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, 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.
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.
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.
Deep Purple: Discolouration in CBD productsMarkus Roggen
Presentation at ACS Spring 2022 conference.
Recently, there has been a flood of cannabidiol (CBD)-containing products, with divers marketing claims for a plethora of use cases. With this new market segment, regulatory oversight is still developing, and label claims of CBD concentration is often verifiable. CBD is unstable in solution and some CBD products are anecdotally reported to turn purple on storage; however, the decomposition products of CBD are mostly unknown.
Delic Lab embarked on a long and painstaking hunt for those decomposition products, established their identity through complementary chemical methods and established reaction pathways between them.
We will present our findings about common CBD oxidation products, who those are highly photochemically unstable and decomposes rapidly. Decomposition leads to a multitude of new cannabinoid derivatives.
Reading and Writing Molecular File Formats for Data Exchange of Small Molecul...NextMove Software
This document discusses various aspects of molecular file formats used for data exchange of small molecules, biopolymers, and reactions. It addresses topics such as representation of hydrogens, valence models, benchmarking different file readers, and preserving labels in files. The author presents results from testing 24 different molecular file readers on their ability to correctly interpret an MDL benchmark file containing over 10,000 connection tables with varying elements, charges, and environments. While many readers can read MDL files, they do not always agree on semantics, though performance is generally better on subsets relevant to pharmaceutical applications. The benchmarking led to improvements in several open-source and commercial toolkits.
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 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 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 Gibbs Free Energy, Equilibrium constant and Cell PotentialLawrence kok
The document discusses the relationship between thermodynamic quantities such as Gibbs free energy (ΔG), equilibrium constant (Kc), cell potential (Ecell), and their significance. It provides equations relating these quantities and explains how ΔG and Kc can be used to predict the spontaneity and extent of chemical reactions. Examples are given to show how ΔG decreases as the reaction progresses towards equilibrium, and how the values of ΔG and Kc indicate the position of the reaction mixture between reactants and products.
IB Chemistry on Absorption Spectrum and Line Emission/Absorption SpectrumLawrence kok
Transition metal complexes can have different colors due to the splitting of the metal ion's d orbitals caused by ligands. Ligands of varying strength cause varying degrees of d orbital splitting, represented by ΔE. Stronger ligands cause greater splitting and absorption of higher energy visible light, resulting in colors like violet or blue. Weaker ligands cause less splitting and absorption of lower energy visible light, appearing as colors like yellow or green. The spectrochemical series orders ligands from weakest to strongest field strength based on the color produced.
IB Chemistry on Redox Design and Nernst EquationLawrence kok
The document outlines research questions and procedures to investigate the effect of various factors on the emf and current of voltaic cells. Specifically, it will study how concentration, temperature, electrode size, salt bridge composition, and metal pairs affect measurements in zinc-copper and copper-copper cells. Tests will be conducted by varying one factor at a time while keeping others standard, and measuring the resulting emf and current.
IB Chemistry on Entropy and Law of ThermodynamicsLawrence kok
This document discusses entropy and the laws of thermodynamics. It defines entropy as a measure of molecular disorder or randomness, and explains that entropy increases as energy and matter disperse and become more randomly distributed. The second law of thermodynamics states that the entropy of the universe always increases for spontaneous processes. Reactions and phase changes that result in higher entropy (more disorder) of the products are spontaneous. The document provides examples and explanations of how entropy changes in different processes.
IB Chemistry on Gibbs Free Energy vs Entropy on spontanietyLawrence 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. The change in internal energy of a system (ΔE) equals heat transferred (q) plus work done (w).
2) The second law of thermodynamics states that the entropy of the universe always increases for spontaneous processes. Entropy (S) is a measure of disorder or randomness at the molecular level. Spontaneous processes result in increased entropy of the universe (ΔSuni > 0).
