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Role of Enzyme and Active Site Conformational Dynamics in the Catalysis by α-Amylase Explored with QM/MM Molecular Dynamics
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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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