Synthesis and Characterization of New Hybrid Organic-Inorganic Metal Halides [(CH3)3SO]M2I3 (M = Cu and Ag)

Recently, all-inorganic copper(I) metal halides have emerged as promising optical materials due to their high light emission efficiencies. This work details the crystal structure of the two hybrid organic-inorganic metal halides [(CH3)3SO]M2I3 (M = Cu and Ag) and their alloyed derivatives [(CH3)3SO]Cu2-xAgxI3 (x = 0.2; 1.25), which were obtained by incorporating trimethylsulfoxonium organic cation (CH3)3SO+ in place of Cs+ in the yellow-emitting all-inorganic CsCu2I3. These compounds are isostructural and centrosymmetric with the space group Pnma, featuring one-dimensional edge-sharing [M2I3]- anionic double chains separated by rows of (CH3)3SO+ cations. Based on density functional theory calculations, the highest occupied molecular orbitals (HOMOs) of [(CH3)3SO]M2I3 (M = Cu and Ag) are dominated by the Cu or Ag d and I p orbitals, while the lowest unoccupied molecular orbitals (LUMOs) are Cu or Ag s and I p orbitals. [(CH3)3SO]Cu2I3 single crystals exhibit a semiconductor resistivity of 9.94 × 109 Ω·cm. Furthermore, a prototype [(CH3)3SO]Cu2I3 single-crystal-based X-ray detector with a detection sensitivity of 200.54 uCGy-1 cm-2 (at electrical field E = 41.67 V/mm) was fabricated, indicating the potential use of [(CH3)3SO]Cu2I3 for radiation detection applications.

The effect of solvent on determining highest occupied molecular orbital energies of semiconducting organic molecules: Insight from a combined computational approach

Although cyclic voltammetry (CV) measurements in solution have been widely used to determine the highest occupied molecular orbital energy (E_HOMO ) of semiconducting organic molecules, an understanding of the experimentally observed discrepancies due to the solvent used is lacking. To explain these differences, we investigate the solvent effects on E_HOMO by combining density functional theory and molecular dynamics calculations for four donor molecules with a common backbone moiety. We compare the experimental E_HOMO values to the calculated values obtained from either implicit or first solvation shell theories. We find that the first solvation shell method can capture the E_HOMO variation arising from the functional groups in solution, unlike the implicit method. We further applied the first solvation shell method to other semiconducting organic molecules measured in solutions for different solvents. We find that the E_HOMO obtained using an implicit method is insensitive to solvent choice. The first solvation shell, however, produces E_HOMO values that are sensitive to solvent choices and agrees with published experimental results. The solvent sensitivity arises from a hierarchy of three effects: (1) the solute electronic state within a surrounding dielectric continuum, (2) ambient temperature or solvent atoms changing the solute geometry, and (3) electronic interactions between the solute and solvents. The implicit method, on the other hand, only captures the effect of a dielectric environment. Our findings suggest that E_HOMO obtained by CV measurements should account for the influence of solvent when the results are reported, interpreted, or compared to other molecules.

Exfoliation procedure-dependent optical properties of solution deposited MoS2 films

The development of high-precision large-area optical coatings and devices comprising low-dimensional materials hinges on scalable solution-based manufacturability with control over exfoliation procedure-dependent effects. As such, it is critical to understand the influence of technique-induced transition metal dichalcogenide (TMDC) optical properties that impact the design, performance, and integration of advanced optical coatings and devices. Here, we examine the optical properties of semiconducting MoS2 films from the exfoliation formulations of four prominent approaches: solvent-mediated exfoliation, chemical exfoliation with phase reconversion, redox exfoliation, and native redox exfoliation. The resulting MoS2 films exhibit distinct refractive indices (n), extinction coefficients (k), dielectric functions (ε1 and ε2), and absorption coefficients (α). For example, a large index contrast of Δn ≈ 2.3 is observed. These exfoliation procedures and related chemistries produce different exfoliated flake dimensions, chemical impurities, carrier doping, and lattice strain that influence the resulting optical properties. First-principles calculations further confirm the impact of lattice defects and doping characteristics on MoS2 optical properties. Overall, incomplete phase reconfiguration (from 1T to mixed crystalline 2H and amorphous phases), lattice vacancies, intraflake strain, and Mo oxidation largely contribute to the observed differences in the reported MoS2 optical properties. These findings highlight the need for controlled technique-induced effects as well as the opportunity for continued development of, and improvement to, liquid phase exfoliation methodologies. Such chemical and processing-induced effects present compelling routes to engineer exfoliated TMDC optical properties toward the development of next-generation high-performance mirrors, narrow bandpass filters, and wavelength-tailored absorbers.

Precision Modification of Monolayer Transition Metal Dichalcogenides via Environmental E-Beam Patterning

Layered Transition Metal Dichalcogenides (TMDs) are an important class of materials that exhibit a wide variety of optoelectronic properties. The ability to spatially tailor their expansive property-space (e.g., conduction behavior, optical emission, surface interactions) is of special interest for applications including, but not limited to, sensing, bioelectronics, and spintronics/valleytronics. Current methods of property modulation focus on the modification of the basal surfaces and edge sites of the TMDs by the introduction of defects, functionalization with organic or inorganic moieties, alloying, heterostructure formation, and phase engineering. A majority of these methods lack the resolution for the development of next-generation nanoscale devices or are limited in the types of functionalities useful for efficient TMD property modification. In this study, we utilize electron-beam patterning on monolayer TMDs (MoSe₂, WSe₂ and MoS₂) in the presence of a pressure-controlled atmosphere of water vapor within an environmental scanning electron microscope (ESEM). A series of parametric studies show local optical and electronic property modification depending on acceleration voltage, beam current, pressure, and electron dose. The ultimate pattern resolution achieved is 67 ± 9 nm. Raman and photoluminescence spectroscopies coupled with Kelvin Probe Force Microscopy reveal electron dose-dependent p-doping in the patterned regions, which we attribute to functionalization from the products of water vapor radiolysis (oxygen and hydroxyl groups). The modulation of the work function through patterning matches well with Density Functional Theory modeling. Finally, post-functionalization of the patterned areas with an organic fluorophore demonstrates a robust method to achieve nanoscale functionalization with high fidelity.

