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Special Issue "Molecular Self-Assembly"

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Recognition".

Deadline for manuscript submissions: closed (31 January 2010)

Special Issue Editor

Guest Editor
Prof. Dr. Vince Rotello (Website)

Department of Chemistry 710 North Pleasant St. University of Massachusetts Amherst, MA 01003 USA
Fax: +1 413 545 4490
Interests: host-guest chemistry; self-assembly; nanomaterials; polymers; bionanotechnology; surfaces

Special Issue Information

Dear Colleagues,

Molecular self-assembly is a "bottom-up" methodology that provides direct access to nanometer-scale devices and nanostructured materials. This approach is inspired by Nature, where billions of years of evolution resulted in an incredibly diverse array of molecular machines (e.g. enzymes) and superstructures. Researchers in the field of self-assembly explore the fundamental attributes of non-covalent interactions while creating molecular building blocks designed to spontaneously assemble into the defined structures desired for functional materials and devices. The strength and versatility of this approach lies in the variety of accessible synthetic systems coupled with the inherent error correction enabled by the thermodynamic nature of self-assembly. The field of self-assembly is currently a science rather than a technology, with much to be learned about the nature and scope of self-assembly. Simultaneously, there are many things that self-assembly can do that are already revolutionizing science, technology, and even our day-to-day life.

Prof. Dr. Vince Rotello
Guest Editor

Keywords

  • supramolecular chemistry
  • nanotechnology
  • intermolecular self-assembly
  • intramolecular self-assembly (folding)
  • hydrogen bonding
  • hydrophobic forces
  • van der Waals forces
  • metal coordination
  • π-π interactions

Related Special Issue

Published Papers (13 papers)

