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Special Issue "Molecular Self-Assembly 2012"

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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 (30 December 2012)

Special Issue Editor

Guest Editor
Prof. Dr. Jurriaan Huskens

Molecular Nanofabrication Group, MESA+ Institute for Nanotechnology, University of Twente, TNW/MNF, PO Box 217, 7500AE Enschede, The Netherlands
Website | E-Mail
Fax: +31 53 4894645
Interests: host-guest chemistry; cyclodextrins; multivalency; supramolecular surface chemistry; supramolecular materials; nanolithography; soft lithography

Keywords

  • self-assembly
  • supramolecular chemistry
  • nanotechnology
  • interfacial assembly
  • cooperativity
  • multivalency
  • dynamics

Published Papers (24 papers)

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Research

Jump to: Review, Other

Open AccessArticle Integrated Self-Assembly of the Mms6 Magnetosome Protein to Form an Iron-Responsive Structure
Int. J. Mol. Sci. 2013, 14(7), 14594-14606; doi:10.3390/ijms140714594
Received: 5 February 2013 / Revised: 9 June 2013 / Accepted: 3 July 2013 / Published: 12 July 2013
Cited by 17 | PDF Full-text (1483 KB) | HTML Full-text | XML Full-text
Abstract
A common feature of biomineralization proteins is their self-assembly to produce a surface consistent in size with the inorganic crystals that they produce. Mms6, a small protein of 60 amino acids from Magnetospirillum magneticum strain AMB-1 that promotes the in vitro growth of
[...] Read more.
A common feature of biomineralization proteins is their self-assembly to produce a surface consistent in size with the inorganic crystals that they produce. Mms6, a small protein of 60 amino acids from Magnetospirillum magneticum strain AMB-1 that promotes the in vitro growth of superparamagnetic magnetite nanocrystals, assembles in aqueous solution to form spherical micelles that could be visualized by TEM and AFM. The results reported here are consistent with the view that the N and C-terminal domains interact with each other within one polypeptide chain and across protein units in the assembly. From studies to determine the amino acid residues important for self-assembly, we identified the unique GL repeat in the N-terminal domain with additional contributions from amino acids in other positions, throughout the molecule. Analysis by CD spectroscopy identified a structural change in the iron-binding C-terminal domain in the presence of Fe3+. A change in the intrinsic fluorescence of tryptophan in the N-terminal domain showed that this structural change is transmitted through the protein. Thus, self-assembly of Mms6 involves an interlaced structure of intra- and inter-molecular interactions that results in a coordinated structural change in the protein assembly with iron binding. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2012)
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Open AccessCommunication Exploiting BSA to Inhibit the Fibrous Aggregation of Magnetic Nanoparticles under an Alternating Magnetic Field
Int. J. Mol. Sci. 2013, 14(3), 5775-5783; doi:10.3390/ijms14035775
Received: 26 November 2012 / Revised: 6 February 2013 / Accepted: 15 February 2013 / Published: 12 March 2013
Cited by 3 | PDF Full-text (495 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The alternating magnetic field was discovered to be capable of inducing the fibrous aggregation of magnetic nanoparticles. However, this anisotropic aggregation may be unfavorable for practical applications. Here, we reported that the adsorption of BSA (bovine serum albumin) on the surfaces of magnetic
[...] Read more.
The alternating magnetic field was discovered to be capable of inducing the fibrous aggregation of magnetic nanoparticles. However, this anisotropic aggregation may be unfavorable for practical applications. Here, we reported that the adsorption of BSA (bovine serum albumin) on the surfaces of magnetic nanoparticles can effectively make the fibrous aggregation of γ-Fe2O3 nanoparticles turn into a more isotropic aggregation in the presence of the alternating magnetic field. Also, the heating curves with and without BSA adsorption under different pH conditions were measured to show the influence of the colloidal aggregation states on the collective calorific behavior of magnetic nanoparticles. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2012)
Open AccessArticle Role of Thermal Process on Self-Assembled Structures of 4'-([2,2':6',2''-Terpyridin]-4'-Yl)-[1,1'-Biphenyl]-4-Carboxylic Acid on Au(III)
Int. J. Mol. Sci. 2013, 14(3), 5686-5693; doi:10.3390/ijms14035686
Received: 23 November 2012 / Revised: 24 January 2013 / Accepted: 18 February 2013 / Published: 11 March 2013
Cited by 2 | PDF Full-text (4031 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The role of dynamic processes on self-assembled structures of 4'-([2,2':6', 2''-terpyridin]-4'-yl)-[1,1'-biphenyl]-4-carboxylic acid (l) molecules on Au(III) has been studied by scanning tunneling microscopy. The as-deposited monolayer is closed-packed and periodic in a short-range due to dipole forces. A thermal annealing process at 110
[...] Read more.
