Solar light harvesting begins with electronic energy transfer in structurally complex lightharves... more Solar light harvesting begins with electronic energy transfer in structurally complex lightharvesting antennae such as the peridinin chlorophyll-a protein from dinoflagellate algae. Peridinin chlorophyll-a protein is composed of a unique combination of chlorophylls sensitized by carotenoids in a 4:1 ratio, and ultrafast spectroscopic methods have previously been utilized
Nonlinear interferometers with quantum correlated photons have been demonstrated to improve optic... more Nonlinear interferometers with quantum correlated photons have been demonstrated to improve optical characterization and metrology. These interferometers can be used in gas spectroscopy, which is of particular interest for monitoring greenhouse gas emissions, breath analysis and industrial applications. Here, we show that gas spectroscopy can be further enhanced via the deployment of crystal superlattices. This is a cascaded arrangement of nonlinear crystals forming interferometers, allowing the sensitivity to scale with the number of nonlinear elements. In particular, the enhanced sensitivity is observed via the maximum intensity of interference fringes that scales with low concentration of infrared absorbers, while for high concentration the sensitivity is better in interferometric visibility measurements. Thus, a superlattice acts as a versatile gas sensor since it can operate by measuring different observables, which are relevant to practical applications. We believe that our ap...
Photosynthetic organisms make structurally complex light-harvesting pigmentprotein complexes with... more Photosynthetic organisms make structurally complex light-harvesting pigmentprotein complexes with high quantum efficiency. The studies presented in this dissertation explore the structure-function relationship in two complexes – peridinin chlorophyll-a protein (PCP) from dinoflagellate Amphidinium carterae and phycocyanin 645 (PC645) from cryptophyte Chroomonas mesostigmatica – using quantum chemistry and ultrafast two-dimensional electronic spectroscopy (2DES). PCP is a protein complex containing eight peridinin and two chlorophyll-a molecules, while PC645 contains eight bilins covalently bonded to a quaternary protein structure. Focus on the functional aspect of these light-harvesting complexes is widespread in literature; their structures serve as starting geometries for chromophoric electronic excited states calculations. This dissertation starts with energy decomposition analyses of the non-covalent interactions between the chromophores and the surrounding environment using sym...
The dye employed in all constructs studied in this work was a custom Cy5 derivative from Integrat... more The dye employed in all constructs studied in this work was a custom Cy5 derivative from Integrated DNA Technologies (IDT; Coralville, IA, USA) that is functionalized with flexible propyl chain linkers attached to the nitrogens of both heterocycle rings. This functionalization scheme enables integration of the Cy5 into the DNA backbone internally via covalent bonding at both the 5' and 3' ends. The structure of the dye with attachment sites indicated is shown below in Figure S 1.1. Figure S 1.1. Structure of the internal Cy5 dye including dual linkers to the DNA backbone (adapted from IDT website). 1.2 DNA Sequences All constructs discussed in the main text are derived from hybridization of two complementary 26 nucleotide (nt) DNA oligomer strand sequences. These strands, herein referred to as "Cy5-A" and its complement, "Cy5-B", have Cy5 molecules internally attached within the DNA's phosphate backbone via dual covalent linkers utilizing a phosphoramidite approach as described above in Section 1.1. Furthermore, the individual complementary oligomer sequences were designed such that, when hybridized, the Cy5 molecules would inhabit the same rung of the DNA duplex. To illustrate how they hybridize, the strand sequences are presented below in Table S 1.1. Table S 1.1. DNA Oligomer Strand Sequences Strand Name End Sequence End Cy5-A 5' CAGTCATAATATGCGA/iCy5/GCGATTATAT 3' Cy5-B 3' GTCAGTATTATACGCT/iCy5/CGCTAATATA 5' Note that throughout the manuscript (and for the remainder of the SI), unless otherwise noted all references to the "monomer" refer to the Cy5-A strand given that the photophysics of the Cy5-A and Cy5-B monomer strands are virtually identical (see Supporting Information S.4: Monomer Photophysics). 1.3 Construct Preparation A detailed description of the construct preparation procedure has been reported previously, 1 but a brief summary follows. DNA oligomers internally functionalized with Cy5 were purchased from IDT as a lyophilized, high-performance liquid chromatography (HPLC) purified powder. Oligomers were rehydrated with ultrapure water (Barnstead Nanopure, Thermo Scientific) to create 100 µM stock solutions of Cy5-A and Cy5-B (Table S 1.1). TAE buffer (10× stock solution, pH 8.0) and MgCl 2 (99% purity) were purchased from Fisher Scientific. The 10× TAE stock solution was diluted to 1× (corresponding to 40 mM tris(hydroxymethyl)aminomethane, 20 mM acetic acid, and 1 mM ethylenediaminetetraacetic acid) with ultrapure water, while the MgCl 2 was dissolved in ultrapure water to create a 1.375 M stock solution. The stock solution of Cy5-A oligomer strands was used to prepare all "monomer" solutions unless otherwise explicitly stated. Hybridization of the oligomers to create DNA duplexes for the J-dimer and Htetramer constructs was accomplished by combining equimolar amounts of complementary Cy5-A and Cy5-B oligomers in a 1× TAE buffer solution to yield a final DNA concentration of 0.1-40 µM. For the Htetramers, aliquots of the stock MgCl 2 solution were added to the diluted (1×) TAE buffer solution to produce a solution with a final magnesium (Mg 2+) concentration of 100 mM MgCl 2. Resulting solutions were then allowed to hybridize for 24 hours at room temperature. 