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Score Dynamics: Scaling Molecular Dynamics with Picoseconds Time Steps via Conditional Diffusion Model
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Coarse-grained modeling of polyethylene melts: Effect on dynamics
The distinctive viscoelastic behavior of polymers results from a coupled interplay of motion on multiple length and time scales. Capturing the broad time and length scales of polymer motion remains a challenge. Using polyethylene (PE) as a model macromolecule, we construct coarse-grained (CG) models of PE with three to six methyl groups per CG bead and probe two critical aspects of the technique: pressure corrections required after iterative Boltzmann inversion (IBI) to generate CG potentials that match the pressure of reference fully atomistic melt simulations and the transferability of CG potentials across temperatures. While IBI produces nonbonded pair potentials that give excellent agreement between the atomistic and CG pair correlation functions, the resulting pressure for the CG models is large compared with the pressure of the atomistic system. We find that correcting the potential to match the reference pressure leads to nonbonded interactions with much deeper minima and slightly smaller effective bead diameter. However, simulations with potentials generated by IBI and pressure-corrected IBI result in similar mean-square displacements (MSDs) and stress autocorrelation functions G( t ) for PE melts. While the time rescaling factor required to match CG and atomistic models is the same for pressure- and non-pressure-corrected CG models, it strongly depends on temperature. Furthermore, transferability was investigated by comparing the MSDs and stress autocorrelation functions for potentials developed at different temperatures.
A Combined Experimental and Computational Study on the Reaction Dynamics of the 1-Propynyl (CH 3 CC)–Acetylene (HCCH) System and the Formation of Methyldiacetylene (CH 3 CCCCH)
We investigated the 1-propynyl (CH 3 CC; X 2 A 1 ) plus acetylene/acetylene-d 2 (HCCH/DCCD; X 1 Σg + ) under single-collision conditions using the crossed molecular beams method. The reaction was found to produce C 5 H 4 plus atomic hydrogen (H) via an indirect reaction mechanism with a reaction energy of -123 ± 18 kJ mol –1 . Using the DCCD isotopologue, we confirmed that the hydrogen atom is lost from the acetylene reactant. Our computational analysis suggests the reaction proceeds by the barrierless addition of the 1-propynyl radical to acetylene, resulting in C 5 H 5 intermediate(s) that dissociate preferentially to methyldiacetylene (CH 3 CCCCH; X 1 A 1 ) via hydrogen atom emission with a computed reaction energy of -123 ± 4 kJ mol –1 . The barrierless nature of this reaction scheme suggests the 1-propynyl radical may be a key intermediate in hydrocarbon chain growth in cold molecular clouds like TMC-1, where methyl-substituted (poly)acetylenes are known to exist.
27 Al Pulsed Field Gradient, Diffusion–NMR Spectroscopy of Solvation Dynamics and Ion Pairing in Alkaline Aluminate Solutions
Here, pulsed field gradient nuclear magnetic resonance (PFG-NMR) measurements were successfully applied to the 27 Al (I = 5/2) nucleus in concentrated electrolytes to investigate the diffusion of aluminate ions [Al(OH) 4 – ] in simulant high-level nuclear waste (3 M NaOH) between 25 and 85 °C. The temperature-dependent diffusion coefficients obtained from 1 H, 23 Na, and 27 Al PFG-NMR were well fit by a Vogel–Fulcher–Tammann model and a power law equation. Comparison of 27 Al diffusion coefficients of 0.1 M Al(OH) 4 – in ~3 M MOH (where M = Na + , K + , (CH 3 ) 4 N + ) at room temperature varied in agreement with the expected changes in solution viscosity via Stokes–Einstein relationship, confirming that the dominant Al species at these conditions are Al(OH) 4 – monomers. This 27 Al PFG-NMR study extends an established methodology to a previously unexplored nucleus enabling this experimental technique to be leverage for exploring ion transport, speciation, and solution structure in concentrated electrolytes.
Reply to “Comment on ‘Dynamics of Phospholipid Membranes beyond Thermal Undulation’”
Recently, Granek postulated a connection of the Brochard-Lennon (BL) “red blood cell” mode with the short time relaxation of liposomes observed by neutron spin echo (NSE) spectroscopy. The experimental observations themselves clearly exclude this BL mode as an explanation. Here, we emphasize that it is an inherent behavior of lipids detectable with different techniques.
Vacancies in Si Can Improve the Concentration-Dependent Lithiation Rate: Molecular Dynamics Studies of Lithiation Dynamics of Si Electrodes
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Spinor Dynamics in Pristine and Mn 2+ -Doped CsPbBr 3 NC: Role of Spin–Orbit Coupling in Ground- and Excited-State Dynamics
Fully inorganic lead halide perovskite nanocrystals (NCs) are of interest for optoelectronic and light-emitting devices because of their photoluminescence (PL) emission properties, which can be tuned/optimized by (I) surface passivation and (II) doping. (I) Surface passivation of the NC affects PL capabilities, as an underpassivated surface can introduce trap states, which reduces PL quantum yields. (II) Doping NCs and quantum dots with transition-metal ions provides stable optical transitions. Doping perovskite NCs with Mn 2+ ions provides high-intensity 4 T 1 → 6 A 1 optical transitions in addition to the bright intrinsic NC emission. In this study, we use noncollinear density functional theory (DFT) to investigate the roles of surface passivation and doping on the PL emission stability of perovskite NCs. Two models are investigated: (i) a pristine NC and (ii) a NC doped with the Mn 2+ ion. The noncollinear DFT includes spin–orbit coupling (SOC) between different spin states and produces spin adiabatic molecular orbitals. These orbitals are used to calculate the transition dipoles between electronic states, oscillator strengths, radiative transition rates, and emission spectra. It was found that the noncollinear spin basis with SOC slows down hole relaxation in the doped NC by 2 orders of magnitude compared to spin-polarized basis. This is attributed to “spin-flip” transition from the perovskite NC to the Mn 2+ dopant and low-probability nonradiative d-d transition.
