the peroxide region. [1] G. Saleh, R. Soave, L. Lo Presti, R. Destro Chem. Eur. J. 2013, 19, 3490. [2] R. F. W. Bader Atoms in Molecules: A Quantum Theory Oxford University Press, Oxford, 1990.

Non-covalent interactions (NCI) define the rules underlying crys- tallisation, self-assembly and drug-re- ceptor docking processes. A novel NCI descriptor, based on the reduced elec- tron density gradient (RDG), that ena- bles easy visualisation of the zones of the electron density (ED) involved in either the supposedly attractive (dis- persive, hydrogen bonding) or allegedly repulsive (steric) intermolecular inter- actions, was recently developed by Johnson et al. Here, it is applied for the first time to EDs derived from single-crystal X-ray diffraction data. A computer code handling both experi- mental and ab initio EDs in the RDG- NCI perspective was purposely written. Three cases spanning a wide range of NCI classes were analysed: 1) benzene, as the prototype of stacking and weak CH···p interactions; 2) austdiol, a heav- ily functionalised fungal metabolite with a complex hydrogen-bonding net- work; 3) two polymorphs of the heter- oatom-rich anti-ulcer drug famotidine, with van der Waals and hydrogen-bond contacts between N- and S-containing groups. Even when applied to experi- mental EDs, the RDG index is a valua- ble NCI descriptor that can highlight their different nature and strength and provide results of comparable quality to ab initio approaches. Combining the RDG-NCI study with Baders ED ap- proach was a key step forward, as the RDG index can depict inherently delo- calised interactions in terms of extend- ed and flat RDG isosurfaces, in con- trast to the bond path analysis, which is often bounded to a too localised and possibly discontinuous (yes/no) descrip- tion. Conversely, the topological tool can provide quantitative insight into the simple, qualitative NCI picture of- fered by the RDG index. Hopefully, this study may pave the way to a deeper analysis of weak interactions in proteins using structural and ED infor- mation from experiment.

The novel non-covalent interaction (NCI) descriptor proposed by Johnson et al. (J. Am. Chem. Soc. 2010, 132, 6498–6506) and based on the reduced density gradient (RDG), is applied to three molecular crystals, spanning a wide range of NCI classes. The key-aspect of this work is to contrast the NCI description obtained using the RDG of the electron density (ED) derived from single-crystal X-ray diffraction data with that calculated from the RDG of the corresponding Independent Atom Model (IAM) density. It is shown that the RDG isosurfaces obtained from the simpler, unperturbed model density are often able to highlight the same interactions revealed by the corresponding surfaces using the crystalline density, but differ systematically in size and are generally much less structured than these latter. A qualitative rationale for such differences is provided for the first time. Our results question the use of the simpler density model to study NCI in large biological systems.

Non covalent interactions (NCI) play a crucial role in biology (protein-drug recognition) and in the design of new materials (self-assembly). A novel electron density (ED) based descriptor of non-covalent interaction was proposed in 2010 by Johnson et al.[1]. It exploits a key quantity in DFT, the reduced density gradient s(r), and reveals NCI in terms of low s-value isosurfaces, defined in low-ED regions and on which the ED is mapped with a colour related to the sign of the local density curvature along the second largest variation direction and to the magnitude of the ED itself. Though directly obtainable from experimental EDs, up to now such descriptor has been applied only to theoretical EDs or to independent atom model (IAM) densities. In this work, we explore the application of this new descriptor to NCI in the bulk, using X-ray derived EDs. In particular, molecular crystals represent ideal supramolecular entities for studying non covalent interactions and the global effect that the crystal field has on them. Austdiol [2], benzene [3] and the two polymorphs of the anti-ulcer drug famotidine [4] were chosen as representative case studies. Atom-centred multipole expansions (XD2006 package [5]) were adopted in the refinement against the experimental structure factors and the grid files for implementing the NCI descriptor were obtained with an ad-hoc code. The NCI isosurfaces obtained from experiment have been also compared with those calculated using ab-initio fully-periodic wavefunctions and the IAM densities. Moreover, the picture provided by this new descriptor was compared with the one obtained using Quantum Theory of Atoms in Molecules, QTAIM [6]. We found that the NCI descriptor is able to distinguish the different types of non-covalent interactions, and also to rank their strength, especially for Hydrogen Bonds (HB). It can also mirror the presence of weak van der Waals interactions, usually difficult to be properly described, in particular using ED-based descriptors. Furthermore, this descriptor turned out to be able to recover the delocalized character of interactions like C-H···? also when QTAIM is not. IAM gives a correct description only for the very weak interactions whose NCI isosurfaces are well separated from the molecular skeleton(s) and for those interactions which are easily anticipated by packing geometry. The very good general agreement we found between theoretical and experimental isosurfaces leads us to conclude that the NCI descriptor can be also successfully applied to experimentally derived multipolar ED. It is therefore an emerging, powerful tool to investigate non-covalent interactions, and able also to give complementary information to the 'conventional' QTAIM approach.

