Coherence in Chemistry: Foundations and Frontiers.

Coherence refers to correlations in waves. Because matter has a wave-particle nature, it is unsurprising that coherence has deep connections with the most contemporary issues in chemistry research (e.g.

Seeking a quantum advantage with trapped-ion quantum simulations of condensed-phase chemical dynamics.

Simulating the quantum dynamics of molecules in the condensed phase represents a longstanding challenge in chemistry. Trapped-ion quantum systems may serve as a platform for the analog-quantum simulation of chemical dynamics that is beyond the reach of current classical-digital simulation. To identify a 'quantum advantage' for these simulations, performance analysis of both analog-quantum simulation on noisy hardware and classical-digital algorithms is needed.

De novo design of drug-binding proteins with predictable binding energy and specificity.

The de novo design of small molecule-binding proteins has seen exciting recent progress; however, high-affinity binding and tunable specificity typically require laborious screening and optimization after computational design. We developed a computational procedure to design a protein that recognizes a common pharmacophore in a series of poly(ADP-ribose) polymerase-1 inhibitors. One of three designed proteins bound different inhibitors with affinities ranging from <5 nM to low micromolar.

design of drug-binding proteins with predictable binding energy and specificity.

The de novo design of small-molecule-binding proteins has seen exciting recent progress; however, the ability to achieve exquisite affinity for binding small molecules while tuning specificity has not yet been demonstrated directly from computation. Here, we develop a computational procedure that results in the highest affinity binders to date with predetermined relative affinities, targeting a series of PARP1 inhibitors. Two of four designed proteins bound with affinities ranging from < 5 nM to low μM, in a predictable manner.

Intra-cluster Charge Migration upon Hydration of Protonated Formic Acid Revealed by Anharmonic Analysis of Cold Ion Vibrational Spectra.

The rates of many chemical reactions are accelerated when carried out in micron-sized droplets, but the molecular origin of the rate acceleration remains unclear. One example is the condensation reaction of 1,2-diaminobenzene with formic acid to yield benzimidazole. The observed rate enhancements have been rationalized by invoking enhanced acidity at the surface of methanol solvent droplets with low water content to enable protonation of formic acid to generate a cationic species (protonated formic acid or PFA) formed by attachment of a proton to the neutral acid.

Synthetic Control of Exciton Dynamics in Bioinspired Cofacial Porphyrin Dimers.

Understanding how the complex interplay among excitonic interactions, vibronic couplings, and reorganization energy determines coherence-enabled transport mechanisms is a grand challenge with both foundational implications and potential payoffs for energy science. We use a combined experimental and theoretical approach to show how a modest change in structure may be used to modify the exciton delocalization, tune electronic and vibrational coherences, and alter the mechanism of exciton transfer in covalently linked cofacial Zn-porphyrin dimers ( linked and linked ). While both and feature zinc porphyrins linked by a 1,2-phenylene bridge, differences in the interporphyrin connectivity set the lateral shift between macrocycles, reducing electronic coupling in and resulting in a localized exciton.

Electron ratcheting in self-assembled soft matter.

Ratcheted multi-step hopping electron transfer systems can plausibly produce directional charge transport over very large distances without requiring a source-drain voltage bias. We examine molecular strategies to realize ratcheted charge transport based on multi-step charge hopping, and we illustrate two ratcheting mechanisms with examples based on DNA structures. The charge transport times and currents that may be generated in these assemblies are also estimated using kinetic simulations.

Delocalization-Assisted Transport through Nucleic Acids in Molecular Junctions.

The flow of charge through molecules is central to the function of supramolecular machines, and charge transport in nucleic acids is implicated in molecular signaling and DNA repair. We examine the transport of electrons through nucleic acids to understand the interplay of resonant and nonresonant charge carrier transport mechanisms. This study reports STM break junction measurements of peptide nucleic acids (PNAs) with a G-block structure and contrasts the findings with previous results for DNA duplexes.

Nonexponential Length Dependence of Molecular Conductance in Acene-Based Molecular Wires.

In the nonresonant regime, molecular conductance decays exponentially with distance, limiting the fabrication of efficient molecular semiconductors at the nanoscale. In this work, we calculate the conductance of a series of acene derivatives connected to gold electrodes using density functional theory (DFT) combined with the nonequilibrium Green's function (NEGF) formalism. We show that these systems have near length-independent conductance and can exhibit a conductance increase with molecular length depending on the connection to the electrodes.

Quantum interference enhances rectification behavior of molecular devices.

We present a theoretical and computational work and demonstrate that cross-conjugated molecules with electron-donating groups are efficient rectifiers with high conductance. The rectification ratios obtained are up to one order of magnitude at an applied bias voltage of 0.3 V.

Symmetry controlled photo-selection and charge separation in butadiyne-bridged donor-bridge-acceptor compounds.

Electron transfer (ET) in donor-bridge-acceptor (DBA) compounds depends strongly on the structural and electronic properties of the bridge. Among the bridges that support donor-acceptor conjugation, alkyne bridges have attractive and unique properties: they are compact, possess linear structure permitting access to high symmetry DBA molecules, and allow torsional motion of D and A, especially for longer bridges. We report conformation dependent electron transfer dynamics in a set of novel DBA compounds featuring butadiyne (C4) bridge, N-isopropyl-1,8-napthalimide (NAP) acceptors, and donors that span a range of reduction potentials (trimethyl silane (Si-C4-NAP), phenyl (Ph-C4-NAP), and dimethyl aniline (D-C4-NAP)).

Unsymmetrical Bis-Alkynyl Complexes Based on Co(III)(cyclam): Synthesis, Ultrafast Charge Separation, and Analysis.

Donor-bridge-acceptor (D-B-A) systems with a polarizable bridge can afford rapid photoinduced electron transfer dynamics that may be susceptible to rate modulation by infrared excitation. We describe the synthesis, characterization, and electronic structure of a class of readily assembled D-B-A structures linked by a cobalt cyclam bridge. The reaction between [Co(cyclam)Cl]Cl and 4-ethynyl--isopropyl-1,8-naphthalimide (HCNAP) yields [Co(cyclam)(CNAP)Cl]Cl (), which reacts with LiCY at -78 °C to afford [Co(cyclam)(CNAP)(CD)]Cl with D as CH-4-NMe (), NAP (), Ph (), and CH-4-N(4-MeOPh) ().