Journal of Computational Chemistry

doi: 10.1002/jcc.26663pmid: N/A

Sarmah, Kangkan; Kalita, Amlan J.; Konwar, Dimpul; Guha, Ankur K.

doi: 10.1002/jcc.26976pmid: 36094074

Quantum chemical calculations have been carried out to investigate the hydrogen storage capacity of Be2(NLi)2 cluster. Calculations reveal that the cluster can take up to eight H2 molecules reaching a maximum gravimetric density of 21.04 wt%. Six H2 molecules bind at the Li atoms and two H2 bind at the Be atoms with moderate binding energy which is required for reversible storage of H2. Symmetry‐adapted perturbation analysis reveals the significant contribution of electrostatic and induction and very minor contribution of dispersion toward the total interaction energy. Molecular dynamics simulations reveal that the H2 molecules are strongly bound at 77 K and get slowly released at elevated temperatures.

Brankin, Alice E.; Fowler, Philip W.

doi: 10.1002/jcc.26979pmid: 36054249

Drug resistant Mycobacterium tuberculosis, which mostly results from single nucleotide polymorphisms in antibiotic target genes, poses a major threat to tuberculosis treatment outcomes. Relative binding free energy (RBFE) calculations can rapidly predict the effects of mutations, but this approach has not been tested on large, complex proteins. We use RBFE calculations to predict the effects of M. tuberculosis RNA polymerase and DNA gyrase mutations on rifampicin and moxifloxacin susceptibility respectively. These mutations encompass a range of amino acid substitutions with known effects and include large steric perturbations and charged moieties. We find that moderate numbers (n = 3–15) of short RBFE calculations can predict resistance in cases where the mutation results in a large change in the binding free energy. We show that the method lacks discrimination in cases with either a small change in energy or that involve charged amino acids, and we investigate how these calculation errors may be decreased.

Zhang, Zheng‐Feng; Su, Ming‐Der

doi: 10.1002/jcc.26980pmid: 36063085

The trapping reactions of carbene analogs G14F2 (G14 = group 14 element) by the benzene‐bridged B/P‐Rea frustrated Lewis pair (FLPs) molecule are studied using density functional theory (B3LYP‐D3(BJ)/def2‐TZVP). Our theoretical investigations predict that only the CF2 intermediate rather than other heavy carbene analogs can be trapped by the B/P‐Rea FLP‐type molecule. Energy decomposition analysis‐natural orbitals for chemical valence (EDA‐NOCV) analyses indicate that the bonding nature of the G14F2 catching reactions by the B/P‐Rea FLP‐type molecule is a donor–acceptor (singlet–singlet) interaction rather than an electron‐sharing (triplet–triplet) interaction. Moreover, EDA‐NOCV and frontier molecular orbital (FMO) theory findings strongly suggest that the lone pair (LP) (P) → vacant p–π‐orbital (G14F2) interaction rather than the empty σ‐orbital (B) ← sp2‐σ‐orbital (G14F2) interaction plays a predominant role in establishing its bonding condition during the G14F2 trapping reaction with the B/P‐Rea FLP‐associated molecule. Our activation strain model findings reveal that the atomic radius of the G14 element of G14F2 plays a key role in determining the activation barrier of the G14F2 trapping reactions by the benzene‐bridged B/P‐Rea FLP. The valence bond state correlation diagram (VBSCD) model developed by Shaik is used to rationalize the calculated results. The VBSCD findings demonstrate that in the present trapping reactions, the singlet triplet splitting of G14F2 plays a significant role in influencing its reaction barrier and reaction enthalpy. Our theoretical results demonstrate that the relationship between the geometrical parameters of the transition states and the corresponding reaction free energy barriers agrees well with the findings based on the Hammond postulate.

Düzenli, Derya; Onal, Isik; Tezsevin, Ilker

doi: 10.1002/jcc.26981pmid: 36054551

In this work, various precious and non‐precious metals reported in the literature as the most effective catalysts for glucose electrooxidation reaction were investigated by the density functional theory (DFT) approach in order to reveal the mechanisms taking place over the catalysts in the fuel cell. The use of a single‐atom catalyst model was adopted by insertion of one Au, Cu, Ni, Pd, Pt, and Zn metal atom on the pyridinic N atoms doped graphene surface (NG). β form of d‐glucose in alkaline solution was used to determine the reaction mechanism and intermediates that formed during the reaction. DFT results showed that the desired glucono‐lactone was formed on the Cu‐3NG electrode in a single‐step reaction pathway whereas it was produced via different two‐step pathways on the Au and Pt‐3NG electrodes. Although the interaction of glucose with Ni, Pd, and Zn‐doped surfaces resulted in the deprotonation of the molecule, lactone product formation did not occur on these electrode surfaces. When the calculation results are evaluated in terms of energy content and product formation, it can be concluded that Cu, Pt, and especially Au doped graphene catalysts are effective for direct glucose oxidation in fuel cells reactor.

Bruce‐Chwatt, Tomás; Naidoo, Kevin J.

doi: 10.1002/jcc.26982pmid: 36054751

Computing the free energies of molecular mechanisms in multidimensional space relies on combinations of geometrically complex reaction coordinates. We show how a graph theory implementation reduces complexity, and illustrate this on the arrangements of hydrogen bonding of a water dimer. The reaction coordinates and forces are computed using graphs that define the dependencies on the atoms in the Free Energy from Adaptive Reaction Coordinate Forces (FEARCF) library. The library can be interfaced with classical molecular dynamics as well as quantum molecular dynamics packages. Multidimensional interdependent reaction coordinates are constructed to produce complex free energy hypersurfaces. The reaction coordinates are graphed from atomic and molecular components to define points, distances, vectors, angles, planes and combinations thereof. The resultant free energy surfaces that are a function of the distance, angles, planes, and so on, can represent molecular mechanisms in reduced dimensions from the component atomic Cartesian coordinate degrees of freedom. The FEARCF library can be interfaced with any molecular package. Here, we demonstrate the link to NWChem to compute a hyperdimensional DFT (aug‐cc‐pVDZ basis set and X3LYP exchange correlation functionals) free energy space of a water dimer. Analysis of the water dimer free energy hypervolume reveals that while the chain and cyclic hydrogen bonding configurations are located in stable minimum energy wells, the bifurcated hydrogen bond configuration is a gateway to instability and dimer dissociation.

Scheiner, Steve

doi: 10.1002/jcc.26983pmid: 36054659

Atoms in molecules, noncovalent index, and natural bond orbital methods are commonly invoked to identify the presence of various noncovalent bonds and to measure their strength. However, there are numerous instances in the literature where these methods provide contradictory or apparently erroneous interpretations of the bonding. The range of reliability of these methods is assessed by calculations of a variety of systems, which include an H‐bond, halogen bond, π‐tetrel bond, CH··HC interaction, and a pairing of two anions. While the results appear to be meaningful for the equilibrium geometries, and those where the two subunits are progressively pulled apart, these techniques erroneously predict a progressively stronger bonding interaction as the two units are compressed and the interaction becomes clearly repulsive. The methods falsely indicate a bonding interaction in the CH··HC arrangement, and incorrectly mimic the behavior of the energy when two anions approach. These approaches are also unreliable for understanding angular deformations.