Effects of inter-radical interactions and scavenging radicals on magnetosensitivity: spin dynamics simulations of proposed radical pairs

Although the magnetosensitivity to weak magnetic fields, such as the geomagnetic field, which was exhibited by radical pairs that are potentially responsible for avian navigation, has been previously investigated by spin dynamics simulations, understanding this behavior for proposed radical pairs in other species is limited. These include, for example, radical pairs formed in the single-cell green alga Chlamydomonas reinhardtii (CraCRY) and in Columba livia (ClCRY4). In addition, the radical pair of FADH^• with the one-electron reduced cyclobutane thymine dimer that was shown to be sensitive to weak magnetic fields has been of interest. In this work, we investigated the directional magnetosensitivity of these radical pairs to a weak magnetic field by spin dynamics simulations. We find significant reduction in the magnetosensitivity by inclusion of dipolar and exchange interactions, which can be mitigated by a scavenging radical, as demonstrated for the [FAD^•- TyrD^•] radical pair in CraCRY, but not for the [FADH^• T□T^•-] radical pair because of the large exchange coupling. The directional magnetosensitivity of the ClCRY4 [FAD^•- TyrE^•] radical pair can survive this adverse effect even without the scavenging reaction, possibly motivating further experimental exploration.

Analysis of localized excitons in strained monolayer WSe2 by first principles calculations

Although there is growing interest in enhancement of single-photon emission (SPE) in two-dimensional transition metal dichalcogenides, particularly when introducing strain by the generation of wrinkles in monolayer WSe₂, understanding the effects of the wrinkle type on the response has been lacking. In this work, by investigating the electronic and optical properties of monolayer WSe₂ with wrinkles by first principles calculations, we gain insight into the tunability of the response, where the band gap is found to be modulated by the wrinkle type. Our detailed analyses of the local electronic structures show that the strain distribution from regions with different local strain magnitudes and types affect the band alignments. We demonstrate that introducing a wrinkle in the monolayer results in a red-shift, including the bright A exciton and the lowest energy dark exciton, and the dependence on strain is consistent with available measurements. The energy difference between the A exciton and the lowest mid-gap energy for a single Se vacancy in the wrinkled WSe₂ monolayer as a function of strain is consistent with a suggestion on the origin of SPE in monolayer WSe₂. Our results will encourage engineering of wrinkle types for enhanced SPE at specific wavelengths, which could potentially originate from hybridization of the localized strained dark exciton and a mid-gap point-defect exciton.

Predicting Van der Waals Heterostructures by a Combined Machine Learning and Density Functional Theory Approach

Van der Waals (vdW) heterostructures are constructed by different two-dimensional (2D) monolayers vertically stacked and weakly coupled by van der Waals interactions. VdW heterostructures often possess rich physical and chemical properties that are unique to their constituent monolayers. As many 2D materials have been recently identified, the combinatorial configuration space of vdW-stacked heterostructures grows exceedingly large, making it difficult to explore through traditional experimental or computational approaches in a trial-and-error manner. Here, we present a computational framework that combines first-principles electronic structure calculations, 2D material database, and supervised machine learning methods to construct efficient data-driven models capable of predicting electronic and structural properties of vdW heterostructures from their constituent monolayer properties. We apply this approach to predict the band gap, band edges, interlayer distance, and interlayer binding energy of vdW heterostructures. Our data-driven model will open avenues for efficient screening and discovery of low-dimensional vdW heterostructures and moiré superlattices with desired electronic and optical properties for targeted device applications.

Computational analysis of the optical response of ZnSe with d-orbital defects

The doping of wide band-gap semiconducting ZnSe by transition metal (TM) atoms finds applications from mid-infrared lasing, sensing, photoelectrochemical cells, to nonlinear optics. Yet understanding the response of these materials at the atomic and electronic level is lacking, particularly in comparing a range of TM dopants, which were studied primarily by phenomenological crystal-field theory. In this work, to investigate bulk ZnSe singly doped with first-row TM atoms, specifically Ti through Cu, we applied a first-principles approach and crystal-field theory to explain the origin of the infrared absorption. We show that the use of an appropriate exchange-correlation functional and a HubbardUcorrection to account for electron correlation improved the determination of the electronic transitions in these systems. We outline an approach for the calculation of the crystal-field splitting from first-principles and find it useful in providing a measure of dopant effects, also in qualitative comparison to our experimental characterization for ZnSe doped with Fe, Cr, and Ni. Our calculated absorption spectra indicate absorption signatures in the mid-infrared range, while the absorption in the visible portion of the spectrum is attributed to the ZnSe host. Our calculations will potentially motivate further experimental exploration of TM-doped ZnSe. Finally, the methods used here provide a route towards computational high-throughput screening of TM dopants in III-V materials through a combination of the electronic band structure and crystal-field theory.

