Alumni Dissertations and Theses

 
 

Alumni Dissertations and Theses

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  • I. The RCM Approach Towards 1,6-methano-bridged[12] & [14]Annulenes and their Bisdehydro-derivatives II. 1,5-bisdehydro[10]Annulene Revisited

    Author:
    Yor-Yu Chen
    Year of Dissertation:
    2010
    Program:
    Chemistry
    Advisor:
    Klaus Grohmann
    Abstract:

    Part I of my dissertation presents a new efficient synthesis of 3,4-benzo-1,6-methano[12]annulene (3). This novel synthetic approach involves a grignard addition to 3,4-benzo-cycloheptatriene-1,6-dialdehyde followed by a ring closing olefin metathesis (RCM) reaction giving the bridged 12-menber ring of 3,4-benzo-1,6-methano[12]annulene (3) was obstained in six steps and an overall yield 44%. This allowed the complete structural and spectroscopic characterization as a paratropic ethano-bridged benzo[12]annulene with a 28% reduction of the paramagnetic ring current relative to the non-benzannulated molecule. A careful comparison of the 1H NMR of (3) with its 9,10-dihydro derivative (104) suggests an extended paratropic 16π system. The RCM approach is general and thus formally presents a 6 steps route to the parent 1,6-methano[12]annulene, previously reported by E. Vogel et al. Combination of cis-selective Wittig reaction of (36) with the ylide derived from 4-bromo-1-butene followed by RCM reaction yielded the 9,12-dihydro-3,4-benzo-1,6-methano[14]annulene (35). Attempts to convert this molecular in to the expectedly diatropic 14π system did not succeed so far. In course of this investigation, an efficient synthesis for 3,4-benzo-1,6-ethynylcycloheptatriene was developed. Diketone (37) obtained through Jones oxidation of the diasteromeric alcohols (26) was converted into the 3,4-benzo-1,6-methano-7,12-bis(dibromomethylene)-8,11-dihydro[12]annulene (38). Treatment of this molecule with two moles of n-butyllithium did not yield the anticipated diacetylene (39). From diketone (37) a series of 7,12-disubstituted bridged [12]annulene can be synthesized, this illustrating the generality of this approach. In part II of my dissertation, approaches toward 1,5-bisdehydro[10]annulenes were investigated with the goal to increase the activation energy for the known Bergmann rearrangement or even mark it impossible for the molecule to undergo it. This would enable us to investigate the expected 10π aromaticity of the 1,5-bisdehydro[10]annulene system. An initial approach utilizing the Ramberg Bakelund rearrangement failed due to the irreproducibility of the formation of the cyclic sulfide (70). Elimination was the major pathway even at pH8, most likely due to the very acidic propargylic hydrogens. The second approach started with the 10 menber ring diyneacetals (78), (85), (91). In course of this investigation a new reaction sequence was discovered as outline on scheme 3-9. This valuable fragmentation deprotection of stable cyclic benzylidene acetals leads directly to allylic alcohols such as compound (86). The introduction of the last double bond via the mesylate followed by treatment with potassium t-butoxide gave unexpectedly Benz(a)anthacene (89) and tetracene (88) in a ratio of 40:1. This result is being interpreted as an initial acetylene-allene isomerization followed by an allene-acetylene cyclization (Myers-Saito cyclization), hydrogen abstraction and aromatization as shown on scheme 3-14. Treatment of the mesylate (93) derived from the allylic alcohol with potassium t-butoxide gave phenanthrene and anthracene in a ratio of 2:3. Treatment of the mesylate with triethylamine gave only anthracene, the expected product of the Bergmann rearrangement.

  • MULTIFERROIC AND CORE-SHELL NANOSTRUCTURES - ADVANCES IN PREPARATIONS AND NOVEL PROPERTIES

    Author:
    I-Wei Chu
    Year of Dissertation:
    2010
    Program:
    Chemistry
    Advisor:
    Nan-Loh Yang
    Abstract:

    This dissertation reports the research findings in two nanoscience areas: (i) facile methods for the preparation of multiferroic bismuth ferrites nanoparticles and the observation of room temperature magnetoelectric coupling and optically induced magnetic and electric orderings in BiFeO3 (BFO) thin film; (ii) preparation and characterization of core-shell nanomaterials based on conducting polymer as components for shell and core. Controlled cargo release from the core as well as from the shell surface was examined for nanospheres with conjugate polymer shell. An unusual enhanced electric polarization was observed for nanospheres with high-k strontium titanate (STO) nanocrystals embedded in conductive polyaniline (PANI) matrix. Multiferroics represent a class of new materials having potential applications for design and preparation of multifunctional material due to the coupling of their coexisting electric and magnetic orderings. Previously, the syntheses of thin film multiferroic materials involve multi-steps in various high temperatures or specific demanding environment. We discovered that nanocrystal thin film and powder of multiferroic BFO could be prepared using new facile procedures: spin-casting and autoclave methods. The room temperature magnetoelectric coupling in nanocrystal BFO was established using scanning probe microscopy, including magnetic force microscopy (MFM) and Kelvin probe force microscopy (KPFM). Magnetic and electrical orderings induced by irradiation 300 to 560 nm were observed. Thus, the "magnetic-electric-optic" coupling at room temperature was observed for the first time in BFO nanocrystal thin film. Core-shell nanospheres of conducting polymer poly(3, 4-ethylenedioxythiophene), PEDOT, with soft template (1-butyl-3-methyimidazolium hexafluorophosphate, bmimPF6) were prepared using interfacial polymerization on the shell surface of the micelle stabilized by surfactant (Triton X-100). The diameter of nanospheres was controlled by bmimPF6-to-surfacnt ratio. The release of cargo from the core and shell of the spheres was trigged by pH control and observed by photometric measurement. Aspect ratio and crystallinity of PEDOT shell increases in high pH value (above 10). In addition, the interaction of electronic polarization with atomic polarization was studied for core-shell nanosphere of PANI matrix with STO nanoparticles embedded. This nanosystem represents the first encapsulated nanospheres with extensive interfacial interaction within the core due to atomic polarizable isolated nano-domains embedded in an electronic polarizable continuous matrix.

  • MULTIFERROIC AND CORE-SHELL NANOSTRUCTURES - ADVANCES IN PREPARATIONS AND NOVEL PROPERTIES

    Author:
    I-Wei Chu
    Year of Dissertation:
    2010
    Program:
    Chemistry
    Advisor:
    Nan-Loh Yang
    Abstract:

    This dissertation reports the research findings in two nanoscience areas: (i) facile methods for the preparation of multiferroic bismuth ferrites nanoparticles and the observation of room temperature magnetoelectric coupling and optically induced magnetic and electric orderings in BiFeO3 (BFO) thin film; (ii) preparation and characterization of core-shell nanomaterials based on conducting polymer as components for shell and core. Controlled cargo release from the core as well as from the shell surface was examined for nanospheres with conjugate polymer shell. An unusual enhanced electric polarization was observed for nanospheres with high-k strontium titanate (STO) nanocrystals embedded in conductive polyaniline (PANI) matrix. Multiferroics represent a class of new materials having potential applications for design and preparation of multifunctional material due to the coupling of their coexisting electric and magnetic orderings. Previously, the syntheses of thin film multiferroic materials involve multi-steps in various high temperatures or specific demanding environment. We discovered that nanocrystal thin film and powder of multiferroic BFO could be prepared using new facile procedures: spin-casting and autoclave methods. The room temperature magnetoelectric coupling in nanocrystal BFO was established using scanning probe microscopy, including magnetic force microscopy (MFM) and Kelvin probe force microscopy (KPFM). Magnetic and electrical orderings induced by irradiation 300 to 560 nm were observed. Thus, the "magnetic-electric-optic" coupling at room temperature was observed for the first time in BFO nanocrystal thin film. Core-shell nanospheres of conducting polymer poly(3, 4-ethylenedioxythiophene), PEDOT, with soft template (1-butyl-3-methyimidazolium hexafluorophosphate, bmimPF6) were prepared using interfacial polymerization on the shell surface of the micelle stabilized by surfactant (Triton X-100). The diameter of nanospheres was controlled by bmimPF6-to-surfacnt ratio. The release of cargo from the core and shell of the spheres was trigged by pH control and observed by photometric measurement. Aspect ratio and crystallinity of PEDOT shell increases in high pH value (above 10). In addition, the interaction of electronic polarization with atomic polarization was studied for core-shell nanosphere of PANI matrix with STO nanoparticles embedded. This nanosystem represents the first encapsulated nanospheres with extensive interfacial interaction within the core due to atomic polarizable isolated nano-domains embedded in an electronic polarizable continuous matrix.

