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Tamblyn I.,University of Ontario Institute of Technology | Refaely-Abramson S.,Weizmann Institute of Science | Neaton J.B.,Lawrence Berkeley National Laboratory | Neaton J.B.,University of California at Berkeley | And 2 more authors.
Journal of Physical Chemistry Letters | Year: 2014

A self-consistent optimally tuned range-separated hybrid density functional (scOT-RSH) approach is developed. It can simultaneously predict accurate geometries, vibrational modes, and frontier orbital energies. This is achieved by optimizing the range-separation parameter, γ to both satisfy the ionization energy theorem and minimize interatomic forces. We benchmark our approach against an established hybrid functional, B3LYP, using the G2 test set. scOT-RSH greatly improves the accuracy of occupied frontier orbital energies, with a mean absolute error (MAE) of only 0.2 eV relative to experimental ionization energies compared to 2.96 eV with B3LYP. Geometries do not change significantly compared to those obtained from B3LYP, with a bond length MAE of 0.012 Å compared to 0.008 Å for B3LYP, and a 6.5% MAE for zero-point energies, slightly larger than that of B3LYP (3.1%). scOT-RSH represents a new paradigm in which accurate geometries and ionization energies can be predicted simultaneously from a single functional approach. © 2014 American Chemical Society.

Xia J.,Columbia University | Dell E.J.,Columbia University | Liu Z.-F.,Lawrence Berkeley National Laboratory | Neaton J.B.,Lawrence Berkeley National Laboratory | And 3 more authors.
Nature Nanotechnology | Year: 2015

Molecular electronics aims to miniaturize electronic devices by using subnanometre-scale active components. A single-molecule diode, a circuit element that directs current flow, was first proposed more than 40years ago and consisted of an asymmetric molecule comprising a donor-bridge-acceptor architecture to mimic a semiconductor p-n junction. Several single-molecule diodes have since been realized in junctions featuring asymmetric molecular backbones, molecule-electrode linkers or electrode materials. Despite these advances, molecular diodes have had limited potential for applications due to their low conductance, low rectification ratios, extreme sensitivity to the junction structure and high operating voltages. Here, we demonstrate a powerful approach to induce current rectification in symmetric single-molecule junctions using two electrodes of the same metal, but breaking symmetry by exposing considerably different electrode areas to an ionic solution. This allows us to control the junction's electrostatic environment in an asymmetric fashion by simply changing the bias polarity. With this method, we reliably and reproducibly achieve rectification ratios in excess of 200 at voltages as low as 370mV using a symmetric oligomer of thiophene-1,1-dioxide. By taking advantage of the changes in the junction environment induced by the presence of an ionic solution, this method provides a general route for tuning nonlinear nanoscale device phenomena, which could potentially be applied in systems beyond single-molecule junctions. © 2015 Macmillan Publishers Limited.

Meji Y.X.,University of California at Berkeley | Meji Y.X.,Max Planck Institute for Biophysical Chemistry | Nudler E.,Howard Hughes Medical Institute | Bustamante C.,University of California at Berkeley | And 2 more authors.
Proceedings of the National Academy of Sciences of the United States of America | Year: 2015

Two components of the RNA polymerase (RNAP) catalytic center, the bridge helix and the trigger loop (TL), have been linked with changes in elongation rate and pausing. Here, single molecule experiments with the WT and two TL-tip mutants of the Escherichia coli enzyme reveal that tip mutations modulate RNAP's pause-free velocity, identifying TL conformational changes as one of two rate-determining steps in elongation. Consistent with this observation, we find a direct correlation between helix propensity of the modified amino acid and pause-free velocity. Moreover, nucleotide analogs affect transcription rate, suggesting that their binding energy also influences TL folding. A kinetic model in which elongation occurs in two steps, TL folding on nucleoside triphosphate (NTP) binding followed by NTP incorporation/pyrophosphate release, quantitatively accounts for these results. The TL plays no role in pause recovery remaining unfolded during a pause. This model suggests a finely tuned mechanism that balances transcription speed and fidelity.