The role of dynamic processes on self-assembled structures of 4'-([2,2':6', 2''-terpyridin]-4'-yl)-[1,1'-biphenyl]-4-carboxylic acid (l) molecules on Au(III) has been studied by scanning tunneling microscopy. The as-deposited monolayer is closed-packed and periodic in a short-range due to dipole forces. A thermal annealing process at 110 degrees drives such disordered monolayer into ordered chain-like structures, determined by the combination of the dipole forces and hydrogen bonding. Further annealing at 130 degrees turns the whole monolayer into a bowknot-like structure in which hydrogen bonding plays the dominant role in the formation of assembled structures. Such dependence of an assembled structure on the process demonstrates that an assembled structure can be regulated and controlled not only by the molecular structure but also by the thermal process to form the assembled structure. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2012)
Open AccessArticle Vascular Endothelial Growth Factor Receptor Family in Ascidians, Halocynthia roretzi (Sea Squirt). Its High Expression in Circulatory System-Containing Tissues
Int. J. Mol. Sci. 2013, 14(3), 4841-4853; doi:10.3390/ijms14034841
Received: 20 November 2012 / Revised: 7 February 2013 / Accepted: 15 February 2013 / Published: 1 March 2013
Cited by 2 | PDF Full-text (657 KB) | HTML Full-text | XML Full-text
Abstract
The vascular endothelial growth factor (VEGF)-VEGF Receptor (VEGFR) system is an important pathway for regulation of angiogenesis. However, its evolutionary development, particularly the step from invertebrates to vertebrates, is still largely unknown. Here, we molecularly cloned the VEGFR-like gene from Halocynthia roretzi, a
[...] Read more.
The vascular endothelial growth factor (VEGF)-VEGF Receptor (VEGFR) system is an important pathway for regulation of angiogenesis. However, its evolutionary development, particularly the step from invertebrates to vertebrates, is still largely unknown. Here, we molecularly cloned the VEGFR-like gene from Halocynthia roretzi, a species belonging to the Tunicata, the chordate subphylum recently considered the sister group of vertebrates. The cDNA encoded a homolog of human VEGFR, including the transmembrane domain, and the tyrosine kinase domain with a kinase-insert region, which was designated S. sq VEGFR (GenBank AB374180). Similar to Tunicates including ascidians in the phylogenetic tree, the Amphioxus, another chordate, is located close to vertebrates. However, S. sq VEGFR has a higher homology than the Amphioxus VEGFR-like molecule (GenBank AB025557) to human VEGFR in the kinase domain-2 region. The S. sq VEGFR mRNA was expressed at highest levels in circulatory system-containing tissues, suggesting that S. sq VEGFR plays an important role in the formation or maintenance of circulatory system in Tunicates, Halocynthia roretzi. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2012)
Open AccessArticle Molecular Self-Assembly at Metal-Electrolyte Interfaces
Int. J. Mol. Sci. 2013, 14(3), 4498-4524; doi:10.3390/ijms14034498
Received: 8 January 2013 / Revised: 10 February 2013 / Accepted: 16 February 2013 / Published: 25 February 2013
Cited by 7 | PDF Full-text (5861 KB) | HTML Full-text | XML Full-text
Abstract
The self-assembly of molecular layers has become an important strategy in modern design of functional materials. However, in particular, large organic molecules may no longer be sufficiently volatile to be deposited by vapor deposition. In this case, deposition from solution may be a
[...] Read more.
The self-assembly of molecular layers has become an important strategy in modern design of functional materials. However, in particular, large organic molecules may no longer be sufficiently volatile to be deposited by vapor deposition. In this case, deposition from solution may be a promising route; in ionic form, these molecules may even be soluble in water. In this contribution, we present and discuss results on the electrochemical deposition of viologen- and porphyrin molecules as well as their co-adsorption on chloride modified Cu(100) and Cu(111) single crystal electrode surfaces from aqueous acidic solutions. Using in situ techniques like cyclic voltametry and high resolution scanning tunneling microscopy, as well as ex-situ photoelectron spectroscopy data the highly ordered self-assembled organic layers are characterized with respect to their electrochemical behavior, lateral order and inner conformation as well as phase transitions thereof as a function of their redox-state and the symmetry of the substrate. As a result, detailed structure models are derived and are discussed in terms of the prevailing interactions. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2012)
Open AccessArticle Immobilization of Ferrocene-Modified SNAP-Fusion Proteins
Int. J. Mol. Sci. 2013, 14(2), 4066-4080; doi:10.3390/ijms14024066
Received: 30 November 2012 / Revised: 4 February 2013 / Accepted: 4 February 2013 / Published: 18 February 2013
Cited by 13 | PDF Full-text (606 KB) | HTML Full-text | XML Full-text
Abstract
The supramolecular assembly of proteins on surfaces has been investigated via the site-selective incorporation of a supramolecular moiety on proteins. To this end, fluorescent proteins have been site-selectively labeled with ferrocenes, as supramolecular guest moieties, via SNAP-tag technology. The assembly of guest-functionalized SNAP-fusion
[...] Read more.
