Initial Maximum Overlap Method for Large Systems by the Quantum Mechanics/Extremely Localized Molecular Orbital Embedding Technique

How Does Mg2+(aq) Interact with ATP(aq)? Biomolecular Structure through the Lens of Liquid-Jet Photoemission Spectroscopy

Liquid-jet photoemission spectroscopy (LJ-PES) allows for a direct probing of electronic structure in aqueous solutions. We show the applicability of the approach to biomolecules in a complex environment, exploring site-specific information on the interaction of adenosine triphosphate in the aqueous phase (ATP(aq)) with magnesium (Mg2+(aq)), highlighting the synergy brought about by the simultaneous analysis of different regions in the photoelectron spectrum. In particular, we demonstrate intermolecular Coulombic decay (ICD) spectroscopy as a new and powerful addition to the arsenal of techniques for biomolecular structure investigation. We apply LJ-PES assisted by electronic-structure calculations to study ATP(aq) solutions with and without dissolved Mg2+. Valence photoelectron data reveal spectral changes in the phosphate and adenine features of ATP(aq) due to interactions with the divalent cation. Chemical shifts in Mg 2p, Mg 2s, P 2p, and P 2s core-level spectra as a function of the Mg2+/ATP concentration ratio are correlated to the formation of [Mg(ATP) 2]6-(aq), [MgATP]2-(aq), and [Mg2ATP](aq) complexes, demonstrating the element sensitivity of the technique to Mg2+-phosphate interactions. The most direct probe of the intermolecular interactions between ATP(aq) and Mg2+(aq) is delivered by the emerging ICD electrons following ionization of Mg 1s electrons. ICD spectra are shown to sensitively probe ligand exchange in the Mg2+-ATP(aq) coordination environment. In addition, we report and compare P 2s data from ATP(aq) and adenosine mono- and diphosphate (AMP(aq) and ADP(aq), respectively) solutions, probing the electronic structure of the phosphate chain and the local environment of individual phosphate units in ATP(aq). Our results provide a comprehensive view of the electronic structure of ATP(aq) and Mg2+-ATP(aq) complexes relevant to phosphorylation and dephosphorylation reactions that are central to bioenergetics in living organisms.

Exploring Ligand-to-Metal Charge-Transfer States in the Photo-Ferrioxalate System Using Excited-State Specific Optimization

The photo-ferrioxalate system (PFS), [Fe(III)(C2O4)]3-, more than an exact chemical actinometer, has been extensively applied in wastewater and environment treatment. Despite many experimental efforts to improve clarity, important aspects of the mechanism of ferrioxalate photolysis are still under debate. In this paper, we employ the recently developed WΓ-CASSCF to investigate the ligand-to-metal charge-transfer states that are key to ferrioxalate photolysis. This investigation provides a qualitative picture of these states and key potential energy surface features related to the photolysis. Our theoretical results are consistent with the prompt charge-transfer picture seen in recent experiments and clarify some features that are not visible in experiments. Two ligand-to-metal charge-transfer states contribute to the photolysis of ferrioxalate, and the avoided crossing barrier between them is low compared with the initial photoexcitation energy. Our data also clarify that one Fe-O bond cleaves first, followed by the C-C bond and the other Fe-O bond.

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.

Fast Method for Excited-State Dynamics in Complex Systems and Its Application to the Photoactivation of a Blue Light Using Flavin Photoreceptor

The excited-state dynamics of molecules embedded in complex (bio)matrices is still a challenging goal for quantum chemical models. Hybrid QM/MM models have proven to be an effective strategy, but an optimal combination of accuracy and computational cost still has to be found. Here, we present a method which combines the accuracy of a polarizable embedding QM/MM approach with the computational efficiency of an excited-state self-consistent field method. The newly implemented method is applied to the photoactivation of the blue-light-using flavin (BLUF) domain of the AppA protein. We show that the proton-coupled electron transfer (PCET) process suggested for other BLUF proteins is still valid also for AppA.

