Rhenium Corrole Dimers: Electrochemical Insights into the Nature of the Metal–Metal Quadruple Bond
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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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Accessing One-Dimensional Chains of Halogenoindates(III) in Organic–Inorganic Hybrids
Organic-inorganic hybrids of halogenoindates(III) are typically represented by one of the zero-dimensional units: InX 4 – , InX 5 2– , InX 6 3– , or In 2 X 11 5– . Higher dimensional anionic forms, although not forbidden, have remained almost elusive. Here, in this study, we report for the first time In 3+ -based organic–inorganic hybrids, (C 4 H 5 N 2 S) 2 InCl 5 and (C 4 H 5 N 2 S) 2 InBr 5 , with 1D anionic chains of trans-halide-bridged InX 6 octahedra whose formation is guided by 2-mercaptopyrimidinium cations (C 4 H 5 N 2 S + ). The chains are characterized by the significant ease of deformation, which is reflected in the elongation of the bridging bonds or the displacement of In 3+ ions. The materials show a robust band gap predominantly governed by C 4 H 5 N 2 S + cations. Dielectric relaxation processes in (C 4 H 5 N 2 S) 2 InBr 5 arise from the cations’ dynamics and suggest the ability of the brominated system to accommodate even larger cations. Our work represents a successful attempt to expand the structural diversity of halogenoindates(III) and opens a pathway to reach multifunctional 1D In 3+ -based hybrids.
36 MATERIALS SCIENCE↗
The Influence of Phosphorus Substituents on the Structures and Solution Speciation of Trivalent Uranium and Lanthanide Phosphinodiboranates
Not Available
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
All-Atom Simulations Uncover Structural and Dynamical Properties of STING Proteins in the Membrane System
Recent studies have shown that the stimulator of interferon gene (STING) protein plays a central role in the immune system by facilitating the production of type I interferons in cells. The STING signaling pathway is also a prominent activator of cancer-killing T cells that initiate a powerful adaptive immune response. Since biomolecular signaling pathways are complicated and not easily identified through traditional experiments, molecular dynamics (MD) has often been used to study structural and dynamical responses of biological pathways. In this work, we carried out MD simulations for full-length chicken and human STING (chSTING and hSTING) proteins. Specifically, we investigated ligand-bound closed (holo) and ligand-unbound open (apo) forms of STING in the membrane system by comparing their conformational and dynamical differences. Our research provides clues for understanding the mechanism of the STING signaling pathway by uncovering detailed insights for the examined systems: the residues from each chain in the binding pocket are strongly correlated to one another in the open STING structure compared with those in the closed STING structure. Ligand-bound closed STING displays ~174° rotation of the ligand-binding domain (LBD) relative to the open STING structure. The dynamical analysis of residue Cys148 located in the linker region of hSTING does not support the earlier hypothesis that Cys148 can form disulfide bonds between adjacent STING dimers. We also demonstrate that using the full-length proteins is critical, since the MD simulations of the LBD portion alone cannot properly describe the global conformational properties of STING.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2
Direct-acting antivirals for the treatment of the COVID-19 pandemic caused by the SARS-CoV-2 virus are needed to complement vaccination efforts. Given the ongoing emergence of new variants, automated experimentation, and active learning based fast workflows for antiviral lead discovery remain critical to our ability to address the pandemic’s evolution in a timely manner. While several such pipelines have been introduced to discover candidates with noncovalent interactions with the main protease (M pro ), here we developed a closed-loop artificial intelligence pipeline to design electrophilic warhead-based covalent candidates. Here, this work introduces a deep learning-assisted automated computational workflow to introduce linkers and an electrophilic “warhead” to design covalent candidates and incorporates cutting-edge experimental techniques for validation. Using this process, promising candidates in the library were screened, and several potential hits were identified and tested experimentally using native mass spectrometry and fluorescence resonance energy transfer (FRET)-based screening assays. We identified four chloroacetamide-based covalent inhibitors of M pro with micromolar affinities (K I of 5.27 μM) using our pipeline. Experimentally resolved binding modes for each compound were determined using room-temperature X-ray crystallography, which is consistent with the predicted poses. The induced conformational changes based on molecular dynamics simulations further suggest that the dynamics may be an important factor to further improve selectivity, thereby effectively lowering KI and reducing toxicity. These results demonstrate the utility of our modular and data-driven approach for potent and selective covalent inhibitor discovery and provide a platform to apply it to other emerging targets.
