Pinacol pinacolone rearrangement involves conversion of 1,2 - diols to carbonyl compounds in presence of acid catalyst with change in carbon skeleton. It is an example of whitmore shift.
Nitrenes are nitrogen analogues of carbenes that contain no charge and are highly reactive and electrophilic. They exist in both singlet and triplet states, with the triplet state being more stable due to the presence of unpaired electrons. Nitrenes can be generated from acyl and alkyl azides, from sulphinylamine, or through insertion reactions. Important reactions involving nitrenes include the Beckmann rearrangement, Hofmann bromamide reaction, Curtius rearrangement, Lossen rearrangement, and Schmidt rearrangement.
Oxidation is any chemical reaction that involves the transfer of electrons. There are two main types of oxidation reactions: reactions involving the elimination of hydrogen from a substrate, and reactions involving the addition of oxygen to a substrate. Common oxidizing agents include chromium trioxide, dichromate, permanganate, and halogens. Alcohols are oxidized to aldehydes and ketones, aldehydes to carboxylic acids, and alkenes can undergo permanganate cleavage. The document provides examples of oxidation reactions and multiple choice questions to test understanding.
The document discusses various electrophilic aromatic substitution reactions including diazotization, formylation, and carboxylation. Diazotization involves treating aromatic amines with nitrous acid to form diazonium salts, which can then couple to other aromatic substrates. Formylation reactions introduce a formyl group onto aromatic compounds, such as through Gatterman-Koch, Vilsmeier-Haack, or Reimer-Tiemann reactions. Carboxylation introduces a carboxylic acid group through reactions like Kolbe-Schmitt carboxylation using sodium phenoxides and carbon dioxide.
This chapter discusses various addition reactions of alkenes, including electrophilic and free radical additions. Electrophilic additions follow Markovnikov's rule, adding the electrophile to the carbon with the greater number of hydrogens. Free radical additions proceed anti-Markovnikov. Other reactions covered include hydroboration-oxidation, oxymercuration-demercuration, halohydrin formation, epoxidation, and hydrogenation. Mechanisms are provided for each reaction type.
This document discusses free radicals. It defines a free radical as a chemical species with an unpaired valence electron. Free radicals are formed through homolytic cleavage of covalent bonds, where the shared electrons are split evenly between the products. Factors like heat, light, peroxides, and other radicals can cause homolytic cleavage. Examples of free radicals include H., Cl., Br., and CH3.. Tertiary radicals are the most stable due to hyperconjugation. Free radicals are highly reactive due to their incomplete valence shells and are paramagnetic. Free radical reactions involve initiation, propagation, and termination steps. Inhibitors like benzoquinone and phenols can slow or stop free radical reactions.
The document discusses inner transition elements, specifically the lanthanide and actinide series. It provides details on their electronic configurations, oxidation states, properties such as color and magnetism, extraction from monazite sand, and separation methods. It also compares the lanthanides and actinides, noting they both show lanthanide/actinide contractions and have similar properties, but the actinides exhibit more variable chemistry and are all radioactive.
This document provides an overview of conjugated unsaturated systems and reactions involving conjugated dienes. Key points include:
1) Conjugated systems have delocalized pi electrons that stabilize the molecule. Allyl radicals, cations, and dienes gain stability through resonance and orbital overlap.
2) Reactions of conjugated dienes like propene and butadiene often give mixtures of 1,2- and 1,4-addition products that depend on kinetic vs. thermodynamic control.
3) The Diels-Alder reaction is a [2+4] cycloaddition of a conjugated diene and a dienophile to form a 6-membered ring product. It
Pinacol pinacolone rearrangement involves conversion of 1,2 - diols to carbonyl compounds in presence of acid catalyst with change in carbon skeleton. It is an example of whitmore shift.
Nitrenes are nitrogen analogues of carbenes that contain no charge and are highly reactive and electrophilic. They exist in both singlet and triplet states, with the triplet state being more stable due to the presence of unpaired electrons. Nitrenes can be generated from acyl and alkyl azides, from sulphinylamine, or through insertion reactions. Important reactions involving nitrenes include the Beckmann rearrangement, Hofmann bromamide reaction, Curtius rearrangement, Lossen rearrangement, and Schmidt rearrangement.
Oxidation is any chemical reaction that involves the transfer of electrons. There are two main types of oxidation reactions: reactions involving the elimination of hydrogen from a substrate, and reactions involving the addition of oxygen to a substrate. Common oxidizing agents include chromium trioxide, dichromate, permanganate, and halogens. Alcohols are oxidized to aldehydes and ketones, aldehydes to carboxylic acids, and alkenes can undergo permanganate cleavage. The document provides examples of oxidation reactions and multiple choice questions to test understanding.
The document discusses various electrophilic aromatic substitution reactions including diazotization, formylation, and carboxylation. Diazotization involves treating aromatic amines with nitrous acid to form diazonium salts, which can then couple to other aromatic substrates. Formylation reactions introduce a formyl group onto aromatic compounds, such as through Gatterman-Koch, Vilsmeier-Haack, or Reimer-Tiemann reactions. Carboxylation introduces a carboxylic acid group through reactions like Kolbe-Schmitt carboxylation using sodium phenoxides and carbon dioxide.
