Cited Article: Hummer, G. Water conduction through the hydrophobic channel of a carbon nanotube
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Title:
Water in the Polar and Nonpolar Cavities of the Protein Interleukin-1 beta
Authors:
Yin, H; Feng, GG; Clore, GM; Hummer, G; Rasaiah, JC
Author Full Names:
Yin, Hao; Feng, Guogang; Clore, G. Marius; Hummer, Gerhard; Rasaiah, Jayendran C.
Source:
JOURNAL OF PHYSICAL CHEMISTRY B 114 (49): 16290-16297 DEC 16 2010
Language:
English
Document Type:
Article
KeyWords Plus:
HIGH-PRESSURE CRYSTALLOGRAPHY; MOLECULAR-DYNAMICS; BOUND WATER; 3-DIMENSIONAL STRUCTURE; HYDROPHOBIC CAVITY; CRYSTAL-STRUCTURE; DISORDERED WATER; NMR-SPECTROSCOPY; AQUEOUS-SOLUTION; FREE-ENERGIES
Abstract:
Water in the protein interior serves important structural and functional roles and is also increasingly recognized as a relevant factor in drug binding. The nonpolar cavity in the protein interleulcin-l beta has been reported to be filled by water on the basis of some experiments and simulations and to be empty on the basis of others. Here we study the thermodynamics of filling the central nonpolar cavity and the four polar cavities of interleukin-1 beta by molecular dynamics simulation. We use different water models (TIP3P and SPC/E) and protein force fields (amber94 and amber03) to calculate the semigrand partition functions term by term that quantify the hydration equilibria. We consistently find that water in the central nonpolar cavity is thermodynamically unstable, independent of force field and water model. The apparent reason is the relatively small size of the cavity, with a volume less than 80 similar to angstrom(3). Our results are consistent with the most recent X
-ray crystallographic and simulation studies but disagree with an earlier interpretation of nuclear magnetic resonance (NMR) experiments probing protein water interactions. We show that, at least semiquantitatively, the measured nuclear Overhauser effects indicating the proximity of water to the methyl groups lining the nonpolar cavity can, in all likelihood, be attributed to interactions with buried and surface water molecules near the cavity. The same methods applied to determine the occupancy of the polar cavities show that they are filled by the same number of water molecules observed in crystallography, thereby validating the theoretical and simulation methods used to study the water occupancy in the nonpolar protein cavity.
Reprint Address:
Hummer, G, NIDDK, Chem Phys Lab, NIH, Bethesda, MD 20892 USA.
Research Institution addresses:
[Clore, G. Marius; Hummer, Gerhard] NIDDK, Chem Phys Lab, NIH, Bethesda, MD 20892 USA; [Yin, Hao; Feng, Guogang; Rasaiah, Jayendran C.] Univ Maine, Dept Chem, Orono, ME 04469 USA
E-mail Address:
Gerhard.Hummer@nih.gov; rasaiah@maine.edu
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Times Cited:
0
Publisher:
AMER CHEMICAL SOC; 1155 16TH ST, NW, WASHINGTON, DC 20036 USA
Subject Category:
Chemistry, Physical
ISSN:
1520-6106
DOI:
10.1021/jp108731r
IDS Number:
690GO
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Title:
Molecular Dynamics Study of the Structures and Dynamics of the Iodine Molecules Confined in AlPO4-11 Crystals
Authors:
Hu, JM; Zhai, JP; Wu, FM; Tang, ZK
Author Full Names:
Hu, J. M.; Zhai, J. P.; Wu, F. M.; Tang, Z. K.
Source:
JOURNAL OF PHYSICAL CHEMISTRY B 114 (49): 16481-16486 DEC 16 2010
Language:
English
Document Type:
Article
KeyWords Plus:
ABSOLUTE FREQUENCY-MEASUREMENT; WALLED CARBON NANOTUBES; ABSORPTION-SPECTRUM; FORCE-FIELD; MECHANICS; SIMULATIONS; ATOMS; LASER; WATER; NM
Abstract:
Structural and dynamical properties of iodine molecules incorporated in one-dimensional elliptic channels of AlPO4-11 (AEL) crystals were studied by means of molecular dynamics (MD) simulations. It was found that the iodine molecules in the AEL channels are restricted in the (101) planes with only two favorite orientations: lying along the channels and standing along the major axes of the ellipses, which are well consistent with the experimental observations. In addition, the iodine structures are largely dependent on the loading level: with the increase of loading, the iodine specimens change their structures accordingly from isolated molecules as in the gas phase to single molecular chains and molecular ribbon sheets. The molecular ribbon sheets are composed of equally distributed and parallel molecules as in the iodine crystals. The simulation results show that the standing iodine molecules in the AEL channels are well restricted due to both the appropriate size of ellipse
s and their alternation throughout the channels. They can diffuse along the channels only after overcoming the rotational barriers to become lying molecules, which indicate that the iodine molecules in the ribbon sheets can keep the configurations without rotational and translational motion. The confined iodine molecules with such structures and properties may be used to improve the accuracy of the frequency standards.