Electrical and chemical properties of vacancy-ordered lead free layered double perovskite nanoparticles

In this work we synthesized vacancy-ordered lead-free layered double perovskite (LDP) nanoparticles. This structure consists of two layers of trivalent metal halide octahedra [B(III)X₆]^3- separated by a layer of divalent metal [B(II)X₆]^4- (B is a divalent or trivalent metal). The chemical formula of this structure is based on A₄B(II)B(III)₂X₁₂ where A is Cs, B(III) is Bi, X is Cl and B(II) is a different ratio between Mn²⁺ and Cd²⁺. Well-defined colloidal nanoplates of Cs₄Cd_xMn_1-xBi₂Cl₁₂ were successfully synthesized. These nanoplates show photoluminescence (PL) in the orange to red region that can be tuned by changing the Cd/Mn ratio. High resolution scanning transmission electron microscopy (HR-STEM) and atomic resolution elemental analysis were performed on these lead free LDP nanoplates revealing two different particle compositions that can be controlled by the Cd/Mn ratio. Ultraviolet Photoelectron Spectroscopy (UPS) and scanning tunneling spectroscopy (STS) reveal the band gap structure of these LDP nanoplates. Density functional theory (DFT) calculations show the existence of [MnCl₆]^4- in-gap states. While the absorption occurs from the valence band maximum (VBM) to the conduction band minimum (CBM), the emission may occur from the CBM to an in-gap band maximum (IGM), which could explain the PL in the orange to red region of these nanoplates. This work provides a detailed picture of the chemical and electronic properties of LDP nanoparticles.

Calculated linear and nonlinear optical absorption spectra of phosphine-ligated gold clusters

Although prediction of optical excitations of ligated gold clusters by time-dependent density functional theory (TDDFT) is relatively well-established, limitations still exist, for example in the choice of the exchange-correlation functional....

Stabilized photoemission from organic molecules in zero-dimensional hybrid Zn and Cd halides

This work explores the utilization of a photoactive organic cation for the preparation of R2MCl4 (M = Zn, Cd; R = (E)-4-styrylpyridinium, C13H12N+).

Interstitial Nature of Mn2+ Doping in 2D Perovskites

Halide perovskites doped with magnetic impurities (such as the transition metals Mn²⁺, Co²⁺, Ni²⁺) are being explored for a wide range of applications beyond photovoltaics, such as spintronic devices, stable light-emitting diodes, single-photon emitters, and magneto-optical devices. However, despite several recent studies, there is no consensus on whether the doped magnetic ions will predominantly replace the octahedral B-site metal via substitution or reside at interstitial defect sites. Here, by performing correlated nanoscale X-ray microscopy, spatially and temporally resolved photoluminescence measurements, and magnetic force microscopy on the inorganic 2D perovskite Cs₂PbI₂Cl₂, we show that doping Mn²⁺ into the structure results in a lattice expansion. The observed lattice expansion contrasts with the predicted contraction expected to arise from the B-site metal substitution, thus implying that Mn²⁺ does not replace the Pb²⁺ sites. Photoluminescence and electron paramagnetic resonance measurements confirm the presence of Mn²⁺ in the lattice, while correlated nano-XRD and X-ray fluorescence track the local strain and chemical composition. Density functional theory calculations predict that Mn²⁺ atoms reside at the interstitial sites between two octahedra in the triangle formed by one Cl^- and two I^- atoms, which results in a locally expanded structure. These measurements show the fate of the transition metal dopants, the local structure, and optical emission when they are doped at dilute concentrations into a wide band gap semiconductor.

Theoretical analysis of structures and electronic spectra of molecular colloidal cadmium sulfide clusters and nanoplatelets

In the present study, we systematically examine structures and absorption spectra for CdS nanoplatelets (NPLs) with thicknesses of two and three monolayers (2 MLs and 3 MLs) and extended lateral dimensions. These nanoplatelet model systems, passivated with formate and acetate ligands, are used to analyze the effects of quantum confinement in the lateral dimension within an extended monolayer and the effects of thickness when changing from two to three monolayers. Based on the computed cubic structures using density functional theory (DFT), we found good agreement between observed and time-dependent DFT-calculated spectra, revealing little ligand participation to influence the color and intensity of low-energy absorption bands as the structures are laterally extended to eight and seven monolayers for 2-ML and 3-ML systems, respectively. The spectral redshift for 3-ML CdS NPLs is attributed to the electron delocalization due to expansion of the nanoplatelet in the lateral and vertical directions.

Two-dimensional MoS2 2H, 1T, and 1T' crystalline phases with incorporated adatoms: theoretical investigation of electronic and optical properties

Although there has been progress in studying the electronic and optical properties of monolayer and near-monolayer (two-dimensional, 2D) MoS₂ upon adatom adsorption and intercalation, understanding the underlying atomic-level behavior is lacking, particularly as related to the optical response. Alkali atom intercalation in 2D transition metal dichalcogenides (TMDs) is relevant to chemical exfoliation methods that are expected to enable large scale production. In this work, focusing on prototypical 2D MoS₂, the adsorption and intercalation of Li, Na, K, and Ca adatoms were investigated for the 2H, 1T, and 1T^' phases of the TMD by the first principles density functional theory in comparison to experimental characterization of 2H and 1T 2D MoS₂ films. Our electronic structure calculations demonstrate significant charge transfer, influencing work function reductions of 1-1.5 eV. Furthermore, electrical conductivity calculations confirm the semiconducting versus metallic behavior. Calculations of the optical spectra, including excitonic effects using a many-body theoretical approach, indicate enhancement of the optical transmission upon phase change. Encouragingly, this is corroborated, in part, by the experimental measurements for the 2H and 1T phases having semiconducting and metallic behavior, respectively, thus motivating further experimental exploration. Overall, our calculations emphasize the potential impact of synthesis-relevant adatom incorporation in 2D MoS₂ on the electronic and optical responses that comprise important considerations toward the development of devices such as photodetectors or the miniaturization of electroabsorption modulator components.

