IB Chemistry on using ICT, 3D software with Jmol, Pymol, Rasmol and ACD for I...Lawrence kok
The document provides a tutorial on using various 3D molecular modeling software like Jmol, Pymol, ACD Lab and Rasmol. It discusses using these programs to measure properties like bond lengths, bond angles, hydrogen bonds and compare protein structures. Links are provided to download the software and view tutorials and examples of using the programs to analyze molecules from the Protein Data Bank and build organic structures. Limitations of computational modeling are also noted.
IB Chemistry on ICT, 3D software, Jmol, Pymol and Rasmol for Internal AssessmentLawrence kok
The document discusses using 3D modeling software and databases to collect data on bond angles and lengths of alcohols and haloalkanes. Data was collected from Jmol, Pymol, Rasmol, ACD Lab and databases like CRC and RSC and averaged. Limitations of computational methods are that they assume non-interacting molecules in isolation. Data from multiple sources should be compared and experimental data is most reliable.
IB Chemistry on using ICT, 3D software with Jmol, Pymol, Rasmol and ACD for I...Lawrence kok
The document provides a tutorial on using various 3D molecular modeling software like Jmol, Pymol, ACD Lab and Rasmol. It discusses using these programs to measure properties like bond lengths, bond angles, hydrogen bonds and compare protein structures. Links are provided to download the software and view tutorials and examples of using the programs to analyze molecules from the Protein Data Bank and build organic structures. Limitations of computational modeling are also noted.
IB Chemistry on ICT, 3D software, Jmol, Pymol and Rasmol for Internal AssessmentLawrence kok
The document discusses using 3D modeling software and databases to collect data on bond angles and lengths of alcohols and haloalkanes. Data was collected from Jmol, Pymol, Rasmol, ACD Lab and databases like CRC and RSC and averaged. Limitations of computational methods are that they assume non-interacting molecules in isolation. Data from multiple sources should be compared and experimental data is most reliable.
IB Chemistry on ICT, 3D software, Jmol, Pymol, Rasmol and ACD for Internal As...Lawrence kok
The document discusses measuring properties of bonds such as length, angle, and strength using various 3D modeling software. It also covers using these programs to analyze protein and enzyme structures from the Protein Data Bank by inputting four-letter codes. Details are provided on tools for molecular modeling and 3D representation in Jmol, PyMol, RasMol, and ACD Labs. Spectroscopic and chemistry databases are listed for reference.
IB Chemistry on ICT, 3D software, Jmol, Rasmol and Pymol for Internal AssessmentLawrence kok
1. The document discusses various molecular modeling software and databases that can be used to measure bond lengths, bond angles, bond strengths, and compare protein and DNA structures between different species.
2. It provides instructions on how to use modeling programs like Jmol, Pymol, Rasmol and ACD Labs to obtain 3D structures from the Protein Data Bank and measure various parameters.
3. The document suggests possible research questions focusing on how factors like element identity, bond type, substituents, and lone pair electrons affect bond angles and lengths based on data collected from both 3D modeling and databases.
IB Chemistry on ICT, 3D software, Jmol, Pymol and Rasmol for Internal AssessmentLawrence kok
1. The document discusses measuring bond lengths, angles, and strengths using molecular modeling software like Jmol, PyMol, RasMol, and ACD Lab.
2. It also discusses using these software and databases like PDB, NCBI, UCSC and Ensembl to collect data on hydrogen bond distances between DNA/RNA base pairs across different species and cell types.
3. Limitations of molecular modeling are considered, like using multiple programs to validate results and checking against reliable databases like CRC and NIST. Accuracy of predicted structures from simulations alone is questioned.
IB Chemistry on ICT, 3D software, Jmol, Rasmol and Pymol for Internal AssessmentLawrence kok
The document provides a tutorial on using various 3D molecular modeling software like Jmol, Pymol, Rasmol and ACD Lab. It discusses how to use these software to generate 3D structures from SMILES or PDB files, optimize structures, measure bond lengths, angles and distances. Possible research questions are outlined focusing on how factors like element identity, double bonds, substituents affect bond angles based on data collected from the software and databases. Limitations of using computational methods are also discussed.
Patent Cheminformatics: Identification of key compounds in patentsSorel Muresan
Patents can contain valuable chemical and biological information not found in scientific journals. This document discusses extracting key compounds from patents, including identifying sources for full-text patents, extracting compounds from text, and predicting key compounds through methods like frequency of group analysis. Predicting key compounds is important as they are often the most biologically active and suitable for further development. The document provides examples of extracting known drug compounds like Bextra, Aciphex, and Aricept from early patents through these methods.
Getting the Big Picture by Joining up the SAR dotsSorel Muresan
Getting the Big Picture by Joining up the SAR dots
This document discusses challenges in integrating structure and bioactivity data at large scales due to the volume and complexity of unstructured data from various sources. It describes efforts to extract chemical entities from text using natural language processing and to standardize structures. The Chemistry Connect knowledge base aims to enable searching across internal and external datasets by developing a chemical dictionary and common representation of concepts.
Automated spelling correction to improve recall rates of name-to-structure to...Sorel Muresan
This document discusses using automated spelling correction to improve the recall rates of name-to-structure tools for chemical text mining. It notes that the biggest cause of missing compounds when extracting chemical entities is the presence of typographical errors. The document introduces CaffeineFix, a chemical nomenclature aware automatic spell checker, that can significantly improve recall rates as a pre-processing step by correcting OCR and other errors in compound names found in patents and other texts.
IB Chemistry on Energetics, Enthalpy Change and ThermodynamicsLawrence kok
1. Heat is the transfer of thermal energy from hot to cold bodies due to a temperature difference. Heat is not a form of energy but rather energy transfer, while temperature is a measure of the average kinetic energy of particles.
2. At the same temperature, different gases have the same average kinetic energy per particle despite differences in mass. Heavier particles move slower than lighter particles at the same temperature.
3. The amount of heat required to change the temperature of a substance depends on its specific heat capacity and mass. Substances with higher specific heat capacity require more heat to change their temperature.
IB Chemistry on Hess's Law, Enthalpy Formation and CombustionLawrence kok
1) Hess's law states that the enthalpy change of a reaction is independent of the pathway and is equal to the sum of the enthalpy changes of the steps.
2) Standard enthalpy changes of formation (ΔHf°) can be used to calculate the enthalpy change (ΔH°) of a reaction by adding the standard enthalpies of formation of products and subtracting the standard enthalpies of formation of reactants.
3) For the reaction 2H2S + SO2 → 3S + 2H2O, the calculated standard enthalpy change is -234 kJ/mol.
IB Chemistry on Mass Spectrometry, Index Hydrogen Deficiency and IsotopesLawrence kok
The document discusses index hydrogen deficiency (IHD), which is a measure of unsaturation in molecules. IHD is calculated based on the number of hydrogen atoms fewer than would be present in a saturated molecule with the same number of carbon atoms. The document provides examples of calculating IHD for various molecules containing double bonds, rings, and heteroatoms like nitrogen. It also describes how mass spectrometry can be used to determine IHD and identify molecular structures based on their fragmentation patterns.
IB Chemistry on Voltaic Cell, Standard Electrode Potential and Standard Hydro...Lawrence kok
This document discusses voltaic cells and the potential differences between half-cells. It explains that connecting two half-cells with different electrode potentials through an external circuit and salt bridge allows electrons to flow spontaneously from the negative half-cell to the positive half-cell. Specifically, it gives the example of a Zn/Cu voltaic cell, where the Zn half-cell acts as the anode undergoing oxidation and the Cu half-cell acts as the cathode undergoing reduction. When connected, the potential difference between the half-cells can be measured as 1.10 volts using a high resistance voltmeter.
