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Rappoport, Dmitrij

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Rappoport

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Dmitrij

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Rappoport, Dmitrij
Author's Publications: search.filters.isAuthorOfPublication.a8aeab65-4adc-4049-b442-953d23fd695e

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Now showing 1 - 10 of 18
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    Electronic Transition Moments of 6-methyl Isoxanthopterin—A Fluorescent Analogue of the Nucleic Acid Base Guanine
    (Oxford University Press, 2012) Widom, Julia; Rappoport, Dmitrij; Perdomo-Ortiz, Alejandro; Thomsen, Hanna; Johnson, Neil P.; von Hippel, Peter H.; Aspuru-Guzik, Alan; Marcus, Andrew H.
    Fluorescent nucleic acid base analogues are important spectroscopic tools for understanding local structure and dynamics of DNA and RNA. We studied the orientations and magnitudes of the electric dipole transition moments (EDTMs) of 6-methyl isoxanthopterin (6-MI), a fluorescent analogue of guanine that has been particularly useful in biological studies. Using a combination of absorption spectroscopy, linear dichroism (LD) and quantum chemical calculations, we identified six electronic transitions that occur within the 25 000–50 000 \(cm^{−1}\) spectral range. Our results indicate that the two experimentally observed lowest-energy transitions, which occur at 29 687 \(cm^{−1}\) (337 nm) and 34 596 \(cm^{−1}\) (289 nm), are each polarized within the plane of the 6-MI base. A third in-plane polarized transition is experimentally observed at 47 547 \(cm^{−1}\) (210 nm). The theoretically predicted orientation of the lowest-energy transition moment agrees well with experiment. Based on these results, we constructed an exciton model to describe the absorption spectra of a 6-MI dinucleotide–substituted double-stranded DNA construct. This model is in good agreement with the experimental data. The orientations and intensities of the low-energy electronic transitions of 6-MI reported here should be useful for studying local conformations of DNA and RNA in biologically important complexes.
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    Can Mixed-Metal Surfaces Provide an Additional Enhancement to SERS?
    (American Chemical Society, 2012) Olivares-Amaya, Roberto; Rappoport, Dmitrij; Camayd-Munoz, Phil; Peng, Paul; Mazur, Eric; Aspuru-Guzik, Alan
    We explore the chemical contribution to surface-enhanced Raman scattering (SERS) in mixed-metal substrates, both experimentally and by computer simulation. These substrates are composed of a chemically active, transition-metal overlayer deposited on an effective SERS substrate. We report improved analytical enhancement factors obtained by using a small surface coverage of palladium or platinum over nanostructured silver substrates. Theoretical predictions of the chemical contribution to the surface enhancement using density functional theory support the experimental results. In addition, these approaches show that the increased enhancement is due not only to an increase in surface coverage of the analyte but also to a higher Raman scattering cross section per molecule. The additional chemical enhancement in mixed-metal SERS substrates correlates with the binding energy of the analyte on the surface and includes both static and dynamical effects. SERS using mixed-metal substrates has the potential to improve sensing for a large group of analyte molecules and to aid the development of chemically specific SERS-based sensors.
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    Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry
    (American Chemical Society (ACS), 2014) Rappoport, Dmitrij; Galvin, Cooper J.; Zubarev, Dmitry Yu.; Aspuru-Guzik, Alan
    While structures and reactivities of many small molecules can be computed efficiently and accurately using quantum chemical methods, heuristic approaches remain essential for modeling complex structures and large-scale chemical systems. Here, we present a heuristics-aided quantum chemical methodology applicable to complex chemical reaction networks such as those arising in cell metabolism and prebiotic chemistry. Chemical heuristics offer an expedient way of traversing high-dimensional reactive potential energy surfaces and are combined here with quantum chemical structure optimizations, which yield the structures and energies of the reaction intermediates and products. Application of heuristics-aided quantum chemical methodology to the formose reaction reproduces the experimentally observed reaction products, major reaction pathways, and autocatalytic cycles.
