Ravindra Venkatramani - Academia.edu (original) (raw)
Uploads
Papers by Ravindra Venkatramani
Journal of the American Chemical Society, 2009
Self-assembled monolayers of single-stranded (ss) peptide nucleic acids (PNAs) containing seven n... more Self-assembled monolayers of single-stranded (ss) peptide nucleic acids (PNAs) containing seven nucleotides (TTTXTTT), a C-terminus cysteine, and an N-terminus ferrocene redox group were formed on gold electrodes. The PNA monomer group (X) was selected to be either cytosine (C), thymine (T), adenine (A), guanine (G), or a methyl group (Bk). The charge transfer rate through the oligonucleotides was found to correlate with the oxidation potential of X. Kinetic measurements and computational studies of the ss-PNA fragments show that a nucleobase mediated charge transport mechanism in the deep tunneling superexchange regime can explain the observed dependence of the kinetics of charge transfer on the PNA sequence. Theoretical analysis suggests that the charge transport is dominantly hole-mediated and takes place through the filled bridge orbitals. The strongest contribution to conductance comes from the highest filled orbitals (HOMO, HOMO-1, and HOMO-2) of individual bases, with a rapid drop off in contributions from lower lying filled orbitals. Our studies further suggest that the linear correlation observed between the experimental charge transfer rates and the oxidation potential of base X arises from weak average interbase couplings and similar stacking geometries for the four TTTXTTT systems.
Springer Series in Chemical Physics, 2003
Biophysical Journal, 2017
Biophysical Journal, 2017
Biophysical Journal, 2016
Biophysical Journal, 2016
Biophysical Journal, 2016
Faraday Discussions, Nov 18, 2014
Faraday discussions, 2014
Faraday discussions, 2014
opened the discussion of the paper by Jenny Nelson: A viable explanation for the initial long-ran... more opened the discussion of the paper by Jenny Nelson: A viable explanation for the initial long-range charge separation step in organic photovoltaic cells is via extremely high non-equilibrium charge mobilities of charge pairs initially formed high in the density of states (DOS). In this model, charge separation would be enhanced by some degree of disorder, including possibly the disorder induced by the packing with the fullerene at the heterojunction.
The Journal of Physical Chemistry C, Aug 8, 2010
... Shahar Keinan*, Ravindra Venkatramani, Alexander Balaeff and David N. Beratan. Departments of... more ... Shahar Keinan*, Ravindra Venkatramani, Alexander Balaeff and David N. Beratan. Departments of Chemistry and Biochemistry, French Family Science Center, Duke University, Durham, North Carolina 27708. J. Phys. Chem. ...
Proceedings of Spie the International Society For Optical Engineering, Aug 1, 2009
We report experimental observations and theoretical modeling of an unusual photoelectric effect i... more We report experimental observations and theoretical modeling of an unusual photoelectric effect in deoxyribonucleic acid (DNA) thin-film devices, under visible and near-infrared illumination. The devices also show diode-type rectifying current-voltage (I-V) characteristics. An equivalent circuit model was constructed that fits the experimental data, and physical processes likely to arise in the devices are discussed. We envisage the formation of a Schottky barrier at the DNA film-metal interface and infer that the photoresponse arises from photoinjection of electrons from the metal into the DNA film.
