Dmitrij Rappoport—Beta Living Through Theoretical Chemistry

Taking on some hard problems in chemistry through new algorithms, tool making, and computation.

Chemical Heuristics in the 21st Century

Chemical heuristics in the esterification reaction
Chemical heuristics in the esterification reaction (right). The elementary reaction steps are represented in terms of bond breaking () and bond making () heuristics. The kinetic feasibility is derived from the energy profile (left) using the arc heuristic criterion Wa (bottom).

Networked Chemistry

Formose reaction network
Some products of the formose reaction  HOCH2CH=O + CH2=O (left). The network of the formose reaction  HOCH2CH=O + 2 CH2=O in the transition network (TN) representation (right).

Conducting Molecules

Tunneling conductance in Cys(Gly)<sub>n</sub> oligopeptides
Model for tunneling conductance in CysGlyn oligopeptide series (left). The highest occupied molecular orbitals (HOMOs) are localized on the S atoms (green). The in-plane peptide bond orbitals are predominantly localized on the C=O groups (red), while the out-of-plane peptide bond orbitals are found on the N atoms (blue). The superexchange model (bottom) predicts a characteristic splitting of the orbital energies (right) for the in-plane (red) and out-of-plane (blue) peptide bond orbitals.

Encoding 3D Molecular Structure

Structure encoding using Morton's Z-curve
Structure encoding of the H2O2 molecule using Morton's Z-curve (top). Schematic representation of the encoding of the four-dimensional space (q, r, θ, and ϕ) using Morton's Z-curve (bottom).

