Cited Article: Hummer, G. Water conduction through the hydrophobic channel of a carbon nanotube
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Title:
Molecular dynamics simulations on the ionic current through charged nanopores
Authors:
Xue, JM; Zou, XQ; Xie, YB; Wang, YG
Author Full Names:
Xue, J. M.; Zou, X. Q.; Xie, Y. B.; Wang, Y. G.
Source:
JOURNAL OF PHYSICS D-APPLIED PHYSICS 42 (10): Art. No. 105308 MAY 21 2009
Language:
English
Document Type:
Article
KeyWords Plus:
PRIMITIVE MODEL ELECTROLYTE; CONTINUUM-THEORIES; BROWNIAN DYNAMICS; CARBON NANOTUBE; SURFACE-CHARGE; TRANSPORT; CONDUCTIVITY; DIFFUSIVITY; CONDUCTANCE; CHANNELS
Abstract:
Molecular dynamics (MD) simulation was performed to investigate the ionic current through charged nanopores, and the results were compared with the calculation of Poisson-Nernst-Planck (PNP) equations based on the continuum theory. Results show that the current obtained by MD simulation is lower than the current calculated by PNP equations, and the discrepancy depends on the surface charge density of the nanopores. Also, MD simulation shows that the contribution of the electro-osmotic flow effect on ionic current could be 10% higher than the results obtained by solving PNP equations. Since the PNP equations do not take the effect of the pore wall into consideration, we suggest that adjusting the diffusion coefficient in the PNP equations can obtain more accurate results when calculating the ionic current through charged nanopores.
Reprint Address:
Xue, JM, Peking Univ, Sch Phys, State Key Lab Nucl Phys & Technol, Beijing 100871, Peoples R China.
Research Institution addresses:
[Xue, J. M.; Zou, X. Q.; Xie, Y. B.; Wang, Y. G.] Peking Univ, Sch Phys, State Key Lab Nucl Phys & Technol, Beijing 100871, Peoples R China; [Xue, J. M.] Peking Univ, Ctr Appl Phys & Technol, Beijing 100871, Peoples R China
E-mail Address:
jmxue@pku.edu.cn
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Cited Reference Count:
33
Times Cited:
0
Publisher:
IOP PUBLISHING LTD; DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND
Subject Category:
Physics, Applied
ISSN:
0022-3727
DOI:
10.1088/0022-3727/42/10/105308
IDS Number:
440CW
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Title:
An exploration of electronic structure and nuclear dynamics in tropolone: II. The A B-1(2) (pi(*)pi) excited state
Authors:
Burns, LA; Murdock, D; Vaccaro, PH
Author Full Names:
Burns, Lori A.; Murdock, Daniel; Vaccaro, Patrick H.
Source:
JOURNAL OF CHEMICAL PHYSICS 130 (14): Art. No. 144304 APR 14 2009
Language:
English
Document Type:
Article
Author Keywords:
bond lengths; chemical exchanges; configuration interactions; coupled cluster calculations; density functional theory; excited states; HF calculations; hydrogen bonds; molecular force constants; organic compounds; perturbation theory; potential energy surfaces; rotational states; vibrational states
KeyWords Plus:
DENSITY-FUNCTIONAL THEORY; COUPLED-CLUSTER METHOD; POTENTIAL-ENERGY SURFACES; PROTON-TRANSFER REACTIONS; JET-COOLED TROPOLONE; GAUSSIAN-BASIS SETS; EXCITATION-ENERGIES; CONFIGURATION-INTERACTION; VIBRATIONAL-EXCITATION; TUNNELING SPLITTINGS
Abstract:
The first excited singlet state of tropolone (A B-1(2)) and the attendant pi(*)<-pi electronic transition have been examined computationally by applying several quantum chemical treatments built upon the aug-cc-pVDZ basis set, including time-dependent density functional theory (TDDFT/B3LYP), configuration interaction singles with perturbative corrections [CIS and CIS(D)], and equation-of-motion coupled-cluster schemes [EOM-CCSD and CR-EOMCCSD(T)]. As in the case of the X (1)A(1) ground state [L. A. Burns, D. Murdock, and P. H. Vaccaro, J. Chem. Phys. 124, 204307 (2006)], geometry optimization procedures and harmonic force-field calculations predict the electronically excited potential surface to support a global minimum-energy configuration of rigorously planar (C-s) symmetry. Minimal Hartree-Fock (HF/CIS) and density-functional (DFT/TDDFT) approaches yield inconsistent results for the X (1)A(1) and A B-1(2) manifolds; however, coupled-cluster (CCSD/EOM-CCSD) methods give fu!
