scholarly journals DFT Study on the Mechanism of Iron-Catalyzed Diazocarbonylation

Molecules ◽  
2020 ◽  
Vol 25 (24) ◽  
pp. 5860
Author(s):  
Tímea R. Kégl ◽  
László Kollár ◽  
Tamás Kégl
Keyword(s):  
Free Energy ◽  
Dft Calculations ◽  
Reaction Rate ◽  
Decomposition Analysis ◽  
Donor Ligands ◽  
Energy Decomposition Analysis ◽  
Doublet State ◽  
Energy Decomposition ◽  
Natural Orbitals ◽  
Free Energy Of Activation

The mechanism of the carbonylation of diazomethane in the presence of iron–carbonyl–phosphine catalysts has been investigated by means of DFT calculations at the M06/def-TZVP//B97D3/def2-TZVP level of theory, in combination with the SMD solvation method. The reaction rate is determined by the formation of the coordinatively unsaturated doublet-state Fe(CO)3(P) precursor followed by the diazoalkane coordination and the N2 extrusion. The free energy of activation is predicted to be 18.5 and 28.2 kcal/mol for the PF3 and PPh3 containing systems, respectively. Thus, in the presence of less basic P-donor ligands with stronger π-acceptor properties, a significant increase in the reaction rate can be expected. According to energy decomposition analysis combined with natural orbitals of chemical valence (EDA–NOCV) calculations, diazomethane in the Fe(CO)3(phosphine)(η1-CH2N2) adduct reveals a π-donor–π-acceptor type of coordination.

How electron-deficient Cp ligand facilitates Rh-catalyzed annulations with alkynes

2022 ◽  
Author(s):  
Han Gao ◽  
Lingfei Hu ◽  
Yanlei Hu ◽  
Xiangying Lv ◽  
Yanbo Wu ◽  
...  
Keyword(s):  
Dft Calculations ◽  
Decomposition Analysis ◽  
Energy Decomposition Analysis ◽  
Energy Decomposition ◽  
Ligand Effects

The mechanism and origin of CpX ligand effects on Rh-catalyzed annulations with alkynes were investigated by using DFT calculations and the approach of energy decomposition analysis (EDA). The results reveal...

scholarly journals Benchmarking lithium amide versus amine bonding by charge density and energy decomposition analysis arguments

2018 ◽  
Vol 9 (12) ◽  
pp. 3111-3121 ◽  
Author(s):  
Felix Engelhardt ◽  
Christian Maaß ◽  
Diego M. Andrada ◽  
Regine Herbst-Irmer ◽  
Dietmar Stalke
Keyword(s):  
Quantum Theory ◽  
Dft Calculations ◽  
Charge Density ◽  
Decomposition Analysis ◽  
Atoms In Molecules ◽  
Energy Decomposition Analysis ◽  
Energy Decomposition ◽  
Lithium Amide ◽  
Experimental Charge Density ◽  
Amide Versus

We investigated [{(Me2NCH2)2(C4H2N)}Li]2 (1) by means of experimental charge density calculations based on the quantum theory of atoms in molecules (QTAIM) and DFT calculations using energy decomposition analysis (EDA).

scholarly journals From Intermolecular Interaction Energies and Observable Shifts to Component Contributions and Back Again: A Tale of Variational Energy Decomposition Analysis

2021 ◽  
Vol 72 (1) ◽  
pp. 641-666
Author(s):  
Yuezhi Mao ◽  
Matthias Loipersberger ◽  
Paul R. Horn ◽  
Akshaya Das ◽  
Omar Demerdash ◽  
...  
Keyword(s):  
Dft Calculations ◽  
Intermolecular Interaction ◽  
Density Functional ◽  
Decomposition Analysis ◽  
Radical Cations ◽  
Energy Decomposition Analysis ◽  
Interaction Energies ◽  
Energy Decomposition ◽  
Functional Theory ◽  
Pauli Repulsion

Quantum chemistry in the form of density functional theory (DFT) calculations is a powerful numerical experiment for predicting intermolecular interaction energies. However, no chemical insight is gained in this way beyond predictions of observables. Energy decomposition analysis (EDA) can quantitatively bridge this gap by providing values for the chemical drivers of the interactions, such as permanent electrostatics, Pauli repulsion, dispersion, and charge transfer. These energetic contributions are identified by performing DFT calculations with constraints that disable components of the interaction. This review describes the second-generation version of the absolutely localized molecular orbital EDA (ALMO-EDA-II). The effects of different physical contributions on changes in observables such as structure and vibrational frequencies upon complex formation are characterized via the adiabatic EDA. Example applications include red- versus blue-shifting hydrogen bonds; the bonding and frequency shifts of CO, N2, and BF bound to a [Ru(II)(NH3)5]2 + moiety; and the nature of the strongly bound complexes between pyridine and the benzene and naphthalene radical cations. Additionally, the use of ALMO-EDA-II to benchmark and guide the development of advanced force fields for molecular simulation is illustrated with the recent, very promising, MB-UCB potential.