IB Chemistry on Free radical substitution, Addition and Nucleophilic substitu...Lawrence kok
This document describes various classes of organic compounds including alkanes, alkenes, alcohols, esters, and their properties. Alkanes are saturated hydrocarbons with the general formula CnH2n+2. Alkenes are unsaturated hydrocarbons containing carbon-carbon double bonds with the general formula CnH2n. Alcohols contain an -OH functional group and have the general formula CnH2n+1OH. Esters are formed from the condensation reaction between carboxylic acids and alcohols, producing water as a byproduct. Common chemical reactions for each class are also outlined such as combustion, addition, oxidation, and esterification
IB Chemistry on Properties of Transition Metal and MagnetismLawrence kok
The document discusses the periodic table and properties of elements. It is divided into blocks based on orbital filling: s, p, d, and f blocks. Transition metals are in the d block and have partially filled d orbitals. They exhibit variable oxidation states, can form colored complexes, and show catalytic activity due to this electronic configuration. Magnetic properties depend on paired or unpaired electrons in the outer shell.
IB Chemistry on Energetics experiment, Thermodynamics and Hess's LawLawrence kok
1. Heat is transferred from hot to cold objects due to a temperature difference, causing the average kinetic energy per particle to equalize.
2. Gases at the same temperature have the same average kinetic energy per particle regardless of mass. Heavier gases have lower average speeds than lighter gases at the same temperature.
3. The amount of heat required to change an object's temperature depends on its mass and specific heat capacity. Substances with higher specific heat capacities require more heat to change their temperature by 1°C.
IB Chemistry on Homologous series and functional groups of organic moleculesLawrence kok
The document discusses organic functional groups and their IUPAC nomenclature rules. It defines classes of organic compounds such as alkanes, alkenes, alkynes, alcohols, ethers, ketones, aldehydes, carboxylic acids, esters, amides, amines, nitriles and haloalkanes based on their functional groups. It provides examples and molecular formulas for different functional groups and discusses IUPAC nomenclature rules for systematically naming organic compounds including identifying the parent chain, functional group, substituents and their positions.
IB Chemistry on Nuclear Magnetic Resonance, Chemical Shift and Splitting PatternLawrence kok
This document discusses various analytical techniques used in chemistry, including both classical and instrumental methods. Classical methods involve qualitative and quantitative analysis using chemical tests, titrations, and gravimetric analysis. Instrumental methods discussed include various types of spectroscopy such as infrared spectroscopy, nuclear magnetic resonance spectroscopy, and chromatography techniques used for separation analysis. The document provides details on the principles, applications, and information provided by different analytical techniques.
IB Chemistry on Bond Enthalpy, Enthalpy formation, combustion and atomizationLawrence kok
This document discusses several methods to calculate enthalpy change (ΔH) for chemical reactions, including using average bond enthalpies, standard enthalpies of formation (ΔHf), standard enthalpies of combustion (ΔHc), and standard enthalpies of atomization (ΔHa). It provides examples of calculating ΔH for reactions involving CH4, CCl4, S8, carbon polymorphs, and the formation of C5H5N from carbon, hydrogen, and nitrogen. The document emphasizes that while average bond enthalpies can be used, ΔHf, ΔHc, and ΔHa are generally more accurate as they consider the specific bonds in the reaction.
IB Chemistry on Gibbs Free Energy and EntropyLawrence kok
This document discusses key concepts in thermodynamics including:
1) The first law of thermodynamics states that energy cannot be created or destroyed, only transferred or changed in form.
2) The second law of thermodynamics states that the entropy of the universe always increases for spontaneous processes. Spontaneous reactions result in an increase in disorder and a more even distribution of energy.
3) Entropy is a measure of molecular disorder/randomness. Higher entropy states correspond to greater dispersal of matter and energy. Phase changes from solid to liquid to gas are accompanied by an increase in entropy.
IB Chemistry on Gibbs Free Energy and Equilibrium constant, KcLawrence kok
This document discusses chemical equilibrium, including the equilibrium constant Kc, factors that affect equilibrium, and the relationship between equilibrium and thermodynamics. At equilibrium, the forward and reverse reaction rates are equal, and the concentrations of reactants and products remain constant. The equilibrium constant Kc is defined as the ratio of product concentrations over reactant concentrations raised to their stoichiometric coefficients. An increase in temperature can shift the position of equilibrium either to the left or right depending on whether the reaction is exothermic or endothermic. The Gibbs free energy change ΔG is related to Kc and can be used to predict spontaneity. A more negative ΔG corresponds to a higher Kc and a greater extent of reaction towards products
IB Chemistry on ICT, 3D software, Jmol, Pymol, Rasmol and ACD for Internal As...Lawrence kok
The document discusses measuring properties of bonds such as length, angle, and strength using various 3D modeling software. It also covers using these programs to analyze protein and enzyme structures from the Protein Data Bank by inputting four-letter codes. Details are provided on tools for molecular modeling and 3D representation in Jmol, PyMol, RasMol, and ACD Labs. Spectroscopic and chemistry databases are listed for reference.
IB Chemistry on ICT, 3D software, Jmol, Rasmol and Pymol for Internal AssessmentLawrence kok
1. The document discusses various molecular modeling software and databases that can be used to measure bond lengths, bond angles, bond strengths, and compare protein and DNA structures between different species.
2. It provides instructions on how to use modeling programs like Jmol, Pymol, Rasmol and ACD Labs to obtain 3D structures from the Protein Data Bank and measure various parameters.
3. The document suggests possible research questions focusing on how factors like element identity, bond type, substituents, and lone pair electrons affect bond angles and lengths based on data collected from both 3D modeling and databases.
IB Chemistry on ICT, 3D software, Jmol, Pymol and Rasmol for Internal AssessmentLawrence kok
1. The document discusses measuring bond lengths, angles, and strengths using molecular modeling software like Jmol, PyMol, RasMol, and ACD Lab.
2. It also discusses using these software and databases like PDB, NCBI, UCSC and Ensembl to collect data on hydrogen bond distances between DNA/RNA base pairs across different species and cell types.
3. Limitations of molecular modeling are considered, like using multiple programs to validate results and checking against reliable databases like CRC and NIST. Accuracy of predicted structures from simulations alone is questioned.
IB Chemistry on ICT, 3D software, Jmol, Rasmol and Pymol for Internal AssessmentLawrence kok
The document provides a tutorial on using various 3D molecular modeling software like Jmol, Pymol, Rasmol and ACD Lab. It discusses how to use these software to generate 3D structures from SMILES or PDB files, optimize structures, measure bond lengths, angles and distances. Possible research questions are outlined focusing on how factors like element identity, double bonds, substituents affect bond angles based on data collected from the software and databases. Limitations of using computational methods are also discussed.
Patent Cheminformatics: Identification of key compounds in patentsSorel Muresan
Patents can contain valuable chemical and biological information not found in scientific journals. This document discusses extracting key compounds from patents, including identifying sources for full-text patents, extracting compounds from text, and predicting key compounds through methods like frequency of group analysis. Predicting key compounds is important as they are often the most biologically active and suitable for further development. The document provides examples of extracting known drug compounds like Bextra, Aciphex, and Aricept from early patents through these methods.
Getting the Big Picture by Joining up the SAR dotsSorel Muresan
Getting the Big Picture by Joining up the SAR dots
This document discusses challenges in integrating structure and bioactivity data at large scales due to the volume and complexity of unstructured data from various sources. It describes efforts to extract chemical entities from text using natural language processing and to standardize structures. The Chemistry Connect knowledge base aims to enable searching across internal and external datasets by developing a chemical dictionary and common representation of concepts.
Automated spelling correction to improve recall rates of name-to-structure to...Sorel Muresan
This document discusses using automated spelling correction to improve the recall rates of name-to-structure tools for chemical text mining. It notes that the biggest cause of missing compounds when extracting chemical entities is the presence of typographical errors. The document introduces CaffeineFix, a chemical nomenclature aware automatic spell checker, that can significantly improve recall rates as a pre-processing step by correcting OCR and other errors in compound names found in patents and other texts.