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Research

Jump to: Review

Open AccessArticle pH Dependent Molecular Self-Assembly of Octaphosphonate Porphyrin of Nanoscale Dimensions: Nanosphere and Nanorod Aggregates
Int. J. Mol. Sci. 2011, 12(3), 1464-1473; doi:10.3390/ijms12031464
Received: 27 January 2011 / Revised: 17 February 2011 / Accepted: 22 February 2011 / Published: 24 February 2011
Cited by 12 | PDF Full-text (342 KB) | HTML Full-text | XML Full-text
Abstract
Self-assembled nanostructures of zwitterionic octaphosphanatoporphyrin 1, of either nanoparticles or nanorods, depending on small changes in the pH, is demonstrated based on the J-aggregates. Porphyrin 1 self-assembled into nanosphere aggregates with a diameter of about 70–80 nm in the pH range [...] Read more.
Self-assembled nanostructures of zwitterionic octaphosphanatoporphyrin 1, of either nanoparticles or nanorods, depending on small changes in the pH, is demonstrated based on the J-aggregates. Porphyrin 1 self-assembled into nanosphere aggregates with a diameter of about 70–80 nm in the pH range 5–7, and nanorod aggregates were observed at pH 8.5. Hydrogen bonding, p-p stacking and hydrophilic interactions play important roles in the formation of this nanostructure morphology. Nanostructures were characterized by UV/Vis absorbance, fluorescence, atomic force microscopy (AFM) and transmission electron microscopy (TEM). This interesting pH dependent self-assembly phenomenon could provide a basis for development of novel biomaterials. Full article
(This article belongs to the Special Issue Molecular Self-Assembly)
Open AccessArticle Self Assembly of Nano Metric Metallic Particles for Realization of Photonic and Electronic Nano Transistors
Int. J. Mol. Sci. 2010, 11(5), 2241-2252; doi:10.3390/ijms11052242
Received: 3 April 2010 / Revised: 19 April 2010 / Accepted: 7 May 2010 / Published: 25 May 2010
Cited by 4 | PDF Full-text (1221 KB) | HTML Full-text | XML Full-text
Abstract
In this paper, we present the self assembly procedure as well as experimental results of a novel method for constructing well defined arrangements of self assembly metallic nano particles into sophisticated nano structures. The self assembly concept is based on focused ion [...] Read more.
In this paper, we present the self assembly procedure as well as experimental results of a novel method for constructing well defined arrangements of self assembly metallic nano particles into sophisticated nano structures. The self assembly concept is based on focused ion beam (FIB) technology, where metallic nano particles are self assembled due to implantation of positive gallium ions into the insulating material (e.g., silica as in silicon on insulator wafers) that acts as intermediary layer between the substrate and the negatively charge metallic nanoparticles. Full article
(This article belongs to the Special Issue Molecular Self-Assembly)
Open AccessArticle Photoinduced Surface Relief Grating Formation for a Single Crystal of 4-Aminoazobenzene
Int. J. Mol. Sci. 2010, 11(4), 1311-1320; doi:10.3390/ijms11041311
Received: 26 January 2010 / Revised: 8 March 2010 / Accepted: 11 March 2010 / Published: 30 March 2010
Cited by 11 | PDF Full-text (209 KB) | HTML Full-text | XML Full-text
Abstract
Photoinduced surface relief grating (SRG) formation for a single crystal of 4-aminoazobenzene was investigated. It was found that SRG could be inscribed on the (001) surface of the crystal, which might suggest that the photoinduced SRG formation is a general phenomenon observed [...] Read more.
Photoinduced surface relief grating (SRG) formation for a single crystal of 4-aminoazobenzene was investigated. It was found that SRG could be inscribed on the (001) surface of the crystal, which might suggest that the photoinduced SRG formation is a general phenomenon observed for single crystals of azobenzene-based molecules as well as for azobenzene-based amorphous systems. In addition, the dependences of the SRG formation upon the orientation of the sample crystal and upon the polarization of the writing beams were found to be different from those observed for previously reported crystalline systems. Full article
(This article belongs to the Special Issue Molecular Self-Assembly)
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Open AccessArticle Monolayer-directed Assembly and Magnetic Properties of FePt Nanoparticles on Patterned Aluminum Oxide
Int. J. Mol. Sci. 2010, 11(3), 1162-1179; doi:10.3390/iijms11031162
Received: 16 November 2009 / Accepted: 3 March 2010 / Published: 19 March 2010
Cited by 13 | PDF Full-text (2207 KB) | HTML Full-text | XML Full-text
Abstract
FePt nanoparticles (NPs) were assembled on aluminum oxide substrates, and their ferromagnetic properties were studied before and after thermal annealing. For the first time, phosph(on)ates were used as an adsorbate to form self-assembled monolayers (SAMs) on alumina to direct the assembly of [...] Read more.
