This document summarizes molecular dynamics simulations of two forms of an electroactive polymer interacting with ions. In one simulation, an amphiphilic polymer forms a charged monolayer interface between a vacuum and an aqueous layer containing ions. The stability of the monolayer under hydrostatic pressure and charge imbalance is investigated. In another simulation, a polythiophene oligomer is twisted into a helix serving as an ion channel between two aqueous regions separated by a phospholipid bilayer membrane.
A molecular-dynamics-investigation-of-the-stability-of-a-charged-electroactiv...Darren Martin Leith
1) A molecular dynamics simulation investigates the stability of a charged electroactive polymer monolayer consisting of an amphiphilic polythiophene on a sodium chloride solution.
2) When the monolayer is chemically reduced, negative charges are conferred on the thiophene rings. This leads to a loss of planarity and buckling of the monolayer, eventually causing it to rupture. It also attracts excess sodium ions to the interface.
3) At low levels of reduction, interface sodium ions are more mobile than sodium ions in the NaCl solution, responding to electric fields by jumping between sites with an energy barrier of 0.33 eV. The instability of the charged polymer membrane is discussed using Gou
Dynamic Stereochemistry and What role does conformation plays on stereochemistry is being exemplified in this presentation. Useful for the Undergraduate and Postgraduates students of Pharmacy, Pharmaceutical Chemistry and Chemical Sciences
Aza Cope Rearrangement of Propargyl Enammonium Cations Catalyzed by a Self-As...Matthew MacLennan
Dr. Kenneth Raymond is a renowned chemist who has received numerous awards and honors over his career. His research focuses on catalyzing the Aza Cope rearrangement of propargyl enammonium cations using a self-assembled "nanozyme" made of gallium ions and ligands. The nanozyme is able to accelerate the rearrangement reaction rate by facilitating a more negative transition state entropy compared to the uncatalyzed reaction. Analysis of reaction kinetics shows the nanozyme displays Michaelis-Menten behavior.
This document summarizes an experiment investigating the behavior of a single fuel cell under different membrane electrode assemblies (MEAs) and fuels. Three MEAs using different catalysts were tested with hydrogen and formic acid as anode fuels and hydrogen, air, or water as cathode reactants. Constant base current with 10A pulses were applied to alleviate carbon monoxide poisoning on the anode. Results including polarization curves and potential/current oscillations are presented. The document also provides background on fuel cells and mechanisms of carbon monoxide poisoning.
The document defines and provides examples of various sigmatropic reactions, including:
1. The Claisen rearrangement, which involves the [3,3] rearrangement of an allyl vinyl ether.
2. The Cope rearrangement, which involves the [3,3] sigmatropic rearrangement of 1,5-dienes.
3. The Oxy-Cope rearrangement, which has a hydroxyl substituent and proceeds faster when deprotonated.
4. Other reactions discussed include the Fischer indole synthesis, aromatic Claisen rearrangement, [2,3]-Wittig rearrangement, Carroll rearrangement, and walk rearrangements. Mechanisms
1. The document discusses electrochemical processes in biology, which involve the transfer of electrons between sites of oxidation and reduction separated by membranes. Energy from electron transfer is stored as electrochemical proton gradients across membranes and used to synthesize ATP.
2. Key components of biological electron transfer systems include quinones, flavins, iron-sulfur proteins, and the electron transfer chains in mitochondria and chloroplasts. These systems facilitate the transduction of chemical energy into work through redox reactions.
3. The concept of redox potential can be applied to small, non-statistical biological systems by considering their equilibrium with larger macrosystems. This explains why electron transfer chains contain many components overlapping a wide range of potential levels
This document discusses electric polarizability dispersion of alumina particles with adsorbed carboxymethyl cellulose. There is debate in the literature about whether condensed counterions along polymer chains are mobile or immobile when an electric field is applied. This experimental study uses electric light scattering to investigate an aqueous suspension of alumina particles with adsorbed carboxymethyl cellulose at different polyelectrolyte concentrations. The results indicate no additional polarizability component from condensed counterions, suggesting they are immobile in a sinusoidal electric field of moderate intensity from 10 Hz to 1 MHz.
A molecular-dynamics-investigation-of-the-stability-of-a-charged-electroactiv...Darren Martin Leith
1) A molecular dynamics simulation investigates the stability of a charged electroactive polymer monolayer consisting of an amphiphilic polythiophene on a sodium chloride solution.
