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  1. Abstract

    Conjugated polymers have received significant attention as potentially lightweight and highly tailorable alternatives to inorganic semiconductors, but their synthesis is often complex, produces toxic byproducts, and they are not typically designed to be degradable or recyclable. These drawbacks necessitate dedicated efforts to discover materials with design motifs that enable targeted and efficient degradation of conjugated polymers. In this vein, the synthetic simplicity of 1,4‐dihydropyrrolo[3,2‐b]pyrroles (DHPPs) is exploited to access azomethine‐containing copolymers via a benign acid‐catalyzed polycondensation protocol. Polymerizations involve reacting a dialdehyde‐functionalized dihydropyrrolopyrrole withp‐phenylenediamine as the comonomer usingp‐toluenesulfonic acid as a catalyst. The inherent dynamic equilibrium of the azomethine bonds subsequently enabled the degradation of the polymers in solution in the presence of acid. Degradation of the polymers is monitored via NMR, UV‐vis absorbance, and fluorescence spectroscopies, and the polymers are shown to be fully degradable. Notably, while absorbance measurements reveal a continued shift to higher energies with extended exposure to acid, fluorescence measurements show a substantial increase in the fluorescence response upon degradation. Results from this study encourage the continued development of environmentally‐conscious polymerizations to attain polymeric materials with useful properties while simultaneously creating polymers with structural handles for end‐of‐life management or/and recyclability.

     
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  2. Abstract

    Aerosol particles are important for our global climate, but the mechanisms and especially the relative importance of various vapors for new particles formation (NPF) remain uncertain. Quantum chemical (QC) studies on organic enhanced nucleation has for the past couple of decades attracted immense attention, but very little remains known about the exact organic compounds that potentially are important for NPF. Here we comprehensively review the QC literature on atmospheric cluster formation involving organic compounds. We outline the potential cluster systems that should be further investigated. Cluster formation involving complex multi‐functional organic accretion products warrant further investigations, but such systems are out of reach with currently applied methodologies. We suggest a “cluster of functional groups” approach to address this issue, which will allow for the identification of the potential structure of organic compounds that are involved in atmospheric NPF.

    This article is categorized under:

    Theoretical and Physical Chemistry > Reaction Dynamics and Kinetics

    Software > Quantum Chemistry

    Theoretical and Physical Chemistry > Thermochemistry

    Molecular and Statistical Mechanics > Molecular Interactions

     
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  3. Abstract

    Charged residues on the surface of proteins are critical for both protein stability and interactions. However, many proteins contain binding regions with a high net charge that may destabilize the protein but are useful for binding to oppositely charged targets. We hypothesized that these domains would be marginally stable, as electrostatic repulsion would compete with favorable hydrophobic collapse during folding. Furthermore, by increasing the salt concentration, we predict that these protein folds would be stabilized by mimicking some of the favorable electrostatic interactions that take place during target binding. We varied the salt and urea concentrations to probe the contributions of electrostatic and hydrophobic interactions for the folding of the yeast SH3 domain found in Abp1p. The SH3 domain was significantly stabilized with increased salt concentrations due to Debye–Huckel screening and a nonspecific territorial ion‐binding effect. Molecular dynamics and NMR show that sodium ions interact with all 15 acidic residues but do little to change backbone dynamics or overall structure. Folding kinetics experiments show that the addition of urea or salt primarily affects the folding rate, indicating that almost all the hydrophobic collapse and electrostatic repulsion occur in the transition state. After the transition state formation, modest yet favorable short‐range salt bridges are formed along with hydrogen bonds, as the native state fully folds. Thus, hydrophobic collapse offsets electrostatic repulsion to ensure this highly charged binding domain can still fold and be ready to bind to its charged peptide targets, a property that is likely evolutionarily conserved over 1 billion years.

     
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  4. Abstract

    Facing the continuous emergence of new psychoactive substances (NPS) and their threat to public health, more effective methods for NPS prediction and identification are critical. In this study, the pharmacological affinity fingerprints (Ph-fp) of NPS compounds were predicted by Random Forest classification models using bioactivity data from the ChEMBL database. The binaryPh-fpis the vector consisting of a compound’s activity against a list of molecular targets reported to be responsible for the pharmacological effects of NPS. Their performance in similarity searching and unsupervised clustering was assessed and compared to 2D structure fingerprints Morgan and MACCS (1024-bits ECFP4 and 166-bits SMARTS-based MACCS implementation of RDKit). The performance in retrieving compounds according to their pharmacological categorizations is influenced by the predicted active assay counts inPh-fpand the choice of similarity metric. Overall, the comparative unsupervised clustering analysis suggests the use of a classification model with Morgan fingerprints as input for the construction ofPh-fp. This combination gives satisfactory clustering performance based on external and internal clustering validation indices.

