journal article
LitStream Collection
Home
Bæk, Kristoffer T.; Kepp, Kasper P.
doi: 10.1002/jcc.26810pmid: 35040492
Accurate prediction of protein stability changes upon mutation (ΔΔG) is increasingly important to evolution studies, protein engineering, and screening of disease‐causing gene variants but is challenged by biases in training data. We investigated 45 linear regression models trained on data sets that account systematically for destabilization bias and mutation‐type bias BM. The models were externally validated on three test data sets probing different pathologies and for internal consistency (symmetry and neutrality). Model structure and performance substantially depended on training data and even fitting method. We developed two final models: SimBa‐IB for typical natural mutations and SimBa‐SYM for situations where stabilizing and destabilizing mutations occur to a similar extent. SimBa‐SYM, despite is simplicity, is essentially non‐biased (vs. the Ssym data set) while still performing well for all data sets (R ~ 0.46–0.54, MAE = 1.16–1.24 kcal/mol). The simple models provide advantage in terms of interpretability, use and future improvement, and are freely available on GitHub.
Simkó, Irén; Chordiya, Kalyani; Császár, Attila G.; Kahaly, Mousumi Upadhyay; Szidarovszky, Tamás
doi: 10.1002/jcc.26811pmid: 35084047
Motivated by recent experiments, the laser‐induced alignment‐and‐orientation (A&O) dynamics of the prolate symmetric top CH3X (X = F, Cl, Br, I) molecules is investigated, with particular emphasis on the effect of halogen substitution on the rotational constants, dipole moments, and polarizabilities of these species, as these quantities determine the A&O dynamics. Insight into possible control schemes for preferred A&O dynamics of halogenated molecules and best practices for A&O simulations are provided, as well. It is shown that for accurate A&O ‐dynamics simulations it is necessary to employ large basis sets and high levels of electron correlation when computing the rotational constants, dipole moments, and polarizabilities. The benchmark‐quality values of these molecular parameters, corresponding to the equilibrium, as well as the vibrationally averaged structures are obtained with the help of the focal‐point analysis (FPA) technique and explicit electronic‐structure computations utilizing the gold‐standard CCSD(T) approach, basis sets up to quintuple‐zeta quality, core‐correlation contributions and, in particular, relativistic effects for CH3Br and CH3I. It is shown that the different A&O behavior of the CH3X molecules in the optical regime is mostly caused by the differences in their polarizability anisotropy, in other terms, the size of the halogen atom. In contrast, the A&O dynamics of the CH3X series induced by an intense few‐cycle THz pulse is mostly governed by changes in the rotational constants, due to the similar dipole moments of the CH3X molecules. The A&O dynamics is most sensitive to the B rotational constant: even the difference between its equilibrium and vibrationally‐averaged values results in noticeably different A&O dynamics. The contribution of rotational states having different symmetry, weighted by nuclear‐spin statistics, to the A&O dynamics is also studied.
doi: 10.1002/jcc.26812pmid: 35108407
The powerful independent gradient model (IGM) method has been increasingly popular in visual analysis of intramolecular and intermolecular interactions in recent years. However, we frequently observed that there is an evident shortcoming of IGM map in graphically studying weak interactions, that is its isosurfaces are usually too bulgy; in these cases, not only the graphical effect is poor, but also the color on some areas on the isosurfaces is inappropriate and may lead to erroneous analysis conclusions. In addition, the IGM method was originally proposed based on promolecular density, which is quite crude and does not take actual electronic structure into account. In this article, we propose an improvement version of IGM, namely IGM based on Hirshfeld partition of molecular density (IGMH), which replaces the free‐state atomic densities involved in the IGM method with the atomic densities derived by Hirshfeld partition of actual molecular electron density. This change makes IGM have more rigorous physical background. A large number of application examples in this article, including molecular and periodic systems, weak and chemical bond interactions, fully demonstrate the important value of IGMH in intuitively understanding interactions in chemical systems. Comparisons also showed that the IGMH usually has markedly better graphical effect than IGM and overcomes known problems in IGM. Currently IGMH analysis has been supported in our wavefunction analysis code Multiwfn (http://sobereva.com/multiwfn). We hope that IGMH will become a new useful method among chemists for exploring interactions in wide variety of chemical systems.