2) When the monolayer is chemically reduced, negative charges are conferred on the thiophene rings. This leads to a loss of planarity and buckling of the monolayer, eventually causing it to rupture. It also attracts excess sodium ions to the interface.
3) At low levels of reduction, interface sodium ions are more mobile than sodium ions in the NaCl solution, responding to electric fields by jumping between sites with an energy barrier of 0.33 eV. The instability of the charged polymer membrane is discussed using Gou
Dynamic Stereochemistry and What role does conformation plays on stereochemistry is being exemplified in this presentation. Useful for the Undergraduate and Postgraduates students of Pharmacy, Pharmaceutical Chemistry and Chemical Sciences
Aza Cope Rearrangement of Propargyl Enammonium Cations Catalyzed by a Self-As...Matthew MacLennan
Dr. Kenneth Raymond is a renowned chemist who has received numerous awards and honors over his career. His research focuses on catalyzing the Aza Cope rearrangement of propargyl enammonium cations using a self-assembled "nanozyme" made of gallium ions and ligands. The nanozyme is able to accelerate the rearrangement reaction rate by facilitating a more negative transition state entropy compared to the uncatalyzed reaction. Analysis of reaction kinetics shows the nanozyme displays Michaelis-Menten behavior.
This document summarizes an experiment investigating the behavior of a single fuel cell under different membrane electrode assemblies (MEAs) and fuels. Three MEAs using different catalysts were tested with hydrogen and formic acid as anode fuels and hydrogen, air, or water as cathode reactants. Constant base current with 10A pulses were applied to alleviate carbon monoxide poisoning on the anode. Results including polarization curves and potential/current oscillations are presented. The document also provides background on fuel cells and mechanisms of carbon monoxide poisoning.
The document defines and provides examples of various sigmatropic reactions, including:
1. The Claisen rearrangement, which involves the [3,3] rearrangement of an allyl vinyl ether.
2. The Cope rearrangement, which involves the [3,3] sigmatropic rearrangement of 1,5-dienes.
3. The Oxy-Cope rearrangement, which has a hydroxyl substituent and proceeds faster when deprotonated.
4. Other reactions discussed include the Fischer indole synthesis, aromatic Claisen rearrangement, [2,3]-Wittig rearrangement, Carroll rearrangement, and walk rearrangements. Mechanisms
1. The document discusses electrochemical processes in biology, which involve the transfer of electrons between sites of oxidation and reduction separated by membranes. Energy from electron transfer is stored as electrochemical proton gradients across membranes and used to synthesize ATP.
2. Key components of biological electron transfer systems include quinones, flavins, iron-sulfur proteins, and the electron transfer chains in mitochondria and chloroplasts. These systems facilitate the transduction of chemical energy into work through redox reactions.
3. The concept of redox potential can be applied to small, non-statistical biological systems by considering their equilibrium with larger macrosystems. This explains why electron transfer chains contain many components overlapping a wide range of potential levels
This document discusses electric polarizability dispersion of alumina particles with adsorbed carboxymethyl cellulose. There is debate in the literature about whether condensed counterions along polymer chains are mobile or immobile when an electric field is applied. This experimental study uses electric light scattering to investigate an aqueous suspension of alumina particles with adsorbed carboxymethyl cellulose at different polyelectrolyte concentrations. The results indicate no additional polarizability component from condensed counterions, suggesting they are immobile in a sinusoidal electric field of moderate intensity from 10 Hz to 1 MHz.
Substitution elimination reaction in cyclohexyl systemDongguk University
The document discusses substitution and elimination reactions in cyclohexyl systems and their stereochemistry. It covers nucleophilic substitution reactions like SN1 and SN2 that can proceed via racemization or inversion of configuration. Neighboring group participation is described as enhancing the rate of some substitution reactions. Allylic bromination of cyclohexene is provided as an example of a radical substitution reaction. Elimination reactions like E2 and cis-elimination are also discussed, noting the effects of substrate conformation on reaction stereochemistry and product formation.
This document describes Michael Ludden's synthesis and characterization of various molybdenum complexes. Three complexes were synthesized - [CpMo(CO)3Me], [CpMo(CO)3Et], and [CpMo(CO)2(COMe)(PPh3)]. They were characterized using NMR and IR spectroscopy. The results confirmed the structures of the complexes and showed how changing ligands affects properties. Kinetic measurements of migratory insertion reactions will be taken using these complexes to understand reaction rate dependence on factors like solvent, temperature and ligand type.