This chapter discusses various addition reactions of alkenes, including electrophilic and free radical additions. Electrophilic additions follow Markovnikov's rule, adding the electrophile to the carbon with the greater number of hydrogens. Free radical additions proceed anti-Markovnikov. Other reactions covered include hydroboration-oxidation, oxymercuration-demercuration, halohydrin formation, epoxidation, and hydrogenation. Mechanisms are provided for each reaction type.
This document discusses free radicals. It defines a free radical as a chemical species with an unpaired valence electron. Free radicals are formed through homolytic cleavage of covalent bonds, where the shared electrons are split evenly between the products. Factors like heat, light, peroxides, and other radicals can cause homolytic cleavage. Examples of free radicals include H., Cl., Br., and CH3.. Tertiary radicals are the most stable due to hyperconjugation. Free radicals are highly reactive due to their incomplete valence shells and are paramagnetic. Free radical reactions involve initiation, propagation, and termination steps. Inhibitors like benzoquinone and phenols can slow or stop free radical reactions.
The document discusses inner transition elements, specifically the lanthanide and actinide series. It provides details on their electronic configurations, oxidation states, properties such as color and magnetism, extraction from monazite sand, and separation methods. It also compares the lanthanides and actinides, noting they both show lanthanide/actinide contractions and have similar properties, but the actinides exhibit more variable chemistry and are all radioactive.
This document provides an overview of conjugated unsaturated systems and reactions involving conjugated dienes. Key points include:
1) Conjugated systems have delocalized pi electrons that stabilize the molecule. Allyl radicals, cations, and dienes gain stability through resonance and orbital overlap.
2) Reactions of conjugated dienes like propene and butadiene often give mixtures of 1,2- and 1,4-addition products that depend on kinetic vs. thermodynamic control.
3) The Diels-Alder reaction is a [2+4] cycloaddition of a conjugated diene and a dienophile to form a 6-membered ring product. It
1) The document summarizes key concepts about ketones and aldehydes from an organic chemistry textbook chapter, including their structures, nomenclature, physical properties, reactions, and industrial uses.
2) Methods of synthesizing ketones and aldehydes are discussed, including oxidation of alcohols, Friedel-Crafts acylation, and reactions of nitriles, acid chlorides, and carboxylic acids.
3) Common reactions of ketones and aldehydes described include nucleophilic addition, hydration, imine and acetal formation, reductions, and oxidations.
This document provides information on acids, bases, and aromaticity. It defines acids and bases according to Arrhenius, Bronsted-Lowry, and Lewis theories. Acids are substances that produce H+ ions or accept electron pairs, while bases produce OH- ions or donate electron pairs. The document discusses factors that determine acid and base strength such as conjugate base stability, bond strength, resonance, induction, and hybridization effects. It also provides examples of acid-base reactions and uses pKa values to predict reaction equilibrium and relative acidities.
New chm-152-unit-4-power-points-sp13-140227172047-phpapp01Cleophas Rwemera
The document discusses acid-base buffers and their properties. It begins by defining an acid-base buffer as a solution that resists changes in pH from the addition of acid or base. It then explains that a buffer usually consists of a conjugate acid-base pair where both species are present in solution. Common examples of buffer systems are given. The document provides examples of how buffers work by lessening the effect of added acid or base through chemical reactions that consume H+ or OH- ions. Graphs and tables are included that illustrate the buffering capacity and buffering range of different solutions. Methods for preparing buffers and calculating buffer parameters are also presented.
The document discusses lattice energy and the Born-Haber cycle. It defines lattice energy as the energy released when one mole of an ionic solid forms from its gaseous ions. It provides the example of NaCl forming from sodium and chlorine gases and ions, and calculates the lattice energy and other thermodynamic values using the Born-Haber cycle. The document also discusses consequences of lattice energies such as the relative thermal stabilities of different ionic solids and how properties like ionic radius affect lattice energy.
The document discusses valence bond theory and hybridization. It explains that valence bond theory describes how covalent bonds form through the overlapping of atomic orbitals to form sigma and pi bonds. It then defines different types of hybridization including sp, sp2, sp3, sp3d, sp3d2, and sp3d3 hybridization. These hybridization types involve the mixing of atomic orbitals to form new hybrid orbitals that determine molecular geometry. Examples are provided to illustrate different bond types and hybridization.
Organozinc reagents play an important role in C-C bond formation through various reactions. They are synthesized through methods such as insertion of zinc metal into alkyl halides, functional group exchange, and transmetallation. Key reactions involving organozinc reagents include the Reformatsky reaction, Simmons-Smith reaction, Negishi coupling, Fukuyama coupling, and Barbier reaction. Organozincates, which involve sodium or lithium zincates, also participate in C-C bond forming reactions.
Grignard reagents are organomagnesium compounds formed by the reaction of an organic halide and magnesium. The reaction proceeds through single electron transfers where radicals are converted to carbanions. Grignard reagents are strong nucleophiles similar to organolithium reagents that can form new carbon-carbon bonds. They were analyzed by decomposing ethylmagnesium iodide with sulfuric acid and directing steam through the apparatus to drive off any ethane, proving it did not appreciably dissolve under experimental conditions.
1. Carbon atoms can form more than 4 bonds through hybridization of orbitals. In methane, carbon's 2s and 2p orbitals hybridize to form 4 equivalent sp3 hybrid orbitals, allowing carbon to form 4 sigma bonds to hydrogen in a tetrahedral structure.