Transient Symmetry Controls Photo Dynamics near Conical Intersections
Excited-state chemistry lacks generalised symmetry rules. With many femtochemistry studies focused on individual cases, it is hard to build up the same level of chemical intuition for excited-states as exists for ground states. Here, we unravel the degrees of freedom involved in ultrafast internal conversion (IC) by mapping the vibrational coherence of the initial wavepacket, and the dependence on molecular symmetry in various cyclic tertiary amines. Molecular symmetry plays an important role in the preservation of vibrational coherence in the transit from one electronic state to another. We show here that it is sufficient for the molecule to simply have the possibility of a more symmetric structure to achieve the preservation of vibrational coherence. It can be transient and still lead to preservation. Furthermore, this finding provides an additional angle on how symmetry influences electronic transitions and an additional piece to the puzzle of establishing symmetry-based selection rules for excited-state processes.
Understanding Strain and Failure of a Knot in Polyethylene Using Molecular Dynamics with Machine-Learned Potentials
A neural network potential (NNP) has been developed by fitting to ab initio electronic structure data on hydrocarbons and is used to study failure of linear and knotted polyethylene (PE) chains. A linear PE chain must be highly strained before breaking as the stress is equally distributed across the chain. In contrast, the stress in a PE chain with a 31 or overhand knot, accumulates at the knot’s entrance/exit. We find the strain energy is greatest when the bond length and angle are strained simultaneously, and that the knot weakens the chain by increasing the variance of the C–C–C angle, thereby allowing rupture at lower bond strains. Here, we extend our analysis to both 51 and 52 knots and find that both break at the entrance/exit of a loop. Notably, molecular scale PE knots exhibit many of the same characteristics as knots in a macroscopic rope, with stick–slip phenomena upon tightening and similar points of failure.
Propane–Water Mixtures Confined within Cylindrical Silica Nanopores: Structural and Dynamical Properties Probed by Molecular Dynamics
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Evolution of Chain Dynamics and Oxidation States with Increasing Chain Length for a Donor–Acceptor-Conjugated Oligomer Series
While it is known that the chain length strongly affects the properties of π-conjugated polymers, the effects of chain length on the molecular structure, chain conformation, and oxidation state properties in donor–acceptor-type conjugated structures remain unclear. This limits our understanding of how the polymer molecular weight impacts material properties. Here, a discrete and monodisperse oligomer series (n = 3, 5, 7, 9, 15, and 21) and polymers (nPB), composed of the donor 3,4-propylenedioxythiophene (ProDOT), the acceptor benzothiadiazole (BTD), and methylthio end-capping groups, are synthesized by C–H-activated cross-coupling. The molecular structure, molecular weight, and dispersity of each oligomer/polymer are thoroughly characterized by nuclear magnetic resonance spectroscopy, mass spectrometry, and gel permeation chromatography. This series reveals a rod-to-coil transition at n = 15 and coil formation at polymer length scales of ~28 units via solution small-angle neutron scattering characterization. The oxidation states are deciphered via cyclic voltammetry, differential pulse voltammetry, spectroelectrochemistry, and density functional theory calculations. Oligomers 3–9 undergo successive one-electron oxidation steps, while 15 and higher undergo multielectron oxidations per step in CH 2 Cl 2 –TBAPF6 at a Pt ultramicroelectrode. The electronic transition of each oxidation state (1+, 2+, 3+, etc.) is tracked by absorption spectroscopy, revealing a “bipolaron to di-polaron” transition at n = 7 at which shorter oligomers prefer bipolaron formation and longer oligomers prefer di-polaron formation in their dication states. Furthermore, oxidized 15 has a lower electronic transition energy compared to its polymer homologue, as shown by spectroelectrochemistry, revealing a synergy between the chain length and the oxidation state properties. This study proves that the convergence limit between small molecule and polymer behavior occurs at approximately 15 units and highlights the property transitions that occur as a function of chain length for a donor–acceptor class of conjugated organic materials.
Three Regimes of Polymer Surface Dynamics under Crowded Conditions
In this work, single-molecule tracking was used to characterize the mobility of poly(ethylene glycol) chains at a solid–liquid interface over a wide range of surface coverage. Trajectories exhibited intermittent motion consistent with a generalized continuous time random walk (CTRW) model, where strongly confined “waiting times” alternated with rapid flights. The presence of three characteristic regimes emerged as a function of surface coverage, based on an analysis of effective short-time diffusion coefficients, mean-squared displacement, and CTRW distributions. The dilute “site-blocking” regime exhibited increasing short-time diffusion, less confined behavior, and shorter waiting times with higher surface coverage, as anomalously strong adsorption sites were increasingly passivated. At intermediate values of surface coverage, the “crowding” regime was distinguished by the exact opposite trends (slower, more confined mobility), presumably due to increasing intermolecular interactions. The trends reversed yet again in the “brush” regime, where adsorbing molecules interacted weakly with a layer of extended overlapping chains.