scholarly journals Differentiation between Enamines and Tautomerizable Imines Oxidation Reaction Mechanism using Electron-Vibration-Vibration Two Dimensional Infrared Spectroscopy

Molecules ◽  
2019 ◽  
Vol 24 (5) ◽  
pp. 869 ◽  
Author(s):  
Fengqin Long ◽  
Zheng Chen ◽  
Keli Han ◽  
Lu Zhang ◽  
Wei Zhuang
Keyword(s):  
Reaction Mechanism ◽  
Reaction Mechanisms ◽  
Theoretical Calculations ◽  
Two Dimensional ◽  
Oxidation Reactions ◽  
Spectral Signatures ◽  
Potential Strength ◽  
Chemical Reaction Mechanisms ◽  
2Dir Spectroscopy ◽  
Two Dimensional Infrared Spectroscopy

Intermediates lie at the center of chemical reaction mechanisms. However, detecting intermediates in an organic reaction and understanding its role in reaction mechanisms remains a big challenge. In this paper, we used the theoretical calculations to explore the potential of the electron-vibration-vibration two-dimensional infrared (EVV-2DIR) spectroscopy in detecting the intermediates in the oxidation reactions of enamines and tautomerizable imines with 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO). We show that while it is difficult to identify the intermediates from their infrared and Raman signals, the simulated EVV-2DIR spectra of these intermediates have well resolved spectral features, which are absent in the signals of reactants and products. These characteristic spectral signatures can, therefore, be used to reveal the reaction mechanism as well as monitor the reaction progress. Our work suggests the potential strength of EVV-2DIR technique in studying the molecular mechanism of organic reactions in general.

A Paramedic Treatment for Modeling Explicitly Solvated Chemical Reaction Mechanisms

2018 ◽  
Author(s):  
Yasemin Basdogan ◽  
John Keith
Keyword(s):  
Reaction Mechanism ◽  
Chemical Reaction ◽  
Reaction Mechanisms ◽  
Reaction Pathway ◽  
Optimization Procedure ◽  
Cost Effective ◽  
Chemical Reaction Mechanisms ◽  
Solvent Molecules ◽  
Dynamics Simulations ◽  
Mbh Reaction

<div> <div> <div> <p>We report a static quantum chemistry modeling treatment to study how solvent molecules affect chemical reaction mechanisms without dynamics simulations. This modeling scheme uses a global optimization procedure to identify low energy intermediate states with different numbers of explicit solvent molecules and then the growing string method to locate sequential transition states along a reaction pathway. Testing this approach on the acid-catalyzed Morita-Baylis-Hillman (MBH) reaction in methanol, we found a reaction mechanism that is consistent with both recent experiments and computationally intensive dynamics simulations with explicit solvation. In doing so, we explain unphysical pitfalls that obfuscate computational modeling that uses microsolvated reaction intermediates. This new paramedic approach can promisingly capture essential physical chemistry of the complicated and multistep MBH reaction mechanism, and the energy profiles found with this model appear reasonably insensitive to the level of theory used for energy calculations. Thus, it should be a useful and computationally cost-effective approach for modeling solvent mediated reaction mechanisms when dynamics simulations are not possible. </p> </div> </div> </div>

Different Spectral Signatures of Octapeptide 310- and α-Helices Revealed by Two-Dimensional Infrared Spectroscopy

2006 ◽  
Vol 110 (12) ◽  
pp. 5834-5837 ◽  
Author(s):  
Hiroaki Maekawa ◽  
Claudio Toniolo ◽  
Alessandro Moretto ◽  
Quirinus B. Broxterman ◽  
Nien-Hui Ge
Keyword(s):  
Infrared Spectroscopy ◽  
Two Dimensional ◽  
Spectral Signatures ◽  
Two Dimensional Infrared Spectroscopy

Acid–base equilibrium dynamics in methanol and dimethyl sulfoxide probed by two-dimensional infrared spectroscopy

2015 ◽  
Vol 17 (27) ◽  
pp. 17557-17561 ◽  
Author(s):  
Chiho Lee ◽  
Hyewon Son ◽  
Sungnam Park
Keyword(s):  
Infrared Spectroscopy ◽  
Dimethyl Sulfoxide ◽  
Acid Dissociation ◽  
Two Dimensional ◽  
Acid Base ◽  
Equilibrium Dynamics ◽  
Dissociation Equilibrium ◽  
Acid Base Equilibrium ◽  
2Dir Spectroscopy ◽  
Two Dimensional Infrared Spectroscopy

Two-dimensional infrared (2DIR) spectroscopy was successfully used to investigate the acid dissociation equilibrium of HN3 in methanol (CH3OH) and dimethyl sulfoxide (DMSO).

scholarly journals Two-dimensional Infrared Spectroscopy Reveals Better Insights of Structure and Dynamics of Protein

Molecules ◽  
2021 ◽  
Vol 26 (22) ◽  
pp. 6893
Author(s):  
Kiran Sankar Maiti
Keyword(s):  
Protein Structure ◽  
Vibrational Spectroscopy ◽  
Structural Information ◽  
Living System ◽  
Ultrafast Dynamics ◽  
Two Dimensional ◽  
Biochemical Processes ◽  
Structure And Dynamics ◽  
2Dir Spectroscopy ◽  
Two Dimensional Infrared Spectroscopy

