Browsing by Author "Rappoport, Dmitrij"

Now showing items 1-18 of 18

    • Anomalously Rapid Tunneling: Charge Transport across Self-Assembled Monolayers of Oligo(ethylene glycol) 

      Baghbanzadeh, Mostafa; Bowers, Carleen M.; Rappoport, Dmitrij; ?aba, Tomasz; Yuan, Li; Kang, Kyungtae; Liao, Kung-Ching; Gonidec, Mathieu; Rothemund, Philipp Josef Michael; Cyganik, Piotr; Aspuru-Guzik, Alan; Whitesides, George McClelland (American Chemical Society (ACS), 2017)
      This paper describes charge transport by tunneling across self-assembled monolayers (SAMs) of thiol-terminated derivatives of oligo(ethylene glycol) (HS(CH2CH2O)nCH3; HS(EG)nCH3); these SAMs are positioned between gold ...

    • The Binding of Benzoarylsulfonamide Ligands to Human Carbonic Anhydrase is Insensitive to Formal Fluorination of the Ligand 

      Lockett, Matthew R.; Lange, Heiko; Breiten, Benjamin; Heroux, Annie; Sherman, Woody; Rappoport, Dmitrij; Yau, Patricia O.; Snyder, Philip W.; Whitesides, George McClelland (Wiley-VCH Verlag Berlin, 2013)
      Auf das Wasser kommt es an: Konservierte Bindungsgeometrie, enthalpiegetriebene Bindungsweise und nichtunterscheidbare Bindungsaffinitäten für fluorierte und nichtfluorierte Liganden von humaner Carbonsäureanhydrase (siehe ...

    • Can Mixed-Metal Surfaces Provide an Additional Enhancement to SERS? 

      Olivares-Amaya, Roberto; Rappoport, Dmitrij; Munoz, Philip Alejandro; Peng, Paul; Mazur, Eric; Aspuru-Guzik, Alan (American Chemical Society, 2012)
      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 ...

    • Characterizing the Metal–SAM Interface in Tunneling Junctions 

      Bowers, Carleen Morris; Liao, Kung-ching; Zaba, Tomasz; Rappoport, Dmitrij; Baghbanzadeh, Mostafa; Breiten, Benjamin; Krzykawska, Anna; Cyganik, Piotr; Whitesides, George McClelland (American Chemical Society (ACS), 2015)
      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 ...

    • Charge Tunneling along Short Oligoglycine Chains 

      Baghbanzadeh, Mostafa; Bowers, Carleen Morris; Rappoport, Dmitrij; Zaba, Tomasz; Gonidec, Mathieu; Al-Sayah, Mohammad; Cyganik, Piotr; Aspuru-Guzik, Alan; Whitesides, George McClelland (Wiley-Blackwell, 2015)
      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 ...

    • Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry 

      Rappoport, Dmitrij; Galvin, Cooper J.; Zubarev, Dmitry; Aspuru-Guzik, Alan (American Chemical Society (ACS), 2014)
      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 ...

    • Electronic Structure Calculations in Arbitrary Electrostatic Environment 

      Watson, Mark A.; Rappoport, Dmitrij; Lee, Elizabeth M. Y.; Olivares-Amaya, Roberto; Aspuru-Guzik, Alan (American Institute of Physics, 2012)
      Modeling of electronic structure of molecules in electrostatic environments is of considerable relevance for surface-enhanced spectroscopy and molecular electronics. We have developed and implemented a novel approach to ...

    • Electronic Transition Moments of 6-methyl Isoxanthopterin—A Fluorescent Analogue of the Nucleic Acid Base Guanine 

      Widom, Julia; Rappoport, Dmitrij; Perdomo-Ortiz, Alejandro; Thomsen, Hanna; Johnson, Neil P.; von Hippel, Peter H.; Aspuru-Guzik, Alan; Marcus, Andrew H. (Oxford University Press, 2012)
      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 ...

    • Introducing Ionic and/or Hydrogen Bonds into the SAM//Ga 2 O 3 Top-Interface of Ag TS /S(CH 2 ) n T//Ga 2 O 3 /EGaIn Junctions 

      Bowers, Carleen Morris; Liao, Kung-ching; Yoon, Hyo Jae; Rappoport, Dmitrij; Baghbanzadeh, Mostafa; Simeone, Felice C.; Whitesides, George McClelland (American Chemical Society (ACS), 2014)
      Junctions with the structure AgTS/S(CH2)nT//Ga2O3/EGaIn (where S(CH2)nT is a self-assembled monolayer, SAM, of n-alkanethiolate bearing a terminal functional group T) make it possible to examine the response of rates of ...