60 APPLIED LIFE SCIENCES↗
Method for accurately predicting solvation structure
Accurately predicting the molecular structure of solutions is a fundamental scientific challenge. Using quantum mechanical density functional theory (DFT) to make these predictions is hindered by significant variation depending on which DFT functional is used. Here, we present a simple metric that can determine the reliability of a DFT functional for predicting solvation structure. We then show that including a simple interaction term to correct this metric leads to quantitative agreement with experimental measurements of liquid structure. We demonstrate the utility of this method by using it to accurately describe the hydration structure around the Na+ a
basis sets, molecular structure, cluster chemistry↗
Atomistic Characterization of Gramicidin Channel Formation
We investigated gramicidin A (gA) subunit dimerization in lipid bilayers using microsecond-long replica-exchange umbrella sampling simulations, millisecond-long unbiased molecular dynamics simulations, and machine learning. Our simulations led to a dimer structure that is indistinguishable from the experimentally determined gA channel structures, with the two gA subunits joined by six hydrogen bonds (6HB). The simulations also uncovered two additional dimer structures, with different gA–gA stacking orientations that were stabilized by four or two hydrogen bonds (4HB or 2HB). When examining the temporal evolution of the dimerization, we found that two bilayer-inserted gA subunits can form the 6HB dimer directly, with no discernible intermediate states, as well as through paths that involve the 2HB and 4HB dimers.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Polarizable Water Potential Derived from a Model Electron Density
A new empirical potential for efficient, large scale molecular dynamics simulation of water is presented. The HIPPO (Hydrogen-like Intermolecular Polarizable POtential) force field is based upon the model electron density of a hydrogen-like atom. This framework is used to derive and parametrize individual terms describing charge penetration damped permanent electrostatics, damped polarization, charge transfer, anisotropic Pauli repulsion, and damped dispersion interactions. Initial parameter values were fit to Symmetry Adapted Perturbation Theory (SAPT) energy components for ten water dimer configurations, as well as the radial and angular dependence of the canonical dimer. The SAPT-based parameters were then systematically refined to extend the treatment to water bulk phases. The final HIPPO water model provides a balanced representation of a wide variety of properties of gas phase clusters, liquid water, and ice polymorphs, across a range of temperatures and pressures. This water potential yields a rationalization of water structure, dynamics, and thermodynamics explicitly correlated with an ab initio energy decomposition, while providing a level of accuracy comparable or superior to previous polarizable atomic multipole force fields. The HIPPO water model serves as a cornerstone around which similarly detailed physics-based models can be developed for additional molecular species.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Comprehensive Basis-Set Testing of Extended Symmetry-Adapted Perturbation Theory and Assessment of Mixed-Basis Combinations to Reduce Cost
Hybrid or “extended” symmetry-adapted perturbation theory (XSAPT) replaces traditional SAPT’s treatment of dispersion with better performing alternatives while at the same time extending two-body (dimer) SAPT to a many-body treatment of polarization using a self-consistent charge embedding procedure. The present work presents a systematic study of how XSAPT interaction energies and energy components converge with respect to the choice of Gaussian basis set. Errors can be reduced in a systematic way using correlation-consistent basis sets, with aug-cc-pVTZ results converged within <0.1 kcal/mol. Similar (if slightly less systematic) behavior is obtained using Karlsruhe basis sets at much lower cost, and we introduce new versions with limited augmentation that are even more efficient. Pople-style basis sets, which are more efficient still, often afford good results if a large number of polarization functions are included. The dispersion models used in XSAPT afford much faster basis-set convergence as compared to the perturbative description of dispersion in conventional SAPT, meaning that “compromise” basis sets (such as jun-cc-pVDZ) are no longer required and benchmark-quality results can be obtained using triple-ζ basis sets. The use of diffuse functions proves to be essential, especially for the description of hydrogen bonds. As a result, the “δ(Hartree–Fock)” correction for high-order induction can be performed in double-ζ basis sets without significant loss of accuracy, leading to a mixed-basis approach that offers 4× speedup over the existing (cubic scaling) XSAPT approach.
