Mechanisms of Porphyrinoid and Carotenoid Spectral Tuning Revealed with Quantum Chemistry

Continued advances in a myriad of biomedical and technological fields require the rational design of molecules or supramolecular architectures with specific photophysical properties. Central to this endeavor is a mechanistic understanding of optical property modulation as a function of molecular structure, conformation, and environment. Natural pigments and protein-pigment complexes constitute a ‘solutions manual’ to challenges in electronic (optical) engineering that has been refined over a few billion years of evolution, and from which design principles can be deduced. In this thesis, unique mechanisms for modulating the optical properties of natural or synthetic porphyrinoid and carotenoid pigments are elucidated with quantum chemical methods. Our investigations add a new conformational mechanism, as well as design principles for regioisomer-dependent electronic substituent effects to the cannon of structural tools for regulating the optical properties of pyrrole-modified porphyrins. The lessons learned provide insight into analogous spectral tuning mechanisms found in nature. We also delineate the molecular factors optimally regulating light harvesting in a natural photosynthetic antenna complex. These discoveries have advanced the fundamental understanding and practical utilization of structure-optical property modulation mechanisms, and may aid the design of next-generation photonic-based technologies

Adapting Advanced Inorganic Chemistry Lecture and Laboratory Instruction for a Legally Blind Student

In this article, the strategies and techniques used to successfully teach advanced inorganic chemistry, in the lecture and laboratory, to a legally blind student are described. At Fairfield University, these separate courses, which have a physical chemistry corequisite or a prerequisite, are taught for junior and senior chemistry and biochemistry majors. A student earns a separate grade in each the lecture (three credits) and the laboratory course (two credits). An overview of the course topics is given, followed by general accommodations and specific approaches that were used. Student assistants were very helpful and provided extra support for the blind student. Student assistants were utilized for the laboratory course, problem sets, and exams. Specific examples and detailed explanations of approaches that were helpful to the legally blind student throughout the entire course are provided. The legally blind student benefited from extensive, verbal description of complexes, figures, and diagrams. In addition, the student benefited from tactile description of figures and models. The student assistants and extra office hours were essential for the blind student to succeed and excel in advanced inorganic chemistry. The approaches discussed in this paper are the product of immediate and continual feedback from the student over the course of the semester. The student would frequently comment after class that he followed the lesson or was confused, and the latter comment elicited experimentation with different approaches

Data_Sheet_1_To be or not to be a cytochrome: electrical characterizations are inconsistent with Geobacter cytochrome ‘nanowires’.pdf

Geobacter sulfurreducens profoundly shapes Earth’s biogeochemistry by discharging respiratory electrons to minerals and other microbes through filaments of a two-decades-long debated identity. Cryogenic electron microscopy has revealed filaments of redox-active cytochromes, but the same filaments have exhibited hallmarks of organic metal-like conductivity under cytochrome denaturing/inhibiting conditions. Prior structure-based calculations and kinetic analyses on multi-heme proteins are synthesized herein to propose that a minimum of ~7 cytochrome ‘nanowires’ can carry the respiratory flux of a Geobacter cell, which is known to express somewhat more (≥20) filaments to increase the likelihood of productive contacts. By contrast, prior electrical and spectroscopic structural characterizations are argued to be physiologically irrelevant or physically implausible for the known cytochrome filaments because of experimental artifacts and sample impurities. This perspective clarifies our mechanistic understanding of physiological metal-microbe interactions and advances synthetic biology efforts to optimize those interactions for bioremediation and energy or chemical production.</p

Carotenoid-Chlorophyll Interactions in a Photosynthetic Antenna Protein: A Supramolecular QM/MM Approach

