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1. Tying Together Multiscale Calculations for Charge Transport in P3HT: Structural Descriptors, Morphology, and Tie-Chains

   https://doi.org/10.3390/polym10121358  

   Miller, Evan ; Jones, Matthew ; Jankowski, Eric ( December 2018 , Polymers)

   Evaluating new, promising organic molecules to make next-generation organic optoelectronic devices necessitates the evaluation of charge carrier transport performance through the semi-conducting medium. In this work, we utilize quantum chemical calculations (QCC) and kinetic Monte Carlo (KMC) simulations to predict the zero-field hole mobilities of ∼100 morphologies of the benchmark polymer poly(3-hexylthiophene), with varying simulation volume, structural order, and chain-length polydispersity. Morphologies with monodisperse chains were generated previously using an optimized molecular dynamics force-field and represent a spectrum of nanostructured order. We discover that a combined consideration of backbone clustering and system-wide disorder arising from side-chain conformations are correlated with hole mobility. Furthermore, we show that strongly interconnected thiophene backbones are required for efficient charge transport. This definitively shows the role “tie-chains” play in enabling mobile charges in P3HT. By marrying QCC and KMC over multiple length- and time-scales, we demonstrate that it is now possible to routinely probe the relationship between molecular nanostructure and device performance.
2. Experimental and theoretical evidence for hydrogen doping in polymer solution-processed indium gallium oxide

   https://doi.org/10.1073/pnas.2007897117  

   Huang, Wei ; Chien, Po-Hsiu ; McMillen, Kyle ; Patel, Sawankumar ; Tedesco, Joshua ; Zeng, Li ; Mukherjee, Subhrangsu ; Wang, Binghao ; Chen, Yao ; Wang, Gang ; et al ( July 2020 , Proceedings of the National Academy of Sciences)

   The field-effect electron mobility of aqueous solution-processed indium gallium oxide (IGO) thin-film transistors (TFTs) is significantly enhanced by polyvinyl alcohol (PVA) addition to the precursor solution, a >70-fold increase to 7.9 cm²/Vs. To understand the origin of this remarkable phenomenon, microstructure, electronic structure, and charge transport of IGO:PVA film are investigated by a battery of experimental and theoretical techniques, including In K-edge and Ga K-edge extended X-ray absorption fine structure (EXAFS); resonant soft X-ray scattering (R-SoXS); ultraviolet photoelectron spectroscopy (UPS); Fourier transform-infrared (FT-IR) spectroscopy; time-of-flight secondary-ion mass spectrometry (ToF-SIMS); composition-/processing-dependent TFT properties; high-resolution solid-state¹H,⁷¹Ga, and¹¹⁵In NMR spectroscopy; and discrete Fourier transform (DFT) analysis with ab initio molecular dynamics (MD) liquid-quench simulations. The⁷¹Ga{¹H} rotational-echo double-resonance (REDOR) NMR and other data indicate that PVA achieves optimal H doping with a Ga···H distance of ∼3.4 Å and conversion from six- to four-coordinate Ga, which together suppress deep trap defect localization. This reduces metal-oxide polyhedral distortion, thereby increasing the electron mobility. Hydroxyl polymer doping thus offers a pathway for efficient H doping in green solvent-processed metal oxide films and the promise of high-performance, ultra-stable metal oxide semiconductor electronics with simple binary compositions.
3. Interpretable molecular models for molybdenum disulfide and insight into selective peptide recognition

   https://doi.org/10.1039/D0SC01443E  

   Liu, Juan ; Zeng, Jin ; Zhu, Cheng ; Miao, Jianwei ; Huang, Yu ; Heinz, Hendrik ( August 2020 , Chemical Science)

