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Journal of Chemical Physics / Volume 136 / Issue 2 / ARTICLES / Biological Molecules, Biopolymers, and Biological Systems
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J. Chem. Phys. 136, 025103 (2012); http://dx.doi.org/10.1063/1.3675486 (10 pages)

Amino acid analogues bind to carbon nanotube via π-π interactions: Comparison of molecular mechanical and quantum mechanical calculations

Zaixing Yang1,2, Zhigang Wang3, Xingling Tian1, Peng Xiu1,2, and Ruhong Zhou4

1Bio-X Lab, Department of Physics, and Soft Matter Research Center, Zhejiang University, Hangzhou 310027, China
2Department of Engineering Mechanics, Zhejiang University, Hangzhou 310027, China
3Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012, China
4Computational Biology Center, IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10598, USA

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(Received 12 September 2011; accepted 15 December 2011; published online 10 January 2012)

Understanding the interaction between carbon nanotubes (CNTs) and biomolecules is essential to the CNT-based nanotechnology and biotechnology. Some recent experiments have suggested that the π-π stacking interactions between protein's aromatic residues and CNTs might play a key role in their binding, which raises interest in large scale modeling of protein-CNT complexes and associated π-π interactions at atomic detail. However, there is concern on the accuracy of classical fixed-charge molecular force fields due to their classical treatments and lack of polarizability. Here, we study the binding of three aromatic residue analogues (mimicking phenylalanine, tyrosine, and tryptophan) and benzene to a single-walled CNT, and compare the molecular mechanical (MM) calculations using three popular fixed-charge force fields (OPLSAA, AMBER, and CHARMM), with quantum mechanical (QM) calculations using the density-functional tight-binding method with the inclusion of dispersion correction (DFTB-D). Two typical configurations commonly found in π-π interactions are used, one with the aromatic rings parallel to the CNT surface (flat), and the other perpendicular (edge). Our calculations reveal that compared to the QM results the MM approaches can appropriately reproduce the strength of π-π interactions for both configurations, and more importantly, the energy difference between them, indicating that the various contributions to π-π interactions have been implicitly included in the van der Waals parameters of the standard MM force fields. Meanwhile, these MM models are less accurate in predicting the exact structural binding patterns (matching surface), meaning there are still rooms to be improved. In addition, we have provided a comprehensive and reliable QM picture for the π-π interactions of aromatic molecules with CNTs in gas phase, which might be used as a benchmark for future force field developments.

© 2012 American Institute of Physics

Article Outline

  1. INTRODUCTION
  2. METHODS
  3. RESULTS AND DISCUSSION
  4. CONCLUSIONS

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KEYWORDS and PACS

Keywords

biochemistry, biomechanics, carbon nanotubes, macromolecules, molecular biophysics, molecular force constants, nanobiotechnology, physiological models, proteins, van der Waals forces

PACS

ARTICLE DATA

Digital Object Identifier
http://dx.doi.org/10.1063/1.3675486

PUBLICATION DATA

ISSN

0021-9606 (print)  
1089-7690 (online)

Publisher

$abstract.society.value is a Member of CrossRef American Institute of Physics

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  82. See supplementary material at http://dx.doi.org/10.1063/1.3675486 for analysis of interaction energies of benzene dimer with different configurations for OPLSAA and CHARMM force fields, complete lists of interaction energies and equilibrium distances of benzene dimer obtained by different methods, nonbonded parameters for aromatic amino acid analogues in MM calculations, snapshots of equilibrium binding structures predicted by QM calculations, and comparison of equilibrium binding structures predicted by QM and MM calculations for the “edge” configuration. [EPAPS]

Figures (click on thumbnails to view enlargements)

FIG.1
Investigated configurations of model aromatic complexes. For benzene dimer (left), four configurations are considered: parallel-displaced C2h (PD), T-shaped tilted Cs (TT), sandwich D6h (S), and T-shaped C2v (T). For indole-benzene complex (right), two configurations are considered: parallel-displaced (flat) and T-shaped (edge).

FIG.1 Download High Resolution Image (.zip file) | Export Figure to PowerPoint

FIG.2
Initial arrangements of the system (side view), using the tryptophan analogue for illustration. Left and right panels show “flat” and “edge” configurations, with the aromatic rings parallel and perpendicular to the carbon nanotube (CNT) surface, respectively. The CNT used here is a hydrogen-terminated (5,5) armchair nanotube.

FIG.2 Download High Resolution Image (.zip file) | Export Figure to PowerPoint

FIG.3
Mapping the interaction energy landscapes for aromatic molecule-CNT complexes with molecular mechanical (MM) calculations, using tryptophan analogue with “flat” configuration and AMBER force field for illustration. (a) Schematic representation of three reaction coordinates used for mapping interaction energy landscapes, d, ϕ, and ψ, where d is the ring-CNT distance, and ϕ and ψ are the angles of aromatic ring rotating along the surface normal and CNT axis, respectively. (b–d) Interaction energy (in kcal/mol) landscapes with three different pairs of reaction coordinates (d, ϕ), (d, ψ), and (ϕ, ψ), respectively. For each landscape, the third reaction coordinate is kept at the optimal position of the final equilibrium structure.

FIG.3 Download High Resolution Image (.zip file) | Export Figure to PowerPoint

FIG.4
Snapshots of the equilibrium structures predicted by different methods for Phe, Tyr, Trp, and benzene [(a–d), respectively] for “flat” configuration, shown in top view.

FIG.4 Download High Resolution Image (.zip file) | Export Figure to PowerPoint

FIG.ch1
Schematic representation of θ used in Table 6 for Phe, Tyr, Trp, and benzene [(a–d), respectively], using the QM predicted equilibrium structures for illustration.

FIG.ch1 Download High Resolution Image (.zip file) | Export Figure to PowerPoint

Supplemental Files (EPAPS)

Tables

Table I. Comparison of interaction energies (kcal/mol) of benzene dimer (A) and benzene-indole complex (B) obtained by different quantum mechanical (QM) methods.

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Table II. Comparison of equilibrium distances (Å) of benzene dimer obtained by different methods.2n1

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Table III. Comparison of QM and MM calculated interaction energies (kcal/mol) of binding for aromatic molecules.3n1

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Table IV. Comparison of QM and MM calculated interaction energies (in kcal/mol) between aromatic molecules and CNTs based on the equilibrium structures predicted by QM calculations.4n1

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Table V. Maximal induced charges on atoms of CNT and induction energies due to aromatic molecules-CNT binding.5n1

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Table VI. Geometrical parameters of equilibrium binding structures for “flat” configuration.6n1

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