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  1. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. Abstract

    The mechanism of isomerization of hydroxyacetone to 2‐hydroxypropanal is studied within the framework of reaction force analysis at the M06‐2X/6‐311++G(d,p) level of theory. Three unique pathways are considered: (a) a step‐wise mechanism that proceeds through the formation of the Z‐isomer of their shared enediol intermediate, (b) a step‐wise mechanism that forms the E‐isomer of the enediol, and (c) a concerted pathway that bypasses the enediol intermediate. Energy calculations show that the concerted pathway has the lowest activation energy barrier at 45.7 kcal mol−1. The reaction force, chemical potential, and reaction electronic flux are calculated for each reaction to characterize electronic changes throughout the mechanism. The reaction force constant is calculated in order to investigate the synchronous/asynchronous nature of the concerted intramolecular proton transfers involved. Additional characterization of synchronicity is provided by calculating the bond fragility spectrum for each mechanism.

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  8. Abstract

    The role of non‐covalent interactions (NCIs) has broadened with the inclusion of new types of interactions and aplethoraof weak donor/acceptor partners. This work illustrates the potential of chirped‐pulse Fourier transform microwave technique, which has revolutionized the field of rotational spectroscopy. In particular, it has been exploited to reveal the role of NCIs’ in the molecular self‐aggregation of difluoromethane where a pentamer, two hexamers and a heptamer were detected. The development of a new automated assignment program and a sophisticated computational screening protocol was essential for identifying the homoclusters in conditions of spectral congestion. The major role of dispersion forces leads to less directional interactions and more distorted structures than those found in polar clusters, although a detailed analysis demonstrates that the dominant interaction energy is the pairwise interaction. The tetramer cluster is identified as a structural unit in larger clusters, representing the maximum expression of bond between dimers.

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  9. Abstract

    The dimerization of glycine is the simplest oligomerization of amino acids and plays an important role in biology. Although this reaction is thermodynamically unfavorable in the aqueous phase, it has been shown to be spontaneous in the gas phase and proceeds via two different concerted reaction mechanisms known ascisandtrans. This may have profound implications in prebiotic chemistry as common atmospheric prenucleation clusters are thought to have participated in gas‐phase reactions in the early Earth's atmosphere. We hypothesize that particular arrangements of water molecules in these clusters could lead to lowering of the reaction barrier of amino acid dimerization and could lead to abiotic catalysis toward polypeptides. We test our hypothesis on a system of thecistransition state of glycine dimerization solvated by one to five water molecules using a combination of a genetic algorithm‐based configurational sampling, density functional theory geometries, and domain‐based local pair natural orbital coupled‐cluster electronic structure. First, we discuss the validity of the model chemistries used to obtain our results. Then, we show that the Gibbs free energy barrier for the concertedcismechanism can indeed be lowered by the addition of up to five water molecules, depending on the temperature.

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  10. Abstract

    In this perspective, two experienced academic administrators who are computational chemists discuss strategies for how to maintain an active research program at a predominately undergraduate institution as your career progresses. More responsibility equates to less time for research, so planning for research to remain a priority is essential. We all have the same amount of time, so figuring out how to use yours better is the key to remaining active. Professional organizations such as Council on Undergraduate Research, consortia of computational chemists such as Molecular Education and Research Consortium in computational chemistRY and Midwest Undergraduate Computational Chemistry Consortium, and attendance at professional conferences can help sustain your research program. Collaborations with faculty at other institutions provide a particularly effective accountability mechanism as well. Perhaps the best way to improve your productivity is to become a better mentor to your undergraduate students. Building a research group that is fun and exciting develops a culture that sustains itself and provides the momentum necessary to maintain progress toward scientific goals.

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