Proteins play an important role in biological and biochemical processes taking place in the living system. To uncover these fundamental processes of the living system, it is an absolutely necessary task to understand the structure and dynamics of the protein. Vibrational spectroscopy is an established tool to explore protein structure and dynamics. In particular, two-dimensional infrared (2DIR) spectroscopy has already proven its versatility to explore the protein structure and its ultrafast dynamics, and it has essentially unprecedented time resolutions to observe the vibrational dynamics of the protein. Providing several examples from our theoretical and experimental efforts, it is established here that two-dimensional vibrational spectroscopy provides exceptionally more information than one-dimensional vibrational spectroscopy. The structural information of the protein is encoded in the position, shape, and strength of the peak in 2DIR spectra. The time evolution of the 2DIR spectra allows for the visualisation of molecular motions.

scholarly journals Insulin dimer dissociation and unfolding revealed by amide I two-dimensional infrared spectroscopy

2010 ◽  
Vol 12 (14) ◽  
pp. 3579-3588 ◽  
Author(s):  
Ziad Ganim ◽  
Kevin C. Jones ◽  
Andrei Tokmakoff
Keyword(s):  
Infrared Spectroscopy ◽  
Two Dimensional ◽  
2Dir Spectroscopy ◽  
Two Dimensional Infrared Spectroscopy

A structurally sensitive probe of the monomer/dimer equilibrium of insulin was developed using 2DIR spectroscopy and interpreted using calculated spectra.

Broadband two dimensional infrared spectroscopy of cyclic amide 2-Pyrrolidinone

2015 ◽  
Vol 17 (38) ◽  
pp. 24998-25003 ◽  
Author(s):  
Kiran Sankar Maiti
Keyword(s):  
Technological Development ◽  
Biological Molecules ◽  
Two Dimensional ◽  
Complex Molecules ◽  
The Past ◽  
Cyclic Amide ◽  
2Dir Spectroscopy ◽  
Physical And Chemical ◽  
Two Dimensional Infrared Spectroscopy ◽  
Half Decade

In the past one-and-a-half decade there has been a significant methodological and technological development of two dimensional infrared (2DIR) spectroscopy, which unfolds many underlying physical and chemical processes of complex molecules, especially for biological molecules.

A Paramedic Treatment for Modeling Explicitly Solvated Chemical Reaction Mechanisms

2018 ◽  
Author(s):  
Yasemin Basdogan ◽  
John Keith
Keyword(s):  
Reaction Mechanism ◽  
Chemical Reaction ◽  
Reaction Mechanisms ◽  
Reaction Pathway ◽  
Optimization Procedure ◽  
Cost Effective ◽  
Chemical Reaction Mechanisms ◽  
Solvent Molecules ◽  
Dynamics Simulations ◽  
Mbh Reaction

<div> <div> <div> <p>We report a static quantum chemistry modeling treatment to study how solvent molecules affect chemical reaction mechanisms without dynamics simulations. This modeling scheme uses a global optimization procedure to identify low energy intermediate states with different numbers of explicit solvent molecules and then the growing string method to locate sequential transition states along a reaction pathway. Testing this approach on the acid-catalyzed Morita-Baylis-Hillman (MBH) reaction in methanol, we found a reaction mechanism that is consistent with both recent experiments and computationally intensive dynamics simulations with explicit solvation. In doing so, we explain unphysical pitfalls that obfuscate computational modeling that uses microsolvated reaction intermediates. This new paramedic approach can promisingly capture essential physical chemistry of the complicated and multistep MBH reaction mechanism, and the energy profiles found with this model appear reasonably insensitive to the level of theory used for energy calculations. Thus, it should be a useful and computationally cost-effective approach for modeling solvent mediated reaction mechanisms when dynamics simulations are not possible. </p> </div> </div> </div>

Insights into the reaction mechanism of propene H/D exchange over acidic zeolite catalysts from theoretical calculations

2016 ◽  
Vol 6 (16) ◽  
pp. 6328-6338 ◽  
Author(s):  
Xianfeng Yi ◽  
Lihong Ding ◽  
Guangchao Li ◽  
Zhiqiang Liu ◽  
Hongqiang Xia ◽  
...  
Keyword(s):  
Reaction Mechanism ◽  
Reaction Mechanisms ◽  
Theoretical Calculations ◽  
Zeolite Catalysts

The reaction mechanisms of propene H/D exchange over deuterated acidic ZSM-5 zeolite have been theoretically revealed.

Determination of Complex Reaction Mechanisms

2006 ◽  
Author(s):  
John Ross ◽  
Igor Schreiber ◽  
Marcel O. Vlad
Keyword(s):  
Reaction Mechanism ◽  
Reaction Mechanisms ◽  
Reaction Pathway ◽  
Chemical Species ◽  
Rate Coefficients ◽  
Chemical System ◽  
Evolutionary Development ◽  
Complex Reaction ◽  
Oscillatory Reactions

In a chemical system with many chemical species several questions can be asked: what species react with other species: in what temporal order: and with what results? These questions have been asked for over one hundred years about simple and complex chemical systems, and the answers constitute the macroscopic reaction mechanism. In Determination of Complex Reaction Mechanisms authors John Ross, Igor Schreiber, and Marcel Vlad present several systematic approaches for obtaining information on the causal connectivity of chemical species, on correlations of chemical species, on the reaction pathway, and on the reaction mechanism. Basic pulse theory is demonstrated and tested in an experiment on glycolysis. In a second approach, measurements on time series of concentrations are used to construct correlation functions and a theory is developed which shows that from these functions information may be inferred on the reaction pathway, the reaction mechanism, and the centers of control in that mechanism. A third approach is based on application of genetic algorithm methods to the study of the evolutionary development of a reaction mechanism, to the attainment given goals in a mechanism, and to the determination of a reaction mechanism and rate coefficients by comparison with experiment. Responses of non-linear systems to pulses or other perturbations are analyzed, and mechanisms of oscillatory reactions are presented in detail. The concluding chapters give an introduction to bioinformatics and statistical methods for determining reaction mechanisms.

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