Bioinspiration and biomimicry in chemistry reverse engineering nature

BIOINSPIRATION AND BIOMIMICRY IN CHEMISTRY BIOINSPIRATION AND BIOMIMICRY IN CHEMISTRY REVERSE-ENGINEERING NATURE Edited by Gerhard F Swiegers A JOHN WILEY & SONS, INC., PUBLICATION Copyright © 2012 by John Wiley & Sons, Inc All rights reserved Published by John Wiley & Sons, Inc., Hoboken, New Jersey Published simultaneously in Canada No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, scanning, or otherwise, except as permitted under Section 107 or 108 of the 1976 United States Copyright Act, without either the prior written permission of the Publisher, or authorization through payment of the appropriate per-copy fee to the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, (978) 750-8400, fax (978) 750-4470, or on the web at www.copyright.com Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030, (201) 748-6011, fax (201) 748-6008, or online at http://www.wiley.com/go/permission Limit of Liability/Disclaimer of Warranty: While the publisher and author have used their best efforts in preparing this book, they make no representations or warranties with respect to the accuracy or completeness of the contents of this book and specifically disclaim any implied warranties of merchantability or fitness for a particular purpose No warranty may be created or extended by sales representatives or written sales materials The advice and strategies contained herein may not be suitable for your situation You should consult with a professional where appropriate Neither the publisher nor author shall be liable for any loss of profit or any other commercial damages, including but not limited to special, incidental, consequential, or other damages For general information on our other products and services or for technical support, please contact our Customer Care Department within the United States at (800) 762-2974, outside the United States at (317) 572-3993 or fax (317) 572-4002 Wiley also publishes its books in a variety of electronic formats Some content that appears in print may not be available in electronic formats For more information about Wiley products, visit our web site at www.wiley.com Library of Congress Cataloging-in-Publication Data: Bioinspiration and biomimicry in chemistry : reverse-engineering nature / edited by Gerhard F Swiegers p cm Includes bibliographical references and index ISBN 978-0-470-56667-1 (cloth) Biomimicry Biomimetics Biomedical engineering Biomedical materials I Swiegers, Gerhard F QP517.B56B478 2012 610.28–dc23 2011049801 Printed in the United States of America 10 Dedicated to Crawford Long, William Thomas Green Morton, and Wilhelm Răontgen CONTENTS Foreword xvii Foreword xix Jean-Marie Lehn Janine Benyus Preface xxiii Contributors xxv Introduction: The Concept of Biomimicry and Bioinspiration in Chemistry Timothy W Hanks and Gerhard F Swiegers 1.1 What is Biomimicry and Bioinspiration? 1.2 Why Seek Inspiration from, or Replicate Biology? 1.2.1 1.2.2 1.2.3 1.3 Biomimicry and Bioinspiration as a Means of Learning from Nature and Reverse-Engineering from Nature Biomimicry and Bioinspiration as a Test of Our Understanding of Nature Going Beyond Biomimicry and Bioinspiration 4 Other Monikers: Bioutilization, Bioextraction, Bioderivation, and Bionics 1.4 Biomimicry and Sustainability 1.5 Biomimicry and Nanostructure 1.6 Bioinspiration and Structural Hierarchies 1.7 Bioinspiration and Self-Assembly 11 1.8 Bioinspiration and Function 12 1.9 Future Perspectives: Drawing Inspiration from the Complex System that is Nature 13 References 14 vii viii CONTENTS Bioinspired Self-Assembly I: Self-Assembled Structures 17 Leonard F Lindoy, Christopher Richardson, and Jack K Clegg 2.1 Introduction 17 2.2 Molecular Clefts, Capsules, and Cages 19 2.2.1 2.2.2 Organic Cage Systems Metallosupramolecular Cage Systems 21 24 Enzyme Mimics and Models: The Example of Carbonic Anhydrase 28 2.4 Self-Assembled Liposome-Like Systems 30 2.5 Ion Channel Mimics 32 2.6 Base-Pairing Structures 34 2.7 DNA–RNA Structures 36 2.8 Bioinspired Frameworks 38 2.9 Conclusion 41 References 41 2.3 Bioinspired Self-Assembly II: Principles of Cooperativity in Bioinspired Self-Assembling Systems 47 Gianfranco Ercolani and Luca Schiaffino 3.1 Introduction 47 3.2 Statistical Factors in Self-Assembly 48 3.3 Allosteric Cooperativity 50 3.4 Effective Molarity 52 3.5 