A complex chemical system is often examined based on their fragments, so fragment-based analysis is the key to chemical understanding. We report the natural fragment bond orbital (NFBO) method for interfragment bonding interaction analysis, as an extension to the well-known natural bond orbital method. NFBOs together with their corresponding natural fragment hybrid orbitals (NFHOs) allow us to derive local bonding and antibonding orbitals among fragments from the delocalized canonical molecular orbitals. In this paper, we provide the algorithm for finding NFBOs and showcase its application to several chemically interesting systems featuring significant interfragment bonding interactions. Through these examples, the NFBO method is shown to be a powerful tool with which to analyze the electronic structures of molecules possessing strong interfragment bonding interactions.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1021/jacs.4c12421 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Natural Fragment Bond Orbital Method for Interfragment Bonding Interaction Analysis.
J Am Chem Soc
December 2024
Department of Chemistry, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China.
A complex chemical system is often examined based on their fragments, so fragment-based analysis is the key to chemical understanding. We report the natural fragment bond orbital (NFBO) method for interfragment bonding interaction analysis, as an extension to the well-known natural bond orbital method. NFBOs together with their corresponding natural fragment hybrid orbitals (NFHOs) allow us to derive local bonding and antibonding orbitals among fragments from the delocalized canonical molecular orbitals.
View Article and Find Full Text PDFDiverse Self-Assembled Molecular Architectures Promoted by C-H···O and C-H···Cl Hydrogen Bonds in a Triad of α-Diketone, α-Ketoimine, and an Imidorhenium Complex: A Unified Analysis Based on XRD, NEDA, SAPT, QTAIM, and IBSI Studies.
ACS Omega
November 2024
Department of Chemistry, St. Paul's Cathedral Mission College, University of Calcutta, 33/1 Raja Rammohan Roy Sarani, Kolkata 700009, India.
X-ray structural elucidation, supramolecular self-assembly, and energetics of existential noncovalent interactions for a triad comprising α-diketone, α-ketoimine, and an imidorhenium complex are highlighted in this report. Molecular packing reveals a self-assembled 2D network stabilized by the C-H···O H-bonds for the α-diketone (benzil), and the first structural report of Brown and Sadanaga stressing on the prevalence of seems to be an oversimplified conjecture. In the α-ketoimine, the imine nitrogen atom undergoes intramolecular N···H interaction to render itself inert toward intermolecular C-H···N interaction and exhibits two types of C-H···O H-bonds in consequence to generate a self-assembled 2D molecular architecture.
View Article and Find Full Text PDFFMOe: Preprocessing and Visualizing Package of the Fragment Molecular Orbital Method for Molecular Operating Environment and Its Applications in Covalent Ligand and Metalloprotein Analyses.
J Chem Inf Model
September 2024
Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
Article Synopsis
- The fragment molecular orbital (FMO) method efficiently analyzes large biomolecules by breaking them into smaller fragments and calculating their interaction energies, which helps understand molecular recognition.
- A graphical user interface was developed to facilitate manual fragmentation of small molecules and enhance the workflow for FMO calculations in the Molecular Operating Environment (MOE).
- The study demonstrated effective fragmentation and interaction analyses for complex cases like cysteine-ligand bonding in SARS-CoV-2 and metal coordination in peptides, indicating potential for advancements in drug discovery.
Exploring the influence of metal cations on individual hydrogen bonds in Watson-Crick guanine-cytosine DNA base pair: An interacting quantum atoms analysis.
J Comput Chem
October 2024
Department of Chemistry, Isfahan University of Technology, Isfahan, Iran.
This study delves into the nature of individual hydrogen bonds and the relationship between metal cations and hydrogen bonding in the Watson-Crick guanine-cytosine (GC) base pair and its alkali and alkaline earth cation-containing complexes (M-GC). The findings reveal how metal cations affect the nature and strength of individual hydrogen bonds. The study employs interacting quantum atoms (IQA) analysis to comprehensively understand three individual hydrogen bonds within the GC base pair and its cationic derivatives.
View Article and Find Full Text PDFMerging the Energy Decomposition Analysis with the Interacting Quantum Atoms Approach.
J Chem Theory Comput
June 2023
Institut de Química Computacional i Catàlisi i Departament de Química, Universitat de Girona, c/ Maria Aurèlia Capmany i Farnés 69, 17003 Girona, Catalonia, Spain.
Energy decomposition analysis (EDA) is a well-established approach to dissect the interaction energy into chemically sound components. Despite the inherent requirement of reference states has been a long-standing object of debate, the direct relation with the molecular orbital analysis helps in building up predictive models. The alternative molecular energy decomposition schemes that decompose the total energy into atomic and diatomic contributions, such as the interacting quantum atoms (IQA), has no external reference requirements and also the intra- and intermolecular interactions are treated on equal footing.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!