Journal of the American Chemical Society, Jun 16, 2010
In molecular electronics, the linker group, which attaches the functional molecular core to the e... more In molecular electronics, the linker group, which attaches the functional molecular core to the electrode, plays a crucial role in determining the overall conductivity of the molecular junction. While much focus has been placed on optimizing molecular core conductivity, there have been relatively few attempts at designing optimal linker groups to metallic or semiconducting electrodes. The vast majority of molecular electronic studies use thiol linker groups; work probing alternative amine linker systems has only recently been explored. Here, we probe single-molecule conductances in phenylene-ethynylene molecules terminated with thiol and carbodithioate linkers, experimentally using STM break-junction methods and theoretically using a nonequilibrium Green's function approach. Experimental studies demonstrate that the carbodithioate linker augments electronic coupling to the metal electrode and lowers the effective barrier for charge transport relative to the conventional thiol linker, thus enhancing the conductance of the linker-phenylene-ethynylene-linker unit; these data underscore that phenylene-ethynylene-based structures are more highly conductive than originally appreciated in molecular electronics applications. The theoretical analysis shows that the nature of sulfur hybridization in these species is responsible for the order-of-magnitude increased conductance in carbodithioate-terminated systems relative to identical conjugated structures that feature classic thiol linkers, independent of the mechanism of charge transport. Interestingly, in these systems, the tunneling current is not dominated by the frontier molecular orbitals. While barriers <k(B)T are expected to produce low beta values, we show that the competition between tunneling and resonant transport processes allows barriers >k(B)T to produce the low beta values seen in our experiments. Taken together, these experimental and theoretical studies indicate a promising role for carbodithioate-based connectivity in molecular-scale electronics applications involving metallic and semiconducting electrodes.
F1000Research, 2013
The long term side effects of any newly introduced drug is a subject of intense research, and oft... more The long term side effects of any newly introduced drug is a subject of intense research, and often raging controversies. One such example is the dipeptidyl peptidase-IV (DPP4) inhibitor used for treating type 2 diabetes, which is inconclusively implicated in increased susceptibility to acute pancreatitis. Previously, based on a computational analysis of the spatial and electrostatic properties of active site residues, we have demonstrated that phosphoinositide-specific phospholipase C (PI-PLC) from is a Bacillus cereus prolyl peptidase using experiments. In the current work, we first report in vivo the inhibition of the native activity of PI-PLC by two DPP4 inhibitors -vildagliptin (LAF-237) and K-579. While vildagliptin inhibited PI-PLC at micromolar concentrations, K-579 was a potent inhibitor even at nanomolar concentrations. Subsequently, we queried a comprehensive, non-redundant set of 5000 human proteins (50% similarity cutoff) with known structures using serine protease (SPASE) motifs derived from trypsin and DPP4. A pancreatic lipase and a gastric lipase are among the proteins that are identified as proteins having promiscuous SPASE scaffolds that could interact with DPP4 inhibitors. The presence of such scaffolds in human lipases is expected since they share the same catalytic mechanism with PI-PLC. However our methodology also detects other proteins, often with a completely different enzymatic mechanism, that have significantly congruent domains with the SPASE motifs. The reported elevated levels of serum lipase, although contested, could be rationalized by inhibition of lipases reported here. In an effort to further our understanding of the spatial and electrostatic basis of DPP4 inhibitors, we have also done a comprehensive analysis of all 76 known DPP4 structures liganded to inhibitors
Public reporting burden for this collection of information is estimated to average I hour per res... more Public reporting burden for this collection of information is estimated to average I hour per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing and reviewing this collection of information. Send comments regarding this burden estimate or any other aspect of this collection of information, including suggestions for reducing this burden to Washington Headquarters Services, Directorate for Information Operations and Reports, 1215 Jefferson Davis Highway, Suite 1204, Arlington, VA 22202-4302, and to the Office of Management and Budget, Pa rwork Reduction Project (0704-0188), Washington, DC 20503
Journal of the American Chemical Society, 2009
Self-assembled monolayers of single-stranded (ss) peptide nucleic acids (PNAs) containing seven n... more Self-assembled monolayers of single-stranded (ss) peptide nucleic acids (PNAs) containing seven nucleotides (TTTXTTT), a C-terminus cysteine, and an N-terminus ferrocene redox group were formed on gold electrodes. The PNA monomer group (X) was selected to be either cytosine (C), thymine (T), adenine (A), guanine (G), or a methyl group (Bk). The charge transfer rate through the oligonucleotides was found to correlate with the oxidation potential of X. Kinetic measurements and computational studies of the ss-PNA fragments show that a nucleobase mediated charge transport mechanism in the deep tunneling superexchange regime can explain the observed dependence of the kinetics of charge transfer on the PNA sequence. Theoretical analysis suggests that the charge transport is dominantly hole-mediated and takes place through the filled bridge orbitals. The strongest contribution to conductance comes from the highest filled orbitals (HOMO, HOMO-1, and HOMO-2) of individual bases, with a rapid drop off in contributions from lower lying filled orbitals. Our studies further suggest that the linear correlation observed between the experimental charge transfer rates and the oxidation potential of base X arises from weak average interbase couplings and similar stacking geometries for the four TTTXTTT systems.
