Secondary structure determines electron transport in peptides.

Proteins play a key role in biological electron transport, but the structure-function relationships governing the electronic properties of peptides are not fully understood. Despite recent progress, understanding the link between peptide conformational flexibility, hierarchical structures, and electron transport pathways has been challenging. Here, we use single-molecule experiments, molecular dynamics (MD) simulations, nonequilibrium Green's function-density functional theory (NEGF-DFT), and unsupervised machine learning to understand the role of secondary structure on electron transport in peptides.

Dinitrogen activation at chromium by photochemically induced Cr-C bond homolysis.

The synthesis of the organochromium(II) complexes [POCOP]Cr(R) (R = -Tol, Bn) is reported. Exposure of [POCOP]Cr(Bn) to visible light promoted homolytic Cr-C bond cleavage and formed {[POCOP]Cr}(η:η-N) a putative [POCOP]Cr(I) species.

Halide-free synthesis of metastable graphitic BC.

Layered BC, a metastable phase within the binary boron-carbon system that is composed of graphite-like sheets with hexagonally symmetric CB units, has never been successfully crystallized. Instead, poorly-crystalline BC-like materials with significant stacking disorder have been isolated, based on the co-pyrolysis of a boron trihalide precursor with benzene at around 800 °C. The halide leaving group (-X) is a significant driving force of these reactions, but the subsequent evolution of gaseous HX species at such high temperatures hampers their scaling up and also prohibits their further use in the presence of hard-casting templates such as ordered silicates.

ENDOR Spectroscopy Reveals the "Free" 5'-Deoxyadenosyl Radical in a Radical SAM Enzyme Active Site Actually is Chaperoned by Close Interaction with the Methionine-Bound [4Fe-4S] Cluster.

H and C hyperfine coupling constants to 5'-deoxyadenosyl (5'-dAdo•) radical trapped within the active site of the radical -adenosyl-l-methionine (SAM) enzyme, pyruvate formate lyase-activating enzyme (PFL-AE), both in the absence of substrate and the presence of a reactive peptide-model of the PFL substrate, are completely characteristic of a classical organic free radical whose unpaired electron is localized in the 2pπ orbital of the sp C5'-carbon ( 12139-12146). However, prior electron-nuclear double resonance (ENDOR) measurements had indicated that this 5'-dAdo• free radical is never truly "free": tight van der Waals contact with its target partners and active-site residues guide it in carrying out the exquisitely precise, regioselective reactions that are hallmarks of RS enzymes. Here, our understanding of how the active site chaperones 5'-dAdo• is extended through the finding that this apparently unexceptional organic free radical has an anomalous g-tensor and exhibits significant Fe, C, N, and H hyperfine couplings to the adjacent, isotopically labeled, methionine-bound [4Fe-4S] cluster cogenerated with 5'-dAdo• during homolytic cleavage of cluster-bound SAM.

Computational Description of Alkylated Iron-Sulfur Organometallic Clusters.

The radical -adenosyl methionine (SAM) enzyme superfamily has widespread roles in hydrogen atom abstraction reactions of crucial biological importance. In these enzymes, reductive cleavage of SAM bound to a [4Fe-4S] cluster generates the 5'-deoxyadenosyl radical (5'-dAdo•) which ultimately abstracts an H atom from the substrate. However, overwhelming experimental evidence has surprisingly revealed an obligatory organometallic intermediate Ω exhibiting an Fe-C5'-adenosyl bond, whose properties are the target of this theoretical investigation.

Cluster Amplitudes and Their Interplay with Self-Consistency in Density Functional Methods.

The front cover artwork is provided by the Mosquera group at Montana State University, Bozeman. The image shows theoretical elements involved in the density-functional calculations that are free of spurious fractional charges. Read the full text of the Research Article at 10.

Color-Tunable Upconversion-Emission Switch Based on Cocrystal-to-Cocrystal Transformation.

Cocrystal engineering, involving the assembly of two or more components into a highly ordered solid-state superstructure, has emerged as a popular strategy for tuning the photophysical properties of crystalline materials. The reversible co-assembly and disassembly of multicomponent cocrystals and their reciprocal transformation in the solid state remain challenging objectives. Herein, we report a color-tunable upconversion-emission switch based on the interconversion between two cocrystals.

Cluster Amplitudes and Their Interplay with Self-Consistency in Density Functional Methods.

