Molecular Dynamics Simulation on Self-Assembly of Fmoc-FF Dipeptide†

doi:10.7503/cjcu20150546

Abstract

Abstract:

Molecular dynamics simulations were performed to investigate the self-assembly of Fmoc-FF dipeptide. The driving force of self-assembly and the effect of water bridge were investigated. During the simulation, Fmoc-FF dipeptides were first dispersed in aqueous solution and then the self-assembly occurred rapidly in a very short simulation time. At last the system reached the dynamics balance and the dipeptide could self-assemble into well-ordered cylindrical nanostructure. Computational analysis of radial distribution function(RDF) between fluorenyl rings showed a typical π-π interaction distance and some well-recognized π-π stacking geometries could be found from the nanostructures such as T-shaped and Herringbone structure. Further the interaction energy between Fmoc-FF dipeptide and water molecules and between different parts of Fmoc-FF dipeptide were calculated to make sure that the Fmoc-FF dipeptide tended to self-assemble into an aggregate and the major interaction was between fluorenyl rings. At last, the properties of hydrogen bond formed between water molecules and certain atoms of Fmoc-FF dipeptide indicated that water bridge structure could exist between two dipeptides and further stabilize the self-assembly aggregate.

Key words: Self-assembly of Fmoc-FF dipeptide, Hydrogel, π-π interaction, Hydrogen bond, Molecular dynamics simulation

CLC Number:

O641

TrendMD:

GUO Kai, ZHANG Heng, SUN Jichao, YUAN Shiling, LIU Chengbu. Molecular Dynamics Simulation on Self-Assembly of Fmoc-FF Dipeptide^†[J]. Chem. J. Chinese Universities, 2015, 36(11): 2171.

Figures/Tables 13

Fig.1 Molecular structure of Fmoc-FF

Fig.2 Views of the configurations at different time(A—E) and top view of configuration at 50 ns(F) Time/ns: (A) 0; (B) 1; (C) 5; (D) 30; (E) 50. Orange represents the fluorenyl group of Fmoc, blue is the peptide chain, and gray is the benzene ring of peptide chain. Fmoc-FF molecules are represented by CPK pattern. Water molecules are represented by red and white lines.

Fig.3 Solvent accessible surface area(SASA) of Fmoc-FF molecule

Fig.4 Non-normalized RDF plot of distance between fluorenyl rings(A) and MD simulation of π-π stacking of the aggregate after 50 ns(B) Water molecules are omitted to show the structure clearly.

Fig.5 Overall interaction energy and the decomposed VDW, Coulomb and hydrogen bond terms (A) The whole interaction energy of dipeptide and water molecules. a. Peptide-peptide; b. peptide-H2O. (B) The individual interaction energy between different parts of Fmoc-FF dipeptide. a. Fmoc-Fmoc; b. Fmoc-Chain; c. Chain-Chain; d. Ben-Ben; e. Ben-Chain; f. Ben-Fmoc. All data are averaged using the last 20 ns MD simulations.

Fig.6 Spatial distribution function between Fmoc-FF molecule and water molecules

Fig.7 Views of water bridge structure (A) Dipeptides formed water bridge through one water molecule; (B) dipeptides formed water bridge by two water molecules.

Fig.8 Mean square displacement-time curves of water around certain atoms of Fmoc-FF dipeptide

Table 1 Dynamic properties of water around certain atoms of Fmoc-FF dipeptide

Certain atoms of Fmoc-FF dipeptide	10⁵Diffusion coefficient(cm²·s^-1)	Residence time, τ_r/ps
O1, O3	3.87	7.09
O4	4.27	9.52
O2, O5	2.91	10.65
N1	4.42	1.71
N2	4.58	1.43

Fig.9 Illustration of definition of Pi Pi(t1)=1 when water molecule in the first shell at t0 and t1.The location of water molecule during t0—t1 does not count.

Fig.10 Time correlation functions of water around certain atoms of Fmoc-FF dipeptide

Table 2 Averaged hydrogen bond number and residence time between certain atoms of Fmoc-FF dipeptide and water molecules

Atom type	Number of hydrogen bonds	Residence time/ps
O1, O3	12.68	16.53
N1H12	0.92	2.23
O4	22.77	12.56
N2H14	1.61	1.01
O2, O5	105.82	9.54

Fig.11 Time correlation function[C(t)] for the hydrogen bonds formed between certain atoms of Fmoc-FF dipeptide and water molecules

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