lly relaxed proton-transfer barrier heights of Delta E-pt(X)=3296.1 cm(-1) and Delta E-pt(A)=1270.6 cm(-1) that are in accordance with the experimentally observed increase in vibrationless tunneling splitting upon electronic excitation. Detailed analyses show that this reduction in Delta E-pt stems from a variety of complementary factors, most notably an overall contraction of the proton-transfer reaction site (whereby the equilibrium O center dot O donor-acceptor distance decreases from 2.53 to 2.46 A) and a concomitant shortening of the intramolecular hydrogen bond. Further refinement of A B-1(2) energies through single-point perturbative triples corrections [CR-EOMCCSD(T)] leads to 1316.1 cm(-1) as the best current estimate for Delta E-pt(A). Direct comparison of the lowest-lying out-of-plane torsional mode [nu(39)(a(2))] for X (1)A(1) and A B-1(2) tropolone reveals that its disparate nature (cf. nu(X)(39)=101.2 cm(-1) and nu(A)(39)=42.0 cm(-1)) mediates vibrational-aver!
aging effects which can account for inertial defects extracted!
by rota
tionally resolved spectroscopic measurements.
Reprint Address:
Burns, LA, Yale Univ, Dept Chem, POB 208107, New Haven, CT 06520 USA.
Research Institution addresses:
[Burns, Lori A.; Murdock, Daniel; Vaccaro, Patrick H.] Yale Univ, Dept Chem, New Haven, CT 06520 USA
E-mail Address:
patrick.vaccaro@yale.edu
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81
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, Atomic, Molecular & Chemical
ISSN:
0021-9606
DOI:
10.1063/1.3089722
IDS Number:
439HC
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Title:
A one-dimensional dipole lattice model for water in narrow nanopores
Authors:
Kofinger, J; Hummer, G; Dellago, C
Author Full Names:
Koefinger, Juergen; Hummer, Gerhard; Dellago, Christoph
Source:
JOURNAL OF CHEMICAL PHYSICS 130 (15): Art. No. 154110 APR 21 2009
Language:
English
Document Type:
Article
Author Keywords:
chemical potential; lattice theory; liquid structure; Monte Carlo methods; nanoporous materials; water
KeyWords Plus:
CARBON NANOTUBE MEMBRANES; PROTON CONDUCTION; MASS-TRANSPORT; ION-TRANSPORT; SIMULATIONS; PROTEINS; CHANNELS; BEHAVIOR
Abstract:
We present a recently developed one-dimensional dipole lattice model that accurately captures the key properties of water in narrow nanopores. For this model, we derive three equivalent representations of the Hamiltonian that together yield a transparent physical picture of the energetics of the water chain and permit efficient computer simulations. In the charge representation, the Hamiltonian consists of nearest-neighbor interactions and Coulomb-like interactions of effective charges at the ends of dipole ordered segments. Approximations based on the charge picture shed light on the influence of the Coulomb-like interactions on the structure of nanopore water. We use Monte Carlo simulations to study the system behavior of the full Hamiltonian and its approximations as a function of chemical potential and system size and investigate the bimodal character of the density distribution occurring at small system sizes.
Reprint Address:
Kofinger, J, Univ Vienna, Fac Phys, Boltzmanngasse 5, A-1090 Vienna, Austria.
Research Institution addresses:
[Koefinger, Juergen; Dellago, Christoph] Univ Vienna, Fac Phys, A-1090 Vienna, Austria; [Hummer, Gerhard] NIDDKD, Phys Chem Lab, NIH, Bethesda, MD 20892 USA
E-mail Address:
christoph.dellago@univie.ac.at
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32
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, Atomic, Molecular & Chemical
ISSN:
0021-9606
DOI:
10.1063/1.3106223
IDS Number:
437KL
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