QM/MM study of N501 involved intermolecular interaction between SARS-CoV-2 receptor binding domain and antibody of human origin

Liu, Yuemin; Sulaiman, Hana F; Johnson, Bruce R.; Ma, Ruina; Gao, Yunxiang; Fernando, Harshica; Amarasekara, Ananda S.; Ashley-Oyewole, Andrea; Fan, Hua‐Jun; Ingram, Heaven N; Briggs, James M.

doi:10.1016/j.compbiolchem.2023.107810

Cited by 2 publications

(2 citation statements)

References 55 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The method nicely correlates chemical reaction and nanoscale molecular motion together, and it has been widely applied to the prediction of reaction mechanisms. 33,34 As a microscopic theory, the length scale of a QM/MM method is on the order of 10 −9 m, and its computational cost is too high for larger systems.…”

Section: Introductionmentioning

confidence: 99%

“…However, it is more and more noticed that the decoupling method is too coarse for many systems, and many coupling theories have been proposed. − One of the most famous theories is the quantum mechanics/molecular mechanics (QM/MM) method. − The QM/MM method divides the system into QM and MM regions, which are examined by quantum theory and molecular simulation, respectively. The method nicely correlates chemical reaction and nanoscale molecular motion together, and it has been widely applied to the prediction of reaction mechanisms. , As a microscopic theory, the length scale of a QM/MM method is on the order of 10 –9 m, and its computational cost is too high for larger systems.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Development of a Reaction–Diffusion–Convection Model and Its Application to NO Oxidation in Reactors

Luo,

Liu

2024

Ind. Eng. Chem. Res.

View full text Add to dashboard Cite

The multiscale modeling of a reaction-transport process is an important issue in both fundamental and applied studies. We introduced a reaction−diffusion−convection model to deal with the reaction-transport process in chemical engineering by combining the reaction kinetics model, classical density functional theory (CDFT), and computational fluid dynamics (CFD). The reaction kinetic model and CDFT are unified into a differential equation, which is coupled with the CFD equation by a boundary condition. The model is applied to NO oxidation in a reactor. The multiscale model reveals the relationship between the microscopic properties and the macroscopic performance of a catalyst/reactor. We examined the dependence of conversion on adsorption strength, the shape and number of catalyst particles, and flow velocity. The multiscale prediction is consistent with the experiment, and there is a selfinhibition effect in the reaction-transport process. The model gives some insight into the design of reactors and has the potential to be applied to other reaction-transport processes.

show abstract

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Development of a Reaction–Diffusion–Convection Model and Its Application to NO Oxidation in Reactors

Luo,

Liu

2024

Ind. Eng. Chem. Res.

View full text Add to dashboard Cite

show abstract

A Quantum Mechanical MP2 Study of the Electronic Effect of Nonplanarity on the Carbon Pyramidalization of Fullerene C60

Liu,

Gao,

Altalhi

et al. 2024

Nanomaterials

View full text Add to dashboard Cite

Among C60’s diverse functionalities, its potential application in CO2 sequestration has gained increasing interest. However, the processes involved are sensitive to the molecule’s electronic structure, aspects of which remain debated and require greater precision. To address this, we performed structural optimization of fullerene C60 using the QM MP2/6–31G* method. The nonplanarity of the optimized icosahedron is characterized by two types of dihedral angles: 138° and 143°. The 120 dihedrals of 138° occur between two hexagons intersecting at C–C bonds of 1.42 Å, while the 60 dihedrals of 143° are observed between hexagons and pentagons at C–C bonds of 1.47 Å. NBO analysis reveals less pyramidal sp1.78 hybridization for carbons at the 1.42 Å bonds and more pyramidal sp2.13 hybridization for the 1.47 Å bonds. Electrostatic potential charges range from −0.04 a.u. to 0.04 a.u. on the carbon atoms. Second-order perturbation analysis indicates that delocalization interactions in the C–C bonds of 1.42 Å (143.70 kcal/mol) and 1.47 Å (34.98 kcal/mol) are 22% and 38% higher, respectively, than those in benzene. MP2/Def2SVP calculations yield a correlation energy of 13.49 kcal/mol per electron for C60, slightly higher than the 11.68 kcal/mol for benzene. However, the results from HOMO-LUMO calculations should be interpreted with caution. This study may assist in the rational design of fullerene C60 derivatives for CO2 reduction systems.

show abstract

QM/MM study of N501 involved intermolecular interaction between SARS-CoV-2 receptor binding domain and antibody of human origin

Cited by 2 publications

References 55 publications

Development of a Reaction–Diffusion–Convection Model and Its Application to NO Oxidation in Reactors

Development of a Reaction–Diffusion–Convection Model and Its Application to NO Oxidation in Reactors

A Quantum Mechanical MP2 Study of the Electronic Effect of Nonplanarity on the Carbon Pyramidalization of Fullerene C60

Contact Info

Product

Resources

About