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Diffusion and Friction Dynamics of Probe Molecules in Liquid n-Alkane Systems: A Molecular Dynamics Simulation Study. J CHEM-NY 2019. [DOI: 10.1155/2019/8134904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
We present a molecular dynamics simulation study of the probe diffusion and friction dynamics of Lennard-Jones particles in a series of liquid n-alkane systems from C12 up to C400 at 318 K, 418 K, 518 K, and 618 K, to investigate the power law dependence of self-diffusion of polymer liquids on their molecular weights. Two LJ particles MY1 with a mass of 114 g/mol and MY2 with a mass of 225 g/mol are used as probes to model methyl yellow. We observed that a clear transition in the power law dependence of n-alkane self-diffusion on the molecular weight (M) of n-alkane, Dself∼M−γ, occurs in the range C120∼C160 at temperatures of 318 K, 418 K, and 518 K, corresponding to a crossover from the “oligomer” to the “Rouse” regime. We also observed that a clear transition in the power law dependence of the diffusion coefficient DMY2 on the molecular weight (M) of n-alkane, DMY2∼M−γ, occurs at low temperatures. The exponent γ for DMY2 shows a sharp transition from 1.21 to 0.52 near C36 at 418 K and from 1.54 to 0.60 near C36 at 318 K. However, no such transition is found for the probe molecule MY2 at temperatures of 518 K and 618 K and for MY1 probe at temperatures of 418 K, 518 K, and 618 K, but the power law exponent γ for MY1 at 318 K shows instead a linear or a rather slow transition. The dependence of the probe diffusion (DMY2) on the matrix molecular weight (M) reflects a significant change of the matrix dynamics associated with the probe diffusion: a crossover from the “solvent-like” to the “oligomer” regime. As the molecular weight of n-alkane increases, the ratio of Dself/DMY2 becomes less than 1 and the probe molecules encounter, in turn, two different microscopic frictions depending on MMY/Mmatrix and the temperature. It is believed that a reduction in the microscopic friction on the probe molecules that diffuse at a rate faster than the solvent fluctuations leads to large deviations of slope from the linear dependence of the friction of MY2 on the chain length of the n-alkane at 318 K and 418 K.
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Forrey C, Saylor DM, Silverstein JS, Douglas JF, Davis EM, Elabd YA. Prediction and validation of diffusion coefficients in a model drug delivery system using microsecond atomistic molecular dynamics simulation and vapour sorption analysis. SOFT MATTER 2014; 10:7480-7494. [PMID: 25115846 DOI: 10.1039/c4sm01297f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Diffusion of small to medium sized molecules in polymeric medical device materials underlies a broad range of public health concerns related to unintended leaching from or uptake into implantable medical devices. However, obtaining accurate diffusion coefficients for such systems at physiological temperature represents a formidable challenge, both experimentally and computationally. While molecular dynamics simulation has been used to accurately predict the diffusion coefficients, D, of a handful of gases in various polymers, this success has not been extended to molecules larger than gases, e.g., condensable vapours, liquids, and drugs. We present atomistic molecular dynamics simulation predictions of diffusion in a model drug eluting system that represent a dramatic improvement in accuracy compared to previous simulation predictions for comparable systems. We find that, for simulations of insufficient duration, sub-diffusive dynamics can lead to dramatic over-prediction of D. We present useful metrics for monitoring the extent of sub-diffusive dynamics and explore how these metrics correlate to error in D. We also identify a relationship between diffusion and fast dynamics in our system, which may serve as a means to more rapidly predict diffusion in slowly diffusing systems. Our work provides important precedent and essential insights for utilizing atomistic molecular dynamics simulations to predict diffusion coefficients of small to medium sized molecules in condensed soft matter systems.
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Affiliation(s)
- Christopher Forrey
- Division of Chemistry and Materials Science, Center for Devices and Radiological Health, US Food and Drug Administration, USA.
