Results 1 to 10 of about 34,457 (165)

Intramolecular Force Mapping at Room Temperature [PDF]

ACS Nano, 2023
Acquisition of dense, three-dimensional, force fields with intramolecular resolution via noncontact atomic force microscopy (NC-AFM) has yielded enormous progress in our ability to characterize molecular and two-dimensional materials at the atomic scale. To date, intramolecular force mapping has been performed exclusively at cryogenic temperatures, due
Brown, T., Blowey, P.J., Henry, J., Sweetman, A.   +3 more
openaire   +4 more sources

Accelerating QM/MM Free Energy Computations via Intramolecular Force Matching [PDF]

Journal of Chemical Theory and Computation, 2018
The calculation of free energy differences between levels of theory has numerous potential pitfalls. Chief among them is the lack of overlap, i.e., ensembles generated at one level of theory (e.g., "low") not being good approximations of ensembles at the other (e.g., "high"). Numerous strategies have been devised to mitigate this issue.
Phillip S. Hudson, Stefan Boresch, David M. Rogers, H. Lee Woodcock   +3 more
openaire   +4 more sources

The Interplay of Inter- and Intramolecular Hydrogen Bonding in Ether Alcohols Related to n-Octanol [PDF]

Molecules
n-Octanol and related ether alcohols are studied via molecular dynamics (MD) simulations using the two classical all-atom force fields OPLS-AA and CHARMM. The ether alcohols studied possess one ether functionality separated by varying n carbon atoms from
Markus M. Hoffmann, Troy N. Smith, Gerd Buntkowsky   +2 more
doaj   +2 more sources

The intramolecular stabilizing effects of O-benzoyl substituents as a driving force of the acid-promoted pyranoside-into-furanoside rearrangement [PDF]

Beilstein Journal of Organic Chemistry
Furanoside derivatives are broadly present in the antigenic structures of pathogenic microorganisms and play a key role in their recognition by the host immune system.
Alexey G. Gerbst, Sofya P. Nikogosova, Darya A. Rastrepaeva, Dmitry A. Argunov, Vadim B. Krylov, Nikolay E. Nifantiev   +5 more
doaj   +2 more sources

Intramolecular proton transfer reaction dynamics using machine-learned ab initio potential energy surfaces

Machine Learning: Science and Technology, 2023
Hydrogen bonding interactions, which are central to various physicochemical processes, are investigated in the present study using ab initio -based machine learning potential energy surfaces.
Shampa Raghunathan, Sai Ajay Kashyap Nakirikanti   +1 more
doaj   +1 more source

Exploring Intramolecular Methyl–Methyl Coupling on a Metal Surface for Edge-Extended Graphene Nanoribbons

Organic Materials, 2021
Intramolecular methyl–methyl coupling on Au (111) is explored as a new on-surface protocol for edge extension in graphene nanoribbons (GNRs). Characterized by high-resolution scanning tunneling microscopy, noncontact atomic force microscopy, and Raman ...
Zijie Qiu, Qiang Sun, Shiyong Wang, Gabriela Borin Barin, Bastian Dumslaff, Pascal Ruffieux, Klaus Müllen, Akimitsu Narita, Roman Fasel   +8 more
doaj   +1 more source

Atomistic Simulation of Lysozyme in Solutions Crowded by Tetraethylene Glycol: Force Field Dependence

Molecules, 2022
The behavior of biomolecules in crowded environments remains largely unknown due to the accuracy of simulation models and the limited experimental data for comparison.
Donglin Liu, Yejie Qiu, Qing Li, Haiyang Zhang   +3 more
doaj   +1 more source

Research progress of single molecule force spectroscopy technology based on atomic force microscopy in polymer materials: Structure, design strategy and probe modification

Nano Select, 2021
With the rapid development of polymer materials, the simultaneous acquisition of micro‐nano structure and mesoscopic mechanical properties from the material surface with the transverse resolution of nanoscale has become a hot spot in the research of ...
Shi Li, Xiao Wang, Zhihua Li, Zhenzhu Huang, Shudong Lin, Jiwen Hu, Yuanyuan Tu   +6 more
doaj   +1 more source

Data scheme and data format for transferable force fields for molecular simulation

Scientific Data, 2023
A generalized data scheme for transferable classical force fields used in molecular simulations, i.e. molecular dynamics and Monte Carlo simulation, is presented. The data scheme is implemented in an SQL-based data format. The data scheme and data format
Gajanan Kanagalingam, Sebastian Schmitt, Florian Fleckenstein, Simon Stephan   +3 more
doaj   +1 more source

Quantum dissipation driven by electron transfer within a single molecule investigated with atomic force microscopy

Nature Communications, 2020
Here, the authors use atomic force microscopy under ultra-high vacuum conditions to study intramolecular single electron transfer within a single molecule.
Jan Berger, Martin Ondráček, Oleksandr Stetsovych, Pavel Malý, Petr Holý, Jiří Rybáček, Martin Švec, Irena G. Stará, Tomáš Mančal, Ivo Starý, Pavel Jelínek   +10 more
doaj   +1 more source