Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userRenormalization of myoglobin-ligand binding energetics by quantum many-body effects
535
0
0.0
(
0
)
Ask ChatGPT about the research
No Arabic abstract
We carry out a first-principles atomistic study of the electronic mechanisms of ligand binding and discrimination in the myoglobin protein. Electronic correlation effects are taken into account using one of the most advanced methods currently available, namely a linear-scaling density functional theory (DFT) approach wherein the treatment of localized iron 3d electrons is further refined using dynamical mean-field theory (DMFT). This combination of methods explicitly accounts for dynamical and multi-reference quantum physics, such as valence and spin fluctuations, of the 3d electrons, whilst treating a significant proportion of the protein (more than 1000 atoms) with density functional theory. The computed electronic structure of the myoglobin complexes and the nature of the Fe-O2 bonding are validated against experimental spectroscopic observables. We elucidate and solve a long standing problem related to the quantum-mechanical description of the respiration process, namely that DFT calculations predict a strong imbalance between O2 and CO binding, favoring the latter to an unphysically large extent. We show that the explicit inclusion of many body-effects induced by the Hunds coupling mechanism results in the correct prediction of similar binding energies for oxy- and carbonmonoxymyoglobin.
rate research
Read More
Myoglobin modulates the binding of diatomic molecules to its heme group via hydrogen-bonding and steric interactions with neighboring residues, and is an important benchmark for computational studies of biomolecules. We have performed calculations on the heme binding site and a significant proportion of the protein environment (more than 1000 atoms) using linear-scaling density functional theory and the DFT+U method to correct for self-interaction errors associated with localized 3d states. We confirm both the hydrogen-bonding nature of the discrimination effect (3.6 kcal/mol) and assumptions that the relative strain energy stored in the protein is low (less than 1 kcal/mol). Our calculations significantly widen the scope for tackling problems in drug design and enzymology, especially in cases where electron localization, allostery or long-ranged polarization influence ligand binding and reaction.
We recently introduced [J. Chem. Phys. 152 2020, 204103] the nuclear-electronic all-particle density matrix renormalization group method (NEAP-DMRG) to solve the molecular Schr{o}dinger equation, based on a stochastically optimized orbital basis, without invoking the Born-Oppenheimer approximation. In this work, we combine the DMRG with nuclear-electronic Hartree-Fock (NEHF-DMRG), treating nuclei and electrons on the same footing. Inter- and intra-species correlations are described within the DMRG without truncating the excitation degree of the full configuration interaction wave function. We extend the concept of orbital entanglement and mutual information to nuclear-electronic wave functions and demonstrate that they are reliable metrics to detect strong correlation effects. We apply NEHF-DMRG to the HeHHe$^+$ molecular ion, to obtain accurate proton densities, ground-state total energies, and vibrational transition frequencies by comparison with state-of-the-art data obtained with grid-based approaches and modern configuration interaction methods. For HCN, we improve on the accuracy of the latter approaches with respect to both ground-state absolute energy and proton density which is a major challenge for multi-reference nuclear-electronic state-of-the-art methods.
We propose a mechanism for binding of diatomic ligands to heme based on a dynamical orbital selection process. This scenario may be described as bonding determined by local valence fluctuations. We support this model using linear-scaling first-principles calculations, in combination with dynamical mean-field theory, applied to heme, the kernel of the hemoglobin metalloprotein central to human respiration. We find that variations in Hunds exchange coupling induce a reduction of the iron 3d density, with a concomitant increase of valence fluctuations. We discuss the comparison between our computed optical absorption spectra and experimental data, our picture accounting for the observation of optical transitions in the infrared regime, and how the Hunds coupling reduces, by a factor of five, the strong imbalance in the binding energies of heme with CO and O_2 ligands.
Coupling a quantum many-body system to an external environment dramatically changes its dynamics and offers novel possibilities not found in closed systems. Of special interest are the properties of the steady state of such open quantum many-body systems, as well as the relaxation dynamics towards the steady state. However, new computational tools are required to simulate open quantum many-body systems, as methods developed for closed systems cannot be readily applied. We review several approaches to simulate open many-body systems and point out the advances made in recent years towards the simulation of large system sizes.
Transition metal complexes are ubiquitous in biology and chemical catalysis, yet they remain difficult to accurately describe with ab initio methods due to the presence of a large degree of dynamic electron correlation, and, in some cases, strong static correlation which results from a manifold of low-lying states. Progress has been hindered by a scarcity of high quality gas-phase experimental data, while exact ab initio predictions are usually computationally unaffordable due to the large size of the systems. In this work, we present a data set of 34 3d metal-containing complexes with gas-phase ligand-dissociation energies that have reported uncertainties of $leq$ 2 kcal/mol. We perform all-electron phaseless auxiliary-field quantum Monte Carlo (ph-AFQMC) utilizing multi-determinant trial wavefunctions selected by a blackbox procedure. We compare the results with those from DFT with various functionals, and DLPNO-CCSD(T). We find MAE of 1.09 $pm$ 0.28 kcal/mol for our best ph-AFQMC method, vs 2.89 kcal/mol for DLPNO-CCSD(T) and 1.57 - 3.87 kcal/mol for DFT. We find maximum errors of 2.96 $pm$ 1.71 kcal/mol for our best ph-AFQMC method, vs 9.15 kcal/mol for DLPNO-CCSD(T) and 5.98 - 13.69 kcal/mol for DFT. The reasonable performance of several functionals is in stark contrast to the much poorer accuracy previously demonstrated for diatomics, suggesting a moderation in electron correlation due to ligand coordination. However, the unpredictably large errors for a small subset of cases with both DFT and DLPNO-CCSD(T) leave cause for concern, especially due to the unreliability of common multi-reference indicators. In contrast, the robust and, in principle, systematically improvable results of ph-AFQMC for these realistic complexes establish it as a useful tool for elucidating the electronic structure of transition metal-containing complexes and predicting their gas-phase properties.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