74 ATOMIC AND MOLECULAR PHYSICS↗
Systematic Evaluation of Counterpoise Correction in Density Functional Theory
A widespread belief persists that the Boys–Bernardi function counterpoise (CP) procedure “overcorrects” supramolecular interaction energies for the effects of basis-set superposition error. To the extent that this is true for correlated wave function methods, it is usually an artifact of low-quality basis sets. The question has not been considered systematically in the context of density functional theory, however, where basis-set convergence is generally less problematic. We present a systematic assessment of the CP procedure for a representative set of functionals and basis sets, considering both benchmark data sets of small dimers and larger supramolecular complexes. The latter include layered composite polymers with ~150 atoms and ligand–protein models with ~300 atoms. Provided that CP correction is used, we find that intermolecular interaction energies of nearly complete-basis quality can be obtained using only double-ζ basis sets. Furthermore, this is less expensive as compared to triple-ζ basis sets without CP correction. CP-corrected interaction energies are less sensitive to the presence of diffuse basis functions as compared to uncorrected energies, which is important because diffuse functions are expensive and often numerically problematic for large systems. Our results upend the conventional wisdom that CP “overcorrects” for basis-set incompleteness. In small basis sets, CP correction is mandatory in order to demonstrate that the results do not rest on error cancellation.
74 ATOMIC AND MOLECULAR PHYSICS↗
Porting Fragmentation Methods to Graphical Processing Units Using an OpenMP Application Programming Interface: Offloading the Fock Build for Low Angular Momentum Functions
Here, a framework to offload four-index two-electron repulsion integrals to graphical processing units (GPUs) using OpenMP is discussed. The method has been applied to the Fock build for low angular momentum s and p functions in both the restricted Hartree–Fock (RHF) and in the effective fragment molecular orbital (EFMO) framework. Benchmark calculations for the GPU code for the pure RHF method show an increasing speedup relative to the existing OpenMP CPU code in GAMESS from 1.04 to 52× for clusters of 70–569 water molecules. The parallel efficiency on 24 NVIDIA V100 GPU boards also increases when increasing the system size: from 75 to 94% for water clusters that contain 303–1120 molecules. In the EFMO framework, the GPU Fock build shows a high linear scalability up to 4608 V100s with a parallel efficiency of 96% for calculations on a solvated mesoporous silica nanoparticle system with ~67,000 basis functions.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Stochastic Real-Time Second-Order Green’s Function Theory for Neutral Excitations in Molecules and Nanostructures
We present a real-time second-order Green’s function (GF) method for computing excited states in molecules and nanostructures, with a computational scaling of O(N e 3 ), where N e is the number of electrons. The cubic scaling is achieved by adopting the stochastic resolution of the identity to decouple the 4-index electron repulsion integrals. To improve the time propagation and the spectral resolution, we adopt the dynamic mode decomposition technique and assess the accuracy and efficiency of the combined approach for a chain of hydrogen dimer molecules of different lengths. We find that the stochastic implementation accurately reproduces the deterministic results for the electronic dynamics and excitation energies. Furthermore, we provide a detailed analysis of the statistical errors, bias, and long-time extrapolation. Overall, the approach offers an efficient route to investigate excited states in extended systems with open or closed boundary conditions.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Comparative Density Functional Theory Study of Magnetic Exchange Couplings in Dinuclear Transition-Metal Complexes
Multicenter transition-metal complexes (MCTMs) with magnetically interacting ions have been proposed as components for information-processing devices and storage units. For any practical application of MCTMs as magnetic units, it is crucial to characterize their magnetic behavior, and in particular, the isotropic magnetic exchange coupling, J, between its magnetic centers. Due to the large size of typical MCTMs, density functional theory is the only practical electronic structure method for evaluating the J coupling. Here, we assess the accuracy of different density functional approximations for predicting the magnetic couplings of eight dinuclear transition-metal complexes, including five dimanganese, two dicopper, and one divanadium with known reliable experimental J couplings spanning from ferromagnetic to strong antiferromagnetic. The density functionals considered include global hybrid functionals which mix semilocal density functional approximations and exact exchange with a fixed admixing parameter, six local hybrid functionals where