Chelate Cooperativity 55 3.6 Interannular Cooperativity 60 3.7 Stability of an Assembly 62 3.8 Conclusion 67 References 67 Bioinspired Molecular Machines 71 Christopher R Benson, Andrew I Share, and Amar H Flood 4.1 Introduction 4.1.1 Inspirational Antecedents: Biology, Engineering, and Chemistry 71 72 (a) (b) (c) Figure 8.16 (a) Fluorescence micrograph and (b) cryo-TEM images of hollow spheres with a lateral nanoporous shell formed by self-assembly of rigid rode amphiphiles in aqueous solution (0.01 wt %) (c) Schematic representation of a reversible open/closed gating motion in the lateral nanopores of the capsules (green, polyether dendrons; yellow, aromatic segments; blue, hydrophobic branches) (Reproduced with permission Copyright Wiley-VCH: Ref 59.) (a) (d) (b) (c) (e) Figure 8.19 (a) Fluorescence spectra of donor-loaded polymerized vesicles in aqueous solution at pH 3.0–11.0 (b) Photograph of donor-loaded polymerized vesicles in aqueous solution at different pH under an ultraviolet lamp (366 nm) (c) CIE 1931 chromaticity diagram The three points indicated by circles signify the fluorescence color coordinates for the donor excimers (0.24, 0.38), perylene membranes (0.52, 0.17), and white fluorescence coordinate (0.32, 0.31) for the donor-loaded polymerized vesicles at pH 9.0 (d) Schematic illustration of the donor-loaded polymerized vesicles with pH-tunable energy transfer On average, 4.0 × 102 donor molecules are loaded into one perylene bisimide vesicle The inner and outer layers of the vesicle consist of 5.2 × 103 and 8.4 × 103 perylene acceptor molecules, respectively Their hydrophilic chains (blue) are exposed to water, with the hydrophobic part (orange) packed together and stabilized by polymerized double bonds (red) (e) pH-dependent energy-transfer efficiency (E, orange line) and overlap integral (J, blue line) of donor-loaded polymerized vesicles at pH 3.0–11.0 (Reproduced with permission Copyright Nature Publishing Group: Ref 68.) (a) (b) (c) (d) (e) (f) Figure 8.21 (a)–(c) Confocal scans of vesicles loaded with 0.3 mM Na2 S (red) and 0.3 mM CdCl2 (green) undergoing fusion (d)–(f) Intensity line profiles along the dashdotted lines indicated by red arrows in (a)–(c), respectively The direction of the field is indicated in (a) Before fusion [(a) and (d)], the vesicle interior shows only background noise similar to the external solution as indicated by the shaded zone in (d) After fusion [(b), (c), (e), and (f)], fluorescence from the product is detected in the interior of the fused vesicle The time after applying the pulse is indicated on the micrographs (Reproduced with permission Copyright Wiley-VCH: Ref 71.) (a) (b) Figure 8.24 (a) Multivesicle assemblies (LSCM) and (b) a sectioned specimen (ca 80 nm thickness) of the multivesicle assembly (TEM) (Reproduced with permission Copyright Wiley-VCH: Ref 73.) mosm/l 350 mosm/l 700 mosm/l 1100 mosm/l GUV Outer membrane 1100 mosm/l Inner membrane 1100 mosm/l Overlay membrane 1100 mosm/l DSV STR+ DSV Figure 8.25 Upper row: Effect of hyperosmotic pressure on GUVs labeled with red dye All images represent different vesicles Middle row: Double-shell giant vesicle at 1100 mosm/L hyperosmotic pressure Double-shell vesicles (DSVs) without surface proteins underwent an outside budding process under hyperosmotic conditions The two membranes stuck together in newly formed nanotubes (yellow signal), or they formed separately new buds and tubes (green and red signals) Lower row: Vesicle coated with a crystalline streptavidin layer on the outer membrane surface (STR+DSV) showed a slight asymmetrical shape deformation without membrane budding (green signal), while the inner membrane released the osmotic pressure, separately forming daughter vesicles (red signal) Scale bars = μm (Reproduced with permission Copyright American Chemical Society: Ref 74.) (a) (b) (c) (d) Figure 10.1 Various colorations provided by living creatures in Nature (a) Blue Morpho butterfly (b) Peacock (c) Longhorn beetles Tmesisternus isabellae (Reproduced with permission from Ref 81 Copyright © 2009, the Optical Society of America.) (d) Myxomycetes Diachea leucopoda (Reproduced with permission Copyright the Optical Society of America: Ref 3.) Stage (a) Motor Hydrophilic substrate (b) (c) Figure 10.4 (a) Schematic illustration of the lifting method During the lifting process, the self-assembly of colloidal