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1. Effects of intervalence charge transfer interaction between π-stacked mixed valent tetrathiafulvalene ligands on the electrical conductivity of 3D metal–organic frameworks

   https://doi.org/10.1039/d1sc04338b  

   Zhang, Shiyu ; Panda, Dillip K. ; Yadav, Ashok ; Zhou, Wei ; Saha, Sourav ( October 2021 , Chemical Science)

   Achieving a molecular-level understanding of how the structures and compositions of metal–organic frameworks (MOFs) influence their charge carrier concentration and charge transport mechanism—the two key parameters of electrical conductivity—is essential for the successful development of electrically conducting MOFs, which have recently emerged as one of the most coveted functional materials due to their diverse potential applications in advanced electronics and energy technologies. Herein, we have constructed four new alkali metal (Na, K, Rb, and Cs) frameworks based on an electron-rich tetrathiafulvalene tetracarboxylate (TTFTC) ligand, which formed continuous π-stacks, albeit with different π–π-stacking and S⋯S distances ( d π–π and d S⋯S ). These MOFs also contained different amounts of aerobically oxidized TTFTC˙ + radical cations that were quantified by electron spin resonance (ESR) spectroscopy. Density functional theory calculations and diffuse reflectance spectroscopy demonstrated that depending on the π–π-interaction and TTFTC˙ + population, these MOFs enjoyed varying degrees of TTFTC/TTFTC˙ + intervalence charge transfer (IVCT) interactions, which commensurately affected their electronic and optical band gaps and electrical conductivity. Having the shortest d π–π (3.39 Å) and the largest initial TTFTC˙ + population (∼23%), the oxidized Na-MOF 1-ox displayed the narrowest band gap (1.33 eV) and the highest room temperature electrical conductivitymore »(3.6 × 10 −5 S cm −1 ), whereas owing to its longest d π–π (3.68 Å) and a negligible TTFTC˙ + population, neutral Cs-MOF 4 exhibited the widest band gap (2.15 eV) and the lowest electrical conductivity (1.8 × 10 −7 S cm −1 ). The freshly prepared but not optimally oxidized K-MOF 2 and Rb-MOF 3 initially displayed intermediate band gaps and conductivity, however, upon prolonged aerobic oxidation, which raised the TTFTC˙ + population to saturation levels (∼25 and 10%, respectively), the resulting 2-ox and 3-ox displayed much narrower band gaps (∼1.35 eV) and higher electrical conductivity (6.6 × 10 −5 and 4.7 × 10 −5 S cm −1 , respectively). The computational studies indicated that charge movement in these MOFs occurred predominantly through the π-stacked ligands, while the experimental results displayed the combined effects of π–π-interactions, TTFTC˙ + population, and TTFTC/TTFTC˙ + IVCT interaction on their electronic and optical properties, demonstrating that IVCT interactions between the mixed-valent ligands could be exploited as an effective design strategy to develop electrically conducting MOFs.« less
2. Coexistence of metallic and nonmetallic properties in the pyrochlore Lu2Rh2O7

   https://doi.org/10.1038/s41535-019-0148-1  

   Hallas, Alannah M. ; Sharma, Arzoo Z. ; Mauws, Cole ; Chen, Qiang ; Zhou, Haidong D. ; Ding, Cui ; Gong, Zizhou ; Tachibana, Makoto ; Sarte, Paul M. ; Attfield, J. Paul ; et al ( March 2019 , npj Quantum Materials)

   Transition metal oxides of the 4dand 5dblock have recently become the targets of materials discovery, largely due to their strong spin–orbit coupling that can generate exotic magnetic and electronic states. Here, we report the high-pressure synthesis of Lu₂Rh₂O₇, a new cubic pyrochlore oxide based on 4d⁵Rh⁴⁺, and characterizations via thermodynamic, electrical transport, and muon spin relaxation measurements. Magnetic susceptibility measurements reveal a large temperature-independent Pauli paramagnetic contribution, while heat capacity shows an enhanced Sommerfeld coefficient,γ = 21.8(1) mJ/mol-Rh K². Muon spin relaxation measurements confirm that Lu₂Rh₂O₇remains paramagnetic down to 2 K. Taken in combination, these three measurements suggest that Lu₂Rh₂O₇is a correlated paramagnetic metal with a Wilson ratio ofR_W = 2.5. However, electric transport measurements present a striking contradiction as the resistivity of Lu₂Rh₂O₇is observed to monotonically increase with decreasing temperature, indicative of a nonmetallic state. Furthermore, although the magnitude of the resistivity is that of a semiconductor, the temperature dependence does not obey any conventional form. Thus, we propose that Lu₂Rh₂O₇may belong to the same novel class of non-Fermi liquids as the nonmetallic metal FeCrAs.
3. Quantum electronic control on chemical activation of methane by collision with spin–orbit state selected vanadium cation

   https://doi.org/10.1039/D0CP04333H  

   Ng, Cheuk-Yiu ; Xu, Yuntao ; Chang, Yih-Chung ; Wannenmacher, Anna ; Parziale, Matthew ; Armentrout, P. B. ( January 2021 , Physical Chemistry Chemical Physics)

