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.
The dissociation of ligands from proteins and other biomacromolecules occurs over a wide range of timescales. For most pharmaceutically relevant inhibitors, these timescales are far beyond those that are accessible by conventional molecular dynamics (MD) simulation. Consequently, to explore ligand egress mechanisms and compute dissociation rates, it is necessary to enhance the sampling of ligand unbinding. Random Acceleration MD (RAMD) is a simple method to enhance ligand egress from a macromolecular binding site, which enables the exploration of ligand egress routes without prior knowledge of…
We consider the recently developed weighted ensemble milestoning (WEM) scheme [J. Chem. Phys. 152, 234114 (2020)], and test its capability of simulating ligand-receptor dissociation dynamics. We performed WEM simulations on the following host-guest systems: Na$^+$/Cl$^-$ ion pair and 4-hydroxy-2-butanone (BUT) ligand with FK506 binding protein (FKBP). As proof or principle, we show that the WEM formalism reproduces the Na$^+$/Cl$^-$ ion pair dissociation timescale and the free energy profile obtained from long conventional MD simulation. To increase accuracy of WEM calculations applied to kine…
Despite the importance of ligand dissociation energies for computational chemistry, obtaining accurate ab initio reference data is difficult and density-functional methods of uncertain reliability are chosen for feasibility reasons. Here, we consider advanced coupled-cluster and multi-configurational approaches to reinvestigate our WCCR10 set of ten gas-phase ligand dissociation energies. We assess the potential multi-configurational character of all molecules involved in these reactions in order to determine where single-reference coupled-cluster approaches can be applied. For some reactions …
Phosphorylation is one of the most important protein modifications, and electron-transfer dissociation tandem mass spectrometry (ETD-MS/MS) is a potentially useful method for the sequencing of phosphopeptides, including determination of the phosphorylation site. Notably, ETD-MS/MS typically provides useful information when the precursor contains more than three positive charges. It is not yet used as an analysis method for large-scale phosphopeptide production due to difficulties occurring in the production of acidic phosphopeptides having more than three positive charges. To increase the char…
The bonding mechanism of ethene to a nickel or palladium center is studied by the density matrix renormalization group algorithm, the complete active space self consistent field method, coupled cluster theory, and density functional theory. Specifically, we focus on the interaction between the metal atom and bis-ethene ligands in perpendicular and parallel orientations. The bonding situation in these structural isomers is further scrutinized using energy decomposition analysis and quantum information theory. Our study highlights the fact that when two ethene ligands are oriented perpendicular …
Protactinium ($Z$ = 91) is a very rare actinide with peculiar physico-chemical properties. Indeed, although one may naively think that it behaves similarly to either thorium or uranium by its position in the periodic table, it may in fact follow its own rules. Because of the quite small energy gap between its valence shells (in particular the 5$f$ and 6$d$ ones) and also the strong influence of relativistic effects on its properties, it is actually a challenging element for theoretical chemists. In this article, we combine experimental information, chemical arguments and standard first-princip…
Molecular Insights into Yb(III) Speciation in Sulfate-Bearing Hydrothermal Fluids from X-ray Absorption Spectra Informed by ab initio Molecular Dynamics
We present the WCCR10 data set of ten ligand dissociation energies of large cationic transition metal complexes for the assessment of approximate exchange--correlation functionals. We analyze nine popular functionals, namely BP86, BP86-D3, B3LYP, B3LYP-D3, B97-D-D2, PBE, TPSS, PBE0, and TPSSh by mutual comparison and by comparison to experimental gas-phase data measured with well-known precision. The comparison of all calculated data reveals a large, system-dependent scattering of results with nonnegligible consequences for computational chemistry studies on transition metal compounds. Conside…