The role of Cr, Mo and W in the electronic delocalization and the metal–ring interaction in metallocene complexes

2018 ◽  
Vol 42 (7) ◽  
pp. 5334-5344 ◽  
Author(s):  
David Arias-Olivares ◽  
Dayán Páez-Hernández ◽  
Rafael Islas
Keyword(s):  
Decomposition Analysis ◽  
Energy Decomposition Analysis ◽  
Metal Ring ◽  
Energy Decomposition ◽  
Natural Orbitals ◽  
Nucleus Independent Chemical Shift ◽  
Electronic Delocalization ◽  
Ring Interaction ◽  
Metallocene Complexes

Metal influence over triple-decker, sandwich-like and pyramidal structured benzenes was studied by means of energy decomposition analysis (Morokuma–Ziegler), combined with extended transition state natural orbitals for chemical valence, and Nucleus Independent Chemical Shift descriptors.

scholarly journals Looking at the big picture in activation strain model/energy decomposition analysis: the case of the ortho–para regioselectivity rule in Diels–Alder reactions

2020 ◽  
Vol 18 (6) ◽  
pp. 1104-1111 ◽  
Author(s):  
Nicolás Grimblat ◽  
Ariel M. Sarotti
Keyword(s):  
Dft Calculations ◽  
Decomposition Analysis ◽  
Diels Alder ◽  
Energy Decomposition Analysis ◽  
Energy Decomposition ◽  
Big Picture ◽  
Strain Model

The regioselectivity of the DA reaction is predicted by the ortho–para rule which has been explained from FMO theory. Using DFT calculations and ASM/EDA, we found that the results vary depending the position where it is performed.

scholarly journals Probing radical–molecule interactions with a second generation energy decomposition analysis of DFT calculations using absolutely localized molecular orbitals

2020 ◽  
Vol 22 (23) ◽  
pp. 12867-12885
Author(s):  
Yuezhi Mao ◽  
Daniel S. Levine ◽  
Matthias Loipersberger ◽  
Paul R. Horn ◽  
Martin Head-Gordon
Keyword(s):  
Dft Calculations ◽  
Second Generation ◽  
Decomposition Analysis ◽  
Closed Shell ◽  
Energy Decomposition Analysis ◽  
Proper Treatment ◽  
Energy Decomposition ◽  
Localized Molecular Orbitals ◽  
Intermolecular Complexes ◽  
Molecule Interactions

Proper treatment of intermolecular complexes formed by radicals and closed-shell molecules in energy decomposition analysis of DFT calculations.

scholarly journals HawkDock: a web server to predict and analyze the protein–protein complex based on computational docking and MM/GBSA

2019 ◽  
Vol 47 (W1) ◽  
pp. W322-W330 ◽  
Author(s):  
Gaoqi Weng ◽  
Ercheng Wang ◽  
Zhe Wang ◽  
Hui Liu ◽  
Feng Zhu ◽  
...  
Keyword(s):  
Free Energy ◽  
Protein Interactions ◽  
Decomposition Analysis ◽  
Scoring Function ◽  
Web Server ◽  
Energy Decomposition Analysis ◽  
Energy Decomposition ◽  
Computational Docking ◽  
Free Energy Decomposition ◽  
Key Residues

Abstract Protein–protein interactions (PPIs) play an important role in the different functions of cells, but accurate prediction of the three-dimensional structures for PPIs is still a notoriously difficult task. In this study, HawkDock, a free and open accessed web server, was developed to predict and analyze the structures of PPIs. In the HawkDock server, the ATTRACT docking algorithm, the HawkRank scoring function developed in our group and the MM/GBSA free energy decomposition analysis were seamlessly integrated into a multi-functional platform. The structures of PPIs were predicted by combining the ATTRACT docking and the HawkRank re-scoring, and the key residues for PPIs were highlighted by the MM/GBSA free energy decomposition. The molecular visualization was supported by 3Dmol.js. For the structural modeling of PPIs, HawkDock could achieve a better performance than ZDOCK 3.0.2 in the benchmark testing. For the prediction of key residues, the important residues that play an essential role in PPIs could be identified in the top 10 residues for ∼81.4% predicted models and ∼95.4% crystal structures in the benchmark dataset. To sum up, the HawkDock server is a powerful tool to predict the binding structures and identify the key residues of PPIs. The HawkDock server is accessible free of charge at http://cadd.zju.edu.cn/hawkdock/.

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