Density functional theory (DFT) provides convenient electronic structure methods for the study of molecular systems and materials. Regular Kohn-Sham DFT calculations rely on unitary transformations to determine the ground-state electronic density, ground state energy, and related properties. However, for dissociation of molecular systems into open-shell fragments, due to the self-interaction error present in a large number of density functional approximations, the self-consistent procedure based on the this type of transformation gives rise to the well-known charge delocalization problem.

Slippery Paraelectric Transition-Metal Dichalcogenide Bilayers.

Traditional ferroelectrics undergo thermally induced phase transitions whereby their structural symmetry increases. The associated higher-symmetry structure is dubbed . Ferroelectric transition-metal dichalcogenide bilayers have been recently shown to become paraelectric, but not much has been said of the atomistic configuration of such a phase.

Theoretical quantum model of two-dimensional propagating plexcitons.

When plasmonic excitations of metallic interfaces and nanostructures interact with electronic excitations in semiconductors, new states emerge that hybridize the characteristics of the uncoupled states. The engendered properties make these hybrid states appealing for a broad range of applications, ranging from photovoltaic devices to integrated circuitry for quantum devices. Here, through quantum modeling, the coupling of surface plasmon polaritons and mobile two-dimensional excitons such as those in atomically thin semiconductors is examined with emphasis on the case of strong coupling.

Atomic-Site-Specific Surface Valence-Band Structure from X-Ray Standing-Wave Excited Photoemission.

X-ray standing-wave (XSW) excited photoelectron emission was used to measure the site-specific valence band (VB) for ½ monolayer (ML) Pt grown on a SrTiO_{3} (001) surface. The XSW induced modulations in the core level (CL), and VB photoemission from the surface and substrate atoms were monitored for three hkl substrate Bragg reflections. The XSW CL analysis shows the Pt to have a face-centered-cubic-like cube-on-cube epitaxy with the substrate.

Thermal properties of single-layer MoS-WS alloys enabled by machine-learned interatomic potentials.

Two-dimensional (2D) quantum materials are poised to transform conventional electronics for a wide spectrum of applications that will encompass chemical sciences. For the study of thermal transport in single-layer (1L) or multi-layer transition metal dichalcogenides (TMDs), this work explores the combination of density functional theory (DFT) and algorithmic training for the generation of a moment tensor potential (MTP) that models 1L-MoS, 1L-WS and their alloys, and demonstrates a synergy of theoretical techniques that is anticipated to play an important role in the field. From a high-performance computing perspective, these yield very convenient inter-atomic (or inter-molecular in other contexts) potentials that are useful to predict the response of quantum materials to thermal perturbations, or other driving forces.

Multipurpose made colorimetric materials for amines, pH change and metal ion detection.

Sensors are routinely developed for specific applications, but multipurpose sensors are challenging, due to stability and poor functional design. We report organic materials that operate in solution and gas phase. They show a strong response behaviour to at least three types of environmental changes: pH, amine and metal ion binding/detection.

l-methionine Adenosylation: Radical Intermediates and the Catalytic Competence of the 5'-Deoxyadenosyl Radical.

Radical -adenosyl-l-methionine (SAM) enzymes employ a [4Fe-4S] cluster and SAM to initiate diverse radical reactions via either H-atom abstraction or substrate adenosylation. Here we use freeze-quench techniques together with electron paramagnetic resonance (EPR) spectroscopy to provide snapshots of the reaction pathway in an adenosylation reaction catalyzed by the radical SAM enzyme pyruvate formate-lyase activating enzyme on a peptide substrate containing a dehydroalanine residue in place of the target glycine. The reaction proceeds via the initial formation of the organometallic intermediate Ω, as evidenced by the characteristic EPR signal with = 2.

Density Functional Calculations Based on the Exponential Ansatz.

This work explores the application of the singles-based exponential ansatz to density functional calculations. In contrast to the standard approach where Kohn-Sham (KS) orbitals are determined prior to computing molecular quantities of interest, we consider the single-reference Hartree-Fock wave function as a starting point. Applying the exponential ansatz to this single reference gives an auxiliary wave function that is employed to calculate the electronic properties of the system.

Second Linear Response Theory and the Analytic Calculation of Excited-State Properties.

