Journal of Computational Chemistry

doi: 10.1002/jcc.25427pmid: N/A

doi: 10.1002/jcc.25430pmid: N/A

Ariyarathna, Isuru R.; Miliordos, Evangelos

doi: 10.1002/jcc.25829pmid: 30920017

Coupled cluster and multireference configuration approaches are employed to study the electronic and geometric structures of mono‐coordinated complexes of lithium, sodium, and beryllium with nitric oxide and its isovalent NS, NSe, and NTe species. Ground and low‐lying excited states were examined for both linear‐bonded and side‐bonded isomers. We show that the ionic M+NX− (M=Li, Na, Be and X=O, S, Se, Te) picture is a more natural representation and can account for the symmetry of the low−lying electronic states as Σ−, Δ, and Σ+, the smaller excitation energies and the larger binding energies for heavier X. An additional electron binds to the positively charged Li and Na terminal creating stable anions. The electron affinity (EA) of LiNX and NaNX species is in the 0.5–0.8 eV range. Despite the negative EA of beryllium and the very small EA of NO, the BeNO molecule has an EA of ~1.0 eV, which is increased to ~1.5 eV for the heavier BeNX species. This is attributed to the fact that the additional electron goes to the beryllium end for BeNO but to a π(MN)π*(NX) orbital of the rest species. Our accurate results contradict previous findings and serve as a guide for future experimental studies. © 2019 Wiley Periodicals, Inc.

Mahler, Andrew; Panno, Kassidy; Janesko, Benjamin G.; Moncho, Salvador; Brothers, Edward N.

doi: 10.1002/jcc.25827pmid: 30901501

Promoter atoms can tune a catalyst's activity and selectivity by transferring charge to and from the active site. Rational design of promoted catalysts, using density functional theory calculations, is today limited by the need to simulate many catalyst and promoter configurations. We present a simple approximation that rapidly captures some trends in promoter effects, at a cost of complexity comparable with simulating unpromoted catalysts. Negative (positive) noninteger point charges introduced into the catalyst simulate how electropositive (electronegative) promoters might affect each predicted intermediate. Calculations return Sabatier plots, relating promoters' predicted efficacy to readily measured properties such as catalyst work functions. We illustrate our approach for two reactions associated with the Fischer–Tropsch process, hydrogen–deuterium scrambling, and carbon monoxide dissociation over ruthenium. Consistent with experiment, electropositive promoters are predicted to accelerate hydrogen scrambling and unassisted CO dissociation. Simulations also provide a new prediction: electronegative promoters accelerate hydrogen‐assisted CO dissociation over hydrogen‐precovered surfaces by stabilizing the initial CO adsorption. © 2019 Wiley Periodicals, Inc.

Manak, Martin

doi: 10.1002/jcc.25828pmid: 30932214

The function of enzymatic proteins is given by their ability to bind specific small molecules into their active sites. These sites can often be found in pockets on a hypothetical boundary between the protein and its environment. Detection, analysis, and visualization of pockets find its use in protein engineering and drug discovery. Many definitions of pockets and algorithms for their computation have been proposed. Kawabata and Go defined them as the regions of empty space into which a small spherical probe can enter but a large probe cannot and developed programs that can compute their approximate shape. In this article, this definition was slightly modified in order to capture the existence of large internal holes, and a Voronoi‐based method for the computation of the exact shape of these modified regions is introduced. The method first puts a finite number of large probes on the protein exterior surface and then, considering both large probes and atomic balls as obstacles for the small probe, the method computes the exact shape of the regions for the small probe. This is all achieved with Voronoi diagrams, which help with the safe navigation of spherical probes among spherical obstacles. Detected regions are internally represented as graphs of vertices and edges describing possible movements of the center of the small probe on Voronoi edges. The surface bounding each region is obtained from this representation and used for visualization, volume estimation, and comparison with other approaches. © 2019 Wiley Periodicals, Inc.

Zhang, Ming‐Xia; Xu, Hong‐Liang

doi: 10.1002/jcc.25830pmid: 30942507

Usually, an extra catalyst (for example, the transition metal complexes) need to be used in catalyzing hydroboration, which involved the cost, environment, and so forth. Here, a greener and controllable catalyst—external electric field (EEF) was used to study its effect on hydroboration of N‐(4‐methylbenzyl)aniline (PhN═CHPhMe) with pinacolboane (HBPin). The results demonstrated that EEF could affect the barrier heights of both two pathways of this reaction. More significantly, flipping the direction of EEF could modify the reaction mechanism to induce a dominant inverse hydroboration at some field strength. That is to say, oriented EEF is a controlling switch for the anti‐ or Markovnikov hydroboration reaction of imines. This investigation is meaningful for the exploration of greener catalyst for chemistry reaction and guide a new method for the Markovnikov hydroboration addition. © 2019 Wiley Periodicals, Inc.

Ma, Zhifeng; Ukaji, Kasumi; Nakatani, Naoki; Fujii, Hiroshi; Hada, Masahiko

doi: 10.1002/jcc.25831pmid: 30938845

The effects of peripheral fluorine atoms on epoxidation reactions of ethylene by oxoiron(IV) porphyrin cation radical complex in the quartet and sextet spin multiplicities are systematically investigated using the DFT method. The overall reaction routes are determined using a model system of ethylene and Fe(IV)OCl‐porphyrin with substituted fluorine atoms. By obtaining the energy diagrams and electron‐ and spin‐density difference contour maps of the transition states and intermediate compounds, we confirm that the electron‐withdrawing by peripheral fluorine atoms enhances the reactivity as the number of fluorine atoms increases, as is observed experimentally. The intersystem crossing between the quartet and sextet spin multiplicities is discussed by means of the intrinsic reaction coordinate method. We conclude that the rate‐determining step is located at the first transition state (TS1) for the activation of CC and FeO bonds, and the ground electronic state changes from quartet to sextet around the TS1. © 2019 Wiley Periodicals, Inc.

Delcey, Mickael G.; Sørensen, Lasse Kragh; Vacher, Morgane; Couto, Rafael C.; Lundberg, Marcus

doi: 10.1002/jcc.25832pmid: 30938847

Electronically excited states play important roles in many chemical reactions and spectroscopic techniques. In quantum chemistry, a common technique to solve excited states is the multiroot Davidson algorithm, but it is not designed for processes like X‐ray spectroscopy that involves hundreds of highly excited states. We show how the use of a restricted active space wavefunction together with a projection operator to remove low‐lying electronic states offers an efficient way to reach single and double‐core‐hole states. Additionally, several improvements to the stability and efficiency of the configuration interaction (CI) algorithm for a large number of states are suggested. When applied to a series of transition metal complexes the new CI algorithm does not only resolve divergence issues but also leads to typical reduction in computational time by 70%, with the largest savings for small molecules and large active spaces. Together, the projection operator and the improved CI algorithm now make it possible to simulate a wide range of single‐ and two‐photon spectroscopies. © 2019 Wiley Periodicals, Inc.