     
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  5. The title compound, [Al 4 (CH 3 ) 8 (C 2 H 7 N) 2 H 2 ], crystallizes as eight-membered rings with –(CH 3 ) 2 Al–(CH 3 ) 2 N–(CH 3 ) 2 Al– moieties connected by single hydride bridges. In the X-ray structure, the ring has a chair conformation, with the hydride H atoms being close to the plane through the four Al atoms. An optimized structure was also calculated by all-electron density functional theory (DFT) methods, which agrees with the X-ray structure but gives a somewhat different geometry for the hydride bridge. Charges on the individual atoms were determined by valence shell occupancy refinements using MoPro and also by DFT calculations analyzed by several different methods. All methods agree in assigning a positive charge to the Al atoms, negative charges to the C, N, and hydride H atoms, and small positive charges to the methyl H atoms. 
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  6. Abstract

    The 3D reference interaction site model (3D‐RISM) of molecular solvation is a powerful tool for computing the equilibrium thermodynamics and density distributions of solvents, such as water and co‐ions, around solute molecules. However, 3D‐RISM solutions can be expensive to calculate, especially for proteins and other large molecules where calculating the potential energy between solute and solvent requires more than half the computation time. To address this problem, we have developed and implemented treecode summation for long‐range interactions and analytically corrected cut‐offs for short‐range interactions to accelerate the potential energy and long‐range asymptotics calculations in non‐periodic 3D‐RISM in the AmberTools molecular modeling suite. For the largest single protein considered in this work, tubulin, the total computation time was reduced by a factor of 4. In addition, parallel calculations with these new methods scale almost linearly and the iterative solver remains the largest impediment to parallel scaling. To demonstrate the utility of our approach for large systems, we used 3D‐RISM to calculate the solvation thermodynamics and density distribution of 7‐ring microtubule, consisting of 910 tubulin dimers, over 1.2 million atoms.

     
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  7. Abstract

    The nature of halogen bonding under different dielectric conditions remains underexplored, especially for inorganic systems. The structural and energetic properties of model halogen bonded complexes (R3M−I—NH3for R=H and F, and M=C, Si, and Ge) are examined computationally for relative permittivities between 1 and 109 using an implicit solvent model. We confirm and assess the exceptionally high maximum potentials at the sigma hole on I (Vs,max) in F3Ge−I relative to cases where M=C or Si. In particular, Ge far outperforms Si in mediating inductive effects. Linear relationships, typically with R2>0.97, are identified betweenVs,max, the full point charge on I in R3M−I, and the interaction energy, and optimized I—N distance in the complexes. An anomalous trend is identified in which, for each M, F3M−I—NH3becomeslessstable as the optimized I—N distance getsshorterin different dielectric environments; it is explained using the F−I—NH3complex as a reference.

     
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  8. Abstract

    AutoMeKin2021 is an updated version of tsscds2018, a program for the automated discovery of reaction mechanisms (J. Comput. Chem.2018,39, 1922). This release features a number of new capabilities: rare‐event molecular dynamics simulations to enhance reaction discovery, extension of the original search algorithm to study van der Waals complexes, use of chemical knowledge, a new search algorithm based on bond‐order time series analysis, statistics of the chemical reaction networks, a web application to submit jobs, and other features. The source code, manual, installation instructions and the website link are available at:https://rxnkin.usc.es/index.php/AutoMeKin

     
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  9. Abstract

    The time‐dependent Schrödinger equation can be rewritten so that its interpretation is no longer probabilistic. Two well‐known and related reformulations are Bohmian mechanics and quantum hydrodynamics. In these formulations, quantum particles follow real, deterministic trajectories influenced by a quantum force. Generally, trajectory methods are not applied to electronic structure calculations as they predict that the electrons in a ground‐state, real, molecular wavefunction are motionless. However, a spin‐dependent momentum can be recovered from the nonrelativistic limit of the Dirac equation. Therefore, we developed new, spin‐dependent equations of motion for the quantum hydrodynamics of electrons in molecular orbitals. The equations are based on a Lagrange multiplier, which constrains each electron to an isosurface of its molecular orbital, as required by the spin‐dependent momentum. Both the momentum and the Lagrange multiplier provide a unique perspective on the properties of electrons in molecules.

     
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  10. Abstract

    In this article, we provide advice and insights, based on our own experiences, for computational chemists who are beginning new tenure‐track positions at primarily undergraduate institutions. Each of us followed different routes to obtain our tenure‐track positions, but we all experienced similar challenges when getting started in our new position. In this article, we discuss our approaches to seven areas that we all found important for engaging undergraduate students in our computational chemistry research, including setting up computational resources, recruiting research students, training research students, designing student projects, managing the lab, mentoring students, and student conference participation.

     
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