   By coupling a newly developed quantum-electronic-state-selected supersonically cooled vanadium cation (V + ) beam source with a double quadrupole-double octopole (DQDO) ion–molecule reaction apparatus, we have investigated detailed absolute integral cross sections ( σ 's) for the reactions, V + [a 5 D J ( J = 0, 2), a 5 F J ( J = 1, 2), and a 3 F J ( J = 2, 3)] + CH 4 , covering the center-of-mass collision energy range of E cm = 0.1–10.0 eV. Three product channels, VH + + CH 3 , VCH 2 + + H 2 , and VCH 3 + + H, are unambiguously identified based on E cm -threshold measurements. No J -dependences for the σ curves ( σ versus E cm plots) of individual electronic states are discernible, which may indicate that the spin–orbit coupling is weak and has little effect on chemical reactivity. For all three product channels, the maximum σ values for the triplet a 3 F J state [ σ (a 3 F J )] are found to be more than ten times larger than those for the quintet σ (a 5 D J ) and σ (a 5 F Jmore ») states, showing that a reaction mechanism favoring the conservation of total electron spin. Without performing a detailed theoretical study, we have tentatively interpreted that a weak quintet-to-triplet spin crossing is operative for the activation reaction. The σ (a 5 D 0 , a 5 F 1 , and a 3 F 2) measurements for the VH + , VCH 2 + , and VCH 3 + product ion channels along with accounting of the kinetic energy distribution due to the thermal broadening effect for CH 4 have allowed the determination of the 0 K bond dissociation energies: D 0 (V + –H) = 2.02 (0.05) eV, D 0 (V + –CH 2 ) = 3.40 (0.07) eV, and D 0 (V + –CH 3 ) = 2.07 (0.09) eV. Detailed branching ratios of product ion channels for the titled reaction have also been reported. Excellent simulations of the σ curves obtained previously for V + generated by surface ionization at 1800–2200 K can be achieved by the linear combination of the σ (a 5 D J , a 5 F J , and a 3 F J ) curves weighted by the corresponding Boltzmann populations of the electronic states. In addition to serving as a strong validation of the thermal equilibrium assumption for the populations of the V + electronic states in the hot filament ionization source, the agreement between these results also confirmed that the V + (a 5 D J , a 5 F J , and a 3 F J ) states prepared in this experiment are in single spin–orbit states with 100% purity.« less
4. Molecular gas in z ∼ 6 quasar host galaxies

   https://doi.org/10.1051/0004-6361/202142871  

   Decarli, Roberto ; Pensabene, Antonio ; Venemans, Bram ; Walter, Fabian ; Bañados, Eduardo ; Bertoldi, Frank ; Carilli, Chris L. ; Cox, Pierre ; Fan, Xiaohui ; Farina, Emanuele Paolo ; et al ( June 2022 , Astronomy & Astrophysics)