We present a method based on second linear response time-dependent density functional theory (TDDFT) to calculate permanent and transition multipoles of excited states, which are required to compute excited-state absorption/emission spectra and multiphoton optical processes, among others. In previous work, we examined computations based on second linear response theory in which linear response TDDFT was employed twice. In contrast, the present methodology requires information from only a single linear response calculation to compute the excited-state properties.

Photophysical implications of ring fusion, linker length, and twisting angle in a series of perylenediimide-thienoacene dimers.

Perylenediimide (PDI) derivatives have been widely studied as electron acceptor alternatives to fullerenes in organic photovoltaics (OPVs) because of their tunable absorption in the visible range, inexpensive synthesis, and photochemical stability. A common motif for improving device efficiency involves joining multiple PDIs together through electron-rich linkers to form a twisted acceptor-donor-acceptor molecule. Molecular features such as ring fusion are further employed to modify the structure locally and in films.

Using Visible Light to Tune Boronic Acid-Ester Equilibria.

We report a series of azobenzene boronic acids that reversibly control the extent of diol binding via photochemical isomerization. When the boronic acid is to the azo group, the thermodynamically favored isomer binds weakly with diols to form boronic esters. The isomerization of the ()-azobenzene to its isomer enhances diol binding, and the magnitude of this enhancement is affected by the azobenzene structure.

Two-photon excited deep-red and near-infrared emissive organic co-crystals.

Two-photon excited near-infrared fluorescence materials have garnered considerable attention because of their superior optical penetration, higher spatial resolution, and lower optical scattering compared with other optical materials. Herein, a convenient and efficient supramolecular approach is used to synthesize a two-photon excited near-infrared emissive co-crystalline material. A naphthalenediimide-based triangular macrocycle and coronene form selectively two co-crystals.

Thermodynamics and Mechanism of a Photocatalyzed Stereoselective [2 + 2] Cycloaddition on a CdSe Quantum Dot.

Colloidal quantum dots (QDs) have shown promise over the last few decades for a range of applications including single photon emission, imaging, and photocatalysis. Recent experiments demonstrated that QDs impart stereoselectivity to triplet excited-state [2 + 2] cycloaddition reactions of alkenes photocatalyzed by the QD through self-assembly of the reagent molecules on the QD surface, but these experiments did not reveal the precise geometries of surface-bound molecules or their interactions with surface atoms. Here, a theoretical mechanistic approach is used to study such interactions for [2 + 2] cycloadditions of 4-vinylbenzoic acid derivatives on CdSe QDs.

Pressure-Induced Optical Transitions in Metal Nanoclusters.

Currently, a comprehensive understanding of the relationship between atomic structures and optical properties of ultrasmall metal nanoclusters with diameters between 1 and 3 nm is lacking. To address this challenge, it is necessary to develop tools for perturbing the atomic structure and modulating the optical properties of metal nanoclusters beyond what can be achieved using synthetic chemistry. Here, we present a systematic high-pressure study on a series of atomically precise ligand-protected metal nanoclusters.

Domain Separated Density Functional Theory for Reaction Energy Barriers and Optical Excitations.

We recently proposed domain separated density functional theory (DS-DFT), a framework that allows for the combination of different levels of theory for the computation of the electronic structure of molecules. This work discusses the application of DS-DFT to the computation of transition-state energy barriers and optical absorption spectra. We considered several hydrogen abstraction reactions and optical spectra of molecule/metal cluster systems, including the absorption of individual species such as carbon monoxide, methane, and molecular hydrogen to a Li cluster.

Efficient Modeling of Organic Chromophores for Entangled Two-Photon Absorption.

The use of a nonclassical light source for studying molecular electronic structure has been of great interest in many applications. Here we report a theoretical study of entangled two-photon absorption (ETPA) in organic chromophores, and we provide new insight into the quantitative relation between ETPA and the corresponding unentangled TPA based on the significantly different line widths associated with entangled and unentangled processes. A sum-over-states approach is used to obtain classical TPA and ETPA cross sections and to explore the contribution of each electronic state to the ETPA process.

Embedding Methods for Quantum Chemistry: Applications from Materials to Life Sciences.

Quantum mechanical embedding methods hold the promise to transform not just the way calculations are performed, but to significantly reduce computational costs and improve scaling for macro-molecular systems containing hundreds if not thousands of atoms. The field of embedding has grown increasingly broad with many approaches of different intersecting flavors. In this perspective, we lay out the methods into two streams: QM:MM and QM:QM, showcasing the advantages and disadvantages of both.