the admixing parameters are extended to be spatially dependent, the SCAN and r 2 SCAN meta-generalized gradient approximations (GGAs), and two widely used GGAs. We found that global hybrids tested in this work have a tendency to over-correct the error in magnetic coupling parameters from the Perdew–Burke–Ernzerhof (PBE) GGA as seen for manganese complexes. The performance of local hybrid density functionals shows no improvement in terms of bias and is scattered without a clear trend, suggesting that more efforts are needed for the extension from global to local hybrid density functionals for this particular property. The SCAN and r 2 SCAN meta-GGAs are found to perform as well as benchmark global hybrids on most tested complexes. We further analyze the charge density redistribution of meta-GGAs as well as global and local hybrid density functionals with respect to that of PBE, in connection to the self-interaction error or delocalization error.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Møller–Plesset and Density-Fixed Adiabatic Connections for a Model Diatomic System at Different Correlation Regimes
In recent years, adiabatic connection (AC) interpolations developed within density functional theory (DFT) have been found to provide good performances in the calculation of interaction energies when used with Hartree–Fock (HF) ingredients. The physical and mathematical reasons for such unanticipated performance have been clarified, to some extent, by studying the strong-interaction limit of the Møller–Plesset (MP) AC. In this work, we calculate both the MP and the DFT AC integrand for the asymmetric Hubbard dimer, which allows for a systematic investigation of different correlation regimes by varying two simple parameters in the Hamiltonian: the external potential, Δv, and the interaction strength, U. Notably, we find that, while the DFT AC integrand appears to be convex in the full parameter space, the MP integrand may change curvature twice. Furthermore, we discuss different aspects of the second-order expansion of the correlation energy in each AC, and we demonstrate why the derivative of the λ-dependent density in the MP AC at λ = 0 (i.e., at the HF density) is zero in the model. Concerning the strong-interaction limit of both ACs in the Hubbard dimer setting, we show that the asymptotic value of the MP AC, W ∞ HF , is lower than (or equal to) its DFT analogue, W ∞ KS , if the two are compared at a given density, just like in real space. Furthermore, we also show that this is not always the case if the two quantities are compared at a given external potential.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
The Effective Fragment Molecular Orbital Method: Achieving High Scalability and Accuracy for Large Systems
The effective fragment molecular orbital (EFMO) method has been developed to predict the total energy of a very large molecular system accurately (with respect to the underlying quantum mechanical method) and efficiently by taking advantage of the locality of strong chemical interactions and employing a two-level hierarchical parallelism. The accuracy of the EFMO method is partly attributed to the accurate and robust intermolecular interaction prediction between distant fragments, in particular, the many-body polarization and dispersion effects, which require the generation of static and dynamic polarizability tensors by solving the coupled perturbed Hartree–Fock (CPHF) and time-dependent HF (TDHF) equations, respectively. Solving the CPHF and TDHF equations is the main EFMO computational bottleneck due to the inefficient (serial) and I/O-intensive implementation of the CPHF and TDHF solvers. In this work, the efficiency and scalability of the EFMO method are significantly improved with a new CPU memory-based implementation for solving the CPHF and TDHF equations that are parallelized by either message passing interface (MPI) or hybrid MPI/OpenMP. Here, the accuracy of the EFMO method is demonstrated for both covalently bonded systems and noncovalently bound molecular clusters by systematically examining the effects of basis sets and a key distance-related cutoff parameter, R cut . R cut determines whether a fragment pair (dimer) is treated by the chosen ab initio method or calculated using the effective fragment potential (EFP) method (separated dimers). Decreasing the value of Rcut increases the number of separated (EFP) dimers, thereby decreasing the computational effort. It is demonstrated that excellent accuracy (<1 kcal/mol error per fragment) can be achieved when using a sufficiently large basis set with diffuse functions coupled with a small R cut value. With the new parallel implementation, the total EFMO wall time is substantially reduced, especially with a high number of MPI ranks. Given a sufficient workload, nearly ideal strong scaling is achieved for the CPHF and TDHF parts of the calculation. For the first time, EFMO calculations with the inclusion of long-range polarization and dispersion interactions on a hydrated mesoporous silica nanoparticle with explicit water solvent molecules (more than 15k atoms) are achieved on a massively parallel supercomputer using nearly 1000 physical nodes. In addition, EFMO calculations on the carbinolamine formation step of an amine-catalyzed aldol reaction at the nanoscale with explicit solvent effects are presented.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NOCI-F Electronic Couplings in Assemblies of Indolonaphthyridine Molecules: From Dimers to the Full Stack