The Brønsted catalysis relationship is a Linear Free Energy Relationship (LFER) that relates ionization of an acid or base which catalyzes a reaction and the rate of the reaction.
Contributed by: Quincy Davis, Jonathan Greenhalgh, Joshua Visser (Undergraduates), University of Utah, 2016
1) Veratrole was electrooxidized on a platinum electrode in acetonitrile solutions containing either tetrabutylammonium perchlorate or lithium perchlorate.
2) A green deposit formed containing hexamethoxytriphenylene radical cation species associated with perchlorate counterions.
3) Spectroelectrochemical experiments showed that oxidation of perchlorate anions above 2.3V dissolved the deposit, but sweeping the potential back regenerated the solid, allowing the process to be cycled.
Theoretical Studies on Mechanism of Xanthine Oxidase and 6-mercaptopurineEDITOR IJCRCPS
The reaction mechanisms of 6-mercaptopurine or hypoxanthine have not been investigated either
theoretically or experimentally. Understanding of the overall mechanism helps to manage the
metabolic properties of potential drug molecules metabolized by XOR. The present theoretical
study is aimed to predict transition state structure, the path of electron transfer and probe plausible
mechanistic route for hydroxylation of 6-mercaptopurine or hypoxanthine and XO by relating the
electronic structure to reactivity. The transition state structure was predicted by linear transit
calculation of series of structures by performing frequency calculation which was confirmed by one
imaginary negative frequency value. The path of coupled electron proton transfer mechanism
proved from Mullikan charge analysis and mechanism of oxidation was proved from geometry
optimization. Density functional theory (DFT)/B3LYP method were used to probe the electronic
structure of metastable structure. Result showed that in transition state structures the energy barrier
for 6-mercaptopurine bound active site was lower than hypoxanthine bound active site by
20kcal/mol in average. The ionocity data revealed the presence of substantial negative charge on
proton which suggests the transfer of hydride from substrate to the active site. Bond length analysis
showed that in the transition stases CRH-Oeq bond length was nearly 98% formed where as the CRHHRH
bond length was only 36.78% broken. Geometry optimization revealed that oxidation of 6-
mercaptopurine or hypoxanthine by XO follow stepwise mechanism. It can be generalized that the
oxidation of 6-mercaptopurine or hypoxanthine by XO follows two step mechanisms namely:
abstraction of proton by Glu1226 from equatorial hydroxide of active site followed by nucleophilic
attach on C2 of substrate and hydride was transferred through concomitant release of oxidized
substrate.
Juornal of Physics Condensed Matter - Article IRossen Hristov
This document summarizes a study that investigated the mobility of counterions condensed on carboxymethyl cellulose (CMC) polymer chains adsorbed onto alumina colloid particles. Previous studies using electro-optical techniques reported that condensed counterions are mobile in alternating electric fields. However, the current study uses an amplitude approach, measuring particle polarizability at increasing CMC concentration rather than frequency dependence. Results indicate condensed counterions do not contribute to particle polarization at 1 kHz, suggesting they are immobile in sinusoidal fields up to 0.5 kV/cm and 1 kHz. Comparison of polarizability and electrophoretic mobility supports the conclusion that condensed counterions are immobilized on the CMC chains.
Cape unit 2 chemistry reactions of halogenoalkanes cram sheetDenison Dwarkah
Everything you'll ever need to know to answer any CAPE chemistry question on halogenoalkanes.
Print double sided for one sheet that will solve all your problems.
Ideal for a five minute revision session just before the exam, or for a first time student wanting to know what's really important in this section of the syllabus.
Some reactions seem to obvious to fail, so what happens when they do? Quantum calculations yield invaluable insight to the nature of a reaction mechanism.
Presented at the Virtual Conference on Computational Chemistry VCCC 2014
Credit due to Guillermo Caballero on whose BSc thesis this presentation is based.
This document summarizes a study that measured the enthalpy change (ΔH) associated with the α-helix to random coil transition of an alanine peptide in water using calorimetry. The researchers synthesized a 50-residue peptide containing primarily alanine residues and determined its ΔH to be between 0.9-1.3 kcal/mol per residue, providing a basic parameter for predicting thermal unfolding of peptide helices. Circular dichroism spectra and melting curves confirmed the peptide adopted an α-helical structure at low temperatures and underwent a reversible helix-coil transition. The ΔH value suggests the peptide backbone, rather than side chains, makes the dominant contribution to helix stability.