Surface Functionalization of Ti3C2Tx MXene Nanosheets with Catechols: Implication for Colloidal Processing

Precise tailoring of two-dimensional nanosheets with organic molecules is critical to passivate the surface and control the reactivity, which is essential for a wide range of applications. Herein, we introduce catechols to functionalize exfoliated MXenes (Ti₃C₂T_x) in a colloidal suspension. Catechols react spontaneously with Ti₃C₂T_x surfaces, where binding is initiated from a charge-transfer complex as confirmed by density functional theory (DFT) and UV-vis. Ti₃C₂T_x sheet interlayer spacing is increased by catechol functionalization, as confirmed by X-ray diffraction (XRD), while Raman and atomic force microscopy-infrared spectroscopy (AFM-IR) measurements indicate binding of catechols at the Ti₃C₂T_x surface occurs through metal-oxygen bonds, which is supported by DFT calculations. Finally, we demonstrate immobilization of a fluorescent dye on the surface of MXene. Our results establish a strategy for tailoring MXene surfaces via aqueous functionalization with catechols, whereby colloidal stability can be modified and further functionality can be introduced, which could provide excellent anchoring points to grow polymer brushes and tune specific properties.

Halogen Etch of Ti3AlC2 MAX Phase for MXene Fabrication

The versatile property suite of two-dimensional MXenes is driving interest in various applications, including energy storage, electromagnetic shielding, and conductive coatings. Conventionally, MXenes are synthesized by a wet-chemical etching of the parent MAX-phase in HF-containing media. The acute toxicity of HF hinders scale-up, and competing surface hydrolysis challenges control of surface composition and grafting methods. Herein, we present an efficient, room-temperature etching method that utilizes halogens (Br₂, I₂, ICl, IBr) in anhydrous media to synthesize MXenes from Ti₃AlC₂. A radical-mediated process depends strongly on the molar ratio of the halogen to MAX phase, absolute concentration of the halogen, the solvent, and temperature. This etching method provides opportunities for controlled surface chemistries to modulate MXene properties.

Toward Architected Nanocomposites: MXenes and Beyond

Achieving excellent electromagnetic interference (EMI) shielding combined with mechanical flexibility, optical transparency, and environmental stability is vital for the future of coatings, electrostatic discharge, electronic displays, and wearable and portable electronic devices. Unfortunately, it is challenging to engineer materials with all of these desired properties due to a lack of understanding of the underlying materials physics and structure-property relationships. Nature has provided numerous examples of a combination of properties through precision engineering of hierarchical structures at multiple length scales with selectively chosen ingredients. This inspiration is reflected in a wide range of synthetic architected nanocomposites. In this Perspective, we provide a brief overview of recent advances in the role of hierarchical architectures in MXene-based thin-film nanocomposites in the quest to achieve multiple functionalities, especially focusing on a combination of excellent EMI shielding, transparency, and mechanical robustness. We also discuss key opportunities, challenges, and prospects.

Systematic Study of the Properties of CdS Clusters with Carboxylate Ligands Using a Deep Neural Network Potential Developed with Data from Density Functional Theory Calculations

Although structures of the inorganic core of CdS atomically precise quantum dots were reported, characterizing the nature of the metal-carboxylate coordination in these materials remains a challenge due to the large number of possible isomers. The computational cost imposed by first-principles methods is prohibitive for such a configurational search, and empirical potentials are not available. In this work, we applied deep neural network algorithms to train a potential for CdS clusters with carboxylate ligands using a database of energies and gradients obtained from density functional theory calculations. The derived potential provided energies and gradients based on a set of reference structures. Our trained potential was then used to accelerate genetic algorithm and molecular dynamics simulations searches of low-energy structures, which in turn, were used to compute the X-ray diffraction and electronic absorption spectra. Our results for CdS clusters with carboxylate ligands, analyzed and compared with experimental findings, demonstrated that the structure of a cluster whose properties agree better with experiment may deviate from the one previously assumed.

Electron transfer and spin dynamics of the radical-pair in the cryptochrome from Chlamydomonas reinhardtii by computational analysis

In an effort to elucidate the origin of avian magnetoreception, it was postulated that a radical-pair formed in a cryptochrome upon light activation provided the basis for the mechanism that enables an inclination compass sensitive to the geomagnetic field. Photoreduction in this case involves formation of a flavin adenine dinucleotide (FAD)-tryptophan (TRP) radical-pair, following electron transfer within a conserved TRP triad in the cryptochrome. Recently, an animal-like cryptochrome from Chlamydomonas reinhardtii (CraCRY) was analyzed, demonstrating the role of a fourth aromatic residue, which serves as a terminal electron donor in the photoreduction pathway, resulting in the creation of a more distal radical-pair and exhibiting fast electron transfer. In this work, we investigated the electron transfer in CraCRY with a combination of free energy molecular dynamics (MD) simulations, frozen density functional theory, and QM/MM MD simulations, supporting the suggestion of a proton coupled electron transfer mechanism. Spin dynamics simulations discerned details on the dependence of the singlet yield on the direction of the external magnetic field for the [FAD^•- TYRH^•+] and [FAD^•- TYR^•] radical-pairs in CraCRY, in comparison with the previously modeled [FAD^•- TRPH^•+] radical-pair.

Theoretical Prediction of Optical Absorption and Emission in Thiolated Gold Clusters

Although the photoluminescence of gold clusters has been extensively studied so far, there are still questions on the origin of the emission in these materials. In this work, we report time-dependent density functional theory calculations on the absorption and emission spectra of the well-studied Au₂₅(SR)₁₈^- cluster, the lowest energy isomer of the Au₃₈(SR)₂₄ cluster, and five isomers of the Au₂₂(SR)₁₈ cluster. Good agreement between the calculated and measured absorption spectra, as well as with the lowest-energy emission values for these clusters, was demonstrated, verifying the accuracy of the theoretical methods employed. Our results for Au₂₅(SR)₁₈^- explain a newly observed feature in the absorption peak, also rationalizing the optical response in terms of the superatom model. The analysis of the absorption and emission characteristics of the Au₂₅(SR)₁₈^- and Au₃₈(SR)₂₄ clusters provides an estimate of the spectral regions, where fluorescence or phosphorescence is predicted to occur. Interestingly, we find that for Au₂₂(SR)₁₈, one of the five proposed structures could be present at a significant concentration in the sample, even though it is not the lowest in energy structure, which can be explained, in part, by solvent effects.