Multichromophoric interactions control the initial events of energy capture and transfer in the light harvesting peridinin-chlorophyll a protein (PCP) from marine algae dinoflagellates. Due to the van der Waals association of the carotenoid peridinin (Per) with chlorophyll a in a unique 4:1 stoichiometric ratio, supramolecular quantum mechanical/molecular mechanical (QM/MM) calculations are essential to accurately describe structure, spectroscopy, and electronic coupling. We show that, by enabling inter-chromophore electronic coupling, substantial effects arise in the nature of the transition dipole moment and the absorption spectrum. We further hypothesize that inter-protein domain Per-Per interactions are not negligible, and are needed to explain the experimental reconstruction features of the spectrum in wild-type PCP

Connectivity-Based Biocompatible Force Field for Thiolated Gold Nanoclusters

Thiolated gold nanoclusters (AuNCs), sub-2 nm Au particles capped by Au­(I) thiolate complexes, promise to have a myriad of applications in biomedical diagnosis and therapy as well as industrial catalysis, energy production, and monitoring of environmental pollutants. Computational simulations are a valuable tool in elucidating design principles for optimizing application-specific physicochemical properties. However, thiolated AuNCs protected, conjugated, and/or interacting with macromolecules often exceed the limit of computational tractability with present-day quantum chemistry software. To facilitate theoretical studies, a molecular mechanics force field, AuSBio, is presented that reasonably reproduces, and retains, characteristic structural features of perhaps the most intensively studied thiolated AuNC, Au₂₅L₁₈ (L = alkylthiolate), over 2 ns finite temperature molecular dynamics simulations. AuSBio was parametrized within the framework of force fields for (bio)­organic simulations to reproduce equilibrium structures and the vibrational density of states for small homoleptic and larger thiolated Au clusters. AuSBio was further validated by the ability to reproduce the experimental structure of Au₃₈L₂₄, as well as bundling of long-chain alkylthiolate ligands, and the nonlinear frequency modulation pattern of a Raman-active vibrational mode, observed experimentally for the Au₂₅ cluster. We envision our AuSBio force field facilitating, in a practical manner, molecular mechanics or hybrid quantum/molecular mechanics simulations on the structure and dynamics of thiolated AuNC bioconjugates and AuNC monolayer-mediated molecular recognition and catalysis events

[3 + 2]-Cycloadditions with Porphyrin β,β′-Bonds: Theoretical Basis of the Counterintuitive <i>meso</i>-Aryl Group Influence on the Rates of Reaction

Removal of a β,β′-bond from meso-tetraarylporphyrin using [3 + 2]-cycloadditions generates meso-tetraarylhydroporphyrins. Literature evidence indicates that meso-tetraphenylporphyrins react more sluggishly with 1,3-dipoles such as ylides and OsO4 (in the presence of pyridine) than meso-tetrakis(pentafluorophenyl)porphyrin. The trend is counterintuitive for the reaction with OsO4, as this formal oxidation reaction is expected to proceed more readily with more electron-rich substrates. This work presents a density functional theory–based computational study of the frontier molecular orbital (FMO) interactions and reaction profile thermodynamics involved in the reaction of archetypical cycloaddition reactions (a simple ylide, OsO4, OsO4·py, OsO4·(py)2, and ozone) with the β,β′-double bonds of variously fluorinated meso-arylporphyrins. The trend observed for the Type I cycloaddition of an ylide is straightforward, as lowering the LUMO of the porphyrin with increasing meso-phenyl-fluorination also lowers the reaction barrier. The corresponding simple FMO analyses of Type III cycloadditions do not correctly model the reaction energetics. This is because increasing fluorination leads to lowering of the porphyrin HOMO–2, thus increasing the reaction barrier. However, coordination of pyridine to OsO4 preorganizes the transition state complex; lowering of the energy barrier by the preorganization exceeds the increase in repulsive orbital interactions, overall accelerating the cycloaddition and rationalizing the counterintuitive experimental findings

Vibrational Coupling Modulation in n-Alkanethiolate Protected Au25(SR)180 Clusters