    • Modeling Coherent Anti-Stokes Raman Scattering with Time-Dependent Density Functional Theory: Vacuum and Surface Enhancement 

      Parkhill, John Anthony; Rappoport, Dmitrij; Aspuru-Guzik, Alan (American Chemical Society, 2011)
      We present the first density functional simulations of coherent anti-Stokes Raman scattering (CARS) and an analysis of the chemical effects upon binding to a metal surface. Spectra are obtained from first-principles ...

    • On the Chemical Bonding Effects in the Raman Response: Benzenethiol Adsorbed on Silver Clusters 

      Saikin, Semion K.; Olivares-Amaya, Roberto; Rappoport, Dmitrij; Stopa, Michael; Aspuru-Guzik, Alán (Royal Society of Chemistry, 2009)
      We study the effects of chemical bonding on Raman scattering from benzenethiol chemisorbed on silver clusters using time-dependent density functional theory (TDDFT). Raman scattering cross sections are computed using a ...

    • Quantum Chemical Approach to Estimating the Thermodynamics of Metabolic Reactions 

      Jinich, Adrian; Rappoport, Dmitrij; Dunn, Ian; Sanchez-Lengeling, Benjamin; Olivares-Amaya, Roberto; Noor, Elad; Even, Arren Bar; Aspuru-Guzik, Alan (Nature Publishing Group, 2014)
      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 ...

    • Separation of Electromagnetic and Chemical Contributions to Surface-Enhanced Raman Spectra on Nanoengineered Plasmonic Substrates 

      Saikin, Semion K.; Chu, Yizhuo; Rappoport, Dmitrij; Crozier, Kenneth B.; Aspuru-Guzik, Alán (American Chemical Society, 2010)
      Raman signals from molecules adsorbed on a noble metal surface are enhanced by many orders of magnitude due to the plasmon resonances of the substrate. Additionally, the enhanced spectra are modified compared to the spectra ...

    • Simplified Sum-Over-States Approach for Predicting Resonance Raman Spectra. Application to Nucleic Acid Bases 

      Rappoport, Dmitrij; Shim, Sangwoo; Aspuru-Guzik, Alan (American Chemical Society, 2011)
      Resonance Raman spectra provide a valuable probe into molecular excited-state structures and properties. Moreover, resonance enhancement is of importance for the chemical contribution to surface-enhanced Raman scattering. ...

    • 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 

      Cabalo, Jerry B.; Saikin, Semion K.; Emmons, Erik D.; Rappoport, Dmitrij; Aspuru-Guzik, Alan (American Chemical Society (ACS), 2014)
      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 ...

    • Temperature-Dependent Conformations of a Membrane Supported Zinc Porphyrin Tweezer by 2D Fluorescence Spectroscopy 

      Widom, Julia R.; Lee, Wonbae; Perdomo-Ortiz, Alejandro; Rappoport, Dmitrij; Molinski, Tadeusz F.; Aspuru-Guzik, Alan; Marcus, Andrew H. (American Chemical Society (ACS), 2013)
      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 ...

    • Tunneling across SAMs Containing Oligophenyl Groups 

      Bowers, Carleen; Rappoport, Dmitrij; Baghbanzadeh, Mostafa; Simeone, Felice; Liao, Kung-ching; Semenov, Sergey N.; Zaba, Tomasz; Cyganik, Piotr; Aspuru-Guzik, Alan; Whitesides, George McClelland (American Chemical Society (ACS), 2016)
      This paper describes rates of charge tunneling across self-assembled monolayers (SAMs) of compounds containing oligophenyl groups, supported on gold and silver, using Ga2O3/EGaIn as the top electrode. It compares the ...

    • Uncertainty of Prebiotic Scenarios: The Case of the Non-Enzymatic Reverse Tricarboxylic Acid Cycle 

      Zubarev, Dmitry Yu; Rappoport, Dmitrij; Aspuru-Guzik, Alán (Nature Publishing Group, 2015)
      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 ...