The supramolecular assembly of proteins on surfaces has been investigated via the site-selective incorporation of a supramolecular moiety on proteins. To this end, fluorescent proteins have been site-selectively labeled with ferrocenes, as supramolecular guest moieties, via SNAP-tag technology. The assembly of guest-functionalized SNAP-fusion proteins on cyclodextrin- and cucurbit[7]uril-coated surfaces yielded stable monolayers. The binding of all ferrocene fusion proteins is specific as determined by surface plasmon resonance. Micropatterns of the fusion proteins, on patterned cyclodextrin and cucurbituril surfaces, have been visualized using fluorescence microscopy. The SNAP-fusion proteins were also immobilized on cyclodextrin vesicles. The supramolecular SNAP-tag labeling of proteins, thus, allows for the assembly of modified proteins via supramolecular host-guest interaction on different surfaces in a controlled manner. These findings extend the toolbox of fabricating supramolecular protein patterns on surfaces taking advantage of the high labeling efficiency of the SNAP-tag with versatile supramolecular moieties. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2012)
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Open AccessArticle Self-Assembly of Pyridine-Modified Lipoic Acid Derivatives on Gold and Their Interaction with Thyroxine (T4)
Int. J. Mol. Sci. 2013, 14(2), 3500-3513; doi:10.3390/ijms14023500
Received: 26 December 2012 / Revised: 30 January 2013 / Accepted: 31 January 2013 / Published: 6 February 2013
PDF Full-text (378 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Pyridyl derivatives of lipoic acid were prepared as ligands for the study of the interaction with thyroxine (T4). Thin self-assembled films of the ligands were prepared in 70% ethanol on gold and their interaction with T4 was studied by titration experiments
[...] Read more.
Pyridyl derivatives of lipoic acid were prepared as ligands for the study of the interaction with thyroxine (T4). Thin self-assembled films of the ligands were prepared in 70% ethanol on gold and their interaction with T4 was studied by titration experiments in an aqueous buffer solution using Surface Plasmon Resonance (SPR). The thickness and refractive index of the ligand layers were calculated from SPR spectra recorded in two media, also allowing for surface coverage and the density of the layers to be estimated. Two ligands, a 4-pyridyl and a bis(2-hydroxyethyl) derivative of lipoic acid, were selected to investigate the feasibility for producing molecularly imprinted self-assembled layers on gold for T4. The methodology was to co-assemble T4 and the ligand onto the gold surface, elute the T4 from the layer under alkaline conditions, and study the rebinding of T4 to the layer. Multiple elution/rebinding cycles were conducted in different buffer solutions, and rebinding of T4 could be observed, with a moderate binding affinity that depended greatly on the solvent used. More optimal binding was observed in HBS buffer, and the affinity of the interaction could be slightly increased when the 4-pyridyl and bis(2-hydroxy-ethyl) derivatives of lipoic acid were combined in the imprinted layer. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2012)
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Open AccessArticle Catalysis of Transesterification Reactions by a Self-Assembled Nanosystem
Int. J. Mol. Sci. 2013, 14(1), 2011-2021; doi:10.3390/ijms14012011
Received: 30 November 2012 / Accepted: 14 January 2013 / Published: 21 January 2013
Cited by 2 | PDF Full-text (461 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Histidine-containing peptides self-assemble on the surface of monolayer protected gold nanoparticles to form a catalytic system for transesterification reactions. Self-assembly is a prerequisite for catalysis, since the isolated peptides do not display catalytic activity by themselves. A series of catalytic peptides and substrates
[...] Read more.
Histidine-containing peptides self-assemble on the surface of monolayer protected gold nanoparticles to form a catalytic system for transesterification reactions. Self-assembly is a prerequisite for catalysis, since the isolated peptides do not display catalytic activity by themselves. A series of catalytic peptides and substrates are studied in order to understand the structural parameters that are of relevance to the catalytic efficiency of the system. It is shown that the distance between the His-residue and the anionic tail does not affect the catalytic activity. On the other hand, the catalytic His-residue is sensitive to the chemical nature of the flanking amino acid residues. In particular, the presence of polar Ser-residues causes a significant increase in activity. Finally, kinetic studies of a series of substrates reveal that substrates with a hydrophobic component are very suitable for this catalytic system. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2012)
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Open AccessArticle Self-Assembly of Discrete Metal Complexes in Aqueous Solution via Block Copolypeptide Amphiphiles
Int. J. Mol. Sci. 2013, 14(1), 2022-2035; doi:10.3390/ijms14012022
Received: 11 December 2012 / Revised: 9 January 2013 / Accepted: 17 January 2013 / Published: 21 January 2013
Cited by 8 | PDF Full-text (2075 KB) | HTML Full-text | XML Full-text
Abstract
The integration of discrete metal complexes has been attracting significant interest due to the potential of these materials for soft metal-metal interactions and supramolecular assembly. Additionally, block copolypeptide amphiphiles have been investigated concerning their capacity for self-assembly into structures such as nanoparticles, nanosheets
[...] Read more.
