A method for 3d nano focusing of optical energy and its application to the surface enhanced raman spectroscopic study of protein 2

Chapter Electromagnetic Theory of 3D Nanofocusing of Surface Plasmon Polariton and its Application to Surface Enhanced Raman Scattering (SERS) In Chapter 2, confined and intense electric fields (the SERS hot-spots) on a spherical metallic nano-particle were shown to be a result of the redistribution of optical energy by the surface plasmon (SP) In this chapter, a coherent fluctuation of surface charges on a flat airmetal interface is discussed (147) Such a “planar” SP or propagating surface plasmon polariton (SPP) has been demonstrated in the electron energy-loss experiments by Powell and Swan (148), and shown to be localized or bound to the interface within the Thomas-Fermi screening thickness of about Å (149) One interesting consequence of an oscillating surface-charge is the resultant transversal and longitudinal electromagnetic field which disappears at |z| →∞, and has its maximum on the surface z = (see Figure 1) Just as the SP fields on a metal particle are capable of Raman enhancement, the same is also true for the SPP fields on a smooth metal surface as will be discussed below 99 SPP Dielectric z Au x Figure Intensity distribution showing the field confinement of the propagating surface plasmon polariton on a the smooth surface of a semi-infinite Au 4.1 General Theory of Propagating Surface Plasmon Polariton on Smooth Surfaces Unlike nano-particle-bound SP fields, which are confined to the north and south poles of the particle (see § 2.3.2 of Chapter 2), a SPP field is non-localized and spread out across the entire metal-dielectric interface The field distribution of a surface-bound SP field can be v v easily found through the Maxwell equation (∇ + κ )E = , which gives E the general form, v ˆ ˆ Ei = (Eix a x + Eiz a z )ei (k ix x + k iz z ) (1) v in which the projected direction of k on the dielectric-metal boundary is assumed to be along the positive x-axis The subscript, i, indicates whether the equation is applicable to the dielectric (i = 1) or the metallic (i = 2) medium One can also see from the Maxwell equation that both kix and k iz are generally complex, satisfying, 100 2 kix + kiz = ω µ iε i (2) ' " where ε is real, and ε , is complex, ε = ε + iε v v Whether the E1 and E2 field is bound to the surface, i.e decays away from the surface |z| > 0, depends primarily on the values of kix and k iz By imposing the boundary conditions, E1 x = E2 x , H1x = H x (3) v v v v and making use of the fact that, ∇ × H = i ωε E and ì E = iàH , it follows that, E1x = H1 y k1z ωε1 , E2 x = H y k2 z ωε (4) thus, k1z ε1 − k2 z ε2 =0 (5) Owing to the continuity of the tangential fields across the interface, one has k1 x = k2 x = k x (6) Since all the k values (i.e k ix and k iz ) are totally described by Eqn 2, and 6, these v v equations thus collectively determine whether the E1 and E2 fields are bound to the interface 101 Now by re-writing Eqn as, ω  k iz = ± ε i   − k ix c (i = 1, 2) (7) and in combination with Eqn 5, one can obtain a dispersion equation that relates k x to ω , kx = ω  ε1ε    c  ε1 + ε    (8) Note that in deriving Eqn 8, the upper sign in Eqn has been chosen for i = 1, and the lower v v sign for i = This is to ensure that the E1 and E2 fields will not increase away from the interface, and thereby result in an unrealistic field Since the current thesis concerns mainly with low-damping noble metals such as Au ' " ' ' and Ag with ε < , ε > ε and ε > ε - true for the metals commonly employed in the majority of SERS studies, k x can thus be approximated as, kx ≈ ' ω  ε1ε    ' c  ε1 + ε    (9) Plotting ω versus k x produces the dispersion curve for SPP (see Figure 2), which describes the allowable SPP modes that can be supported on a planar metal surface for a range of ω The shaded region bound by the light line ε ω / c and the ω -axis in Figure represents v points where both k x ( = k x ) and k1z are real, i.e where E1 is propagating away from the 102 surface The fact that the SPP dispersion curve is not included in this particular region indicates that the k x (or k x ) for the SPP modes must be greater than ε ω / c , and thus the corresponding k1z must be a pure positive imaginary according to Eqn Hence, as expected, v v the E1 field of the SPP is decaying away (i.e E1 field is surface bound) from the surface rather than propagating away Inside the metal (i = 2), on the other hand, k z of the SPP will v possess a negative imaginary part (see Eqn and 7), which suggests that the E2 field should reduce as z → -∞ Thus, the SPP dispersion curve represents “non-radiative” surface-bound field with exponentially decreasing intensities above and below the dielectric-metal boundary z > (Figure 1) Note that the dispersion curve does not increase monotonically with k x , but levels at ω sp = ωp ' 1+ ε , where ωsp and ω p is respectively the SPP frequency and the ' bulk plasma frequency of the metal With increasing ε , the value of ω sp reduced One can E also conclude that, according to Eqn 1, ∠ iz E  ix  k  = ∠ ix  k   iz  π ≈  for a supported SPP field on  the interface, suggesting the longitudinal and transverse fields, i.e Eix and Eiz , are always 90 º out of phase 103 Dispersion Curve for SPP on semi-infinite Au Light-line Freq (1e15 rad/s) ω sp Dispersion 1 10 k (10e7) Figure Dispersion curve for a planar surface plasmon Finally, through the divergence theorem, expression for the SPP charges across the interface can be obtained, v ρ (s ) = ε o (ε1E1+z − ε E2+z )  k  = ε o  ε1 − ε z1  E1+z  kz2     k v ˆ = ε o  ε1 − ε z1  E2 ( x, y )a z  kz2    (10) where the plus sign indicates the field is measured immediately above the metal surface, and v s is a surface vector ( x, y ) 104 4.2 Excitation and Evidence of Propagating Surface Plasmon v An electron penetrating a solid can transfer its momentum hq and energy ∆Eo to the v v electrons of the solid The projection of q upon the surface kx determines the plasmon wave vector and, together with the dispersion relation, the energy loss of the scattered electron ∆Eo = hω (see Figure 3) can be determined Since the electrons