SIMONA CAVALU_Rotational Correlation Times of proteinsSimona Cavalu
Noncovalent spin labeled proteins (ovalbumin, bovine serum albumin, hemoglobin, and cytochrome c) were
investigated in order to follow the different type of interactions between the nitroxide radical of 3-carbamoyl-
2,2,5,5-tetramethyl-3-pyrrolin-1-yloxy spin label and functional groups of heme and nonheme proteins as
well as the pH influence on molecular motion of the label with respect to these proteins. EPR spectra were
recorded at room temperature and the computer simulation analysis of spectra was made in order to obtain
the magnetic parameters. Noncovalent labeling of proteins can give valuable information on the magnetic
interaction between the label molecule and the paramagnetic center of the proteins. The relevance of this
interaction can be obtained from line shape analysis: computer simulations for nonheme proteins assume
a Gaussian line shape, whereas for heme proteins, a weighted sum of Lorentzian and Gaussian components
is assumed. In the framework of the “moderate jump diffusion” model for rotational diffusion, the rotational
correlation time is strongly influenced by pH, because of the electrostatic interactions and hydrogen bonding.
This document summarizes experiments investigating the roles of various organic additives in facilitating coupling reactions between haloarenes and arenes using potassium tert-butoxide (KOtBu). Amino acids like sarcosine and proline were found to initiate these reactions via electron transfer, forming aryl radicals. Secondary amino acids were more effective than primary or tertiary amino acids. Piperazinedione derivatives formed from the condensation of amino acids were also found to initiate reactions by forming electron-rich enolates or dianions that act as electron donors. Alcohols, 1,2-diols, and 1,2-diamines were also investigated for their ability to form electron donors that initiate these coupling reactions.
This document outlines a graduate program on mass spectral analysis of alcohols, phenols, and ethers. It discusses the objectives to introduce mass spectroscopy, principles, functions, ionization techniques, and fragmentation patterns of various compounds. Specifically, it describes how primary, secondary, tertiary, and cyclic alcohols can be differentiated by their mass spectrometry peaks. It also examines the fragmentation of aromatic alcohols, phenols, and various types of ethers including aliphatic and aromatic ethers. The summary provides key differences in molecular ion peaks and fragmentation patterns between these compound classes.
This document summarizes an investigation of the adsorption of carboxymethyl cellulose (NaCMC) onto gamma-aluminum oxide (γ-Al2O3) particles. Key findings include:
1) Electrophoretic and electro-optical measurements both show that NaCMC adsorption causes the particle charge to be overcompensated above a concentration of 1x10-3 g/L NaCMC.
2) Frequency plateaus in electro-optical effect measurements shift to lower frequencies with NaCMC adsorption, indicating a decrease in particle relaxation frequency.
3) Relaxation times increase with NaCMC concentration as the adsorbed polymer enlarges the particle size, though the effect is
Fragmentation techniques in mass spectroscopyMahendra G S
Fragmentation in mass spectrometry involves the breakdown of molecular ions into smaller daughter ions. There are several types of fragmentation including homolytic cleavage, heterolytic cleavage, and rearrangement reactions. Homolytic cleavage involves equal transfer of electrons to both atoms, forming a radical and cation. Heterolytic cleavage involves both electrons being taken by one atom, forming an even electron cation and radical. Rearrangement reactions require changes to multiple bonds and can eliminate smaller molecules. Common rearrangements include McLafferty rearrangement and elimination reactions. Fragmentation patterns provide information about functional groups present in molecules.
Basic principles & questions and answers of organic chemistry Bryar Ali Rus
this is some basic principles and question & answers of previous years of organic chemistry with notes on dr.emad manhal's examination , school of pharmacy , university of sulaimani .
The document discusses the McLafferty rearrangement, which is an intramolecular atomic rearrangement during fragmentation that results in rearrangement ions. To undergo a McLafferty rearrangement, a molecule must possess an appropriately located heteroatom like oxygen or nitrogen, a π system usually a double bond, and an abstractable hydrogen atom next to the carbonyl system. Rearrangement peaks can be identified by considering whether the mass number of the fragment ion is even or odd relative to the molecular ion.
In mass spectrometry, fragmentation is the dissociation of energetically unstable molecular ions formed from passing the molecules in the ionization chamber of a mass spectrometer. The fragments of a molecule cause a unique pattern in the mass spectrum.