3) The third law of thermodynamics states that the entropy of a perfectly crystalline substance is zero at absolute zero temperature
IB Chemistry on Stereoisomers, E/Z, Cis Trans, Geometric, Optical and Polarim...Lawrence kok
There are two types of isomerism: structural isomerism and stereoisomerism. Structural isomers have the same molecular formula but different structural formulas or arrangements of atoms. Stereoisomers have the same molecular formula and structural formula but different spatial arrangements of atoms. Examples of stereoiosmers include geometric isomers, which require a double bond or ring structure to prevent bond rotation, and optical isomers. The E/Z or Cahn-Ingold-Prelog system is used to name geometric isomers based on atomic mass priorities of substituents.
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, 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.
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.
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.
Deep Purple: Discolouration in CBD productsMarkus Roggen
Presentation at ACS Spring 2022 conference.
Recently, there has been a flood of cannabidiol (CBD)-containing products, with divers marketing claims for a plethora of use cases. With this new market segment, regulatory oversight is still developing, and label claims of CBD concentration is often verifiable. CBD is unstable in solution and some CBD products are anecdotally reported to turn purple on storage; however, the decomposition products of CBD are mostly unknown.
Delic Lab embarked on a long and painstaking hunt for those decomposition products, established their identity through complementary chemical methods and established reaction pathways between them.
We will present our findings about common CBD oxidation products, who those are highly photochemically unstable and decomposes rapidly. Decomposition leads to a multitude of new cannabinoid derivatives.
Reading and Writing Molecular File Formats for Data Exchange of Small Molecul...NextMove Software
This document discusses various aspects of molecular file formats used for data exchange of small molecules, biopolymers, and reactions. It addresses topics such as representation of hydrogens, valence models, benchmarking different file readers, and preserving labels in files. The author presents results from testing 24 different molecular file readers on their ability to correctly interpret an MDL benchmark file containing over 10,000 connection tables with varying elements, charges, and environments. While many readers can read MDL files, they do not always agree on semantics, though performance is generally better on subsets relevant to pharmaceutical applications. The benchmarking led to improvements in several open-source and commercial toolkits.
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 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 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 Gibbs Free Energy, Equilibrium constant and Cell PotentialLawrence kok
The document discusses the relationship between thermodynamic quantities such as Gibbs free energy (ΔG), equilibrium constant (Kc), cell potential (Ecell), and their significance. It provides equations relating these quantities and explains how ΔG and Kc can be used to predict the spontaneity and extent of chemical reactions. Examples are given to show how ΔG decreases as the reaction progresses towards equilibrium, and how the values of ΔG and Kc indicate the position of the reaction mixture between reactants and products.
IB Chemistry on Absorption Spectrum and Line Emission/Absorption SpectrumLawrence kok
Transition metal complexes can have different colors due to the splitting of the metal ion's d orbitals caused by ligands. Ligands of varying strength cause varying degrees of d orbital splitting, represented by ΔE. Stronger ligands cause greater splitting and absorption of higher energy visible light, resulting in colors like violet or blue. Weaker ligands cause less splitting and absorption of lower energy visible light, appearing as colors like yellow or green. The spectrochemical series orders ligands from weakest to strongest field strength based on the color produced.
IB Chemistry on Redox Design and Nernst EquationLawrence kok
The document outlines research questions and procedures to investigate the effect of various factors on the emf and current of voltaic cells. Specifically, it will study how concentration, temperature, electrode size, salt bridge composition, and metal pairs affect measurements in zinc-copper and copper-copper cells. Tests will be conducted by varying one factor at a time while keeping others standard, and measuring the resulting emf and current.
IB Chemistry on Entropy and Law of ThermodynamicsLawrence kok
This document discusses entropy and the laws of thermodynamics. It defines entropy as a measure of molecular disorder or randomness, and explains that entropy increases as energy and matter disperse and become more randomly distributed. The second law of thermodynamics states that the entropy of the universe always increases for spontaneous processes. Reactions and phase changes that result in higher entropy (more disorder) of the products are spontaneous. The document provides examples and explanations of how entropy changes in different processes.