scatter at different angles θ , v different momenta hk x are transferred to the metal surface Thus measurements of the energy loss ∆Eo over a range of θ , allow the dispersion relation of the SPPs to be measured up to v large kx , beyond the Brillouin zone (149) The physics of SPPs has thus been studied extensively with electrons, especially with fast electrons, and the fundamental properties of SPP have been found in good agreement with theory (150) v kel Incident electron v Projection of hq onto the metal surface v kx Thin metal film Scattered v electron k ' v hq el - + Energy loss measurement Figure An energy loss measurement for determining the dispersion relation of SPP on a v' v thin metal film kel is the final momentum of the incident electron after collision, while hq is the momentum transferred to an electron within the metal 105 While fast electrons are good tools for the study of the dispersion relation at very v large kx (~0.3 Å-1) as has been performed previously in order to study the slow increase of the dispersion relation in Al (150-153), it is however not convenient to reach the region of v small kx because of the difficulties in producing an extremely narrow incident electron beam v with a low kel required for such a measurement This limits the experimental uncertainty in v the measurable kx value via electron loss to about × 10-3 Å-1, which is comparable with the extension of the whole linear region of the dispersion relation Hence, either a fast- or a slow- v electrons beam is not suitable for exciting SPP in the low kx value range of interest to the current study Visible light, on the other hand, possesses a low momentum in the × 10-3 Å-1, range, and can thus allow for the excitation of SPPs on a smooth metal surface However, this is not straightforward since it is not possible for a radiative beam to launch a SPP on a metal v surface via a direct incidence, simply because the projection of k of the light onto the surface (i.e k x = ω c ε sin θ o , where θ o is the incident angle, and ε is the dielectric constant of the medium above the metal surface) is always less than the SPP momentum ' ω  ε 1ε    (see ' c  ε1 + ε    ' ' Eqn and recalling that ε < and ε > ε ) for any incident angle between º to 90 º; the incident photon must at least gain an extra momentum ω  c  '  ε 1ε  ε +ε '  ∆k in the order of   ω − ε sin θ o  in order to induce a SPP  c    Conventionally, this is achieved through a three-layer configuration as shown in Figure First, the exciting beam is launched into the top medium (i.e region 0), normally a glass semi-cylindrical prism, which has a high refractive index (normally a glass) to up the k x 106 to ω c ε sin θ o (where ε o > ) before impinging upon the 0/1 interface Due to electromagnetic theory and the theory of conservation of momentum, this momentum ( k x ) is carried across region and reaches the 1/2 interface Depending on whether a KrestchmanRaether (1 = metal, = dielectic) or an Otto configuration (1 = dielectric, = metal) is used, one of the regions and can be a metal, while the other a dielectric (149, 154) In any case, it is possible to choose an appropriate ε so that k x = ω c ε sin θ o = ω  ε 1ε    , which c  ε1 + ε    matches the SPP wave vector at the 1/2 interface The incident angle at which this condition is satisfied is thus simply,  ε 1ε   ε + ε  ε o   θ o, sp = sin −1       (11) Note that ε must always be sufficiently large compared to, | ε1 | in the case of a Krestchman-Raether setup, or | ε | in the case of Otto setup, in order for θ o , sp to be a real value, i.e in order to have a realistic incident angle 107 High refractive index θ Incident beam kx Reflected beam ε0 0/1 ε1 kx 1/2 ε2 Figure A three-layer configuration for exciting surface plasmons 4.3 Exciting Propagating Surface Plasmon Optically 4.3.1 Exciting Surface Plasmons via Krestchman-Raether Configuration Figure shows a typical Krestchman-Raether configuration with the three layers respectively being glass (or quartz) (0), metal (1), and a dielectric medium (2) exhibiting a refractive index lower than that in In this particular configuration, the incident field gains its momentum while traversing through region before reaching the metal film layer in which the field decreases exponentially in amplitude prior to impinging on the 1/2 interface If the field is p-polarized and the incident angle θ o is such that the k x of the field matches ksp ( R ω  ε 1' ε  c  ε 1' + ε    ) at the 1/2 interface, a SPP is excited in which case the reflected intensity   (see Figure 5) reduces to a minimum as a result of the incident energy being completely converted to the excited SPP mode Such a dependence of the reflected light with the incident 108 The electric field on the metal surface above the nano-cavity can be derived once (s) v Ect is known; ∞ v v v ˆ ~ ˆv E c = E1i + ∑ ∫∫∫ e −ik + ⋅ha z Ts e ks+ m ,n with ~ Ts ( p ) ( ( (s) v ~ ˆv ˆ E ct e ks+ + T p e kvp+ ) ( being a tensor that relates the wave surface to the transmitted wave v ~ ˆv E s ( p ) = Ts ( p ) eks (+p )   v s( p) E = (a − b )   , where v E s( p) v E s( p) v 2 k1 − k1 x v k1 ˆs ekv (+p ) (s) v ˆ E ct e kvp+ )) (VII.56) directing from the cavity toward the in the dielectric medium above the metal, i.e has the form,  k  k   −ik x − ik z ik z 1 ˆ ˆ ˆ  e x a x + a  v x  e z a z + b v x  e z a z k  k        v with a and b being some complex constants, and k1 being the wave vector in the dielectric at the light frequency ( ω ) of interest Reference C Flammer, in Spheroidal Wave Functions, Dover Pubns, New York (2005) xl Publications and Conference Abstracts Publications Kho KW, Koh ZY, Shen ZX, Watt F, Olivo MC, “3D Nanofocusing and Confined Guiding of Optical Energy by Nonspherical Nanocavity”, Physical Review A 2009 (submitted) Kho KW, Koh ZY, Shen ZX, Mhaisalkar S, White TJ, Watt F, Olivo MC, “Fabrication of a Smooth Metal Substrate with Embedded Spherical and Non-spherical Nanocavities”, Langmuir 2009 (submitted) Kho KW, Shen ZX, Lei Z, Watt F, Soo KC, Olivo M, “Investigation into a surface plasmon related heating effect in surface enhanced Raman spectroscopy”, Anal Chem 2007 Dec 1; 79(23): 8870-82 Kho KW, Shen ZX, Zeng