03 - Structure and Stereochemistry of Alkanes - Wade 7thNattawut Huayyai
This document summarizes key concepts about alkanes from Chapter 3 of an organic chemistry textbook. It discusses the structures, properties, nomenclature and conformations of alkanes. It also covers cycloalkanes and their ring strains. Specific topics covered in 3 sentences or less include:
- Alkanes are hydrocarbons with the general formula CnH2n+2. They exist as gases at low molecular weights and liquids/solids at higher weights. Their physical properties depend on molecular weight.
- Constitutional isomers have the same molecular formula but different connectivities. Conformations result from bond rotations and include staggered, eclipsed, gauche and anti arrangements.
- Cyclo
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive functioning. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
This document outlines the key points from a seminar on leadership and ministry presented by Dennis W. Wiley at Vanderbilt Divinity School in 1999. The seminar covered definitions of leadership and ministry, biblical principles of servant leadership, challenges facing church leaders in the 21st century, and how churches may change in response. Major topics included the declining influence of institutional churches, motivations for churchgoers, and tensions within the Black church since the Civil Rights movement.
Substitution elimination reaction in cyclohexyl systemDongguk University
The document discusses substitution and elimination reactions in cyclohexyl systems and their stereochemistry. It covers nucleophilic substitution reactions like SN1 and SN2 that can proceed via racemization or inversion of configuration. Neighboring group participation is described as enhancing the rate of some substitution reactions. Allylic bromination of cyclohexene is provided as an example of a radical substitution reaction. Elimination reactions like E2 and cis-elimination are also discussed, noting the effects of substrate conformation on reaction stereochemistry and product formation.
This document describes Michael Ludden's synthesis and characterization of various molybdenum complexes. Three complexes were synthesized - [CpMo(CO)3Me], [CpMo(CO)3Et], and [CpMo(CO)2(COMe)(PPh3)]. They were characterized using NMR and IR spectroscopy. The results confirmed the structures of the complexes and showed how changing ligands affects properties. Kinetic measurements of migratory insertion reactions will be taken using these complexes to understand reaction rate dependence on factors like solvent, temperature and ligand type.
The Brønsted catalysis relationship is a Linear Free Energy Relationship (LFER) that relates ionization of an acid or base which catalyzes a reaction and the rate of the reaction.
Contributed by: Quincy Davis, Jonathan Greenhalgh, Joshua Visser (Undergraduates), University of Utah, 2016
1) Veratrole was electrooxidized on a platinum electrode in acetonitrile solutions containing either tetrabutylammonium perchlorate or lithium perchlorate.
2) A green deposit formed containing hexamethoxytriphenylene radical cation species associated with perchlorate counterions.
3) Spectroelectrochemical experiments showed that oxidation of perchlorate anions above 2.3V dissolved the deposit, but sweeping the potential back regenerated the solid, allowing the process to be cycled.
Theoretical Studies on Mechanism of Xanthine Oxidase and 6-mercaptopurineEDITOR IJCRCPS
The reaction mechanisms of 6-mercaptopurine or hypoxanthine have not been investigated either
theoretically or experimentally. Understanding of the overall mechanism helps to manage the
metabolic properties of potential drug molecules metabolized by XOR. The present theoretical
study is aimed to predict transition state structure, the path of electron transfer and probe plausible
mechanistic route for hydroxylation of 6-mercaptopurine or hypoxanthine and XO by relating the
electronic structure to reactivity. The transition state structure was predicted by linear transit
calculation of series of structures by performing frequency calculation which was confirmed by one
imaginary negative frequency value. The path of coupled electron proton transfer mechanism
proved from Mullikan charge analysis and mechanism of oxidation was proved from geometry
optimization. Density functional theory (DFT)/B3LYP method were used to probe the electronic
structure of metastable structure. Result showed that in transition state structures the energy barrier
for 6-mercaptopurine bound active site was lower than hypoxanthine bound active site by
20kcal/mol in average. The ionocity data revealed the presence of substantial negative charge on
proton which suggests the transfer of hydride from substrate to the active site. Bond length analysis
showed that in the transition stases CRH-Oeq bond length was nearly 98% formed where as the CRHHRH
bond length was only 36.78% broken. Geometry optimization revealed that oxidation of 6-
mercaptopurine or hypoxanthine by XO follow stepwise mechanism. It can be generalized that the
oxidation of 6-mercaptopurine or hypoxanthine by XO follows two step mechanisms namely:
abstraction of proton by Glu1226 from equatorial hydroxide of active site followed by nucleophilic
attach on C2 of substrate and hydride was transferred through concomitant release of oxidized
substrate.