IB Chemistry on Gibbs Free Energy vs Entropy on spontanietyLawrence 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. The change in internal energy of a system (ΔE) equals heat transferred (q) plus work done (w).
2) The second law of thermodynamics states that the entropy of the universe always increases for spontaneous processes. Entropy (S) is a measure of disorder or randomness at the molecular level. Spontaneous processes result in increased entropy of the universe (ΔSuni > 0).
3) The third law of thermodynamics states that the entropy of a perfectly crystalline substance is zero at absolute zero temperature
IB Chemistry on Stereoisomers, E/Z, Cis Trans, Geometric, Optical and Polarim...Lawrence kok
There are two types of isomerism: structural isomerism and stereoisomerism. Structural isomers have the same molecular formula but different structural formulas or arrangements of atoms. Stereoisomers have the same molecular formula and structural formula but different spatial arrangements of atoms. Examples of stereoiosmers include geometric isomers, which require a double bond or ring structure to prevent bond rotation, and optical isomers. The E/Z or Cahn-Ingold-Prelog system is used to name geometric isomers based on atomic mass priorities of substituents.
IB Chemistry on Structural Isomers and Benzene StructureLawrence kok
The document discusses organic functional groups and their naming conventions. It provides examples of common organic compound classes including alkanes, alkenes, alkynes, alcohols, ethers, ketones, aldehydes, carboxylic acids, esters, amides, amines, nitriles, and halogenoalkanes. It also discusses IUPAC nomenclature rules for systematically naming organic molecules based on functional groups, carbon chain length and position of substituents. Additionally, it briefly touches on isomerism, which refers to compounds with the same molecular formula but different structural or spatial arrangements of atoms.
This document provides an overview of analytical techniques used in chemistry, including both classical and instrumental methods. Classical methods involve qualitative and quantitative analysis using chemical tests, flame tests, and titration. Instrumental methods discussed include various types of spectroscopy such as infrared spectroscopy, nuclear magnetic resonance spectroscopy, and chromatography techniques used for separation analysis. Specific analytical techniques are described including their applications and mechanisms. Key concepts covered include electromagnetic radiation, molecular vibration, factors that influence infrared absorption frequencies, and interpreting infrared spectra to determine functional groups in organic compounds.
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 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 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 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 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 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 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.
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.
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.
A label free and enzyme-free aptasensor for visual cd2+ detection based on sp...Vincent Paul Schmitz
The document describes a label-free and enzyme-free aptasensor for visual detection of Cd2+ based on split G-quadruplex DNAzyme fragments. The sensing system utilizes a three-way junction structure constructed from three hairpin molecules. In the presence of Cd2+, the aptamer binds Cd2+ and initiates branch migration of the hairpins, forming the junction. This brings the split G-quadruplex fragments into proximity to form an intact G-quadruplex upon addition of hemin. The formed G-quadruplex DNAzymes catalyze a color change reaction, providing naked-eye visual detection of Cd2+ with high sensitivity down to 10 pM concentration. The biosensor
The document discusses catalytic interfaces and techniques for probing their dynamics. It defines catalytic interfaces as boundaries between different phases, such as solid-gas or solid-liquid, where catalysis occurs. Dynamic processes at these interfaces include surface restructuring, oxidation/reduction, and atom migration. In situ techniques like environmental transmission electron microscopy (ETEM) and high pressure scanning tunneling microscopy allow observing these interface dynamics under reaction conditions. ETEM studies have visualized phenomena like carbon nanofiber growth, nanoparticle sintering, and surface reconstructions during catalysis. These techniques provide insights into catalyst deactivation mechanisms and ways to improve activity.
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.
A fuel cell membrane test stand was designed and fabricated to evaluate three new solid polymer electrolyte membranes. The test stand allowed for measurement of temperature, pressure, humidity, and oxygen concentration at the reactant-catalyst-electrolyte interface. Characterizations were performed of the membranes and gas diffusion electrodes using optical microscopy, scanning electron microscopy, and atomic force microscopy. Performance testing generated polarization curves and power curves to compare the experimental membranes to Nafion 117. Challenges were encountered with sensors shorting out but were addressed with design modifications.