FePt nanoparticles (NPs) were assembled on aluminum oxide substrates, and their ferromagnetic properties were studied before and after thermal annealing. For the first time, phosph(on)ates were used as an adsorbate to form self-assembled monolayers (SAMs) on alumina to direct the assembly of NPs onto the surface. The Al2O3 substrates were functionalized with aminobutylphosphonic acid (ABP) or phosphonoundecanoic acid (PNDA) SAMs or with poly(ethyleneimine) (PEI) as a reference. FePt NPs assembled on all of these monolayers, but much less on unmodified Al2O3, which shows that ligand exchange at the NPs is the most likely mechanism of attachment. Proper modification of the Al2O3 surface and controlling the immersion time of the modified Al2O3 substrates into the FePt NP solution resulted in FePt NPs assembly with controlled NP density. Alumina substrates were patterned by microcontact printing using aminobutylphosphonic acid as the ink, allowing local NP assembly. Thermal annealing under reducing conditions (96%N2/4%H2) led to a phase change of the FePt NPs from the disordered FCC phase to the ordered FCT phase. This resulted in ferromagnetic behavior at room temperature. Such a process can potentially be applied in the fabrication of spintronic devices. Full article
(This article belongs to the Special Issue Molecular Self-Assembly)
Open AccessArticle Lipid Vesicle Aggregation Induced by Cooling
Int. J. Mol. Sci. 2010, 11(2), 754-761; doi:10.3390/ijms11020754
Received: 6 January 2010 / Accepted: 10 February 2010 / Published: 21 February 2010
PDF Full-text (109 KB) | HTML Full-text | XML Full-text
Abstract
Lipid bilayer fusion is a complex process requiring several intermediate steps. Initially, the two bilayers are brought into close contact following removal of intervening water layers and overcoming electrostatic repulsions between opposing bilayer head groups. In this study we monitor by light [...] Read more.
Lipid bilayer fusion is a complex process requiring several intermediate steps. Initially, the two bilayers are brought into close contact following removal of intervening water layers and overcoming electrostatic repulsions between opposing bilayer head groups. In this study we monitor by light scattering the reversible aggregation of phosphatidylcholine single shell vesicles during which adhesion occurs but stops prior to a fusion process. Light scattering measurements of dimyristoyl-sn-glycero-3-phosphocholine (DMPC), dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) in water show that lowering the temperature of about 0.14 micron single shell vesicles of DPPC (from 20 °C to 5 °C) and about 2 micron vesicles of DSPC (from 20 °C to 15 °C), but not of 1 micron vesicles of DMPC, results in extensive aggregation within 24 hours that is reversible by an increase in temperature. Aggregation of DSPC vesicles was confirmed by direct visual observation. Orientation of lipid head groups parallel to the plane of the bilayer and consequent reduction of the negative surface charge can account for the ability of DPPC and DSPC vesicles to aggregate. Retention of negatively charged phosphates on the surface and the burial of positively charged cholines within the bilayer offer an explanation for the failure of DMPC vesicles to aggregate. Lowering the temperature of 1,2-dipalmitoyl-sn-glycero-3-phosphoserine (DPPS) vesicles from 20 °C to 5 °C failed to increase aggregation within 24 hours at Mg++/DPPS ratios that begin to initiate aggregation and fusion. Full article
(This article belongs to the Special Issue Molecular Self-Assembly)
Open AccessArticle Self-Assembly of Diamondoid Molecules and Derivatives (MD Simulations and DFT Calculations)
Int. J. Mol. Sci. 2010, 11(1), 288-303; doi:10.3390/ijms11010288
Received: 7 December 2009 / Revised: 10 January 2010 / Accepted: 17 January 2010 / Published: 21 January 2010
Cited by 15 | PDF Full-text (1457 KB) | HTML Full-text | XML Full-text
Abstract
We report self-assembly and phase transition behavior of lower diamondoid molecules and their primary derivatives using molecular dynamics (MD) simulation and density functional theory (DFT) calculations. Two lower diamondoids (adamantane and diamantane), three adamantane derivatives (amantadine, memantine and rimantadine) and two artificial [...] Read more.
We report self-assembly and phase transition behavior of lower diamondoid molecules and their primary derivatives using molecular dynamics (MD) simulation and density functional theory (DFT) calculations. Two lower diamondoids (adamantane and diamantane), three adamantane derivatives (amantadine, memantine and rimantadine) and two artificial molecules (ADM•Na and DIM•Na) are studied separately in 125-molecule simulation systems. We performed DFT calculations to optimize their molecular geometries and obtained atomic electronic charges for the corresponding MD simulation, by which we predicted self-assembly structures and simulation trajectories for the seven different diamondoids and derivatives. Our radial distribution function and structure factor studies showed clear phase transitions and self-assemblies for the seven diamondoids and derivatives. Full article
(This article belongs to the Special Issue Molecular Self-Assembly)
Open AccessArticle Characterization and Purification of Polydisperse Reconstituted Lipoproteins and Nanolipoprotein Particles
Int. J. Mol. Sci. 2009, 10(7), 2958-2971; doi:10.3390/ijms10072958
Received: 3 June 2009 / Accepted: 22 June 2009 / Published: 2 July 2009
Cited by 10 | PDF Full-text (380 KB) | HTML Full-text | XML Full-text
Abstract
Heterogeneity is a fact that plagues the characterization and application of many self-assembled biological constructs. The importance of obtaining particle homogeneity in biological assemblies is a critical goal, as bulk analysis tools often require identical species for reliable interpretation of the results—indeed, [...] Read more.
