The Anisotropy of the Molecular Reorientational Motions in Liquid Methanol

1995 ◽  
Vol 50 (2-3) ◽  
pp. 211-216 ◽  
Author(s):  
R. Ludwig ◽  
Ph. A. Bopp ◽  
M. D. Zeidler
Keyword(s):  
Molecular Dynamics ◽  
Nuclear Magnetic Resonance ◽  
Low Temperatures ◽  
Nmr Relaxation ◽  
Md Simulations ◽  
Pure Liquid ◽  
Correlation Times ◽  
Detailed Understanding ◽  
Nmr Relaxation Time ◽  
Reorientational Dynamics

Abstract Nuclear magnetic resonance (NMR) relaxation time measurements on isotopically substituted samples yield a detailed understanding of the molecular reorientational dynamics in liquids. Reorientational correlation times obtained from such experiments are reported for two molecule-fixed vectors in pure liquid methanol. While the reorientational motions of single molecules are nearly isotropic at temperatures below 250 K, at 308 K the reorientational correlation time of the O-H vector becomes 2.3 times larger than that of the O-C vector. Molecular dynamics (MD) simulations give access to the complete correlation functions of the reorientational motions. Correlation times extracted from these functions fit well to the experiment in case of the O-C vector. At low temperatures, however, these times lie markedly above those obtained in the experiment for the O-H vector. Thus, the simulation yields reorientation times for the O-H vector that are, independent of the temperature, twice as large as those of the O-C vector.

Silver nitrate in aqueous solution and as molten salt: A molecular dynamics simulation and NMR relaxation study

1994 ◽  
Vol 72 (11) ◽  
pp. 2278-2285 ◽  
Author(s):  
Aatto Laaksonen ◽  
Helena Kovacs
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Silver Nitrate ◽  
Nmr Relaxation ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Correlation Times ◽  
Nitrate Ion ◽  
Relaxation Measurements ◽  
Dynamics Simulations

Using molecular dynamics simulations, the motion and intermolecular interactions of the ions of silver nitrate are studied in aqueous solution and compared to the results obtained from simulations of molten AgNO3. The particularly interesting and experimentally frequently studied modes of reorientational motion (in-plane and end-over-end) of the planar nitrate ion have been determined from the simulation results. In accordance with earlier experimental results, the correlation times for the end-over-end rotation in aqueous solution are longer than those for the in-plane rotation, while the opposite is found to hold in the melt. In addition, the rotational motion of the nitrate ion in aqueous solution is experimentally studied using 14N relaxation measurements. Good agreement is found between the reorientational correlation times obtained from MD simulations and from NMR relaxation measurements.

scholarly journals A method to construct the dynamic landscape of a bio-membrane with experiment and simulation

2022 ◽  
Vol 13 (1) ◽  
Author(s):  
Albert A. Smith ◽  
Alexander Vogel ◽  
Oskar Engberg ◽  
Peter W. Hildebrand ◽  
Daniel Huster
Keyword(s):  
Molecular Dynamics ◽  
Nmr Relaxation ◽  
Dynamics Simulation ◽  
Comprehensive Description ◽  
Correlation Times ◽  
Wide Range ◽  
Dynamic Landscape ◽  
C Nmr ◽  
Analysis Of Motion

AbstractBiomolecular function is based on a complex hierarchy of molecular motions. While biophysical methods can reveal details of specific motions, a concept for the comprehensive description of molecular dynamics over a wide range of correlation times has been unattainable. Here, we report an approach to construct the dynamic landscape of biomolecules, which describes the aggregate influence of multiple motions acting on various timescales and on multiple positions in the molecule. To this end, we use 13C NMR relaxation and molecular dynamics simulation data for the characterization of fully hydrated palmitoyl-oleoyl-phosphatidylcholine bilayers. We combine dynamics detector methodology with a new frame analysis of motion that yields site-specific amplitudes of motion, separated both by type and timescale of motion. In this study, we show that this separation allows the detailed description of the dynamic landscape, which yields vast differences in motional amplitudes and correlation times depending on molecular position.

Molecular Dynamics of Cellulose-Water Systems Investigated by NMR Relaxation Method

Holzforschung ◽  
2000 ◽  
Vol 54 (5) ◽  
pp. 501-504 ◽  
Author(s):  
K. Banas ◽  
B. Blicharska ◽  
W. Dietrich ◽  
M. Kluza
Keyword(s):  
Molecular Dynamics ◽  
Relaxation Time ◽  
Nmr Relaxation ◽  
Relaxation Method ◽  
Water Systems ◽  
Motion Model ◽  
Cellulose Pulp ◽  
Time Dependencies ◽  
Nmr Relaxation Time ◽  
Different Origin

Summary On the basis of the proton NMR relaxation time dependencies on temperature and frequency in cellulose pulp a simple two-motion model of molecular dynamics has been proposed. The parameters, activation energies and correlation times, describing the model may be correlated with structure features such as level of crystallinity of cellulose with different origin, as well as degree of paper devastation.

scholarly journals Predicting NMR Relaxation of Proteins from Molecular Dynamics Simulations with Accurate Methyl Rotation Barriers

2020 ◽  
Author(s):  
Falk Hoffmann ◽  
Frans Mulder ◽  
Lars V. Schäfer
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Force Fields ◽  
Nmr Relaxation ◽  
Md Simulations ◽  
Quantitative Agreement ◽  
Relaxation Rates ◽  
Protein Force Fields ◽  
Dynamics Simulations ◽  
Methyl Rotation

