Optical vs. chemical driving for molecular machines

2016 ◽  
Vol 195 ◽  
pp. 583-597 ◽  
Author(s):  
R. D. Astumian
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Thermodynamic Parameters ◽  
Energy Surface ◽  
Molecular Machines ◽  
Coarse Grained ◽  
Power Stroke ◽  
Microscopic Reversibility ◽  
Single Time ◽  
External Modulation

Molecular machines use external energy to drive transport, to do mechanical, osmotic, or electrical work on the environment, and to form structure. In this paper the fundamental difference between the design principles necessary for a molecular machine to use light or external modulation of thermodynamic parameters as an energy sourcevs.the design principle for using an exergonic chemical reaction as a fuel will be explored. The key difference is that for catalytically-driven motors microscopic reversibility must hold arbitrarily far from equilibrium. Applying the constraints of microscopic reversibility assures that a coarse grained model is consistent with an underlying model for motion on a single time-independent potential energy surface. In contrast, light-driven processes, and processes driven by external modulation of the thermodynamic parameters of a system cannot in general be described in terms of motion on a single time-independent potential energy surface, and the rate constants are not constrained by microscopic reversibility. The results presented here call into question the value of the so-called power stroke model as an explanation of the function of autonomous chemically-driven molecular machines such as are commonly found in biology.

Smoothing potential energy surface of proteins by hybrid coarse grained approach

2017 ◽  
Vol 26 (5) ◽  
pp. 050202
Author(s):  
Yukun Lu ◽  
Xin Zhou ◽  
ZhongCan OuYang
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Energy Surface ◽  
Coarse Grained

An accurate, global, ab initio potential energy surface for the H + 3 molecule

2000 ◽  
Vol 98 (5) ◽  
pp. 261-273 ◽  
Author(s):  
Oleg L. Polyansky, Rita Prosmiti, Wim Kl
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Energy Surface

Active Learning Accelerates Ab Initio Molecular Dynamics on Pericyclic Reactive Energy Surfaces

2020 ◽  
Author(s):  
Shi Jun Ang ◽  
Wujie Wang ◽  
Daniel Schwalbe-Koda ◽  
Simon Axelrod ◽  
Rafael Gomez-Bombarelli
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Transition State ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Energy Surface ◽  
Computational Cost ◽  
Reactive Trajectories ◽  
Dynamics Simulations ◽  
Energy Surfaces

<div>Modeling dynamical effects in chemical reactions, such as post-transition state bifurcation, requires <i>ab initio</i> molecular dynamics simulations due to the breakdown of simpler static models like transition state theory. However, these simulations tend to be restricted to lower-accuracy electronic structure methods and scarce sampling because of their high computational cost. Here, we report the use of statistical learning to accelerate reactive molecular dynamics simulations by combining high-throughput ab initio calculations, graph-convolution interatomic potentials and active learning. This pipeline was demonstrated on an ambimodal trispericyclic reaction involving 8,8-dicyanoheptafulvene and 6,6-dimethylfulvene. With a dataset size of approximately</div><div>31,000 M062X/def2-SVP quantum mechanical calculations, the computational cost of exploring the reactive potential energy surface was reduced by an order of magnitude. Thousands of virtually costless picosecond-long reactive trajectories suggest that post-transition state bifurcation plays a minor role for the reaction in vacuum. Furthermore, a transfer-learning strategy effectively upgraded the potential energy surface to higher</div><div>levels of theory ((SMD-)M06-2X/def2-TZVPD in vacuum and three other solvents, as well as the more accurate DLPNO-DSD-PBEP86 D3BJ/def2-TZVPD) using about 10% additional calculations for each surface. Since the larger basis set and the dynamic correlation capture intramolecular non-covalent interactions more accurately, they uncover longer lifetimes for the charge-separated intermediate on the more accurate potential energy surfaces. The character of the intermediate switches from entropic to thermodynamic upon including implicit solvation effects, with lifetimes increasing with solvent polarity. Analysis of 2,000 reactive trajectories on the chloroform PES shows a qualitative agreement with the experimentally-reported periselectivity for this reaction. This overall approach is broadly applicable and opens a door to the study of dynamical effects in larger, previously-intractable reactive systems.</div>

Rotational de-excitations of C3H+ (1Σ+) by collision with He: new ab initio potential energy surface and scattering calculations

2020 ◽  
Vol 494 (4) ◽  
pp. 5675-5681 ◽  
Author(s):  
Sanchit Chhabra ◽  
T J Dhilip Kumar
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Cross Sections ◽  
Energy Surface ◽  
Molecular Ions ◽  
Basis Set ◽  
Rate Coefficients ◽  
Close Coupling ◽  
Collisional Rate Coefficients

ABSTRACT Molecular ions play an important role in the astrochemistry of interstellar and circumstellar media. C3H+ has been identified in the interstellar medium recently. A new potential energy surface of the C3H+–He van der Waals complex is computed using the ab initio explicitly correlated coupled cluster with the single, double and perturbative triple excitation [CCSD(T)-F12] method and the augmented correlation consistent polarized valence triple zeta (aug-cc-pVTZ) basis set. The potential presents a well of 174.6 cm−1 in linear geometry towards the H end. Calculations of pure rotational excitation cross-sections of C3H+ by He are carried out using the exact quantum mechanical close-coupling approach. Cross-sections for transitions among the rotational levels of C3H+ are computed for energies up to 600 cm−1. The cross-sections are used to obtain the collisional rate coefficients for temperatures T ≤ 100 K. Along with laboratory experiments, the results obtained in this work may be very useful for astrophysical applications to understand hydrocarbon chemistry.

scholarly journals Probing the location of the unpaired electron in spin–orbit changing collisions of NO with Ar

2020 ◽  
Vol 22 (39) ◽  
pp. 22289-22301
Author(s):  
Cornelia G. Heid ◽  
Imogen P. Bentham ◽  
Victoria Walpole ◽  
Razvan Gheorghe ◽  
Pablo G. Jambrina ◽  
...  
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Unpaired Electron ◽  
Energy Surface ◽  
Spin Orbit ◽  
Selective Sampling

The ability to orient NO molecules prior to collision with Ar atoms allows selective sampling of different potential energy surface regions and elucidation of the associated collision pathways.

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