Introduction of a weighting scheme for the X-ray restrained wavefunction approach: advantages and drawbacks

In a quite recent study [Genoni et al. (2017). IUCrJ, 4, 136-146], it was observed that the X-ray restrained wavefunction (XRW) approach allows a more efficient and larger capture of electron correlation effects on the electron density if high-angle reflections are not considered in the calculations. This is due to the occurrence of two concomitant effects when one uses theoretical X-ray diffraction data corresponding to a single-molecule electron density in a large unit cell: (i) the high-angle reflections are generally much more numerous than the low- and medium-angle ones, and (ii) they are already very well described at unrestrained level. Nevertheless, since high-angle data also contain important information that should not be disregarded, it is not advisable to neglect them completely. For this reason, based on the results of the previous investigation, this work introduces a weighting scheme for XRW calculations to up-weight the contribution of low- and medium-angle reflections, and, at the same time, to reasonably down-weight the importance of the high-angle data. The proposed strategy was tested through XRW computations with both theoretical and experimental structure-factor amplitudes. The tests have shown that the new weighting scheme works optimally if it is applied with theoretically generated X-ray diffraction data, while it is not advantageous when traditional experimental X-ray diffraction data (even of very high resolution) are employed. This also led to the conclusion that the use of a specific external parameter λ_J for each resolution range might not be a suitable strategy to adopt in XRW calculations exploiting experimental X-ray data as restraints.

Initial Maximum Overlap Method Embedded with Extremely Localized Molecular Orbitals for Core-Ionized States of Large Systems

Despite great advances in X-ray absorption spectroscopy for the investigation of small molecule electronic structure, the application to biosystems of experimental techniques developed within this research field remains a challenge. To partially circumvent the problem, users resort to theoretical methods to interpret or predict the X-ray absorption spectra of large molecules. To accomplish this task, only low-cost computational strategies can be exploited. For this reason, some of them are single Slater determinant wavefunction approaches coupled with multiscale embedding techniques designed to treat large systems of biological interest. Therefore, in this work, we propose to apply the recently developed IMOM/ELMO embedding method to the determination of core-ionized states. The IMOM/ELMO technique resulted from the combination of the single Slater determinant Δself-consistent-field-initial maximum overlap approach (ΔSCF-IMOM) with the QM/ELMO (quantum mechanics/extremely localized molecular orbital) embedding strategy, a method where only the chemically relevant region of the examined system is treated at fully quantum chemical level, while the rest is described through transferred and frozen extremely localized molecular orbitals (ELMOs). The IMOM/ELMO technique was initially validated by computing core-ionization energies for small molecules, and it was afterwards exploited to study larger biosystems. The obtained results are in line with those reported in previous studies that applied alternative ΔSCF approaches. This makes us envisage a possible future application of the proposed method to the interpretation of X-ray absorption spectra of large molecules.

Spin-Orbit Couplings for Nonadiabatic Molecular Dynamics at the ΔSCF Level

A procedure for the calculation of spin-orbit coupling (SOC) at the delta self-consistent field (ΔSCF) level of theory is presented. Singlet and triplet excited electronic states obtained with the ΔSCF method are expanded into a linear combination of singly excited Slater determinants composed of ground electronic state Kohn-Sham orbitals. This alleviates the nonorthogonality between excited and ground electronic states and introduces a framework, similar to the auxiliary wave function at the time-dependent density functional theory (TD-DFT) level, for the calculation of observables. The ΔSCF observables of the formaldehyde system were compared to reference TD-DFT values. Our procedure gives all components (energies, gradients, nonadiabatic couplings, and SOC terms) at the ΔSCF level of theory for conducting efficient, full-atomistic nonadiabatic molecular dynamics with intersystem crossing, particularly in condensed phase systems.

The ΔSCF method for non-adiabatic dynamics of systems in the liquid phase

Computational studies of ultrafast photoinduced processes give valuable insights into the photochemical mechanisms of a broad range of compounds. In order to accurately reproduce, interpret, and predict experimental results, which are typically obtained in a condensed phase, it is indispensable to include the condensed phase environment in the computational model. However, most studies are still performed in vacuum due to the high computational cost of state-of-the-art non-adiabatic molecular dynamics (NAMD) simulations. The quantum mechanical/molecular mechanical (QM/MM) solvation method has been a popular model to perform photodynamics in the liquid phase. Nevertheless, the currently used QM/MM embedding techniques cannot sufficiently capture all solute-solvent interactions. In this Perspective, we will discuss the efficient ΔSCF electronic structure method and its applications with respect to the NAMD of solvated compounds, with a particular focus on explicit quantum mechanical solvation. As more research is required for this method to reach its full potential, some challenges and possible directions for future research are presented as well.