Difference between revisions of "Team:Tec-Chihuahua/Modeling"

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<h2> Modeling</h2>
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<h4>Note</h4>
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                <li><a href="https://2015.igem.org/Team:Tec-Chihuahua">Home</a></li>
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<p>In order to be considered for the <a href="https://2015.igem.org/Judging/Awards#SpecialPrizes">Best Model award</a>, you must fill out this page.</p>
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                <li><a href="https://2015.igem.org/Team:Tec-Chihuahua/Attributions">Team</a></li>
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<p>Mathematical models and computer simulations provide a great way to describe the function and operation of BioBrick Parts and Devices. Synthetic Biology is an engineering discipline, and part of engineering is simulation and modeling to determine the behavior of your design before you build it. Designing and simulating can be iterated many times in a computer before moving to the lab. This award is for teams who build a model of their system and use it to inform system design or simulate expected behavior in conjunction with experiments in the wetlab.</p>
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                <li><a href="https://2015.igem.org/Team:Tec-Chihuahua/Modeling">Modeling</a></li>
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Here are a few examples from previous teams:
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                <h1 id="modeling-title">Modeling</h1>
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                <h2>Introduction</h2>
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                <p>Computational chemistry and molecular modeling are considered as prediction tools that give explanation to phenomena and chemical reactions, using approaches that are based on the laws of quantum mechanics and classical mechanics. In this particular case, we could infer whether a reaction may be given spontaneously by conducting experimentation. This minimizes the use of reagents and the generation of hazardous waste.</p>
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                <p>The methodology used is based on the electron density of atoms, that’s why only a representative part of the carbon nanotube (CNT) is used, this part contains a carboxyl group which interact directly with the carbodiimide EDC forming an unstable compound with a group which will react with the poliethylamide later, therefore, that’s why only one monomer is used.
 
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                <h2>Methodology</h2>
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<li><a href="https://2014.igem.org/Team:ETH_Zurich/modeling/overview">ETH Zurich 2014</a></li>
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                <p>The theoretical study was carried out using the theory of density functional (DFT) implemented in the Gaussian 09 package, review A.02 and using the graphical display Gauss View 5.0. to make the calculations we use the B3LYP functional and the 6-31G basis set (d). Structures optimizations were conducted using water as the solvent with IEFPCM model. The energy of formation of the amidation reaction was obtained. The optimized structures with their respective energy are in Table 1</p>
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<li><a href="https://2014.igem.org/Team:Waterloo/Math_Book">Waterloo 2014</a></li>
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                <img class="modeling-equation" src="https://static.igem.org/mediawiki/2015/8/81/Tec-chihuahua-table1.png" >
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                <h2>Results</h2>
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                <p>The equation to determinate the energy of reaction is:</p>
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                <img class="modeling-equation" src="https://static.igem.org/mediawiki/2015/e/e8/Tec-chihuahua-mod1.png" >
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                <p>With thermal correction:</p>
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                <img class="modeling-equation" src="https://static.igem.org/mediawiki/2015/8/88/Tec-chihuahua-mod2.png" >
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                <p>With thermal correction:</p>
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                <img class="modeling-equation" src="https://static.igem.org/mediawiki/2015/3/30/Tec-chihuahua-mod3.png" >
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                <p>With thermal correction:</p>
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                <img class="modeling-equation" src="https://static.igem.org/mediawiki/2015/e/e9/Tec-chihuahua-mod4.png" >
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                <p>The results indicate that the reaction is going to be spontaneous.</p>
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                <h2>Recomendations</h2>
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                <p>It is feasible to establish an equation where the constant value of the reactants and products are set and they are not altered when ethyl-amide units increase or if is necessary to change the molecule that will bind to the CNT.</p>
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                <p>The equations is:</p>
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                <img class="modeling-equation" src="https://static.igem.org/mediawiki/2015/7/7e/Tec-chihuahua-mod5.png" >
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                <p>Conditions:</p>
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                <p>To give the reaction spontaneously, it requires that the constant value always presents a negative amount bigger than the sum of the variable values.</p>
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                <img class="modeling-equation" src="https://static.igem.org/mediawiki/2015/2/25/Tec-chihuahua-mod6.png" >
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                    <p>Address</p>
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                    <p>Av. Heróico Colegio Militar 4700 Col. Nombre de Dios, Zip Code: 31300 </p>
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Latest revision as of 03:43, 18 September 2015

Carbon carriers Carbon carriers

Modeling

Introduction

Computational chemistry and molecular modeling are considered as prediction tools that give explanation to phenomena and chemical reactions, using approaches that are based on the laws of quantum mechanics and classical mechanics. In this particular case, we could infer whether a reaction may be given spontaneously by conducting experimentation. This minimizes the use of reagents and the generation of hazardous waste.

The methodology used is based on the electron density of atoms, that’s why only a representative part of the carbon nanotube (CNT) is used, this part contains a carboxyl group which interact directly with the carbodiimide EDC forming an unstable compound with a group which will react with the poliethylamide later, therefore, that’s why only one monomer is used.

Methodology

The theoretical study was carried out using the theory of density functional (DFT) implemented in the Gaussian 09 package, review A.02 and using the graphical display Gauss View 5.0. to make the calculations we use the B3LYP functional and the 6-31G basis set (d). Structures optimizations were conducted using water as the solvent with IEFPCM model. The energy of formation of the amidation reaction was obtained. The optimized structures with their respective energy are in Table 1

Results

The equation to determinate the energy of reaction is:

With thermal correction:

With thermal correction:

With thermal correction:

The results indicate that the reaction is going to be spontaneous.

Recomendations

It is feasible to establish an equation where the constant value of the reactants and products are set and they are not altered when ethyl-amide units increase or if is necessary to change the molecule that will bind to the CNT.

The equations is:

Conditions:

To give the reaction spontaneously, it requires that the constant value always presents a negative amount bigger than the sum of the variable values.

Address

Av. Heróico Colegio Militar 4700 Col. Nombre de Dios, Zip Code: 31300

Phone Number

+52 (614) 439 5000 (Ext. 3009)

Email

igem_chih@outlook.com