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68 Publications visible to you, out of a total of 68
PSIXAS : A Psi4 plugin for efficient simulations of X‐ray absorption spectra based on the transition‐potential and Δ‐Kohn–Sham method

Abstract (Expand)

Near edge X‐ray absorption fine structure (NEXAFS) spectra and their pump‐probe extension (PP‐NEXAFS) offer insights into valence‐ and core‐excited states. We present PSIXAS, a recent implementation … for simulating NEXAFS and PP‐NEXAFS spectra by means of the transition‐potential and the Δ‐Kohn–Sham method. The approach is implemented in form of a software plugin for the Psi4 code, which provides access to a wide selection of basis sets as well as density functionals. We briefly outline the theoretical foundation and the key aspects of the plugin. Then, we use the plugin to simulate PP‐NEXAFS spectra of thymine, a system already investigated by others and us. It is found that larger, extended basis sets are needed to obtain more accurate absolute resonance positions. We further demonstrate that, in contrast to ordinary NEXAFS simulations, where the choice of the density functional plays a minor role for the shape of the spectrum, for PP‐NEXAFS simulations the choice of the density functional is important. Especially hybrid functionals (which could not be used straightforwardly before to simulate PP‐NEXAFS spectra) and their amount of “Hartree‐Fock like” exact exchange affects relative resonance positions in the spectrum.

Authors: Christopher Ehlert, Tillmann Klamroth

Date Published: 15th Jul 2020

Publication Type: Journal

Au 21 cage structures and their magic number tri‐cations

Abstract (Expand)

We examine the stability and properties of three Au21 cage structures, one with D3 symmetry and denoted as Au21 (D3), which is novel, and the other two with C2v symmetry. One, denoted as Au21 (C2v-1), … has been previously reported but the other, denoted as Au21 (C2v-2), is novel. As reference Au21 structures, we also examine a sheet isomer and a compact isomer, Au21 (Cs-Tetra), formed by adsorbing an Au atom on Au20 (Td). For all structures, we consider charge ranging from −1 to +4. For the Au21 cage structures, a primary property of interest is their spherical aromaticity, as measured by their nucleus independent chemical shift. Our focus is on charge +3 since each gold atom is assumed to contribute one (6s) valence electron, and 18 is a magic number for shell closing. We find that, although Au21 (D3)+3 has the largest aromaticity, it is not the most stable urn:x-wiley:00207608:media:qua26191:qua26191-math-0001 cage species. Surprisingly, Au21 (C2v-2), which is not even stable as a neutral cage species, is the most stable tri-cation cage species. We also examine the stability of (neutral) Au21Xn cage structures relative to Au21Xn structures derived from Au21 (Cs-Tetra) (with X = F, Cl, Br, I and n = 1, 3, 5). We find that, although Au21F3 derived from Au21 (D3) has the largest aromaticity, it is not the most stable Au21F3 cage structure. Nonetheless, all cage structures are stabilized relative to Au21 (Cs-Tetra) and, remarkably, for the trichlorinated, tribrominated, and triiodineated clusters, at least one cage structure is more stable than its Au21 (Cs-Tetra) counterpart.

Authors: Christopher Ehlert, Xiaojing J. Liu, Ian P. Hamilton

Date Published: 5th Jun 2020

Publication Type: Journal

Conceptual Framework of Organic Electronics

Abstract (Expand)

In this account, we discuss the common molecular features and the related chemistry concepts across several different areas of organic electronics, including molecular semiconductors and single-molecule … junctions. Despite seemingly diverse charge transport mechanisms and device set-ups, various molecular electronics systems can benefit from the same fundamental principles of physical organic chemistry, based upon the electronic structure and geometry of their molecular building blocks and the intermolecular interactions between them. This is not an exhaustive review of organic electronics, but rather a focused account of primarily our own recent efforts aimed at developing a unified approach to understanding and designing conductive molecular species for diverse electronic applications.