2. In ethene and ethyne, carbon's orbitals hybridize differently to form pi bonds in addition to sigma bonds. Ethene carbons hybridize to form 3 sp2 orbitals and 1 p orbital, allowing 2 sigma bonds and 1 pi bond to other carbons. Ethyne carbons hybridize to form 2 sp orbitals and 2 p orbitals, allowing 1 sigma bond and 1 pi bond to each
The document discusses pH titration curves for different acid-base reactions. It explains that the equivalence point occurs when reactants are mixed in exact proportions according to the balanced chemical equation. The end point is seen by a color change in the indicator. Titration curves show a steep pH change near the equivalence point. Curves are provided for strong acid-strong base, strong acid-weak base, weak acid-strong base, and weak acid-weak base reactions. More complex curves are discussed for reactions producing multiple products.
Point Group Borazine and Bis(benzene)chromiumRohanSinghMaggo
Borazine has the point group D3h. It is a planar molecule with a C3 principal axis and three perpendicular C2 axes of symmetry. It also has an inversion center and horizontal plane of symmetry.
Bis(benzene)chromium has the point group D6d. It is a non-planar molecule that has a C6 axis of rotation and C2 axes of rotation perpendicular to the C6 axis. It does not have a horizontal plane of symmetry.
Pyridinium chlorochromate (PCC) is a mild and selective oxidizing reagent used to convert primary and secondary alcohols to aldehydes and ketones respectively. It was first described in 1975 by Elias Corey and J. William Suggs as an efficient reagent for alcohol oxidation. PCC is prepared by adding pyridine to a solution of chromium trioxide in hydrochloric acid. It is a stable, yellow-orange solid that is soluble in organic solvents. PCC oxidizes alcohols more selectively than related reagents like Jones reagent with little chance of over-oxidation to carboxylic acids. While still used, its usage has declined in recent decades as
Neighbouring group participation, organic chemistry, M.SC.2JOYNA123
This document summarizes a student's report on neighbouring group participation in organic chemistry. It defines neighbouring group participation as the interaction of a reaction center with electrons in an adjacent atom, sigma bond, or pi bond. The document notes that NGP reactions proceed through an SN2 mechanism, involving attack of an internal nucleophile in the first step followed by substitution of an external nucleophile in the second step. This can lead to unexpected retention of configuration and a first-order reaction. Examples of NGP involving pi bonds and aromatic rings are also mentioned.
This document provides an introduction to organic chemistry, covering topics such as:
- The definition of organic chemistry as the study of carbon compounds.
- Electronic structure of atoms and how they bond through ionic and covalent bonding.
- Resonance structures and how they are used to represent molecules.
- Factors that influence acidity such as electronegativity, size, and resonance.
- The definitions of nucleophiles and electrophiles and their roles in bond formation.
Carbocations and factors affecting their stabilitykoskal
A carbocation is a species where a carbon atom bonds to three carbon atoms and has a positive charge. Carbocations are electron deficient species and therefore very reactive and unstable. Anything which donates electron density to the electron-deficient center will help to stabilize them.
this presentation includes all the important oxidation and reduction definitions. all oxidizing and reducing agents. oxidation reactions of organic chemistry. reactions involving hydrogen from substrates. oxidation of alcohols, swern oxidation. reactions involving addition of oxygen to the substrates; oxidation of aldehydes and ketones, baeyer villiger reaction, oxidation of alkenes with peroxyacids, hydroxylation of alkenes, oxidative cleavage of diols, ozonolysis, etard reaction, sharpless epoxidation.
This document discusses interhalogen compounds and pseudohalogens. It describes how interhalogen compounds are formed between different halogen elements and can be categorized based on their molecular structure. Properties like physical state, color, boiling point, and reactivity are explained. Examples of specific interhalogen compounds such as IBr, ClF3, IF5, and IF7 are provided along with their methods of preparation and properties. Pseudohalogens are introduced as groups formed from p-block elements that behave similarly to halogens. Their properties and an example of (SCN)2 are outlined. Interhalogen compounds and pseudohalogens have various applications as solvents, catalysts, and oxidizing agents
1. The document outlines different elimination reaction mechanisms including E2, E1, and E1cb.
2. It discusses the regiochemistry and stereochemistry of elimination reactions and how Zaytzeff's rule and Hofmann's rule apply.
3. The key differences between the E2, E1, and E1cb mechanisms are described along with factors that determine whether substitution or elimination will occur for a given reaction.
This document provides tips for preparing for the CSIR NET Chemical Sciences exam, which is conducted biyearly by NTA for the Junior Research Fellowship or Lectureship. It outlines important topics in inorganic chemistry, organic chemistry, and physical chemistry that carry higher weightage. Preparation tips recommended by toppers include thoroughly learning the syllabus and high-weightage topics, creating a study schedule, practicing with previous years' papers and mock tests, and discussing concepts with others.
1) The document summarizes key concepts about ketones and aldehydes from an organic chemistry textbook chapter, including their structures, nomenclature, physical properties, reactions, and industrial uses.
2) Methods of synthesizing ketones and aldehydes are discussed, including oxidation of alcohols, Friedel-Crafts acylation, and reactions of nitriles, acid chlorides, and carboxylic acids.
3) Common reactions of ketones and aldehydes described include nucleophilic addition, hydration, imine and acetal formation, reductions, and oxidations.
