Journal of Computational Chemistry

doi: 10.1002/jcc.25927pmid: N/A

doi: 10.1002/jcc.25928pmid: N/A

Hussain, Razak; Yadav, Rolly; Ahmed, Mushtaq; Khan, Tabreiz A.; Kumar, Devesh; Akhter, Yusuf

doi: 10.1002/jcc.26177pmid: 32067246

Tri11 (now renamed as tri22) encoded cytochrome P450 monooxygenase in Trichoderma brevicompactum catalyzes the C‐4 C‐H hydroxylation of 12, 13‐epoxytrichothec‐9‐ene (EPT) to produce trichodermol in the biosynthetic pathway of trichodermin/harzianum A. The density functional theory (DFT)‐quantum mechanics (QM) approach is applied to elucidate the hydroxylation of EPT by using a model active species of P450 (Cpd I). The QM calculations were performed on the active site complex, to find out transition‐state structure, intermediate, and product complexes for the two spin states at different potential energy surfaces. The two state reactivity rebound‐free product formation resulted from the interplay of two spin states (doublet and quartet).

Evarestov, Robert A.; Kuzmin, Alexei

doi: 10.1002/jcc.26178pmid: 32091135

Pressure‐induced insulator‐to‐metal transition (IMT) has been studied in the van der Waals compound iron thiophosphate (FePS3) using first‐principles calculations within the periodic linear combination of atomic orbitals method with hybrid Hartree–Fock‐DFT B3LYP functional. Our calculations reproduce correctly the IMT at ∼15 GPa, which is accompanied by a reduction of the unit cell volume and of the vdW gap. We found from the detailed analysis of the projected density of states that the 3p states of phosphorus atoms contribute significantly at the bottom of the conduction band. As a result, the collapse of the band gap occurs due to changes in the electronic structure of FePS3 induced by relative displacements of phosphorus or sulfur atoms along the c‐axis direction under pressure.

Joseph, Newlyn N.; Roy, Raktim N.; Steitz, Thomas A.

doi: 10.1002/jcc.26179pmid: 32091136

Pistol ribozymes comprise a class of small, self‐cleaving RNAs discovered via comparative genomic analysis. Prior work in the field has probed the kinetics of the cleavage reaction, as well as the influence of various metal ion cofactors that accelerate the process. In the current study, we performed unbiased and unconstrained molecular dynamics simulations from two current high‐resolution pistol crystal structures, and we analyzed trajectory data within the context of the currently accepted ribozyme mechanistic framework. Root‐mean‐squared deviations, radial distribution functions, and distributions of nucleophilic angle‐of‐attack reveal insights into the potential roles of three magnesium ions with respect to catalysis and overall conformational stability of the molecule. A series of simulation trajectories containing in silico mutations reveal the relatively flexible and partially interchangeable roles of two particular magnesium ions within solvated hydrogen‐bonding distances from the catalytic center.

Andoh, Yoshimichi; Yoshii, Noriyuki; Okazaki, Susumu

doi: 10.1002/jcc.26180pmid: 32100899

The fast multipole method (FMM) is an order N method for the numerically rigorous calculation of the electrostatic interactions among point charges in a system of interest. The FMM is utilized for massively parallelized software for molecular dynamics (MD) calculations. However, an inconvenient limitation is imposed on the implementation of the FMM: In three‐dimensional case, a cubic MD unit cell is hierarchically divided by the octree partitioning under isotropic periodic boundary conditions along three axes. Here, we extended the FMM algorithm adaptive to a rectangular MD unit cell with different periodicity along the axes by applying an anisotropic hierarchical partitioning. The algorithm was implemented into the parallelized general‐purpose MD calculation software designed for a system with uniform distribution of point charges in the unit cell. The partition tree can be a mixture of binary and ternary branches, the branches being chosen arbitrarily with respect to the coordinate axes at any levels. Errors in the calculated electrostatic interactions are discussed in detail for a selected partition tree structure. The extension enables us to execute MD calculations under more general conditions for the shape of the unit cell, partition tree, and boundary conditions, keeping the accuracy of the calculated electrostatic interactions as high as that with the conventional FMM. An extension of the present FMM algorithm to other prime number branches, such as 5 and 7, is straightforward.

