Paramagnetic adsorbates on graphene: a charge transfer analysis

We introduce a modified version of the Hirshfeld charge analysis method and demonstrate its accurateness by calculating the charge transfer between the paramagnetic molecule NO2 and graphene. The charge transfer between paramagnetic molecules and a graphene layer as calculated with ab initio methods can crucially depend on the size of the supercell used in the calculation. This has important consequences for adsorption studies involving paramagnetic molecules such as NO2 physisorbed on graphene or on carbon nanotubes.Comment: 4 pages, 4 figures, submitted to Applied Physics Letter

Reply to 'Comment on "Extending Hirshfeld-I to bulk and periodic materials" '

The issues raised in the comment by T.A. Manz are addressed through the presentation of calculated atomic charges for NaF, NaCl, MgO, SrTiO$_3$ and La$_2$Ce$_2$O$_7$, using our previously presented method for calculating Hirshfeld-I charges in Solids [J. Comput. Chem.. doi: 10.1002/jcc.23088]. It is shown that the use of pseudo-valence charges is sufficient to retrieve the full all-electron Hirshfeld-I charges to good accuracy. Furthermore, we present timing results of different systems, containing up to over $200$ atoms, underlining the relatively low cost for large systems. A number of theoretical issues is formulated, pointing out mainly that care must be taken when deriving new atoms in molecules methods based on "expectations" for atomic charges.Comment: 7 pages, 2 Tables, 2 figure

Ab initio data-analytics study of carbon-dioxide activation on semiconductor oxide surfaces

The excessive emissions of carbon dioxide (CO$_2$) into the atmosphere threaten to shift the CO$_2$ cycle planet-wide and induce unpredictable climate changes. Using artificial intelligence (AI) trained on high-throughput first principles based data for a broad family of oxides, we develop a strategy for a rational design of catalytic materials for converting CO$_2$ to fuels and other useful chemicals. We demonstrate that an electron transfer to the $\pi^*$-antibonding orbital of the adsorbed molecule and the associated bending of the initially linear molecule, previously proposed as the indicator of activation, are insufficient to account for the good catalytic performance of experimentally characterized oxide surfaces. Instead, our AI model identifies the common feature of these surfaces in the binding of a molecular O atom to a surface cation, which results in a strong elongation and therefore weakening of one molecular C-O bond. This finding suggests using the C-O bond elongation as an indicator of CO$_2$ activation. Based on these findings, we propose a set of new promising oxide-based catalysts for CO$_2$ conversion, and a recipe to find more

Performance of 3D-space-based atoms-in-molecules methods for electronic delocalization aromaticity indices

Several definitions of an atom in a molecule (AIM) in three-dimensional (3D) space, including both fuzzy and disjoint domains, are used to calculate electron sharing indices (ESI) and related electronic aromaticity measures, namely, Iringand multicenter indices (MCI), for a wide set of cyclic planar aromatic and nonaromatic molecules of different ring size. The results obtained using the recent iterative Hirshfeld scheme are compared with those derived from the classical Hirshfeld method and from Bader's quantum theory of atoms in molecules. For bonded atoms, all methods yield ESI values in very good agreement, especially for C-C interactions. In the case of nonbonded interactions, there are relevant deviations, particularly between fuzzy and QTAIM schemes. These discrepancies directly translate into significant differences in the values and the trends of the aromaticity indices. In particular, the chemically expected trends are more consistently found when using disjoint domains. Careful examination of the underlying effects reveals the different reasons why the aromaticity indices investigated give the expected results for binary divisions of 3D spaceM.S. is grateful for the nancial help furnished by the Spanish MICINN Project No. CTQ2008-03077/BQU and by the Catalan DIUE through project No. 2009SGR63

Assessment of atomic charge models for gas-phase computations on polypeptides

The concept of the atomic charge is extensively used to model the electrostatic properties of proteins. Atomic charges are not only the basis for the electrostatic energy term in biomolecular force fields but are also derived from quantum mechanical computations on protein fragments to get more insight into their electronic structure. Unfortunately there are many atomic charge schemes which lead to significantly different results, and it is not trivial to determine which scheme is most suitable for biomolecular studies. Therefore, we present an extensive methodological benchmark using a selection of atomic charge schemes [Mulliken, natural, restrained electrostatic potential, Hirshfeld-I, electronegativity equalization method (EEM), and split-charge equilibration (SQE)] applied to two sets of penta-alanine conformers. Our analysis clearly shows that Hirshfeld-I charges offer the best compromise between transferability (robustness with respect to conformational changes) and the ability to reproduce electrostatic properties of the penta-alanine. The benchmark also considers two charge equilibration models (EEM and SQE), which both clearly fail to describe the locally charged moieties in the zwitterionic form of penta-alanine. This issue is analyzed in detail because charge equilibration models are computationally much more attractive than the Hirshfeld-I scheme. Based on the latter analysis, a straightforward extension of the SQE model is proposed, SQE+Q0, that is suitable to describe biological systems bearing many locally charged functional groups

Information-theoretic approaches to atoms-in-molecules : Hirshfeld family of partitioning schemes

Many population analysis methods are based on the precept that molecules should be built from fragments (typically atoms) that maximally resemble the isolated fragment. The resulting molecular building blocks are intuitive (because they maximally resemble well-understood systems) and transferable (because if two molecular fragments both resemble an isolated fragment, they necessarily resemble each other). Information theory is one way to measure the deviation between molecular fragments and their isolated counterparts, and it is a way that lends itself to interpretation. For example, one can analyze the relative importance of electron transfer and polarization of the fragments. We present key features, advantages, and disadvantages of the information-theoretic approach. We also codify existing information-theoretic partitioning methods in a way, that clarifies the enormous freedom one has within the information-theoretic ansatz

Effect of pressure on the crystal structure of alpha-glycylglycine to 4.7 GPa; application of Hirshfeld surfaces to analyse contacts on increasing pressure

The crystal structure of alpha-glycylglycine (alpha-GLYGLY) has been determined at room temperature at pressures between 1.4 and 4.7 GPa. The structure can be considered to consist of layers. The arrangement of molecules within each layer resembles the antiparallel beta-sheet motif observed in proteins, except that in alpha-GLYGLY the motif is constructed through NH center dot center dot center dot O hydrogen bonds rather than covalent amide links. Compression of alpha-GLYGLY proceeds via the reduction in void sizes. Voids close in such a way as to decrease the distances of stabilizing interactions such as hydrogen bonds and dipolar contacts. The largest reductions in interaction distances tend to occur for those contacts which are longest at ambient pressure. These longer interactions are formed between the beta-sheet-like layers, and the largest component of the strain tensor lies in the same direction. The N center dot center dot center dot O distance in one NH center dot center dot center dot O hydrogen bond measures 2.624 (9) angstrom at 4.7 GPa. This is very short for this kind of interaction and the crystal begins to break up above 5.4 GPa, presumably as the result of a phase transition. The changes that occur have been analysed using Hirshfeld surfaces. Changes in the appearance of these surfaces enable rapid assessment of the structural changes that occur on compression.</p