   We investigate the molecular gas content of z  ∼ 6 quasar host galaxies using the Institut de Radioastronomie Millimétrique Northern Extended Millimeter Array. We targeted the 3 mm dust continuum, and the line emission from CO(6–5), CO(7–6), and [C  I ] 2−1 in ten infrared–luminous quasars that have been previously studied in their 1 mm dust continuum and [C  II ] line emission. We detected CO(7–6) at various degrees of significance in all the targeted sources, thus doubling the number of such detections in z  ∼ 6 quasars. The 3 mm to 1 mm flux density ratios are consistent with a modified black body spectrum with a dust temperature T dust  ∼ 47 K and an optical depth τ ν  = 0.2 at the [C  II ] frequency. Our study provides us with four independent ways to estimate the molecular gas mass, M H2 , in the targeted quasars. This allows us to set constraints on various parameters used in the derivation of molecular gas mass estimates, such as the mass per luminosity ratios α CO and α [CII] , the gas-to-dust mass ratio δ g/d , and the carbon abundance [C]/H 2 . Leveraging either on the dust, CO, [C  I ], ormore »[C  II ] emission yields mass estimates of the entire sample in the range M H2  ∼ 10 10 –10 11 M ⊙ . We compared the observed luminosities of dust, [C  II ], [C  I ], and CO(7–6) with predictions from photo-dissociation and X-ray dominated regions. We find that the former provide better model fits to our data, assuming that the bulk of the emission arises from dense ( n H  > 10 4 cm −3 ) clouds with a column density N H  ∼ 10 23 cm −2 , exposed to a radiation field with an intensity of G 0  ∼ 10 3 (in Habing units). Our analysis reiterates the presence of massive reservoirs of molecular gas fueling star formation and nuclear accretion in z  ∼ 6 quasar host galaxies. It also highlights the power of combined 3 mm and 1 mm observations for quantitative studies of the dense gas content in massive galaxies at cosmic dawn.« less
5. Simulation Data for Design of Peptides that Fold and Self-Assemble on Graphite

   https://doi.org/10.5281/zenodo.6426152  

   Comer, Jeffrey ; Thakkar, Ravindra ; Velásquez-Silva, Astrid ; Miranda-Carvajal, Ingrid ( January 2022 )