The document summarizes a student's final project to design and construct a low pressure capacitively coupled plasma etcher. Key points:
- The objective was to design a plasma etch source that can hold a vacuum and create a stable plasma for etching.
- The initial design was simplified using aluminum and graphite electrodes. The final design maintained the materials due to cost but added insulation on the electrodes.
- Construction involved machining parts and assembling the chamber, which was then tested and optimized by addressing leaks and plasma instability issues.
- Diagnostics using optical emission spectroscopy were planned to analyze the plasma properties and etch species.
- Future work proposed improving the design and experimenting with
Visible and near-infrared emission properties of melt-grown Dy doped CsPbCl3 ...samuel uba
Doping of lead halides perovskites with rare-earth metals ions has become of significant current interest for possible applications in optoelectronics. In this research, we studied the material preparation and the visible to near IR optical properties of Dy3+ doped CsPbCl3. The crystal was synthesized from purified starting materials and melt-grown by vertical Bridgman technique. Visible emission studies under resonant-intra-4f excitation at ~450nm revealed bright yellow emission centered at 575nm arising from the 4F9/2 to 4H13/2 transition of Dy3+ ions. Additional emission bands arising from the 4F9/2 excited states were centered at 485nm, 664nm and 752nm. The decay time of the 4F9/2 level was non-exponential with an average lifetime of ~320 µs. Near-infrared emission studies were performed using a 808 nm diode lasers and revealed several IR bands located at 1.14 µm (6H7/2+6F9/2 ->6H15/2), 1.33 µm(6H9/2+6F11/2 ->6H15/2) , 1.55 µm (6F5/2 ->6H11/2), and ~1.7 µm (6H11/2 ->6H15/2) arising from lower excited states of Dy3+ ions. More details of the emission spectra and dynamics of Dy: CsPbCl3 as well as a comparison to Dy: KPbCl2 will be presented at the conference
A presentation on Diamond-like Carbon Thin Film with Controlled Zeta Potential for Medical Application made by Deepak Rajput. It was presented as a course requirement at the University of Tennessee Space Institute in Fall 2008.
Yutong Liu - Poster - ACF-PEDOT SupercapYutong Liu
This document summarizes research on activated carbon fiber (ACF) and poly(3,4-ethylenedioxythiophene) (PEDOT) based supercapacitors. The introduction provides background on supercapacitors and the materials used. Experimental details are given on vapor phase polymerization to coat ACF with PEDOT. Characterization with SEM, EDS, and Raman spectroscopy show the ACF is well-coated. Electrochemical testing reveals the supercapacitors have stable capacitance over cycles and scan rates. Gravimetric capacitance reaches over 100 F/g, and coating ACF with high purity PEDOT could further increase this. In conclusion, ACF/PEDOT nanocomposites show potential
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.
Cooper Environmental’s Xact® 625i is designed for high time resolution multi-metals monitoring of ambient air, with detection limits that rival those of laboratory analysis. The Xact® 625i comes standard with a solid-state meteorological sensor and Cooper Environmental’s proprietary ADAPT analysis package, making the instrument one of the most powerful air pollution source detection offerings in the industry. ask info here: https://etserv.be/product/cooper-environmental-xact-625i/
The document summarizes a hyphenated technique combining capillary electrophoresis (CE) and inductively coupled plasma mass spectrometry (ICP-MS) for elemental speciation analysis. It discusses the CE-ICP-MS instrumentation including interface designs, applications to analyze arsenic and chromium species in preserved wood and soil, and preliminary results examining interface configurations and gas flow rates.