This document provides information on acids, bases, and aromaticity. It defines acids and bases according to Arrhenius, Bronsted-Lowry, and Lewis theories. Acids are substances that produce H+ ions or accept electron pairs, while bases produce OH- ions or donate electron pairs. The document discusses factors that determine acid and base strength such as conjugate base stability, bond strength, resonance, induction, and hybridization effects. It also provides examples of acid-base reactions and uses pKa values to predict reaction equilibrium and relative acidities.
New chm-152-unit-4-power-points-sp13-140227172047-phpapp01Cleophas Rwemera
The document discusses acid-base buffers and their properties. It begins by defining an acid-base buffer as a solution that resists changes in pH from the addition of acid or base. It then explains that a buffer usually consists of a conjugate acid-base pair where both species are present in solution. Common examples of buffer systems are given. The document provides examples of how buffers work by lessening the effect of added acid or base through chemical reactions that consume H+ or OH- ions. Graphs and tables are included that illustrate the buffering capacity and buffering range of different solutions. Methods for preparing buffers and calculating buffer parameters are also presented.
The document discusses lattice energy and the Born-Haber cycle. It defines lattice energy as the energy released when one mole of an ionic solid forms from its gaseous ions. It provides the example of NaCl forming from sodium and chlorine gases and ions, and calculates the lattice energy and other thermodynamic values using the Born-Haber cycle. The document also discusses consequences of lattice energies such as the relative thermal stabilities of different ionic solids and how properties like ionic radius affect lattice energy.
The document discusses valence bond theory and hybridization. It explains that valence bond theory describes how covalent bonds form through the overlapping of atomic orbitals to form sigma and pi bonds. It then defines different types of hybridization including sp, sp2, sp3, sp3d, sp3d2, and sp3d3 hybridization. These hybridization types involve the mixing of atomic orbitals to form new hybrid orbitals that determine molecular geometry. Examples are provided to illustrate different bond types and hybridization.
Organozinc reagents play an important role in C-C bond formation through various reactions. They are synthesized through methods such as insertion of zinc metal into alkyl halides, functional group exchange, and transmetallation. Key reactions involving organozinc reagents include the Reformatsky reaction, Simmons-Smith reaction, Negishi coupling, Fukuyama coupling, and Barbier reaction. Organozincates, which involve sodium or lithium zincates, also participate in C-C bond forming reactions.
Grignard reagents are organomagnesium compounds formed by the reaction of an organic halide and magnesium. The reaction proceeds through single electron transfers where radicals are converted to carbanions. Grignard reagents are strong nucleophiles similar to organolithium reagents that can form new carbon-carbon bonds. They were analyzed by decomposing ethylmagnesium iodide with sulfuric acid and directing steam through the apparatus to drive off any ethane, proving it did not appreciably dissolve under experimental conditions.
1. Carbon atoms can form more than 4 bonds through hybridization of orbitals. In methane, carbon's 2s and 2p orbitals hybridize to form 4 equivalent sp3 hybrid orbitals, allowing carbon to form 4 sigma bonds to hydrogen in a tetrahedral structure.
2. In ethene and ethyne, carbon's orbitals hybridize differently to form pi bonds in addition to sigma bonds. Ethene carbons hybridize to form 3 sp2 orbitals and 1 p orbital, allowing 2 sigma bonds and 1 pi bond to other carbons. Ethyne carbons hybridize to form 2 sp orbitals and 2 p orbitals, allowing 1 sigma bond and 1 pi bond to each
The document discusses pH titration curves for different acid-base reactions. It explains that the equivalence point occurs when reactants are mixed in exact proportions according to the balanced chemical equation. The end point is seen by a color change in the indicator. Titration curves show a steep pH change near the equivalence point. Curves are provided for strong acid-strong base, strong acid-weak base, weak acid-strong base, and weak acid-weak base reactions. More complex curves are discussed for reactions producing multiple products.
Point Group Borazine and Bis(benzene)chromiumRohanSinghMaggo
Borazine has the point group D3h. It is a planar molecule with a C3 principal axis and three perpendicular C2 axes of symmetry. It also has an inversion center and horizontal plane of symmetry.
Bis(benzene)chromium has the point group D6d. It is a non-planar molecule that has a C6 axis of rotation and C2 axes of rotation perpendicular to the C6 axis. It does not have a horizontal plane of symmetry.
Pyridinium chlorochromate (PCC) is a mild and selective oxidizing reagent used to convert primary and secondary alcohols to aldehydes and ketones respectively. It was first described in 1975 by Elias Corey and J. William Suggs as an efficient reagent for alcohol oxidation. PCC is prepared by adding pyridine to a solution of chromium trioxide in hydrochloric acid. It is a stable, yellow-orange solid that is soluble in organic solvents. PCC oxidizes alcohols more selectively than related reagents like Jones reagent with little chance of over-oxidation to carboxylic acids. While still used, its usage has declined in recent decades as
Neighbouring group participation, organic chemistry, M.SC.2JOYNA123
This document summarizes a student's report on neighbouring group participation in organic chemistry. It defines neighbouring group participation as the interaction of a reaction center with electrons in an adjacent atom, sigma bond, or pi bond. The document notes that NGP reactions proceed through an SN2 mechanism, involving attack of an internal nucleophile in the first step followed by substitution of an external nucleophile in the second step. This can lead to unexpected retention of configuration and a first-order reaction. Examples of NGP involving pi bonds and aromatic rings are also mentioned.
This document provides an introduction to organic chemistry, covering topics such as:
- The definition of organic chemistry as the study of carbon compounds.
- Electronic structure of atoms and how they bond through ionic and covalent bonding.