The integration of discrete metal complexes has been attracting significant interest due to the potential of these materials for soft metal-metal interactions and supramolecular assembly. Additionally, block copolypeptide amphiphiles have been investigated concerning their capacity for self-assembly into structures such as nanoparticles, nanosheets and nanofibers. In this study, we combined these two concepts by investigating the self-assembly of discrete metal complexes in aqueous solution using block copolypeptides. Normally, discrete metal complexes such as [Au(CN)2], when molecularly dispersed in water, cannot interact with one another. Our results demonstrated, however, that the addition of block copolypeptide amphiphiles such as K183L19 to [Au(CN)2] solutions induced one-dimensional integration of the discrete metal complex, resulting in photoluminescence originating from multinuclear complexes with metal-metal interactions. Transmission electron microscopy (TEM) showed a fibrous nanostructure with lengths and widths of approximately 100 and 20 nm, respectively, which grew to form advanced nanoarchitectures, including those resembling the weave patterns of Waraji (traditional Japanese straw sandals). This concept of combining block copolypeptide amphiphiles with discrete coordination compounds allows the design of flexible and functional supramolecular coordination systems in water. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2012)
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Open AccessArticle Photophysical Property and Photocatalytic Activity of New Gd2InSbO7 and Gd2FeSbO7 Compounds under Visible Light Irradiation
Int. J. Mol. Sci. 2013, 14(1), 999-1021; doi:10.3390/ijms14010999
Received: 3 December 2012 / Revised: 21 December 2012 / Accepted: 24 December 2012 / Published: 7 January 2013
Cited by 3 | PDF Full-text (762 KB) | HTML Full-text | XML Full-text
Abstract
Gd2InSbO7 and Gd2FeSbO7 were synthesized first, and their structural and photocatalytic properties were studied. The lattice parameters and the band gaps for Gd2InSbO7 and Gd2FeSbO7 were 10.449546 Å, 10.276026 Å, 2.897
[...] Read more.
Gd2InSbO7 and Gd2FeSbO7 were synthesized first, and their structural and photocatalytic properties were studied. The lattice parameters and the band gaps for Gd2InSbO7 and Gd2FeSbO7 were 10.449546 Å, 10.276026 Å, 2.897 eV and 2.151 eV. The photocatalytic degradation of rhodamine B was performed with Gd2InSbO7 and Gd2FeSbO7 under visible light irradiation. Gd2InSbO7 and Gd2FeSbO7 had higher catalytic activity compared with Bi2InTaO7. Gd2FeSbO7 exhibited higher catalytic activity than Gd2InSbO7. The photocatalytic degradation of rhodamine B followed with the first-order reaction kinetics, and the first-order rate constant k was 0.01606, 0.02220 or 0.00329 min−1 with Gd2InSbO7, Gd2FeSbO7 or Bi2InTaO7 as photocatalyst. Complete removal of rhodamine B was observed after visible light irradiation for 225 min or 260 min with Gd2FeSbO7 or Gd2InSbO7 as photocatalyst. The evolution of CO2 was realized, and it indicated continuous mineralization of rhodamine B during the photocatalytic process. The possible photocatalytic degradation pathway of rhodamine B was proposed. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2012)
Open AccessArticle Synthesis and Self-Organization of Fluorene-Conjugated Bisimidazolylporphyrin and Its Optical Properties
Int. J. Mol. Sci. 2013, 14(1), 322-331; doi:10.3390/ijms14010322
Received: 26 November 2012 / Revised: 14 December 2012 / Accepted: 17 December 2012 / Published: 21 December 2012
PDF Full-text (284 KB) | HTML Full-text | XML Full-text
Abstract
A conjugated-bisimidazolylporphyrin bridged by bis(ethynylfluorene) was synthesized and organized into linear polymer through self-coordination having mean molecular weights, Mw and Mn, of ~2.1 × 105 Da and ~1.6 × 105 Da, respectively. A large two-photon absorption cross section
[...] Read more.
A conjugated-bisimidazolylporphyrin bridged by bis(ethynylfluorene) was synthesized and organized into linear polymer through self-coordination having mean molecular weights, Mw and Mn, of ~2.1 × 105 Da and ~1.6 × 105 Da, respectively. A large two-photon absorption cross section value of 3.4 × 105 GM (per dimer unit) was observed. This value was comparable to that of the previously reported self-assembled linear polymer consisting of butadiyne-bridged imidazolylporphyrins. The two-photon absorption properties could be controlled by tuning the wavelength and absorption intensity of the one-photon absorption. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2012)
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Open AccessArticle Turn-On Fluorescent Chemosensor for Hg2+ Based on Multivalent Rhodamine Ligands
Int. J. Mol. Sci. 2012, 13(12), 16822-16832; doi:10.3390/ijms131216822
Received: 22 November 2012 / Accepted: 4 December 2012 / Published: 7 December 2012
Cited by 6 | PDF Full-text (1357 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Rhodamine-based fluorescent chemosensors 1 and 2 exhibit selective fluorescence enhancement to Fe3+ and Hg2+ over other metal ions at 580 nm in CH3CN/H2O (3/1, v/v) solution. Bis(rhodamine) chemosensor 1, under optimized conditions (CH
[...] Read more.