  • Development of Cell-Active Inhibitors and Activity-Based Probe of Cysteine Cathepsins

    Author:
    Dibyendu Dana
    Year of Dissertation:
    2014
    Program:
    Chemistry
    Advisor:
    SANJAI KUMAR
    Abstract:

    Cysteine cathepsins are an important class of enzymes that coordinate a variety of important cellular processes, and are implicated in various types of human diseases. Still however, many of their cellular function remain poorly understood. Chemical biology approaches employing small molecules can be utilized for this purpose. Unfortunately small molecule probes that are cell-permeable and non-peptidyl in nature are scarcely available. In this work, first a library of sulfonyloxiranes is synthesized. From this library, 2-(2-ethylphenylsulfonyl)oxirane is identified as a selective inhibitor of cysteine cathepsins. Cell-based study reveals that 2-(2-ethylphenylsulfonyl)oxirane is a cell-permeable, covalent, and irreversible inhibitor of cathepsin B with modest efficacy. Next, a hybrid-design approach is undertaken to develop a highly potent and selective peptidyl vinylsulfonates inhibitor (KD-1) of human cathepsin L. Studies involving human breast carcinoma MDA-MB-231 cells establishes that this inhibitor can successfully block intracellular cathepsin L activity, and retards the cell-migratory potential of these highly metastatic cells. This work has been further extended to develop an activity-based probe (KDP-1) of cathepsin L by suitable modification of KD-1 inhibitory scaffold. KDP-1 has been found to be so far the most potent activity-based probe of cathepsin L. Cell-based studies are currently underway to demonstrate the cellular efficacy of KDP-1. Further, KDP-1 is anticipated to find extensive applications in proteome-wide analysis of cathepsin L activity in both normal and diseased cells.

  • MODIFICATION OF HYDROXYAPATITE (HAP) WITH 1-HYDROXYETHANE-1, 1-DIPHOSPHONIC ACID (HEDP) FOR THE SELECTIVE SORPTION OF METAL IONS FROM WATER

    Author:
    Yasmine Daniels
    Year of Dissertation:
    2013
    Program:
    Chemistry
    Advisor:
    Spiro Alexandratos
    Abstract:

    The United States Center for Disease Control and Prevention (CDC) has linked several diseases to water pollution. Metal ions such as lead, cadmium and copper are among the biggest contributors to water pollution and can leach into water from corroded plumbing, battery and paint discharges, glass and electronic production wastes and natural deposits. Toxic amounts of these metals have been shown to cause kidney failure, liver damage, developmental delay and several forms of cancer. The effect of groundwater pollution on disease has created a dire need to safely remove toxic metal ions from groundwater systems. The application of organophosphate-modified hydroxyapatite (mHAP) for water remediation is presented in this study. Hydroxyapatite (HAP) was modified with complexant 1-hydroxyethane 1, 1-diphosphonic acid (HEDP) and its effect on metal ion affinity and selectivity was determined. HAP was synthesized from calcium hydroxide and phosphoric acid, calcined at 700oC and modified by a post-functionalization method with HEDP. The influence of time and temperature on the extent of modification was investigated. An increasing concentration of HEDP (0.01 to 0.50 M) resulted in more modification. Both untreated and HEDP-treated HAP were characterized using Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), scanning electron microscopy (SEM), energy dispersive x-ray spectroscopy (EDS), ICP-OES and specific surface area (SSA) measurements. Ca/P ratios, acid capacities and phosphorus elemental analyses provide information about the effect of modification on mHAP composition, surface characteristics and interactions. A high reaction temperature during modification produced new, distinct phosphate bands (993cm-1, 1082cm-1, 1144cm-1) indicating the presence of HEDP. This was independent of reaction time. HAP modified at both high temperature and long reaction time had the highest HEDP loading and revealed the sharpest XRD peaks. The emergence of new HAP-HEDP strands was observed in SEM images for treated samples while EDS and ICP showed high phosphorus contents in these strands. HAP modified at high temperature for the long reaction also had a high acid capacity and more organic phosphorus than the controls, resulting from the presence of additional P-OH groups in HEDP. Selectivity for Pb(II) (90%) and Cd(II) (80%) over Zn(II) (25%), Ni(II) (18%) and Cu(II) (0%) from 10-4 N nitrate solutions was high for this sample compared to the metal ion sorption of unmodified HAP and HAP modified for the short reaction time at low temperature. The newly synthesized mHAP was not only selective for Pb(II) and Cd(II) but had unique chemical properties that were different from HAP-HEDP salts prepared by alternative pre-functionalization methods and different from Ca-HEDP salts.

