Toward Post-Hartree-Fock Accuracy for Protein-Ligand Affinities Using the Molecules-in-Molecules Fragmentation-Based Method.

The complexity and size of large molecular systems, such as protein-ligand complexes, pose computational challenges for accurate post-Hartree-Fock calculations. This study delivers a thorough benchmarking of the Molecules-in-Molecules (MIM) method, presenting a clear and accessible strategy for layer/theory selections in post-Hartree-Fock computations on substantial molecular systems, notably protein-ligand complexes. An approach is articulated, enabling augmented computational efficiency by strategically canceling out common subsystem energy terms between complexes and proteins within the supermolecular equation. Employing DLPNO-based post-Hartree-Fock methods in conjunction with the three-layer MIM method (MIM3), this study demonstrates the achievement of protein-ligand binding energies with remarkable accuracy (errors <1 kcal mol-1), while significantly reducing computational costs. Furthermore, noteworthy correlations between theoretically computed interaction energies and their experimental equivalents were observed, with R2 values of approximately 0.90 and 0.78 for CDK2 and BZT-ITK sets, respectively, thus validating the efficacy of the MIM method in calculating binding energies. By highlighting the crucial role of diffuse or small Pople-style basis sets in the middle layer for reducing energy errors, this work provides valuable insights and practical methodologies for interaction energy computations in large molecular complexes and opens avenues for their application across a diverse range of molecular systems.

Vibrational Analysis of Constrained Molecular Systems.

Vibrational spectroscopy, including infrared (IR), Raman spectroscopy, and vibrational circular dichroism, is instrumental in determining the structure and composition of molecules. These techniques are highly sensitive to molecular conformations. However, full molecular optimization, necessary for theoretical vibrational spectra, can lead to unintended conformational changes, especially in large biomolecules like polypeptides. To address this, dihedral angle constraints can be imposed during optimization to preserve the molecule's native conformation. Constraint-optimized molecular geometries, not being true stationary points in the full configurational space, pose challenges for traditional vibrational analysis. We address this by considering such geometries as subspace minima, reformulating vibrational analysis to incorporate constraints. Normal modes and spectra consistent with these constraints are obtained by projecting the force constant matrix onto a space orthogonal to the constrained coordinates. This method, illustrated by the example of enkephalin, yields 3N - 6 - m nonzero frequencies after constraint projection, demonstrating its applicability to biomolecules with flexible conformations. Our approach offers a comprehensive mathematical framework to compute vibrational spectra of molecules with conformationally flexible subunits under environmental constraints.

14 examples of how LLMs can transform materials science and chemistry: a reflection on a large language model hackathon.

Large-language models (LLMs) such as GPT-4 caught the interest of many scientists. Recent studies suggested that these models could be useful in chemistry and materials science. To explore these possibilities, we organized a hackathon. This article chronicles the projects built as part of this hackathon. Participants employed LLMs for various applications, including predicting properties of molecules and materials, designing novel interfaces for tools, extracting knowledge from unstructured data, and developing new educational applications. The diverse topics and the fact that working prototypes could be generated in less than two days highlight that LLMs will profoundly impact the future of our fields. The rich collection of ideas and projects also indicates that the applications of LLMs are not limited to materials science and chemistry but offer potential benefits to a wide range of scientific disciplines.

Tris(carbene)borates; alternatives to cyclopentadienyls in organolanthanide chemistry.

The chemistry of the tris-carbene anion phenyltris(3-alkyl-imidazoline-2-yliden-1-yl)borate, [C3Me]- ligand, is initiated for f-block metal cations. Neutral, molecular complexes of the form Ln(C3)2I are formed for cerium(III), while a separated ion pair [Ln(C3)2]I forms for ytterbium(III). DFT/QTAIM computational analyses of the complexes and related tridentate tris(pyrazolyl)borate (Tp) - supported analogs demonstrates the anticipated strength of the σ donation and confirms greater covalency in the metal-carbon bonds of the [C3Me]- complexes in comparison with those in the TpMe,Me complexes. The DFT calculations demonstrate the crucial role of THF solvent in accurately reproducing the contrasting molecular and ion-pair geometries observed experimentally for the Ce and Yb complexes.