Heterogeneity is a fact that plagues the characterization and application of many self-assembled biological constructs. The importance of obtaining particle homogeneity in biological assemblies is a critical goal, as bulk analysis tools often require identical species for reliable interpretation of the results—indeed, important tools of analysis such as x-ray diffraction typically require over 90% purity for effectiveness. This issue bears particular importance in the case of lipoproteins. Lipid-binding proteins known as apolipoproteins can self assemble with liposomes to form reconstituted high density lipoproteins (rHDLs) or nanolipoprotein particles (NLPs) when used for biotechnology applications such as the solubilization of membrane proteins. Typically, the apolipoprotein and phospholipids reactants are self assembled and even with careful assembly protocols the product often contains heterogeneous particles. In fact, size polydispersity in rHDLs and NLPs published in the literature are frequently observed, which may confound the accurate use of analytical methods. In this article, we demonstrate a procedure for producing a pure, monodisperse NLP subpopulation from a polydisperse self-assembly using size exclusion chromatography (SEC) coupled with high resolution particle imaging by atomic force microscopy (AFM). In addition, NLPs have been shown to self assemble both in the presence and absence of detergents such as cholate, yet the effects of cholate on NLP polydispersity and separation has not been systematically examined. Therefore, we examined the separation properties of NLPs assembled in both the absence and presence of cholate using SEC and native gel electrophoresis. From this analysis, NLPs prepared with and without cholate showed particles with well defined diameters spanning a similar size range. However, cholate was shown to have a dramatic affect on NLP separation by SEC and native gel electrophoresis. Furthermore, under conditions where different sized NLPs were not sufficiently separated or purified by SEC, AFM was used to deconvolute the elution pattern of different sized NLPs. From this analysis we were able to purify an NLP subpopulation to 90% size homogeneity by taking extremely fine elutions from the SEC. With this purity, we generate high quality NLP crystals that were over 100 μm in size with little precipitate, which could not be obtained utilizing the traditional size exclusion techniques. This purification procedure and the methods for validation are broadly applicable to other lipoprotein particles. Full article
(This article belongs to the Special Issue Molecular Self-Assembly)
Open AccessArticle Temperature-Dependent Phase Behaviors in Cylinder-Forming Block Copolymers
Int. J. Mol. Sci. 2009, 10(5), 2169-2189; doi:10.3390/ijms10052169
Received: 4 April 2009 / Revised: 30 April 2009 / Accepted: 13 May 2009 / Published: 15 May 2009
Cited by 2 | PDF Full-text (496 KB) | HTML Full-text | XML Full-text
Abstract
We demonstrate that the temperature-dependent phase behaviors of parallel and perpendicular cylinder-forming block copolymers are governed by domain-domain segregation forces inherently present in block copolymer material itself. With increasing temperature, a parallel cylinder-forming block copolymer experienced a parallel cylinder straightening process before [...] Read more.
We demonstrate that the temperature-dependent phase behaviors of parallel and perpendicular cylinder-forming block copolymers are governed by domain-domain segregation forces inherently present in block copolymer material itself. With increasing temperature, a parallel cylinder-forming block copolymer experienced a parallel cylinder straightening process before the order-disorder transition (ODT) and did not show long-range composition fluctuations near the ODT temperature due to the weak segregation forces between the block domains. A perpendicular cylinder-forming block copolymer with a strong segregation force between the block domains displayed cylinder orientation transition from perpendicular to parallel below the ODT temperature. On the other hand, a perpendicular cylinder-forming block copolymer material with an exceptionally strong segregation force between the block domains maintained its initial perpendicular cylinder orientation up to near the ODT temperature. In both cases of perpendicular cylinder-forming block copolymers, submicrometer-scale long-range composition fluctuations were observed well above the ODT temperature due to their intrinsically strong segregation forces between the block domains. Full article
(This article belongs to the Special Issue Molecular Self-Assembly)
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Open AccessArticle The Effect of Self-Assembling Peptide RADA16-I on the Growth of Human Leukemia Cells in Vitro and in Nude Mice
Int. J. Mol. Sci. 2009, 10(5), 2136-2145; doi:10.3390/ijms10052136
Received: 31 March 2009 / Revised: 30 April 2009 / Accepted: 12 May 2009 / Published: 14 May 2009
Cited by 11 | PDF Full-text (714 KB) | HTML Full-text | XML Full-text
Abstract
Nanofiber scaffolds formed by self-assembling peptide RADA16-I have been used for the study of cell proliferation to mimic an extracellular matrix. In this study, we investigated the effect of RADA16-I on the growth of human leukemia cells in vitro and in nude [...] Read more.