crystals takes place at the air–liquid interface, due to the capillary force and the evaporation of solvent The lifting speed can be precisely controlled by the computer (b) SEM images of the obtained highly ordered PC films (c) PC films with various distinct brilliant structural color fabricated by using colloidal crystals with different diameters (Reproduced with permission Copyright the American Chemical Society: Ref 31.) (a) 0.20 (b) water NaBr NH4NO3 NaBF4 NaCIO4 NH4PF6 LiTf2N Absorbance (c) 0.15 0.10 0.05 550 (d) Water Br– NO–3 BF–4 CIO–4 600 650 700 Wavelength (nm) PF–6 750 Tf2N– Figure 10.9 SEM images of the anion-sensitive ionic liquid based inverse opal film with (a) opened pore structures and (b) closed pore structures (c) Stop band shift of the film in response to various kinds of anion aqueous solutions (d) Color presented by the film when soaking into different kinds of anion aqueous solutions Different colors will be exhibited in response to the anions due to the change of the solubility and the refraction index, which can be directly recognized by the naked eye (Reproduced with permission Copyright Wiley-VCH: Ref 73.) A (a) Hred A′ A w A′ d Flo Sequential ultraviolet pattern C Magnetic field intensity Hblue > Hgreen > Hred dblue > dgreen > dred Hblue Hgreen Hred Ultraviolet DMD dynamic mask (b) Time (c) (d) Figure 10.10 (a) Schematic illustration of high-throughput bioassays generated from M-ink with the help of an external magnetic field and a computer-controlled spatial light modulator as mask Taking advantage of both spectral encoding and graphical encoding, various barcodes can be obtained (b–d) (b) Hexagon-type 2D color-barcoded microparticles; (c) microparticles with various shapes and colors; (d) bar-type 1D color-barcoded microparticles (Reproduced with permission Copyright Nature Publishing Group: Ref 79.) (a) (b) Reflection (%) 100 200nm 214nm 223nm 232nm 246nm 80 260nm 60 40 20 400 450 500 550 600 650 700 Wavelength (nm) (c) Figure 10.11 (a) Microscope image of various kinds of inverse opal beads fabricated through microfluidic technology by using polystyrene spheres with different size as sacrificial templates (b) Reflection spectra of these beads These optical signals are quite stable and have close relationships with the size of colloidal crystals used for the fabrication (c) SEM images of the inverse opal beads The insert shows that they have a porous surface Further investigation found that both the surface and bulk of the beads are composed of well-ordered 3D periodical structures, providing a rather high specific surface area for the potential application in the bioassays (Reproduced with permission Copyright Wiley-VCH: Ref 78.) (a) (b) (c) (d) (e) (f) Figure 10.12 Living creatures with tunable colors in Nature They can change their body color in response to the external stimulation to adapt themselves to the surrounding environment (a)–(c) Chameleon (Reproduced with permission from Michael Monge, Copyright by FL Chams, Inc.) (d)–(f) Beetles charidotella egregia (Reproduced with permission Copyright the American Physical Society: Ref 80.) (a) PC film PDLC Holophote UV light (b) (c) 50 Reflectance (%) 40 30 UV light Visible light 20 10 500 550 600 650 700 Wavelength (nm) Figure 10.13 (a) Schematic illustration of a reversible photonic device composed of PC film and liquid crystals, which can conveniently be modulated by UV and visible light; (b) characteristics presented by the photonic devices; (c) reflection spectra change of the film under the irradiation of UV light These changes can be reversed to the original state under the irradiation of visible light The insets show the colors before and after UV irradiation (Reproduced with permission Copyright the American Institute of Physics: Ref 84.) Diffraction intensity/a.u (b) 30.2°C 80 29.2°C Creatinine diffuses into hydrogel and binds to enzyme 26.8°C 24.7°C Washing 23.0°C Creatinine hydrolysis produces OH– 21.5°C 18.1°C 15.7°C – OH deprotonates nitrophenol Hydrogel swells causing red-shift Diffraction red shift/nm (a) 60 40 pH 6.5 pH 7.3 pH pH 9.1 pH 4.4 pKa = 7.34 450 500 λ/nm 550 600 20 OH 450 500 550 600 650 λ/nm (c) 1) pH mM 10 mM 15 mM 20 mM 2) 400 500 600 λ/nm 700 800 Figure 10.14 Responsive photonic materials-based PCs and their responsiveness to specific external stimulation such as temperature, pH, and chemicals (a) Temperature dependence of the reflection spectra of the porous NIPA gel made using close-packed silica colloidal crystals as template (Reproduced with permission Copyright the American Chemical Society: Ref 86.) (b) Schematic illustration of pH-responsive polymerized crystalline colloidal array (left) and the pH dependence of reflection spectra of this intelligent sensing array (right) (Reproduced with permission Copyright the American Chemical Society: Ref 88.) (c) Photographs (left) and reflection spectra (right) of the periodically ordered interconnecting porous poly(NIPA-co-AAPBA) gel in response to different concentrations of glucose (Reproduced with permission Copyright Wiley-VCH: Ref 87.) d2 PS beads PDMS Swelling Shrinking d2 (b) Intensity (a.u.) (a) 400 PDMS swollen with solvent Before swelling After swelling 600 500 Wavelength (nm) 700 (c) Figure 10.15 Patterned photonic films fabricated by taking advantage of the swelling process of polymer matrix (a) Schematic illustration of the swelling and shrinking process of tunable colloidal crystals The lattice constant will be increased by swelling the PDMS matrix with an appropriate solvent, while it will shrink back to the original state after the evaporation of solvent (b) The change of reflection spectra before and after the swelling process (c) Letters printed on the surface of the matrix using a rubber stamp (Reproduced with permission Copyright the American Chemical Society: Ref 89.) PS sphere (a) (b) d PDMS elastomer Stretched Initial Released Stretched Reflectance (a.u.) (c) 520 540 560 580 600 620 640 Wavelength (nm) Figure 10.16 External mechanical-force-responsive photonic films fabricated by embedding colloidal crystals in PDMS matrix (a) Schematic illustration of the reversible elastic deformation of the composite colloidal crystal film The lattice constant can easily be modulated by the stretch rate of the film (b) Digital photographs of the composite colloidal crystal film before (top) and after (down) stretch (c) The change of reflection spectra during the stretching process (Reproduced with permission Copyright the American Chemical Society: Ref 91.) Increasing voltage (b) Reflectivity (a) Wavelength Figure 10.17 Electric-field-induced tunable photonic materials (a) Schematic illustration of the operation of voltage-tunable full-color opal film As the film was obtained by embedding the silica colloidal crystals into the matrix of polyferrocenylsilane gel, modulation of the voltage causes a change in the lattice constant (b) Photographs of the tunable opal film in response to the voltage change This kind of film has a tuning range covering the whole visible region (Reproduced with permission Copyright Elsevier: Ref 37.) (a) (b) a (c) c e (d) 40 R/% 30 20 10 450 500 550 600 650 700 750 800 λ/nm Figure 10.18 Magnetically tunable photonic crystals With the help of an external magnetic field, they have a tuning range covering the whole visible region (a) Magnetic colloidal crystals exhibiting various Bragg colors due to the inhomogeneous field gradient, which compresses or relaxes the crystal lattice (Reproduced with permission Copyright the American Chemical Society: Ref 96.) (b) Photographs of magnetic colloidal crystals in response to an external magnetic field The magnetic crystals will exhibit various colors while gradually altering the magnet–sample distance (c) Optical microscope images of magnetic colloidal crystal solution enclosed in a glass capillary under an increasing magnetic field (d) External magnetic field intensity dependence of the reflection spectra of the magnetic colloidal crystals (Panels (b) and (d) reproduced with permission Copyright 2007 Wiley-VCH: Ref 98 Panel (c) reproduced with permission Copyright the American Chemical Society: Ref 99.) ... Means of Learning from Nature and Reverse- Engineering from Nature Biomimicry and Bioinspiration as a Test of Our Understanding of Nature Going Beyond Biomimicry and Bioinspiration 4 Other Monikers:... BIOINSPIRATION AND BIOMIMICRY IN CHEMISTRY BIOINSPIRATION AND BIOMIMICRY IN CHEMISTRY REVERSE- ENGINEERING NATURE Edited by Gerhard F Swiegers A JOHN WILEY & SONS, INC., PUBLICATION... Bioderivation, and Bionics 1.4 Biomimicry and Sustainability 1.5 Biomimicry and Nanostructure 1.6 Bioinspiration and Structural Hierarchies 1.7 Bioinspiration and Self-Assembly 11 1.8 Bioinspiration and