IB Chemistry on Energetics, Enthalpy Change and ThermodynamicsLawrence kok
1. Heat is the transfer of thermal energy from hot to cold bodies due to a temperature difference. Heat is not a form of energy but rather energy transfer, while temperature is a measure of the average kinetic energy of particles.
2. At the same temperature, different gases have the same average kinetic energy per particle despite differences in mass. Heavier particles move slower than lighter particles at the same temperature.
3. The amount of heat required to change the temperature of a substance depends on its specific heat capacity and mass. Substances with higher specific heat capacity require more heat to change their temperature.
IB Chemistry on Hess's Law, Enthalpy Formation and CombustionLawrence kok
1) Hess's law states that the enthalpy change of a reaction is independent of the pathway and is equal to the sum of the enthalpy changes of the steps.
2) Standard enthalpy changes of formation (ΔHf°) can be used to calculate the enthalpy change (ΔH°) of a reaction by adding the standard enthalpies of formation of products and subtracting the standard enthalpies of formation of reactants.
3) For the reaction 2H2S + SO2 → 3S + 2H2O, the calculated standard enthalpy change is -234 kJ/mol.
IB Chemistry on Mass Spectrometry, Index Hydrogen Deficiency and IsotopesLawrence kok
The document discusses index hydrogen deficiency (IHD), which is a measure of unsaturation in molecules. IHD is calculated based on the number of hydrogen atoms fewer than would be present in a saturated molecule with the same number of carbon atoms. The document provides examples of calculating IHD for various molecules containing double bonds, rings, and heteroatoms like nitrogen. It also describes how mass spectrometry can be used to determine IHD and identify molecular structures based on their fragmentation patterns.
IB Chemistry on Voltaic Cell, Standard Electrode Potential and Standard Hydro...Lawrence kok
This document discusses voltaic cells and the potential differences between half-cells. It explains that connecting two half-cells with different electrode potentials through an external circuit and salt bridge allows electrons to flow spontaneously from the negative half-cell to the positive half-cell. Specifically, it gives the example of a Zn/Cu voltaic cell, where the Zn half-cell acts as the anode undergoing oxidation and the Cu half-cell acts as the cathode undergoing reduction. When connected, the potential difference between the half-cells can be measured as 1.10 volts using a high resistance voltmeter.
IB Chemistry on Free radical substitution, Addition and Nucleophilic substitu...Lawrence kok
This document describes various classes of organic compounds including alkanes, alkenes, alcohols, esters, and their properties. Alkanes are saturated hydrocarbons with the general formula CnH2n+2. Alkenes are unsaturated hydrocarbons containing carbon-carbon double bonds with the general formula CnH2n. Alcohols contain an -OH functional group and have the general formula CnH2n+1OH. Esters are formed from the condensation reaction between carboxylic acids and alcohols, producing water as a byproduct. Common chemical reactions for each class are also outlined such as combustion, addition, oxidation, and esterification
IB Chemistry on Properties of Transition Metal and MagnetismLawrence kok
The document discusses the periodic table and properties of elements. It is divided into blocks based on orbital filling: s, p, d, and f blocks. Transition metals are in the d block and have partially filled d orbitals. They exhibit variable oxidation states, can form colored complexes, and show catalytic activity due to this electronic configuration. Magnetic properties depend on paired or unpaired electrons in the outer shell.
IB Chemistry on Energetics experiment, Thermodynamics and Hess's LawLawrence kok
1. Heat is transferred from hot to cold objects due to a temperature difference, causing the average kinetic energy per particle to equalize.
2. Gases at the same temperature have the same average kinetic energy per particle regardless of mass. Heavier gases have lower average speeds than lighter gases at the same temperature.
3. The amount of heat required to change an object's temperature depends on its mass and specific heat capacity. Substances with higher specific heat capacities require more heat to change their temperature by 1°C.
IB Chemistry on Homologous series and functional groups of organic moleculesLawrence kok
The document discusses organic functional groups and their IUPAC nomenclature rules. It defines classes of organic compounds such as alkanes, alkenes, alkynes, alcohols, ethers, ketones, aldehydes, carboxylic acids, esters, amides, amines, nitriles and haloalkanes based on their functional groups. It provides examples and molecular formulas for different functional groups and discusses IUPAC nomenclature rules for systematically naming organic compounds including identifying the parent chain, functional group, substituents and their positions.
IB Chemistry on Nuclear Magnetic Resonance, Chemical Shift and Splitting PatternLawrence kok
This document discusses various analytical techniques used in chemistry, including both classical and instrumental methods. Classical methods involve qualitative and quantitative analysis using chemical tests, titrations, and gravimetric analysis. Instrumental methods discussed include various types of spectroscopy such as infrared spectroscopy, nuclear magnetic resonance spectroscopy, and chromatography techniques used for separation analysis. The document provides details on the principles, applications, and information provided by different analytical techniques.
IB Chemistry on Bond Enthalpy, Enthalpy formation, combustion and atomizationLawrence kok
This document discusses several methods to calculate enthalpy change (ΔH) for chemical reactions, including using average bond enthalpies, standard enthalpies of formation (ΔHf), standard enthalpies of combustion (ΔHc), and standard enthalpies of atomization (ΔHa). It provides examples of calculating ΔH for reactions involving CH4, CCl4, S8, carbon polymorphs, and the formation of C5H5N from carbon, hydrogen, and nitrogen. The document emphasizes that while average bond enthalpies can be used, ΔHf, ΔHc, and ΔHa are generally more accurate as they consider the specific bonds in the reaction.
IB Chemistry on Gibbs Free Energy and EntropyLawrence kok
This document discusses key concepts in thermodynamics including:
1) The first law of thermodynamics states that energy cannot be created or destroyed, only transferred or changed in form.
2) The second law of thermodynamics states that the entropy of the universe always increases for spontaneous processes. Spontaneous reactions result in an increase in disorder and a more even distribution of energy.
3) Entropy is a measure of molecular disorder/randomness. Higher entropy states correspond to greater dispersal of matter and energy. Phase changes from solid to liquid to gas are accompanied by an increase in entropy.
IB Chemistry on Gibbs Free Energy and Equilibrium constant, KcLawrence kok
This document discusses chemical equilibrium, including the equilibrium constant Kc, factors that affect equilibrium, and the relationship between equilibrium and thermodynamics. At equilibrium, the forward and reverse reaction rates are equal, and the concentrations of reactants and products remain constant. The equilibrium constant Kc is defined as the ratio of product concentrations over reactant concentrations raised to their stoichiometric coefficients. An increase in temperature can shift the position of equilibrium either to the left or right depending on whether the reaction is exothermic or endothermic. The Gibbs free energy change ΔG is related to Kc and can be used to predict spontaneity. A more negative ΔG corresponds to a higher Kc and a greater extent of reaction towards products
IB Chemistry on Organic nomenclature and functional groups.Lawrence kok
The document discusses organic functional groups and their naming conventions. It provides the suffixes used to name different classes of organic compounds based on their functional groups, including -ane for alkanes, -ene for alkenes, -yne for alkynes, -ol for alcohols, and -one for ketones. It also gives examples of compound names and formulas for different functional groups like ethane for alkanes and ethene for alkenes.
IB Chemistry on Standard Reduction Potential, Standard Hydrogen Electrode and...Lawrence kok
The document discusses standard electrode potentials and how they are measured. It explains that the standard hydrogen electrode is used as a reference with a potential of 0 V. Other half-cell potentials are measured against this to determine their standard electrode potential. Common half-cells include metal/metal ion, gas/ion, and ion/ion systems. Standard conditions of 1 M concentrations, 1 atm pressure, and 298K temperature must be used. The potentials of zinc/zinc ion, iron III/iron II, and chlorine/chloride ion half-cells are given as examples.