- Resonance structures and how they are used to represent molecules.
- Factors that influence acidity such as electronegativity, size, and resonance.
- The definitions of nucleophiles and electrophiles and their roles in bond formation.
Carbocations and factors affecting their stabilitykoskal
A carbocation is a species where a carbon atom bonds to three carbon atoms and has a positive charge. Carbocations are electron deficient species and therefore very reactive and unstable. Anything which donates electron density to the electron-deficient center will help to stabilize them.
this presentation includes all the important oxidation and reduction definitions. all oxidizing and reducing agents. oxidation reactions of organic chemistry. reactions involving hydrogen from substrates. oxidation of alcohols, swern oxidation. reactions involving addition of oxygen to the substrates; oxidation of aldehydes and ketones, baeyer villiger reaction, oxidation of alkenes with peroxyacids, hydroxylation of alkenes, oxidative cleavage of diols, ozonolysis, etard reaction, sharpless epoxidation.
This document discusses interhalogen compounds and pseudohalogens. It describes how interhalogen compounds are formed between different halogen elements and can be categorized based on their molecular structure. Properties like physical state, color, boiling point, and reactivity are explained. Examples of specific interhalogen compounds such as IBr, ClF3, IF5, and IF7 are provided along with their methods of preparation and properties. Pseudohalogens are introduced as groups formed from p-block elements that behave similarly to halogens. Their properties and an example of (SCN)2 are outlined. Interhalogen compounds and pseudohalogens have various applications as solvents, catalysts, and oxidizing agents
1. The document outlines different elimination reaction mechanisms including E2, E1, and E1cb.
2. It discusses the regiochemistry and stereochemistry of elimination reactions and how Zaytzeff's rule and Hofmann's rule apply.
3. The key differences between the E2, E1, and E1cb mechanisms are described along with factors that determine whether substitution or elimination will occur for a given reaction.
This document provides tips for preparing for the CSIR NET Chemical Sciences exam, which is conducted biyearly by NTA for the Junior Research Fellowship or Lectureship. It outlines important topics in inorganic chemistry, organic chemistry, and physical chemistry that carry higher weightage. Preparation tips recommended by toppers include thoroughly learning the syllabus and high-weightage topics, creating a study schedule, practicing with previous years' papers and mock tests, and discussing concepts with others.
The document discusses developing novel molecular descriptors for antimicrobial peptides (AMPs) using machine learning methods. It aims to use distances between transmembrane proteins of different organisms as descriptors in quantitative structure-activity relationship (QSAR) models to improve selectivity predictions of AMPs. A workflow is proposed that involves selecting homogeneous AMP datasets, developing QSAR models using genetic algorithms and artificial neural networks, defining new distance-based metrics between proteomes, and testing the novel molecular descriptors.
This document is a thesis submitted by Federica Campana for a PhD in molecular dynamics investigations of drug-cell membrane interactions. It summarizes research on how drug molecules interact with and influence cell membranes. Key findings include that membrane cholesterol content influences the effects of membrane fluidizers and heat shock protein co-inducers. Hydroxylamine derivatives were found to modify membrane physical state and induce heat shock proteins. Hydroxy arachidonic acid was identified as a potential new non-steroidal anti-inflammatory drug that targets cyclooxygenase enzymes with less affinity than arachidonic acid.
This document summarizes Federica Campana's doctoral thesis on investigating drug-cell membrane interactions using molecular dynamics simulations. The thesis examines how membrane composition influences the effects of membrane fluidizers and heat shock protein co-inducers. It also analyzes the binding of anti-inflammatory molecules like hydroxyarachidonic acid to cyclooxygenase enzymes. The overall goal is to better understand how drug molecules interact with and modulate lipid bilayer properties at a molecular level.
The document summarizes 4 projects being conducted as part of a PhD program:
1) Studying the effect of G protein lipids on membrane structure using molecular dynamics simulations. Results show the lipids interact differently with the membrane.
2) Examining 2-hydroxy arachidonic acid as a potential anti-inflammatory drug through binding energy and docking analyses with COX enzymes. It may have advantages over arachidonic acid.
3) Investigating how the drug BGP-15 remodels plasma membrane rafts using density profiles. It enhances docking with cholesterol-rich regions and increases order.
4) Developing GRIMD, a system for distributed molecular dynamics simulations across multiple machines
This document provides a summary of the history of MDMA from its discovery and early uses in psychotherapy to its prohibition and rise in recreational use. Some key points:
- MDMA was first synthesized in 1912 and studied by the US Army for potential use in chemical warfare in the 1950s. Psychotherapist Leo Zeff popularized its use in therapy in the 1970s, calling it "Adam".
- MDMA gained popularity in psychotherapy in the 1980s but its recreational use also increased, especially in the rave scene. Catholic priest Michael Clegg popularized the name "Ecstasy".
- The DEA banned MDMA in 1985 despite protests from therapists about its benefits. Its legal status fluctuated but
This document summarizes a study that used molecular dynamics (MD) simulations and mesoscopic simulations to model the compatibility of polystyrene (PS) and poly(methyl methacrylate) (PMMA) blends. The study calculated Flory-Huggins interaction parameters via MD simulations which indicated immiscibility. Mesoscopic simulations then examined how the phase morphology of PS/PMMA blends was influenced by adding a block copolymer, applying shear, doping with nanoparticles, and surface roughness. The study provided insights into using inducing effects to control phase separation in polymer blends.