HC, Soo KC, Olivo M, “Deposition method for preparing SERSactive gold nanoparticle substrates”, Anal Chem 2005 Nov 15; 77(22): 7462-71 Conference Abstracts Kho KW, Koh ZY, Shen ZX, Watt F, Olivo MC, Surface Enhanced Raman Spectroscopy xli Using a Smooth Planar Metal Surface with Embedded Nano-Cavities, XX1st International Conference on Raman Spectroscopy, 19 August, 2008, London, UK Kho KW, Olivo MC, Colloguium Spectroscopium Internationale XXXV, Xiamen, China, September 22 – 28, 2007 Kho KW, Shen ZX, Watt F, Soo KC, Olivo M Plasmon-induced Heating effect in Surface Enhanced Raman Scattering In: International Symposium Photonic West 2006 xlii References D Otzen, "Differential adsorption of variants of the Thermomyces lanuginosus lipase on a hydrophobic surface suggests a role for local flexibility," Col Surf B 64( ), 223-228 (2008) F Ferrato, F Carriere, L Sarda and R Verger, "A critical reevaluation of the phenomenon of interfacial activation " Meth Enzymol 286( ), 327-347 (1997) R D Schmid and R Verger, "Lipases: Interfacial Enzymes with Attractive Applications," Angew Chem Int Ed 37(12), 1608-1633 (1998) H Xu, X Zhao, C Grant, J R Lu, D E Williams and J Penfold, "Orientation of a Monoclonal Antibody Adsorbed at the Solid/Solution Interface: A Combined Study Using Atomic Force Microscopy and Neutron Reflectivity," Langmuir 22( ), 6313-6320 (2006) M Malmsten, "Formation of Adsorbed Protein Layers " J Colloid Interface Sci 207(2), 186-199 (1998) C Lou, Z Wang and S W Wang, "Two-Dimensional Protein Crystals on a Solid Substrate: Effect of Surface Ligand Concentration," Langmuir 23( ), 9752-9759 (2007) M Tanaka and E Sackmann, "Polymer-supported membranes as models of the cell surface " Nat 437 ( ), 656-663 (2005) Y Kumashiro, Y Ikezoe, K Tamada and M Hara, "Dynamic Interfacial Properties of Poly(ethylene glycol)-Modified Ferritin at the Solid/Liquid Interface," J Phys Chem B 112(28), 8291-8297 (2008) L Stryer, "Proteins: Conformation, Dynamics, and Function," in Biochemistry, pp 145-180, W H Freeman and Company, New York (2000) 10 A McPherson, "Protein crystallization in the structural genomics era," J Struct Funct Genomics 5(1-2), 3-12 (2004) 11 A McPherson, "Macromolecular crystallization in the structural genomics era," J Struc Biol 142(1), 1-2 (2003) 12 K Wuthrich, "NMR Studies of structure and function of bioogical macromolecules," in Nobel Lecture (2002) 13 S K Straus, "Recent developments in solid-state magic angle spinning, nuclear magnetic resonance of fully and significantly isotopically labelled peptides and proteins " Phil Trans R Soc Lond B 359(1), 997-1008 (2004) 14 Makrodimitris K, Masica DL, Kim ET and G JJ, "Structure prediction of proteinsolid surface interactions reveals a molecular recognition motif of statherin for hydroxyapatite," J Am Chem Soc 129(44), 13713-13722 (2007) 15 W Guo and N Hu, "Interaction of myoglobin with poly(methacrylic acid) at different pH in their layer-by-layer assembly films: An electrochemical study," Biophys Chem 129( ), 163-171 (2007) 16 H Sota, Y Hasegawa and M Iwakura, "Detection of conformational changes in an immobilized protein using surface plasmon resonance," Anal Chem 70(10), 2019-2024 (1998) 17 F Cecchet, B D Meersman, S D Champagne, B Nysten and A M Jonas, "One Step Growth of Protein Antifouling Surfaces: Monolayers of Poly(ethylene oxide) (PEO) Derivatives on Oxidized and Hydrogen-Passivated Silicon Surfaces," Langmuir 22( ), 1173-1181 (2006) 18 F A Armstrong, H A O Hill and N J Walton, "Direct electrochemistry of redox proteins," Acc Chem Res 21(11), 407-413 (1988) 19 K E v Holde, W C Johnson and P S Ho, "Linear and Circular Dichroism," in Principles of Physical Biochemistry, Cambridge University, New York (1988) xliii 20 Kensal C J., van Holde E and Pui Shing Ho, "Biological Macromolecules," in Principles of Physical Biochemistry, Prentice Hall, New York (2005) 21 Zubay, in Principles of Biochemistry, McGraw-Hill College (1995) 22 A Coutinho, C García, J González-Rodríguez and M P Lillo, "Conformational changes in human integrin αIIbβ3 after platelet activation, monitored by FRET " Biophys Chem 130(1-2), 76-87 (2007) 23 R Tuma, H Tsuruta, J M Benevides, P E J Prevelige and G J J Thomas, "Characterization of subunit structural changes accompanying assembly of the bacteriophage P22 procapsid," Biochemistry 40(3), 665-674 (2001) 24 B Lassen and M Malmsten, "Structure of Protein Layers during Competitive Adsorption " J Colloid Interface Sci 180(2), 339-349 (1996) 25 V Krisdhasima, J McGuire and R Sproull, "Surface hydrophobic influences on β-lactoglobulin adsorption kinetics " J Colloid Interface Sci 154(2), 337-350 (1992) 26 M Wahlgrena and U Elofssonb, "Simple Models for Adsorption Kinetics and Their Correlation to the Adsorption of β-Lactoglobulin A and B," J Colloid Interface Sci 188(1), 121-129 (1997) 27 C E Giacomelli, M J Esplandiu, P I Ortiz, M J Avena and C P De Pauli, "Ellipsometric Study of Bovine Serum Albumin Adsorbed onto Ti/TiO2 Electrodes," J Colloid Interface Sci 218(2), 404-411 (1999) 28 A R Bizzarri, B Bonanni, G Costantini and S Cannistraro, "A Combined Atomic Force Microscopy and Molecular Dynamics Simulation Study on a Plastocyanin Mutant Chemisorbed on a Gold Surface," ChemPhysChem 4( ), 11891195 (2003) 29 J Zhou, J Zheng and S Jiang, "Molecular Simulation Studies of the Orientation and Conformation of Cytochrome c adsorbed on Self-Assembled Monolayers," J Phys Chem B 108( 45), 17418-17424 (2004) 30 M H Donna, W S Shalaby and A L J Robert, "Direct correlation between adsorption-induced changes in protein structure and platelet adhesion," J Biomed Mat Res P A 73(3), 349-358 (2005) 31 G Raffaini and F Ganazzoli, "Sequential adsorption of proteins and the surface modification of biomaterials: a molecular dynamics study," J Mater Sci Mater Med 18(2), 300-316 (2007) 32 M Skepö, P Linse and T Arnebrant, "Coarse-grained modeling of proline rich protein (PRP-1) in bulk solution and adsorbed to a negatively charged surface.," J Phys Chem B 110(21), 12141-12148 (2006) 33 M R Oberholzer, N J Wagner and A M Lenhoff, "Grand canonical Brownian dynamics simulation of colloidal adsorption," J Chem Phys 107( ), 9157 (1997) 34 J