IB Chemistry on Electrolysis and Faraday's LawLawrence kok
This document discusses types of voltaic and electrolytic cells. It provides information on redox reactions, conversion of chemical to electrical energy and vice versa, and factors that affect which ions are discharged during electrolysis. Specifically:
- Voltaic cells convert chemical energy to electrical energy via spontaneous redox reactions. Electrolytic cells require an external voltage to drive non-spontaneous reactions that convert electrical to chemical energy.
- Key components of voltaic and electrolytic cells are discussed, including electrodes, electrolytes, and direction of electron and ion flow.
- Standard reduction potentials are provided for many half-cell reactions to allow calculation of overall cell potentials.
- Examples of specific vol
IB Chemistry on Redox, Reactivity Series and Displacement reactionLawrence kok
The document discusses the reactivity series of metals and non-metals. It explains that metals can be arranged based on their tendency to lose electrons and form positive ions through oxidation. More reactive metals oxidize less reactive ones in displacement reactions. Carbon and aluminum are strong reducing agents that can displace iron from its oxide to extract iron. The reactivity of non-metals increases from fluorine to iodine as they have a higher tendency to gain electrons and form negative ions through reduction reactions.
IB Chemistry on Redox, Oxidizing, Reducing Agents and writing half redox equa...Lawrence kok
The document discusses oxidation numbers (also called oxidation states), which are used to keep track of electrons in chemical reactions. Some key points:
- Oxidation numbers are assigned to each atom in a chemical species by assuming ionic bonding and counting electrons.
- Common rules are outlined for assigning oxidation numbers to elements, such as metals in Group 1 have a +1 oxidation state and nonmetals in Group 7 have a -1 oxidation state.
- Oxidation numbers can be used to determine if a reaction is a redox reaction by looking for changes in oxidation numbers between reactants and products.
- Transition metals can have multiple common oxidation states. Roman numerals are used to distinguish, such as
IB Chemistry on Reactivity Series vs Electrochemical SeriesLawrence kok
The document discusses the reactivity and electrochemical series of group 1 alkali metals lithium, sodium, and potassium. While lithium has the most negative standard reduction potential, indicating it is most easily oxidized, potassium is the most reactive when reacting with water and acids due to lower kinetic barriers. The electrochemical series is a thermodynamic measurement based on standard potentials, while the reactivity series considers reaction kinetics. Thus, there is a correlation but not perfect agreement between the two series.
IB Chemistry on Crystal Field Theory and Splitting of 3d orbitalLawrence kok
The document discusses the properties and behaviors of transition metals. Transition metals are d-block elements that have partially filled d orbitals. They can exist in multiple oxidation states and form colored complexes due to their variable electron configurations. Transition metals are also good catalysts as their partially filled d orbitals allow them to easily gain or lose electrons and form weak bonds with reactants to lower the activation energy of chemical reactions.
IB Chemistry on HNMR Spectroscopy and Spin spin couplingLawrence kok
Spectroscopy measures the interaction of molecules with electromagnetic radiation. Different types of spectroscopy use different regions of the electromagnetic spectrum and provide information about molecular structure. Nuclear magnetic resonance spectroscopy specifically uses radio waves to investigate nuclear spin properties and can determine organic molecular structures. It works by applying a magnetic field to nuclei with an odd number of protons and neutrons, which have a net spin and magnetic moment.
This document provides an overview of protein structure analysis tools and techniques:
1) It describes exploring the Protein Data Bank (PDB) to view and analyze X-ray crystallography and NMR protein structures, comparing similar structures, and using tools like FoldX for in silico mutagenesis and homology modeling.
2) Key concepts covered include PDB file formats, atomic coordinates, B-factors, resolution, RMSD, and the principles of X-ray crystallography, NMR structure determination, and homology modeling.
3) Visualization software like YASARA, SwissPDBViewer and PyMOL are introduced for viewing protein structures from the PDB.
This document discusses the use of positron annihilation spectroscopy to analyze the free volume nanohole distribution in polymers and its correlation to the physico-chemical properties of polymers. It provides background on positron annihilation spectroscopy and how it can be used to measure free volume in polymers. The document then describes several studies that use this technique to analyze the influence of free volume properties on the swelling of polymer hydrogels, structure-property relationships in modified epoxy resins, and free volume and interfacial interactions in epoxy clay composites.
This document summarizes Bing Hsieh's research journey from 1990 to 2014. It covers his work in conducting polymers for OLEDs from 1990-2002, then toner and cartridge recycling from 2003-2007. From 2008-2011 he worked on solid electrolytes and ionic liquids for lithium batteries. From 2011-2014 his focus was on printed organic electronics and graphene supercapacitors. The document provides details on his research into issues with printed transistors, block copolymers as solid electrolytes, dendrite formation in batteries, and preliminary work printing graphene oxide inks for supercapacitors. Diagrams and images supplement the technical descriptions.
OECD Webinar | Assessing the dispersion stability and dissolution (rate) of n...OECD Environment
On Thursday 25 February 2021, Anne Gourmelon (Environment Directorate, OECD), Kathrin Schwirn (German Environment Agency, Umweltbundesamt, UBA); Frank von der Kammer (University of Vienna) Research and Development Center) and Doris Völker (German Environment Agency, Umweltbundesamt, UBA) presented the scope, content, and use of the Test Guideline No. 318: Dispersion Stability of Nanomaterials in Simulated Environmental Media and its accompanying Guidance Document. Further discussions focused on the scope of the upcoming Test Guideline.
The increased production and wide usage of manufactured nanomaterials suggest a higher probability of finding them in the environment. Therefore, testing the dissolution rate and dispersion stability for toxicity assessment are of paramount importance for adequate hazard assessment.
Dislocation Density in Multicomponent Alloys CoNi, CoFeNiIRJET Journal
This document discusses dislocation density in multi-component alloys CoNi and CoFeNi. It begins with an introduction to high entropy alloys and their properties. It then discusses the definition and calculation of dislocation density using X-ray diffraction peak broadening analysis. The document describes preparing CoNi, CoFeNi alloys by mechanical alloying and casting and characterizing the structural properties using X-ray diffraction to analyze dislocation density behavior.
Simultaneous voltammetric determination of paracetamol anddomperidone based o...Pramod Kalambate
Graphene oxide and hexachloroplatinic acid were electrochemically reduced on a glassy carbon elec-trode (GCE) surface so as to form a graphene (Gr)–platinum nanoparticles (PtNP) composite. This nanocomposite was then coated with nafion (NAF) film so as to form NAF/PtNP/Gr/GCE. In this work, anelectrochemical method based on adsorptive stripping square wave voltammetry (AdSSWV) employ-ing NAF/PtNP/Gr/GCE has been proposed for the subnanomolar determination of paracetamol (PCT) anddomperidone (DOM) simultaneously. The electrode material was characterized by scanning electronmicroscopy, energy dispersive X-ray spectroscopy, and X-ray diffraction. The electrochemical perfor-mance of PCT and DOM on modified electrode was investigated by cyclic voltammetry, electrochemicalimpedance spectroscopy, and chronocoulometry. A sixteen fold enhancement in the AdSSWV signal wasobserved at NAF/PtNP/Gr/GCE in pH 6.0, phosphate buffer, as compared to GCE. Under the optimized con-ditions, the method allowed simultaneous determination of PCT and DOM in the linear working range of8.2 × 10−6–1.6 × 10−9M with detection limits (3 × SD/s) of 1.06 × 10−10and 4.37 × 10−10M for PCT andDOM respectively. The practical analytical utilities of the modified electrode were demonstrated by thedetermination of PCT and DOM in pharmaceutical formulations, human urine, and blood serum samples.This proposed method was validated by HPLC and the results are in agreement at the 95% confidencelevel. Simultaneous voltammetric determination of PCT and DOM has been reported for the first time.
