David Hennessey Waldeck

Publications (3)17.79 Total impact

• Article: The Effect of Oxygen Heteroatoms on the Single Molecule Conductance of Saturated Chains.

  Emil Wierzbinski, Xing Yin, Keith Werling, David Hennessey Waldeck
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  ABSTRACT: Single molecule conductance measurements on alkanedithiols and alkoxydithiols (dithiolated oligoethers) were performed using the STM-controlled Break Junction method in order to ascertain how the oxygen heteroatoms in saturated linear chains impact the molecular conductance. The experimental results show that the difference in conductance increases with chain length, over the range studied. Comparisons with electronic structure calculations and previous work on alkanes indicate that the conductance of the oligoethers is lower than that of alkane chains with the same length. Electronic structure calculations allow the difference in the conductance of these two families of molecules to be traced to differences in the spatial distribution of the molecular orbitals that contribute most to the conductance. A pathway analysis of the electronic coupling through the chain is used to explain how the difference in conductance between the alkane and oligoether molecules depends on the chain length.
  The Journal of Physical Chemistry B 10/2012; · 3.70 Impact Factor
• Article: Effect of backbone flexibility on charge transfer rates in peptide nucleic acid duplexes.

  Emil Wierzbinski, Arnie de Leon, Xing Yin, Alexander Balaeff, Kathryn L Davis, Srinivas Reppireddy, Ravindra Venkatramani, Shahar Keinan, Danith H Ly, Marcela Madrid, David N Beratan, Catalina Achim, David H Waldeck
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  ABSTRACT: Charge transfer (CT) properties are compared between peptide nucleic acid structures with an aminoethylglycine backbone (aeg-PNA) and those with a γ-methylated backbone (γ-PNA). The common aeg-PNA is an achiral molecule with a flexible structure, whereas γ-PNA is a chiral molecule with a significantly more rigid structure than aeg-PNA. Electrochemical measurements show that the CT rate constant through an aeg-PNA bridging unit is twice the CT rate constant through a γ-PNA bridging unit. Theoretical calculations of PNA electronic properties, which are based on a molecular dynamics structural ensemble, reveal that the difference in the CT rate constant results from the difference in the extent of backbone fluctuations of aeg- and γ-PNA. In particular, fluctuations of the backbone affect the local electric field that broadens the energy levels of the PNA nucleobases. The greater flexibility of the aeg-PNA gives rise to more broadening, and a more frequent appearance of high-CT rate conformations than in γ-PNA.
  Journal of the American Chemical Society 04/2012; 134(22):9335-42. · 9.91 Impact Factor
• Article: Charge transfer through modified peptide nucleic acids.

  Emil Wierzbinski, Arnie de Leon, Kathryn L Davis, Silvia Bezer, Matthäus A Wolak, Matthew J Kofke, Rudy Schlaf, Catalina Achim, David H Waldeck
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  ABSTRACT: We studied the charge transfer properties of bipyridine-modified peptide nucleic acid (PNA) in the absence and presence of Zn(II). Characterization of the PNA in solution showed that Zn(II) interacts with the bipyridine ligands, but the stability of the duplexes was not affected significantly by the binding of Zn(II). The charge transfer properties of these molecules were examined by electrochemistry for self-assembled monolayers of ferrocene-terminated PNAs and by conductive probe atomic force microscopy for cysteine-terminated PNAs. Both electrochemical and single molecular studies showed that the bipyridine modification and Zn(II) binding do not affect significantly the charge transfer of the PNA duplexes.
  Langmuir 01/2012; 28(4):1971-81. · 4.19 Impact Factor