Teodoro Laino

Surface-assisted cyclodehydrogenation provides a synthetic route towards easily processable and chemically tailored nanographenes

Atomically thin sheets of sp(2)-hybridized carbon--graphene--have enormous potential for applications in future electronic devices. Particularly promising are nanostructured (sub)units of graphene, the electronic properties of which can be tuned by changing the spatial extent or the specific edge termination of the carbon network. Processability and precise tailoring of graphene-derived structures are, however, still major obstacles in developing applications; both bottom-up and top-down routes are presently under investigation in attempts to overcome this limitation. Here, we propose a surface chemical route that allows for the atomically precise fabrication of tailored nanographenes from polyphenylene precursors. The cyclodehydrogenation of a prototypical polyphenylene on Cu(111) is studied using scanning tunnelling microscopy and density functional theory. We find that the thermally induced cyclodehydrogenation proceeds via several intermediate steps, two of which can be stabilized on the surface, yielding unprecedented insight into a dehydrogenative intramolecular aryl-aryl coupling reaction.

An Efficient Real Space Multigrid QM/MM Electrostatic Coupling.

A popular strategy for simulating large systems where quantum chemical effects are important is the use of mixed quantum mechanical/molecular mechanics methods (QM/MM). While the cost of solving the Schrödinger equation in the QM part is the bottleneck of these calculations, evaluating the Coulomb interaction between the QM and the MM part is surprisingly expensive. In fact it can be just as time-consuming as solving the QM part. We present here a novel real space multigrid approach that handles Coulomb interactions very effectively and implement it in the CP2K code. This novel scheme cuts the cost of this part of the calculation by 2 orders of magnitude. The method does not need very fine-tuning or adjustable parameters, and it is quite accurate, leading to a dynamics with very good energy conservation. We exemplify the validity of our algorithms with simulations of water and of a zwitterionic dipeptide solvated in water.

An Efficient Linear-Scaling Electrostatic Coupling for Treating Periodic Boundary Conditions in QM/MM Simulations

A new linear-scaling method based on a multigrid approach to treat long-range electrostatic interactions in hybrid quantum mechanics/molecular mechanics (QM/MM) simulations is described. The scheme has been implemented in the context of a QM calculation based on density functional theory (DFT). The method is tested on an analytical model to validate the new algorithm. Two realistic problems in α-quartz crystals and a zwitterionic dipeptide (GLY-ALA) in water have been chosen as further tests. Results from QM/MM calculations with periodic boundary conditions (PBC) show that the use of PBC is essential when studying highly ordered crystal structures, unless a carefully designed MM crystal is used for the calculation. With a general shaped MM subsystem, the absence of PBC leads to an incorrect description of Kohn-Sham band gaps and charge density. The present method allows periodic boundary conditions to be used in molecular simulations of biological and material science systems.

Endocyclic cleavage in glycosides with 2,3-trans cyclic protecting groups.

An endocyclic pathway is proposed as a reaction mechanism for the anomerization from the β (1,2-trans) to the α (1,2-cis) configuration observed in glycosides carrying 2,3-trans cyclic protecting groups. This reaction occurs in the presence of a weak Lewis or Brønsted acid, while endocyclic cleavage (endocleavage) in typical glycosides was observed only when mediated by protic media or strong Lewis acids. To rationalize the behavior of this class of compounds, the reaction mechanism and the promoting factors of the endocleavage are investigated using quantum-mechanical (QM) calculations and experimental studies. We examine anomerization reactions of thioglycosides carrying 2,3-trans cyclic protecting groups, employing boron trifluoride etherate (BF(3)·OEt(2)) as a Lewis acid. The estimated theoretical reactivity, based on a simple model to predict transition state (TS) energies from the strain caused by the fused rings, is very close to the TS energies calculated by the TS search along the C1-C2 bond rotation after the endo C-O bond breaking. Excellent agreement is found between the predicted TS energies and the experimental reactivity ranking. The series of calculations and experiments strongly supports the predominance of the endocyclic rather than the exocyclic mechanism. Furthermore, these investigations suggest that the inner strain is the primary factor enhancing the endocleavage reaction. The effect of the cyclic protecting group in restricting the pyranoside ring to a (4)C(1) conformation, extensively discussed in conjunction with the stereoelectronic effect theory, is shown to be a secondary factor.

A Revisited Picture of the Mechanism of Glycerol Dehydration

The dehydration mechanism of neutral glycerol in the gas phase was investigated by means of metadynamics simulations. Structures, vibrational frequencies, Gibbs free energy barriers, and rate constants at 800 K were computed for the different steps involved in the pyrolytic process. In this article, we provide a novel mechanism for the dehydration of neutral glycerol, proceeding via formation of glycidol with a barrier of 66.8 kcal/mol. The formation of glycidol is the rate limiting step of the overall decomposition process. Once formed, glycidol converts into 3-hydroxypropanal with a barrier of 49.5 kcal/mol. 3-Hydroxypropanal can decompose further into acrolein or into formaldehyde and vinyl-alcohol with barriers of 53.9 and 35.3 kcal/mol, respectively. These findings offer new insights to available experimental data based on glycerol pyrolysis studies performed with isotopic labeling and on the interpretation of the chemistry of glycerol and sugars in pyrolytic conditions.