  • Recruitment of the ribosomal 40S subunit to the 3'untranslated region of a viral mRNA, via the eIF4 complex, facilitates cap-independent translation.

    Author:
    Sohani Das Sharma
    Year of Dissertation:
    2014
    Program:
    Chemistry
    Advisor:
    Dixie Goss
    Abstract:

    Translation of uncapped plant viral RNAs can be facilitated by either an internal ribosomal entry site (IRES) in the 5' untranslated region (UTR) or a cap-independent translation element (CITE) in the 3' UTR. Barley yellow dwarf virus (BYDV) mRNA, which lacks both cap and poly(A) tail, has a translation element (3'BTE) in its 3' UTR that is essential for efficient translation initiation at the 5'-proximal AUG. This mechanism requires binding of the eukaryotic initiation factor 4G (eIF4G) subunit of the heterodimer eIF4F to the 3'BTE and base pairing between the 3'BTE and the 5' UTR. Here we investigate how this interaction recruits the ribosome to the 5' end of the mRNA. Using fluorescence anisotropy, SHAPE analysis and toe printing, we found that (i) 40S ribosomal subunits bind to the 3'BTE, (ii) the helicase complex eIF4F-eIF4A-eIF4B-ATP increases affinity of 40S subunit binding to the conserved SL-I of the 3' BTE by exposing more unpaired bases of the 3'BTE and (iii) long-distance base pairing transfers this complex to the 5' end of the mRNA where translation initiates. These results reveal an utterly novel mechanism of ribosome recruitment to an mRNA.

  • CORRELATION BETWEEN EXCITED STATE ORBITAL PARENTAGE AND EXCITED STATE ACID-BASE BEHAVIOR IN TRANSITION METAL COMPLEXES

    Author:
    Jim Dimitrakopoulos
    Year of Dissertation:
    2013
    Program:
    Chemistry
    Advisor:
    Harry Gafney
    Abstract:

    Chromium (III) polypyridyl and rhodium (III) polypyridyl complexes have been the subjects of considerable interest because of their extraordinary rich photophysical and photochemical properties. The following complexes were synthesized and studied: bis(2,2'-bipyridine) (2,3-bis (pyridyl)pyrazine) chromium(III) Hexafluorophosphate, tris(2,2'-bipyridine) chromium(III) Hexafluorophosphate, bis(1,10-phenanthroline) (2,3-bis(pyridyl)pyrazine) chromium(III) Hexafluorophosphate, bis(2,2'-bipyridine)(2,3-bis(pyridyl)pyrazine) rhodium(III) Nitrate, tris(2,2'-bipyridine) rhodium(III) Nitrate, and bis(2,2'-bipyridine)bis chloride rhodium(III)Hexafluorophosphate. All chromium polypyridyl complexes studied exhibit only metal-centered emissions (d-d); they display a fluorescence signal at approximately 695 nm (4A2g © 4T2g) and a phosphorescence signal at approximately 730 nm (4A2g© 2Eg). Quenching of both emissions occurs at high pH, while emission is enhanced at low pH. The [Rh(bpy)2dpp]3+ complex is found to display both metal-centered and ligand-centered emissions. The metal-centered emission (d-d) is the dominant luminescence feature at 77 K in ethanol-methanol glasses (4:1 v/v), but the ligand-centered (&pi ¨ &pi*) emission is enhanced relative to the metal-centered luminescence in fluid acetonitrile solutions. The bis complex, [Rh(bpy)2C12]+, displays a dominant metal centered emission under all conditions that were studied. The [Rh(bpy)3]3+ complex emits only from ligand-centered excited states at 77K. From this thesis, it became clear that the excited-state properties of a complex are related to the energy ordering of its low-energy excited states and, particularly, to the orbital nature of its lowest excited state. The energy positions of the MC, MLCT, and LC excited states depend on the ligand field strength, the redox properties of metal and ligands, and intrinsic properties of the ligands, respectively. Thus, in a series of complexes of the same metal ion, the energy ordering of the various excited states, and particularly the orbital nature of the lowest excited state, can be controlled by the choice of suitable ligands. It is therefore possible to design complexes having, at least to a certain degree, desired properties.

  • Synthesis of Drug/Dye Incorporated Copolymer-Protein Hybrids and Novel Curcumin Derivatives for Imaging and Therapeutic Applications.