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Sun MF, Yang SC, Chang KW, Tsai TY, Chen HY, Tsai FJ, Lin JG, Chen CYC. Screening from TCM Database@Taiwan and QSAR model for identifying HER2 inhibitors. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2011.569550] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Sun MF, Chang TT, Chen KC, Yang SC, Chang KW, Tsai TY, Chen HY, Tsai FJ, Lin JG, Chen CYC. Treat Alzheimer's disease by traditional Chinese medicine? MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2011.577074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Chang TT, Sun MF, Chen KC, Wong YH, Yang SC, Chen HY, Tsai FJ, Fisher M, Lee CL, Fang WC, Chen CYC. Drug discovery for DNA break repair system by screening from TCM database and molecular dynamics approach. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2010.548388] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Tung-Ti Chang
- a Department of Chinese Pediatrics , China Medical University Hospital , Taichung, Taiwan ROC
| | - Mao-Feng Sun
- b Department of Acupuncture , China Medical University Hospital , Taichung, Taiwan ROC
| | - Kuan-Chung Chen
- c Laboratory of Computational and Systems Biology , School of Chinese Medicine, China Medical University , Taichung, 40402, Taiwan ROC
| | - Yung-Hao Wong
- c Laboratory of Computational and Systems Biology , School of Chinese Medicine, China Medical University , Taichung, 40402, Taiwan ROC
| | - Shun-Chieh Yang
- c Laboratory of Computational and Systems Biology , School of Chinese Medicine, China Medical University , Taichung, 40402, Taiwan ROC
| | - Hsin-Yi Chen
- c Laboratory of Computational and Systems Biology , School of Chinese Medicine, China Medical University , Taichung, 40402, Taiwan ROC
| | - Fuu-Jen Tsai
- d Department of Bioinformatics , Asia University , Taichung, 41354, Taiwan ROC
- e Department of Medical Genetics, Pediatrics and Medical Research , College of Chinese Medicine, China Medical University , Taichung, 40402, Taiwan ROC
| | - Mark Fisher
- f Harvard-MIT Division of Health Sciences and Technology , 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Chun-Lin Lee
- g Department of Business Administration , National Taipei University , Taipei, Taiwan ROC
| | - Wen-Chang Fang
- g Department of Business Administration , National Taipei University , Taipei, Taiwan ROC
| | - Calvin Yu-Chian Chen
- c Laboratory of Computational and Systems Biology , School of Chinese Medicine, China Medical University , Taichung, 40402, Taiwan ROC
- d Department of Bioinformatics , Asia University , Taichung, 41354, Taiwan ROC
- f Harvard-MIT Division of Health Sciences and Technology , 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- h Computational and Systems Biology , Massachusetts Institute of Technology , Cambridge, MA, 02139, USA
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Chang TT, Sun MF, Chang KW, Chen HY, Tsai FJ, Fisher M, Lin JG, Chen CYC. Screening from the world's largest TCM database for inhibiting DNA repair protein XRCC4. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2011.554550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Chang TT, Sun MF, Chen HY, Tsai FJ, Fisher M, Lin JG, Chen CYC. Novel hemagglutinin inhibitors for H1N1 influenza virus screening from TCM database. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2010.543973] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Tung-Ti Chang
- a Laboratory of Computational and Systems Biology, School of Chinese Medicine, China Medical University , Taichung, 40402, Taiwan, ROC
- b Department of Chinese Pediatrics , China Medical University Hospital , Taichung, 40402, Taiwan, ROC
| | - Mao-Feng Sun
- a Laboratory of Computational and Systems Biology, School of Chinese Medicine, China Medical University , Taichung, 40402, Taiwan, ROC
- c Department of Acupuncture , China Medical University Hospital , Taichung, 40402, Taiwan, ROC
| | - Hsin-Yi Chen
- d Department of Bioinformatics , Asia University , Taichung, 41354, Taiwan, ROC
| | - Fuu-Jen Tsai
- d Department of Bioinformatics , Asia University , Taichung, 41354, Taiwan, ROC
- e Department of Medical Genetics , China Medical University , Taichung, 40402, Taiwan, ROC
| | - Mark Fisher
- f Harvard-MIT Division of Health Sciences and Technology , 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Jaung-Geng Lin
- a Laboratory of Computational and Systems Biology, School of Chinese Medicine, China Medical University , Taichung, 40402, Taiwan, ROC
| | - Calvin Yu-Chian Chen
- a Laboratory of Computational and Systems Biology, School of Chinese Medicine, China Medical University , Taichung, 40402, Taiwan, ROC
- d Department of Bioinformatics , Asia University , Taichung, 41354, Taiwan, ROC
- f Harvard-MIT Division of Health Sciences and Technology , 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- g Computational and Systems Biology, Massachusetts Institute of Technology , Cambridge, MA, 02139, USA
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Li CL, Chang TT, Sun MF, Chen HY, Tsai FJ, Fisher M, Chen CYC, Lee CL, Fang WC, Wong YH. Structure-based and ligand-based drug design for microsomal prostaglandin E synthase-1 inhibitors. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2010.538054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Lai CY, Chang TT, Sun MF, Chen HY, Tsai FJ, Lin JG, Chen CYC. Molecular dynamics analysis of potent inhibitors of M2 proton channel against H1N1 swine influenza virus. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2010.543972] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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