High Speed Parameter Estimation for a Homogenized Energy Model- Doctoral Defe...Jon Ernstberger
I used this presentation when making my final doctoral defense at NC State University in June 2008. My defense was entitled "High Speed Parameter Estimation for a Homogenized Energy Model". Dr. Ralph C. Smith was my advisor.
This document discusses the automation of computational chemistry calculations and protocols to reliably generate molecular property data. It addresses validating computational methods, analyzing results for errors and outliers, and comparing output to experimental data. The goal is to provide high-quality "experimental" data through automated high-throughput computation while ensuring valid results and identifying unusual computations. Workflows, parsing tools, and dissemination methods are presented for managing large numbers of jobs and analyzing results.
An update version of the genome assembly including the mention of techniques such as HiC and Bionano. Also include the QC. These are the same slides used in the course for the UNL in Argentina.
The document discusses several topics related to semiconductor manufacturing processes and design for manufacturability (DFM). It summarizes resolution enhancement techniques used in lithography like RET and OPC. It also discusses DFM techniques like process characterization of IP libraries using yield models, addressing systematic and random yield loss mechanisms, and the need for proactive DFM using accurate process models early in the design flow. Finally, it briefly mentions the use of automated test equipment for testing chips after manufacturing.
This document discusses the design and synthesis of functionalized ligands for adsorptive separation of CO2/N2 and CO2/CH4 mixtures. It describes the synthesis of various aliphatic and heterocyclic ligand functionalized polystyrene adsorbents and evaluates their performance for CO2 capture based on equilibrium adsorption studies, FTIR characterization, and pulse chromatography experiments. The adsorbents showed high CO2 capture capacity and selectivity over N2 and CH4 due to interactions between CO2 and the tertiary amine ligands.
Dna data compression algorithms based on redundancyijfcstjournal
Carl Jung said, 'Collective unconscious' i.e. we are all connected to each other in some way or the other via our DNA.In frequent cases there are four bases in a DNA. They are a (Adenine),c (Cytosine),g(Guanine)
and t (Thymine).Each of these bases can be represented by two bits as 2 powers 2 =4 i.e.a–00,c–01,g–11 and t–10 respectively, although this choice is random.Soredundancy within a sequence is more likely to exist.That’s why in this paper wehave explored different types of repeat to compress DNA.These are direct repeats, palindrome or reverse direct repeat , inverted exact repeats or complementary palindrome or exact reverse complement, inverted approximate repeats or approximate complementary palindrome or approximate reverse complement, interspersed or dispersed repeats,
flanking repeats or terminal repeats etc. Better compression gives better network speed and save storage space.
The document discusses investigation of hexagonal boron nitride (BN) using terahertz time-domain spectroscopy. The analysis revealed differences in refractive indices and transmission loss between four grades of hot pressed BN related to their porosity and binder content. It also provided an indication of particle and pore sizes. Terahertz time-domain spectroscopy was shown to provide structural insight into opaque ceramic materials like various grades of BN.
Experiment 4 - Testing of Materials in Tension Object .docxSANSKAR20
Experiment 4 - Testing of Materials in Tension
Object: The object of this experiment is to measure the tensile properties of two polymeric
materials, steel and aluminum at a constant strain rate on the Tension testing machine.
Background: For structural applications of materials such as bridges, pressure vessels, ships,
and automobiles, the tensile properties of the metal material set the criteria for a safe design.
Polymeric materials are being used more and more in structural applications, particularly in
automobiles and pressure vessels. New applications emerge as designers become aware of
the differences in the properties of metals and polymers and take full advantage of them. The
analyses of structures using metals or plastics require that the data be available.
Stress-Strain: The tensile properties of a material are obtained by pulling a specimen of
known geometry apart at a fixed rate of straining until it breaks or stretches to the machines
limit. It is useful to define the load per unit area (stress) as a parameter rather than load to
avoid the confusion that would arise from the fact that the load and the change in length are
dependent on the cross-sectional area and original length of the specimen. The stress,
however, changes during the test for two reasons: the load increases and the cross-sectional
area decreases as the specimen gets longer.
Therefore, the stress can be calculated by two formulae which are distinguished as
engineering stress and true stress, respectively.
(1) = P/Ao= Engineering Stress (lbs/in
2 or psi)
P = load (lbs)
Ao= original cross-sectional area (in
2)
(2) T= P/Ai = True Stress
Ai = instantaneous cross-sectional area (in
2)
Likewise, the elongation is normalized per unit length of specimen and is called strain. The
strain may be based on the original length or the instantaneous length such that
(3) =(lf - lo)/ lo = l / lo = Engineering Strain, where
lf= final gage length (in)
lo= original gage length (in)
(4) T= ln ( li / lo ) = ln (1 +) = True Strain, where
li = instantaneous gage length (in)
ln = natural logarithm
For a small elongation the engineering strain is very close to the true strain when l=1.2 lo,
then = 0.2 and T= ln 1.2 = 0.182. The engineering stress is related to the true stress by
(5) T= (1 + )
The true stress would be 20% higher in the case above where the specimen is 20% longer
than the original length. As the relative elongation increases, the true strain will become
significantly less than the engineering strain while the true stress becomes much greater than
the engineering stress. When l= 4.0 lo then = 3.0 but the true strain =ln 4.0 = 1.39.
Therefore, the true strain is less than 1/2 of the engineering strain. The true stress (T) = (1+
3.0) = 4, or the true stress is 4 times the engineering stress.
Tensile Test Nom ...
W. Phippen Deisgn Optmization of CFRP Satellite Solar Panel Structures - MECH461William Phippen
The document describes the design optimization of a carbon fiber reinforced polymer (CFRP) satellite solar panel structure using Altair's HyperWorks software. The goal was to maximize stiffness while minimizing cost and meeting stress and deflection constraints. The model was optimized over 4 iterations for CFRP properties and loading cases of launch and orbital deployment. The final design yielded a 71.2% mass reduction while satisfying all constraints.
This document summarizes an experiment conducted to determine the significant parameters affecting the shear strength of hot-air welds between polypropylene rod material and twintex composite material. The experiment tested different welding temperatures, feed rates, and fan speeds using a designed experiment approach. Samples were tested and data was analyzed to make recommendations for further testing.
1. The document describes calculations of the geometric parameters, energies, and electronic properties of a donor-π-bridge-acceptor molecular system using density functional theory with the B3LYP/6-31G(d,p) basis set.
2. The results show that substituting groups onto the phenyl ring bridge leads to a new molecular system with a smaller energy gap than the individual donor, acceptor, or bridge components.
3. The donor-π-bridge-acceptor system was found to have suitable properties for charge transfer, including a large dipole moment and polarizability, indicating it may be a better electrophilic system for charge transport applications.
1. The author tested different molecules like PEG and OTS to attach plasmid DNA to silicon surfaces for potential use in nanotechnology circuits, as the commonly used APTES binds DNA too strongly.
2. Imaging with an atomic force microscope showed that DNA appeared more relaxed on the neutral PEG layer than on the positively charged APTES layer.
3. Restriction enzymes were used to cut the plasmid DNA into linearized pieces to better observe the effects of the different attachment molecules on the DNA structure at the nanoscale level.
The document discusses performing molecular dynamics simulations using GROMACS to minimize the energy of a protein structure. It describes converting protein data files, setting up the simulation box, running the simulation with tools like grompp and mdrun, and analyzing the results by visualizing trajectories and the minimized protein structure.
This document summarizes a study that investigated stress concentrations in laser-cut polymethylmethacrylate (PMMA) material under static and centripetal loading. Tensile tests were performed on standardized specimens with varying fillet radii. Additional centripetal tests were done on laser-cut fan blades. Finite element analysis was used to model the tests and compare results. Tensile testing showed stress concentration factors lower than literature values. Centripetal testing yielded variable fracture speeds. Finite element analysis correlated well with tensile testing but was less predictive for centripetal loading due to complex blade geometry.