Rhodamine-based fluorescent chemosensors 1 and 2 exhibit selective fluorescence enhancement to Fe3+ and Hg2+ over other metal ions at 580 nm in CH3CN/H2O (3/1, v/v) solution. Bis(rhodamine) chemosensor 1, under optimized conditions (CH3CN/HEPES buffer (0.02 M, pH = 7.0) (95/5, v/v)), shows a high selectivity and sensitivity to Hg2+, with a linear working range of 0–50 μM, a wide pH span of 4–10, and a detection limit of 0.4 μM Hg2+. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2012)
Open AccessArticle Effects of Intramolecular Distance between Amyloidogenic Domains on Amyloid Aggregation
Int. J. Mol. Sci. 2012, 13(10), 12169-12181; doi:10.3390/ijms131012169
Received: 10 August 2012 / Revised: 13 September 2012 / Accepted: 13 September 2012 / Published: 25 September 2012
PDF Full-text (600 KB) | HTML Full-text | XML Full-text
Abstract
Peptide/protein aggregation is implicated in many amyloid diseases. Some amyloidogenic peptides/proteins, such as those implicated in Alzheimer’s and Parkinson’s diseases, contain multiple amyloidogenic domains connected by “linker” sequences displaying high propensities to form turn structures. Recent studies have demonstrated the importance of physicochemical
[...] Read more.
Peptide/protein aggregation is implicated in many amyloid diseases. Some amyloidogenic peptides/proteins, such as those implicated in Alzheimer’s and Parkinson’s diseases, contain multiple amyloidogenic domains connected by “linker” sequences displaying high propensities to form turn structures. Recent studies have demonstrated the importance of physicochemical properties of each amino acid contained in the polypeptide sequences in amyloid aggregation. However, effects on aggregation related to the intramolecular distance between amyloidogenic domains, which may be determined by a linker length, have yet to be examined. In the study presented here, we created peptides containing two copies of KFFE, a simple four-residue amyloidogenic domain, connected by GS-rich linker sequences with different lengths yet similar physicochemical properties. Our experimental results indicate that aggregation occurred most rapidly when KFFE domains were connected by a linker of an intermediate length. Our experimental findings were consistent with estimated entropic contribution of a linker length toward formation of (partially) structured intermediates on the aggregation pathway. Moreover, inclusion of a relatively short linker was found to inhibit formation of aggregates with mature fibril morphology. When the results are assimilated, our study demonstrates that intramolecular distance between amyloidogenic domains is an important yet overlooked factor affecting amyloid aggregation. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2012)
Open AccessArticle Effects of Humidity and Surfaces on the Melt Crystallization of Ibuprofen
Int. J. Mol. Sci. 2012, 13(8), 10296-10304; doi:10.3390/ijms130810296
Received: 19 July 2012 / Revised: 4 August 2012 / Accepted: 16 August 2012 / Published: 17 August 2012
Cited by 4 | PDF Full-text (578 KB) | HTML Full-text | XML Full-text
Abstract
Melt crystallization of ibuprofen was studied to understand the effects of humidity and surfaces. The molecular self-assembly during the amorphous-to-crystal transformation was examined in terms of the nucleation and growth of the crystals. The crystallization was on Al, Au, and self-assembled monolayers with
[...] Read more.
Melt crystallization of ibuprofen was studied to understand the effects of humidity and surfaces. The molecular self-assembly during the amorphous-to-crystal transformation was examined in terms of the nucleation and growth of the crystals. The crystallization was on Al, Au, and self-assembled monolayers with –CH3, –OH, and –COOH functional groups. Effects of the humidity were studied at room temperature (18–20 °C) with relative humidity 33%, 75%, and 100%. Effects of the surfaces were observed at −20 °C (relative humidity 36%) to enable close monitoring with slower crystal growth. The nucleation time of ibuprofen was faster at high humidity conditions probably due to the local formation of the unfavorable ibuprofen melt/water interface. The crystal morphologies of ibuprofen were governed by the nature of the surfaces, and they could be associated with the growth kinetics by the Avrami equation. The current study demonstrated the effective control of the melt crystallization of ibuprofen through the melt/atmosphere and melt/surface interfaces. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2012)

Review

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Open AccessReview Statistical Mechanical Treatments of Protein Amyloid Formation
Int. J. Mol. Sci. 2013, 14(9), 17420-17452; doi:10.3390/ijms140917420
Received: 27 June 2013 / Revised: 5 August 2013 / Accepted: 9 August 2013 / Published: 23 August 2013
Cited by 1 | PDF Full-text (3271 KB) | HTML Full-text | XML Full-text
Abstract
Protein aggregation is an important field of investigation because it is closely related to the problem of neurodegenerative diseases, to the development of biomaterials, and to the growth of cellular structures such as cyto-skeleton. Self-aggregation of protein amyloids, for example, is a complicated
[...] Read more.