Hirao, Kimihiko; Chan, Bun; Song, Jong‐Won; Bhattarai, Kamala; Tewary, Subrata

doi: 10.1002/jcc.26181pmid: 32108955

A new simple and conceptual theoretical scheme is proposed for estimating one‐electron excitation energies using Kohn–Sham (KS) solutions. One‐electron transitions that are dominated by the promotion from one initially occupied orbital to one unoccupied orbital of a molecular system can be expressed in a two‐step process, ionization, and electron attachment. KS with long‐range corrected (LC) functionals satisfies Janak's theorem and LC total energy varies almost linearly as a function of its fractional occupation number between the integer electron points. Thus, LC reproduces ionization energies (IPs) and electron affinities (EAs) with high accuracy and one‐electron excitation energies are expressed as the difference between the occupied orbital energy of a neutral molecule and the corresponding unoccupied orbital energy of its cation. Two such expressions can be used, with one employing the orbital energies for the neutral and cationic systems, while the other utilizes orbital energies of just the cation. Because the EA of a molecule is the IP of its anion, if we utilize this identity, the two expressions coincide and give the same excitation energies. Reasonable results are obtained for valence and core excitations using only orbital energies.

Ananthaneni, Sahithi; Rankin, Rees B.

doi: 10.1002/jcc.26182pmid: 32100900

Among all the pollutants in the atmosphere, CO2 has the highest impact on global warming, and with the rising levels of this pollutant, studies on developing various technologies to convert CO2 into carbon‐neutral fuels and chemicals have become more valuable. In this work, we present a detailed computational study of electrochemical reduction of CO2 reaction (the CO2RR) to methane and/or methanol over different transition metal‐p block catalysts using density functional theory calculations. In addition to the catalyst structure, we studied reaction mechanisms using free energy diagrams that explain the product selectivity with respect to the competing hydrogen evolution reaction. Furthermore, we developed scaling relations between all the active C bound intermediate species with ΔG(CO*) and O bound species with ΔG(OH*) The limiting potential lines with ΔG(OH*) as the descriptor are much less negative compared to UL lines with ΔG(CO*) as the descriptor indicating that catalyst materials following pathways via OH− bound intermediate species require more negative potentials than CO*→ HCO* and CO2→ COOH* steps to convert into products. We developed thermodynamic volcano plots with two descriptors; the CO* and OH* binding free energies and determined the best catalyst material among the initially investigated catalyst materials expecting this plot will provide guidance to the future work on improving the activity of transition metal‐p block catalysts for this important reduction reaction.

Alberto, Marta Erminia; De Simone, Bruna Clara; Liuzzi, Simona; Marino, Tiziana; Russo, Nino; Toscano, Marirosa

doi: 10.1002/jcc.26183pmid: 32104925

The search for new dyes to be used as photosensitizers in photodynamic therapy (PDT) is a field of great interest from both experimental and theoretical viewpoints. In this study, the main photophysical properties (excitation energies, singlet‐triplet energy gap, and spin orbit coupling matrix elements) of some unsubstituted and iodine substituted phosphorus corrole complexes have been determined by using density functional theory and its time‐dependent formulation. Results show that these compounds can be proposed as photosensitizers in PDT. The heavy atom effects have been rationalized on the basis of El‐Sayed rules.

Hernández, Belén; Pflüger, Fernando; Ghomi, Mahmoud

doi: 10.1002/jcc.26184pmid: 32109325

Anionic species of aspartic acid, Asp−, having a zwitterionic backbone and a deprotonated side chain, appears to be a good example for analyzing dipole‐ion and ion pair interactions. Density functional theory calculations were herein performed to investigate the low energy conformers of Asp− embedded in a dielectric continuum modeling an aqueous environment, through a scan of the potential energy as a function of the side chain (χ1, χ2) torsion angles. The most energetically favorable conformers having g+g− and g−g+ side chain orientations are found to be stabilized by charge‐enhanced intramolecular H‐bonding involving the positively charged (NH3+) and the two negatively charged (COO−) groups. These conformers were further used to analyze Asp− + nW clusters (W: water, n = 1 or 3), and Asp−/Asp− pair formation. COO− groups were found to be the most attractive sites for hosting a water molecule (binding energy: −6.0 ± 1.5 kcal/mol), compared to NH3+ groups (binding energy: −4.7 ± 1.1 kcal/mol). Energy separation between g+g− and g−g+ conformers increases upon explicit hydration. Asp−/Asp− ion pairs, stabilized by the interaction between the NH3+ group of a partner and the COO− group of the other, shows a quite constant binding energy (−8.1 ± 0.2 kcal/mol), whatever the pair type, and the relative orientation of the two interacting partners. This study suggests a first step to achieve a more realistic image of intermolecular interactions in aqueous environment, especially upon increasing concentration. It can also be considered as a preliminary attempt to assess the interactions of the Lys+…Asp−/Glu− ion pairs stabilizing intra‐ and interchain interactions in proteins.