scholarly journals Ab-Initio Computational Study : The Activation Energy Changes and Steric Effects In Peptide Synthesis Of Ac-AA-NH2 and Ac-AP-NH2

Molekul ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. 137
Author(s):  
Indah Pratiwi ◽  
Bambang Cahyono ◽  
Parsaoran Siahaan
Keyword(s):  
Activation Energy ◽  
Reaction Mechanism ◽  
Ab Initio ◽  
Peptide Synthesis ◽  
Reaction Mechanisms ◽  
Steric Effect ◽  
Computational Study ◽  
Computational Method ◽  
Side Chain ◽  
Concerted Reaction

Ab-Initio computational method can be used for simulating reaction mechanisms, such as concerted reaction mechanism on peptide synthesis. The concerted reaction is one of many possible pathways on how peptide can be synthesized. The purpose of this study are probing the concerted reaction mechanism and comparing the steric effect to the reaction, given by different side-chain of alanine (A) and proline (P). Two dipeptides formed from alanine and proline were computed at HF-SCF/6-31G** theory level: Ac-AA-NH2 and Ac-AP-NH2. The res.lts show the activation energy of Ac-AA-NH2  and Ac-AP-NH2 forming via concerted pathway are 167.541 kJ/mol and 161.044 kJ/mol, respectively. The steric difference in side-chain affects the dihedral angle of the structure, and also gives difference to the entropy value of reaction.

scholarly journals Theoretical study on pegylation reaction mechanisms of IFN-α-2a, IFN-α-2b and IFN-β-1a

2017 ◽  
Vol 82 (7-8) ◽  
pp. 841-850
Author(s):  
Mohammad Taqavian ◽  
Daryoush Abedi ◽  
Fatemeh Zigheimat ◽  
Leila Zeidabadinejad
Keyword(s):  
Polyethylene Glycol ◽  
Reaction Mechanism ◽  
Dft Calculations ◽  
Transition State ◽  
Reaction Mechanisms ◽  
Theoretical Study ◽  
Computational Study ◽  
Single Transition ◽  
Experimental Works ◽  
Ab Initio And Dft

Ab initio and DFT calculations have been carried out to study the reaction mechanism between interferons (IFNs) ?-2a, ?-2b and ?-1a and polyethylene glycol (PEG) group. The calculations show that the mechanisms are concerted, in agreement with the results of experimental works. However, although it appears that there is one single transition state, the characteristics of its structure reveal a very synchronous reaction mechanism. The reactions are clearly exothermic and as well have feasible activation energies. Our computational study shows that the lowest transition state energies are related to Lys 134, His 34 and Met 1 of IFN-?-2a, IFN-?-2b and IFN-?-1a, respectively.

SOLVENT AND SUBSTITUENT EFFECTS ON THE INTRAMOLECULAR AMIDE HYDROLYSIS OF N-METHYLMALEAMIC ACID

2009 ◽  
Vol 08 (06) ◽  
pp. 1217-1226 ◽  
Author(s):  
JUN CAI ◽  
ZHIJIAN WU
Keyword(s):  
Reaction Mechanism ◽  
Gas Phase ◽  
Reaction Mechanisms ◽  
Substituent Effects ◽  
Phase Reaction ◽  
Gas Phase Reaction ◽  
Amide Hydrolysis ◽  
Reaction Barriers ◽  
Hydrolysis Of ◽  
Concerted Reaction

Intramolecular amide hydrolysis of N-methylmaleamic acid is revisited at the B3LYP/6-311G(2df, p)//B3LYP/6-31G(d, p) + ZVPE level, including solvent effects at the CPCM-B3LYP/6-311G(2df, p)//Onsager-B3LYP/6-31G(d, p) + ZPVE level. The concerted reaction mechanism is energetically favorable over stepwise reaction mechanisms in both the gas phase and solution. The calculated reaction barriers are significantly lower in solution than in the gas phase. In addition, it is concluded that the substituents of the four N-methylmaleamic acid derivatives considered herein have a significant effect on the gas-phase reaction barriers but a smaller, or little, effect on the barriers in solution.

scholarly journals Sublimation Kinetic Studies of theZr(tmhd)4Complex

2013 ◽  
Vol 2013 ◽  
pp. 1-5 ◽  
Author(s):  
T. S. Arul Jeevan ◽  
K. S. Nagaraja
Keyword(s):  
Activation Energy ◽  
Reaction Mechanism ◽  
Heating Rate ◽  
Reaction Mechanisms ◽  
Kinetic Studies ◽  
Nitrogen Atmosphere ◽  
Dynamic Measurements ◽  
Pure Nitrogen ◽  
Value Analysis ◽  
Pure Nitrogen Atmosphere

The thermal behaviour of tetrakis(2,2,6,6-tetramethyl-3,5-heptanedionato)zirconium(IV), [Zr(tmhd)4] was investigated by nonisothermal and isothermal thermogravimetric methods in a high pure nitrogen atmosphere. The influence of the heating rate in dynamic measurements (6, 8, 10, and 12°C/min) on activation energy was also studied. The nonisothermal sublimation activation energy values determined following the procedures of Arrhenius, Coats and Redfern, Kissinger, and Flynn-Wall yielded76±5,92±2,81±8, and72±7 kJ/mol, respectively, and the isothermal sublimation activation energy was found to be87±4 kJ/mol over the temperature range of 411–462 K. Different reaction mechanisms were used to compare with this value. Analysis of the experimental results suggested that the actual reaction mechanism was anRndeceleration type.