Juornal of Physics Condensed Matter - Article IRossen Hristov
This document summarizes a study that investigated the mobility of counterions condensed on carboxymethyl cellulose (CMC) polymer chains adsorbed onto alumina colloid particles. Previous studies using electro-optical techniques reported that condensed counterions are mobile in alternating electric fields. However, the current study uses an amplitude approach, measuring particle polarizability at increasing CMC concentration rather than frequency dependence. Results indicate condensed counterions do not contribute to particle polarization at 1 kHz, suggesting they are immobile in sinusoidal fields up to 0.5 kV/cm and 1 kHz. Comparison of polarizability and electrophoretic mobility supports the conclusion that condensed counterions are immobilized on the CMC chains.
Cape unit 2 chemistry reactions of halogenoalkanes cram sheetDenison Dwarkah
Everything you'll ever need to know to answer any CAPE chemistry question on halogenoalkanes.
Print double sided for one sheet that will solve all your problems.
Ideal for a five minute revision session just before the exam, or for a first time student wanting to know what's really important in this section of the syllabus.
Some reactions seem to obvious to fail, so what happens when they do? Quantum calculations yield invaluable insight to the nature of a reaction mechanism.
Presented at the Virtual Conference on Computational Chemistry VCCC 2014
Credit due to Guillermo Caballero on whose BSc thesis this presentation is based.
This document summarizes a study that measured the enthalpy change (ΔH) associated with the α-helix to random coil transition of an alanine peptide in water using calorimetry. The researchers synthesized a 50-residue peptide containing primarily alanine residues and determined its ΔH to be between 0.9-1.3 kcal/mol per residue, providing a basic parameter for predicting thermal unfolding of peptide helices. Circular dichroism spectra and melting curves confirmed the peptide adopted an α-helical structure at low temperatures and underwent a reversible helix-coil transition. The ΔH value suggests the peptide backbone, rather than side chains, makes the dominant contribution to helix stability.
SIMONA CAVALU_Rotational Correlation Times of proteinsSimona Cavalu
Noncovalent spin labeled proteins (ovalbumin, bovine serum albumin, hemoglobin, and cytochrome c) were
investigated in order to follow the different type of interactions between the nitroxide radical of 3-carbamoyl-
2,2,5,5-tetramethyl-3-pyrrolin-1-yloxy spin label and functional groups of heme and nonheme proteins as
well as the pH influence on molecular motion of the label with respect to these proteins. EPR spectra were
recorded at room temperature and the computer simulation analysis of spectra was made in order to obtain
the magnetic parameters. Noncovalent labeling of proteins can give valuable information on the magnetic
interaction between the label molecule and the paramagnetic center of the proteins. The relevance of this
interaction can be obtained from line shape analysis: computer simulations for nonheme proteins assume
a Gaussian line shape, whereas for heme proteins, a weighted sum of Lorentzian and Gaussian components
is assumed. In the framework of the “moderate jump diffusion” model for rotational diffusion, the rotational
correlation time is strongly influenced by pH, because of the electrostatic interactions and hydrogen bonding.
This document summarizes experiments investigating the roles of various organic additives in facilitating coupling reactions between haloarenes and arenes using potassium tert-butoxide (KOtBu). Amino acids like sarcosine and proline were found to initiate these reactions via electron transfer, forming aryl radicals. Secondary amino acids were more effective than primary or tertiary amino acids. Piperazinedione derivatives formed from the condensation of amino acids were also found to initiate reactions by forming electron-rich enolates or dianions that act as electron donors. Alcohols, 1,2-diols, and 1,2-diamines were also investigated for their ability to form electron donors that initiate these coupling reactions.
This document outlines a graduate program on mass spectral analysis of alcohols, phenols, and ethers. It discusses the objectives to introduce mass spectroscopy, principles, functions, ionization techniques, and fragmentation patterns of various compounds. Specifically, it describes how primary, secondary, tertiary, and cyclic alcohols can be differentiated by their mass spectrometry peaks. It also examines the fragmentation of aromatic alcohols, phenols, and various types of ethers including aliphatic and aromatic ethers. The summary provides key differences in molecular ion peaks and fragmentation patterns between these compound classes.
