Journal of Computational Chemistry

doi: 10.1002/jcc.27155pmid: N/A

Sridharan, Bhuvanesh; Sinha, Animesh; Bardhan, Jai; Modee, Rohit; Ehara, Masahiro; Priyakumar, U. Deva

doi: 10.1002/jcc.27354pmid: 38698628

Reinforcement learning (RL) has been applied to various domains in computational chemistry and has found wide‐spread success. In this review, we first motivate the application of RL to chemistry and list some broad application domains, for example, molecule generation, geometry optimization, and retrosynthetic pathway search. We set up some of the formalism associated with reinforcement learning that should help the reader translate their chemistry problems into a form where RL can be used to solve them. We then discuss the solution formulations and algorithms proposed in recent literature for these problems, the advantages of one over the other, together with the necessary details of the RL algorithms they employ. This article should help the reader understand the state of RL applications in chemistry, learn about some relevant actively‐researched open problems, gain insight into how RL can be used to approach them and hopefully inspire innovative RL applications in Chemistry.

Devereux, Mike; Boittier, Eric D.; Meuwly, Markus

doi: 10.1002/jcc.27367pmid: 38695412

The impact of targeted replacement of individual terms in empirical force fields is quantitatively assessed for pure water, dichloromethane (CH 2Cl 2), and solvated K + and Cl − ions. For the electrostatic interactions, point charges (PCs) and machine learning (ML)‐based minimally distributed charges (MDCM) fitted to the molecular electrostatic potential are evaluated together with electrostatics based on the Coulomb integral. The impact of explicitly including second‐order terms is investigated by adding a fragment molecular orbital (FMO)‐derived polarization energy to an existing force field, in this case CHARMM. It is demonstrated that anisotropic electrostatics reduce the RMSE for water (by 1.4 kcal/mol), CH 2Cl 2 (by 0.8 kcal/mol) and for solvated Cl − clusters (by 0.4 kcal/mol). An additional polarization term can be neglected for CH 2Cl 2 but further improves the models for pure water (by ∼1.0 kcal/mol) and hydrated Cl − (by 0.4 kcal/mol), and is key for solvated K +, reducing the RMSE by 2.3 kcal/mol. A 12‐6 Lennard‐Jones functional form performs satisfactorily with PC and MDCM electrostatics, but is not appropriate for descriptions that account for the electrostatic penetration energy. The importance of many‐body contributions is assessed by comparing a strictly 2‐body approach with self‐consistent reference data. Two‐body interactions suffice for CH 2Cl 2 whereas water and solvated K + and Cl − ions require explicit many‐body corrections. Finally, a many‐body‐corrected dimer potential energy surface exceeds the accuracy attained using a conventional empirical force field, potentially reaching that of an FMO calculation. The present work systematically quantifies which terms improve the performance of an existing force field and what reference data to use for parametrizing these terms in a tractable fashion for ML fitting of pure and heterogeneous systems.

Ferreira, Bruna R.; Martins, Francisco A.; Freitas, Matheus P.

doi: 10.1002/jcc.27368pmid: 38695838

Compounds containing the thiophene moiety find several applications in physics and chemistry, such as electrical conduction, which depends on specific conformations to properly exhibiting the desired properties. In turn, chalcogen bonding has found to modulate the conformation of some N‐thiophen‐2‐ylfomamides. Since halogens participate in a kin interaction (halogen bonding) and are abundant in agrochemicals, pharmaceuticals, and materials, we have quantum‐chemically explored the interaction between organic halogen and thiophene as a conformational modulator in some model compounds. Although such interaction indeed appears, as demonstrated by atoms in molecules and natural bond orbital analysis, it is inefficient to control the conformational equilibrium. An energy decomposition analysis scheme demonstrated that halomethane and thiophene tend to move away from one another due to a core component (Pauli repulsion and exchange), which is mainly due to a deformation term. Therefore, chalcogen bonds with halogens appear weaker than with other chalcogens.

Boyd, Russell J.

doi: 10.1002/jcc.27383pmid: 38700431

Deng, Zhihao; Liu, Chang; Li, Zhongwei; Zhang, Yingsheng

doi: 10.1002/jcc.27386pmid: 38703182

In symmetry‐adapted perturbation theory (SAPT), accurate calculations on non‐covalent interaction (NCI) for large complexes with more than 50 atoms are time‐consuming using large basis sets. More efficient ones with smaller basis sets usually result in poor prediction in terms of dispersion and overall energies. In this study, we propose two composite methods with baseline calculated at SAPT2/aug‐cc‐pVDZ and SAPT2/aug‐cc‐pVTZ with dispersion term corrected at SAPT2+ level using bond functions and smaller basis set with δMP2 corrections respectively. Benchmark results on representative NCI data sets, such as S22, S66, and so forth, show significant improvements on the accuracy compared to the original SAPT Silver standard and comparable to SAPT Gold standard in some cases with much less computational cost.

Cernatic, Filip; Fromager, Emmanuel

doi: 10.1002/jcc.27387pmid: 38700389

A recent work (arXiv:2401.04685) has merged N‐centered ensembles of neutral and charged electronic ground states with ensembles of neutral ground and excited states, thus providing a general and in‐principle exact (so‐called extended N‐centered) ensemble density functional theory of neutral and charged electronic excitations. This formalism made it possible to revisit the concept of density‐functional derivative discontinuity, in the particular case of single excitations from the highest occupied Kohn–Sham (KS) molecular orbital, without invoking the usual “asymptotic behavior of the density” argument. In this work, we address a broader class of excitations, with a particular focus on double excitations. An exact implementation of the theory is presented for the two‐electron Hubbard dimer model. A thorough comparison of the true physical ground‐ and excited‐state electronic structures with that of the fictitious ensemble density‐functional KS system is also presented. Depending on the choice of the density‐functional ensemble as well as the asymmetry of the dimer and the correlation strength, an inversion of states can be observed. In some other cases, the strong mixture of KS states within the true physical system makes the assignment “single excitation” or “double excitation” irrelevant.