A topological study of chemical bonds under pressure: solid hydrogen as a model case.

It is now well recognized that a fundamental understanding of the rules that govern chemistry under pressure is still lacking. Hydrogen being the "simplest" element as well as a central core to high pressure physics, we undertake a general study of the changes in the chemical bonding under pressure. We start from a simple trimer unit that has been found in high pressure phases, whose behavior has been found to reveal the basics of hydrogen polymerization under pressure. Making use of bond analysis tools, mainly the NCI (noncovalent interactions) index, we show that polymerization takes place in three steps: dipolar attraction, repulsion and bond formation. The use of a 1D Wigner-Seitz radius allowed us to extend the conclusions to 3D networks and to analyze their degree of polymerization. On the one hand, this approach provides new insight into the polymerization of hydrogen. On the other hand, it shows that complicated molecular solids can be understood from cluster models, where correlated methods can be applied, main differences in solid state arising at the transition points, where breaking/forming of bonds happens at once instead of continuously like in the cluster model.

Binding of Thioflavin T and Related Probes to Polymorphic Models of Amyloid-ß Fibrils.

Alzheimer's disease is a challenge of the utmost importance for contemporary society. An early diagnosis is essential for the development of treatments and for establishing a network of support for the patient. In this light, the deposition in the brain of amyloid-ß fibrillar aggregates, which is a distinctive feature of Alzheimer, is key for an early detection of this disease. In this work we propose an atomistic study of the interaction of amyloid tracers with recently published polymorphic models of amyloid-ß 1-40 and 1-42 fibrils, highlighting the relationship between marker architectures and binding affinity. This work uncovers the importance of quaternary structure, and in particular of junctions between amyloid-ß protofilaments, as the key areas for marker binding.

Decoupling the Effects of Mass Density and Hydrogen-, Oxygen-, and Aluminum-Based Defects on Optoelectronic Properties of Realistic Amorphous Alumina.

The search for functional materials is currently hindered by the difficulty to find significant correlation between constitutive properties of a material and its functional properties. In the case of amorphous materials, the diversity of local structures, chemical composition, impurities and mass densities makes such a connection difficult to be addressed. In this Letter, the relation between refractive index and composition has been investigated for amorphous AlOx materials, including nonstoichiometric AlOx, emphasizing the role of structural defects and the absence of effect of the band gap variation. It is found that the Newton-Drude (ND) relation predicts the refractive index from mass density with a rather high level of precision apart from some structures displaying structural defects. Our results show especially that O- and Al-based defects act as additive local disturbance in the vicinity of band gap, allowing us to decouple the mass density effects from defect effects (n = n[ND] + Δndefect).

Microhydration of Protonated Nα-Acetylhistidine: A Theoretical Approach.

Extensive exploration of the potential energy surfaces of protonated Nα-acetylhistidine hydrated by 0-3 molecules of water was performed. The methodology combined hierarchical and genealogical (Darwin family tree) approaches using polarizable AMOEBA force field and M06 functional. It is demonstrated that this mixed approach allows recovering a larger number of conformers than the number recovered by using any one of the two methods alone. Hydration enthalpies of protonated Nα-acetylhistidine and of model compounds have been computed using higher theoretical methods, up to the G4MP2 procedure. Excellent agreement with experiment is observed for successive hydration of methylamonium and imidazolium cations using MP2/6-311++G(2d,2p)//M06/6-311++G(d,p) and G4MP2 methods, thereby validating the theory levels used for hydrated protonated Nα-acetylhistidine. It is found that the first hydration enthalpy of protonated Nα-acetylhistidine is ca. 10 kJ mol(-1) lower than that of imidazolium, a result explained by the local environment of the positively charged imidazolium moiety.

Benchmarking DFT and TD-DFT Functionals for the Ground and Excited States of Hydrogen-Rich Peptide Radicals.

