Understanding the initial events of the oxidative damage and protection mechanisms of the AA9 lytic polysaccharide monooxygenase family.

Lytic polysaccharide monooxygenase (LPMO) is a new class of oxidoreductases that boosts polysaccharide degradation employing a copper active site. This boost may facilitate the cost-efficient production of biofuels and high-value chemicals from polysaccharides such as lignocellulose. Unfortunately, self-oxidation of the active site inactivates LPMOs. Other oxidoreductases employ hole-hopping mechanisms as protection against oxidative damage, but little is generally known about the details of these mechanisms. Herein, we employ highly accurate theoretical models based on density functional theory (DFT) molecular mechanics (MM) hybrids to understand the initial steps in LPMOs' protective measures against self-oxidation; we identify several intermediates recently proposed from experiment, and quantify which are important for protective hole-hopping pathways. Investigations on two different LPMOs show consistently that a tyrosine residue close to copper is crucial for protection: this explains recent experiments, showing that LPMOs without this tyrosine are more susceptible to self-oxidation.

Extracting Quantitative Information at Quantum Mechanical Level from Noncovalent Interaction Index Analyses.

The noncovalent interaction (NCI) index is nowadays a well-known strategy to detect NCIs in molecular systems. Even though it initially provided only qualitative descriptions, the technique has been recently extended to also extract quantitative information. To accomplish this task, integrals of powers of the electron distribution were considered, with the requirement that the overall electron density can be clearly decomposed as sum of distinct fragment contributions to enable the definition of the (noncovalent) integration region. So far, this was done by only exploiting approximate promolecular electron densities, which are given by the sum of spherically averaged atomic electron distributions and thus represent too crude approximations. Therefore, to obtain more quantum mechanically (QM) rigorous results from NCI index analyses, in this work, we propose to use electron densities obtained through the transfer of extremely localized molecular orbitals (ELMOs) or through the recently developed QM/ELMO embedding technique. Although still approximate, the electron distributions resulting from the abovementioned methods are fully QM and, above all, are again partitionable into subunit contributions, which makes them completely suitable for the NCI integral approach. Therefore, we benchmarked the integrals resulting from NCI index analyses (both those based on the promolecular densities and those based on ELMO electron distributions) against interaction energies computed at a high quantum chemical level (in particular, at the coupled cluster level). The performed test calculations have indicated that the NCI integrals based on ELMO electron densities outperform the promolecular ones. Furthermore, it was observed that the novel quantitative NCI-(QM/)ELMO approach can be also profitably exploited both to characterize and evaluate the strength of specific interactions between ligand subunits and protein residues in protein-ligand complexes and to follow the evolution of NCIs along trajectories of molecular dynamics simulations. Although further methodological improvements are still possible, the new quantitative ELMO-based technique could be already exploited in situations in which fast and reliable assessments of NCIs are crucial, such as in computational high-throughput screenings for drug discovery.

The N,N,N-trimethylammonium moiety as tetrel bond donor site: crystallographic and computational studies.

Five structures bearing the N,N,N-trimethylammonium unit have been investigated to address the ability of the N+-CH3 unit to function as a tetrel bond donor site. Charged and neutral electron density donors display close contacts with different carbon atoms of methyl groups on the ammonium moiety. The Hirshfeld atom refinement (HAR) technique was used on selected structures to accurately and precisely determine the hydrogen atom positions and, consequently, to get better insights into the N+-C⋯Nu (Nu = nucleophile) interactions occurring in the crystals. In particular, the performed analyses highlighted specific geometrical features of the moieties involved in the interactions and allowed distinguishing between tetrel and hydrogen bonds.

Nickel and Palladium Complexes of a PP(O)P Pincer Ligand Based upon a peri-Substituted Acenaphthyl Scaffold and a Secondary Phosphine Oxide.

