The reaction mechanism of polyalcohol dehydration in hot pressurized water

The use of high-temperature liquid water (HTW) as a reaction medium is a very promising tech- nology in the field of green chemistry. In order to fully exploit this technology, it is crucial to unravel the reaction mechanisms of the processes carried out in HTW. In this work, the reaction mecha- nism of 2,5-hexanediol dehydration in HTW has been studied by means of three different ab initio simulations: string method, metadynamics and molecular dynamics in real time. It is found that the whole reaction involving the protonation, bond exchange and the deprotonation occurs in a single step without a stable intermediate. The hydrogen bonded network of surrounding water has a vital role in assisting an efficient proton relay at the beginning and at the end of the reaction. It is confirmed that the reaction is energetically most favorable in the SN2 pathway with an estimated barrier of 36 kcal/mol, which explains the high stereoselectivity and the reaction rate observed in experiment. The mechanistic insights provided by our study are relevant for a prominent class of reactions in the context of sustainable biomass processing, namely dehydration reactions of polyalcohol molecules

The Effect of tensile stress on the conformational free energy landscape of disulfide bonds

Disulfide bridges are no longer considered to merely stabilize protein structure, but are increasingly recognized to play a functional role in many regulatory biomolecular processes. Recent studies have uncovered that the redox activity of native disulfides depends on their C-C-S-S dihedrals, and . Moreover, the interplay of chemical reactivity and mechanical stress of disulfide switches has been recently elucidated using force-clamp spectroscopy and computer simulation. The and angles have been found to change from conformations that are open to nucleophilic attack to sterically hindered, so-called closed states upon exerting tensile stress. In view of the growing evidence of the importance of C-C-S-S dihedrals in tuning the reactivity of disulfides, here we present a systematic study of the conformational diversity of disulfides as a function of tensile stress. With the help of force-clamp metadynamics simulations, we show that tensile stress brings about a large stabilization of the closed conformers, thereby giving rise to drastic changes in the conformational free energy landscape of disulfides. Statistical analysis shows that native TDi, DO and interchain Ig protein disulfides prefer open conformations, whereas the intrachain disulfide bridges in Ig proteins favor closed conformations. Correlating mechanical stress with the distance between the two -carbons of the disulfide moiety reveals that the strain of intrachain Ig protein disulfides corresponds to a mechanical activation of about 100 pN. Such mechanical activation leads to a severalfold increase of the rate of the elementary redox reaction step. All these findings constitute a step forward towards achieving a full understanding of functional disulfides

Selective nanomechanics of aromatic versus aliphatic thiolates on gold surfaces

Thiolated gold nanointerfaces play a key role in numerous fields of science, technology, as well as modern medicine to coat, functionalize, and protect. Our computational study reveals that the mechanical vs thermal stabilities of aliphatic thiolates on gold surfaces are strikingly different from those of aromatic thiolates. The aliphatic thiolates feature, at the same time, a higher thermal desorption energy but a lower mechanical rupture force than thiophenolates. Our analysis discloses that this most counterintuitive property is due to different mechanochemical detachment mechanisms. Electronic structure analyses along the detachment pathways trace this back to the distinct electronic properties of the S─Au bond in stretched nanojunctions. The discoveries that it is a higher thermal stability that entails a lower mechanical stability and that mechanical loads generate different local nanostructures depending on the nature of the thiolate are highly relevant for the rational design of improved thiol-gold nanocontacts

Thermal spin crossover in Fe(ii) and Fe(iii). Accurate spin state energetics at the solid state

The thermal spin crossover (SCO) phenomenon refers to an entropy-driven spin transition in some materials based on d6-d9 transition metal complexes. While its molecular origin is well known, intricate SCO behaviours are increasingly common, in which the spin transition occurs concomitantly to e.g. phase transformations, solvent absorption/desorption, or order-disorder processes. The computational modelling of such cases is challenging, as it requires accurate spin state energies in the solid state. Density Functional Theory (DFT) is the best framework, but most DFT functionals are unable to balance the spin state energies. While a few hybrid functionals perform better, they are still too expensive for solid-state minima searches in moderate-size systems. The best alternative is to dress cheap local (LDA) or semi-local (GGA) DFT functionals with a Hubbard-type correction (DFT+U). However, the parametrization of U is not straightforward due to the lack of reference values, and because ab initio parametrization methods perform poorly. Moreover, SCO complexes undergo notable structural changes upon transition, so intra- and inter-molecular interactions might play an important role in stabilizing either spin state. As a consequence, the U parameter depends strongly on the dispersion correction scheme that is used. In this paper, we parametrize U for nine reported SCO compounds (five based on FeII, 1-5 and four based on FeIII, 6-9) when using the D3 and D3-BJ dispersion corrections. We analyze the impact of the dispersion correction treatments on the SCO energetics, structure, and the unit cell dimensions. The average U values are different for each type of metal ion (FeIIvs. FeIII), and dispersion correction scheme (D3 vs. D3-BJ) but they all show excellent transferability, with mean absolute errors (MAE) below chemical accuracy (i.e. MAE <4 kJ mol−1). This enables a better description of SCO processes and, more generally, of spin state energetics, in materials containing FeII and FeIII ions

Nanomechanics of bidentate thiolate ligands of gold surfaces

The effect of the chain length separating sulfur atoms in bidentate thiols attached to defective gold surfaces on the rupture of the respective molecule-gold junctions has been studied computationally. Thermal desorption always yields cyclic disulfides. In contrast, mechanochemical desorption leads to cyclic gold complexes, where metal atoms are extracted from the surface and kept in tweezer-like arrangements by the sulfur atoms. This phenomenon is rationalized in terms of directional mechanical manipulation of Au-Au bonds and Au-S coordination numbers. Moreover, the flexibility of the chain is shown to crucially impact on the mechanical strength of the junction