Authors: Ganna Gryn'ova, Clémence Corminboeuf

Date Published: 24th Apr 2019

Publication Type: Journal

Topology-Driven Single-Molecule Conductance of Carbon Nanothreads

Abstract (Expand)

Highly conductive single-molecule junctions typically involve π-conjugated molecular bridges, whose frontier molecular orbital energy levels can be fine-tuned to best match the Fermi level of the leads. … Fully saturated wires, e.g., alkanes, are typically thought of as insulating rather than highly conductive. However, in this work, we demonstrate in silico that significant zero-bias conductance can be achieved in such systems by means of topology. Specifically, caged saturated hydrocarbons offering multiple σ-conductance channels afford transmission far beyond what could be expected based upon conventional superposition laws, particularly if these pathways are composed entirely from quaternary carbon atoms. Computed conductance of molecular bridges based on carbon nanothreads, e.g., polytwistane, is not only of appreciable magnitude; it also shows a very slow decay with increasing nanogap, similarly to the case of π-conjugated wires. These findings offer a way to manipulate the transport properties of molecular systems by means of their topology, alternatively to the traditionally invoked electronic structure.

Authors: Ganna Gryn’ova, Clémence Corminboeuf

Date Published: 11th Feb 2019

Publication Type: Journal

Experimental Evidence for Long-Range Stabilizing and Destabilizing Interactions between Charge and Radical Sites in Distonic Ions

Abstract (Expand)

Polarizable radical sites in distonic radical anions are stabilized by ostensibly remote negative charges. Computational evidence suggests bond dissociation energies of closed-shell precursors are … significantly lowered by through-space interactions with a proximate negative charge, however direct experimental confirmation has proved challenging. Herein, we exploit two complementary tandem mass spectrometry strategies to probe the influence of a remote charge on the stability of nitroxyl radicals, and vice versa. Dissociation of negatively charge-tagged alkoxyamines reveals that the energetic onset of radical formation is dependent on the proximity and basicity of the charged group, thus providing direct evidence for a charge-induced stabilization of the nitroxyl radical. Complementary kinetic method experiments on a series of proton-bound dimers demonstrate that the presence of a nitroxyl radical decreases the proton affinity for a selection of proximate ionic groups. These data show excellent agreement with quantum-chemical calculations and provide a general framework to explore the magnitude and direction of charge-radical interactions through systematic exploration of the identity, polarity and the proximity of the ion to the radical site. These findings expand our fundamental understanding of radical ion energetics that underpin the application of distonic ions as models for neutral radical reactivity, and open new avenues for exploiting these interactions as chemical switches.

Authors: David L. Marshall, Ganna Gryn’ova, Berwyck L.J. Poad, Steven E. Bottle, Adam J. Trevitt, Michelle L. Coote, Stephen J. Blanksby

Date Published: 2019

Publication Type: Journal

The Evolution of Multiple Active Site Configurations in a Designed Enzyme

Abstract (Expand)

Developments in computational chemistry, bioinformatics, and laboratory evolution have facilitated the de novo design and catalytic optimization of enzymes. Besides creating useful catalysts, the … generation and iterative improvement of designed enzymes can provide valuable insight into the interplay between the many phenomena that have been suggested to contribute to catalysis. In this work, we follow changes in conformational sampling, electrostatic preorganization, and quantum tunneling along the evolutionary trajectory of a designed Kemp eliminase. We observe that in the Kemp Eliminase KE07, instability of the designed active site leads to the emergence of two additional active site configurations. Evolutionary conformational selection then gradually stabilizes the most efficient configuration, leading to an improved enzyme. This work exemplifies the link between conformational plasticity and evolvability and demonstrates that residues remote from the active sites of enzymes play crucial roles in controlling and shaping the active site for efficient catalysis.

Authors: Nan-Sook Hong, Dušan Petrović, Richmond Lee, Ganna Gryn’ova, Miha Purg, Jake Saunders, Paul Bauer, Paul D. Carr, Ching-Yeh Lin, Peter D. Mabbitt, William Zhang, Timothy Altamore, Chris Easton, Michelle L. Coote, Shina C. L. Kamerlin, Colin J. Jackson

Date Published: 1st Dec 2018

Publication Type: Journal

Read between the Molecules: Computational Insights into Organic Semiconductors

Abstract (Expand)

The performance and key electronic properties of molecular organic semiconductors are dictated by the interplay between the chemistry of the molecular core and the intermolecular factors of which … manipulation has inspired both experimentalists and theorists. This Perspective presents major computational challenges and modern methodological strategies to advance the field. The discussion ranges from insights and design principles at the quantum chemical level, in-depth atomistic modeling based on multiscale protocols, morphological prediction and characterization as well as energy-property maps involving data-driven analysis. A personal overview of the past achievements and future direction is also provided.

Authors: Ganna Gryn’ova, Kun-Han Lin, Clémence Corminboeuf

Date Published: 5th Nov 2018

Publication Type: Journal

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