High Capacity Planar Supercapacitors and Lithium-Ion Batteries byModular Man...Bing Hsieh
High Capacity Planar Supercapacitors and Lithium Ion Batteries by Modular Manufacturing
Novel planar supercapacitors (SC) and lithium ion batteries (LIB) having interdigitated electrodes for large format applications will be presented. We will discuss the design principles of the new planar structures, their potential to give > 5X improvement in capacity over current supercapacitors, their pack designs, as well as low cost fabrication by modular manufacturing. The drawings given in the following link depict the plan view (top) and the cross-sectional view (bottom) of a planar LIB, wherein the dotted and the hatched areas are the positive and the negative electrodes respectively; the gray areas are the current collectors and the gray lines are the grid lines. Unlike the known interdigitated thin film microsupercapacitor design where the current collectors are situated on the top or bottom surfaces of the electrodes and paralleled to the plane of the substrate and can only exert limited weak fringe fields, the current collectors in our new design are running along the sidewalls of the electrodes and are perpendicular to the substrate and can thus provide strong direct fields, as indicated by the purple arrow, to promote facile ion movement across the entire thickness of the electrodes (20-100 µm). In addition, the relatively narrow inter-spaces between two opposite electrodes (20-100 µm) may allow much higher power densities than ever. Due to their scalability and low cost modular manufacturing processes by printing, the new planar SC/LIB may be designed for a wide range of applications such as mobile devices, transportation, and grid and distributed energy storage.
https://drive.google.com/file/d/0B7fDeNQTYRc9VDdOTTVYRmh2QWc/view?usp=sharing
This is a little presentation I gave to Roald Hoffmann's group at Cornell. What are the industrial applications of computational chemistry? How to people work differently in academia vs. industry? What are the sorts of things students should think about if they plan to work in the corporate world?
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.
5th International Conference : Workshop - Energyicarb
This document summarizes a meeting about developing consistent methods for accounting carbon emissions from wind power generation. The meeting agenda included presentations on different life cycle carbon assessment approaches, including process-based, cost-based, and hybrid models. Attendees included policymakers, academics, and environmental groups. The meeting aimed to discuss case studies, get feedback on carbon accounting guidelines, and explore applying lessons to other sectors. Presenters also discussed normalizing varied life cycle assessment results and understanding how wind interacts with the electric grid. The document proposes developing a standard framework and accreditation for carbon accounting through the Initiative for Carbon Accounting.
The document discusses the use of X-ray photoelectron spectroscopy (XPS) to analyze soot samples. XPS can be used to determine the elemental composition, carbon oxidation state through identification of oxygen functional groups, and carbon nanostructure of soot. The document provides examples of low-resolution XPS scans of jet aircraft and diesel engine emissions that show elemental composition. Higher resolution scans of soot samples show differences in oxygen functional groups and carbon bonding that provide information about oxidation conditions. XPS analysis of carbon nanostructure may provide an alternative to lattice fringe analysis using HRTEM images. Correlating XPS results with reactivity could help understand the effects of fuels and nanostructure on soot properties.
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.
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
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.
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 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.
Walmart Business+ and Spark Good for Nonprofits.pdfTechSoup
"Learn about all the ways Walmart supports nonprofit organizations.
You will hear from Liz Willett, the Head of Nonprofits, and hear about what Walmart is doing to help nonprofits, including Walmart Business and Spark Good. Walmart Business+ is a new offer for nonprofits that offers discounts and also streamlines nonprofits order and expense tracking, saving time and money.
The webinar may also give some examples on how nonprofits can best leverage Walmart Business+.
The event will cover the following::
Walmart Business + (https://business.walmart.com/plus) is a new shopping experience for nonprofits, schools, and local business customers that connects an exclusive online shopping experience to stores. Benefits include free delivery and shipping, a 'Spend Analytics” feature, special discounts, deals and tax-exempt shopping.
Special TechSoup offer for a free 180 days membership, and up to $150 in discounts on eligible orders.
Spark Good (walmart.com/sparkgood) is a charitable platform that enables nonprofits to receive donations directly from customers and associates.
Answers about how you can do more with Walmart!"