   Molybdenum disulfide (MoS 2 ) is a layered material with outstanding electrical and optical properties. Numerous studies evaluate the performance in sensors, catalysts, batteries, and composites that can benefit from guidance by simulations in all-atom resolution. However, molecular simulations remain difficult due to lack of reliable models. We introduce an interpretable force field for MoS 2 with record performance that reproduces structural, interfacial, and mechanical properties in 0.1% to 5% agreement with experiments. The model overcomes structural instability, deviations in interfacial and mechanical properties by several 100%, and empirical fitting protocols in earlier models. It is compatible with several force fields for molecular dynamics simulation, including the interface force field (IFF), CVFF, DREIDING, PCFF, COMPASS, CHARMM, AMBER, and OPLS-AA. The parameters capture polar covalent bonding, X-ray structure, cleavage energy, infrared spectra, bending stability, bulk modulus, Young's modulus, and contact angles with polar and nonpolar solvents. We utilized the models to uncover the binding mechanism of peptides to the MoS 2 basal plane. The binding strength of several 7mer and 8mer peptides scales linearly with surface contact and replacement of surface-bound water molecules, and is tunable in a wide range from −86 to −6 kcal mol −1 . The binding selectivitymore »is multifactorial, including major contributions by van-der-Waals coordination and charge matching of certain side groups, orientation of hydrophilic side chains towards water, and conformation flexibility. We explain the relative attraction and role of the 20 amino acids using computational and experimental data. The force field can be used to screen and interpret the assembly of MoS 2 -based nanomaterials and electrolyte interfaces up to a billion atoms with high accuracy, including multiscale simulations from the quantum scale to the microscale.« less
4. Simulation of pH-Dependent Conformational Transitions in Membrane Proteins: The CLC-ec1 Cl−/H+ Antiporter

   https://doi.org/10.3390/molecules26226956  

   Kots, Ekaterina ; Shore, Derek M. ; Weinstein, Harel ( November 2021 , Molecules)

   Intracellular transport of chloride by members of the CLC transporter family involves a coupled exchange between a Cl− anion and a proton (H+), which makes the transport function dependent on ambient pH. Transport activity peaks at pH 4.5 and stalls at neutral pH. However, a structure of the WT protein at acidic pH is not available, making it difficult to assess the global conformational rearrangements that support a pH-dependent gating mechanism. To enable modeling of the CLC-ec1 dimer at acidic pH, we have applied molecular dynamics simulations (MD) featuring a new force field modification scheme—termed an Equilibrium constant pH approach (ECpH). The ECpH method utilizes linear interpolation between the force field parameters of protonated and deprotonated states of titratable residues to achieve a representation of pH-dependence in a narrow range of physiological pH values. Simulations of the CLC-ec1 dimer at neutral and acidic pH comparing ECpH-MD to canonical MD, in which the pH-dependent protonation is represented by a binary scheme, substantiates the better agreement of the conformational changes and the final model with experimental data from NMR, cross-link and AFM studies, and reveals structural elements that support the gate-opening at pH 4.5, including the key glutamates Gluin and Gluex.
5. Development of Cu ²⁺ -Based Distance Methods and Force Field Parameters for the Determination of PNA Conformations and Dynamics by EPR and MD Simulations

   https://doi.org/10.1021/acs.jpcb.0c05509  

   Gamble Jarvi, Austin ; Sargun, Artur ; Bogetti, Xiaowei ; Wang, Junmei ; Achim, Catalina ; Saxena, Sunil ( August 2020 , The Journal of Physical Chemistry B)

   Peptide nucleic acids (PNAs) are a promising group of synthetic analogues of DNA and RNA that offer several distinct advantages over the naturally occurring nucleic acids for applications in biosensing, drug delivery, and nanoelectronics. Because of its structural differences from DNA/RNA, methods to analyze and assess the structure, conformations, and dynamics are needed. In this work, we develop synergistic techniques for the study of the PNA conformation. We use CuQ2, a Cu(II) complex with 8-hydroxyquinoline (HQ), as an alternative base pair and as a spin label in electron paramagnetic resonance (EPR) distance methods. We use molecular dynamics (MD) simulations with newly developed force field parameters for the spin labels to interpret the distance constraints determined by EPR. We complement these methods by UV–vis and circular dichroism measurements and assess the efficacy of the Cu(II) label on a PNA duplex whose backbone is based on aminoethylglycine and a duplex with a hydroxymethyl backbone modification. We show that the Cu(II) label functions efficiently within the standard PNA and the hydroxymethyl-modified PNA and that the MD parameters may be used to accurately reproduce our EPR findings. Through the combination of EPR and MD, we gain new insights into the PNA structure and conformationsmore »as well as into the mechanism of orientational selectivity in Cu(II) EPR at X-band. These results present for the first time a rigid Cu(II) spin label used for EPR distance measurements in PNA and the accompanying MD force fields for the spin label. Our studies also reveal that the spin labels have a low impact on the structure of the PNA duplexes. The combined MD and EPR approach represents an important new tool for the characterization of the PNA duplex structure and provides valuable information to aid in the rational application of PNA at large.« less