scholarly journals Kinetic and products of C3H3 and C4H2 reaction: theoretical and computational study

2018 ◽  
Vol 10 (2) ◽  
pp. 102
Author(s):  
Antonius Indarto
Keyword(s):  
Ab Initio ◽  
Master Equation ◽  
Reaction Kinetic ◽  
Computational Study ◽  
Molecular Structures ◽  
Computational Method ◽  
Propargyl Radical ◽  
Ring Molecules ◽  
Hydrocarbon Molecules ◽  
High Concentrations

The formation of first aromatic ring was suggested to be a crucial step of the PAHs and soot growth mechanism. In general, four-, five-, six-, or seven-membered ring molecules could be formed by the addition reaction of two hydrocarbon molecules resulted from many different pathways. Small hydrocarbon molecules with numerous concentrations during combustion/pyrolysis are suspected to play an important role. Propargyl radical (•C3H3) and butadiene (C4H2) have been chosen as the initial reactants in this discussion, since they are found at relatively high concentrations in flame experiments to examine the above particular reaction. Following initial addition mechanisms, their adduct intermediate can form a ring molecule and undergo subsequent rearrangement. All possible molecular structures were considered and the viability of each channel was assessed through a “RRKM + master equation” kinetic study. This study is an attemp and example to develop and apply molecular computational method for solving problems in the chemical engineering.Keywords: reaction kinetic, ab-initio calculation, RRKM theory, unimolecular reaction, propargyl, butadiene.AbstrakReaksi pembentukan cincin aromatic pada senyawa hidrokarbon merupakan mekanisme awal terpenting dari pembentukan Polisiklik Aromatik Hidrokarbon (PAH) dan jelaga karbon. Secara umum, senyawa hidrokarbon dengan cincin berjumlah empat, lima, enam, atau tujuh dapat dibentuk oleh reaksi gabungan dua molekul hidrokarbon. Molekul hidrokarbon dengan jumlah atom karbon rendah akan memainkan peranan penting ditinjau dari besarnya konsentrasi senyawa ini saat pembakaran/pirolisis. Dalam diskusi ini, reaksi propargil radikal (•C3H3) dan butadiena (C4H2) digunakan sebagai studi kasus karena konsentrasinya yang relatif tinggi dalam percobaan laboratorium dengan menggunakan bunsen. Secara garis besar, reaksi pembentukan rantai lingkar (cincin) dapat tercapai baik secara langsung setelah reaksi adisi atau melalui penataan ulang molekul. Berbagai struktur molekul dan mekanisme yang mungkin ada dalam reaksi ini akan dianalisis melalui studi kinetika "RRKM + persamaan master (master equation)". Studi ini juga ditujukan sebagai usaha dan contoh untuk memperkenalkan penggunaan kimia komputasi molekuler dalam menyelesaikan berbagai problem di bidang teknik kimia.Kata kunci: kinetika reaksi, perhitungan ab-initio, teori RRKM, reaksi unimolekular, propargil, butadiena.

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>

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.

Fmoc Solid Phase Peptide Synthesis

1999 ◽  
Keyword(s):  
Peptide Synthesis ◽  
Solid Phase ◽  
Solid Phase Peptide Synthesis ◽  
Peptide Chain ◽  
Standard Approach ◽  
Side Chain ◽  
Complex Structures ◽  
Protein Conjugation ◽  
Chemoselective Ligation ◽  
Routine Production

In the years since the publication of Atherton and Sheppard's volume, the technique of Fmoc solid-phase peptide synthesis has matured considerably and is now the standard approach for the routine production of peptides. The basic problems outstanding at the time of publication of this earlier work have now been, for the most part, solved. As a result, innovators in the field have focussed their efforts to develop methodologies and chemistry for the synthesis of more complex structures. The focus of this new volume is much broader, and covers not only the essential procedures for the production of linear peptides but also more advanced techniques for preparing cyclic, side-chain modified, phospho- and glycopeptides. Many other methods also deserving attention have been included: convergent peptide synthesis; peptide-protein conjugation; chemoselective ligation; and chemoselective purification. The difficult preparation of cysteine and methionine-containing peptides is also covered, as well as methods for overcoming aggregation during peptide chain assembly and a survey of available automated instrumentation.

scholarly journals A computational study for the reaction mechanism of metal-free cyanomethylation of aryl alkynoates with acetonitrile

RSC Advances ◽  
2021 ◽  
Vol 11 (30) ◽  
pp. 18246-18251
Author(s):  
Selçuk Eşsiz
Keyword(s):  
Density Functional Theory ◽  
Reaction Mechanism ◽  
Density Functional ◽  
Computational Study ◽  
Coupled Cluster ◽  
Functional Theory ◽  
Metal Free ◽  
Coupled Cluster Methods ◽  
High Level ◽  
Cluster Methods

A computational study of metal-free cyanomethylation and cyclization of aryl alkynoates with acetonitrile is carried out employing density functional theory and high-level coupled-cluster methods, such as [CCSD(T)].

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