1.4 Purification Procedure To remove any excess monomer or unwanted secondary structures that formed, aggregate (J-dimer and H-tetramer) constructs were purified using native polyacrylamide gel electrophoresis (PAGE). 10% PAGE gels were cast using 1× TAE buffer with no MgCl 2 added for J-dimers and 100 mM MgCl 2 added for H-tetramers. Samples were prepared at a concentration of 42 μM and allowed to hybridize at room temperature for at least 24 hours. A solution with a 5:1 ratio of 6× loading buffer (New England Biolabs) to DNA sample was prepared, and the DNA/loading buffer mixtures were injected into the gels, which were allowed to run 60-90 minutes at 100-150 V. Gels were run in a 1× TAE buffer with 0 mM and 100mM MgCl 2 added for the J-dimer and H-tetramer solutions, respectively. After the bands were sufficiently separated from the loading buffer, the gels were imaged using a FluoroChemQ imaging system as shown in Figure S 1.2 and Figure S 1.3. Figure S 1.2. 10% PAGE gels of J-dimer constructs run in 1× TAE buffer. The image on the left is obtained when the gel is excited with 245 nm light and the bands cast shadows onto an underlying phosphor plate. The image on the right is obtained when the gel
Solar light harvesting begins with electronic energy transfer in structurally complex light-harve... more Solar light harvesting begins with electronic energy transfer in structurally complex light-harvesting antennae such as the peridinin chlorophyll-a protein from dinoflagellate algae. Peridinin chlorophyll-a protein is composed of a unique combination of chlorophylls sensitized by carotenoids in a 4:1 ratio, and ultrafast spectroscopic methods have previously been utilized in elucidating their energy-transfer pathways and timescales. However, due to overlapping signals from various chromophores and competing pathways and timescales, a consistent model of intraprotein electronic energy transfer has been elusive. Here, we used a broad-band two-dimensional electronic spectroscopy, which alleviates the spectral congestion by dispersing excitation and detection wavelengths. Interchromophoric couplings appeared as cross peaks in two-dimensional electronic spectra, and these spectral features were observed between the peridinin S 2 states and chlorophyll-a Q x and Q y states. In addition, t...
Solar light harvesting begins with electronic energy transfer in structurally complex lightharves... more Solar light harvesting begins with electronic energy transfer in structurally complex lightharvesting antennae such as the peridinin chlorophyll-a protein from dinoflagellate algae. Peridinin chlorophyll-a protein is composed of a unique combination of chlorophylls sensitized by carotenoids in a 4:1 ratio, and ultrafast spectroscopic methods have previously been utilized
Nonlinear interferometers with quantum correlated photons have been demonstrated to improve optic... more Nonlinear interferometers with quantum correlated photons have been demonstrated to improve optical characterization and metrology. These interferometers can be used in gas spectroscopy, which is of particular interest for monitoring greenhouse gas emissions, breath analysis and industrial applications. Here, we show that gas spectroscopy can be further enhanced via the deployment of crystal superlattices. This is a cascaded arrangement of nonlinear crystals forming interferometers, allowing the sensitivity to scale with the number of nonlinear elements. In particular, the enhanced sensitivity is observed via the maximum intensity of interference fringes that scales with low concentration of infrared absorbers, while for high concentration the sensitivity is better in interferometric visibility measurements. Thus, a superlattice acts as a versatile gas sensor since it can operate by measuring different observables, which are relevant to practical applications. We believe that our ap...
Photosynthetic organisms make structurally complex light-harvesting pigmentprotein complexes with... more Photosynthetic organisms make structurally complex light-harvesting pigmentprotein complexes with high quantum efficiency. The studies presented in this dissertation explore the structure-function relationship in two complexes – peridinin chlorophyll-a protein (PCP) from dinoflagellate Amphidinium carterae and phycocyanin 645 (PC645) from cryptophyte Chroomonas mesostigmatica – using quantum chemistry and ultrafast two-dimensional electronic spectroscopy (2DES). PCP is a protein complex containing eight peridinin and two chlorophyll-a molecules, while PC645 contains eight bilins covalently bonded to a quaternary protein structure. Focus on the functional aspect of these light-harvesting complexes is widespread in literature; their structures serve as starting geometries for chromophoric electronic excited states calculations. This dissertation starts with energy decomposition analyses of the non-covalent interactions between the chromophores and the surrounding environment using sym...