Key electronic processes related to molecular excitonic states of finite stacks of indolonaphthyridine molecules are analyzed via the non-orthogonal configuration interaction with fragments (NOCI-F) method. Indolonaphthyridine is an organic chromophore that can undergo several electronic photoexcitation-related intermolecular processes, such as exciton and electron transfer. The structures studied here are noncrystalline arrangements built as either ordered stacks of indolonaphthyridine or stacks extracted from molecular dynamics simulations including thermal disorder. Taking dimers or trimers from either model, we performed CASSCF and NOCI-F calculations to quantify the intermolecular electronic couplings governing singlet fission, excited singlet and triplet diffusion, and hole and electron diffusion processes. Also, comparing the results for the different models, we studied the effect of structural disorder and distortion on these couplings. Finally, we present a newly developed, advanced postanalysis tool. It takes the NOCI-F data as input to carry out a multifragment full Hamiltonian procedure that involves the complete stack, providing physical information not available from the dimer/trimer models, hence giving access to additional insight into the material’s properties.
coupling reactions↗
Diabatization with Electrostatic Embedding for Studying Photophysics in Organic Molecular Crystals
Highly emissive organic molecular crystals find applications in several areas, such as organic electronics, solar cells, and sensors. Understanding the excited-state mechanisms underlying these applications is essential for optimizing and controlling them effectively. Exciton models coupled with nonadiabatic dynamics, particularly quantum dynamics, provide crucial insights into photochemical and photophysical processes in molecular crystals. Nevertheless, there remains a lack of general tools and automated workflows to facilitate such simulations. In this paper, we present a computational strategy to investigate the photoactivated dynamics of organic molecular crystals, bridging methodologies traditionally used for molecular systems and materials science, with a particular focus on the interplay between local excitations and charge transfer (CT) processes. We have implemented an interface between the fromage and Overdia programs, enabling the construction of vibronic Hamiltonians for molecular crystals within an excited-state ONIOM(QM:QM′) framework, incorporating long-range electrostatics through a RESP-based Ewald summation. Fragment-based diabatization provides a route to quantum dynamics simulations in weak-to-intermediate coupling regimes. The method was applied to the photophysics of dibenzo[g,p]chrysene (DBC) crystals using time-dependent DFT. The fromage/ Overdia interface was employed to compute the couplings of local excitations and CT states for 18 unique DBC dimers in the crystal and to quantify the influence of electrostatic embedding, which was found to be modest (10−20%). Simulations on π-stacked dimers reproduced the small red shift observed experimentally from solution to crystal, attributed to electronic interactions among fixed monomers rather than crystal electrostatics. Quantum dynamics simulations revealed ultrafast population transfer from bright local excitations to CT states. This approach establishes a robust framework linking molecular and solid-state excited-state dynamics, with potential applications for studying excitations, defects, and impurities in molecular crystals.
Crystals↗
Linear-Scaling Asymmetric Triples Correction through the Solution of the DLPNO–CCSD Lambda Equations: DLPNO–CCSD(T) Λ
In this research, we derive equations for solving for the stationary points of the DLPNO–CCSD Lagrangian, in the t 1 -transformed formalism introduced earlier and as currently implemented in the P SI 4 quantum chemistry software package. These lambda equations in the local pair natural orbital basis allow for the evaluation of CCSD(T) Λ energetics with linear-scaling computational effort, also known as the asymmetric triples correction. This DLPNO–CCSD(T) Λ method allows for accurate triples contributions to be computed for larger molecules, especially in cases that CCSD(T) is known to be insufficient, such as with multireference systems and bond-breaking systems. We showcase the accuracy of our code on reaction energies, barrier heights, and noncovalent interaction energies. Also showcased are the capabilities of our code by evaluating DLPNO–CCSD(T) Λ energetics on large noncovalent dimers up to 112 atoms, as well as a rhodium catalyst complex containing 66 atoms.
Cluster chemistry↗