Molecular mechanics (MM4) studies have been carried out on the catenane (C13H26)2, specifically 13-13D2. The structure obtained is in general agreement with second-order perturbation theory. More importantly, the MM4 structure allows a breakdown of the energy of the molecule into its component classical parts. This allows an understanding of why the structure is so distorted, in terms of C-C bonding and nonbonding interactions, van der Waals repulsion, C-C-C and C-C-H angle bending, torsional energies, stretch-bend, torsion-stretch, and bend-torsion-bend interactions. Clearly, the hole in 113-membered ring is too small for the other ring to fit through comfortably. There are too many atoms trying to fit into the limited space at the same time, leading to large van der Waals repulsions. The rings distort in such a way as to enlarge this available space, and lower the total energy of the molecule. While the distortions are spread around the rings, one of the nominally tetrahedral C-C-C bond angles in each ring is opened to 147.9° by MM4 (146.8° by MP2). The stability of the compound is discussed in terms of the strain energy.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1002/jcc.24193 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Correction: Engineering extracellular vesicles for ROS scavenging and tissue regeneration.
Nano Converg
January 2025
Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA.
Hybrid molecular-scale and continuum modeling of two-dimensional flow between inhomogeneous solid surfaces and its application to the thrust bearing.
J Mol Model
January 2025
College of Mechanical Engineering, Changzhou University, Changzhou, Jiangsu Province, China.
Context: The flow equations are derived for describing the two-dimensional hybrid molecular-scale and continuum flows in the very small surface separation with inhomogeneous solid surfaces and they can be applied for designing the specific bearings. The aim of the present study is to solve this specific flow problem in engineering with normal computational cost. The flow factor approach model describes the flow of the molecule layer adjacent to the solid surface and the Newtonian fluid model describes the flow of the intermediate continuum fluid.
View Article and Find Full Text PDFDeep Learning of CYP450 Binding of Small Molecules by Quantum Information.
J Chem Inf Model
January 2025
Industrial and Molecular Pharmaceutics, Purdue University, West Lafayette, Indiana 47907, United States.
Drug-drug interaction can lead to diminished therapeutic effects or increased toxicity, posing significant risks, especially in polypharmacy, and cytochrome P450 plays an indispensable role in this interaction. Cytochrome P450, responsible for the metabolism and detoxification of most drugs, metabolizes about 90% of Food and Drug Administration-approved drugs, making early detection of potential drug-drug interactions. Over the years, in-silico modeling has become a valuable tool for predicting drug-drug interactions.
View Article and Find Full Text PDFMolecular dynamics work on thermal conductivity of SiGe nanotubes.
J Mol Model
January 2025
School of Mechanics and Safety Engineering, Zhengzhou University, Zhengzhou, 450001, People's Republic of China.
Context: SiGe nanotubes (SiGeNTs) hold significant promise for applications in nanosolar cells, optoelectronic systems, and interconnects, where thermal conductivity is critical to performance. This study investigates the effects of length, diameter, temperature, and axial strain on the thermal conductivity of armchair and zigzag SiGeNTs through molecular dynamics simulations. Results indicate that thermal conductivity increases with sample length due to ballistic heat transport and decreases with temperature as phonon scattering intensifies.
View Article and Find Full Text PDFHydration Effects Driving Network Remodeling in Hydrogels during Cyclic Loading.
ACS Macro Lett
January 2025
Materials Science and Engineering Department, Technion-Israel Institute of Technology, Haifa 3200003, Israel.
In complex networks and fluids such as the extracellular matrix, the mechanical properties are substantially affected by the movement of polymers both part of and entrapped in the network. As many cells are sensitive to the mechanical remodeling of their surroundings, it is important to appreciate how entrapped polymers may inhibit or facilitate remodeling in the network. Here, we explore a molecular-level understanding of network remodeling in a complex hydrogel environment through successive compressive loading and the role that noninteracting polymers may play in a dynamic network.
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!