Journal of Computational Chemistry

doi: 10.1002/jcc.26909pmid: N/A

Guan, Xiao‐Ling; Sun, Rui; Jin, Bo; Yuan, Caixia; Wu, Yan‐Bo

doi: 10.1002/jcc.27096pmid: 36872591

In designing three‐dimensional (3‐D) molecular stars, it is very difficult to enhance the molecular rigidity through forming the covalent bonds between the axial and equatorial groups because corresponding axial groups will generally break the delocalized π bond over equatorial frameworks and thus break their star‐like arrangement. In this work, exemplified by designing the 3‐D stars Be2©Be5E5+ (E = Au, Cl, Br, I) with three delocalized σ bonds and delocalized π bond over the central Be2©Be5 moiety, we propose that the desired covalent bonding can be achieved by forming the delocalized σ bond(s) and delocalized π bond(s) simultaneously between the axial groups and equatorial framework. The covalency and rigidity of axial bonding can be demonstrated by the total Wiberg bond indices of 1.46–1.65 for axial Be atoms and ultrashort Be‐Be distances of 1.834–1.841 Å, respectively. Beneficial also from the σ and π double aromaticity, these mono‐cationic 3‐D molecular stars are dynamically viable global energy minima with well‐defined electronic structures, as reflected by wide HOMO‐LUMO gaps (4.68–5.06 eV) and low electron affinities (4.70–4.82 eV), so they are the promising targets in the gas phase generation, mass‐separation, and spectroscopic characterization.

Seidler, Leopold Maximilian; Laun, Joachim; Bredow, Thomas

doi: 10.1002/jcc.27097pmid: 36905233

Consistent basis sets of triple‐zeta valence quality for the elements La‐Lu were derived for periodic quantum‐chemical solid‐state calculations. They are an extension of the pob‐TZVP‐rev2 [D. Vilela Oliveira, et al., J. Comput. Chem. 2019, 40(27), 2364–2376], [J. Laun and T. Bredow, J. Comput. Chem. 2021, 42(15), 1064–1072], [J. Laun and T. Bredow, J. Comput. Chem. 2022, 43(12), 839–846] basis sets and are based on the fully relativistic effective core potentials of the Stuttgart/Cologne group and on the def2‐TZVP valence basis of the Ahlrichs group. The basis sets are constructed to minimize the basis set superposition error in crystalline systems. The contraction scheme, orbital exponents, and contraction coefficients were optimized in order to ensure robust and stable self‐consistent‐field convergence for a set of compounds and metals. For the applied PW1PW hybrid functional, the average deviations of the calculated lattice constants from experimental references are smaller with pob‐TZV‐rev2 than with standard basis sets available from the CRYSTAL basis set database. After augmentation with single diffuse s‐ and p‐functions, reference plane‐wave band structures of metals can be accurately reproduced.

Rahali, Emna; Oussama Zouaghi, Mohamed; Sanz, Javier Fernandez; Raouafi, Noureddine; Arfaoui, Youssef

doi: 10.1002/jcc.27098pmid: 36905299

Recently, halogen bonding (XB) has received increased attention as a new type of non‐covalent interaction widely present in nature. In this work, quantum chemical calculations at DFT level have been carried out to investigate halogen bonding interactions between COn(n = 1 or 2) and dihalogen molecules XY (X = F, Cl, Br, I and Y = Cl, Br, I). Highly accurate all‐electron data, estimated by CCSD(T) calculations, were used to benchmark the different levels of computational methods with the objective of finding the best accuracy/computational cost. Molecular electrostatic potential, interaction energy values, charge transfer, UV spectra, and natural bond orbital (NBO) analysis were determined to better understand the nature of the XB interaction. Density of states (DOS) and projected DOS were also computed. Hence, according to these results, the magnitude of the halogen bonding is affected by the halogen polarizability and electronegativity, where for the more polarizable and less electronegative halogen atoms, the σ‐hole is bigger. Furthermore, for the halogen‐bonded complexes involving CO and XY, the OC∙∙∙XY interaction is stronger than the CO∙∙∙XY interaction. Thus, the results presented here can establish fundamental characteristics of halogen bonding in media, which would be very helpful for applying this noncovalent interaction for the sustainable capture of carbon oxides.