Similar to IB Chemistry on ICT, 3D software, Avogadro, Jmol, Swiss PDB, Pymol for Internal Assessment on aromaticity (20)
IA on efficiency of immobilized enzyme amylase (yeast extract) in alginate be...Lawrence kok
Sodium alginate reacts with calcium chloride to form calcium alginate beads that can immobilize enzymes like amylase from yeast extract. These beads were added to a solution of starch and iodine, which produces a blue-black color. As the immobilized amylase breaks down the starch into maltose and simple sugars over 3 minutes, the blue-black color fades. The rate of starch hydrolysis was measured by the decrease in absorbance of the blue-black color over time using a colorimeter.
IA on effect of duration on efficiency of immobilized MnO2 in alginate beads ...Lawrence kok
Sodium alginate and calcium chloride were used to immobilize MnO2 catalyst particles in alginate beads. MnO2-loaded beads were prepared using 3% sodium alginate and 2% calcium chloride solutions and tested in the decomposition of hydrogen peroxide over 4 days. The rate of reaction and efficiency decreased slightly each day, from an initial rate of 0.1976 kPas-1 and 100% efficiency on day 1 to 0.1528 kPas-1 and 77% efficiency on day 4, demonstrating the durability of the immobilized MnO2 catalyst beads over multiple reuse cycles.
IA on effect of concentration of sodium alginate and calcium chloride in maki...Lawrence kok
The document investigates the effect of sodium alginate and calcium chloride concentration on forming alginate beads. Various concentrations of sodium alginate (1%, 2%, 3%) and calcium chloride (1%, 2%, 3%) were used to form beads. 3% sodium alginate added to 2% calcium chloride produced the strongest, biggest beads. This combination will be used to immobilize the catalyst MnO2 in alginate beads so that it can be reused instead of being discarded after reaction with H2O2.
IA on effect of duration (steeping time) on polyphenol (tannins) of tea, usin...Lawrence kok
This document examines the effect of steeping time on the polyphenol content of green tea, as measured by potassium permanganate titration. Green tea bags were steeped in a water bath at 90C for durations ranging from 1 to 5 minutes. The polyphenol content was found to increase linearly with steeping time, ranging from 1247 mg/L after 1 minute to 2078 mg/L after 5 minutes. The titration procedure involved adding tea steeped for different times to a solution with an indicator, and titrating with potassium permanganate solution until the endpoint was reached.
IA on polyphenol quantification using potassium permanganate titration (Lowen...Lawrence kok
This document describes the quantification of polyphenols using potassium permanganate titration. Some key points:
1. Polyphenols are antioxidants found in fruits like grapes, berries, and cider that can be quantified using a redox titration with potassium permanganate.
2. The procedure involves preparing a 0.004M potassium permanganate solution and titrating fruit extracts with it using indigo carmine as an indicator, until the solution turns greenish yellow at the endpoint.
3. The volume of permanganate used corresponds to the amount of polyphenols present, with green grapes containing the most at 665 mg/L tannic acid equivalents based on the titration
How to Make a Field Mandatory in Odoo 17Celine George
In Odoo, making a field required can be done through both Python code and XML views. When you set the required attribute to True in Python code, it makes the field required across all views where it's used. Conversely, when you set the required attribute in XML views, it makes the field required only in the context of that particular view.
How to Fix the Import Error in the Odoo 17Celine George
An import error occurs when a program fails to import a module or library, disrupting its execution. In languages like Python, this issue arises when the specified module cannot be found or accessed, hindering the program's functionality. Resolving import errors is crucial for maintaining smooth software operation and uninterrupted development processes.
How to Build a Module in Odoo 17 Using the Scaffold MethodCeline George
Odoo provides an option for creating a module by using a single line command. By using this command the user can make a whole structure of a module. It is very easy for a beginner to make a module. There is no need to make each file manually. This slide will show how to create a module using the scaffold method.
How to Manage Your Lost Opportunities in Odoo 17 CRMCeline George
Odoo 17 CRM allows us to track why we lose sales opportunities with "Lost Reasons." This helps analyze our sales process and identify areas for improvement. Here's how to configure lost reasons in Odoo 17 CRM
This slide is special for master students (MIBS & MIFB) in UUM. Also useful for readers who are interested in the topic of contemporary Islamic banking.
Reimagining Your Library Space: How to Increase the Vibes in Your Library No ...Diana Rendina
Librarians are leading the way in creating future-ready citizens – now we need to update our spaces to match. In this session, attendees will get inspiration for transforming their library spaces. You’ll learn how to survey students and patrons, create a focus group, and use design thinking to brainstorm ideas for your space. We’ll discuss budget friendly ways to change your space as well as how to find funding. No matter where you’re at, you’ll find ideas for reimagining your space in this session.
How to Setup Warehouse & Location in Odoo 17 InventoryCeline George
In this slide, we'll explore how to set up warehouses and locations in Odoo 17 Inventory. This will help us manage our stock effectively, track inventory levels, and streamline warehouse operations.
A review of the growth of the Israel Genealogy Research Association Database Collection for the last 12 months. Our collection is now passed the 3 million mark and still growing. See which archives have contributed the most. See the different types of records we have, and which years have had records added. You can also see what we have for the future.
it describes the bony anatomy including the femoral head , acetabulum, labrum . also discusses the capsule , ligaments . muscle that act on the hip joint and the range of motion are outlined. factors affecting hip joint stability and weight transmission through the joint are summarized.
हिंदी वर्णमाला पीपीटी, hindi alphabet PPT presentation, hindi varnamala PPT, Hindi Varnamala pdf, हिंदी स्वर, हिंदी व्यंजन, sikhiye hindi varnmala, dr. mulla adam ali, hindi language and literature, hindi alphabet with drawing, hindi alphabet pdf, hindi varnamala for childrens, hindi language, hindi varnamala practice for kids, https://www.drmullaadamali.com
IB Chemistry on ICT, 3D software, Avogadro, Jmol, Swiss PDB, Pymol for Internal Assessment on aromaticity
1. Measure bond length/angle
Measure number H2 bonds
Measure bond strength
Protein 1, 2 , 3O structure
Presence of disulfide bond
Presence alpha and beta pleated sheet
Organic softwarefor 3D model
Click here download Rasmol Click here download PyMolClick here download ACD Click here download Jmol Click here Chem EDDL
Click here ChemDraw editor
Click here download(Accelrys)
Click here chemical search.
Click here CRC database Click here RSC Databooklet
Modelling and 3D representation
Chemistry Database
Click here Spectra database(OhioState) Click here Spectra database (NIST)
Click here chem finder.
Spectroscopic Database
Click here download Swiss PDB Viewer
Modelling and 3D representation
✓ ✓
2. Electrostatic Potential (ESP)
Measure polarization
Electron Map density
Electron distribution
Dipole Moment
Measure bond length/angle
Measure bond strength
Organic softwarefor 3D model
Click here download Rasmol
Click here download PyMolClick here download Jmol
Click here Chem EDDL
Click here chemical search.
Click here CRC database
Modelling and 3D representation
Chemistry Database
Click here Spectra database(OhioState) Click here Spectra database (NIST)
Click here chem finder.