Reprint Address:
Tang, ZK, Hong Kong Univ Sci & Technol, Dept Phys, Kowloon, Hong Kong, Peoples R China.
Research Institution addresses:
[Hu, J. M.; Tang, Z. K.] Hong Kong Univ Sci & Technol, Dept Phys, Kowloon, Hong Kong, Peoples R China; [Hu, J. M.; Tang, Z. K.] Hong Kong Univ Sci & Technol, Inst Nano Sci & Technol, Kowloon, Hong Kong, Peoples R China; [Zhai, J. P.] Shenzhen Univ, Coll Elect Sci & Technol, Shenzhen 518060, Peoples R China; [Wu, F. M.] Zhejiang Normal Univ, Inst Condensed Matter Phys, Jinhua 321004, Zhejiang, Peoples R China
E-mail Address:
phzktang@ust.hk
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0
Publisher:
AMER CHEMICAL SOC; 1155 16TH ST, NW, WASHINGTON, DC 20036 USA
Subject Category:
Chemistry, Physical
ISSN:
1520-6106
DOI:
10.1021/jp1076615
IDS Number:
690GO
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Title:
Kinetics and Solvent-Dependent Thermodynamics of Water Capture by a Fullerene-Based Hydrophobic Nanocavity
Authors:
Frunzi, M; Baldwin, AM; Shibata, N; Iwamatsu, SI; Lawler, RG; Turro, NJ
Author Full Names:
Frunzi, Michael; Baldwin, Anne M.; Shibata, Nobuyuki; Iwamatsu, Sho-Ichi; Lawler, Ronald G.; Turro, Nicholas J.
Source:
JOURNAL OF PHYSICAL CHEMISTRY A 115 (5): 735-740 FEB 10 2011
Language:
English
Document Type:
Article
KeyWords Plus:
OPEN-CAGE FULLERENE; CARBON NANOTUBES; MOLECULES; ENCAPSULATION; NMR; COMPLEXES; CHEMISTRY; PROTEINS; CLUSTERS; CAVITIES
Abstract:
Kinetic and thermodynamic properties of water encapsulation from organic solution by an open-cage [60]fullerene derivative have been investigated. 2D exchange NMR spectroscopy (EXSY) measurements were employed to determine the association and dissociation constants at 300 330 K (k(a) = 4.3 M-1 x s(-1) and k(d) = 0.42 s(-1) at 300 K) in 1,1,2,2-tetrachloroethane-d(2) as well as the activation energies (E-a,E-ass = 27 kJ mol(-1) E-a,E-diss 50 kJ mol(-1)). The equilibrium constants and thermodynamic parameters in various solvents (benzene-d(6), 1,2-dichlorobenzene-d(4), and dimethylsulfwdde-d(6)) were estimated using 1D-H-1 NMR spectroscopy. The parameters were dependent on the polarity of the solvent; Delta H depended linearly on the solvent polarity, becoming increasingly unfavorable as polarity increased. Mixtures of polar dimethylsulfoxide-do in less polar 1,1,2,2-tetrachloroethane-d(2) showed a similar trend.
Reprint Address:
Turro, NJ, Columbia Univ, Dept Chem, New York, NY 10027 USA.
Research Institution addresses:
[Frunzi, Michael; Baldwin, Anne M.; Turro, Nicholas J.] Columbia Univ, Dept Chem, New York, NY 10027 USA; [Shibata, Nobuyuki; Iwamatsu, Sho-Ichi] Nagoya Univ, Grad Sch Environm Studies, Chikusa Ku, Nagoya, Aichi 4648601, Japan; [Lawler, Ronald G.] Brown Univ, Dept Chem, Providence, RI 02912 USA
E-mail Address:
njt3@columbia.edu
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40
Times Cited:
0
Publisher:
AMER CHEMICAL SOC; 1155 16TH ST, NW, WASHINGTON, DC 20036 USA
Subject Category:
Chemistry, Physical; Physics, Atomic, Molecular & Chemical
ISSN:
1089-5639
DOI:
10.1021/jp110832m
IDS Number:
714HH
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Title:
The coupled vibration of fluid-filled multiwalled carbon nanotubes with intertube deformation
Authors:
Wang, XY; Chen, W
Author Full Names:
Wang, X. Y.; Chen, W.