A PP(O)P pincer ligand based upon a peri-substituted acenaphthyl (Ace) scaffold and a secondary phosphine oxide, (5-Ph2P-Ace-6-)2P(O)H, was prepared and fully characterized including a neutron diffraction study. The reaction with [Ni(H2O)6]Cl2 and PdCl2 produced ionic metal(II) complexes [κ3-P,P',P''((5-Ph2P-Ace-6-)2P(OH))MCl]Cl, which upon addition of Et3N gave rise to zwitterionic metal(II) complexes κ3-P,P',P''((5-Ph2P-Ace-6-)2P(O))MCl (M = Ni, Pd). The reaction with Ni(COD)2 (COD = cyclooctadiene) provided the η3-cyclooctenyl Ni(II) complex κ3-P,P',P''((5-Ph2P-Ace-6-)2P(O))Ni(η3-C8H13). A detailed complementary bonding analysis of the P-H, P-O, and P-M interactions was carried out (M = Ni, Pd).

QM/ELMO: A Multi-Purpose Fully Quantum Mechanical Embedding Scheme Based on Extremely Localized Molecular Orbitals.

The development of computationally advantageous methods for the study of large systems is a long-standing research topic in theoretical chemistry. Among these techniques, a prominent place is certainly occupied by the multiscale embedding strategies, from the well-known QM/MM (quantum mechanics/molecular mechanics) methods to the latest and promising fully quantum mechanical approaches. In this Feature Article, we will briefly review the recently proposed QM/ELMO (quantum mechanics/extremely localized molecular orbital) scheme, namely a new multiscale embedding strategy in which the most chemically relevant region of the investigated system is treated at fully quantum chemical level, while the remaining part (namely, the environment) is described by means of transferred extremely localized molecular orbitals that remain frozen throughout the computation. Other than highlighting the theoretical bases, here we will also review the main results obtained through all the currently available variants of the novel method. In particular, we will show how the QM/ELMO embedding scheme has been successfully exploited to perform both ground and excited state calculations, reproducing the results of corresponding fully quantum mechanical computations but with a much lower computational cost. A first application to crystallography will be also discussed, and we will describe how the QM/ELMO approach has been recently coupled with the Hirshfeld atom refinement technique to accurately determine the positions of hydrogen atoms from X-ray diffraction data. Given the reliability and quality of the obtained results, future applications of the current versions of the QM/ELMO embedding strategy to different types of chemical problems are to be expected in the near future. Moreover, further algorithmic improvements and methodological developments are also envisaged, such as the development of a polarizable QM/ELMO scheme accounting for the effects of the QM region on the ELMO subsystem or the use of the new embedding approach in the context of quantum crystallography to perform unprecedented accurate refinements of macromolecular crystal structures.

A Step toward the Quantification of Noncovalent Interactions in Large Biological Systems: The Independent Gradient Model-Extremely Localized Molecular Orbital Approach.

The independent gradient model (IGM) is a recent electron density-based computational method that enables to detect and quantify covalent and noncovalent interactions. When applied to large systems, the original version of the technique still relies on promolecular electron densities given by the sum of spherically averaged atomic electron distributions, which leads to approximate evaluations of the inter- and intramolecular interactions occurring in systems of biological interest. To overcome this drawback and perform IGM analyses based on quantum mechanically rigorous electron densities also for macromolecular systems, we coupled the IGM approach with the recently constructed libraries of extremely localized molecular orbitals (ELMOs) that allow fast and reliable reconstructions of polypeptide and protein electron densities. The validation tests performed on small polypeptides and peptide dimers have shown that the novel IGM-ELMO strategy provides results that are systematically closer to the fully quantum mechanical ones and outperforms the IGM method based on the crude promolecular approximation, but still keeping a quite low computational cost. The results of the test calculations carried out on proteins have also confirmed the trends observed for the IGM analyses conducted on small systems. This makes us envisage the future application of the novel IGM-ELMO approach to unravel complicated noncovalent interaction networks (e.g., in protein-protein contacts) or to rationally design new drugs through molecular docking calculations and virtual high-throughput screenings.

Climbing Jacob's Ladder of Structural Refinement: Introduction of a Localized Molecular Orbital-Based Embedding for Accurate X-ray Determinations of Hydrogen Atom Positions.