Zhou, H K Tsao, Y J Sheng and S Jiang, "Monte Carlo simulations of antibody adsorption and orientation on charged surfaces," J Chem Phys 121( ), 1050 (2004) 35 J Zhou, S Chen and S Jiang, "Orientation of Adsorbed Antibodies on Charged Surfaces by Computer Simulation Based on a United-Residue Model," Langmuir 19(8), 3472-3478 (2003) 36 A H Juffer, P Argos and J d Vlieg, "Adsorption of proteins onto charged surfaces: A Monte Carlo approach with explicit ions," J Comput Chem 17(16), 1783-1803 (1996) 37 S Ravichandran, J D Madura and J Talbot, "A Brownian Dynamics Study of the Initial Stages of Hen Egg-White Lysozyme Adsorption at a Solid Interface," J Phys Chem B 105(17), 3610-3613 (2001) xliv 38 X Chen, R Ferrigno, J Yang and G M Whitesides, "Redox Properties of Cytochrome c Adsorbed on Self-Assembled Monolayers: A Probe for Protein Conformation and Orientation," Langmuir 18(18), 7009-7015 (2002) 39 S W Raso, P L Clark, C Haase-Pettingell, J King and G J Thomas, "Distinct Cysteine Sulfhydryl Environments Detected by Analysis of Raman S-H Markers of Cys – Ser Mutant Proteins " J Mol Biol 307(899-911 (2001) 40 K E v Holde, W C Johnson and P S Ho, "Absorption spectroscopy," in Principles of Physical Biochemistry, Pearson, , New Jersey (2006) 41 R L McCreery, in Raman Spectroscopy for Chemical Analysis J D Winefordner, Ed., John Wiley & Sons Inc., New york (2000) 42 E Shaw, "Cysteinyl proteinases and their selective inactivation," Adv Enzymol Relat Areas Mol Biol 63(271-347 (1990) 43 N Darby and T E Creighton, "Disulfide bonds in protein folding and stability," Methods Mol Biol 40(219-252 (1995) 44 P R Carey, "Raman spectroscopy, the sleeping giant in structural biology, awakes.," J Biol Chem 274(38), 26625-26628 (1999) 45 H Deng, J Wang, R H Callender, J C Grammer and R G Yount, "Raman Difference Spectroscopic Studies of the Myosin S1 MgADP Vanadate Complex," Biochemistry 37(31), 10972-10979 (1998) 46 R J Weesie, J C Merlin, H J de Groot, G Britton, J Lugtenburg, F J Jansen and J P Cornard, "Resonance raman spectroscopy and quantum chemical modeling studies of protein-astaxanthin interactions in alpha-crustacyanin (major blue carotenoprotein complex in carapace of lobster, Homarus gammarus," Biospec 5(6), 358 - 370 (1999) 47 M Hammel, D Nemecek, J A Keightley, G J Jr Thomas and B V Geisbrecht, "The Staphylococcus aureus extracellular adherence protein (Eap) adopts an elongated but structured conformation in solution," Prot Sci 16(12), 26052617 (2007) 48 M Moskovits, "Surface Enhanced Spectroscopy," Reviews of Modern Physics 57(3), 783-825 (1985) 49 M Fleischmann, P J Hendra and A J McQuillan, "M Fleischmann, P J Hendra, A J McQuillan," Chem Phys Lett 26(2), 163-166 (1974) 50 D L Jeanmaire and R P V Duyne, "Surface raman spectroelectrochemistry: Part I Heterocyclic, aromatic, and aliphatic amines adsorbed on the anodized silver electrode " J Electroanal Chem 84(1), 1-20 (1977) 51 M G Albrecht and J A Creighton, "Anomalously intense Raman spectra of pyridine at a silver electrode," J Am Chem Soc 99(15), 5215-5217 (1977) 52 M Moskovits, "The dependence of the metal—molecule vibrational frequency on the mass of the adsorbate and its relevance to the role of adatoms in surface-enhanced raman scattering " Chem Phys Lett 98(5), 498-502 (1983) 53 P N Sanda, J M Warlaumont, J E Demuth, J C Tsang, K Christmann and J A Bradley, "Surface-Enchanced Raman Scattering from Pyridine on Ag(111)," Phys Rev Lett 45(18), 1519-1523 (1980) 54 R K Chang and T E Furtak, in Surface Enhanced Raman Scattering, p 315, Plenum Press., New York (1982) 55 T H Wood, "Role of atomic-scale roughness in surface-enhanced Raman scattering," Phys Rev B 24(4), 2289-2291 (1981) 56 S G Schultza, M J Czachor and R P V Duyne, "Surface enhanced Raman spectroscopy: A re-examination of the role of surface roughness and electrochemical anodization," Surf Sci 104(2-3), 419-434 (1981) xlv 57 J E Rowe, C V Shank, D A Zwemer and C A Murray, "Ultrahigh-Vacuum Studies of Enhanced Raman Scattering from Pyridine on Ag Surfaces," Phys Rev Lett 44(26), 1770-1773 (1980) 58 P B Dorain, K U Vonraben, R K Chang and B L Laube, "Catalytic formation of SO32− and SO42− from SO2 on silver observed by surface-enhanced raman scattering " Chem Phys Lett 84(2), 405-409 (1981) 59 W Krasser and A J Renouprez, "Enhanced Raman scattering of benzene chemisorbed on small platinum clusters " Solid State Commun 41(3), 231-235 (1982) 60 Benner R E., Von Raben K U., Lee K C., Owen J F., Chang R K and L B L., "Raman scattering from Pt(CN)42− adsorbed on Pt colloids," Chem Phys Lett 96(1), 65-69 (1983) 61 W L Parker, R M Hexter and A R Siedle, "Raman spectroscopy as a probe of adsorption on rhodium particles " Chem Phys Lett 107(1), 96-98 (1984) 62 L Surbhi, K G Nathaniel, K Janardan, S L b Carly and L J B J H Naomi, "Tailoring plasmonic substrates for surface enhanced spectroscopies," Chem.Soc.Rev 37( ), 898-911 (2008) 63 R E Holt and T M Cotton, "Free flavin interference in surface enhanced resonance Raman spectroscopy of glucose oxidase," J Am Chem Soc 109(6), 1841-1845 (1987) 64 F J Adrian, "Charge transfer effects in surface enhanced Raman scattering," J Chem Phys 77(11), 5302-5314 (1982) 65 Z Chen, A Taflove and V Backman, "Photonic nanojet enhancement of backscattering of light by nanoparticles: a potential novel visible-light ultramicroscopy technique," Opt Express 12(7), 1214-1220 (2004) 66 X Li, Z Chen, A Taflove and V Backman, "Optical analysis of nanoparticles via enhanced backscattering facilitated by 3-D photonic nanojets," Opt Express 13(2), 526-533 (2005) 67 S Lecler, Y Takakura and P Meyrueis, "Properties of a three-dimensional photonic jet," Opt Express 30(19), 2641-2643 (2005) 68 A V Itagi and W A Challener, "Optics of photonic nanojets," J Opt Soc Am A Opt Image Sci Vis 22(12), 2847-2858 (2005) 69 A Heifetz, J J Simpson, S.