The internal dynamics of proteins occurring on time scales from picoseconds to nanoseconds can be sensitively probed by nuclear magnetic resonance (NMR) spin relaxation experiments, as well as by molecular dynamics (MD) simulations. This complementarity offers unique opportunities, provided that the two methods are compared at a suitable level. Recently, several groups have used MD simulations to compute the spectral density of backbone and side-chain molecular motions, and to predict NMR relaxation rates from these. Unfortunately, in the case of methyl groups in protein side-chains, inaccurate energy barriers to methyl rotation were responsible for a systematic discrepancy in the computed relaxation rates, as demonstrated for the AMBER ff99SB*-ILDN force field (and related parameter sets), impairing quantitative agreement between simulations and experiments. However, correspondence could be regained by emending the MD force field with accurate coupled cluster quantum chemical calculations. Spurred by this positive result, we tested whether this approach could be generally applicable, in spite of the fact that different MD force fields employ different water models. Improved methyl group rotation barriers for the CHARMM36 and AMBER ff15ipq protein force fields were derived, such that the NMR relaxation data obtained from the MD simulations now also display very good agreement with experiment. Results herein showcase the performance of present-day MD force fields, and manifest their refined ability to accurately describe internal protein dynamics.

scholarly journals Predicting NMR Relaxation of Proteins from Molecular Dynamics Simulations with Accurate Methyl Rotation Barriers

2019 ◽  
Author(s):  
Falk Hoffmann ◽  
Frans Mulder ◽  
Lars V. Schäfer
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Force Fields ◽  
Nmr Relaxation ◽  
Md Simulations ◽  
Quantitative Agreement ◽  
Relaxation Rates ◽  
Protein Force Fields ◽  
Dynamics Simulations ◽  
Methyl Rotation

The internal dynamics of proteins occurring on time scales from picoseconds to nanoseconds can be sensitively probed by nuclear magnetic resonance (NMR) spin relaxation experiments, as well as by molecular dynamics (MD) simulations. This complementarity offers unique opportunities, provided that the two methods are compared at a suitable level. Recently, several groups have used MD simulations to compute the spectral density of backbone and side-chain molecular motions, and to predict NMR relaxation rates from these. Unfortunately, in the case of methyl groups in protein side-chains, inaccurate energy barriers to methyl rotation were responsible for a systematic discrepancy in the computed relaxation rates, as demonstrated for the AMBER ff99SB*-ILDN force field (and related parameter sets), impairing quantitative agreement between simulations and experiments. However, correspondence could be regained by emending the MD force field with accurate coupled cluster quantum chemical calculations. Spurred by this positive result, we tested whether this approach could be generally applicable, in spite of the fact that different MD force fields employ different water models. Improved methyl group rotation barriers for the CHARMM36 and AMBER ff15ipq protein force fields were derived, such that the NMR relaxation data obtained from the MD simulations now also display very good agreement with experiment. Results herein showcase the performance of present-day MD force fields, and manifest their refined ability to accurately describe internal protein dynamics.

scholarly journals Predicting NMR Relaxation of Proteins from Molecular Dynamics Simulations with Accurate Methyl Rotation Barriers

2019 ◽  
Author(s):  
Falk Hoffmann ◽  
Frans Mulder ◽  
Lars V. Schäfer
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Force Fields ◽  
Nmr Relaxation ◽  
Md Simulations ◽  
Quantitative Agreement ◽  
Relaxation Rates ◽  
Protein Force Fields ◽  
Dynamics Simulations ◽  
Methyl Rotation

The internal dynamics of proteins occurring on time scales from picoseconds to nanoseconds can be sensitively probed by nuclear magnetic resonance (NMR) spin relaxation experiments, as well as by molecular dynamics (MD) simulations. This complementarity offers unique opportunities, provided that the two methods are compared at a suitable level. Recently, several groups have used MD simulations to compute the spectral density of backbone and side-chain molecular motions, and to predict NMR relaxation rates from these. Unfortunately, in the case of methyl groups in protein side-chains, inaccurate energy barriers to methyl rotation were responsible for a systematic discrepancy in the computed relaxation rates, as demonstrated for the AMBER ff99SB*-ILDN force field (and related parameter sets), impairing quantitative agreement between simulations and experiments. However, correspondence could be regained by emending the MD force field with accurate coupled cluster quantum chemical calculations. Spurred by this positive result, we tested whether this approach could be generally applicable, in spite of the fact that different MD force fields employ different water models. Improved methyl group rotation barriers for the CHARMM36 and AMBER ff15ipq protein force fields were derived, such that the NMR relaxation data obtained from the MD simulations now also display very good agreement with experiment. Results herein showcase the performance of present-day MD force fields, and manifest their refined ability to accurately describe internal protein dynamics.

Water inside carbon nanotubes: structure and dynamics

2016 ◽  
Vol 5 (3) ◽  
Author(s):  
Jamal Hassan ◽  
Georgios Diamantopoulos ◽  
Dirar Homouz ◽  
Georgios Papavassiliou
Keyword(s):  
Carbon Nanotubes ◽  
Molecular Dynamics ◽  
Nuclear Magnetic Resonance ◽  
Md Simulations ◽  
Liquid Transport ◽  
Comprehensive Review ◽  
Structure And Dynamics ◽  
Potential Applications ◽  
Nmr Methods ◽  
Theoretical Results

AbstractStudying the properties of water confined in carbon nanotubes (CNTs) have gained a lot of interest in recent years due to the vast potential applications of systems in nanoscale liquid transport as well as biology functions. This article presents a comprehensive review of recent experimental and theoretical results using nuclear magnetic resonance (NMR) and molecular dynamics (MD) simulations. Different NMR methods including

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