Journals and Book Chapters

  1. Rappoport, D.; Furche, F. Photoinduced intramolecular charge transfer in 4-(dimethyl)-aminobenzonitrile—A theoretical perspective. J. Am. Chem. Soc. , 126, 1277–1284.
  2. Bark, T.; Zelewsky, von, A.; Rappoport, D.; Neuburger, M.; Schaffner, S.; Lacour, J.; Jodry, J. Synthesis and stereochemical properties of chiral square complexes of iron(II). Chem. Eur. J. , 10, 4839–4845.
  3. Rappoport, D.; Furche, F. Analytical time-dependent density functional derivative methods within the RI–J approximation, an approach to excited states of large molecules. J. Chem. Phys. , 122, 064105.
  4. Furche, F.; Rappoport, D. Density functional methods for excited states: Equilibrium structure and electronic spectra. In Computational Photochemistry; Olivucci, M., Ed.; Elsevier: Amsterdam, , pp. 93-128.
  5. Rappoport, D.; Furche, F. Excited States and Photochemistry. In Time-Dependent Density Functional Theory; Marques, M. A. L.; Ullrich, C. A.; Nogueira, F.; Rubio, A.; Burke, K.; Gross, E. K. U., Eds.; Springer: Berlin, Heidelberg, , pp. 337–354.
  6. Rappoport, D.; Furche, F. Lagrangian approach to molecular vibrational Raman intensities using time-dependent hybrid density functional theory. J. Chem. Phys. , 126, 201104.
  7. Chow, H. S.; Constable, E. C.; Frantz, R.; Housecroft, C. E.; Lacour, J.; Neuburger, M.; Rappoport, D.; Schaffner, S. Conformationally-locked metallomacrocycles—Prototypes for a novel type of axial chirality. New J. Chem. , 33, 376–385.
  8. Rappoport, D., Furche, F. Structure of Endohedral Fullerene Eu@C74. Phys. Chem. Chem. Phys. , 11, 6353–6358.
  9. Rappoport, D.; Crawford, N. R. M.; Furche, F.; Burke, K. Approximate Density Functionals: Which Should I Choose? In Encyclopedia of Inorganic Chemistry. Computational Inorganic and Bioinorganic Chemistry; Solomon, E. I.; King, R. B.; Scott, R. A., Eds.; Wiley: Chichester, , pp. 159–172.
  10. Saikin, S. K.; Olivares-Amaya, R.; Rappoport, D.; Stopa, M.; Aspuru-Guzik, A. On the chemical bonding effects in the Raman response: Benzenethiol adsorbed on silver clusters. Phys. Chem. Chem. Phys. , 11, 9401–9411.
  11. Rappoport, D.; Furche, F. Property-optimized Gaussian basis sets for molecular response calculations. J. Chem. Phys. , 133, 134105.
  12. Saikin, S. K.; Chu, Y.; Rappoport, D.; Crozier, K. B.; Aspuru-Guzik, A. Separation of Electromagnetic and Chemical Contributions to Surface-Enhanced Raman Spectra on Nanoengineered Plasmonic Substrates. J. Phys. Chem. Lett. , 1, 2740–2746.
  13. Rappoport, D.; Shim, S.; Aspuru-Guzik, A. Simplified Sum-Over-States Approach for Predicting Resonance Raman Spectra. Application to Nucleic Acid Bases. J. Phys. Chem. Lett. , 2, 1254–1260.
  14. Parkhill, J. A.; Rappoport, D.; Aspuru-Guzik, A. Modeling Coherent Anti-Stokes Raman Scattering with Time-Dependent Density Functional Theory: Vacuum and Surface Enhancement. J. Phys. Chem. Lett. , 2, 1849–1854.
  15. Rappoport, D. Basis-set quality and basis-set bias in molecular property calculations. ChemPhysChem, , 12, 3404–3413.
  16. Watson, M. A.; Rappoport, D.; Lee, E. M. Y.; Olivares-Amaya, R.; Aspuru-Guzik, A. Electronic structure calculations in arbitrary electrostatic environments. J. Chem. Phys. , 136, 024101.
  17. Rappoport, D.; Hutter, J. Excited-State Properties and Dynamics. In Fundamentals of Time-Dependent Density Functional Theory; Marques, M. A. L.; Maitra, N. T.; Nogueira, F. M. S.; Gross, E. K. U.; Rubio, A., Eds.; Springer: Berlin Heidelberg, , pp. 317–336.
  18. Olivares-Amaya, R.; Rappoport, D.; Munoz, P. A.; Peng, P.; Mazur, E.; Aspuru-Guzik, A. Can Mixed-Metal Surfaces Provide an Additional Enhancement to SERS? J. Phys. Chem. C, , 116, 15568–15575.
  19. Widom, J. R.; Rappoport, D.; Perdomo-Ortiz, A.; Thomsen, H.; Johnson, N. P.; Hippel, von, P. H.; Aspuru-Guzik, A.; Marcus, A. H. Electronic transition moments of 6-methyl isoxanthopterin—A fluorescent analogue of the nucleic acid base guanine. Nucleic Acids Res., , 41, 995–1004.
  20. Widom, J. R.; Lee, W.; Perdomo-Ortiz, A.; Rappoport, D.; Molinski, T. F.; Aspuru-Guzik, A.; Marcus, A. H. Temperature-dependent conformations of a membrane supported zinc porphyrin tweezer by 2D fluorescence spectroscopy. J. Phys. Chem. A, , 117, 6171–6184.
  21. Lockett, M. R.; Lange, H.; Breiten, B.; Héroux, A.; Sherman, W.; Rappoport, D.; Yau, P. O.; Snyder, P. W.; Whitesides, G. M. The binding of benzoarylsulfonamide ligands to human carbonic anhydrase is insensitive to formal fluorination of the ligand. Angew. Chem. Int. Ed., , 52, 7714–7717.
  22. Rappoport, D.; Galvin, C. J.; Zubarev, D. Yu.; Aspuru-Guzik, A. Complex chemical reaction networks from heuristics-aided quantum chemistry. J. Chem. Theory Comput., , 10, 897–907.
  23. Bowers, C. M.; Liao, K.-C.; Yoon, H. J.; Rappoport, D.; Baghbanzadeh, M.; Simeone, F. C; Whitesides, G. M. Introducing ionic and/or hydrogen bonds into the SAM//Ga2O3 top-interface of AgTS/S(CH2)nT//Ga2O3/EGaIn junctions. Nano Lett., , 14, 3521–3526.
  24. Cabalo, J. B.; Saikin, S. K.; Emmons, E. D.; Rappoport, D; Aspuru-Guzik, A. A state-by-state investigation of destructive interference in resonance Raman spectra of neutral tyrosine and tyrosinate anion with the simplified sum-over-states approach. J. Phys. Chem. A, , 118, 9675–9686.
  25. Jinich, A.; Rappoport, D.; Dunn, I.; Sanchez-Lengeling, B.; Olivares-Amaya, R.; Noor, E.; Bar Even; A.; Aspuru-Guzik, A. Quantum chemical approach to estimating the thermodynamics of metabolic reactions. Sci. Rep., , 4, 7022.
  26. Hellweg, A.; Rappoport, D. Development of new auxiliary basis functions of the Karlsruhe segmented contracted basis sets including diffuse basis functions (def2-SVPD, def2-TZVPPD, and def2-QVPPD) for RI-MP2 and RI-CC calculations. Phys. Chem. Chem. Phys, , 17, 1010–1017.
  27. Bowers, C. M.; Liao, K.-C.; Żaba, T.; Rappoport, D.; Breiten, B.; Baghbanzadeh, M.; Krzykawska, A.; Cyganik, P.; Whitesides, G. M. Characterizing the metal–SAM interface in tunneling junctions. ACS Nano, , 9, 1471–1477.
  28. Zubarev, D. Yu.; Rappoport, D.; Aspuru-Guzik, A. Uncertainty of prebiotic scenarios: The case of the non-enzymatic reverse tricarboxylic acid cycle. Sci. Rep., , 5, 8009.
  29. Baghbanzadeh, M.; Bowers, C. M.; Rappoport, D.; Żaba, T.; Gonidec, M.; Al-Sayah, M. H.; Cyganik, P.; Whitesides, G. M. Charge tunneling along short oligoglycine chains. Angew. Chem. Int. Ed., , 54, 14743–14747.
  30. Bowers, C. M.; Rappoport, D.; Baghbanzadeh, M.; Simeone, F. C.; Liao, K.-C.; Semenov, S. N.; Żaba, T.; Cyganik, P.; Aspuru-Guzik, A.; Whitesides, G. M. Tunneling across SAMs containing oligophenyl groups. J. Phys. Chem. C, , 120, 11331–11337.
  31. Markovich, T.; Blood-Forsythe, M.; Rappoport, D.; Kim, D.; Aspuru-Guzik, A. Calibration of the many-body dispersion range-separation parameter. , arXiv:1605.04987.
  32. Jasrasaria, D.; Pyzer-Knapp, E. O.; Rappoport, D.; Aspuru-Guzik, A. Space-filling curves as a novel crystal structure representation for machine learning models. , arXiv:1608.05747.
  33. Baghbanzadeh, M.; Bowers, C. M.; Rappoport, D.; Zaba, T.; Yuan, L.; Kang, K.; Liao, K.-C.; Gonidec, M.; Rothemund, P.; Cyganik, P.; Aspuru-Guzik, A.; Whitesides, G. M. Anomalously Rapid Tunneling: Charge Transport across SAMs of Oligoethylene Glycol. J. Am. Chem. Soc. .