-C Kong, A Taflove and V Backman, "Subdiffraction optical resolution of a gold nanosphere located within the nanojet of a Mie-resonant dielectric microsphere," Opt Express 15(25), 17334-17342 (2007) 70 P Ferrand, J Wenger, A Devilez, M Pianta, B Stout, N Bonod, E Popov and H Rigneault, "Direct imaging of photonic nanojets," Opt Express 16(10), 6930-6940 (2008) 71 Y T Sylvain Lecler, and Patrick Meyrueis "Properties of a three-dimensional photonic jet," Opt Express 30(19), 2641-2643 (2005) 72 M Born and E Wolf, Principles of Optics: Electromagnetic Theory of Propagation, Interference and Diffraction of Light, Cambridge University Press, London (1999) 73 P B Johnson and R W Christy, "Optical Constants of the Noble Metals," Phys Rev B 6(12), 4370-4379 (1972) 74 K J Yi, H Wang, Y F Lu and Z Y Yang, "Enhanced Raman scattering by selfassembled silica spherical microparticles " J Appl Phys 101(063528 (2007) 75 H Xu, J Aizpurua, M Käll and P Apell, "Electromagnetic contributions to single-molecule sensitivity in surface-enhanced Raman scattering," Phys Rev E 62(3), 4318-4324 (2000) 76 A Kudelski, "Analytical applications of Raman spectroscopy," Talanta 76( ), 18 (2008) xlvi 77 M Moskovits, "Surface-enhanced Raman spectroscopy: a brief retrospective," J Raman Spectrosc 36(6-7), 485-496 (2005) 78 X.-M Qian and S M Nie, "Single-molecule and single-nanoparticle SERS: from fundamental mechanisms to biomedical applications," Chem Soc Rev 37( ), 912920 (2008) 79 K W Kho, Z X Shen, H C Zeng, K C Soo and M Olivo, "Deposition method for preparing SERS-active gold nanoparticle substrates," Anal Chem 77(22), 74627471 (2005) 80 A D McFarland, M A Young, J A Dieringer and R P VanDuyne, "Wavelength-Scanned Surface-Enhanced Raman Excitation Spectroscopy," J Phys Chem B 109(22), 11279-11285 (2005) 81 F J G d Abajo and J Aizpurua, "Numerical simulation of electron loss near inhomogeneous dielectrics," Phys Rev B 56(24), 15873-15884 (1997) 82 M Ringler, T A Klar, A Schwemer, A S Susha, J Stehr, G Raschke, S Funk, M Borowski, A Nichtl, K Kürzinger, R T Phillips and J Feldmann, "Moving Nanoparticles with Raman Scattering," Nano Lett 7(9), 2753-2757 (2007) 83 J Grand, M Lamy de la Chapelle, J L Bijeon, P M Adam, A Vial and P Royer, "Role of localized surface plasmons in surface-enhanced Raman scattering of shape-controlled metallic particles in regular arrays," Phys Rev B 72(3), 033407033410 (2005) 84 B T Draine and P J Flatau, "Discrete-dipole approximation for scattering calculations," J Opt Soc Am A Opt Image Sci Vis 11( ), 1491-1499 (1994) 85 S A Maier, P G Kik and H A Atwater, "Optical pulse propagation in metal nanoparticle chain waveguides," Phys Rev B 67( ), 205402 (2003) 86 F J García-Vidal and J B Pendry, "Collective Theory for Surface Enhanced Raman Scattering," Phys Rev Lett 77(6), 1163-1166 (1996) 87 M Fleischmann, P J Hendra and A J McQuillan, "Raman spectra of pyridine adsorbed at a silver electrode," Chem Phys Lett 26(2), 163-166 (1974) 88 S Lal, N K Grady, G P Goodrich and N J Halas, "Profiling the Near Field of a Plasmonic Nanoparticle with Raman-Based Molecular Rulers," Nano Lett 6(10), 23382343 (2006) 89 K Kim, H B Lee, Y M Lee and K S Shin, "Rhodamine B isothiocyanatemodified Ag nanoaggregates on dielectric beads: a novel surface-enhanced Raman scattering and fluorescent imaging material," Biosens Bioelectron 24(7), 1864-1869 (2009) 90 A Barhoumi, D Zhang and N J Halas, "Correlation of molecular orientation and packing density in a dsDNA self-assembled monolayer observable with surfaceenhanced Raman spectroscopy," J Am Chem Soc 130(43), 14040-14041 (2008) 91 C D Keating, K K Kovaleski and M J Natan, "Heightened Electromagnetic Fields between Metal Nanoparticles: Surface Enhanced Raman Scattering from Metal−Cytochrome c-Metal Sandwiches," J Phys Chem B 102(47), 9414-9425 (1998) 92 T M Cotton, J.-H Kim and G D Chumanov, "Application of surfaceenhanced Raman spectroscopy to biological systems," J Raman Spectrosc 22(12), 729-742 (1991) 93 S Lal, N K Grady, G P Goodrich and N J Halas, "Profiling the Near Field of a Plasmonic Nanoparticle with Raman-Based Molecular Rulers," Nano Lett 6(10), 23382343 (2006) 94 K E Shafer-Peltier, C L Haynes, M R Glucksberg and R P V Duyne, "Toward a glucose biosensor based on surface-enhanced Raman scattering," J Am Chem Soc 125(2), 588-593 (2005) xlvii 95 J A Dieringer, A D McFarland, N C Shah, D A Stuart, A V Whitney, C R Yonzon, M A Young, X Zhang and R P V Duyne, "Surface enhanced Raman spectroscopy: new materials, concepts, characterization tools, and applications," Faraday Discuss 132( ), 9-26 (2006) 96 I Tunc, S Suzer, M A Correa-Duarte and L M Liz-Marzan, "XPS Characterization of Au (Core)/SiO2 (Shell) Nanoparticles," J Phys Chem B 100( ), 7597-7600 (2005) 97 L M Liz-Marzan, M Giersig and P Mulvaney, "Synthesis of Nanosized GoldSilica Core-Shell Particles," Langmuir 12( ), 4329-4335 (1996) 98 I Tunc, S Suzer, M A Correa-Duarte and L M Liz-Marzán, "XPS Characterization of Au (Core)/SiO2 (Shell) Nanoparticles," J Phys Chem B 109(16), 7597-7600 (2005) 99 K S Praveen, N S Ramgir and S Bhansali, "Metal decotated silica nanowires: An active surface enhanced Raman substrate for cancer biomarker detection," J Phys Chem C 112(1729-1734 (2008) 100 N S Lee, R S Sheng, M D Morris and L M Schopfer, "The active species in surface-enhanced Raman scattering of flavins on silver colloids," J Am Chem Soc 108(20), 6179-6183 (1986) 101 J Xu, R L Birke and J R Lombardi, "Surface-enhanced Raman spectroscopy from flavins adsorbed on a silver electrode: observation of the unstable semiquinone intermediate," J Am Chem Soc 109(19), 5646-5649 (1987) 102 M A De Jesús, K S Giesfeldt and M J Sepaniak, "Use of a Sample Translation Technique to Minimize Adverse Effects of Laser Irradiation in Surface-Enhanced Raman Spectrometry," Appl Spectrosc 57(4), 428-438 (2003) 103 J.