Spectroscopic Database
Click here down Swiss PDB
Modelling and 3D representation
✓ ✓
Click here NIST data
✓Click here download Arguslab
Click here chem axon
Click here download Avagrado
Click here chem EdDL
3. Measure bond length/angle
Measure number H2 bonds
Measure bond strength
Protein 1, 2 , 3O structure
Presence of disulfide bond
Presence alpha and beta pleated sheet
Chemical viewer 3D structure (Jmol)
Uses molecular modelling
1
J mol executable file
final product
J mol executable file
1
Designing benzene molecule
Open model kit
Drag to bond – choose carbon
Drag to bond – choose oxygen
Choose double bond – cursor center
Model kit – Minimize structure
Choose ruler for measurement
Measure bond angle CCC
Measure bond length C – C
Click here J mol tutorial
2
2
3
File – Get MOL – type – benzene/napthalene
Right click – Computation – Optimize structure
Measure C – C – C bond angle
Press 3D Optimization before measurement
Get structure from
PDB and MOL
Right click to get console
Measure
distance/angle
Model kit to
design molecule
To create ESP - Insert benzene file type . mol2 to Jmol
Right click – Surface – Molecular Surface Potential
3
Electrostatic Potential
Red – Oxygen region
(High electron density)
White – Hydrogen
(Low electron density)
Click here J mol download
4. Measure bond length/angle
Measure number H2 bonds
Measure bond strength
Protein 1, 2 , 3O structure
Presence of disulfide bond
Presence alpha and beta pleated sheet
Type -PDB ID - 4 letter code to J mol
Protein Data Bank
Protein database key in - PDB 4 letter code
1
2
3
Uses molecular modelling
1
2
Chemical viewer 3D structure (Avogadro)
Click here for pdb files
Click here download Avogadro
File – open benzene.sdf file
Extension – Optimize geometry
Select measure bond angle
Obtain file from any site as sdf/xml
Select measure
measure bond angle
Select E
Optimize geometry
View – Bond angle
View – Bond angle
4
Extension – Create surface
Type – Van Der Waals
- Electrostatic potential
- Calculate
5
Save file type as. Mol2 type
Electrostatic Potential
Red – Oxygen region
(High electron density)
White – Hydrogen
(Low electron density)
Insert file. mol2 to Jmol
Right click – Surface – Molecular Surface Potential
5. Measure bond length/angle
Measure number H2 bonds
Measure bond strength
Protein 1, 2 , 3O structure
Presence of disulfide bond
Presence alpha and beta pleated sheet
Protein Data Bank
Protein database key in - PDB 4 letter code
1
2
Uses molecular modelling
White – Hydrogen
(Low electron density)
1
2
Chemicalviewer 3D structure(Argus Lab)
Click here for pdb files
File – open benzene pdb file
Surface – Quick plot ESP
Click here download Arguslab
Red – Oxygen region
(High electron density)
Quantitative
measurement
3
6. Measure bond length/angle
Measure number H2 bonds
Measure bond strength
Protein 1, 2 , 3O structure
Presence of disulfide bond
Presence alpha and beta pleated sheet
Organic softwarefor 3D model (Pymol)
download pdb file text
1
1
Click here - Protein Data Bank
Protein database key in - PDB 4 letter code
3
Click here download PyMol
Click here Pymol video tutorialClick here Pymol video tutorial
Click here for pdb files
2
Wizard – measurement
- measure bond angle/length benzene
Uses molecular modelling
2
3
Look for benzene from PubChem
Down load 3D as sdf . file type
File – open from Pymol
7. Measure bond length/angle
Measure number H2 bonds
Measure bond strength
Protein 1, 2 , 3O structure
Presence of disulfide bond
Presence alpha and beta pleated sheet
Organic softwarefor 3D model (ACD Lab)
Click here download ACD Lab
Finish product in 3D viewer
Uses molecular modelling
1
Draw benzene
Press copy to 3D or press 3D viewer
Measure C – C bond length/ C – C – C bond angle
Press 3D Optimizationbefore measurement
Compareit to J mol
Compareit to CRC Data booklet
Compareit to Chem EDDL
Compute the average bond length /angle C - C - C
Measure distance Measure distanceSelect atom
1
Draw napthalene
Press copy to 3D or press 3D viewer
Measure C – C bond length/ bond angle
Press optimizationbefore measurement
Compareit to J mol
Compareit to CRC Data booklet
Compareit to Chem EDDL
Compute the average bond length /angle
Finish product in 3D viewer
22
3
3
8. Possible ResearchQuestion
DataCollection 3D modelling (Benzene/Napthalene)
Data Collection using 3D modelling
Data Collection using Database
Click here Jmol Click here PyMol
Click here ACD Click here Avagrado
Are aromatic moleculeplanar/flat
Do fused aromatic ring undergo delocalization
Do they obey Huckel rule
Are their angle of 120o
Are their bond length the same
Is there single/double bond present
What is their bond length/angle
Are all c in ring – sp2 hybrid
How ESP shown in aromatic ring
Click here chem axon Click here NIST data
CRC database
Chem spider.
Benzene ACD Pymol Jmol Avogadro Mean
Planar/flat Flat Flat Flat Flat Flat
ESP Planar Planar Planar Planar Planar
Bond length 140 139 139 140 139
Bond angle 120.02 120.01 120.05 120.03 120.2
DataCollectionDatabase (Benzene/Napthalene)
Napthalene ACD Pymol Jmol Avogadro Mean
Planar/flat Flat Flat Flat Flat Flat
ESP Planar Planar Planar Planar Planar
Bond length 136/140 138/141 139/140 137/140 138/140
Bond angle 120.04 120.02 120.01 120.01 120.2
Benzene NIST CRC Chemspi Chemaxon Mean
Bond length 139 139 139 140 139
Bond angle 120.01 120.01 120.02 120.01 120.1
napthalene
benzene
Benzene NIST CRC Chemspi Chemaxon Mean
Bond length 136
141
137
140
137
141
137
141
137
141
Bond angle 120.01 120.01 120.02 120.01 120.1
How planarity and delocalization affect aromaticity?
Huckel rule = 4n + 2
n = 1 = 6π electron
n= 2 = 10 π electron
n = 3 = 14 π electron 6π 10π 14π
9. How planarity and delocalization affect aromaticity?
Possible ResearchQuestion Data Collection using 3D modelling
Data Collection using Database
Click here Jmol Click here PyMol
Click here ACD Click here Avagrado
Are aromatic moleculeplanar/flat
Do fused aromatic ring undergo delocalization
Do they obey Huckel rule
Are their angle of 120o
Are their bond length the same
Is there single/double bond present
What is their bond length/angle
Are all c in ring – sp2 hybrid
How ESP shown in aromatic ring
Click here chem axon Click here NIST data
CRC database
Chem spider.
Evaluationand Limitationusing 3D modelling
Must use a variety of sources/programmeto verify/validatethe validity and reliability of data collected
Average is computedfrom diff software and checked with databaseto confirm.
Check on methodological limitationusing 3D model. (MUST perform 3D Optimization to most stable form structure.
Criticaland skeptical of result produced by computationalchemistry.
Major limitationof computation,they assume non-interactingmolecule. (Ideal situation, ex molecule in vacuum or isolated state)
Most appropriatemolecule are those whose coordinates are not theoreticalbut derive from experimentalstructuraldetermination
(using X ray diffraction)
Be carefulof predicted arrangement from simulation /3D model
Datasources are supported using diff method/3D model/database
Certain databaselike NIST and CRC are more reliable source
Check if there is a good agreement bet CRC, diff databases and 3D model predictionbefore making conclusion
Computation programmeis always based on approximationand we cannot conclusive prove anything
Reflect of validity and reliability of data
Is model a true representation of reality?
10. Click here ring strain (wiki)
Click here angle strain (master organic)
Angle strain – smaller angle (higher angle strain)
– more energeticbond
– more unstable/reactive
Angle strain destabilize molecule - higher reactivity
Angle strain leads to elevated heat of combustion.
Max bond strength result from effective overlap of atomic orbital.
Angle strain and torsional strain combine to create ring strain
Both affect stability of cyclic molecules
Angle strain- deviation from ideal angle
Ideal angle = 109o Angle = 60o
49o deviate from 109o
(angle/torsional strain)
Angle = 90o
49o deviate from 109o
(angle/torsional strain)
Angle = 108o
1o deviate from 109o
(angle/torsional strain)
Angle = 120o
11o deviate from 109o
(angle/torsional strain)
Molecule is NOT FLAT!!!!!
Possible ResearchQuestion – How planarityand delocalizationaffect aromaticity?