Analysis of the acting forces in a theory of catalysis and mechanochemistry

The theoretical description of a chemical process resulting from the application of mechanical or catalytical stress to a molecule is performed by the generation of an effective potential energy surface (PES). Changes for minima and saddle points by the stress are described by Newton trajectories (NTs) on the original PES. From the analysis of the acting forces we postulate the existence of pulling corridors built by families of NTs that connect the same stationary points. For different exit saddles of different height we discuss the corresponding pulling corridors; mainly by simple two-dimensional surface models. If there are different exit saddles then there can exist saddles of index two, at least, between. Then the case that a full pulling corridor crosses a saddle of index two is the normal case. It leads to an intrinsic hysteresis of such pullings for the forward or the backward reaction. Assuming such relations we can explain some results in the literature. A new finding is the existence of roundabout corridors that can switch between different saddle points by a reversion of the direction. The findings concern the mechanochemistry of molecular systems under a mechanical load as well as the electrostatic force and can be extended to catalytic and enzymatic accelerated reactions. The basic and ground ansatz includes both kinds of forces in a natural way without an extra modification

Toward a theory of mechanochemistry: simple models from the very beginnings

A core idea in the context of mechanochemistry is that applying an external tensile force along a reaction coordinate should enhance the chemical reaction of interest. Here we analyze perturbed generic molecular structures: schematic models of triatomics, ABC, and tetraatomics, AABB. They are used to demonstrate that pulling does usu- ally not use the 'reaction coordinate', but opens new reaction pathways. Within de- velopment of these models we use the concept of Newton trajectories for a theory of mechanochemistry. However, we find cases where the theory of Newton trajectories is not applicable. For all cases we define the curve of force-displaced stationary points, and we discuss the importance of barrier breakdown points and valley-ridge inflection points. The examples use Morse potentials for bonds and simple angle functions and are demonstrated by assumed real values for the potential parameters. On the basis of the systematic study of some generic models we explain a set of already observed experimental mechanochemical phenomena in specific molecular systems and we apply the results to the strength of chemical bonds

Origin of bistability in the butyl-substituted spirobiphenalenyl-based neutral radical material

One of the most remarkable bistable materials reported so far is made of pi dimers of a butyl-substituted spirobiphenalenyl boron radical (butyl-SBP). The phase transition of this material, which is accompanied by changes in its optical, conductive, and magnetic properties, occurs with a hysteretic loop 25 K wide centered at 335 K. Herein, a computational study is presented aimed at deciphering the origin of this hysteresis. The phase transition of butyl-SBP consists of a spin transition of the constituent pi dimers coupled with an order-disorder transition involving the butyl chains linked to the nitrogen atoms of the superimposed phenalenyl rings of the pi dimer. Below 335 K, the terminal methyl group of the butyl chains adopts a gauche conformation with respect to the methylene unit bonded to the nitrogen atom. Above 335 K, the methyl group is in an anti conformation and exhibits dynamic disorder. The gauche -> anti conformational rearrangement triggers the spin transition of the pi dimers and is responsible for the hysteretic behavior of butyl-SBP. Specifically, the onset of the phase transition in the heating mode, and thus, the width of the hysteresis loop, are governed by the high energy cost and strong structural cooperative effects associated with this conformational change. Our results show that coupling a spin switch with a conformational switch in a molecular crystal provides a promising strategy in the design of new bistable materials

On the zeroth-order Hamiltonian for CASPT2 calculations of spin crossover compounds

Complete active space self-consistent field theory (CASSCF) calculations and subsequent second-order perturbation theory treatment (CASPT2) are discussed in the evaluation of the spin-states energy difference (ΔHelec) of a series of seven spin crossover (SCO) compounds. The reference values have been extracted from a combination of experimental measurements and DFT  +  U calculations, as discussed in a recent article (Vela et al., Phys Chem Chem Phys 2015, 17, 16306). It is definitely proven that the critical IPEA parameter used in CASPT2 calculations of ΔHelec, a key parameter in the design of SCO compounds, should be modified with respect to its default value of 0.25 a.u. and increased up to 0.50 a.u. The satisfactory agreement observed previously in the literature might result from an error cancellation originated in the default IPEA, which overestimates the stability of the HS state, and the erroneous atomic orbital basis set contraction of carbon atoms, which stabilizes the LS states

Lattice-solvent effects in the spin-crossover of an Fe(II)-based material. The key role of intermolecular interactions between solvent molecules

The spin transition of Fe(II) complexes is the subject of intensive synthetic and computational efforts. In this manuscript, we analyze the spin crossover (SCO) of [Fe(Edpsp)(2)](2+) (1), which features a spin transition depending on the cocrystallizing solvent molecules. Whereas the use of acetone results in a hysteretic spin transition at similar to 170 K, the use of propylene carbonate (PC) results in a permanent diamagnetic signal up to 300 K. By means of DFT+U+D2 calculations in the solid state of the material, we unravel the reasons for such different behavior. Our results allow us to ascribe the relatively low transition temperature of 1(BF4)(2.) acetone to the distorted arrangement of the SCO molecules in the low-spin state of the material. In turn, intermolecular interactions play the primary role in the case of 1(BF4)(2).2PC. In particular, we found that solvent-solvent interactions actively promote the stability of the low-spin state due to the formation of PC dimers. These dimers would appear at larger distances in the high-spin phase, with the subsequent loss of phase stability. This is yet another proof of how subtle is the spin transition phenomenon in Fe(II)-based architectures