Journal of Computational Chemistry

doi: 10.1002/jcc.26667pmid: N/A

Kossaka Macedo, Gabriel; Haiduke, Roberto Luiz Andrade

doi: 10.1002/jcc.26985pmid: 36053978

This work is focused on evaluating the performance of exchange‐correlation functionals from density functional theory in providing descriptor values derived from the electron density of saddle point structures (transition states) in chemical reactions. The properties investigated were obtained from the quantum theory of atoms in molecules, including atomic charges and electron density topological data at the bond critical points. In addition, parameters from the Interacting quantum atom energy partition were used as well in this comparative study. The reference values are attained in coupled cluster calculations with iterative single and double excitations (CCSD). Six elementary reactions are considered here: CO + H2 ↔ H2CO, CO + H2O ↔ HCOOH, HCN ↔ HNC, H + F2 ↔ HF + F, H + N2 ↔ HN2, and H + CO ↔ HCO. In general, the BB1K functional (hybrid‐meta‐generalized gradient approximation) provides the best description of these properties. Our study indicates that an intermediate percentage of nonlocal exact exchange, around 40%–55% (perhaps even larger), is probably required for attaining more accurate values with actual functionals, although this condition is not able of explaining all the trends observed.

Muz, İskender; Kurban, Mustafa

doi: 10.1002/jcc.26986pmid: 36054565

We have investigated the adsorption of CH4 and CO2 gases on zinc oxide nanoclusters (ZnO NCs) using density functional theory (DFT). It was found that the CH4 tends to be physically adsorbed on the surface of all the ZnO NCs with adsorption energy in the range −11 to −14 kcal/mol. Even though, the CO2 is favorably chemisorbed on the Zn12O12 and Zn15O15 NCs, with adsorption energy about −38 kcal/mol at B3LYP/6‐311G(d,p) level of theory. When the CH4 and CO2 gases are adsorbed on the ZnO NCs, their electrical conductivities are decreased, and thus the studied ZnO NCs do not generate an electrical signal in the presence of CH4 and CO2 gases. Interestingly, both pure and gas adsorbed Zn22O22 NC exhibited more favorable electronic and reactive properties than other NCs. Comparison of the structural, electronic, and optical data predicted by DFT/B3LYP and TD‐DFT/CAM‐B3LYP calculations with those experimentally obtained show good agreement.

Muñoz‐Castro, Alvaro; Dias, H. V. Rasika

doi: 10.1002/jcc.26987pmid: 36073752

The π‐complexes of cationic coinage metal ions (Cu(I), Ag(I), Au(I)) provide useful experimental support for understanding fundamental characteristics of bonding and 13C‐NMR patterns of the group 11 triad. Here, we account for the role of relativistic effects on olefin‐coinage metal ion interaction for cationic, homoleptic tris‐ethylene, and tris‐norbornene complexes, [M(η2‐C2H4)3]+ and [M(η2‐C7H10)3]+ (M = Cu, Ag, Au), as representative case of studies. The M‐(CC) bond strength in the cationic, tris‐ethylene complexes is affected sizably for Au and to a lesser extent for Ag and Cu (48.6%, 16.7%, and 4.3%, respectively), owing to the influence on the different stabilizing terms accounting for the interaction energy in the formation of coinage metal cation‐π complexes. The bonding elements provided by olefin → M σ‐donation and olefin ← M π‐backbonding are consequently affected, leading to a lesser covalent interaction going down in the triad if the relativistic effects are ignored. Analysis of the 13C‐NMR tensors provides further understanding of the observed experimental values, where the degree of backbonding charge donation to π2*‐olefin orbital is the main influence on the observed high‐field shifts in comparison to the free olefin. This donation is larger for ethylene complexes and lower for norbornene counterparts. However, the bonding energy in the later complexes is slightly stabilized given by the enhancement in the electrostatic character of the interaction. Thus, the theoretical evaluation of metal‐alkene bonds, and other metal‐bonding situations, benefits from the incorporation of relativistic effects even in lighter counterparts, which have an increasing role going down in the group.

Otlyotov, Arseniy A.; Minenkov, Yury

doi: 10.1002/jcc.26988pmid: 36053781

Performance of contemporary tight‐binding semiempirical GFNn‐xTB methods for the conformational energies of singly charged sodium clusters Na+(S)n (n = 4–8) with 3 protic and 8 aprotic solvents is examined against the reference RI‐MP2/CBS method. The median Pearson correlation coefficients of ρ = 0.84 (GFN2‐xTB) and ρ = 0.82 (GFN1‐xTB) do not give the clear preference to any tested approach. GFN1‐xTB method demonstrates more stable performance than its GFN2‐xTB successor with the average mean absolute errors (MAEs)/mean signed errors (MSEs) of 1.2/0.2 and 2.3/1.6 kcal mol−1, respectively. Conformational energies produced by the computationally efficient DFT functional PBE and double‐ζ basis set complemented with –D3(BJ) dispersion correction are suitable for the preliminary sampling (median ρ = 0.93), but should be used with a caution for the calculations of the average ensemble properties (MAE/MSE = 1.7/1.1 kcal mol−1). Higher‐ranking PBE0‐D3(BJ) and ωB97M‐V with triple‐ζ basis sets yield significantly lower MAEs/MSEs of 0.55/0.20 and 0.51/0.23 kcal mol−1, respectively.

Shiga, Motoyuki

doi: 10.1002/jcc.26989pmid: 36094104

An approximate approach to quantum vibrational dynamics, “Brownian chain molecular dynamics (BCMD),” is proposed to alleviate the chain resonance and curvature problems in the imaginary time‐based path integral (PI) simulation. Here the non‐centroid velocity is randomized at each step when solving the equation of motion of path integral molecular dynamics. This leads to a combination of the Newton equation and the overdamped Langevin equation for the centroid and non‐centroid variables, respectively. BCMD shares the basic properties of other PI approaches such as centroid and ring polymer molecular dynamics: It gives the correct Kubo‐transformed correlation function at short times, conserves the time symmetry, has the correct high‐temperature/classical limits, gives exactly the position and velocity autocorrelations of harmonic oscillator systems, and does not have the zero‐point leakage problem. Numerical tests were done on simple molecular models and liquid water. On‐the‐fly ab initio BCMD simulations were performed for the protonated water cluster, H5O2+, and its isotopologue, D5O2+.

Jiang, Runxuan; Gogineni, Tarun; Kammeraad, Joshua; He, Yifei; Tewari, Ambuj; Zimmerman, Paul M.

doi: 10.1002/jcc.26984pmid: 36000759

Conformer‐RL is an open‐source Python package for applying deep reinforcement learning (RL) to the task of generating a diverse set of low‐energy conformations for a single molecule. The library features a simple interface to train a deep RL conformer generation model on any covalently bonded molecule or polymer, including most drug‐like molecules. Under the hood, it implements state‐of‐the‐art RL algorithms and graph neural network architectures tuned specifically for molecular structures. Conformer‐RL is also a platform for researching new algorithms and neural network architectures for conformer generation, as the library contains modular class interfaces for RL environments and agents, allowing users to easily swap components with their own implementations. Additionally, it comes with tools to visualize and save generated conformers for further analysis. Conformer‐RL is well‐tested and thoroughly documented with tutorials for each of the functionalities mentioned above, and is available on PyPi and Github: https://github.com/ZimmermanGroup/conformer-rl.