Scientific Presentations

  1. Practical aspects of molecular TDDFT calculations. 2nd International Workshop on TDDFT, , Benasque (Spain).
  2. Computational aspects of molecular TDDFT calculations. University of Illinois, , Urbana-Champaign, IL.
  3. Optimized Gaussian basis sets for linear and nonlinear response properties. 44th Symposium on Theoretical Chemistry, , Ramsau (Austria).
  4. TDDFT in chemistry and biochemistry III and IV. TDDFT Winter School, , Benasque (Spain).
  5. New approaches to analysis of resonant Raman spectra. 240th ACS National Meeting, , Boston, MA.
  6. Optimized basis sets and accuracy of electronic excitation energies in molecules. 242th ACS National Meeting, , Denver, CO.
  7. Prediction of coherent anti-stokes Raman (CARS) and surface-enhanced CARS spectra using density functional theory. 242th ACS National Meeting, , Denver, CO.
  8. Parametrized exciton dynamics in multichromophoric aggregates. 48th Symposium on Theoretical Chemistry, , Karlsruhe (Germany).
  9. New theoretical approaches to resonant and nonlinear Raman spectroscopies. Edgewood Chemical Biological Center, , Edgewood, MD.
  10. Construction and properties of prebiotic chemical reaction networks. 248th ACS National Meeting, , San Francisco, CA.
  11. Reaction networks. A simplification attempt. Advanced Methods for De Novo Prediction Of Chemical Reaction Networks Workshop, , Telluride, CO.

Open-Source Code

  1. colibri is your lightweight and gregarious chemistry explorer.
  2. molz is an experimental molecular structure encoder using Morton's space-filling curve.