We assess the pros and cons of a large panel of DFT exchange-correlation functionals for the prediction of the electronic structure of hydrogen-rich peptide radicals formed after electron attachment on a protonated peptide. Indeed, despite its importance in the understanding of the chemical changes associated with the reduction step, the question of the attachment site of an electron and, more generally, of the reduced species formed in the gas phase through electron-induced dissociation (ExD) processes in mass spectrometry is still a matter of debate. For hydrogen-rich peptide radicals in which several positive groups and low-lying π* orbitals can capture the incoming electron in ExD, inclusion of full Hartree-Fock exchange at long-range interelectronic distance is a prerequisite for an accurate description of the electronic states, thereby excluding several popular exchange-correlation functionals, e.g., B3LYP, M06-2X, or CAM-B3LYP. However, we show that this condition is not sufficient by comparing the results obtained with asymptotically correct range-separated hybrids (M11, LC-BLYP, LC-BPW91, ωB97, ωB97X, and ωB97X-D) and with reference CASSCF-MRCI and EOM-CCSD calculations. The attenuation parameter ω significantly tunes the spin density distribution and the excited states vertical energies. The investigated model structures, ranging from methylammonium to hexapeptide, allow us to obtain a description of the nature and energy of the electronic states, depending on (i) the presence of hydrogen bond(s) around the cationic site(s), (ii) the presence of π* molecular orbitals (MOs), and (iii) the selected DFT approach. It turns out that, in the present framework, LC-BLYP and ωB97 yields the most accurate results.

Gas-phase structures and thermochemistry of neutral histidine and its conjugated acid and base.

Extensive exploration of the conformational space of neutral, protonated and deprotonated histidine has been conducted at the G4MP2 level. Theoretical protonation and deprotonation thermochemistry as well as heats of formation of gaseous histidine and its ionized forms have been calculated at the G4 level considering either the most stable conformers or an equilibrium population of conformers at 298 K. These theoretical results were compared to evaluated experimental determinations. Recommended proton affinity and protonation entropy deduced from these comparisons are PA(His) = 980 kJ mol(-1) and ΔpS(His) ∼ 0 J mol(-1) K(-1), thus leading to a gas-phase basicity value of GB(His) = 947.5 kJ mol(-1). Similarly, gas phase acidity parameters are ΔacidH(o)(His) = 1373 kJ mol(-1), ΔacidS(His) ∼ 10 J mol(-1) K(-1) and ΔacidG(o)(His) = 1343 kJ mol(-1). Computed G4 heats of formation values are equal to -290, 265 and -451 kJ mol(-1) for gaseous neutral histidine and its protonated and deprotonated forms, respectively. The present computational data correct, and complete, previous thermochemical parameter estimates proposed for gas-phase histidine and its acido-basic properties.

Acid-base thermochemistry of gaseous oxygen and sulfur substituted amino acids (Ser, Thr, Cys, Met).

Acid-base thermochemistry of isolated amino acids containing oxygen or sulfur in their side chain (serine, threonine, cysteine and methionine) have been examined by quantum chemical computations. Density functional theory (DFT) was used, with B3LYP, B97-D and M06-2X functionals using the 6-31+G(d,p) basis set for geometry optimizations and the larger 6-311++G(3df,2p) basis set for energy computations. Composite methods CBS-QB3, G3B3, G4MP2 and G4 were applied to large sets of neutral, protonated and deprotonated conformers. Conformational analysis of these species, based on chemical approach and AMOEBA force field calculations, has been used to identify the lowest energy conformers and to estimate the population of conformers expected to be present at thermal equilibrium at 298 K. It is observed that G4, G4MP2, G3B3, CBS-QB3 composite methods and M06-2X DFT lead to similar conformer energies. Thermochemical parameters have been computed using either the most stable conformers or equilibrium populations of conformers. Comparison of experimental and theoretical proton affinities and Δ(acid)H shows that the G4 method provides the better agreement with deviations of less than 1.5 kJ mol(-1). From this point of view, a set of evaluated thermochemical quantities for serine, threonine, cysteine and methionine may be proposed: PA = 912, 919, 903, 938; GB = 878, 886, 870, 899; Δ(acid)H = 1393, 1391, 1396, 1411; Δ(acid)G = 1363, 1362, 1367, 1382 kJ mol(-1). This study also confirms that a non-negligible ΔpS° is associated with protonation of methionine and that the most acidic hydrogen of cysteine in the gas phase is that of the SH group. In several instances new conformers were identified thus suggesting a re-examination of several IRMPD spectra.