Journal of Computational Chemistry

doi: 10.1002/jcc.26611pmid: N/A

Das, Prasenjit; Chattaraj, Pratim Kumar

doi: 10.1002/jcc.26845pmid: 35322887

Density functional theory (DFT) is used to explore the structure, stability, and bonding in CSiGaAl2−/0 and CGeGaAl2−/0 systems having planar tetracoordinate carbon (ptC). The neutral systems have 17 valence electrons and the mono‐anionic systems have 18 valence electrons. The ab initio molecular dynamics simulations for 2000 fs time at two different temperatures (300 and 500 K) supported the kinetic stability of the systems. From the natural bond orbital (NBO) analysis it is shown that there is a strong electron donation from the ligand atoms to the ptC atom. We have used Li+ ion for the neutralization of the mono‐anionic systems and more interestingly it does not disrupt the planar structure. The most preferable site for binding of Li+ ion is along the AlAl bond in both of the mono‐anionic systems. All the systems in this work have both σ and π aromaticity which is predicted from the computations of nucleus independent chemical shift (NICS). Although the anionic species obey the 18 valence electronic rule, the neutral systems break the rule with 17 valence electrons. However, both sets of systems are stable in the planar form. The bonding analysis of the systems includes molecular orbital, adaptive natural density partitioning (AdNDP), quantum theory of atoms in molecules (QTAIM), electron localization function (ELF) basin, and aromaticity analyses. The energy decomposition analysis (EDA) determines the interaction of Li+ ion with CSiGaAl2− and CGeGaAl2− in Li@SiGaAl2 and Li@GeGaAl2, respectively.

Xiong, Yuqing; Zeng, Juan; Xia, Fei; Cui, Qiang; Deng, Xianming; Xu, Xin

doi: 10.1002/jcc.26846pmid: 35324017

The human Son of Sevenless (SOS) activates the signal‐transduction protein Ras by forming the complex SOS·Ras and accelerating the guanosine triphosphate (GTP) exchange in Ras. Inhibition of SOS·Ras could regulate the function of Ras in cells and has emerged as an effective strategy for battling Ras related cancers. A key factor to the success of this approach is to understand the conformational change of Ras during the GTP exchange process. In this study, we perform an extensive molecular dynamics simulation to characterize the specific conformations of Ras without and with guanine nucleotide exchange factors (GEFs) of SOS, especially for the substates of State 1 of HRasGTP∙Mg2+. The potent binding pockets on the surfaces of the RasGDP∙Mg2+, the S1.1 and S1.2 substates in State 1 of RasGTP∙Mg2+ and the ternary complexes with SOS are predicted, including the binding sites of other domains of SOS. These findings help to obtain a more thorough understanding of Ras functions in the GTP cycling process and provide a structural foundation for future drug design.

Daré, Joyce K.; Freitas, Matheus P.

doi: 10.1002/jcc.26848pmid: 35315534

Conformation has a key role in the mechanism of interaction between small molecules and biological receptors. However, encoding this type of information in molecular descriptors for the construction of robust quantitative structure–activity relationships (QSAR) models is not an easy task and, so far, the dependence of these models on such feature has not been thoroughly investigated. In the present study, the authors explore the effects of conformational information on a 3D‐QSAR technique by comparing models built with descriptors that encode fully described tridimensional aspects (structures docked inside a biological target), with descriptors in which this information is suppressed (flat structures) or not fully described (structures with quantum‐chemically optimized geometries). As a result, the validation parameters indicate that the robustness of the models seems to be more related to the alignment aspect of the structures than to how well their tridimensional features are described.

Kirschbaum, Thorren; Petit, Tristan; Dzubiella, Joachim; Bande, Annika

doi: 10.1002/jcc.26849pmid: 35322429

Nanodiamonds (NDs) are modern high‐potential materials relevant for applications in biomedicine, photocatalysis, and various other fields. Their electronic surface properties, especially in the liquid phase, are key to their function in the applications, but we show that they are sensitively modified by their interactions with the environment. Two important interaction modes are those with oxidative aqueous adsorbates as well as ND self‐aggregation towards the formation of ND clusters. For planar diamond surfaces it is known that the electron density migrates from the diamond towards oxidative adsorbates, which is known as transfer doping. Here, we quantify this effect for highly curved NDs of varying sizes (35–147 C atoms) and surface terminations (H, OH, F), focusing on their interactions with the most abundant aqueous oxidative adsorbates (H3O+, O2, O3). We prove that the concept of transfer doping stays valid for the case of the high‐curvature NDs and can be tuned via the ND's specific properties. Secondly, we investigate the electronic structures of clusters of NDs which are known to form in particular in aqueous dispersions. Upon cluster formation, we find that the optical gaps of the structures are significantly reduced, which explains why different experimental values were obtained for the optical gap of the same structures, and the cluster's LUMO shapes resemble atom‐type orbitals, as in the case of isolated spherical NDs. Our findings have implications for ND applications as photocatalysts or electronic devices, where the specific electronic properties are key to the functionality of the ND material.

Roe, Daniel R.; Bergonzo, Christina

doi: 10.1002/jcc.26847pmid: 35318701

Setting up molecular dynamics simulations from experimentally determined structures is often complicated by a variety of factors, particularly the inclusion of carbohydrates, since these have several anomer types which can be linked in a variety of ways. Here we present a stand‐alone tool implemented in the widely‐used software CPPTRAJ that can be used to automate building structures and generating a “ready to run” parameter and coordinate file pair. This tool automatically identifies carbohydrate anomer type, configuration, linkage, and functional groups, and performs topology modifications (e.g., renaming residue/atom names) required to build the final system using state of the art GLYCAM force field parameters. It will also generate the necessary commands for bonding carbohydrates and creating any disulfide bonds.