The dye employed in all constructs studied in this work was a custom Cy5 derivative from Integrat... more The dye employed in all constructs studied in this work was a custom Cy5 derivative from Integrated DNA Technologies (IDT; Coralville, IA, USA) that is functionalized with flexible propyl chain linkers attached to the nitrogens of both heterocycle rings. This functionalization scheme enables integration of the Cy5 into the DNA backbone internally via covalent bonding at both the 5' and 3' ends. The structure of the dye with attachment sites indicated is shown below in Figure S 1.1. Figure S 1.1. Structure of the internal Cy5 dye including dual linkers to the DNA backbone (adapted from IDT website). 1.2 DNA Sequences All constructs discussed in the main text are derived from hybridization of two complementary 26 nucleotide (nt) DNA oligomer strand sequences. These strands, herein referred to as "Cy5-A" and its complement, "Cy5-B", have Cy5 molecules internally attached within the DNA's phosphate backbone via dual covalent linkers utilizing a phosphoramidite approach as described above in Section 1.1. Furthermore, the individual complementary oligomer sequences were designed such that, when hybridized, the Cy5 molecules would inhabit the same rung of the DNA duplex. To illustrate how they hybridize, the strand sequences are presented below in Table S 1.1. Table S 1.1. DNA Oligomer Strand Sequences Strand Name End Sequence End Cy5-A 5' CAGTCATAATATGCGA/iCy5/GCGATTATAT 3' Cy5-B 3' GTCAGTATTATACGCT/iCy5/CGCTAATATA 5' Note that throughout the manuscript (and for the remainder of the SI), unless otherwise noted all references to the "monomer" refer to the Cy5-A strand given that the photophysics of the Cy5-A and Cy5-B monomer strands are virtually identical (see Supporting Information S.4: Monomer Photophysics). 1.3 Construct Preparation A detailed description of the construct preparation procedure has been reported previously, 1 but a brief summary follows. DNA oligomers internally functionalized with Cy5 were purchased from IDT as a lyophilized, high-performance liquid chromatography (HPLC) purified powder. Oligomers were rehydrated with ultrapure water (Barnstead Nanopure, Thermo Scientific) to create 100 µM stock solutions of Cy5-A and Cy5-B (Table S 1.1). TAE buffer (10× stock solution, pH 8.0) and MgCl 2 (99% purity) were purchased from Fisher Scientific. The 10× TAE stock solution was diluted to 1× (corresponding to 40 mM tris(hydroxymethyl)aminomethane, 20 mM acetic acid, and 1 mM ethylenediaminetetraacetic acid) with ultrapure water, while the MgCl 2 was dissolved in ultrapure water to create a 1.375 M stock solution. The stock solution of Cy5-A oligomer strands was used to prepare all "monomer" solutions unless otherwise explicitly stated. Hybridization of the oligomers to create DNA duplexes for the J-dimer and Htetramer constructs was accomplished by combining equimolar amounts of complementary Cy5-A and Cy5-B oligomers in a 1× TAE buffer solution to yield a final DNA concentration of 0.1-40 µM. For the Htetramers, aliquots of the stock MgCl 2 solution were added to the diluted (1×) TAE buffer solution to produce a solution with a final magnesium (Mg 2+) concentration of 100 mM MgCl 2. Resulting solutions were then allowed to hybridize for 24 hours at room temperature. 1.4 Purification Procedure To remove any excess monomer or unwanted secondary structures that formed, aggregate (J-dimer and H-tetramer) constructs were purified using native polyacrylamide gel electrophoresis (PAGE). 10% PAGE gels were cast using 1× TAE buffer with no MgCl 2 added for J-dimers and 100 mM MgCl 2 added for H-tetramers. Samples were prepared at a concentration of 42 μM and allowed to hybridize at room temperature for at least 24 hours. A solution with a 5:1 ratio of 6× loading buffer (New England Biolabs) to DNA sample was prepared, and the DNA/loading buffer mixtures were injected into the gels, which were allowed to run 60-90 minutes at 100-150 V. Gels were run in a 1× TAE buffer with 0 mM and 100mM MgCl 2 added for the J-dimer and H-tetramer solutions, respectively. After the bands were sufficiently separated from the loading buffer, the gels were imaged using a FluoroChemQ imaging system as shown in Figure S 1.2 and Figure S 1.3. Figure S 1.2. 10% PAGE gels of J-dimer constructs run in 1× TAE buffer. The image on the left is obtained when the gel is excited with 245 nm light and the bands cast shadows onto an underlying phosphor plate. The image on the right is obtained when the gel
Solar light harvesting begins with electronic energy transfer in structurally complex light-harve... more Solar light harvesting begins with electronic energy transfer in structurally complex light-harvesting antennae such as the peridinin chlorophyll-a protein from dinoflagellate algae. Peridinin chlorophyll-a protein is composed of a unique combination of chlorophylls sensitized by carotenoids in a 4:1 ratio, and ultrafast spectroscopic methods have previously been utilized in elucidating their energy-transfer pathways and timescales. However, due to overlapping signals from various chromophores and competing pathways and timescales, a consistent model of intraprotein electronic energy transfer has been elusive. Here, we used a broad-band two-dimensional electronic spectroscopy, which alleviates the spectral congestion by dispersing excitation and detection wavelengths. Interchromophoric couplings appeared as cross peaks in two-dimensional electronic spectra, and these spectral features were observed between the peridinin S 2 states and chlorophyll-a Q x and Q y states. In addition, t...
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