We have studied, both experimentally and theoretically, the Raman vibrational spectra of a series of nalkanethiolate protected Au25(SCnH2n+1)18 clusters, with n = 2, 3, 4, 5, 6, 8, 10, 12, and 14. The C 12H stretching region of the infrared spectra reveals that, while shorter chains are flexible, longer chains are more ordered with a propensity toward extended all-trans conformation. The different behavior of long and short chains is also reflected in the low-frequency Raman spectra of the clusters, which are broadened for the longer chains due to interchain interactions and formation of bundles. The experimental low-frequency modes in the Raman spectra, associated with Au 12S stretching vibrations, change drastically and in an apparently unsystematic way as a function of chain length. For example, a band around 320 cm 121 associated with tangential Au 12S stretching character shifts up in frequency, then down and then up again as the carbon chain is increased. DFT calculations reveal that this behavior is due to a nonlinear coupling of this mode to torsional and bending modes of the alkyl chain. The frequencies of these modes strongly depend on the chain length and, as a consequence, also their coupling with the Au 12S stretching modes, which explains the erratic behavior of this band in the spectra. This behavior is well described by calculations on a mimic cluster model that considers only one staple motif. For the ethanethiolate-protected cluster, the entire cluster was included in the calculation of the Raman spectrum, and this allowed for the first time to compare directly experimental and calculated Raman spectra of the same cluster. Furthermore, our study shows that the entire ligand has to be considered for the calculation of the low frequency vibrations of the Au 12S interface, as this spectral region is sensitive to coupling with low-frequency ligand modes

Light Harvesting by Equally Contributing Mechanisms in a Photosynthetic Antenna Protein

We report supramolecular quantum mechanics/molecular mechanics simulations on the peridinin–chlorophyll <i>a</i> protein (PCP) complex from the causative algal species of red tides. These calculations reproduce for the first time quantitatively the distinct peridinin absorptions, identify multichromophoric molecular excitations, and elucidate the mechanisms regulating the strongly allowed S₀ (1¹A_g^–) → S₂ (1¹B_u⁺) absorptions of the bound peridinins that span a 58 nm spectral range in the region of maximal solar irradiance. We discovered that protein binding site-imposed conformations, local electrostatics, and electronic coupling contribute equally to the spectral inhomogeneity. Electronic coupling causes coherent excitations among the densely packed pigments. Complementary pairing of tuning mechanisms is the result of a competition between pigment–pigment and pigment–environment interactions. We found that the aqueous solvent works in concert with the charge distribution of PCP to produce a strong correlation between peridinin spectral bathochromism and the local dielectric environment

Delineating redox cooperativity in water-soluble and membrane multiheme cytochromes through protein design

Nature has evolved diverse electron transport proteins and multiprotein assemblies essential to the generation and transduction of biological energy. However, substantially modifying or adapting these proteins for user-defined applications or to gain fundamental mechanistic insight can be hindered by their inherent complexity. De novo protein design offers an attractive route to stripping away this confounding complexity, enabling us to probe the fundamental workings of these bioenergetic proteins and systems, while providing robust, modular platforms for constructing completely artificial electron-conducting circuitry. Here, we use a set of de novo designed mono-heme and di-heme soluble and membrane proteins to delineate the contributions of electrostatic micro-environments and dielectric properties of the surrounding protein medium on the inter-heme redox cooperativity that we have previously reported. Experimentally, we find that the two heme sites in both the water-soluble and membrane constructs have broadly equivalent redox potentials in isolation, in agreement with Poisson-Boltzmann Continuum Electrostatics calculations. BioDC, a Python program for the estimation of electron transfer energetics and kinetics within multiheme cytochromes, also predicts equivalent heme sites, and reports that burial within the low dielectric environment of the membrane strengthens heme-heme electrostatic coupling. We conclude that redox cooperativity in our diheme cytochromes is largely driven by heme electrostatic coupling and confirm that this effect is greatly strengthened by burial in the membrane. These results demonstrate that while our de novo proteins present minimalist, new-to-nature constructs, they enable the dissection and microscopic examination of processes fundamental to the function of vital, yet complex, bioenergetic assemblies.</p

Size-selective Pt siderophores based on redox active azo-aromatic ligands

10.1039/d0sc02683bChemical Science11349226-923