Protein aggregation is an important field of investigation because it is closely related to the problem of neurodegenerative diseases, to the development of biomaterials, and to the growth of cellular structures such as cyto-skeleton. Self-aggregation of protein amyloids, for example, is a complicated process involving many species and levels of structures. This complexity, however, can be dealt with using statistical mechanical tools, such as free energies, partition functions, and transfer matrices. In this article, we review general strategies for studying protein aggregation using statistical mechanical approaches and show that canonical and grand canonical ensembles can be used in such approaches. The grand canonical approach is particularly convenient since competing pathways of assembly and dis-assembly can be considered simultaneously. Another advantage of using statistical mechanics is that numerically exact solutions can be obtained for all of the thermodynamic properties of fibrils, such as the amount of fibrils formed, as a function of initial protein concentration. Furthermore, statistical mechanics models can be used to fit experimental data when they are available for comparison. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2012)
Open AccessReview DNA Self-Assembly: From Chirality to Evolution
Int. J. Mol. Sci. 2013, 14(4), 8252-8270; doi:10.3390/ijms14048252
Received: 20 February 2013 / Revised: 3 March 2013 / Accepted: 21 March 2013 / Published: 15 April 2013
Cited by 6 | PDF Full-text (7721 KB) | HTML Full-text | XML Full-text
Abstract
Transient or long-term DNA self-assembly participates in essential genetic functions. The present review focuses on tight DNA-DNA interactions that have recently been found to play important roles in both controlling DNA higher-order structures and their topology. Due to their chirality, double helices are
[...] Read more.
Transient or long-term DNA self-assembly participates in essential genetic functions. The present review focuses on tight DNA-DNA interactions that have recently been found to play important roles in both controlling DNA higher-order structures and their topology. Due to their chirality, double helices are tightly packed into stable right-handed crossovers. Simple packing rules that are imposed by DNA geometry and sequence dictate the overall architecture of higher order DNA structures. Close DNA-DNA interactions also provide the missing link between local interactions and DNA topology, thus explaining how type II DNA topoisomerases may sense locally the global topology. Finally this paper proposes that through its influence on DNA self-assembled structures, DNA chirality played a critical role during the early steps of evolution. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2012)
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Open AccessReview Aggregation of p-Sulfonatocalixarene-Based Amphiphiles and Supra-Amphiphiles
Int. J. Mol. Sci. 2013, 14(2), 3140-3157; doi:10.3390/ijms14023140
Received: 30 November 2012 / Revised: 24 January 2013 / Accepted: 24 January 2013 / Published: 4 February 2013
Cited by 28 | PDF Full-text (1076 KB) | HTML Full-text | XML Full-text
Abstract
p-Sulfonatocalixarenes are a special class of water soluble macrocyclic molecules made of 4-hydroxybenzenesulfonate units linked by methylene bridges. One of the main features of these compounds relies on their ability to form inclusion complexes with cationic and neutral species. This feature, together
[...] Read more.
p-Sulfonatocalixarenes are a special class of water soluble macrocyclic molecules made of 4-hydroxybenzenesulfonate units linked by methylene bridges. One of the main features of these compounds relies on their ability to form inclusion complexes with cationic and neutral species. This feature, together with their water solubility and apparent biological compatibility, had enabled them to emerge as one the most important host receptors in supramolecular chemistry. Attachment of hydrophobic alkyl chains to these compounds leads to the formation of macrocyclic host molecules with amphiphilic properties. Like other oligomeric surfactants, these compounds present improved performance with respect to their monomeric counterparts. In addition, they hold their recognition abilities and present several structural features that depend on the size of the macrocycle and on the length of the alkyl chain, such as preorganization, flexibility and adopted conformations, which make these molecules very interesting to study structure-aggregation relationships. Moreover, the recognition abilities of p-sulfonatocalixarenes enable them to be applied in the design of amphiphiles constructed from non-covalent, rather than covalent, bonds (supramolecular amphiphiles). In this review, we summarize the developments made on the design and synthesis of p-sulfonatocalixarenes-based surfactants, the characterization of their self-assembly properties and on how their structure affects these properties. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2012)
Open AccessReview S-Layer Protein Self-Assembly
Int. J. Mol. Sci. 2013, 14(2), 2484-2501; doi:10.3390/ijms14022484
Received: 14 December 2012 / Revised: 14 January 2013 / Accepted: 16 January 2013 / Published: 25 January 2013
Cited by 29 | PDF Full-text (6818 KB) | HTML Full-text | XML Full-text
Abstract
Crystalline S(urface)-layers are the most commonly observed cell surface structures in prokaryotic organisms (bacteria and archaea). S-layers are highly porous protein meshworks with unit cell sizes in the range of 3 to 30 nm, and thicknesses of ~10 nm. One of the key
[...] Read more.