ISO/IEC 27001, ISO/IEC 42001, and GDPR: Best Practices for Implementation and...PECB
Denis is a dynamic and results-driven Chief Information Officer (CIO) with a distinguished career spanning information systems analysis and technical project management. With a proven track record of spearheading the design and delivery of cutting-edge Information Management solutions, he has consistently elevated business operations, streamlined reporting functions, and maximized process efficiency.
Certified as an ISO/IEC 27001: Information Security Management Systems (ISMS) Lead Implementer, Data Protection Officer, and Cyber Risks Analyst, Denis brings a heightened focus on data security, privacy, and cyber resilience to every endeavor.
His expertise extends across a diverse spectrum of reporting, database, and web development applications, underpinned by an exceptional grasp of data storage and virtualization technologies. His proficiency in application testing, database administration, and data cleansing ensures seamless execution of complex projects.
What sets Denis apart is his comprehensive understanding of Business and Systems Analysis technologies, honed through involvement in all phases of the Software Development Lifecycle (SDLC). From meticulous requirements gathering to precise analysis, innovative design, rigorous development, thorough testing, and successful implementation, he has consistently delivered exceptional results.
Throughout his career, he has taken on multifaceted roles, from leading technical project management teams to owning solutions that drive operational excellence. His conscientious and proactive approach is unwavering, whether he is working independently or collaboratively within a team. His ability to connect with colleagues on a personal level underscores his commitment to fostering a harmonious and productive workplace environment.
Date: May 29, 2024
Tags: Information Security, ISO/IEC 27001, ISO/IEC 42001, Artificial Intelligence, GDPR
-------------------------------------------------------------------------------
Find out more about ISO training and certification services
Training: ISO/IEC 27001 Information Security Management System - EN | PECB
ISO/IEC 42001 Artificial Intelligence Management System - EN | PECB
General Data Protection Regulation (GDPR) - Training Courses - EN | PECB
Webinars: https://pecb.com/webinars
Article: https://pecb.com/article
-------------------------------------------------------------------------------
For more information about PECB:
Website: https://pecb.com/
LinkedIn: https://www.linkedin.com/company/pecb/
Facebook: https://www.facebook.com/PECBInternational/
Slideshare: http://www.slideshare.net/PECBCERTIFICATION
Communicating effectively and consistently with students can help them feel at ease during their learning experience and provide the instructor with a communication trail to track the course's progress. This workshop will take you through constructing an engaging course container to facilitate effective communication.
Gender and Mental Health - Counselling and Family Therapy Applications and In...PsychoTech Services
A proprietary approach developed by bringing together the best of learning theories from Psychology, design principles from the world of visualization, and pedagogical methods from over a decade of training experience, that enables you to: Learn better, faster!
Gender and Mental Health - Counselling and Family Therapy Applications and In...
IB Chemistry on ICT, 3D software, Avogadro, Jmol, Swiss PDB, Pymol for Internal Assessment on Fullerenes and Buckyballs
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
✓ ✓
Click here download nano modeller
Click here download nano modeller
fullerene library
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. Organic softwarefor 3D model
Click here download software
fullerenes/nanotube pdb file
1
File – open bucky ball file
3
Tools – recalculatebonds
4
Display bond angle
2
Organic softwarefor 3D model
Click here download software
fullerenes/nanotube pdb files
1
2
3
Measure conductivity Click here – bucky ball
Select type bucky ball
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
Chemicalviewer 3D structure(Avogadro)
Click here for pdb files
Click here download Avogadro
File – open C60. xyz or pdb file
Extension – Optimize geometry
Select measure bond angle
Obtain file from any site as xyz/pdb
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
Chemicalviewer 3D structure(Jmol)
Uses molecular modelling
1
J mol executable file
final product
J mol executable file
1
Designing C60 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 – C60
Save file type as Mol2 in Avogadro – transfer to Jmol
Right click – Computation – Optimize structure
Press 3D Optimization before measurement
Measure C – C bond length/angle
Get structure from
PDB and MOL
Right click to get console
Measure
distance/angle
Model kit to
design molecule
To create ESP - Insert C60 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
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 C60
Uses molecular modelling
2
3
Look for C60 from PubChem
Download as sdf /pdb/xyz 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
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 C60 pdb/xyz file
Surface – Quick plot ESP
Click here download Arguslab
Red – Oxygen region
(High electron density)
Quantitative
measurement
3
8. 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 C60
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 fullerene
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
9. Files resources for Fullerenes
Diff bucky balls
Bucky ball C60 - containpentagonal and hexagonal ring
No two pentagons share an edge (pentalene).