Interaction-Deletion: A Composite Energy Method for the Optimization of Molecular Systems Selectively Removing Specific Nonbonded Interactions.

The complex interactions between different portions of a large molecule can be challenging to analyze through traditional electronic structure calculations. Moreover, standard methods cannot easily quantify the physical consequences of individual pairwise interactions inside a molecule. By creating a set of molecular fragments, we propose a composite energy method to explore changes in a molecule caused by removing selected nonbonded interactions between different molecular portions. Energies and forces are easily obtained with this composite approach, allowing geometry optimizations that lead to chemically meaningful structures that describe how the omitted interactions contribute to changes in the local geometrical minima. We illustrate the application of our new hybrid scheme by computing the influence of intramolecular hydrogen-bonding interactions in two small molecules: 1,6-(tG+G+TG+G+g-)-hexanediol and a cyclic analogue, cis-1,4-cyclohexanediol. The resulting structural and energetic changes are interpreted to yield key physical insights and quantify concepts such as "preparation energy" or "reorganization energy". We demonstrate that the composite method can be extended to larger molecular systems by showing its application on a Si(100) surface model containing interactions between dissociated ammonia molecules on adjacent surface dimers. The scheme's efficacy is also tested by applying it to systems having multiple intramolecular interactions, viz., 310-polyglycine and H+GPGG. Furthermore, the cooperative nature of intramolecular hydrogen bonds is explored by using interaction-deletion in 2-nitrobenzene-1,3-diol.

The striking influence of oxophilicity differences in heterometallic Mo-Mn oxide cluster reactions with water.

Mixed-metal oxides have proven to be effective catalysts for the hydrogen evolution reaction, often outperforming either of the binary metal oxides. The reactivity of MnxMoOy - (x = 1, 2; y = 3, 4) clusters toward H2O was investigated via time-of-flight mass spectrometry with clear evidence of cluster oxidation and corresponding H2 production, specifically for MnxMoO3 - (x = 1, 2) clusters. Unlike previously studied MoxOy - clusters, which assumed a broad distribution of stoichiometries (typically x ≤ y ≤ 3x), both MnMoOy - and Mn2MoOy - preferentially formed y = 3 and 4 compositions in significant quantities under our source conditions. The electronic and molecular structures of the MnxMoOy (x = 1, 2; y = 3, 4) anion and neutral clusters were probed with anion photoelectron spectroscopy and analyzed with supporting density functional theory calculations. Our studies suggest that both metal centers are involved in initial cluster-water complex formation, while Mo is the center that undergoes oxidation; hence, reactivity terminates when Mo is saturated in its highest oxidation state of +6. Across these four clusters, Mn remains relatively reduced and is stable in a high-spin electronic configuration. The preferential reactivity of water molecules toward the Mo center rather than Mn is rationalized by the much lower relative oxophilicity of Mn.

Mo Insertion into the H2 Bond in MoxSy- + H2 Reactions.

A combined experimental and computational study of H2 reactions with small 98MoxSy- clusters ranging from subsulfide (x ∼ y) to hypersulfide (y > 2x) is presented. Results suggest that the subsulfides react with H2 primarily by insertion of a more reduced Mo center into the H-H bond, forming a dihydride product. We find that this reaction occurs up to Mo oxidation states of +4. For the subsulfides containing a second metal in a sufficiently low oxidation state, a second insertion of H2 occurs, leading to a tetrahydride product. The reaction mechanisms of the sulfides are found to be very similar, albeit slightly higher energetically to those of the analogous oxosulfides that are also observed at low abundances in the experiments. In addition, the experimental results show an overall reduction of hypersulfides in the presence of H2, suggesting loss of H2S neutral molecules.