Accelerated Discovery of Efficient Solar-cell Materials using Quantum and Machine-learning Methods

Solar-energy plays an important role in solving serious environmental problems and meeting high-energy demand. However, the lack of suitable materials hinders further progress of this technology. Here, we present the largest inorganic solar-cell material search to date using density functional theory (DFT) and machine-learning approaches. We calculated the spectroscopic limited maximum efficiency (SLME) using Tran-Blaha modified Becke-Johnson potential for 5097 non-metallic materials and identified 1997 candidates with an SLME higher than 10%, including 934 candidates with suitable convex-hull stability and effective carrier mass. Screening for 2D-layered cases, we found 58 potential materials and performed G0W0 calculations on a subset to estimate the prediction-uncertainty. As the above DFT methods are still computationally expensive, we developed a high accuracy machine learning model to pre-screen efficient materials and applied it to over a million materials. Our results provide a general framework and universal strategy for the design of high-efficiency solar cell materials. The data and tools are publicly distributed at: https://www.ctcms.nist.gov/~knc6/JVASP.html, https://www.ctcms.nist.gov/jarvisml/, https://jarvis.nist.gov/ and https://github.com/usnistgov/jarvis.

Tunability in the optical response of defective monolayer WSe2 by computational analysis

In aiming to achieve red-shifted single-photon emitters that result from localized excitons in monolayer WSe2, we report in this work a theoretical investigation on the optical properties of nanostructures with vacancies and rotational defects. We find that for pristine monolayer WSe2, the complex excitonic manifold, namely, the energies of the bright and dark excitons and the exciton binding energy, agree well with the experimental data when using the GW (Green's function approximation with a screened Coulomb interaction W)-Bethe Salpeter Equation (GW-BSE) method, including spin-orbit coupling. The predicted second and third lowest dark excitons are close in energy and appear below the second bright exciton. Upon introduction of single or double Se vacancies, or a single W vacancy within monolayer WSe2, accurate computational results demonstrate emergence of deeper defect excitons in comparison to shallower values observed for edges, which are consistent with measured emissions upon Ar+ plasma treatment of WSe2 for longer periods of time. Furthermore, using corrected RPA (random phase approximation) calculations, we find that defect excitons red-shift significantly for large rotational defects that pattern the monolayer. Finally, interestingly, first-order Raman intensity calculations demonstrate that a comparison between pristine and defective monolayer WSe2 with a single vacancy can provide a fingerprint for defect characterization. Overall, our results will encourage experimental defect engineering to enable the development of red-shifted single-photon emitters, such as by inducing extended patterning of monolayer WSe2.

Coupling Drosophila melanogaster Cryptochrome Light Activation and Oxidation of the Kvβ Subunit Hyperkinetic NADPH Cofactor

Motivated by the observations on the involvement of light-induced processes in the Drosophila melanogaster cryptochrome (DmCry) in regulation of the neuronal firing rate, which is achieved by a redox-state change of its voltage-dependent K⁺ channel Kvβ subunit hyperkinetic (Hk) reduced nicotinamide adenine dinucleotide phosphate (NADPH) cofactor, we propose in this work two hypothetical pathways that may potentially enable such coupling. In the first pathway, triggered by blue-light-induced formation of a radical pair [FAD^•-TRP^•+] in DmCry, the hole (TRP^•+) may hop to Hk, for example, through a tryptophan chain and oxidize NADPH, possibly leading to inhibition of the N-terminus inactivation in the K⁺ channel. In a second possible pathway, DmCry's FAD^•- is reoxidized by molecular oxygen, producing H₂O₂, which then diffuses to Hk and oxidizes NADPH. In this work, by applying a combination of quantum and empirical-based methods for free-energy calculations, we find that the oxidation of NADPH by TRP^•+ or H₂O₂ and the reoxidation of FAD^•- by O₂ are thermodynamically feasible. Our results may have an implication in identifying a magnetic sensing signal transduction pathway, specifically upon Drosophila's Hk NADPH cofactor oxidation, with a subsequent inhibition of the K⁺ channel N-terminus inactivation gate, permitting K⁺ flux.

Theoretical Analysis of Optical Absorption and Emission in Mixed Noble Metal Nanoclusters

In this work, we studied theoretically two hybrid gold-silver clusters, which were reported to have dual-band emission, using density functional theory (DFT) and linear and quadratic response time-dependent DFT (TDDFT). Hybrid functionals were found to successfully predict absorption and emission, although explanation of the NIR emission from the larger cluster (cluster 1) requires significant vibrational excitation in the final state. For the smaller cluster (cluster 2), the Δ H(0-0) value calculated for the T1 → S0 transition, using the PBE0 functional, is in good agreement with the measured NIR emission, and the calculated T2 → S0 value is in fair agreement with the measured visible emission. The calculated T1 → S0 phosphorescence Δ H(0-0) for cluster 1 is close to the measured visible emission energy. In order for the calculated phosphorescence for cluster 1 to agree with the intense NIR emission reported experimentally, the vibrational energy of the final state (S0) is required to be about 0.7 eV greater than the zero-point vibrational energy.