The positions of hydrogen atoms in molecules are fundamental in many aspects of chemistry. Nevertheless, most molecular structures are obtained from refinements of X-ray data exploiting the independent atom model (IAM), which uses spherical atomic densities and provides bond lengths involving hydrogen atoms that are too short compared to the neutron reference values. To overcome the IAM shortcomings, the wave function-based Hirshfeld atom refinement (HAR) method has been recently proposed, emerging as a promising strategy able to give element-hydrogen bond distances in excellent agreement with the neutron ones in terms of accuracy and precision. In this Letter, we propose a significant improvement of HAR based on the idea of describing the crystal environment explicitly in the underlying wave function calculation through a quantum mechanical embedding strategy that exploits extremely localized molecular orbitals. Test-bed refinements on a crystal structure characterized by strong intermolecular interactions are also discussed.

Similarities and Differences between Crystal and Enzyme Environmental Effects on the Electron Density of Drug Molecules.

The crystal interaction density is generally assumed to be a suitable measure of the polarization of a low-molecular weight ligand inside an enzyme, but this approximation has seldomly been tested and has never been quantified before. In this study, we compare the crystal interaction density and the interaction electrostatic potential for a model compound of loxistatin acid (E64c) with those inside cathepsin B, in solution, and in vacuum. We apply QM/MM calculations and experimental quantum crystallography to show that the crystal interaction density is indeed very similar to the enzyme interaction density. Less than 0.1 e are shifted between these two environments in total. However, this difference has non-negligible consequences for derived properties.

Localized Molecular Orbital-Based Embedding Scheme for Correlated Methods.

Embedding strategies currently provide the best compromise between accuracy and computational cost in modeling chemical properties and processes of large and complex systems. In this framework, different methods have been proposed all over the years, from the very popular QM/MM approaches to the more recent and very promising density matrix and density functional embedding techniques. Here, we present a further development of the quantum mechanics/extremely localized molecular orbital technique (QM/ELMO) method, a recently proposed multiscale embedding strategy in which the chemically active region of the investigated system is treated at a fully quantum mechanical level, while the rest is described by frozen extremely localized molecular orbitals previously transferred from proper libraries or tailor-made model molecules. In particular, in this work we discuss and assess in detail the extension of the QM/ELMO approach to density functional theory and post-Hartree-Fock techniques by evaluating its performances when it is used to describe chemical reactions, bond dissociations, and intermolecular interactions. The preliminary test calculations have shown that, in the investigated cases, the new embedding strategy enables the results of the corresponding fully quantum mechanical computations to be reproduced within chemical accuracy in almost all the cases but with a significantly reduced computational cost, especially when correlated post-Hartree-Fock strategies are used to describe the quantum mechanical subsystem. In light of the obtained results, we already envisage the future application of the new correlated QM/ELMO techniques to the investigation of more challenging problems, such as the modeling of enzyme catalysis, the study of excited states of biomolecules, and the refinement of macromolecular X-ray crystal structures.

Fast and Accurate Quantum Crystallography: From Small to Large, from Light to Heavy.

The coupling of the crystallographic refinement technique Hirshfeld atom refinement (HAR) with the recently constructed libraries of extremely localized molecular orbitals (ELMOs) gives rise to the new quantum-crystallographic method HAR-ELMO. This method is significantly faster than HAR but as accurate and precise, especially concerning the free refinement of hydrogen atoms from X-ray diffraction data, so that the first fully quantum-crystallographic refinement of a protein is presented here. However, the promise of HAR-ELMO exceeds large molecules and protein crystallography. In fact, it also renders possible electron-density investigations of heavy elements in small molecules and facilitates the detection and isolation of systematic errors from physical effects.

NCI-ELMO: A New Method To Quickly and Accurately Detect Noncovalent Interactions in Biosystems.

Accurate determinations of noncovalent interactions in biological systems are fundamental to rationalize the structure and to get insights into the functions and the dynamics of macromolecules. Here we propose a new tool for the efficient identification of noncovalent interactions in proteins. The noncovalent interaction (NCI) method, a well-established strategy to detect noncovalent interactions in chemical systems, is coupled with the libraries of extremely localized molecular orbitals (ELMOs), which allow instantaneous reconstruction of quantum mechanically rigorous electron distributions of polypeptides and proteins. Test calculations performed on different interactions show that the new NCI-ELMO strategy always outperforms the original NCI method based on the promolecular approximation, while it is in close agreement with original NCI analyses based on fully quantum mechanical calculations. The new technique allows for unraveling the network of interactions in biological systems and to rapidly monitor their evolutions with time, with possible consequences on the design of new drugs.