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    The Binding of Benzoarylsulfonamide Ligands to Human Carbonic Anhydrase is Insensitive to Formal Fluorination of the Ligand
    (Wiley-VCH Verlag Berlin, 2013) Lockett, Matthew R.; Lange, Heiko; Breiten, Benjamin; Heroux, Annie; Sherman, Woody; Rappoport, Dmitrij; Yau, Patricia O.; Snyder, Philip W.; Whitesides, George
    Auf das Wasser kommt es an: Konservierte Bindungsgeometrie, enthalpiegetriebene Bindungsweise und nichtunterscheidbare Bindungsaffinitäten für fluorierte und nichtfluorierte Liganden von humaner Carbonsäureanhydrase (siehe Bild) stützen die Theorie, dass das Schlüssel-Schloss-Modell einen wichtigen Bestandteil des Bindungsvorgangs unbeachtet lässt: das Wasser, das die Bindungstasche des Proteins füllt und den Liganden umgibt.
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    Temperature-Dependent Conformations of a Membrane Supported Zinc Porphyrin Tweezer by 2D Fluorescence Spectroscopy
    (American Chemical Society (ACS), 2013) Widom, Julia R.; Lee, Wonbae; Perdomo-Ortiz, Alejandro; Rappoport, Dmitrij; Molinski, Tadeusz F.; Aspuru-Guzik, Alan; Marcus, Andrew H.
    We studied the equilibrium conformations of a zinc porphyrin tweezer composed of two carboxylphenyl-functionalized zinc tetraphenyl porphyrin subunits connected by a 1,4-butyndiol spacer, which was suspended inside the amphiphilic regions of 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) liposomes. By combining phase-modulation two-dimensional fluorescence spectroscopy (2D FS) with linear absorbance and fluorimetry, we determined that the zinc porphyrin tweezer adopts a mixture of folded and extended conformations in the membrane. By fitting an exciton-coupling model to a series of data sets recorded over a range of temperatures (17–85°C) and at different laser center wavelengths, we determined that the folded form of the tweezer is stabilized by a favorable change in the entropy of the local membrane environment. Our results provide insights toward understanding the balance of thermodynamic factors that govern molecular assembly in membranes.
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    Quantum Chemical Approach to Estimating the Thermodynamics of Metabolic Reactions
    (Nature Publishing Group, 2014) Jinich, Adrian; Rappoport, Dmitrij; Dunn, Ian; Sanchez-Lengeling, Benjamin; Olivares-Amaya, Roberto; Noor, Elad; Even, Arren Bar; Aspuru-Guzik, Alan
    Thermodynamics plays an increasingly important role in modeling and engineering metabolism. We present the first nonempirical computational method for estimating standard Gibbs reaction energies of metabolic reactions based on quantum chemistry, which can help fill in the gaps in the existing thermodynamic data. When applied to a test set of reactions from core metabolism, the quantum chemical approach is comparable in accuracy to group contribution methods for isomerization and group transfer reactions and for reactions not including multiply charged anions. The errors in standard Gibbs reaction energy estimates are correlated with the charges of the participating molecules. The quantum chemical approach is amenable to systematic improvements and holds potential for providing thermodynamic data for all of metabolism.