Mechanistic Analysis of Oxygen Vacancy-Driven Conductive Filament Formation in Resistive Random Access Memory Metal/NiO/Metal Structures

Electrically switchable resistive random access memories have drawn much interest as nonvolatile memory device candidates based on metal-insulator-metal (MIM) structure concepts. However, atomic level mechanisms that lead to conductive filament (CF) formation in MIM structures are often lacking, such as for the system with NiO as the oxide layer, which was found promising for resistive random access memory (RRAM) device applications. In this work, using density functional theory with a Hubbard-type on-site Coulomb correction, which we carefully benchmarked, we analyzed the intrinsic propensity toward CF formation in NiO upon introduction of oxygen vacancies, including interfacial effects of Ag or Pt electrodes. First, for stoichiometric MIM structural models, contributions from metal-induced gap states to the electronic density of states (DOS) were identified, accommodating oxygen vacancy states and showing that the interface region is reduced more easily than the bulklike region, for example, for the Ag/NiO/Ag structure. Moreover, a tendency toward oxygen vacancy clustering was demonstrated, important for CF formation. Indeed, by introducing ordered oxygen vacancies into the oxide layer for both MIM models, several extended defect states within the forbidden gap have resulted, which lead to defect-assisted transport. These were shown to be influenced by the spatial distribution and number of oxygen vacancies in the filament, where the degree of reduction of Ni atoms changes based on the immediate surroundings. Projected electronic DOS for individual Ni atoms in regions near and away from oxygen vacancies indicated that those Ni close to oxygen vacancies contribute most to the conductivity. Interestingly, based on charge analyses, these atoms are revealed to undergo significant reduction, generating a locally conductive region in the oxide layer that consists of metallic/near-metallic Ni (Ni⁰), formed through local reduction.

A Theoretical Investigation of the Structure and Optical Properties of a Silver Cluster in Solid Form and in Solution

Using density functional theory (DFT) and linear and quadratic response time-dependent DFT, we investigated the structure and optical properties of a silver sulfide cluster with the interesting property of dual emission that was observed when in crystal form but not in solution. Since the dual fluorescence is observed only in the crystal, a supposition of stabilization of a higher-energy excited state by an excimer-like complex was analyzed by calculations for a cluster dimer, formed through π-stacking of aromatic groups bonded to the sulfur atoms. However, because of the complexity of the system, a simple one-dimensional method for dimer optimization, which works moderately well in predicting the red-shifted fluorescence compared to its absorption in a naphthalene dimer, predicts only partially the red shift for the emission energy. Interestingly, calculations of the two-photon absorption (TPA) cross-section on the optimized isolated cluster as well as the crystal structure geometry indicate significant off-resonance TPA. While some materials have significantly larger TPA cross-sections, such a TPA cross-section off-resonance could be useful. The high density of states in the dimer system results in a higher probability for significant resonance enhancement and thus much larger TPA cross-sections.

Bound Flavin-Cytochrome Model of Extracellular Electron Transfer in Shewanella oneidensis: Analysis by Free Energy Molecular Dynamics Simulations

Flavins are known to enhance extracellular electron transfer (EET) in Shewanella oneidensis MR-1 bacteria, which reduce electron acceptors through outer-membrane (OM) cytochromes c. Free-shuttle and bound-redox cofactor mechanisms were proposed to explain this enhancement, but recent electrochemical reports favor a flavin-bound model, proposing two one-electron reductions of flavin, namely, oxidized (Ox) to semiquinone (Sq) and semiquinone to hydroquinone (Hq), at anodic and cathodic conditions, respectively. In this work, to provide a mechanistic understanding of riboflavin (RF) binding at the multiheme OM cytochrome OmcA, we explored binding configurations at hemes 2, 5, 7, and 10. Subsequently, on the basis of molecular dynamics (MD) simulations, binding free energies and redox potential shifts upon RF binding for the Ox/Sq and Sq/Hq reductions were analyzed. Our results demonstrated an upshift in the Ox/Sq and a downshift in the Sq/Hq redox potentials, consistent with a bound RF-OmcA model. Furthermore, binding free energy MD simulations indicated an RF binding preference at heme 7. MD simulations of the OmcA-MtrC complex interfacing at hemes 5 revealed a small interprotein redox potential difference with an electron transfer rate of 10(7)-10(8)/s.

Theoretical analysis of the combined effects of sulfur vacancies and analyte adsorption on the electronic properties of single-layer MoS2

We report a first-principles theoretical investigation on the electronic structure and electron transport of defective single-layer (SL) MoS2, as well as of corresponding structures adsorbed with benzyl viologen (BV), which was shown to provide improved performance of a field effect transistor. O2 adsorption was included to gain an understanding of the response upon air-exposure. Following analysis of the structure and stability of sulfur single vacancy and line defects in SL MoS2, we investigated the local transport at the adsorbed sites via a transport model that mimics a scanning tunneling spectroscopy experiment. Distinct current-voltage characteristics were indicated for adsorbed oxygen species at a sulfur vacancy. The electronic structures of defective MoS2 indicated the emergence of impurity states in the bandgap due to sulfur defects and oxygen adsorption. Electron transport calculations for the MoS2 surface with an extended defect in a device setting demonstrated that physisorption of BV enhances the output current, while facile chemisorption by O2 upon air-exposure causes degradation of electron transport.

Photo-thermal oxidation of single layer graphene

Photo-thermal oxidation yields no pores in the graphene layer and suggests pathways for oxygen defect engineering in a controlled manner.

Calculation of One-Photon and Two-Photon Absorption Spectra of Porphyrins Using Time-Dependent Density Functional Theory

Time-dependent density functional theory has been used to calculate the one-photon and two-photon absorption spectra of free-base porphyrin, a substituted zinc porphyrin, and a zinc porphyrin dimer, in order to assess the validity of the method to reproduce the large increase in the two-photon absorption (TPA) cross-section for the dimer. Three hybrid functionals with varying amounts of exact exchange were tested, and the calculated one-photon absorption spectra for each of the molecular systems were shown to be in qualitative agreement with the measured spectra. All three functionals predict a large enhancement in the TPA cross-section for the dimer relative to the monomer, in agreement with experimental results. However, because of the sensitivity of the resonance enhancement factor to small differences in the relevant state energies, quantitative prediction of the TPA cross-section by this method is still a challenge.