   Abstract

   <p>This data set for the manuscript entitled &#34;Design of Peptides that Fold and Self-Assemble on Graphite&#34; includes all files needed to run and analyze the simulations described in the this manuscript in the molecular dynamics software NAMD, as well as the output of the simulations. The files are organized into directories corresponding to the figures of the main text and supporting information. They include molecular model structure files (NAMD psf or Amber prmtop format), force field parameter files (in CHARMM format), initial atomic coordinates (pdb format), NAMD configuration files, Colvars configuration files, NAMD log files, and NAMD output including restart files (in binary NAMD format) and trajectories in dcd format (downsampled to 10 ns per frame). Analysis is controlled by shell scripts (Bash-compatible) that call VMD Tcl scripts or python scripts. These scripts and their output are also included.</p> <p>Version: 2.0</p> <p>Changes versus version 1.0 are the addition of the free energy of folding, adsorption, and pairing calculations (Sim_Figure-7) and shifting of the figure numbers to accommodate this addition.</p> <p><br /> Conventions Used in These Files<br /> &#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;</p> <p>Structure Files<br /> ----------------<br /> - graph_*.psf or sol_*.psf (original NAMD (XPLOR?) format psf file including atom details (type, charge, mass), as well as definitions of bonds, angles, dihedrals, and impropers for each dipeptide.)</p> <p>- graph_*.pdb or sol_*.pdb (initial coordinates before equilibration)<br /> - repart_*.psf (same as the above psf files, but the masses of non-water hydrogen atoms have been repartitioned by VMD script repartitionMass.tcl)<br /> - freeTop_*.pdb (same as the above pdb files, but the carbons of the lower graphene layer have been placed at a single z value and marked for restraints in NAMD)<br /> - amber_*.prmtop (combined topology and parameter files for Amber force field simulations)<br /> - repart_amber_*.prmtop (same as the above prmtop files, but the masses of non-water hydrogen atoms have been repartitioned by ParmEd)</p> <p>Force Field Parameters<br /> ----------------------<br /> CHARMM format parameter files:<br /> - par_all36m_prot.prm (CHARMM36m FF for proteins)<br /> - par_all36_cgenff_no_nbfix.prm (CGenFF v4.4 for graphene) The NBFIX parameters are commented out since they are only needed for aromatic halogens and we use only the CG2R61 type for graphene.<br /> - toppar_water_ions_prot_cgenff.str (CHARMM water and ions with NBFIX parameters needed for protein and CGenFF included and others commented out)</p> <p>Template NAMD Configuration Files<br /> ---------------------------------<br /> These contain the most commonly used simulation parameters. They are called by the other NAMD configuration files (which are in the namd/ subdirectory):<br /> - template_min.namd (minimization)<br /> - template_eq.namd (NPT equilibration with lower graphene fixed)<br /> - template_abf.namd (for adaptive biasing force)</p> <p>Minimization<br /> -------------<br /> - namd/min_*.0.namd</p> <p>Equilibration<br /> -------------<br /> - namd/eq_*.0.namd</p> <p>Adaptive biasing force calculations<br /> -----------------------------------<br /> - namd/eabfZRest7_graph_chp1404.0.namd<br /> - namd/eabfZRest7_graph_chp1404.1.namd (continuation of eabfZRest7_graph_chp1404.0.namd)</p> <p>Log Files<br /> ---------<br /> For each NAMD configuration file given in the last two sections, there is a log file with the same prefix, which gives the text output of NAMD. For instance, the output of namd/eabfZRest7_graph_chp1404.0.namd is eabfZRest7_graph_chp1404.0.log.</p> <p>Simulation Output<br /> -----------------<br /> The simulation output files (which match the names of the NAMD configuration files) are in the output/ directory. Files with the extensions .coor, .vel, and .xsc are coordinates in NAMD binary format, velocities in NAMD binary format, and extended system information (including cell size) in text format. Files with the extension .dcd give the trajectory of the atomic coorinates over time (and also include system cell information). Due to storage limitations, large DCD files have been omitted or replaced with new DCD files having the prefix stride50_ including only every 50 frames. The time between frames in these files is 50 * 50000 steps/frame * 4 fs/step &#61; 10 ns. The system cell trajectory is also included for the NPT runs are output/eq_*.xst.</p> <p>Scripts<br /> -------<br /> Files with the .sh extension can be found throughout. These usually provide the highest level control for submission of simulations and analysis. Look to these as a guide to what is happening. If there are scripts with step1_*.sh and step2_*.sh, they are intended to be run in order, with step1_*.sh first.</p> <p><br /> CONTENTS<br /> &#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;</p> <p>The directory contents are as follows. The directories Sim_Figure-1 and Sim_Figure-8 include README.txt files that describe the files and naming conventions used throughout this data set.</p> <p>Sim_Figure-1: Simulations of N-acetylated C-amidated amino acids (Ac-X-NHMe) at the graphite–water interface.</p> <p>Sim_Figure-2: Simulations of different peptide designs (including acyclic, disulfide cyclized, and N-to-C cyclized) at the graphite–water interface.</p> <p>Sim_Figure-3: MM-GBSA calculations of different peptide sequences for a folded conformation and 5 misfolded/unfolded conformations.</p> <p>Sim_Figure-4: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite–water interface at 370 K.</p> <p>Sim_Figure-5: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite–water interface at 295 K.</p> <p>Sim_Figure-5_replica: Temperature replica exchange molecular dynamics simulations for the peptide cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) with 20 replicas for temperatures from 295 to 454 K.</p> <p>Sim_Figure-6: Simulation of the peptide molecule cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) in free solution (no graphite).</p> <p>Sim_Figure-7: Free energy calculations for folding, adsorption, and pairing for the peptide CHP1404 (sequence: cyc(GTGSGTG-GPGG-GCGTGTG-SGPG)). For folding, we calculate the PMF as function of RMSD by replica-exchange umbrella sampling (in the subdirectory Folding_CHP1404_Graphene/). We make the same calculation in solution, which required 3 seperate replica-exchange umbrella sampling calculations (in the subdirectory Folding_CHP1404_Solution/). Both PMF of RMSD calculations for the scrambled peptide are in Folding_scram1404/. For adsorption, calculation of the PMF for the orientational restraints and the calculation of the PMF along z (the distance between the graphene sheet and the center of mass of the peptide) are in Adsorption_CHP1404/ and Adsorption_scram1404/. The actual calculation of the free energy is done by a shell script (&#34;doRestraintEnergyError.sh&#34;) in the 1_free_energy/ subsubdirectory. Processing of the PMFs must be done first in the 0_pmf/ subsubdirectory. Finally, files for free energy calculations of pair formation for CHP1404 are found in the Pair/ subdirectory.</p> <p>Sim_Figure-8: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) where the peptides are far above the graphene–water interface in the initial configuration.</p> <p>Sim_Figure-9: Two replicates of a simulation of nine peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite–water interface at 370 K.</p> <p>Sim_Figure-9_scrambled: Two replicates of a simulation of nine peptide molecules with the control sequence cyc(GGTPTTGGGGGGSGGPSGTGGC) at the graphite–water interface at 370 K.</p> <p>Sim_Figure-10: Adaptive biasing for calculation of the free energy of the folded peptide as a function of the angle between its long axis and the zigzag directions of the underlying graphene sheet.</p> <p> </p>
   

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   This material is based upon work supported by the US National Science Foundation under grant no. DMR-1945589. A majority of the computing for this project was performed on the Beocat Research Cluster at Kansas State University, which is funded in part by NSF grants CHE-1726332, CNS-1006860, EPS-1006860, and EPS-0919443. This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant number ACI-1548562, through allocation BIO200030.
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