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    State-by-State Investigation of Destructive Interference in Resonance Raman Spectra of Neutral Tyrosine and the Tyrosinate Anion with the Simplified Sum-over-States Approach
    (American Chemical Society (ACS), 2014) Cabalo, Jerry B.; Saikin, Semion K.; Emmons, Erik D.; Rappoport, Dmitrij; Aspuru-Guzik, Alan
    UV resonance Raman scattering is uniquely sensitive to the molecular electronic structure as well as intermolecular interactions. To better understand the relationship between electronic structure and resonance Raman cross section, we carried out combined experimental and theoretical studies of neutral tyrosine and the tyrosinate anion. We studied the Raman cross sections of four vibrational modes as a function of excitation wavelength, and we analyzed them in terms of the contributions of the individual electronic states as well as of the Albrecht A and B terms. Our model, which is based on time-dependent density functional theory (TDDFT), reproduced the experimental resonance Raman spectra and Raman excitation profiles for both studied molecules with good agreement. We found that for the studied modes, the contributions of Albrecht’s B terms in the Raman cross sections were important across the frequency range spanning the La,b and Ba,b electronic excitations in tyrosine and the tyrosinate anion. Furthermore, we demonstrated that interference with high-energy states had a significant impact and could not be neglected even when in resonance with a lower-energy state. The symmetry of the vibrational modes served as an indicator of the dominance of the A or B mechanisms. Excitation profiles calculated with a damping constant estimated from line widths of the electronic absorption bands had the best consistency with experimental results.
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    Uncertainty of Prebiotic Scenarios: The Case of the Non-Enzymatic Reverse Tricarboxylic Acid Cycle
    (Nature Publishing Group, 2015) Zubarev, Dmitry Yu.; Rappoport, Dmitrij; Aspuru-Guzik, Alan
    We consider the hypothesis of the primordial nature of the non-enzymatic reverse tricarboxylic acid (rTCA) cycle and describe a modeling approach to quantify the uncertainty of this hypothesis due to the combinatorial aspect of the constituent chemical transformations. Our results suggest that a) rTCA cycle belongs to a degenerate optimum of auto-catalytic cycles, and b) the set of targets for investigations of the origin of the common metabolic core should be significantly extended.
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    Charge Tunneling along Short Oligoglycine Chains
    (Wiley-Blackwell, 2015) Baghbanzadeh, Mostafa; Bowers, Carleen; Rappoport, Dmitrij; Zaba, Tomasz; Gonidec, Mathieu; Al-Sayah, Mohammad; Cyganik, Piotr; Aspuru-Guzik, Alan; Whitesides, George
    This work examines charge transport (CT) through self-assembled monolayers (SAMs) of oligoglycines having an N-terminal cysteine group that anchors the molecule to a gold substrate, and demonstrate that CT is rapid (relative to SAMs of n-alkanethiolates). Comparisons of rates of charge transport-using junctions with the structure AuTS /SAM//Ga2 O3 /EGaIn (across these SAMs of oligoglycines, and across SAMs of a number of structurally and electronically related molecules) established that rates of charge tunneling along SAMs of oligoglycines are comparable to that along SAMs of oligophenyl groups (of comparable length). The mechanism of tunneling in oligoglycines is compatible with superexchange, and involves interactions among high-energy occupied orbitals in multiple, consecutive amide bonds, which may by separated by one to three methylene groups. This mechanistic conclusion is supported by density functional theory (DFT).
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    Characterizing the Metal–SAM Interface in Tunneling Junctions
    (American Chemical Society (ACS), 2015) Bowers, Carleen; Liao, Kung-ching; Zaba, Tomasz; Rappoport, Dmitrij; Baghbanzadeh, Mostafa; Breiten, Benjamin; Krzykawska, Anna; Cyganik, Piotr; Whitesides, George
    his paper investigates the influence of the interface between a gold or silver metal electrode and an n-alkyl SAM (supported on that electrode) on the rate of charge transport across junctions with structure Met(Au or Ag)TS/A(CH2)nH//Ga2O3/EGaIn by comparing measurements of current density, J(V), for Met/AR = Au/thiolate (Au/SR), Ag/thiolate (Ag/SR), Ag/carboxylate (Ag/O2CR), and Au/acetylene (Au/C≡CR), where R is an n-alkyl group. Values of J0 and β (from the Simmons equation) were indistinguishable for these four interfaces. Since the anchoring groups, A, have large differences in their physical and electronic properties, the observation that they are indistinguishable in their influence on the injection current, J0 (V = 0.5) indicates that these four Met/A interfaces do not contribute to the shape of the tunneling barrier in a way that influences J(V).