Coordination chemistry relies on harnessing active metal sites within organic matrices. Polynuclear complexes - consisting of organic ligands binding to clusters of several metal atoms are of particular interest, owing to their electronic/magnetic properties and potential for functional reactivity pathways. However, their synthesis remains challenging; only a limited number of geometries and configurations have been achieved. Here, we synthesise - via supramolecular chemistry on a noble metal surface - one-dimensional metal-organic nanostructures composed of terpyridine (tpy)-based molecules c…
In this contribution I critically revise the alchemical reversible approach in the context of the statistical mechanics theory of non covalent bonding in drug receptor systems. I show that most of the pitfalls and entanglements for the binding free energies evaluation in computer simulations are rooted in the equilibrium assumption that is implicit in the reversible method. These critical issues can be resolved by using a non-equilibrium variant of the alchemical method in molecular dynamics simulations, relying on the production of many independent trajectories with a continuous dynamical evo…
Coordination compounds with tin centre surrounded by both organic and inorganic ligands ([SnI4{(C6H5)3PO}2], [SnI4{(C6H5)2SO}2] and [SnI4(C5H5NO)2]), acting as molecular semiconductors are in the spotlight of this article. This is a new class of hybrid semiconducting materials where optoelectronic properties of inorganic core (SnI4) were tuned by organic ligands. The valence band is located at inorganic part of the molecule while the conduction band is made of carbon-based orbitals. This suggests a great importance of hydrogen bonds where iodine atoms play the role of an acceptor. Weak intermo…
Polonium (Z = 84) is one of the rarest elements on Earth. More than a century after its discovery, its chemistry remains poorly known and even basic questions are not yet satisfactorily addressed. In this work, we perform a systematic study of the geometries, interactions energies and bonding in basic polonium(IV) species, namely the hydrated [Po(H$_2$O)$_n$]$^{4+}$ and chlorinated [PoCl$_n$]$^{4-n}$ complexes by means of gas-phase electronic structure calculations. We show that while up to nine water molecules can fit in the first coordination sphere of the polonium(IV) ion, its coordination …
Test of the Orbital-Based LI3 Index as a Predictor of the Height of the 3MLCT to 3MC Transition-State Barrier for [Ru(N N)3]2+ Polypyridine Complexes in CH3CN
The luminescence properties of the $\mathrm{[UO_2Cl_4]^{2-}}$ complex in an organic phase, especially the influence of large organic counter cations, have been studied by time-resolved laser-induced fluorescence spectroscopy (TRLFS) and ab initio modeling. The experimental spectrum was assigned by vibronic Franck-Condon calculations on quantum chemical models based on relativistic density functional approaches. The shape of the luminescence spectrum of the uranyl tetrachloride complex is determined by symmetrical vibrations and geometrical change upon emission. The possible change of the lumin…
A dispersion-corrected density functional theory study of the photosensitizer [Ir(ppy)$_2$(bpy)]$^+$ and its derivatives bound to silver clusters Ag$_n$ ($n$=2-20, 92) is performed. The goal is to provide a new system-specific set of $C_{\rm 6}^{}$ interaction parameters for Ag and Ir atoms. To this end a QM:QM scheme is employed using the PBE functional and RPA as well as MP2 calculation as a reference. The obtained $C_{\rm 6}^{}$ coefficients were applied to calculate dissociation curves of selected IrPS-Ag$_n$ complexes and binding energies of derivatives containing oxygen and sulphur as he…
Efficient training of generative models from multireference simulations and its application to the design of Dy complexes with large magnetic anisotropy
School of Physics, AMBER and CRANN Institute, Trinity College, Dublin 2, Ireland（都柏林三一学院物理学院、AMBER和CRANN研究所）
Test of the Orbital-Based LI3 Index as a Predictor of the Height of the $^3$MLCT $\rightarrow$ $^3$MC Transition-State Barrier for Gas-Phase [Ru(N$^\wedge$N)$_3$]$^{2+}$ Polypyridine Complexes
The bond dissociation energies of a set of 44 3d transition metal-containing diatomics are computed with phaseless auxiliary-field quantum Monte Carlo (ph-AFQMC) utilizing a correlated sampling technique. We investigate molecules with H, N, O, F, Cl, and S ligands, including those in the 3dMLBE20 database first compiled by Truhlar and co-workers with calculated and experimental values that have since been revised by various groups. In order to make a direct comparison of the accuracy of our ph-AFQMC calculations with previously published results from 10 DFT functionals, CCSD(T), and icMR-CCSD(…