Theoretical analysis of structures and electronic spectra in molecular cadmium chalcogenide clusters

We present calculated structural and optical properties of molecular cadmium chalcogenide nonstoichiometric clusters with a size range of less than 1 nm to more than 2 nm with well-defined chemical compositions and structures in comparison to experimental characterization and previous theoretical work. A unified treatment of these clusters to obtain a fundamental understanding of the size, ligand, and solvation effects on their optical properties has not been heretofore presented. The clusters belong to three topological classes, specifically supertetrahedral (Tn), penta-supertetrahedral (Pn), and capped supertetrahedral (Cn), where n is the number of metal layers in each cluster. The tetrahedrally shaped Tn clusters examined in this work are Cd(ER)4(2-) (T1), Cd4(ER)10(2-) (T2), and Cd10E4 (')(ER)16(4-) (T3), where R is an organic group, E and E' are chalcogen atoms (sulfur or selenium). The first member of the Pn series considered is M8E'(ER)16(2-). For the Cn series, we consider the first three members, M17E4 (')(ER)28(2-), M32E14 (')(ER)36L4, and M54E32 (')(ER)48L4(4-) (L = neutral ligand). Mixed ligand clusters with capping ER groups replaced by halogen or neutral ligands were also considered. Ligands and solvent were found to have a large influence on the color and intensity of the electronic absorption spectra of small clusters. Their effects are generally reduced with increasing cluster sizes. Blueshifts were observed for the first electronic transition with reduced size for both cadmium sulfide and cadmium selenide series. Due to weakly absorbing and forbidden transitions underlying the one-photon spectra, more care is needed in interpreting the quantum confinement from the clusters' lowest-energy absorption bands.

Photoactivation of cryptochromes from Drosophila melanogaster and Sylvia borin: insight into the chemical compass mechanism by computational investigation

Although behavioral studies demonstrated light-induced magnetoreception in the insect Drosophila melanogaster, gaining insight into the possibility that a radical-pair mechanism accounts for the magnetic response of the cryptochrome (DmCry1) is complicated by a number of factors. In addition, the mechanism of magnetoreception for the cryptochrome from the garden warbler bird Sylvia borin (gwCry1a), which demonstrated a long-lived radical pair by transient optical absorption measurements, has also not been rationalized. To assess potential feasibility of a radical-pair mechanism in DmCry1 and gwCry1a, formed by excitation and electron transfer between a Trp-triad and flavin adenine dinucleotide (FAD), further separated by electron transfer within the triad, we applied a combination of theoretical methods, including homology modeling and molecular dynamics (MD) for structure refinement, high-level ab initio theory, and MD simulations using a polarizable force-field for prediction of pKa and the electron transfer rate. Calculated excitation energies, followed by electron transfer in model compounds of DmCry1 that assume proton transfer in conjunction with electron transfer from Trp (W420) to FAD and the predicted pKa for the proximate residue to FAD (Cys416), support a radical-pair mechanism. Furthermore, free-energy and reorganization energies for the Trp-triad in DmCry1 demonstrate facile electron transfer, explained by the local protein environment and exposure to solvent, which in turn enables a large enough distance separation for the radical-pair partners. Results for gwCry1a demonstrated the importance of accounting for relaxed excited-state geometries in validating the first stage of a radical-pair mechanism. This work provides insight into the so-called chemical compass mechanism to explain magnetic-field sensing in DmCry1 and gwCry1a, expanding on previous work on the cyrptochrome from the plant Arabidopsis thaliana (Solov'yov et al. J. Am. Chem. Soc. 2012, 134, 18046-18052. Solov'yov et al., Sci. Rep. 2014, 4, 1-8.).

Density functional theory based generalized effective fragment potential method

We present a generalized Kohn-Sham (KS) density functional theory (DFT) based effective fragment potential (EFP2-DFT) method for the treatment of solvent effects. Similar to the original Hartree-Fock (HF) based potential with fitted parameters for water (EFP1) and the generalized HF based potential (EFP2-HF), EFP2-DFT includes electrostatic, exchange-repulsion, polarization, and dispersion potentials, which are generated for a chosen DFT functional for a given isolated molecule. The method does not have fitted parameters, except for implicit parameters within a chosen functional and the dispersion correction to the potential. The electrostatic potential is modeled with a multipolar expansion at each atomic center and bond midpoint using Stone's distributed multipolar analysis. The exchange-repulsion potential between two fragments is composed of the overlap and kinetic energy integrals and the nondiagonal KS matrices in the localized molecular orbital basis. The polarization potential is derived from the static molecular polarizability. The dispersion potential includes the intermolecular D3 dispersion correction of Grimme et al. [J. Chem. Phys. 132, 154104 (2010)]. The potential generated from the CAMB3LYP functional has mean unsigned errors (MUEs) with respect to results from coupled cluster singles, doubles, and perturbative triples with a complete basis set limit (CCSD(T)/CBS) extrapolation, of 1.7, 2.2, 2.0, and 0.5 kcal/mol, for the S22, water-benzene clusters, water clusters, and n-alkane dimers benchmark sets, respectively. The corresponding EFP2-HF errors for the respective benchmarks are 2.41, 3.1, 1.8, and 2.5 kcal/mol. Thus, the new EFP2-DFT-D3 method with the CAMB3LYP functional provides comparable or improved results at lower computational cost and, therefore, extends the range of applicability of EFP2 to larger system sizes.