Coto P.B.,Friedrich - Alexander - University, Erlangen - Nuremberg | Sharifzadeh S.,Lawrence Berkeley National Laboratory | Neaton J.B.,Lawrence Berkeley National Laboratory | Neaton J.B.,University of California at Berkeley | And 2 more authors.
Journal of Chemical Theory and Computation | Year: 2015

The lowest-lying electronic excited states of pentacene and its oligomers are investigated using accurate multireference wave function methods (CASPT2/CASSCF) and the many-body Greenss function approach (GW/BSE). The results obtained for dimers and trimers of different geometry reveal a complex electronic structure, which includes locally excited, charge transfer, and multiexciton states. For singlets of single-excitation character, both approaches yield excitation energies that are in good overall quantitative agreement. While the multiexciton states are located relatively high in energy in all systems investigated, charge transfer states exist in close proximity to the lowest-lying absorbing states. The implications of the results for the mechanisms of singlet fission in pentacene are discussed. © 2014 American Chemical Society.

Liu Z.-F.,Lawrence Berkeley National Laboratory | Wei S.,Columbia University | Yoon H.,Yonsei University | Adak O.,Columbia University | And 8 more authors.
Nano Letters | Year: 2014

Using scanning tunneling microscope break-junction experiments and a new first-principles approach to conductance calculations, we report and explain low-bias charge transport behavior of four types of metal-porphyrin-gold molecular junctions. A nonequilibrium Green's function approach based on self-energy corrected density functional theory and optimally tuned range-separated hybrid functionals is developed and used to understand experimental trends quantitatively. Importantly, due to the localized d states of the porphyrin molecules, hybrid functionals are essential for explaining measurements; standard semilocal functionals yield qualitatively incorrect results. Comparing directly with experiments, we show that the conductance can change by nearly a factor of 2 when different metal cations are used, counter to trends expected from gas-phase ionization energies which are relatively unchanged with the metal center. Our work explains the sensitivity of the porphyrin conductance with the metal center via a detailed and quantitative portrait of the interface electronic structure and provides a new framework for understanding transport quantitatively in complex junctions involving molecules with localized d states of relevance to light harvesting and energy conversion. © 2014 American Chemical Society.

Poloni R.,CNRS Materials Science and Engineering | Poloni R.,University of California at Berkeley | Poloni R.,Lawrence Berkeley National Laboratory | Lee K.,University of California at Berkeley | And 6 more authors.
Journal of Physical Chemistry Letters | Year: 2014

Using van der Waals-corrected density functional theory and a local chemical bond analysis, we study and explain trends in the binding between CO2 and open-metal coordination sites within a series of two metal-organic frameworks (MOFs), BTT, and MOF-74 for Ca, Mg, and nine divalent transition-metal cations. We find that Ti and V result in the largest CO 2 binding energies and show that for these cations the CO2 binding energies for both structure types are twice the value expected based on pure electrostatics. We associate this behavior with the specific electronic configuration of the divalent cations and symmetry of the metal coordination site upon CO2 binding, which result in empty antibonding orbitals between CO2 and the metal cation. We demonstrate that a chemical bond analysis and electrostatic considerations can be used to predict trends of CO2 binding affinities to MOFs with transition-metal cations. © 2014 American Chemical Society.

Sharifzadeh S.,Lawrence Berkeley National Laboratory | Sharifzadeh S.,Boston University | Wong C.Y.,University of California at Berkeley | Wu H.,University of California at Berkeley | And 8 more authors.
Advanced Functional Materials | Year: 2015

Theory and experiment are combined to investigate the nature of low-energy excitons within ordered domains of 6,13-bis(triisopropylsilylethynyl)-pentacene (TIPS-PEN) polycrystalline thin films. First-principles density functional theory and many-body perturbation theory calculations, along with polarization-dependent optical absorption spectro-microscopy on ordered domains, show multiple low-energy absorption peaks that are composed of excitonic states delocalized over several molecules. While the first absorption peak is composed of a single excitonic transition and retains the polarization-dependent behavior of the molecule, higher energy peaks are composed of multiple transitions with optical properties that can not be described by those of the molecule. The predicted structure-dependence of polarization-dependent absorption reveals the exact inter-grain orientation within the TIPS-PEN film. Additionally, the degree of exciton delocalization can be significantly tuned by modest changes in the solid-state structure and the spatial extent of the excitations along a given direction is correlated with the degree of electronic dispersion along the same direction. These findings pave the way for tailoring the singlet fission efficiency of organic crystals by solid-state structure. © 2014 Wiley-VCH Verlag GmbH & Co. KGaA.