Nanofiber scaffolds formed by self-assembling peptide RADA16-I have been used for the study of cell proliferation to mimic an extracellular matrix. In this study, we investigated the effect of RADA16-I on the growth of human leukemia cells in vitro and in nude mice. Self-assembly assessment showed that RADA16-I molecules have excellent self-assembling ability to form stable nanofibers. MTT assay displayed that RADA16-I has no cytotoxicity for leukemia cells and human umbilical vein endothelial cells (HUVECs) in vitro. However, RADA16-I inhibited the growth of K562 tumors in nude mice. Furthermore, we found RADA16-I inhibited vascular tube-formation by HUVECs in vitro. Our data suggested that nanofiber scaffolds formed by RADA16-I could change tumor microenvironments, and inhibit the growth of tumors. The study helps to encourage further design of self-assembling systems for cancer therapy. Full article
(This article belongs to the Special Issue Molecular Self-Assembly)
Open AccessCommunication Rupture Pathway of Phosphatidylcholine Liposomes on Silicon Dioxide
Int. J. Mol. Sci. 2009, 10(4), 1683-1696; doi:10.3390/ijms10041683
Received: 9 February 2009 / Revised: 3 April 2009 / Accepted: 10 April 2009 / Published: 17 April 2009
Cited by 30 | PDF Full-text (234 KB) | HTML Full-text | XML Full-text
Abstract
We have investigated the pathway by which unilamellar POPC liposomes upon adsorption undergo rupture and form a supported lipid bilayer (SLB) on a SiO2 surface. Biotinylated lipids were selectively incorporated in the outer monolayer of POPC liposomes to create liposomes with [...] Read more.
We have investigated the pathway by which unilamellar POPC liposomes upon adsorption undergo rupture and form a supported lipid bilayer (SLB) on a SiO2 surface. Biotinylated lipids were selectively incorporated in the outer monolayer of POPC liposomes to create liposomes with asymmetric lipid compositions in the outer and inner leaflets. The specific binding of neutravidin and anti-biotin to SLBs formed by liposome fusion, prior to and after equilibrated flip-flop between the upper and lower monolayers in the SLB, were then investigated. It was concluded that the lipids in the outer monolayer of the vesicle predominantly end up on the SLB side facing the SiO2 substrate, as demonstrated by having maximum 30-40% of lipids in the liposome outer monolayer orienting towards the bulk after forming the SLB. Full article
(This article belongs to the Special Issue Molecular Self-Assembly)
Open AccessArticle AFM and Multiple Transmission-Reflection Infrared Spectroscopy (MTR-IR) Studies on Formation of Air-Stable Supported Lipid Bilayers
Int. J. Mol. Sci. 2009, 10(3), 1407-1418; doi:10.3390/ijms10031407
Received: 31 January 2009 / Revised: 11 March 2009 / Accepted: 19 March 2009 / Published: 26 March 2009
Cited by 1 | PDF Full-text (402 KB) | HTML Full-text | XML Full-text
Abstract
Supported lipid bilayers (SLBs) were prepared by deposition of unilamellar vesicles on a silicon substrate. Atomic force microscopy (AFM) and a new Multiple Transmission-Reflection Infrared Spectroscopy (MTR-IR) developed by us were used to trace the dynamic formation of lipid bilayers on the [...] Read more.
Supported lipid bilayers (SLBs) were prepared by deposition of unilamellar vesicles on a silicon substrate. Atomic force microscopy (AFM) and a new Multiple Transmission-Reflection Infrared Spectroscopy (MTR-IR) developed by us were used to trace the dynamic formation of lipid bilayers on the silicon surfaces. The evolution from deformation of vesicles to formation of bilayers can be distinguished clearly by AFM imaging. MTR-IR provided high quality infrared spectra of ultrathin lipid bilayers with high sensitivity and high signal to noise ratio (SNR). The structural and orientational changes during vesicle’s fusion were monitored with MTR-IR. MTR-IR shows superiority over other infrared approaches for ultrathin films on standard silicon wafers in view of its economy and high sensitivity. Both MTR-IR and AFM results were consistent with each other and they provided more information for understanding the self-assembling procedure of SLBs. Full article
(This article belongs to the Special Issue Molecular Self-Assembly)
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Open AccessArticle Ordering and Reverse Ordering Mechanisms of Triblock Copolymers in the Presence of Solvent
Int. J. Mol. Sci. 2009, 10(3), 805-816; doi:10.3390/ijms10030805
Received: 21 January 2009 / Revised: 24 February 2009 / Accepted: 24 February 2009 / Published: 27 February 2009
Cited by 1 | PDF Full-text (268 KB) | HTML Full-text | XML Full-text
Abstract
Self-consistent field theory is used to study the self-assembly of a triblock copolymer melt. Two different external factors (temperature and solvent) are shown to affect the self-assembly. Either one or two-step self-assembly can be found as a function of temperature in the [...] Read more.
Self-consistent field theory is used to study the self-assembly of a triblock copolymer melt. Two different external factors (temperature and solvent) are shown to affect the self-assembly. Either one or two-step self-assembly can be found as a function of temperature in the case of a neat triblock melt, or as a function of increasing solvent content (for non-selective solvents) in the case of a triblock-solvent mixture. For selective solvents, it is shown that increasing the solvent content leads to more complicated self-assembly mechanisms, including a reversed transition where order is found to increase instead of decreasing as expected, and re-entrant behavior where order is found to increase at first, and then decrease to a previous state of disorder. Full article
(This article belongs to the Special Issue Molecular Self-Assembly)
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Review