Aromatic ring/fuse benzene ring/ heterocyclic
Benzene/aromatic – sp2 – 120 – no angle strain
Angle = 120o
NO deviate from 120o
(No angle strain)
Molecule is FLAT!!
11. Aromatic ring/fuse benzene ring/ heterocyclic Huckel rule
- 4n+2 electronundergo delocalization
- conjugated p-orbitalcloud
- molecule is planar/cyclic
- atom in ring participatein delocalizing e
by having p-orbital/unsharedelectron.
- 4n+2 electrons→ n = 1 → C6H6 (Benzene)
Are these molecule planar/flat
Do they obey Huckel rule
Do they have angle of 120o
Are their bond length the same
Is there single/double bond present
What is their bond length/angle
Are all c in ring – sp2 hybrid
How are ESP shown in ring
Benzene/aromatic – sp2 – 120o – no angle strain
Furan thiphene pyrrole pyridine pyran
oxazine thiazine pyrimidine piperazine thipyran
Possible ResearchQuestion – How planarityand delocalizationaffect aromaticity?
Aromatic can be heterocyclic if contain
non-carbon, with oxy, nitrogen, or sulfur They do not obey Huckel rule
Why ?
12. Are these molecule planar/flat
Do they obey Huckel rule
Do they have angle of 120o
Are their bond length the same
Is there single/double bond present
What is their bond length/angle
Are all c in ring – sp2 hybrid
How are ESP shown in ring
Aromatic ring/fuse benzene ring/ heterocyclic) Huckel rule
- 4n+2 electronundergo delocalization
- conjugated p-orbitalcloud
- molecule is planar/cyclic
- atom in ring participatein delocalizing e
by having p-orbital/unsharedelectron.
- 4n+2 electrons→ n = 1 → C6H6 (Benzene)
Benzene/aromatic – sp2 – 120o – no angle strain
Possible ResearchQuestion –How planarityand delocalizationaffect aromaticity?
They do not obey Huckel rule
Why ?
Aromatic can be heterocyclic if contain
non-carbon, with oxy, nitrogen, or sulfur
13. Delocalizationof electron
Resonance
• Describing delocalizationof electron within a molecule/polyatomic ion
where bonding cant be express by ONE single Lewis structure
•Delocalizationof π bond – π electron spread over more than 2 nuclei
•π electron are shared/spread – more stable
Resonance structurebenzene
Benzene 6HC6
resonance structure 1 resonance structure 2
Resonance hybrid
• All bond C6H6 identical in length/strength
• Hybrid of 2 resonance structures
• No C-C (single) or C=C (double) bond
• Only C ----- C bond
• Intermediate character bet single/double bond
• Bond Order = 1.5
• Unhybridised p orbital
• Delocalization electron above below plane
• sp2 hybridization on carbon center
Click here to view
Delocalizedelectrons
Kekulé structure
Cyclohexa- 1,3,5 triene
χ ✓
Benzene
Hexagonal, planar
Resonance Hybrid more stable than any of resonance structure
✓
Click here to view
Kekule
14. Resonance/DelocalizationEnergy
ΔH cyclohexene = -120 kJmol-1
ΔH cyclohexa 1,3 diene = -240 kJmol-1
ΔH cyclohexa 1,3,5 triene = -360 kJmol-1
ΔH Benzene = -208 kJmol-1
Enthalpy change hydrogenation
✓
✓
……
• Benzene lower in energy by 150 kJ
• More stable due to delocalization
of π electron
150kJ
C-C
Single bond
C=C
Double bond
C=C
Benzene
Bond length/pm 154 134 140
Bond
enthalpy/kJmol-1
346 614 507
1
2
• X ray hit benzene crystal
• Interact with electron (electron density map)
• X ray diffraction produced
• Bond length measured
X ray crystallography
NO single/double bond detected ✓
✓
3 Addition rxn for unsaturatedC=C
✓
Addition rxn
Substitution rxn
NO double bond
- 360χ
- 240
- 150
H H Br Br
׀ ׀ ׀ ׀
C = C + Br2 → H – C – C – H
׀ ׀ ׀ ׀
H H H H
3 Evidence for Benzene structure
15. Resonance structure methanoate
resonance structure 1 resonance structure 2
• All CO bond are identical in length/strength
• Hybrid of 2 resonance structure
• NO C-O (single) or C=O (double) bond
• Only C ----- O bond
• Intermediate character bet single and double bond
• Bond Order = 1.5
Methanoate ion
HCOO
Click here to view
resonance hybrid
Click here to view
Resonance structureethanoate
Ethanoate ion
COOCH3
resonance structure 1 resonance structure 2
resonance hybrid
HH
CH3
Delocalizationof electron
Resonance
• Describing delocalizationof electron within a molecule/polyatomic ion
where bonding cant be express by ONE single Lewis structure
• Delocalization of π bond – π electron spread over more than 2 nuclei
• π electron are shared/spread – more stable
16. Delocalizationof electron
Resonance structurecarbonateion
2
3CO
resonance structure 1 resonance structure 2 resonance structure 3
Resonance hybrid
• All bond CO3
2-
are identical in length /strength
• Hybrid of 3 resonance structure
• Negative charge equally distributed over all oxy
• No O-O (single) or O=O (double) bond.
• Only O ----- O bond
• Intermediate in character bet single and double bond
• Bond Order = 1.3
Carbonate Ion
Charge 2- delocalized into 2/3-
Lower charge – more stable
Click here on video carbonate
C
Resonance
• Describing delocalizationof electron within a molecule/polyatomic ion
where bonding cant be express by ONE single Lewis structure
• Delocalizationof π bond – π electron spread over more than2 nuclei
• π electron are shared/spread– more stable
17. Resonance structurenitrate ion
3NO
resonance structure 1 resonance structure 2 resonance structure 3
resonance hybrid
• All bond NO3
-
are identical in length/strength
• Hybrid of 3 resonance structure
• Negative charge equally distributed over all oxy
• No N-O (single) or N=O (double) bond
• Only N ----- O bond
• Intermediate in character bet single and double bond
• Bond Order = 1.3
Nitrate Ion
Charge 1- delocalized into 1/3-
Lower charge – more stable
Click here to view video
1/3
1/31/3
Delocalizationof electron
Resonance
• Describing delocalizationof electron within a molecule/polyatomic ion
where bonding cant be express by ONE single Lewis structure
• Delocalization of π bond – π electron spread over more than 2 nuclei
• π electron are shared/spread – more stable
18. Resonance structurenitrite ion
2NO
resonance structure 1 resonance structure 2
resonance hybrid
• All bonds NO2
-
are identical in length and strength
• Hybrid of 2 resonance structures
• Negative charge equally distributed over all oxygen
• NO N-O (single) or N=O (double) bonds found
• Only N ----- O bond
• Intermediate in character bet single and double bond
• Bond Order = 1.5
Nitrite Ion
charge 1- delocalized into 1/2-
Lower charge – more stable
Click here video nitrite
Delocalizationof electron
Resonance
• Describing delocalizationof electron within a molecule/polyatomic ion
where bonding cant be express by ONE single Lewis structure
•Delocalizationof π bond – π electron spread over more than 2 nuclei
•π electron are shared/spread – more stable
19. Resonance structuresulfur dioxide
2SO
resonance structure 1 resonance structure 2
• All SO2 bond are identical in length/strength
• Hybrid of 2 resonance structure
• Negative charge equally distributed over all oxy
• NO S-O (single) or S=O (double) bond
• Only S ----- O bond
• Intermediate in character bet single and double bond
• Bond Order = 1.5
Sulfur Dioxide
Click here to view
S
resonance hybrid
Delocalizationof electron
Resonance
• Describing delocalizationof electron within a molecule/polyatomic ion
where bonding cant be express by ONE single Lewis structure
•Delocalizationof π bond – π electron spread over more than 2 nuclei
•π electron are shared/spread – more stable