    Author:
    Sukanta Dolai
    Year of Dissertation:
    2010
    Program:
    Chemistry
    Advisor:
    Krishnaswami Raja
    Abstract:

    This thesis describes novel synthetic methodologies towards: (a) novel polymer-protein hybrids with a significantly increased number of functional units attached per protein and (b) the synthesis of curcumin derivatives with increased solubility and amplified bioactivity. Azide terminated poly(tert-butyl acrylate) was synthesized via atom transfer radical polymerization [ATRP]. Subsequent deprotection was performed to yield poly(acrylic acid) (PAA) possessing a reactive chain-end. A one pot sequential amidation of the PAA with the amine derivatives of a near infrared fluorescent dye (ADS832WS) and glucose produced NIRF dye incorporated water soluble copolymers. End-group modifications were performed to produce alkyne/biotin terminated copolymers which were further employed to generate dye incorporated polymer-protein hybrids via the biotin-avidin interaction with avidin or "click" bioconjugation with azide modified bovine serum albumen or apoferritin. We have overcome two fundamental limitations in the synthesis of bioconjugates: (a) the basic restriction in the diversity of copolymers which can be synthesized for producing bioconjugates, (b) the limitation in the number of dyes/drug molecules that can be attached per protein molecule. The copolymers possessed enhanced optical properties compared to the dye due to increased solubility in water. Potential utility of these copolymers and conjugates in multiwell plate based assays, cell surface imaging and in vivo animal imaging were explored. In order to overcome the difficulties associated with the low water/plasma solubility of the potent anti-oxidant, anti-inflammatory, anti-carcinogenic, anti-Alzheimer's active curcumin we have successfully synthesized several mono-functional derivatives via one-two step covalent modification methods. Freely water soluble derivatives or adducts of curcumin e.g. curcumin sugar conjugate, dendrimer-curcumin conjugate were synthesized. Antibody-curcumin adduct was produced to develop an intelligent drug delivery system. The curcumin mono-carboxylic acid was able to stain and dissolute amyloid-beta plaques at a much lower concentrations compared to curcumin. A curcumin sugar conjugate which was able to modulate Aβ aggregation in nM concentrations was synthesized compared to curcumin which is effective in μM concentrations, the sugar conjugate is ~1000 times more potent. The curcumin sugar conjugate was found to be neuro-protective as well. The curcumin dimer which have the same numbers of free phenolic-OH as curcumin, was able to selectively destroy human neurotumor cells. The dendrimer-curcumin conjugate displays curcumin in a polyvalent architecture, it was freely soluble in water and was effective against BT459 mammalian cancer cells at much lower concentrations than curcumin. Towards the synthesis of targeted drug delivery module for curcumin, the synthesis of Antibody-curcumin adduct showed a great promise in destroying GL261 glioblastoma cells as well as B16F10 melanoma cells in nM concentrations compared to curcumin which is effective in μM concentrations. The in vivo studies in both glioblastoma and melanoma models for brain tumors indicated that mice treated with antibody-curcumin conjugate resulted in significant decrease in tumor size and a significant increase in survival life span.

  • Synthesis of Drug/Dye Incorporated Copolymer-Protein Hybrids and Novel Curcumin Derivatives for Imaging and Therapeutic Applications.

    Author:
    Sukanta Dolai
    Year of Dissertation:
    2010
    Program:
    Chemistry
    Advisor:
    Krishnaswami Raja
    Abstract:

    This thesis describes novel synthetic methodologies towards: (a) novel polymer-protein hybrids with a significantly increased number of functional units attached per protein and (b) the synthesis of curcumin derivatives with increased solubility and amplified bioactivity. Azide terminated poly(tert-butyl acrylate) was synthesized via atom transfer radical polymerization [ATRP]. Subsequent deprotection was performed to yield poly(acrylic acid) (PAA) possessing a reactive chain-end. A one pot sequential amidation of the PAA with the amine derivatives of a near infrared fluorescent dye (ADS832WS) and glucose produced NIRF dye incorporated water soluble copolymers. End-group modifications were performed to produce alkyne/biotin terminated copolymers which were further employed to generate dye incorporated polymer-protein hybrids via the biotin-avidin interaction with avidin or "click" bioconjugation with azide modified bovine serum albumen or apoferritin. We have overcome two fundamental limitations in the synthesis of bioconjugates: (a) the basic restriction in the diversity of copolymers which can be synthesized for producing bioconjugates, (b) the limitation in the number of dyes/drug molecules that can be attached per protein molecule. The copolymers possessed enhanced optical properties compared to the dye due to increased solubility in water. Potential utility of these copolymers and conjugates in multiwell plate based assays, cell surface imaging and in vivo animal imaging were explored. In order to overcome the difficulties associated with the low water/plasma solubility of the potent anti-oxidant, anti-inflammatory, anti-carcinogenic, anti-Alzheimer's active curcumin we have successfully synthesized several mono-functional derivatives via one-two step covalent modification methods. Freely water soluble derivatives or adducts of curcumin e.g. curcumin sugar conjugate, dendrimer-curcumin conjugate were synthesized. Antibody-curcumin adduct was produced to develop an intelligent drug delivery system. The curcumin mono-carboxylic acid was able to stain and dissolute amyloid-beta plaques at a much lower concentrations compared to curcumin. A curcumin sugar conjugate which was able to modulate Aβ aggregation in nM concentrations was synthesized compared to curcumin which is effective in μM concentrations, the sugar conjugate is ~1000 times more potent. The curcumin sugar conjugate was found to be neuro-protective as well. The curcumin dimer which have the same numbers of free phenolic-OH as curcumin, was able to selectively destroy human neurotumor cells. The dendrimer-curcumin conjugate displays curcumin in a polyvalent architecture, it was freely soluble in water and was effective against BT459 mammalian cancer cells at much lower concentrations than curcumin. Towards the synthesis of targeted drug delivery module for curcumin, the synthesis of Antibody-curcumin adduct showed a great promise in destroying GL261 glioblastoma cells as well as B16F10 melanoma cells in nM concentrations compared to curcumin which is effective in μM concentrations. The in vivo studies in both glioblastoma and melanoma models for brain tumors indicated that mice treated with antibody-curcumin conjugate resulted in significant decrease in tumor size and a significant increase in survival life span.

  • 2D & 3D NANOMATERIAL FABRICATION WITH BIOLOGICAL MOLECULAR FRAMEWORKS

    Author:
    Kristina Fabijanic
    Year of Dissertation:
    2014
    Program:
    Chemistry
    Advisor:
    HIROSHI MATSUI
    Abstract:

    Recently, there has been a heightened amount of work done in the field of biomineralization. By taking inspiration from natures' phenomenonal individualities as a means to develop new and interesting nanostructures of varying sizes and dimensions, there is a newly developed design, namely Biomimetic Crystallization Nanolithography (BCN). With this method, the simultaneous nano-patterning and crystallization has been achieved using urease as the nucleation point and the hydrolysis of urea to obtain patterns of oxide semiconductor material, namely zinc oxide, at room temperature and aqueous solvent. The new and interesting characteristic of BCN involves the construction of amorphous inks of ZnO through the use of an enzyme, its hydrolyzing abilities, and Zn-precursors. These inks are nano-patterned with the tip of an atomic force microscope, which has found to induce the crystallization of the amorphous inks into crystalline patterns. Also, a micro-contact printing process was developed and utilized as a means to directly pattern enzymes in a single step without the loss of enzyme activity after printing. By modifying the substrate to display aldehyde groups, the direct stamping of urease enables the simultaneous patterning and covalent cross-linking of urease under the reducing agent NaCNBH4, which does not degrade the enzyme activity. The exposed urease particles on the substrate, free from the cross-linker, were still catalytically active and utilized to grow crystalline ZnO nanoparticles on the enzyme patterns in ambient conditions and in aqueous solution. Recently, there has been a growing demand to have the ability of fabricating nanosized structures that are 3D in orientation, produced in large quantities and yield uniform shapes and sizes. Biomimetic assembly has been given attention in that it relies on the use of bio-inspired materials that are characteristically organized from the macroscale all the way to the nanoscale. Peptides are one of nature's building blocks that have the ability to take an active role in self-assembly and that can further be integrated to consequently yield the self-organization of structures with interesting properties in high quantities. In this study, first, micron-sized assembly of streptavidin-functionalized Au nanoparticles and biotinylated collagen peptides into cubic structures was demonstrated as assembled peptide frameworks incorporate nanoparticles in the exact position of unit cell, and then other fluorescent molecules or nanoparticles with biotin moieties were co-assembled to generate complex 3D nanoparticle assemblies. Energy transfer (FRET) and excitonic lifetime change of between QDs (donors) and AuNPs (acceptors) in these assemblies were investigated. As the interparticle distance was changed, the FRET efficiency also changed, shown by emission lifetime measurements. The energy transfer efficiency was also affected by the number of acceptor nanoparticles around the donor QDs. This type of robust large-scale 3D material assembly technique with precise positioning could be beneficial for future bottom-up device assembly such as solar cells, batteries, and metamaterials.