Springer Series in Chemical Physics, 2003
Biophysical Journal, 2017
Biophysical Journal, 2017
Biophysical Journal, 2016
Biophysical Journal, 2016
Biophysical Journal, 2016
Faraday Discussions, Nov 18, 2014
Faraday discussions, 2014
Faraday discussions, 2014
opened the discussion of the paper by Jenny Nelson: A viable explanation for the initial long-ran... more opened the discussion of the paper by Jenny Nelson: A viable explanation for the initial long-range charge separation step in organic photovoltaic cells is via extremely high non-equilibrium charge mobilities of charge pairs initially formed high in the density of states (DOS). In this model, charge separation would be enhanced by some degree of disorder, including possibly the disorder induced by the packing with the fullerene at the heterojunction.
The Journal of Physical Chemistry C, Aug 8, 2010
... Shahar Keinan*, Ravindra Venkatramani, Alexander Balaeff and David N. Beratan. Departments of... more ... Shahar Keinan*, Ravindra Venkatramani, Alexander Balaeff and David N. Beratan. Departments of Chemistry and Biochemistry, French Family Science Center, Duke University, Durham, North Carolina 27708. J. Phys. Chem. ...
Proceedings of Spie the International Society For Optical Engineering, Aug 1, 2009
We report experimental observations and theoretical modeling of an unusual photoelectric effect i... more We report experimental observations and theoretical modeling of an unusual photoelectric effect in deoxyribonucleic acid (DNA) thin-film devices, under visible and near-infrared illumination. The devices also show diode-type rectifying current-voltage (I-V) characteristics. An equivalent circuit model was constructed that fits the experimental data, and physical processes likely to arise in the devices are discussed. We envisage the formation of a Schottky barrier at the DNA film-metal interface and infer that the photoresponse arises from photoinjection of electrons from the metal into the DNA film.
Journal of the American Chemical Society, Jun 16, 2010
In molecular electronics, the linker group, which attaches the functional molecular core to the e... more In molecular electronics, the linker group, which attaches the functional molecular core to the electrode, plays a crucial role in determining the overall conductivity of the molecular junction. While much focus has been placed on optimizing molecular core conductivity, there have been relatively few attempts at designing optimal linker groups to metallic or semiconducting electrodes. The vast majority of molecular electronic studies use thiol linker groups; work probing alternative amine linker systems has only recently been explored. Here, we probe single-molecule conductances in phenylene-ethynylene molecules terminated with thiol and carbodithioate linkers, experimentally using STM break-junction methods and theoretically using a nonequilibrium Green's function approach. Experimental studies demonstrate that the carbodithioate linker augments electronic coupling to the metal electrode and lowers the effective barrier for charge transport relative to the conventional thiol linker, thus enhancing the conductance of the linker-phenylene-ethynylene-linker unit; these data underscore that phenylene-ethynylene-based structures are more highly conductive than originally appreciated in molecular electronics applications. The theoretical analysis shows that the nature of sulfur hybridization in these species is responsible for the order-of-magnitude increased conductance in carbodithioate-terminated systems relative to identical conjugated structures that feature classic thiol linkers, independent of the mechanism of charge transport. Interestingly, in these systems, the tunneling current is not dominated by the frontier molecular orbitals. While barriers <k(B)T are expected to produce low beta values, we show that the competition between tunneling and resonant transport processes allows barriers >k(B)T to produce the low beta values seen in our experiments. Taken together, these experimental and theoretical studies indicate a promising role for carbodithioate-based connectivity in molecular-scale electronics applications involving metallic and semiconducting electrodes.