Ag and Sn are the major components of solder alloys adopted to assemble printed circuit boards. The qualities that make them the alloys of choice for the modern electronic industry are related to their physical and chemical properties. For corrosion resistance and solderability, surface properties are particularly important. Yet, atomic-level information about the surfaces of these alloys is not known. Here we fill this gap by presenting an extensive ab initio investigation of composition, energetics, structure and reactivity of Ag-Sn alloy surfaces. The structure and stability of various surfaces is evaluated, and the main factors determining the energetics of surface formation are uncovered. Oxygen and sulphur chemisorptions are studied and discussed in the framework of corrosion tendency, an important issue for printed circuit boards. Adsorption energy trends are rationalized based on the analysis of structural and electronic features.

The Source Function (SF) [1,2] enables one to view chemical bonding and other chemical paradigms under a new perspective and using only information from the electron density observable, rho, and its derivatives. Being completely independent from the tools used to get rho, the SF represents a very useful descriptor, able in some cases to bridge the gap between the rich information one gains from an ab-initio wavefunction of an ideal system and that, quite often more limited, but referred to a real system, obtained from an experimental rho derived from X-ray diffraction data. The potential uses of the SF are, however, yet not fully explored. In a preliminary work, we addressed the question of whether the SF is or is not capable to reveal electron conjugation [3]. Question arose because of a recent claim [4] according to which pi-electron delocalization in the benzene ring is not manifest in the SF when the reference point (rp) - the point at which the atomic sources for its density are calculated - is taken at the C-C bond critical point (bcp)". Reasoning behind this statement is the null contribution from pi molecular orbitals (MOs) to rho in their nodal plane. However, since sigma and pi-distributions are not independent, but self-consistently interrelated, we conjectured that some, albeit small, effect of electron conjugation could also be manifest when the rp lies in the pi-orbitals-nodal plane, even though pi-orbitals do not obviously yield direct contributions to rho in that plane. Results on a series of increasingly pi-conjugated systems demonstrate that this is actually the case. By looking at the C-C bcp electron density for the shortest bond(s) in cyclohexene, cyclohexadiene, benzene, i.e. those bonds with largest double-bond character, one observes that both the SF and the SF% contributions of the C atoms other than those directly involved in such a bond increase with decreasing double bond character and electron localization of the bond. The enhanced S% value then becomes largely more evident when analysed using rps for which the effect of pi-electron conjugation takes place directly through pi-electron distribution rather than, indirectly, through sigma-pi electron interdependency. In this work, the analysis is extended to more complex systems, formed by more than one ring, with fully conjugated or partially interrupted sequence of formal double-bonds and with planar or non planar geometry. In the case of benzene, the analysis is also performed on a rho derived through multipole refinement of a set of X-ray diffraction data taken on a benzene molecular crystal. In the inspected cases and regardless of the theoretical or experimental origin of rho, the SF reveals capable to detect electron conjugation. Such an ability is independent from a sigma and pi separation of rho, since the SF tool was applied to the total rho. This observation is important in view of the possibility to recover electron conjugation effects using both rho's derived experimentally (hence without sigma and pi separation being allowed) and rho's where the departure from symmetry inhibits a proper separation of sigma and pi contributions. Using a MO approach, the sigma and pi contributions to the SF values can also be revealed and quantified.