-J K Y -S Choia, S Miyajimab, "Diffusive loss of surface adatoms and surface enhanced Raman scattering intensity " Chem Phys Lett 255(1-3), 45-48 (1996) 104 Y S Choia, J J Kima and S Miyajimab, "Diffusive loss of surface adatoms and surface enhanced Raman scattering intensity " Chem Phys Lett 255(1-3), 45-48 (1996) 105 G H Amir Weiss, "Time-Dependent Single-Molecule Raman Scattering as a Probe of Surface Dynamics," J Phys Chem 105(49), 12348-12354 (2001) 106 Y Sharaabi, T Shegai and G Haran, "Two-state analysis of single-molecule Raman spectra of crystal violet " Chem Phys 318(1-2), 44-49 (2005) 107 J L McHale, "Raman and Resonance Raman Scattering," in Molecular Spectroscopy, p 390, Prentice Hall, New Jersey (1999) 108 P G Etchegoin, C Galloway and E C LeRu, "Polarization-dependent effects in surface-enhanced Raman scattering (SERS)," Phys Chem Chem Phys 8(26242628 (2006) 109 F A Khan, T G Kreutz, L Zhu, G W Flynn and R E Weston, "Temperature dependence of rotationally resolved excitation of carbon dioxide (0001) by collisions with hot hydrogen atoms," J Phys Chem 92(22), 6171-6478 (1988) 110 C Y Panicker, H T Varghese, A John, D Philip, K Istvane and G Kereszturye, "FT-IR, FT-Raman and FT-SERS spectra of 4-aminosalicylic acid sodium salt dihydrate " Spectrochim Acta Part A 58(2), 281-287 (2002) 111 W Kiefer and H J Bernstein, "A Cell for Resonance Raman Excitation with Lasers in Liquids," Appl Spectrosc 25(4), 500-501 (1971) 112 R A A Kam, J Duff and C P Tripp, "Evolution of the Molecular Organization in Bis(n-propylimido)perylene Films under Thermal Annealing," Chem Mater 10(1), 172-176 (1998) xlviii 113 M Moskovits and J S Suh, "Surface geometry change in 2-naphthoic acid adsorbed on silver," J Phys Chem 92(22), 6327-6329 (1988) 114 X Gao, J P Davies and M J Weaver, "Test of surface selection rules for surface-enhanced Raman scattering: the orientation of adsorbed benzene and monosubstituted benzenes on gold," J Phys Chem 94(17), 6858-6864 (1990) 115 C S Allen and R P V Duyne, "Orientational specificity of Raman scattering from molecules adsorbed on silver electrodes " Chem Phys Lett 63(3), 455-459 (1979) 116 J D Jiang, E Burstein and H Kobayashi, "Resonant Raman Scattering by Crystal-Violet Molecules Adsorbed on a Smooth Gold Surface: Evidence for a Charge-Transfer Excitation," Phys Rev Lett 57(14), 1793-1796 (1986) 117 J W Gadzuk, "Hot Electrons and Photodesorption Dynamics: Theory," in Laser Spectroscopy and Photochemistry on Metal Surfaces, W H H-L Dai, Ed., p 897, World Scientific, Singapore (1995) 118 I Hussla, H Seki, T J Chuang, Z W Gortel, H J Kreuzer and P Piercy, "Infrared-laser-induced photodesorption of NH3 and ND3 adsorbed on single-crystal Cu(100) and Ag film," Phys Rev B 32(6), 3489-3501 (1985) 119 K J Laidler and J H Meiser, "Chemical Kinetics I The Basic Ideas.," in Physical Chemistry, pp 353-406, Houghton Mifflin, Boston (1995) 120 L Y Olson LG, Beebe TP Jr, Harris JM., "Characterization of silane-modified immobilized gold colloids as a substrate for surface-enhanced Raman spectroscopy," Anal Chem 73(17), 4268-4276 (2001) 121 B Jirgensons and M E Straumanis, "The Electrical Properties of Colloids," in A Short Textbook of Colloid Chemistry, pp 127-155, Macmilan, New York (1962) 122 H Xu and M Käll, "Surface-Plasmon-Enhanced Optical Forces in Silver Nanoaggregates," Phys Rev Lett 89(24), 246802-246805 (2002) 123 M S Peter Hildebrandt, "Cytochrome c at charged interfaces Conformational and redox equilibria at the electrode/electrolyte interface probed by surface-enhanced resonance Raman spectroscopy," Biochem 28(16), 6710-6721 (1898) 124 M S Peter Hildebrandt, "Cytochrome c at charged interfaces Complexes with negatively charged macromolecular systems studied by resonance Raman spectroscopy," Biochem 28(16), 6722-6728 (1989) 125 T Heimburg, P Hildebrandt and D Marsh, "Cytochrome c-lipid interactions studied by resonance Raman and phosphorus-31 NMR spectroscopy Correlation between the conformational changes of the protein and the lipid bilayer," Biochem 30(37), 9084-9089 (1991) 126 P Hildebrandt and M Stockburger, "Surface-enhanced resonance Raman spectroscopy of cytochrome c at room and low temperatures," J Phys Chem 90(22), 6017-6024 (1986) 127 G C Morgan S Sibbald, and Therese M Cotton, "Reduction of Cytochrome c by Halide-Modified, Laser-Ablated Silver Colloids," J Phys Chem 100(11), 4672-4678 (1996) 128 Y Maeda, H Yamamoto and H Kitano, "Self-Assembled Monolayers as Novel Biomembrane Mimetics Characterization of Cytochrome c Bound to SelfAssembled Monolayers on Silver by Surface-Enhanced Resonance Raman Spectroscopy," J Phys Chem 99(13), 4837-4841 (1995) 129 I D G Macdonald and W E Smith, "Orientation of Cytochrome c Adsorbed on a Citrate-Reduced Silver Colloid Surface," Langmuir 12(3), 706-713 (1996) xlix 130 G Niaura, A K Gaigalas and V L Vilker, "Non-resonant SERS study of the adsorption of cytochrome c on a silver electrode " J Electroanal Chem 416(1-2), 167-178 (1996) 131 D Hobara, K Niki, C Zhou, G Chumanov and T M Cotton, "Characterization of cytochurome c immobilized on modified gold and silver electrodes by surfaceenhanced Raman spectroscopy " Colloids Surf A 93(241-250 (1994) 132 P L Edmiston, J E Lee, S.-S Cheng and S S Saavedra, "Molecular Orientation Distributions in Protein Films Cytochrome c Adsorbed to Substrates of Variable Surface Chemistry," J Am Chem Soc 119(3), 560-570 (1997) 133 J E Lee and S S Saavedra, "Molecular Orientation in Heme Protein Films Adsorbed to Hydrophilic and Hydrophobic Glass Surfaces," Langmuir 12(16), 40254032 (1996) 134 A N Strahler, "The Evolution/Creation Controversy," in Science and Earth History, Prometheus Books, New York (1999) 135 M.-E Aubin-Tam and K Hamad-Schifferli, "Gold Nanoparticle−Cytochrome c Complexes: The Effect of Nanoparticle Ligand Charge on Protein Structure," Langmuir 21(26), 12080-12084 (2005) 136 P Unneberg, J J Merelo, P Chacón and F Morán, "SOMCD: Method for evaluating protein secondary structure from UV circular dichroism spectra, Proteins: Structure, Function, and Genetics," pp 460-470 (2001) 137 R A Scott and A G Mauk, Cytochrome C : a multidisciplinary approach, University Science Books, Sausalito, Calif (1996) 138 A C Albrecht, "On the Theory of Raman Intensities," J Chem Phys 34(5), 1476-1480 (1961) 139 A C Albrecht and M C Hutley, "On the Dependence of Vibrational Raman Intensity on the Wavelength of Incident Light," J Chem Phys 55(9), 4438-4440 (1971) 140 M H Perrin, M Gouterman and C L Perrin, "Vibronic Coupling VI Vibronic Borrowing in Cyclic Polyenes and Porphyrin," J Chem Phys 50(10), 4137-4150 (1969) 141 J Tang and A C Albrecht, "Developments in the theories of vibrational Raman intensities," in Raman Spectroscopy Theory and Practice H A Szymanski, Ed., pp 33-68, Plenum Press, New York (1970) 142 M S Peter Hildebrandt, "Cytochrome c at charged interfaces