Notes on “Ewald summation of electrostatic multipole interactions up to quadrupolar level” [J. Chem. Phys. 119, 7471 (2003)]

In an article [A. Aguado and P. A. Madden, J. Chem. Phys. 119, 7471 (2003)] published in this journal, Ewald summation expressions were derived for the energy, interatomic forces, pressure tensor, electrostatic field, and electrostatic field gradients in simulation system composed of molecules with charges, induced dipoles, and quadrupoles. In this letter we propose an alternative formulation of the reciprocal space terms generalized to higher multipoles, providing, at the same time, a few important corrections for previously published derivations. The present expressions, more compact than the ones proposed in the original work, provide a straightforward approach to implement an Ewald summation scheme for multipole interactions in codes where a standard Ewald summation is already available. A major result of the present derivation is an increase in the computational efficiency compared to the previous implementation of the several different electrostatic terms.

Mechanisms of Propylene Glycol and Triacetin Pyrolysis

Propylene glycol and triacetin are chemical compounds, commonly used as food additives. Though the usage of the pure chemicals is not considered harmful when used as dietary supplements, little is known about the nature of their thermal degradation products and the impact they may have on human health. For these reasons, in this manuscript we investigate the thermal decomposition mechanisms of both neutral propylene glycol and triacetin in the gas phase by a novel simulation framework. This is based on a free energy sampling methodology followed by an accurate energy refinement. Structures, Gibbs free energy barriers, and rate constants at 800 K were computed for the different steps involved in the two pyrolytic processes. The thermal decomposition mechanisms found theoretically for propylene glycol and triacetin were validated by a qualitative experimental investigation using gas-phase chromatography-mass spectroscopy, with excellent agreement. The results provide a validation of the novel simulation framework and shed light on the potential hazard to the health that propylene glycol and triacetin may have when exposed to high temperatures.

Chemical reactivity of aprotic electrolytes on a solid Li2O2 surface: screening solvents for Li–air batteries

Nowadays, simulation techniques are routinely used to generate accurate models of the structures of crystalline and amorphous solids, to study surfaces, defects and the properties of complex systems, and to screen possible candidate materials for the most diverse types of technological applications. The screening of novel molecular structures has been so far pursued by calculation of intrinsic properties with first-principle methods. Still, the use of intrinsic properties as scoring functions may not always be optimal for systems of high complexity. In these cases, increasingly detailed and realistic simulations that take into account the interaction with the surrounding molecules are of crucial importance. In this paper, we present an effective way to screen different solvents with respect to their chemical stability versus Li2O2 solid particles. To achieve this, the minimum energy paths for different types of reactions of a series of aprotic solvents (acetonitrile and pivalonitrile, dimethyl sulphoxide, N-methyl-2-pyrrolidone and some of its derivatives, penta ethylene glycol (PEG-5) and a fluorinated derivative) with solid Li2O2 are computed and reported. From these data, we can extract the reaction energy barriers, which compare extremely well with the available experimental data and offer a convenient way for screening and designing suitable solvents for Li–air batteries from first-principle calculations.

The adaptive buffered force QM/MM method in the CP2K and AMBER software packages

The implementation and validation of the adaptive buffered force (AdBF) quantum‐mechanics/molecular‐mechanics (QM/MM) method in two popular packages, CP2K and AMBER are presented. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM‐MM interface errors by discarding forces near the boundary according to the buffered force‐mixing approach. New adaptive thermostats, needed by force‐mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl‐phosphate hydrolysis using various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the AdBF QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force‐mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies.

Semiempirical self-consistent polarization description of bulk water, the liquid-vapor interface, and cubic ice.

We have applied an efficient electronic structure approach, the semiempirical self-consistent polarization neglect of diatomic differential overlap (SCP-NDDO) method, previously parametrized to reproduce properties of water clusters by Chang, Schenter, and Garrett [ J. Chem. Phys. 2008 , 128 , 164111 ] and now implemented in the CP2K package, to model ambient liquid water at 300 K (both the bulk and the liquid-vapor interface) and cubic ice at 15 and 250 K. The SCP-NDDO potential retains its transferability and good performance across the full range of conditions encountered in the clusters and the bulk phases of water. In particular, we obtain good results for the density, radial distribution functions, enthalpy of vaporization, self-diffusion coefficient, molecular dipole moment distribution, and hydrogen bond populations, in comparison to experimental measurements.