Journal of Computational Chemistry

doi: 10.1002/jcc.25984pmid: N/A

Chamkin, Aleksandr A.; Serkova, Elena S.

doi: 10.1002/jcc.26398pmid: 32812657

The reaction between ferrocenium and trimethylphosphine was studied using density functional theory (DFT), domain‐based local pair natural orbital coupled cluster theory with single‐, double‐, and perturbative triple excitations (DLPNO‐CCSD(T)), and N‐electron valence state perturbation theory (NEVPT2). The accuracy of the DFT functionals decreases compared to the DLPNO‐CCSD(T) level in the following order: M06‐L > TPSS > M06, BLYP > PBE, PBE0, B3LYP > > PWPB95 > > DSD‐BLYP. The roles of thermochemical, continuum solvation (SMD), and counterpoise corrections were evaluated. Grimme's D3 empirical dispersion correction is essential for all functionals studied except M06 and M06‐L. The reliability of the frequency calculations performed directly within the SMD was confirmed. The systems showed no significant multireference character according to T1 and T2 diagnostics and the fractional occupation number (FOD) weighted electron density analysis. The multireference NEVPT2 calculations gave qualitatively valid conclusions about the reaction mechanism. However, a multireference approach is generally not recommended because it requires arbitrary chosen active spaces.

Jana, Gourhari; Chattaraj, Pratim K.

doi: 10.1002/jcc.26403pmid: 32827169

The effect of substitution in the dodecahedrane (C20H20) cage on bonding in the confined He dimer is analyzed. The HeHe distances inside the halogenated dodecahedrane C20X20 (X = FBr) cages are found to be less than half of that in the free He dimer. Comparing the equilibrium structure of He2@C20H20 with He2@C20X20 at ωB97XD/def2‐TZVPP level, it is found that the He‐He distances are relatively larger in the latter cases indicating the influence of halogen groups on the interaction between the cage and the trapped He pair. The viability of the He2@C20X20 complexes is reflected in the presence of a very high activation energy barrier against the thermochemically feasible dissociation process producing free He2 and C20X20. Quantum theory of atoms in molecules (QTAIM) approach reveals a partial covalent interaction between He pair.

Yoshidome, Takashi; Ikeguchi, Mitsunori; Ohta, Masateru

doi: 10.1002/jcc.26406pmid: 32815201

Hydration is a critical factor in the ligand binding process. Herein, to examine the hydration states of ligand binding sites, the three‐dimensional distribution function for the water oxygen site, gO(r), is computed for 3,706 ligand‐free protein structures based on the corresponding small molecule–protein complexes using the 3D‐RISM theory. For crystallographic waters (CWs) close to the ligand, gO(r) reveals that several CWs are stabilized by interaction networks formed between the ligand, CW, and protein. Based on the gO(r) for the crystallographic binding pose of the ligand, hydrogen bond interactions are dominant in the highly hydrated regions while weak interactions such as CH‐O are dominant in the moderately hydrated regions. The polar heteroatoms of the ligand occupy the highly hydrated and moderately hydrated regions in the crystallographic (correct) and wrongly docked (incorrect) poses, respectively. Thus, the gO(r) of polar heteroatoms may be used to distinguish the correct binding poses.

Chenouf, Jamal; Boutahir, Mourad; Fakrach, Brahim; Rahmani, Abdelhai; Chadli, Hassane; Hermet, Patrick; Mejía‐López, Jose; Rahmani, Abdelali

doi: 10.1002/jcc.26408pmid: 32844488

We developed a hybrid approach, combining the density functional theory, molecular mechanics, bond polarizability model and the spectral moment's method to compute the nonresonant Raman spectra of a single quaterthiophene (4T) molecule encapsulated into a single‐walled carbon nanotube (metallic or semiconducting). We reported the optimal tube diameter allowing the 4T encapsulation. The influence of the encapsulation on the Raman modes of the 4T molecule and those of the nanotube (radial breathing modes and tangential modes) are analyzed. An eventual charge transfer between the 4T oligomer and the nanotube is discussed.

Friis, Ida; Verkhovtsev, Alexey; Solov'yov, Ilia A.; Solov'yov, Andrey V.

doi: 10.1002/jcc.26399pmid: 32851682

Ion‐induced DNA damage is an important effect underlying ion beam cancer therapy. This article introduces the methodology of modeling DNA damage induced by a shock wave caused by a projectile ion. Specifically it is demonstrated how single‐ and double strand breaks in a DNA molecule could be described by the reactive CHARMM (rCHARMM) force field implemented in the program MBN Explorer. The entire workflow of performing the shock wave simulations, including obtaining the crucial simulation parameters, is described in seven steps. Two exemplary analyses are provided for a case study simulation serving to: (a) quantify the shock wave propagation and (b) describe the dynamics of formation of DNA breaks. The article concludes by discussing the computational cost of the simulations and revealing the possible maximal computational time for different simulation set‐ups.