Conformational and redox equilibria at the electrode/electrolyte interface probed by surface-enhanced resonance Raman spectroscopy," Biochem 28(16), 6710-6721 (1989) 143 H Xu and M Käll, "Polarization-Dependent Surface-Enhanced Raman Spectroscopy of Isolated Silver Nanoaggregates," ChemPhysChem 4(9), 1001-1005 (2003) 144 Y Feng and S W Englander, "Salt-dependent structure change and ion binding in cytochrome c studied by two-dimensional proton NMR," Biochem 29(14), 3505-3509 (1990) 145 O Joshi, J McGuire and D Q Wang, "Absorption and function of recombinant factor VIII at solid-water interfaces in the presence of Tween-80," J Phar Sci 97(11), 4741-4755 (2008) 146 V P Drachev, V C Nashine, M D Thoreson, D Ben-Amotz, V J Davison and V M Shalaev, "Adaptive silver films for detection of antibody-antigen binding," Langmuir 21(18), 8368-8373 (2005) 147 R H Ritchie, "Plasma Losses by Fast Electrons in Thin Films," Phys Rev 106(5), 874-881 (1957) 148 C J Powell and J B Swan, "Effect of Oxidation on the Characteristic Loss Spectra of Aluminum and Magnesium," Phys Rev 118(640-3), (1960) l 149 H Raether, Plasmons on smooth and rough surfaces and on gratings, Springer-Verlag, Berlin (1998) 150 H Raether, in Excitation of Plasmons and Interband Transitions by Electrons, Springer-Verlag, Berlin, Heidelberg, New York (1980) 151 L Eckertova, in Physics of Thin Films, p 145, Plenum Press, New York (1977) 152 H Raether, Physics of Thin Films, Academic Press, New York (1977) 153 F Forstman and R R Gerhardts, Metal Optics Near the Plasma Frequency, Springer Tracts in Modern Physics, Springer, Berlin, Heidelberg, New York (1986) 154 M Futamata, P Borthen, J Thomassen, D Schumacher and A Otto, "Application of an ATR Method in Raman Spectroscopy," Appl Spectrosc 48(2), 252260 (1994) 155 W H Weber and G W Ford, "Optical electric-field enhancement at a metal surface arising from surface-plasmon excitation," Opt Express 6(3), 122-124 (1981) 156 C E Reed, J Giergiel, J Hemminer and S Ushioda, "Dipole radiation in a multilayer geometry," Phys Rev B 36(9), 4990-5003 (1987) 157 H Reather, Surface Plasmon, Springer, Berlin (1988) 158 J Giergiel, C E Reed, J C Hemminger and S Ushoids, "Surface plasmon polariton enhancement of Raman scattering in a Kretschmann geometry," J Phys Chem 92(19), 5357-5365 (1988) 159 A Otto, "Spectroscopy of Surface Polaritons by Attenuated Total Reflection.," in Optical Properties of Solids B O Seraphin, Ed., p 677, Amesterdam, North-Holland (1976) 160 S Ushioda and Y Sasaki, "Raman scattering mediated by surface-plasmon polariton resonance," Phys Rev B 27(2), 1401-1404 (1983) 161 A Otto, Polaritons, Pergamon Press, Oxford (1974) 162 R P Cooney, Advances in Infrared and Raman Spectroscopy, Heyden & Sons, Chichester (1982) 163 Y J Chen, W P Chen and E Burstein, "Surface-Electromagnetic-WaveEnhanced Raman Scattering by Overlayers on Metals," Phys Rev Lett 36(20), 12071210 (1976) 164 M Futamata, "Surface Plasmon Polariton Enhanced Raman Scattering from Adsorbates on a "Smooth" Metal Surface: The Effect of Thickness and Dielectric Properties of Constituents," Langmuir 11(10), 3894-3901 (1995) 165 M Futamata, "Surface Plasmon Polariton Enhanced Raman Scattering from Self-Assembled Monolayers of p-Nitrothiophenol and p-Aminothiophenol on Silver," J Phys Chem 99(31), 119091-119098 (1995) 166 K Kurosawa, R M Pierce, S Ushioda and J C Hemminger, "Raman scattering and attenuated-total-reflection studies of surface-plasmon polaritons," Phys Rev B 33(1), 789-789 (1986) 167 H J Simon, D E Mitchell and J G Watson, "Optical Second-Harmonic Generation with Surface Plasmons in Silver Films," Phys Rev Lett 33(26), 1531-1534 (1974) 168 A Girlando, M R Philpott, D Heitmann, J D Swalen and R Santo, "Raman spectra of thin organic films enhanced by plasmon surface polaritons on holographic metal gratings " J Chem Phys 72(9), 5187-5190 (1980) 169 G Sun and C T Chan, "Frequency-selective absorption characteristics of a metal surface with embedded dielectric microspheres," Phys Rev E 73 73(3), 036613036617 (2006) 170 A Modinos, "Scattering of electromagnetic waves by a plane of spheresformalism " Physica A 141(2-3), 575-588 (1987) li 171 H Yan, C F Blanford, B T Holland, M Parent, W H Smyrl and A Stein, "A Chemical Synthesis of Periodic Macroporous NiO and Metallic Ni," Adv Mater 11(12), 1003-1006 (1999) 172 P Jiang, J Cizeron, J F Bertone and V L Colvin, "Preparation of Macroporous Metal Films from Colloidal Crystals," J Am Chem Soc 121(34), 79577958 (1999) 173 O D Velev, P M Tessier, A M Lenhoff and E W Kaler, "Materials: A class of porous metallic nanostructures," Nat 401( ), 548 (1999) 174 H Yan, C F Blanford, A Stein and W H Smyrl, "Preparation and structure of 3D ordered macroporous alloys by PMMA colloidal crystal templating " chem Commun 1477-1478 (2000) 175 T Sumida, Y Wada, T Kitamura and S Yanagida, "Electrochemical preparation of macroporous polypyrrole films with regular arrays of interconnected spherical voids," Chem Commun 1613-1614 (2000) 176 P N Bartlett, M A Ghanem, I S E Hallag, P d Groot and A Zhukov, "Electrochemical deposition of macroporous magnetic networks using colloidal templates," J Mater Chem 13( ), 2596-2602 (2003) 177 P N Bartlett, J J Baumberg, P R Birkin, M A Ghanem and M C Netti, "Highly Ordered Macroporous Gold and Platinum Films Formed by Electrochemical Deposition through Templates Assembled from Submicron Diameter Monodisperse Polystyrene Spheres," Chem Mater 14(5), 2199-2208 (2002) 178 M Hegner, P Wagner and G Semenza, "Ultralarge atomically flat templatestripped Au surfaces for scanning probe microscopy," Surf Sci 291( ), 39-46 (1993) 179 F Burmeister, C Schafle, T Matthes, M Boăhmisch, J Boneberg and P Leiderer, "Colloid Monolayers as Versatile Lithographic Masks," Langmuir 13( ), 29832987 (1997) 180 H W Deckman and J H Dunsmuir, "Natural lithography," Appl Phys Lett 41( ), 377 (1982) 181 A S Dimitrov and K Nagayama, "Continuous Convective Assembling of Fine Particles into Two-Dimensional Arrays on Solid Surfaces," Langmuir 12( ), 1303-1311 (1996) 182 H W Deckman and J H Dunsmuir, "Applications of surface textures produced with natural lithography," J Vat Sci Technol B 1(4), 1109-1112 (1983) 183 H W Deckman and J H Dunsmuir, "Natural lithography," Appl Phys Lett 41( 4), 377-379 (1982) 184 A Sharma, "Stability and Breakup of Thin Evaporating Water Films: Role of Hydrophobic Interaction," J Colloid Interface Sci 99( ), 212 - 214 (1997) 185 L Malaquin, T Kraus, H Schmid, E Delamarche and H Wolf, "Controlled Particle Placement through Convective and Capillary Assembly," Langmuir 23( ), 11513-11521 (2007) 186 E Matijevic, "Uniform inorganic colloid dispersions Achievements and challenges," Langmuir 10(1), 8-16 (1994) 187 E Snoeks, A v Blaaderen, T v Dillen, C M v Kats, M L Brongersma and A Polman, "Colloidal Ellipsoids with Continuously Variable Shape," Adv Mater 12(20), 1511-1514 (2000) 188 J A Champion, Y K Katare and S Mitragotri, "Making polymeric micro- and nanoparticles of complex shapes.," Proc Natl Acad Sci U S A 104(29), 11901-11904 (2007) 189 K Y Champion JA, Mitragotri S., "Making polymeric micro- and nanoparticles of complex shapes.," Proc Natl Acad Sci U S A 104(29), 11901-11904 (2007) lii 190 P Wager, M Hagner, H J Guntherodt and G Semenza, "Formation and in situ modification of monolayers chemisorbed on ultraflat template stripped gold surface," Langmuir 11(3867-3875 (1995) 191 D W Mosley, B Y Chow and J M Jacobson, "Solid-State Bonding Technique for Template-Stripped Ultraflat Gold Substrates," Langmuir 22( ), 2437-2440 (2006) 192 J Zhou, J Zheng and S Jiang, "Molecular Simulation Studies of the Orientation and Conformation of Cytochrome c Adsorbed on Self-Assembled Monolayers," J Phys Chem B 108( ), 17418-17424 (2004) 193 K Edinger, A Goelzhaeuser, K Demota, C Woell and M Grunze, "Formation of self-assembled monolayers of n-alkanethiols on gold: a scanning tunneling microscopy study on the modification of substrate morphology," Langmuir 9(1), 4-8 (1993) 194 C A Widrig, C A Alves and M D Porter, "Scanning tunneling microscopy of ethanethiolate and n-octadecanethiolate monolayers spontaneously absorbed at gold surfaces," J Am Chem Soc 113(8), 2805-2810 (1991) 195 Y T Kim and A J Bard, "Imaging and etching of self-assembled noctadecanethiol layers on gold with the scanning tunneling microscope," Langmuir 8(4), 1096-1102 (1992) 196 L Häussling, B Michel, H Ringsdorf and H Rohrer, "Direct Observation of Streptavidin Specifically Adsorbed on Biotin-Functionalized Self-Assembled Monolayers with the Scanning Tunneling Microscope," Ang Chem Int Ed Engl 30(5), 569-572 (2003) 197 C A Widrig, C A Alves and M D Porter, "Scanning tunneling microscopy of ethanethiolate and n-octadecanethiolate monolayers spontaneously absorbed at gold surfaces," J Am Chem Soc 113(8), 2805-2810 (1991) 198 W.-H Kao, V J Weibel and M J Root, "The influence of Potassium Ion on the Electrodeposition and Electrochemistry of Electrolytic Manganese Dioxide," J Electrochem Soc 139(5), 1223-1226 (1992) 199 C Schoenenberger, J A M Sondag-Huethorst, J Jorritsma and L G J Fokkink, "What Are the "Holes" in Self-Assembled Monolayers of Alkanethiols on Gold?," Langmuir 10(3), 611-614 (1994) 200 K W Kho, K Z Qing, Z X Shen, I B Ahmad, S S Lim, S Mhaisalkar, T J White, F Watt, K C Soo and M Olivo, "Polymer-based microfluidics with surface-enhanced Raman-spectroscopy-active periodic metal nanostructures for biofluid analysis.," J Biomed Opt 13(5), 054026 (2008) 201 B D Adair, J P Xiong, C Maddock, S L Goodman, M A Arnaout and M Yeager, "Three-dimensional EM structure of the ectodomain of Integrin alphaVbeta3 in a complex with fibronectin," J Cell Biol 168(7), 1109-1118 (2005) 202 A N Strahler, in Science and Earth History: The Evolution/Creation Controversy, Prometheus Books, New York (1999) 203 L Stryer, "Oxidative phosphorylation," in Biochemistry, pp 529-558, W H Freeman and company, New York (2000) 204 Y.-L P Ow, D R Green, Z Hao and T W Mak, "Cytochrome : c: : functions beyond respiration " Nat Rev Mol Cell Bio 9(532-542 (2008) 205 J Z Jian Zhou, Shaoyi Jiang, "Molecular Simulation Studies of the Orientation and Conformation of Cytochrome c Adsorbed on Self-Assembled Monolayers," J Phys Chem B 108(45), 17418-17424 (2004) 206 L A Dick, A J Haes and R P VanDuyne, "Distance and Orientation Dependence of Heterogeneous Electron Transfer: A Surface-Enhanced Resonance Raman Scattering Study of Cytochrome c Bound to Carboxylic Acid Terminated liii Alkanethiols Adsorbed on Silver Electrodes," j phys Chem B 104(49), 11752-11762 (2000) 207 L L Wood, S.-S Cheng, P L Edmiston and S S Saavedra, "Molecular Orientation Distributions in Protein Films Site-Directed Immobilization of Yeast Cytochrome c on Thiol-Capped, Self-Assembled Monolayers," J Am Chem Soc 119(3), 571-576 (1997) 208 P L Edmiston, J E Lee, L L Wood and S S Saavedra, "Dipole Orientation Distributions in Langmuir−Blodgett Films by Planar Waveguide Linear Dichroism and Fluorescence Anisotropy," J Phys Chem 100(2), 775-784 (1996) 209 B R Herr and C A Mirkin, "Self-Assembled Monolayers of Ferrocenylazobenzenes: Monolayer Structure vs Response," J Am Chem Soc 116(3), 1157-1158 (1994) 210 K L Prime and G M Whitesides, "Self-assembled organic monolayers: model systems for studying adsorption of proteins at surfaces " Sci 24(1164-1167 (1991) 211 J F Calvert, J L Hill and A Dong, "Redox-dependent Conformational Changes are common Structural Features of Cytochrom c from various Species," Arch Biochem Biophys 346(2), (1997) 212 J A Dieringer, A D McFarland, N C Shah, D A Stuart, A V Whitney, C R Yonzon, M A Young, X Zhang and R P V Duyne, "Surface enhanced Raman spectroscopy: new materials, concepts, characterization tools, and applications," Faraday Discuss 132( ), 9-26 (2006) liv ... and Christy’s previous publication (73), 117 4.4 Surface Plasmon Polariton Assisted Surface Enhanced Raman Scattering on Ultrasmooth Metal Surface The theory for an enhanced field near a metal... distance of the center of the cavity to the surface is h The major and minor axis of the cavity are denoted ˆ as a and b respectively a y -axis is pointing perpendicularly out of the image plane... from the surface rather than propagating away Inside the metal (i = 2) , on the other hand, k z of the SPP will v possess a negative imaginary part (see Eqn and 7), which suggests that the E2 field