Carreon‐Gonzalez, Mirzam; Muñoz‐Rugeles, Leonardo; Vivier‐Bunge, Annik; Alvarez‐Idaboy, Juan Raul
doi: 10.1002/jcc.26813pmid: 35106786
Thiophenols are chemical species with multiple desirable biological properties, including their primary and secondary antioxidant capacity. In this work, the repairing antioxidant activity of eight different thiophenols has been investigated for damaged leucine and tryptophane. The investigation was carried out employing quantum mechanical and transition state methods to calculate the thermodynamic and kinetic data of the reactions involved, while simulating the biological conditions at physiological pH and aqueous and lipidic medium. The analysis of the atomic charges and the spin densities at each of the points on the potential energy surface was the tool that allowed the elucidation of the reaction mechanisms through which thiophenols repair the oxidative damage caused to the amino acids leucine and tryptophan. It was found that thiophenols can repair leucine via a hydrogen atom transfer mechanism in a manner which is similar to the one used by glutathione to repair the carbon‐centered radicals of guanosine. In addition, thiophenols can also restore tryptophane, a nitrogen‐centered radical, via proton‐coupled electron transfer and single electron transfer mechanisms. Moreover, both processes occur at close to diffusion‐controlled rates.
Nguyen, Anh L. P.; Izgorodina, Ekaterina I.
doi: 10.1002/jcc.26814pmid: 35137436
The counterpoise (CP) correction by Boys and Bernardi has been well accepted as a reliable strategy to account for basis set superposition error (BSSE) in intermolecular complexes. The behavior of the CP correction was thoroughly studied in individual molecules of molecular complexes. This work studies the performance of the CP correction in many‐body clusters including three‐body clusters of organic compounds in the 3B‐69 dataset. Additionally, we used crystal structures of polymorphs of benzene, aspirin, and oxalyl dihydrazide (ODH) to construct a many‐body cluster dataset, abbreviated as the MBC‐36 dataset, consisting of two, four and eight molecules, and 16 molecules in the case of benzene. A series of Dunning's basis sets—cc‐pXZ and aug‐cc‐pXZ (X = D and T)—were used to predict CP‐corrected Hartree–Fock (HF) interaction energies of the 3B‐69 and MBC‐36 datasets. The CP‐corrected interaction energies were found to be basis‐set independent, whereas the non‐CP corrected interaction energies were found not to a follow a smooth exponential fitting as previously found for electronic energies of individual molecules. This observation was attributed to the presence of non‐additive induction forces in some clusters. Two 2 × 2 × 2 supercells of benzene polymorphs were constructed to explore the local nature of BSSE effects. A cut‐off radius of 10 Å was demonstrated to be sufficient to fully recover these effects. Although the behavior of CP correction was found to be non‐conventional in many‐body clusters of organic compounds, the use of a small basis set such as cc‐pVDZ showed excellent performance in the prediction of HF interaction energies.
Boziki, Ariadni; Baudin, Pablo; Liberatore, Elisa; Ashari Astani, Negar; Rothlisberger, Ursula
doi: 10.1002/jcc.26815pmid: 35146764
Transient absorption spectra (TAS) of lead halide perovskites can provide important insights into the nature of the photoexcited state dynamics of this prototypical class of materials. Here, we perform ground and excited state molecular dynamics (MD) simulations within a restricted open shell Kohn‐Sham (ROKS) approach in order to interpret the characteristic features of the TAS of CsPbBr3. Our results reveal that properties such as the finite temperature band gap, the Stokes shift, and therefore, also the TAS are strongly size‐dependent. Our TAS simulations show an early positive red‐shifted feature on the fs scale that can be explained by geometric relaxation in the excited state. As excited‐state processes can crucially affect the electronic properties of this class of photoactive materials, our observations are an important ingredient for further optimization of lead halide based optoelectronic devices.
Showing 1 to 7 of 7 Articles