Crystalline S(urface)-layers are the most commonly observed cell surface structures in prokaryotic organisms (bacteria and archaea). S-layers are highly porous protein meshworks with unit cell sizes in the range of 3 to 30 nm, and thicknesses of ~10 nm. One of the key features of S-layer proteins is their intrinsic capability to form self-assembled mono- or double layers in solution, and at interfaces. Basic research on S-layer proteins laid foundation to make use of the unique self-assembly properties of native and, in particular, genetically functionalized S-layer protein lattices, in a broad range of applications in the life and non-life sciences. This contribution briefly summarizes the knowledge about structure, genetics, chemistry, morphogenesis, and function of S-layer proteins and pays particular attention to the self-assembly in solution, and at differently functionalized solid supports. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2012)
Open AccessReview Molecular Motions in Functional Self-Assembled Nanostructures
Int. J. Mol. Sci. 2013, 14(2), 2303-2333; doi:10.3390/ijms14022303
Received: 11 December 2012 / Revised: 11 January 2013 / Accepted: 11 January 2013 / Published: 24 January 2013
Cited by 11 | PDF Full-text (989 KB) | HTML Full-text | XML Full-text
Abstract
The construction of “smart” materials able to perform specific functions at the molecular scale through the application of various stimuli is highly attractive but still challenging. The most recent applications indicate that the outstanding flexibility of self-assembled architectures can be employed as a
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The construction of “smart” materials able to perform specific functions at the molecular scale through the application of various stimuli is highly attractive but still challenging. The most recent applications indicate that the outstanding flexibility of self-assembled architectures can be employed as a powerful tool for the development of innovative molecular devices, functional surfaces and smart nanomaterials. Structural flexibility of these materials is known to be conferred by weak intermolecular forces involved in self-assembly strategies. However, some fundamental mechanisms responsible for conformational lability remain unexplored. Furthermore, the role played by stronger bonds, such as coordination, ionic and covalent bonding, is sometimes neglected while they can be employed readily to produce mechanically robust but also chemically reversible structures. In this review, recent applications of structural flexibility and molecular motions in self-assembled nanostructures are discussed. Special focus is given to advanced materials exhibiting significant performance changes after an external stimulus is applied, such as light exposure, pH variation, heat treatment or electromagnetic field. The crucial role played by strong intra- and weak intermolecular interactions on structural lability and responsiveness is highlighted. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2012)
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Open AccessReview Aqueous Self-Sorting in Extended Supramolecular Aggregates
Int. J. Mol. Sci. 2013, 14(1), 1541-1565; doi:10.3390/ijms14011541
Received: 6 December 2012 / Revised: 27 December 2012 / Accepted: 4 January 2013 / Published: 14 January 2013
Cited by 19 | PDF Full-text (1610 KB) | HTML Full-text | XML Full-text
Abstract
Self-organization and self-sorting processes are responsible for the regulation and control of the vast majority of biological processes that eventually sustain life on our planet. Attempts to unveil the complexity of these systems have been devoted to the investigation of the binding processes
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Self-organization and self-sorting processes are responsible for the regulation and control of the vast majority of biological processes that eventually sustain life on our planet. Attempts to unveil the complexity of these systems have been devoted to the investigation of the binding processes between artificial molecules, complexes or aggregates within multicomponent mixtures, which has facilitated the emergence of the field of self-sorting in the last decade. Since, artificial systems involving discrete supramolecular structures, extended supramolecular aggregates or gel-phase materials in organic solvents or—to a lesser extent—in water have been investigated. In this review, we have collected diverse strategies employed in recent years to construct extended supramolecular aggregates in water upon self-sorting of small synthetic molecules. We have made particular emphasis on co-assembly processes in binary mixtures leading to supramolecular structures of remarkable complexity and the influence of different external variables such as solvent and concentration to direct recognition or discrimination processes between these species. The comprehension of such recognition phenomena will be crucial for the organization and evolution of complex matter. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2012)
Open AccessReview VCD Studies on Chiral Characters of Metal Complex Oligomers
Int. J. Mol. Sci. 2013, 14(1), 964-978; doi:10.3390/ijms14010964
Received: 11 December 2012 / Revised: 27 December 2012 / Accepted: 31 December 2012 / Published: 7 January 2013
Cited by 17 | PDF Full-text (722 KB) | HTML Full-text | XML Full-text
Abstract
The present article reviews the results on the application of vibrational circular dichroism (VCD) spectroscopy to the study of stereochemical properties of chiral metal complexes in solution. The chiral characters reflecting on the vibrational properties of metal complexes are revealed by measurements of
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The present article reviews the results on the application of vibrational circular dichroism (VCD) spectroscopy to the study of stereochemical properties of chiral metal complexes in solution. The chiral characters reflecting on the vibrational properties of metal complexes are revealed by measurements of a series of β-diketonato complexes with the help of theoretical calculation. Attention is paid to the effects of electronic properties of a central metal ion on vibrational energy levels or low-lying electronic states. The investigation is further extended to the oligomers of β-diketonato complex units. The induction of chiral structures is confirmed by the VCD spectra when chiral inert moieties are connected with labile metal ions. These results have demonstrated how VCD spectroscopy is efficient in revealing the static and dynamic properties of mononuclear and multinuclear chiral metal complexes, which are difficult to clarify by means of other spectroscopes. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2012)