C60 is truncatedicosahedron - 20 hexagons and 12 pentagons
C60 avoid having double bond in pentagonal ring, which make
electron delocalizationpoor
C60 not "superaromatic".C60 - like electrondeficient alkene
React with electron rich species – addition rxn
ResearchQuestion – How diff fullerene affect aromaticity,,delocalization and conductivity ?
6:6 ring (bet two hexagon) - double bond - shorter
6:5 ring (bet hexagon and pentagon)- longer
Average bond length is 1.4A
Electrondensity – higher in 6 carbon ring than in 5 carbon ring
Undergo addition rather than substitutionrxn
Small degree – aromatic character
Still have localized C =C and single C – C bond
Super alkene ratherthan aromatic compound
6:6 ring (C=C)
6:5 ring (C- C)
Fullerene, n carbon atoms has n pi elec, free to delocalize over whole molecule.
Smallest spherical fullerene – C20
Most common – C60
They exist as - C70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90
C20 C60 C70 C80 C90
Click here view excellent fullerene xyz file Click here view excellent fullerene pdb file Click here fullerene pdb file
10. Possible ResearchQuestion
DataCollection 3D modelling
Data Collection using 3D modelling
Data Collection using Database
Click here Jmol Click here PyMol
Click here ACD Click here Avagrado
How diff fullerenes/shapeaffect aromaticity
Are they still aromatic and is Huckel rule obey
How shape fullerene affect conductivity/delocalization
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
Click here chem axon Click here NIST data
CRC database
Chem spider.
C60 ACD Pymol Jmol Avogadro Mean
Bond angle
Hexagon
Pentagon
< 120
< 118
< 120
< 117
< 120
< 115
< 120
< 114
< 120
< 115
Bond length
C = C
C – C
139
142
141
144
141
143
139
143
139
142
Data Collection Database
How diff fullerenes affect aromaticity, delocalization and conductivity ?
C60
6:6 ring (C=C) 6:5 ring (C- C)
Graphene ACD Pymol Jmol Avogadro Mean
Bond angle
Hexagon
120 120 120 120 120
Bond length
C - C
143 142 143 142 142
C60 NIST CRC Chemaxo Chemspi Mean
Bond angle
Hexagon
Pentagon
< 120
< 113
< 120
< 117
< 120
< 115
< 120
< 114
< 120
< 116
Bond length
C = C
C – C
140
143
142
144
141
143
141
143
140
143
Graphene
Graphene NIST CRC Chemaxo Chenspi Mean
Bond angle
Hexagon
120 120 120 120 120
Bond length
C - C
142 142 143 142 142
Graphene C60 Nanotubes
11. Possible ResearchQuestion Data Collection using 3D modelling
Data Collection using Database
Click here Jmol Click here PyMol
Click here ACD Click here Avagrado
How diff fullerenes/shapeaffect aromaticity
Are they still aromatic and is Huckel rule obey
How shape fullerene affect conductivity/delocalization
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
Click here chem axon Click here NIST data
CRC database
Chem spider.
How diff fullerenes affect aromaticity, delocalization and conductivity ?
Graphene C60 Nanotubes
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?
12. Allotropes of Carbon
Diamond Fullerene, C60
• Carbon- sp2 hybridization
• Bonded in geodesic shape
• 60 carbon spherical - 20 hexagon/12 pentagon
• 1 π electron free to delocalized.
• Surface is not planar, but sphere
• Electrons NOT able to flow easily.