1. Flexible protein-protein docking is challenging due to the large number of degrees of freedom which increases computational time and the likelihood of false positives.
2. Existing docking methods limit flexibility to certain types of motions like backbone or side chain flexibility. They often only allow one protein to be flexible.
3. Flexible docking is generally divided into preprocessing, rigid docking, refinement, and scoring stages. In preprocessing, flexible regions are identified and modeled. Rigid docking generates initial solutions which refinement then optimizes with small motions and adjustments. Scoring ranks solutions by parameters like binding energy.
1) The document describes molecular dynamics simulations studying the interactions of palmitic acid, myristic acid, and geranylgeraniol lipids with model cell membranes, and the interactions of the antitumor molecule BGP-15 with sphingomyelin-cholesterol membrane bilayers.
2) The simulations showed that palmitic acid and myristic acid interact more strongly with phosphatidylcholine membranes than geranylgeraniol, which decreases membrane pressure. Geranylgeraniol also increases non-lamellar membrane phases.
3) The BGP-15 simulations revealed that BGP-15 spontaneously inserts into sphingomyelin-cholesterol
1. Seconda parte bis Teorie atomiche. Configurazione elettronica. Il legame chimico Prof. Stefano Piotto – Prof. SimonaConcilio Universitàdi Salerno
2. Seconda parte bis Proprietà periodiche Raggio atomico Energia di ionizzazione Affinità elettronica Elettronegatività Elementi di sistematica Legame ionico Legame metallico Legami deboli Van derWaals London Legame a idrogeno
3. Proprietà periodiche I chimici hanno sempre tentato di ordinare le sostanze studiate in base a somiglianze che permettessero, in qualche modo, di raggrupparle in modo schematico; questa esigenza divenne progressivamente più sentita nel secolo scorso, quando il progresso delle tecniche di analisi permise di scoprire nuove sostanze semplici. LEGGE PERIODICA: le proprietà dei corpi semplici, come le forme e le proprietà delle combinazioni, sono funzione periodica della grandezza del peso atomico. (1868)
11. Trucco per ricordare il riempimento degli orbitali Il riempimento degli orbitali segue le frecce
12. Effetto di altri elettroni negli orbitali interni Gli elettroni interni schermano molto efficacemente gli elettroni esterni e aumentano notevolmente l’energia dell’orbitale.
13. Carica nucleare efficace Zeff≈ Z – (n° di e- presenti nei livelli inferiori) Per es. Na ha 11 e- (1s2 2s2 2p6 3s1) n°di e- livelli inferiori = 10 Quindi Zeff ≈ 1
16. Ciascuno dei due elettroni schermaparzialmente l’altro nei confronti della carica nucleare completa e aumenta l’energia dell’orbitale e diminuisce l’E. Ion. Effetto della carica nucleare e di un elettrone addizionale nello stesso orbitale L’aumento della carica nucleare fa diminuire l’energia dell’orbitale e aumenta l’En. Ionizz.
17. Energia di ionizzazione L'energia di ionizzazione di un atomo o di una molecola è l'energia minima richiesta per strappargli un elettrone e portarlo a distanza infinita. Quindi è l'energia necessaria per far avvenire il seguente processo: X(g) -> X+(g) + e− L'energia di ionizzazione decresce lungo un gruppo della Tavola periodica, e aumenta da sinistra a destra attraverso il periodo. Gli elettroni degli atomi più piccoli sono più attratti dal nucleo, quindi l'energia di ionizzazione è maggiore. Negli atomi più grandi gli elettroni non sono trattenuti così fortemente e quindi l'energia di ionizzazione richiesta è minore.
18. Affinità elettronica L'affinità elettronica di un atomo è l'energia che si libera quando l'atomo in fase gassosa cattura un elettrone, trasformandosi in uno ione negativo; in altre parole è la misura della tendenza di un atomo all'acquisto di elettroni. L'affinità elettronica varia in modo caratteristico: cresce da sinistra a destra per i primi due periodi e decresce lungo i gruppi dall'alto in basso. L'affinità elettronica è massima per gli elementi in alto a destra della tavola periodica (fluoro, ossigeno, zolfo, cloro, bromo, iodio), ai quali manca un solo elettrone per completare l'"ottetto".
20. Elettronegatività Si definisce “elettronegatività” di un atomo la sua relativa tendenza ad attrarre verso di sé i cosiddetti “elettroni di legame”, ossia quegli elettroni che lo tengono unito ad un altro atomo per formare una molecola. L’elettronegatività aumenta lungo un periodo (da sinistra verso destra) e diminuisce lungo un gruppo (dall’alto verso il basso), così come accade per l’affinità elettronica. I motivi di questo andamento sono i seguenti: L’aumento che si verifica andando verso destra in un periodo deriva dalle sempre più ridotte dimensioni degli atomi, per cui c’è un minore effetto di schermo e quindi una maggiore attrazione degli elettroni; La diminuzione che si ha, invece, scendendo lungo un gruppo deriva sia dall’aumento delle dimensioni atomiche sia dall’aumento dell’effetto schermo.
