Entropic Path Sampling: Computational Protocol to Evaluate Entropic Profile along a Reaction Path

2021 ◽  
pp. 10713-10719
Author(s):  
Zhi-Xin Qin ◽  
Matthew Tremblay ◽  
Xin Hong ◽  
Zhongyue J. Yang
Keyword(s):  
Reaction Path ◽  
Path Sampling ◽  
Computational Protocol

scholarly journals Entropic Path Sampling: Computational Protocol to Evaluate Entropic Profile along a Reaction Path

2021 ◽  
Author(s):  
Zhi-Xin Qin ◽  
Matthew Tremblay ◽  
Xin Hong ◽  
Zhongyue Yang
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Reaction Path ◽  
Product Formation ◽  
Conformational Flexibility ◽  
Model Reaction ◽  
Energy Minimum ◽  
Path Sampling ◽  
Free Energy Minimum ◽  
Computational Protocol

Fleeting intermediates constitute dynamically-stepwise mechanisms. They have been characterized in molecular dynamics trajectories, but whether these intermediates form a free energy minimum to become entropic intermediate remains elusively defined. We developed a computational protocol known as entropic path sampling to evaluate the entropic variation of reacting species along a reaction path based on an ensemble of trajectories. Using cyclopentadiene dimerization as a model reaction, we observed a shallow entropic trap (–T∆S = –0.8 kcal/mol) along the reaction path which originates from an enhanced conformational flexibility as the reacting species enter into a flat energy region. As the reacting species further approach product formation, unfavorable entropic restriction fails to offset the potential energy drop, resulting in no free energy minimum along the post-TS pathway. Our results show that cyclopentadiene dimerization involves an entropic trap that leads to dynamic intermediates with elongated lifetime, but the reaction does not involve entropic intermediates.

Use of 2½ D imaging in analysis of NiTi martensite

1978 ◽  
Vol 36 (1) ◽  
pp. 610-611
Author(s):  
G. M. Michal
Keyword(s):  
Memory Effect ◽  
Monoclinic Phase ◽  
Reaction Path ◽  
Structural Characteristics ◽  
Salient Feature ◽  
Martensite Phase ◽  
Orientation Relationships ◽  
Low Symmetry ◽  
Hydride Phases ◽  
Unusual Shape

Several TEM investigations have attempted to correlate the structural characteristics to the unusual shape memory effect in NiTi, the consensus being the essence of the memory effect is ostensible manifest in the structure of NiTi transforming martensitic- ally from a B2 ordered lattice to a low temperature monoclinic phase. Commensurate with the low symmetry of the martensite phase, many variants may form from the B2 lattice explaining the very complex transformed microstructure. The microstructure may also be complicated by the enhanced formation of oxide or hydride phases and precipitation of intermetallic compounds by electron beam exposure. Variants are typically found in selfaccommodation groups with members of a group internally twinned and the twins themselves are often observed to be internally twinned. Often the most salient feature of a group of variants is their close clustering around a given orientation. Analysis of such orientation relationships may be a key to determining the nature of the reaction path that gives the transformation its apparently perfect reversibility.

Stability of radical anions derived from substituted 5-nitrofurans investigated by ESR spectroscopy

1985 ◽  
Vol 50 (7) ◽  
pp. 1594-1601 ◽  
Author(s):  
Jiří Klíma ◽  
Larisa Baumane ◽  
Janis Stradinš ◽  
Jiří Volke ◽  
Romualds Gavars
Keyword(s):  
Radical Anion ◽  
High Stability ◽  
Esr Spectroscopy ◽  
Reaction Path ◽  
Order Reaction ◽  
Second Order ◽  
Radical Anions ◽  
Second Order Reaction ◽  
Unpaired Electron Density ◽  
The Stability

It has been found that the decay in dimethylformamide and dimethylformamide-water mixtures of radical anions in five of the investigated 5-nitrofurans is governed by a second-order reaction. Only the decay of the radical anion generated from 5-nitro-2-furfural III may be described by an equation including parallel first- and second-order reactions; this behaviour is evidently caused by the relatively high stability of the corresponding dianion, this being an intermediate in the reaction path. The presence of a larger conjugated system in the substituent in position 2 results in a decrease of the unpaired electron density in the nitro group and, consequently, an increase in the stability of the corresponding radical anions.

Electrolytic reduction of o-nitrobenzyl thiocyanate in buffered solutions on mercury

1985 ◽  
Vol 50 (1) ◽  
pp. 33-41 ◽  
Author(s):  
Jaromír Hlavatý
Keyword(s):  
Acidic Medium ◽  
Reaction Path ◽  
Electrolytic Reduction ◽  
Buffer System ◽  
Height Ratio ◽  
Preparative Electrolysis ◽  
Clear Explanation ◽  
Ec Mechanism ◽  
Controlled Potential

