Free energy profile analysis to identify factors activating the aggregation-induced emission of a cyanostilbene derivative

2021 ◽  
Author(s):  
Norifumi Yamamoto
Keyword(s):  
Free Energy ◽  
Profile Analysis ◽  
Energy Profile ◽  
Contributing Factors ◽  
Free Energy Profile ◽  
Aggregation Induced Emission ◽  
Energy Profiles ◽  
Free Energy Profiles

The contributing factors that cause the aggregation-induced emission (AIE) are determined by identifying characteristic differences in the free energy profiles of the AIE processes of the AIE-active E-form of CN-MBE and the inactive Z-form.

scholarly journals Accelerated Computation of Free Energy Profile at ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semi-Empirical Reference Potential. II. Recalibrating Semi-Empirical Parameters with Force Matching

2019 ◽  
Author(s):  
Xiaoliang Pan ◽  
Pengfei Li ◽  
Junming Ho ◽  
Jingzhi Pu ◽  
Ye Mei ◽  
...  
Keyword(s):  
Free Energy ◽  
Ab Initio ◽  
Quantum Mechanical ◽  
Energy Profile ◽  
Free Energy Profile ◽  
Force Matching ◽  
Energy Profiles ◽  
Reference Potential ◽  
Semi Empirical ◽  
Free Energy Profiles

An efficient and accurate reference potential simulation protocol is proposed for producing ab initio quantum mechanical molecular mechanical (AI-QM/MM) quality free energy profiles for chemical<br>reactions in a solvent or macromolecular environment. This protocol involves three stages: (a) using force matching to recalibrate a semi-empirical quantum mechanical (SE-QM) Hamiltonian for the specific reaction under study; (b) employing the recalibrated SE-QM Hamiltonian (in combination with molecular mechanical force fields) as the reference potential to drive umbrella samplings along the reaction pathway; and (c) computing AI-QM/MM energy values for collected configurations from the sampling and performing weighted thermodynamic perturbation to acquire AI-QM/MM corrected reaction free energy profile. For three model reactions (identity SN2 reaction, Menshutkin reaction, and glycine proton transfer reaction) in aqueous solution and one enzyme reaction (Claisen arrangement in chorismate mutase), our simulations using recalibrated PM3 SE-QM Hamiltonians well reproduced AI-QM/MM free energy profiles (at the B3LYP/6-31G* level of theory) all within 1 kcal/mol with a 20 to 45 fold reduction in the computer time.

scholarly journals Temperature Dependent Entropy Driven Water Uptake in Phase Separated Aerosol from Steered Molecular Dynamics and Intrinsic Surface Analysis

2021 ◽  
Author(s):  
Mária Lbadaoui-Darvas ◽  
Satoshi Takahama ◽  
Athanasios Nenes
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Water Uptake ◽  
Energy Profile ◽  
Temperature Dependent ◽  
Finite Velocity ◽  
Free Energy Profile ◽  
Energy Profiles ◽  
Accommodation Coefficients ◽  
Free Energy Profiles

&lt;p&gt;Dynamic water uptake by aerosol is a major driver of cloud droplet activation and growth. Interfacial mass transfer&amp;#8212; that governs water uptake if the mean free path of molecules in the vapour phase is comparable to particle size &amp;#8212; is represented in models by the mass accommodation coefficient. Although widely used, this approach neglects &lt;em&gt;i&lt;/em&gt;) other internal interfaces (e.g., liquid-liquid that may be important for water uptake), and, &lt;em&gt;ii&lt;/em&gt;) fluctuations of the liquid surface from capillary waves that modulate the surface and induce ambiguity in the estimation of mass accommodation coefficients. These issues can be addressed if the full path of the water molecule &amp;#8211; from vapour to the bulk aqueous phase - is considered.&lt;span&gt;&amp;#160;&lt;/span&gt;&lt;/p&gt;&lt;p&gt;We demonstrate, using steered molecular simulations, that a full treatment of the water uptake process reveals important details of the mechanism. The simulations are used to reconstruct the free energy profile of water transport across a vapour/hydroxy cis-pinonic acid/water double interface at 300 K and 200 K. In steered molecular dynamics the transferred molecule is pulled with a finite velocity along an aptly chosen reaction coordinate and the work exerted is used to reconstruct the free energy profile. Due to the finite velocity pulling, this method takes the effect of friction on the transport mechanism into account, which is important for phases of considerably different friction coefficients and is neglected by&lt;span&gt;&amp;#160; &lt;/span&gt;quasi equilibrium free energy methods. Free energy profiles are used to estimate surface and bulk uptake coefficients and are decomposed into entropic and enthalpic contributions.&lt;span&gt;&amp;#160;&lt;/span&gt;&lt;/p&gt;&lt;p&gt;Surface accommodation coefficients are unity at both temperatures, while bulk uptake at 300 K from the internal interface is strongly hindered (k&lt;sub&gt;b&lt;/sub&gt;=0.05) by the increased density and molecular order in the first layer of the aqueous phase, which results in decreased orientational entropy. The difference between bulk and surface uptake coefficients also implies that water accumulates in the organic shell, which cannot be predicted using a single uptake coefficient for the whole particle. The minimum of the free energy profile at the organic/water interface, rationalised by increased conformational entropy due to local mixing and the depleted system density, results in a concentration gradient which helps maintain low surface tension and phase separation. Low surface tensions may explain increased CCN activity. These entropic features of the free energy profiles diminish at low temperature, which invokes a completely different mechanism of water uptake. Our results point out the need to describe water uptake in aerosol growth models using a temperature dependent parametrisation.&lt;/p&gt;

scholarly journals Accelerated Computation of Free Energy Profile at ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semi-Empirical Reference Potential. II. Recalibrating Semi-Empirical Parameters with Force Matching