21. L'elettronegatività, forza F esercitata dal nucleo sugli elettroni di valenza, è definita dalla relazione: F = Z*/r2 = Z S/r2 in cui: Z* = carica nucleare efficace = Z*S Z = carica nucleare totale (cioè il numero atomico, corripondente al numero di protoni del nucleo) S = costante di schermo elettronico (dovuto agli elettroni sottostanti a quelli di valenza) r = raggio covalente espresso in Å (10-8 cm = 10-10 m)
26. Il carattere metallico, che e’ una proprietà composita, degli elementi sistemati nella tavola periodica, va diminuendo da sinistra verso destra e dal basso verso l’alto. Regola di Sanderson > 0 metalli n-m = -1 o -2 semimetalli < -2 non metalli n numero del periodo m numero di elettroni nello strato esterno
29. Metalli alcalini (Gruppi I e II) Tutti i metalli del Gruppo I hanno un elettrone s nello strato esterno (ns1), mentre i metalli del Gruppo II anno due elettroni s esterni (ns2); gli elettroni esterni debolmente trattenuti dal nucleo, rendono molto reattivi questi metalli, che perdono facilmente gli elettroni esterni e formano ioni stabili (con carica +1 per i metalli alcalini, +2 per gli alcalino-terrosi). Ad esempio: Na Na+ + e- Ca Ca2+ + 2e-
30. esempio 2 Li + 2 H2O 2 Li+ + 2 OH- + H2(g)2 Na + 2 H2O 2 Na+ + 2 OH- + H2(g)2 Na + 2 C2H5OH 2 Na+ + 2 C2H5O- + H2 (g)2 K + 2 H2O 2 K+ + 2 OH- + H2(g) Reattivita’ di Li, Na e K
31. Alogeni (gruppo VII) Caratterizzati tutti da molecole biatomiche, gli alogeni possono presentarsi in diversi stati fisici (lo iodio è solido, il bromo è liquido, cloro e fluoro sono gas); il loro nome, che significa “generatori di sali”, sottolinea la forte reattività di questi non metalli che mostrano, nonostante alcune differenze, proprietà molto simili tra loro, conseguenza della somiglianza tra le strutture elettroniche (ns2 np5, 7 elettroni nello strato esterno). Diversamente dagli elementi del blocco s, possono assumere nei composti diversi numeri di ossidazione.
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33. Metalli di transizione Gli elementi dallo scandio (Z = 21) allo zinco (Z = 30) formano la prima serie degli elementi di transizione; analogamente, nei periodi successivi possono essere individuate una seconda ed una terza serie. Nelle tre serie si ha il riempimento degli orbitali 3d, 4d e 5d, rispettivamente. Possono essere considerati metalli di transizione quelli che formano almeno uno ione con orbitale d parzialmente riempito; la vicinanza di energia tra gli orbitali d ed s fa sì che essi possano presentare stati di ossidazione variabili. Inoltre, le ridotte dimensioni degli atomi e la struttura compatta che li caratterizzano (ogni atomo è circondato da altri 12 atomi) conferiscono loro alti punti di ebollizione e di fusione.
36. Momento dipolare Quando, in una molecola, il baricentro delle cariche positive e negative non coincide: esiste un momento dipolare m Esso è un vettore il cui modulo è dato dal prodotto della carica q per la distanza r tra i due baricentri delle cariche positive e negative:
41. Legame chimico – Legame ionico Si realizza quando atomi di un elemento fortemente elettropositivo (bassa energia di ionizzazione) si combinano con atomi di un elemento fortemente elettronegativo (elevata affinità elettronica) Il sale NaCl è formato da un grandissimo numero di atomi di sodio e cloro aggregati in un solido ionico cristallino
43. Legame chimico – Legame ionico Requisiti per la formazione di un legame ionico:
44. Legame chimico – Legame ionico Energia Reticolare: energia che si acquista nella formazione del reticolo cristallino.
45. Legame ionico Esiste qualcosa di simile ad un “legame ionico”? La distanza dell’elettrone indicato dal nucleo di Li è minore quando è legato che quando è presente nel atomo di Li isolato Come vedete in figura un elettrone è più vicino quando è stato “perso” dal Li che quando era sul Li stesso. La risposta alla domanda è al tempo stesso si e no: Sì, l’elettrone che era nell’orbitale 2s del Li è ora nell’orbitale 2p del F, ma no, l’elettrone è più vicino ora e quindi come può essere stato “perso”? Una cosa indubbiamente vera è che ora ci saranno più elettroni vicini ai nuclei di quanto non fossero prima, con Li e F separati. Ma questa è appunto il fondamento stesso della teoria VB: il legame chimico si forma quando elettroni sono simultaneamente vicini ai due nuclei. Stando così le cose, c’è veramente una reale differenza tra legame covalente e ionico? Ci sono molti dubbi su quanto sia realistica l’immagine di un solido fatto di soli ioni. Lo schema che sta emergendo è quello in cui gli orbitali occupati di atomi adiacenti sono semplicemente deformati così da accomodare una maggiore densità elettronica intorno agli elementi “negativi” che intorno a quelli “positivi”. Occorre comunque ricordare che il modello ionico di legame chimico è molto utile per i nostri scopi e non c’è nulla di sbagliato nel usare il termine “legame ionico” per descrivere le interazioni tra atomi in solidi ionici come LiF e NaCl.
49. Teoria degli orbitali molecolari gli elettroni di valenza sono delocalizzati gli orbitali molecolari si formano per la sovrapposizione di orbitali atomici gli elettroni di valenza sono negli orbitali molecolari, che sono delocalizzati sull’intera molecola Tutti gli elettroni sono localizzati in orbitali che appartengono all’intera molecola (da qui il nome orbitali molecolari) e NON negli orbitali di ciascun atomo costituente la molecola.