The o-nitrobenzyl thiocyanate (I) behaves differently on the DME and on a large mercury pool electrode. Polarography did not give a sufficiently clear explanation of the reaction mechanism, only the preparative experiments yielded useful results. Whereas polarographic curves in solutions of Britton-Robinson buffer system with 50% by vol. ethanol exhibit two cathodic waves within the pH region 1-12, corresponding according to their height ratio to an uptake of 4 e and 2 e respectively, the controlled potential preparation electrolysis (CPE) and coulometry results indicate a more complicated reaction path. In the CPE carried out at the concentration of I 1 . 10 -2 mol/l the electroreductive splitting of CH2-SCN occurs as the first step. Nitrobenzyl radicals so formed react in the follow-up dimerization resulting in dibenzyl or toluene structures. Simultaneously or at a later stage the completion of the electrolytic reduction of the nitro group proceeds to the hydroxylamino group. In solution of 9 > pH > 1 the CPE of nitro compound I takes place by an ECEC mechanism yielding dibenzodiazocine III, its N-oxide IV and 2,2'-dimethylazoxybenzene (V). In course of preparative electrolysis in strongly acidic medium 2-amino-benzo(l,3)-thiazine-l-oxide (II) is formed by an EC mechanism.

Rare event simulation

2017 ◽  
Author(s):  
Michael P. Allen ◽  
Dominic J. Tildesley
Keyword(s):  
Rare Event ◽  
Path Sampling ◽  
Rapid Progress ◽  
Computationally Efficient ◽  
Transition Path ◽  
Transition Path Sampling ◽  
Event Simulation ◽  
Reaction Coordinates ◽  
Simulation Techniques ◽  
Transition Interface

The development of techniques to simulate infrequent events has been an area of rapid progress in recent years. In this chapter, we shall discuss some of the simulation techniques developed to study the dynamics of rare events. A basic summary of the statistical mechanics of barrier crossing is followed by a discussion of approaches based on the identification of reaction coordinates, and those which seek to avoid prior assumptions about the transition path. The demanding technique of transition path sampling is introduced and forward flux sampling and transition interface sampling are considered as rigorous but computationally efficient approaches.

Accurate prediction of 195Pt NMR chemical shifts for a series of Pt(ii) and Pt(iv) antitumor agents by a non-relativistic DFT computational protocol

2014 ◽  
Vol 43 (14) ◽  
pp. 5409-5426 ◽  
Author(s):  
Athanassios C. Tsipis ◽  
Ioannis N. Karapetsas
Keyword(s):  
Dft Calculations ◽  
Anticancer Agents ◽  
Antitumor Agents ◽  
Chemical Shifts ◽  
Accurate Prediction ◽  
Nmr Chemical Shifts ◽  
Relativistic Dft ◽  
Square Planar ◽  
Wide Range ◽  
Computational Protocol

Exhaustive benchmark DFT calculations reveal that the non-relativistic GIAO-PBE0/SARC-ZORA(Pt)∪6-31+G(d)(E) computational protocol predicts accurate 195Pt NMR chemical shifts for a wide range of square planar Pt(ii) and octahedral Pt(iv) anticancer agents.

scholarly journals The Hydrothermal Stability and the Properties of Non- and Strongly-Interacting Rh Species over Rh/γ, θ-Al2O3 Catalysts

Catalysts ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 99
Author(s):  
Guanghao Cheng ◽  
Gurong Shen ◽  
Jun Wang ◽  
Yunhao Wang ◽  
Weibo Zhang ◽  
...  
Keyword(s):  
Activation Energy ◽  
Apparent Activation Energy ◽  
Aging Time ◽  
Reaction Path ◽  
Aging Treatment ◽  
Hydrothermal Stability ◽  
Hydrothermal Aging ◽  
Strongly Interacting

The present work reports the effects of γ-, θ-phase of alumina on the hydrothermal stability and the properties of non- and strongly-interacting Rh species of the Rh/Al2O3 catalysts. Comparing to γ-Al2O3, θ-Al2O3 can not only reduce the amount of occluded Rh but also better stabilize Rh during hydrothermal aging treatment. When the aging time was prolonged to 70 h, all the non-interacting Rh was transformed into strongly-interacting Rh and occluded Rh. The XPS results indicated that non- and strongly-interacting Rh might exist in the form of Rh/Rh3+ and Rh4+, respectively. CO-NO reaction was chosen as a probe reaction to research more information about non- and strongly-interacting Rh. The two Rh species had similar apparent activation energy (Eapp) of 170 kJ/mol, which indicated that non- and strongly-interacting Rh follow the same reaction path. The non-interacting Rh was removed from aged samples by the acid-treated method, and obtained results showed that only 2.5% and 4.0% non-interacting Rh was maintained in aged Rh/γ-Al2O3 and Rh/θ-Al2O3.

scholarly journals Catalytic Mechanism of Processive GlfT2: Transition Path Sampling Investigation of Substrate Translocation

ACS Omega ◽  
2020 ◽  
Vol 5 (34) ◽  
pp. 21374-21384
Author(s):  
Pavel Janoš ◽  
Igor Tvaroška ◽  
Christoph Dellago ◽  
Jaroslav Koča
Keyword(s):  
Catalytic Mechanism ◽  
Path Sampling ◽  
Transition Path ◽  
Transition Path Sampling
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