Graphene
• Carbon- sp2 hybridization
• Carbon bond to 3 others form hexagon (120o)
• Exist chicken wire/honeycomb-1 layer
Click here to viewClick here to view Click here to view
• Carbon- sp3 hybridization
• Bonded tetrahedrally
• Strong hard covalent network
• Carbon- sp2 hybridization
• Bonded Trigonal planar (layers)
• Giant covalent structure (2D)
• Strong covalent network within layers
• Weak Van Der Waals force bet layers
Giant covalent structure (3D)
Giant covalent structure (2D)
Molecular structure
✓
✓
✓
Giant covalent structure (2D) ✓
Uses of graphene
Graphite
Bond to 4 C atoms
Bond to 3 C atoms
Bond to 3 C atoms
…
Element exist in different form/physical state
13. Allotropes of Carbon
Diamond Fullerene, C60GrapheneGraphite
Electricalconductivity
Special property
Electricalconductivity Electricalconductivity Electricalconductivity
Special property
Good
- Within layer, C sp2 hybridized
- ONE free delocalized π electron
Very Good
- Within layer, C sp2 hybridized
- ONE free delocalized π electron
moving across the layer easily
Poor
- C sp3 hybridized
- No free moving electron
Semiconductor✓✗
- Surfacesphere, not planar
- ElectronsCANNOT flow easily.
- Lower electron mobility
- Soft, layer slide
across each other
- Hardest substance
- Jewellery
Special property
graphite lubricant electrode
Lightest/strongest material
replacing silicon in photovoltaic cell
Drug delivery Transistor/Electronic
Transparentconducting
electrode
Click here uses graphene
Drug in graphene
Element exist in different form/physical state
14. Allotropes of Carbon
Fullerene, C60Graphene
Click here to view touch screen
Electron in hexagonal rings dont
delocalized over whole molecule.
6:6 bond shorter than 6:5
6:5 bond bet hexagon and pentagon
Macroscopicproperties
• High tensile strength
• High electrical/heat conductivity
• High ductility and chemical inactivity
Potential medicinal use
• Trap/bind drug inside/outside cage
• Target cancer cells
Drug inside Drug bind outside
• sp2 hybridization
• Exist as 2D/chicken wire/honeycomb
• Stronger than diamond, x200 stronger steel
• Conductivethan copper
• Flexible/Transparent/lighterthan rubber
• Solar cell and batteries
Graphene touch screen and photovoltaic cell
Click here for application of graphene
Single sheet conductor Rool into conductive nanotubes
Electrical contact
photovoltaic cell
Lightest and strongest replacing silicon in photovoltaic cell
6:6 bond length bet two hexagon
Double bond
Single bond
Element exist in different form/physical state
60 carbon in spherical
(20 hexagon/12 pentagon)
15. Uses of Carbon Allotropes
• Conduct current/heatvery well
• Conduct current at speed of light
• Electron delocalized above/belowplane
• High electron mobility
Click here discovery graphene Click here CNT Click here to view
sp2 hybridization
graphene
rool into rool into
Carbon Nanotube (CNT)
CNT- fullerene family of carbon allotropes.
Hollow cylindrical molecule
Rolling single or multiple layers of graphene sheet.
Single-wall SWNT/ multi-wall MWCNT
High tensile, stable, unreactive
Single wall Nanotube (SWNT) Multi wall Nanotubes (MWNT)
Click here TEDtalk graphene
1 layer thick
Uses of CNT
Strong tubes as
space elevator
Filter off salt
(desalination)
Drug delivery to body Attachment drug
therapeutics
16. 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!!!!!
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!!
ResearchQuestion – How diff fullerene affect aromaticity,,delocalization and conductivity ?
17. 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
Aromatic can be heterocyclic if contain
non-carbon, with oxy, nitrogen, or sulfur They do not obey Huckel rule
Why ?
ResearchQuestion – How diff fullerene affect aromaticity,,delocalization and conductivity ?
18. 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
19. 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