Jump to: Research

Open AccessReview Self-Assembly of Optical Molecules with Supramolecular Concepts
Int. J. Mol. Sci. 2009, 10(5), 1950-1966; doi:10.3390/ijms10051950
Received: 24 March 2009 / Accepted: 24 April 2009 / Published: 27 April 2009
Cited by 9 | PDF Full-text (460 KB) | HTML Full-text | XML Full-text
Abstract
Fabrication of nano-sized objects is one of the most important issues in nanoscience and nanotechnology. Soft nanomaterials with flexible properties have been given much attention and can be obtained through bottom-up processing from functional molecules, where self-assembly based on supramolecular chemistry and [...] Read more.
Fabrication of nano-sized objects is one of the most important issues in nanoscience and nanotechnology. Soft nanomaterials with flexible properties have been given much attention and can be obtained through bottom-up processing from functional molecules, where self-assembly based on supramolecular chemistry and designed assembly have become crucial processes and techniques. Among the various functional molecules, dyes have become important materials in certain areas of nanotechnology and their self-assembling behaviors have been actively researched. In this short review, we briefly introduce recent progress in self-assembly of optical molecules and dyes, based mainly on supramolecular concepts. The introduced examples are classified into four categories: self-assembly of (i) low-molecular-weight dyes and (ii) polymeric dyes and dye self-assembly (iii) in nanoscale architectures and (iv) at surfaces. Full article
(This article belongs to the Special Issue Molecular Self-Assembly)
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