Byun, Jinyoung; Vellampatti, Srivithya; Chatterjee, Prathit; Hwang, Sun Ha; Kim, Byoung Choul; Lee, Juyong

doi: 10.1002/jcc.27100pmid: 36988355

A major difference between amyloid precursor protein (APP) isoforms (APP695 and APP751) is the existence of a Kunitz type protease inhibitor (KPI) domain which has a significant impact on the homo‐ and hetero‐dimerization of APP isoforms. However, the exact molecular mechanisms of dimer formation remain elusive. To characterize the role of the KPI domain in APP dimerization, we performed a single molecule pull down (SiMPull) assay where homo‐dimerization between tethered APP molecules and soluble APP molecules was highly preferred regardless of the type of APP isoforms, while hetero‐dimerization between tethered APP751 molecules and soluble APP695 molecules was limited. We further investigated the domain level APP‐APP interactions using coarse‐grained models with the Martini force field. Though the model initial ternary complexes (KPI‐E1, KPI‐KPI, KPI‐E2, E1‐E1, E2‐E2, and E1‐E2) generated using HADDOCK (HD) and AlphaFold2 (AF2), the binding free energy profiles and the binding affinities of the domain combinations were investigated via the umbrella sampling with Martini force field. Additionally, membrane‐bound microenvironments at the domain level were modeled. As a result, it was revealed that the KPI domain has a stronger attractive interaction with itself than the E1 and E2 domains, as reported elsewhere. Thus, the KPI domain of APP751 may form additional attractive interactions with E1, E2 and the KPI domain itself, whereas it is absent in APP695. In conclusion, we found that the APP751 homo‐dimer formation is predominant than the homodimerization in APP695, which is facilitated by the presence of the KPI domain.

Mondal, Sukanta; Jana, Gourhari; Srivastava, Hemant K.; Sastry, Garikapati N.; Chattaraj, Pratim Kumar

doi: 10.1002/jcc.27102pmid: 36916825

The intrinsic ability of clathrate hydrates to encage gaseous molecules is explored. Encapsulation ability depends on the cavity size and the type of guest gaseous species in addition to the physical parameters, temperature and pressure. Here we have reported the structure, stability and nature of interaction in dissimilar guest occupied sH hydrate cavity. Diatomic gas molecules and small polyatomic hydrocarbons are considered as guests. The irregular icosahedron (51268) cavity of sH hydrate is the host. Different thermodynamic parameters for the guest molecules encapsulation were calculated using three different hybrid DFT functionals, B3LYP, M05‐2X, M06, and moreover using dispersion correction (PBE0‐D3). With the consideration of large H‐bonded systems the 6‐31G* and cc‐pVTZ basis sets were used for two set of computations. To disclose the nature of interaction between the host‐guest systems as well as the interaction between the guest molecules inside the host the non‐covalent interaction (NCI) indices and energy decomposition analysis (EDA) were done. Impact of host‐guest and guest‐guest interactions are discussed.

Brzeski, Jakub

doi: 10.1002/jcc.27104pmid: 36905170

Quantum‐chemical calculations were used to describe both the acidity of aluminabenzene‐based Lewis acids and stability of aluminabenzene‐based anions. Aluminabenzene itself was found to exhibit greater acidity than antimony pentaflouride, and thus can be qualified as a Lewis superacid. Substitution of the heterocyclic ring with electron withdrawing groups results in formation of extremely strong Lewis superacids. Two of them, namely AlC5Cl5 and AlC5(CN)5 are the strongest Lewis acids described in the literature so far. Whereas, anions formed after the addition of fluoride anion to substituted aluminabenzene‐based Lewis acids, while characterized by somewhat lower electronic stability than the least coordinating anions hitherto known, are considerably more stable in terms of thermodynamic stability (measured by the propensity to electrophile attack). On this account they are expected to act as counterions for the most reactive cations. The proposed Lewis acids may be prone to the isomerization and dimerization, whereas studied anions are expected to be stable with regard to such processes.