Goldman D.H.,University of California at Berkeley | Kaiser C.M.,University of California at Berkeley | Kaiser C.M.,Johns Hopkins University | Milin A.,University of California at Berkeley | And 6 more authors.
Science | Year: 2015

Protein synthesis rates can affect gene expression and the folding and activity of the translation product. Interactions between the nascent polypeptide and the ribosome exit tunnel represent one mode of regulating synthesis rates. The SecM protein arrests its own translation, and release of arrest at the translocon has been proposed to occur by mechanical force. Using optical tweezers, we demonstrate that arrest of SecM-stalled ribosomes can indeed be rescued by force alone and that the force needed to release stalling can be generated in vivo by a nascent chain folding near the ribosome tunnel exit. We formulate a kinetic model describing how a protein can regulate its own synthesis by the force generated during folding, tuning ribosome activity to structure acquisition by a nascent polypeptide. © 2015, American Association for the Advancement of Science. All rights reserved.

Lee K.,Lawrence Berkeley National Laboratory | Lee K.,University of California at Berkeley | Howe J.D.,Lawrence Berkeley National Laboratory | Howe J.D.,University of California at Berkeley | And 7 more authors.
Chemistry of Materials | Year: 2015

Using density functional theory, we systematically compute and investigate the binding enthalpies of 14 different small molecules in a series of isostructural metal-organic frameworks, M-MOF-74, with M = Mg, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, and Zn. The small molecules we consider include major flue-gas components, trace gases, and small hydrocarbons, i.e., H2, CO, CO2, H2O, H2S, N2, NH3, SO2, CH4, C2H2, C2H4, C2H6, C3H6, and C3H8. In total, the adsorption energetics of 140 unique systems are presented and discussed. Dispersion interactions are included by employing a nonlocal van der Waals density functional, vdW-DF2. Hubbard U corrections are applied to the localized d electrons of transition metal atoms, and the impact of such corrections is assessed quantitatively. For systems for which measured binding enthalpies have been reported, our calculations lead to excellent overall agreement with experimentally determined structures and isosteric heats of adsorption. For systems that have yet to be realized or characterized, this study provides quantitative predictions, establishes a better understanding of the role of different transition-metal cations in small-molecule binding at open-metal sites, and identifies routes for predicting potential candidates for energy-related gas-separation applications. For example, we predict that Cu-MOF-74 will exhibit selectivity of CO2 over H2O and that Mn-MOF-74 can be used to separate trace flue-gas impurities and toxic gases from gas mixtures. © 2014 American Chemical Society.

Egger D.A.,Weizmann Institute of Science | Liu Z.-F.,Lawrence Berkeley National Laboratory | Neaton J.B.,Lawrence Berkeley National Laboratory | Neaton J.B.,University of California at Berkeley | And 2 more authors.
Nano Letters | Year: 2015

A key quantity for molecule-metal interfaces is the energy level alignment of molecular electronic states with the metallic Fermi level. We develop and apply an efficient theoretical method, based on density functional theory (DFT) that can yield quantitatively accurate energy level alignment information for physisorbed metal-molecule interfaces. The method builds on the "DFT+Σ" approach, grounded in many-body perturbation theory, which introduces an approximate electron self-energy that corrects the level alignment obtained from conventional DFT for missing exchange and correlation effects associated with the gas-phase molecule and substrate polarization. Here, we extend the DFT+Σ approach in two important ways: first, we employ optimally tuned range-separated hybrid functionals to compute the gas-phase term, rather than rely on GW or total energy differences as in prior work; second, we use a nonclassical DFT-determined image-charge plane of the metallic surface to compute the substrate polarization term, rather than the classical DFT-derived image plane used previously. We validate this new approach by a detailed comparison with experimental and theoretical reference data for several prototypical molecule-metal interfaces, where excellent agreement with experiment is achieved: benzene on graphite (0001), and 1,4-benzenediamine, Cu-phthalocyanine, and 3,4,9,10-perylene-tetracarboxylic-dianhydride on Au(111). In particular, we show that the method correctly captures level alignment trends across chemical systems and that it retains its accuracy even for molecules for which conventional DFT suffers from severe self-interaction errors. (Figure Presented). © 2015 American Chemical Society.

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