Source:
JOURNAL OF APPLIED PHYSICS 108 (11): Art. No. 114307 DEC 1 2010
Language:
English
Document Type:
Article
KeyWords Plus:
WAVE-PROPAGATION ANALYSIS; CONVEYING FLUID; ELASTIC MEDIUM; INSTABILITY; MODULUS; MODEL; WATER; FLOW
Abstract:
Carbon nanotubes hold substantial and exciting promise as nanocontainers filled with fluid or nanopipes conveying fluid in their hollow cavity in nanotechnology. This paper studies the coupled vibration of embedded fluid-filled multiwalled carbon nanotubes (MWNTs) subject to axial load using the multiple-Euler beam model and considering the distinctive intertube deformation of carbon MWNTs. Through the numerical examples, the effective scope of the single-beam model is examined, and the effect of the internal fluid on the coupled vibration for various geometric dimensions, mass densities of the fluid, Winkler constants, axial loads, and mode numbers, is investigated. It is found that the influence of fluid coupling effect on the natural vibrating frequencies of fluid-filled MWNTs increases as the density of the fluid increases, or as the diameter of the innermost tube increases, or as the mode number studied decreases, and, the higher mode number n or density of the fluid rho
(f) is, the more intense the vibration of inner tubes are than that of outer tubes, and the more the vibration tends towards noncoaxial. (c) 2010 American Institute of Physics. [doi:10.1063/1.3480987]
Reprint Address:
Wang, XY, Hohai Univ, Coll Mech & Mat, Dept Engn Mech, Nanjing 210098, Jiangsu Prov, Peoples R China.
Research Institution addresses:
[Wang, X. Y.; Chen, W.] Hohai Univ, Coll Mech & Mat, Dept Engn Mech, Nanjing 210098, Jiangsu Prov, Peoples R China
E-mail Address:
xywang223@sina.com
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Cited Reference Count:
55
Times Cited:
0
Publisher:
AMER INST PHYSICS; CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA
Subject Category:
Physics, Applied
ISSN:
0021-8979
DOI:
10.1063/1.3480987
IDS Number:
696XG
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Title:
Effect of Surface Morphology on the Ordered Water Layer at Room Temperature
Authors:
Wang, CL; Zhou, B; Xiu, P; Fang, HP
Author Full Names:
Wang, Chunlei; Zhou, Bo; Xiu, Peng; Fang, Haiping
Source:
JOURNAL OF PHYSICAL CHEMISTRY C 115 (7): 3018-3024 FEB 24 2011
Language:
English
Document Type:
Article
KeyWords Plus:
HYDROPHOBIC NANOPORES; PROTEIN SURFACES; CONTACT-ANGLE; DYNAMICS; NANOTUBES; HYDRATION; DEFECTS; INTERFACES; POLARITY; CHANNEL
Abstract:
The behavior of water, particularly the first water layer residing on solid surfaces with various unit cell sizes and charge defects, is studied by molecular dynamics simulations at room temperature. We found that both the unit cell size and presence of defects greatly affected the configurations of the first water layer, specifically the structure and stability of the two-dimensional hydrogen.-bond network within this layer. Consequently, the wetting behavior of water on the solid surface is significantly influenced. On certain wetted solid surfaces with water droplets distributed over the first water layer, the presence of defects at low ratios leads to partial disruption of the structure of the two-dimensional hydrogen-bond network within the first water layer and the existence of the irregular droplet profiles different from the conventional circular shapes. Due to the adsorption of the surface, the dwell time of the first water layer is extremely large and is about 1 ord
er of magnitude larger than the rest of the water layers.
Reprint Address:
Fang, HP, Chinese Acad Sci, Shanghai Inst Appl Phys, POB 800-204, Shanghai 201800, Peoples R China.
Research Institution addresses:
[Wang, Chunlei; Zhou, Bo; Fang, Haiping] Chinese Acad Sci, Shanghai Inst Appl Phys, Shanghai 201800, Peoples R China; [Wang, Chunlei; Zhou, Bo] Chinese Acad Sci, Grad Sch, Beijing 100080, Peoples R China; [Xiu, Peng] Zhejiang Univ, Dept Phys, Bio X Lab, Hangzhou 310027, Peoples R China; [Fang, Haiping] Chinese Acad Sci, Theoret Phys Ctr Sci Facil, Beijing 100049, Peoples R China
E-mail Address:
fanghaiping@sinap.ac.cn
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Cited Reference Count:
60
Times Cited:
0
Publisher:
AMER CHEMICAL SOC; 1155 16TH ST, NW, WASHINGTON, DC 20036 USA
Subject Category:
Chemistry, Physical; Nanoscience & Nanotechnology; Materials Science, Multidisciplinary
ISSN:
1932-7447
DOI:
10.1021/jp108595d
IDS Number:
721FD
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