Plasmon-induced transparency in the visible region via self-assembled gold nanorod heterodimers

The phenomenon of plasmon-induced transparency holds immense potential for high sensitivity sensors and optical information processing due to the extreme dispersion and slowing of light within a narrow spectral window. Unfortunately plasmonic metamaterials demonstrating this effect has been restricted to infrared and greater wavelengths due to requisite precision in structure fabrication. Here we report a novel metamaterial synthesized by bottom-up self-assembly of gold nanorods. The small dimensions (≤ 50/20 nm, length/diameter), atomically smooth surfaces, and nanometer resolution enable the first demonstration of plasmon-induced transparency at visible wavelengths. The slow-down factors within the reduced symmetry heterodimer cluster are comparable to longer wavelength counterparts. The inherent spectral tunability and facile large-scale integration afforded by self-assembled metamaterials will open a new paradigm for physically realizable on-chip photonic device designs.

Electronic properties of a graphene device with peptide adsorption: insight from simulation

In this work, to explain doping behavior of single-layer graphene upon HSSYWYAFNNKT (P1) and HSSAAAAFNNKT (P1-3A) adsorption in field-effect transistors (GFETs), we applied a combined computational approach, whereby peptide adsorption was modeled by molecular dynamics simulations, and the lowest energy configuration was confirmed by density functional theory calculations. On the basis of the resulting structures of the hybrid materials, electronic structure and transport calculations were investigated. We demonstrate that π-π stacking of the aromatic residues and proximate peptide backbone to the graphene surface in P1 have a role in the p-doping. These results are consistent with our experimental observation of the GFET's p-doping even after a 24-h annealing procedure. Upon substitution of three of the aromatic residues to Ala in (P1-3A), a considerable decrease from p-doping is observed experimentally, demonstrating n-doping as compared to the nonadsorbed device, yet not explained based on the atomistic MD simulation structures. To gain a qualitative understanding of P1-3A's adsorption over a longer simulation time, which may differ from aromatic amino acid residues' swift anchoring on the surface, we analyzed equilibrated coarse-grain simulations performed for 500 ns. Desorption of the Ala residues from the surface was shown computationally, which could in turn affect charge transfer, yet a full explanation of the mechanism of n-doping will require elucidation of differences between various aromatic residues as dependent on peptide composition, and inclusion of effects of the substrate and environment, to be considered in future work.

Plasmonic resonances in self-assembled reduced symmetry gold nanorod structures

Self-assembled plasmonic Dolmen structures consisting of small gold nanorods (length = 50 nm and diameter = 20 nm) with a few nanometer gaps are observed to show coherent effects of super-radiance and characteristics of Fano resonance due to the significantly reduced symmetry of the structure. Relative to previous larger structures from top-down electron-beam lithography, the single crystallinity and atomically smooth surfaces of these self-assembled plasmonic structures result in 50% narrower resonances, and the small gaps with associated strong coupling enable observation of multiple dark and bright modes. By tilting the cap monomer with respect to the base dimer an order of magnitude increase in E-field enhancement at the Fano dip is obtained. In addition, a spectrally broad mode is observed indicating the strong impact of the geometry of the structure on the nature of coupled modes. The highly localized electric near-fields in the gaps will enable strong light matter interactions and the narrow resonances will be useful for improved figure of merits in inexpensive chemical and biosensing.

Inhibition of biocatalysis in [Fe-Fe] hydrogenase by oxygen: molecular dynamics and density functional theory calculations

Designing O(2)-tolerant hydrogenases is a major challenge in applying [Fe-Fe]H(2)ases for H(2) production. The inhibition involves transport of oxygen through the enzyme to the H-cluster, followed by binding and subsequent deactivation of the active site. To explore the nature of the oxygen diffusion channel for the hydrogenases from Desulfovibrio desulfuricans (Dd) and Clostridium pasteurianum (Cp), empirical molecular dynamics simulations were performed. The dynamic nature of the oxygen pathways in Dd and Cp was elucidated, and insight is provided, in part, into the experimental observation on the difference of oxygen inhibition in Dd and the hydrogenase from Clostridium acetobutylicum (Ca, assumed homologous to Cp). Further, to gain an understanding of the mechanism of oxygen inhibition of the [Fe-Fe]H(2)ase, density functional theory calculations of model compounds composed of the H-cluster and proximate amino acids are reported. Confirmation of the experimentally based suppositions on inactivation by oxygen at the [2Fe](H) domain is provided, validating the model compounds used and oxidation state assumptions, further explaining the mode of damage. This unified approach provides insight into oxygen diffusion in the enzyme, followed by deactivation at the H-cluster.

On modeling biomolecular-surface nonbonded interactions: application to nucleobase adsorption on single-wall carbon nanotube surfaces

In this work we explored the selectivity of single nucleobases towards adsorption on chiral single-wall carbon nanotubes (SWCNTs) by density functional theory calculations. Specifically, the adsorption of molecular models of guanine (G), adenine (A), thymine (T), and cytosine (C), as well as of AT and GC Watson-Crick (WC) base pairs on chiral SWCNT C(6, 5), C(9, 1) and C(8, 3) model structures, was analyzed in detail. The importance of correcting the exchange-correlation functional for London dispersion was clearly demonstrated, yet limitations in modeling such interactions by considering the SWCNT as a molecular model may mask subtle effects in a molecular-macroscopic material system. The trend in the calculated adsorption energies of the nucleobases on same diameter C(6, 5) and C(9, 1) SWCNT surfaces, i.e., G > A > T > C, was consistent with related computations and experimental work on graphitic surfaces, however contradicting experimental data on the adsorption of single-strand short homo-oligonucleotides on SWCNTs that demonstrated a trend of G > C > A > T (Albertorio et al 2009 Nanotechnology 20 395101). A possible role of electrostatic interactions in this case was partially captured by applying the effective fragment potential method, emphasizing that the interplay of the various contributions in modeling nonbonded interactions is complicated by theoretical limitations. Finally, because the calculated adsorption energies for Watson-Crick base pairs have shown little effect upon adsorption of the base pair farther from the surface, the results on SWCNT sorting by salmon genomic DNA could be indicative of partial unfolding of the double helix upon adsorption on the SWCNT surface.