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Open AccessReview Spontaneous Crystallization in Athermal Polymer Packings
Int. J. Mol. Sci. 2013, 14(1), 332-358; doi:10.3390/ijms14010332
Received: 28 November 2012 / Accepted: 14 December 2012 / Published: 24 December 2012
Cited by 12 | PDF Full-text (2276 KB) | HTML Full-text | XML Full-text
Abstract
We review recent results from extensive simulations of the crystallization of athermal polymer packings. It is shown that above a certain packing density, and for sufficiently long simulations, all random assemblies of freely-jointed chains of tangent hard spheres of uniform size show a
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We review recent results from extensive simulations of the crystallization of athermal polymer packings. It is shown that above a certain packing density, and for sufficiently long simulations, all random assemblies of freely-jointed chains of tangent hard spheres of uniform size show a spontaneous transition into a crystalline phase. These polymer crystals adopt predominantly random hexagonal close packed morphologies. An analysis of the local environment around monomers based on the shape and size of the Voronoi polyhedra clearly shows that Voronoi cells become more spherical and more symmetric as the system transits to the ordered state. The change in the local environment leads to an increase in the monomer translational contribution to the entropy of the system, which acts as the driving force for the phase transition. A comparison of the crystallization of hard-sphere polymers and monomers highlights similarities and differences resulting from the constraints imposed by chain connectivity. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2012)
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Open AccessReview Natural Biomolecules and Protein Aggregation: Emerging Strategies against Amyloidogenesis
Int. J. Mol. Sci. 2012, 13(12), 17121-17137; doi:10.3390/ijms131217121
Received: 29 November 2012 / Revised: 12 December 2012 / Accepted: 12 December 2012 / Published: 14 December 2012
Cited by 15 | PDF Full-text (281 KB) | HTML Full-text | XML Full-text
Abstract
Biomolecular self-assembly is a fundamental process in all organisms. As primary components of the life molecular machinery, proteins have a vast array of resources available to them for self-assembly in a functional structure. Protein self-assembly, however, can also occur in an aberrant way,
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Biomolecular self-assembly is a fundamental process in all organisms. As primary components of the life molecular machinery, proteins have a vast array of resources available to them for self-assembly in a functional structure. Protein self-assembly, however, can also occur in an aberrant way, giving rise to non-native aggregated structures responsible for severe, progressive human diseases that have a serious social impact. Different neurodegenerative disorders, like Huntington’s, Alzheimer’s, and spongiform encephalopathy diseases, have in common the presence of insoluble protein aggregates, generally termed “amyloid,” that share several physicochemical features: a fibrillar morphology, a predominantly beta-sheet secondary structure, birefringence upon staining with the dye Congo red, insolubility in common solvents and detergents, and protease resistance. Conformational constrains, hydrophobic and stacking interactions can play a key role in the fibrillogenesis process and protein–protein and peptide–peptide interactions—resulting in self-assembly phenomena of peptides yielding fibrils—that can be modulated and influenced by natural biomolecules. Small organic molecules, which possess both hydrophilic and hydrophobic moieties able to bind to peptide/protein molecules through hydrogen bonds and hydrophobic and aromatic interactions, are potential candidates against amyloidogenesis. In this review some significant case examples will be critically discussed. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2012)

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Open AccessCase Report Successful Treatment of Liver Aspergilloma by Caspofungin Acetate First-Line Therapy in a Non-Immunocompromised Patient
Int. J. Mol. Sci. 2012, 13(9), 11063-11070; doi:10.3390/ijms130911063
Received: 18 July 2012 / Revised: 20 August 2012 / Accepted: 29 August 2012 / Published: 6 September 2012
Cited by 4 | PDF Full-text (1292 KB) | HTML Full-text | XML Full-text
Abstract
Aspergillosis remains to be a life-threatening complication in immunocompromised patients. However, Aspergillus infection can be observed in non-immunocompromised individuals in rare cases. We report a case of liver aspergilloma in a chronic aplastic anemia patient under relatively intact immune status. Therapeutic strategy for
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Aspergillosis remains to be a life-threatening complication in immunocompromised patients. However, Aspergillus infection can be observed in non-immunocompromised individuals in rare cases. We report a case of liver aspergilloma in a chronic aplastic anemia patient under relatively intact immune status. Therapeutic strategy for this rare condition was extensively discussed and caspofungin acetate single agent first-line therapy was applied after careful consideration. Encouraging clinical and radiologic improvements were achieved in response to the antifungal salvage. Our long-term follow-up study also revealed a favorable prognosis. Based on this experience, we suggest caspofungin acetate as first-line therapy for treatment plans of liver aspergilloma. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2012)

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