F1000Research, 2013
The long term side effects of any newly introduced drug is a subject of intense research, and oft... more The long term side effects of any newly introduced drug is a subject of intense research, and often raging controversies. One such example is the dipeptidyl peptidase-IV (DPP4) inhibitor used for treating type 2 diabetes, which is inconclusively implicated in increased susceptibility to acute pancreatitis. Previously, based on a computational analysis of the spatial and electrostatic properties of active site residues, we have demonstrated that phosphoinositide-specific phospholipase C (PI-PLC) from is a Bacillus cereus prolyl peptidase using experiments. In the current work, we first report in vivo the inhibition of the native activity of PI-PLC by two DPP4 inhibitors -vildagliptin (LAF-237) and K-579. While vildagliptin inhibited PI-PLC at micromolar concentrations, K-579 was a potent inhibitor even at nanomolar concentrations. Subsequently, we queried a comprehensive, non-redundant set of 5000 human proteins (50% similarity cutoff) with known structures using serine protease (SPASE) motifs derived from trypsin and DPP4. A pancreatic lipase and a gastric lipase are among the proteins that are identified as proteins having promiscuous SPASE scaffolds that could interact with DPP4 inhibitors. The presence of such scaffolds in human lipases is expected since they share the same catalytic mechanism with PI-PLC. However our methodology also detects other proteins, often with a completely different enzymatic mechanism, that have significantly congruent domains with the SPASE motifs. The reported elevated levels of serum lipase, although contested, could be rationalized by inhibition of lipases reported here. In an effort to further our understanding of the spatial and electrostatic basis of DPP4 inhibitors, we have also done a comprehensive analysis of all 76 known DPP4 structures liganded to inhibitors
Public reporting burden for this collection of information is estimated to average I hour per res... more Public reporting burden for this collection of information is estimated to average I hour per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing and reviewing this collection of information. Send comments regarding this burden estimate or any other aspect of this collection of information, including suggestions for reducing this burden to Washington Headquarters Services, Directorate for Information Operations and Reports, 1215 Jefferson Davis Highway, Suite 1204, Arlington, VA 22202-4302, and to the Office of Management and Budget, Pa rwork Reduction Project (0704-0188), Washington, DC 20503
Metalloproteins carry out diverse biological functions including metal transport, electron transf... more Metalloproteins carry out diverse biological functions including metal transport, electron transfer, and catalysis. At present, the influence of metal cofactors on metalloprotein stability is not well understood. Here, we report the mechanical stability and unfolding pathway of azurin, a cupredoxin family protein with β-barrel topology and type I copper-binding centre. Single-molecule force spectroscopy (SMFS) experiments reveal 2-state and 3-state unfolding pathways for apo-azurin. The intermediate in the 3-state pathway occurs at an unfolding contour length of 7.5 nm from the native state. Steered molecular dynamics (SMD) simulations show that apo-azurin unfolds via a first transition state (TS) where β2Β–β8 and β7–β8 strand pairs rupture to form the intermediate, which subsequently unfolds by the collective rupture of remaining strands. SMFS experiments on holo-azurin exhibit an additional 4-state pathway besides the 2-state and 3-state pathways. The unfolding contour length leading to the first intermediate is 6.7 nm suggesting a sequestration of ~1 nm polypeptide chain length by the copper. SMD simulations reveal atomistic details of the copper sequestration and predict a combined β4–β7 pair and copper coordination sphere rupture to create the third TS in the 4-state pathway. Our systematic studies provide detailed mechanistic insights on modulation of protein mechanical properties by metal-cofactors.