Evaluation of the ONIOM Method for Interpretation of Infrared Spectra of Gas-Phase Molecules of Biological Interest

QM/MM investigations of organic chemistry oriented questions

About 35 years after its first suggestion, QM/MM became the standard theoretical approach to investigate enzymatic structures and processes. The success is due to the ability of QM/MM to provide an accurate atomistic picture of enzymes and related processes. This picture can even be turned into a movie if nuclei-dynamics is taken into account to describe enzymatic processes. In the field of organic chemistry, QM/MM methods are used to a much lesser extent although almost all relevant processes happen in condensed matter or are influenced by complicated interactions between substrate and catalyst. There is less importance for theoretical organic chemistry since the influence of nonpolar solvents is rather weak and the effect of polar solvents can often be accurately described by continuum approaches. Catalytic processes (homogeneous and heterogeneous) can often be reduced to truncated model systems, which are so small that pure quantum-mechanical approaches can be employed. However, since QM/MM becomes more and more efficient due to the success in software and hardware developments, it is more and more used in theoretical organic chemistry to study effects which result from the molecular nature of the environment. It is shown by many examples discussed in this review that the influence can be tremendous, even for nonpolar reactions. The importance of environmental effects in theoretical spectroscopy was already known. Due to its benefits, QM/MM can be expected to experience ongoing growth for the next decade.In the present chapter we give an overview of QM/MM developments and their importance in theoretical organic chemistry, and review applications which give impressions of the possibilities and the importance of the relevant effects. Since there is already a bunch of excellent reviews dealing with QM/MM, we will discuss fundamental ingredients and developments of QM/MM very briefly with a focus on very recent progress. For the applications we follow a similar strategy.

Gas-phase structure of amyloid-β (12-28) peptide investigated by infrared spectroscopy, electron capture dissociation and ion mobility mass spectrometry

The gas-phase structures of doubly and triply protonated Amyloid-β12-28 peptides have been investigated through the combination of ion mobility (IM), electron capture dissociation (ECD) mass spectrometry, and infrared multi-photon dissociation (IRMPD) spectroscopy together with theoretical modeling. Replica-exchange molecular dynamics simulations were conducted to explore the conformational space of these protonated peptides, from which several classes of structures were found. Among the low-lying conformers, those with predicted diffusion cross-sections consistent with the ion mobility experiment were further selected and their IR spectra simulated using a hybrid quantum mechanical/semiempirical method at the ONIOM DFT/B3LYP/6-31 g(d)/AM1 level. In ECD mass spectrometry, the c/z product ion abundance (PIA) has been analyzed for the two charge states and revealed drastic differences. For the doubly protonated species, N - Cα bond cleavage occurs only on the N and C terminal parts, while a periodic distribution of PIA is clearly observed for the triply charged peptides. These PIA distributions have been rationalized by comparison with the inverse of the distances from the protonated sites to the carbonyl oxygens for the conformations suggested from IR and IM experiments. Structural assignment for the amyloid peptide is then made possible by the combination of these three experimental techniques that provide complementary information on the possible secondary structure adopted by peptides. Although globular conformations are favored for the doubly protonated peptide, incrementing the charge state leads to a conformational transition towards extended structures with 310- and α-helix motifs.

The assessment of density functionals for DNA–protein stacked and T-shaped complexes

The present work uses 129 nucleobase – amino acid CCSD(T)/CBS stacking and T-shaped interaction energies as reference data to test the ability of various density functionals with double-zeta quality basis sets, as well as some semi-empirical and molecular mechanics methods, to accurately describe noncovalent DNA–protein π–π and π+–π interactions. The goal of this work is to identify methods that can be used in hybrid approaches (QM/MM, ONIOM) for large-scale modeling of enzymatic systems involving active-site (substrate) π–π contacts. Our results indicate that AMBER is a more appropriate choice for the lower-level method in hybrid techniques than popular semi-empirical methods (AM1, PM3), and suggest that AMBER accurately describes the π–π interactions found throughout DNA–protein complexes. The M06–2X and PBE-D density functionals were found to provide very promising descriptions of the 129 nucleobase – amino acid interaction energies, which suggests that these may be the most suitable methods for describing high-level regions. Therefore, M06–2X and PBE-D with both the 6–31G(d) and 6–31+G(d,p) basis sets were further examined through potential-energy surface scans to better understand how these techniques describe DNA–protein π–π interactions in both minimum and nonminimum regions of the potential-energy surfaces, which is critical information when modeling enzymatic reaction pathways. Our results suggest that studies of stacked nucleobase – amino acid systems should implement the PBE-D/6–31+G(d,p) method. However, if T-shaped contacts are involved and (or) smaller basis sets must be considered due to limitations in computational resources, then M06–2X/6–31G(d) provides an overall excellent description of both nucleobase – amino acid stacking and T-shaped interactions for a range of DNA–protein π–π and π+–π interactions.