2019 ◽  
Author(s):  
Xiaoliang Pan ◽  
Pengfei Li ◽  
Junming Ho ◽  
Jingzhi Pu ◽  
Ye Mei ◽  
...  
Keyword(s):  
Free Energy ◽  
Ab Initio ◽  
Quantum Mechanical ◽  
Energy Profile ◽  
Free Energy Profile ◽  
Force Matching ◽  
Energy Profiles ◽  
Reference Potential ◽  
Semi Empirical ◽  
Free Energy Profiles

An efficient and accurate reference potential simulation protocol is proposed for producing ab initio quantum mechanical molecular mechanical (AI-QM/MM) quality free energy profiles for chemical<br>reactions in a solvent or macromolecular environment. This protocol involves three stages: (a) using force matching to recalibrate a semi-empirical quantum mechanical (SE-QM) Hamiltonian for the specific reaction under study; (b) employing the recalibrated SE-QM Hamiltonian (in combination with molecular mechanical force fields) as the reference potential to drive umbrella samplings along the reaction pathway; and (c) computing AI-QM/MM energy values for collected configurations from the sampling and performing weighted thermodynamic perturbation to acquire AI-QM/MM corrected reaction free energy profile. For three model reactions (identity SN2 reaction, Menshutkin reaction, and glycine proton transfer reaction) in aqueous solution and one enzyme reaction (Claisen arrangement in chorismate mutase), our simulations using recalibrated PM3 SE-QM Hamiltonians well reproduced AI-QM/MM free energy profiles (at the B3LYP/6-31G* level of theory) all within 1 kcal/mol with a 20 to 45 fold reduction in the computer time.

scholarly journals Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanical accuracy via a semi-empirical reference potential. II. Recalibrating semi-empirical parameters with force matching

2019 ◽  
Vol 21 (37) ◽  
pp. 20595-20605 ◽  
Author(s):  
Xiaoliang Pan ◽  
Pengfei Li ◽  
Junming Ho ◽  
Jingzhi Pu ◽  
Ye Mei ◽  
...  
Keyword(s):  
Free Energy ◽  
Ab Initio ◽  
Quantum Mechanical ◽  
Energy Profile ◽  
Force Matching ◽  
Energy Profiles ◽  
Reference Potential ◽  
Simulation Protocol ◽  
Semi Empirical ◽  
Free Energy Profiles

An efficient and accurate reference potential simulation protocol is proposed for producing ab initio quantum mechanical/molecular mechanical (AI-QM/MM) quality free energy profiles for chemical reactions in a solvent or macromolecular environment.

scholarly journals Chemical-state-dependent free energy profile from single-molecule trajectories of biomolecular motor: Application to processive chitinase

2019 ◽  
Author(s):  
Kei-ichi Okazaki ◽  
Akihiko Nakamura ◽  
Ryota Iino
Keyword(s):  
Free Energy ◽  
Single Molecule ◽  
Chemical State ◽  
Energy Profile ◽  
Free Energy Profile ◽  
Energy Profiles ◽  
Biomolecular Motors ◽  
State Dependent ◽  
Chitinase A ◽  
State Changes

ABSTRACTThe mechanism of biomolecular motors has been elucidated using single-molecule experiments for visualizing motor motion. However, it remains elusive that how changes in the chemical state during the catalytic cycle of motors lead to unidirectional motions. In this study, we use singlemolecule trajectories to estimate an underlying diffusion model with chemical-state-dependent free energy profile. To consider nonequilibrium trajectories driven by the chemical energy consumed by biomolecular motors, we develop a novel framework based on a hidden Markov model, wherein switching among multiple energy profiles occurs reflecting the chemical state changes in motors. The method is tested using simulation trajectories and applied to singlemolecule trajectories of processive chitinase, a linear motor that is driven by the hydrolysis energy of a single chitin chain. The chemical-state-dependent free energy profile underlying the burnt- bridge Brownian ratchet mechanism of processive chitinase is determined. The novel framework allows us to connect the chemical state changes to the unidirectional motion of biomolecular motors.

scholarly journals Particle Diffusivity and Free-Energy Profiles in Hydrogels from Time-Resolved Penetration Data

2021 ◽  
Author(s):  
Amanuel Wolde-Kidan ◽  
Anna Herrmann ◽  
Albert Prause ◽  
Michael Gradzielski ◽  
Rainer Haag ◽  
...  
Keyword(s):  
Free Energy ◽  
Time Resolved ◽  
Energy Profiles ◽  
Penetration Data ◽  
Free Energy Profiles
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