Journal of Molecular Graphics and Modelling 58 (2015) 10–15
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Journal of Molecular Graphics and Modelling j ourna l h om epa ge: www.elsev ier .com/ locate /JMGM
A dimension map for molecular aggregates
Department of a r t i c l
Accepted 22 F
Aggregation m the pr lar ag ggreg the d wo b struc e stru n the rovid of a
Aggrega occurs in m associated together to form fibrils in a number of human diseases; phospholipid molecules in water can spontaneously aggregate into bilayer membranes; organic molecules possessing polyaromatic (PA) cores, such as perylene tetracarboxylic diimide, can assemble into semiconductors of nanobelt structures in solutions; heavy aromatics in crude oil known as asphaltenes aggregate during petrole mechanism ing spheric have been electron mi tron micros small-angle (MD) simul define the s employed i of them are and hence, and general facilitate di helps not o ∗ Correspon
E-mail add 1 Present ad wood, CA 9030 ates forc map based on a pair of unitless quantities, defined from the ratios between the principal radii of gyration of the aggregated structures, as a simple way to quantify their dimension characteristics. Applications of the dimension map are demonstrated using aggregates formed by biomolecules as well as PA compounds in water and organic solvents, obtained from MD simulations. Its potential use http://dx.doi.o 1093-3263/© um processing [1–5]. Depending on the aggregation s, various shapes can be formed, examples includal micelles or rod-like micelles [6–8]. These structures revealed by imaging techniques such as scanning croscopy, atomic force microscopy, transmission eleccopy, circular dichroism, nuclear magnetic resonance, neutron scattering, as well as molecular dynamics ations [4,6–11]. Many parameters have been used to hapes of various aggregates, such as radii of curvature n the work of Israelachvili et al. . However, most difficult to obtain numerically and/or experimentally, are not widely used. On the other hand, a consistent ized method quantifying dimension characteristics will rect comparison among different observations, which nly to track the morphology variations of molecular ding author. Tel.: +1 780 492 5467; fax: +1 780 492 2200. ress: firstname.lastname@example.org (T. Tang). dress: Water Planet Engineering, 721D, South Glasgow Avenue, Ingle1, United States. Tel.: +1 424 331 7702. in experimental studies, such as microscopic analysis of molecular aggregates, is discussed.
Seven different compounds selected from the categories of peptides, lipids and PA compounds were simulated using MD.
Their chemical structures are shown in Fig. 1. Tetra-peptide (TYR-TYR-TYR-TYR, TYR-4; Fig. 1a) was selected as a representative for peptide. Dodecylphosphocholine (DPC; Fig. 1b) and dipalmitoylphosphatidylcholine (DPPC; Fig. 1c) were chosen as representatives for single- and double-chained lipids, respectively.
Peptides and lipids are known to aggregate in aqueous environment [1,2]; hence they were simulated in water. PA compounds are often used as surrogates in petroleum engineering for probing the aggregation behaviors of asphaltenes , which are defined as toluene soluble but n-heptane insoluble heavy aromatic compounds [14–17]. Four PA models, developed from Viloanthrone-78 [18,19], were employed in the MD simulations. These four models have the same PA core but differ by the length of their aliphatic side chains. Based on the number of interconnected aliphatic hydrocarbons on each chain, the four models are respectively referred to as VO-4C (Fig. 1d), VO-8C (Fig. 1e), VO-12C (Fig. 1f) and VO16C (Fig. 1g). Three solvents (water, toluene and n-heptane) were rg/10.1016/j.jmgm.2015.02.003 2015 Elsevier Inc. All rights reserved.ian, Tian Tang ∗, Subir Bhattacharjee1
Mechanical Engineering, University of Alberta, Edmonton, AB T6G 2G8, Canada e i n f o ebruary 2015 e 2 March 2015 s p regates anner echanism a b s t r a c t
A pair of gyradius ratios, defined from that describes the geometry of molecu simulations were performed on the a pounds to demonstrate application of the dimension map were bounded by t regions representing three groups of planar structures or short-cylinder-lik ining the location of the aggregates o type and solute material parameter p and to study solubility and mechanism tion of molecules is a universal phenomenon which any processes. For instance, proteins or peptides are aggreg drivingincipal radii of gyration, are used to generate a dimension map gregates in water and in organic solvents. Molecular dynamics ation of representative biomolecules and polyaromatic comimension map. It was shown that molecular aggregate data on oundary curves, and that the map could be separated into three tures: one-dimensional rod-like structures; two-dimensional ctures; and three-dimensional sphere-like structures. Examdimension map and how the location changes with solvent es a simple yet effective way to infer the aggregation manner ggregation. © 2015 Elsevier Inc. All rights reserved. but also gain insight into the aggregation manner and es. In this communication, we introduce a dimension
C. Jian et al. / Journal of Molecular Graphics and Modelling 58 (2015) 10–15 11
PPC, ( used in the all of which on the GRO tem was su 30 to 180 n
Fig. 2 s obtained at ment of dy
Information exhibit diffe
VO-8C in nture not ob describe the less quantit gyration (gy the three p y, z and the
The detailed of inertia an mation, Sec [27–29]:
Rx = (
Ry = (
Rz = (
Izz∑ im mi an and n alwFig. 1. Molecular structures employed in this study: (a) TYR-4, (b) DPC, (c) D ir MD simulations. In total, 15 systems were studied, were simulated using GROMACS 4.0.7 [20–23] based