58. Proviamo a visualizzare la densita’ elettronica (in modalità onda stazionaria) Proviamo a visualizzare questi elettroni Proviamo a visualizzare gli elettroni di valenza (in modalità corpuscolare)
59. Conduttori, isolanti e semiconduttori Isolante Banda di valenza satura e separata dalla banda di conduzione da un dislivello (GAP) energetico molto elevato
60. Conduttori, isolanti e semiconduttori Semiconduttore Banda di valenza satura e separata dalla banda di conduzione da un dislivello (GAP) energetico piccolo
62. Conducibilità termica Ognuno sa che, a temperatura ambiente, una superficie metallica appare al tatto più fredda di una superficie di legno. L’alta conducibilità termica dei metalli permette al calore di fluire dal nostro corpo verso l’esterno molto più efficacemente rispetto a legno o plastica. Per la stessa ragione, una superficie metallica a T superiore a quella corporea apparirà molto più caldo. L’alta conducibilità termica è attribuita ad eccitazioni vibrazionali degli elettroni de localizzati; queste eccitazioni si diffondono molto rapidamente nel cristallo e molto più lentamente in struttura meno organizzate come il legno
63. Lucentezza Quando parliamo di “lucentezza” o di “tipico effetto metallico” ci riferiamo alla capacità di un metallo di riflettere la luce. Quando la luce colpisce un metallo, il campo EM oscillante induce simili oscillazioni negli elettroni debolmente legati di superficie. Una carica vibrante è di per sé un emettitore di radiazioni elettromagnetiche, così che l’effetto è una remissione, o riflessione, della luce incidente.
66. Sommario delle forze di interazione Ione Ione + - Carica ionica- Carica ionica Ione dipolo + Carica ionica-dipolo -+ Aumento forza di interazione dipolo (incluso H) dipolo Dipolo-dipolo -+ -+ dipolo indotto dipolo indotto Dipolo indotto-dipolo indotto - + - +
67. Energia potenziale tra le particelle interagenti Energia potenziale totale Distanza internucleare più stabile E =ENERGIA DI ATTRAZIONE+ ENERGIA DI REPULSIONE
68. Interazioni intermolecolari 1 d 1 d2 1 d3 1 d6 Distanza di separazione Energia potenziale per l’interazione tra ioni energia Energia potenziale per l’interazione dipolo-dipolo Energia potenziale per l’interazione dipolo indotto – dipolo indotto (interazione di Van der Waals
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70. Interazioni di van der Waals Interazioni ione-dipolo (ione Na+ e ione Cl- solvatati in acqua)
71. Polarità e proprietà chimiche Forti interazioni dipolo – dipolo fra molecole della stessa specie comportano temperature di ebollizione alte => es. fase condensata a pressione atmosferica (H2O) Deboli interazioni dipolo – dipolo o nulle (molecole apolari) comportano temperature di ebollizione basse => fase gassosa a pressione atmosferica (CO2)
73. Forze di London Le forze di dispersione di London possono essere indotte in molecole non polari, come idrogeno gassoso (H2), diossido di carbonio (CO2), azoto (N2), ed in gas nobili (He, Ne, Ar, Kr, etc). Es. Gli elettroni del Neon si muovono casualmente e in un dato momento si trovano tutti da un lato del nucleo. Ciò crea un dipolo istantaneo nell’atomo #1 , il quale induce un dipolo istantaneo anche sull’ atomo di Neon #2, poiché i suoi elettroni vengono respinti dal primo atomo. Questa polarità temporanea indotta consente ai due atomi di attrarsi l’un l’altro debolmente quando la parte negativa dell’atomo #1 è attratta dalla zona positiva dell’atomo #2
75. Cristalli liquidi Sono delle fasi intermedie tra i solidi e i liquidi. Ovvero presentano un ordine a corto raggio in una direzione e a lungo raggio in un’altra.
76. S è il parametro d’ordine La tendenza delle molecole di LC ad allinearsi lungo una direzione si definisce anisotropia Cristalli liquidi
79. Se vuoi divertirti a scoprire i cristalli liquidi visita questo sito (è in inglese) http://plc.cwru.edu/tutorial/enhanced/lab/lab.htm
80. Legame a Idrogeno Il legame di idrogeno è dovuto a interazione di atomi H legati ad atomi elettronegativi, con atomi analoghi di altre molecole
81. Legame a Idrogeno Link a un tutorial in inglese L'acqua liquida è tale perché esistono infiniti legami a idrogeno tra gli atomi H e O; il fenomeno è dovuto al fatto che, essendo O molto elettronegativo, gli H ad esso legati hanno una parziale carica positiva, che tendono a compensare interagendo con i doppietti liberi degli O di altre molecole: ogni O è praticamente legato parzialmente a 4 H, in una struttura pressoché tetraedrica. Per NH3 il fenomeno incide poco; per CH4 non conta nulla (infatti C è poco elettronegativo rispetto ad H).
82. Il legame a idrogeno nell’acqua determina la formazione di un reticolo cristallino tetraedrico ordinato. Ecco perché l’acqua allo stato solido è meno densa dell’acqua allo stato liquido Struttura del ghiaccio L’acqua liquida mantiene solo in parte la struttura del ghiaccio, dato che al crescere della temperatura si rompe un certo numero di legami ad idrogeno A quattro gradi la densità dell’acqua è massima.