This document summarizes an investigation of the adsorption of carboxymethyl cellulose (NaCMC) onto gamma-aluminum oxide (γ-Al2O3) particles. Key findings include:
1) Electrophoretic and electro-optical measurements both show that NaCMC adsorption causes the particle charge to be overcompensated above a concentration of 1x10-3 g/L NaCMC.
2) Frequency plateaus in electro-optical effect measurements shift to lower frequencies with NaCMC adsorption, indicating a decrease in particle relaxation frequency.
3) Relaxation times increase with NaCMC concentration as the adsorbed polymer enlarges the particle size, though the effect is
Fragmentation techniques in mass spectroscopyMahendra G S
Fragmentation in mass spectrometry involves the breakdown of molecular ions into smaller daughter ions. There are several types of fragmentation including homolytic cleavage, heterolytic cleavage, and rearrangement reactions. Homolytic cleavage involves equal transfer of electrons to both atoms, forming a radical and cation. Heterolytic cleavage involves both electrons being taken by one atom, forming an even electron cation and radical. Rearrangement reactions require changes to multiple bonds and can eliminate smaller molecules. Common rearrangements include McLafferty rearrangement and elimination reactions. Fragmentation patterns provide information about functional groups present in molecules.
Basic principles & questions and answers of organic chemistry Bryar Ali Rus
this is some basic principles and question & answers of previous years of organic chemistry with notes on dr.emad manhal's examination , school of pharmacy , university of sulaimani .
The document discusses the McLafferty rearrangement, which is an intramolecular atomic rearrangement during fragmentation that results in rearrangement ions. To undergo a McLafferty rearrangement, a molecule must possess an appropriately located heteroatom like oxygen or nitrogen, a π system usually a double bond, and an abstractable hydrogen atom next to the carbonyl system. Rearrangement peaks can be identified by considering whether the mass number of the fragment ion is even or odd relative to the molecular ion.
In mass spectrometry, fragmentation is the dissociation of energetically unstable molecular ions formed from passing the molecules in the ionization chamber of a mass spectrometer. The fragments of a molecule cause a unique pattern in the mass spectrum.
03 - Structure and Stereochemistry of Alkanes - Wade 7thNattawut Huayyai
This document summarizes key concepts about alkanes from Chapter 3 of an organic chemistry textbook. It discusses the structures, properties, nomenclature and conformations of alkanes. It also covers cycloalkanes and their ring strains. Specific topics covered in 3 sentences or less include:
- Alkanes are hydrocarbons with the general formula CnH2n+2. They exist as gases at low molecular weights and liquids/solids at higher weights. Their physical properties depend on molecular weight.
- Constitutional isomers have the same molecular formula but different connectivities. Conformations result from bond rotations and include staggered, eclipsed, gauche and anti arrangements.
- Cyclo
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive functioning. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
This document outlines the key points from a seminar on leadership and ministry presented by Dennis W. Wiley at Vanderbilt Divinity School in 1999. The seminar covered definitions of leadership and ministry, biblical principles of servant leadership, challenges facing church leaders in the 21st century, and how churches may change in response. Major topics included the declining influence of institutional churches, motivations for churchgoers, and tensions within the Black church since the Civil Rights movement.
Vitamins are essential nutrients that support growth, maintenance and regulation of bodily processes. There are 13 vitamins that are divided into fat-soluble and water-soluble categories. Fat-soluble vitamins include A, D, E and K which are stored in the body and have different deficiency and toxicity symptoms compared to water-soluble vitamins like C and the B vitamins which are not stored and require more regular intake. A balanced diet with variety is important to obtain the necessary vitamins, while too little or too much of certain vitamins can cause harm.
Este documento presenta una unidad sobre viajes en inglés para el I.E.P. «Nuestra Señora de Guadalupe». La unidad incluye vocabulario común para viajes como maleta, tarjeta de crédito, monedero, snorkel, paraguas, aletas y cheques de viajero. También incluye ejercicios para ordenar y completar estas palabras relacionadas con los viajes.
Teorías y descripciones de la etapa adultaEmagister
1) Las teorías de Erikson y Peck describen las etapas de la vida adulta media, enfocándose en retos como la productividad vs el estancamiento y cambios físicos, mentales y sociales. Otras teorías como las de Levinson y Sheehy también describen esta etapa y transiciones alrededor de los 40-50 años relacionadas con reexaminar metas y prioridades. 2) Los estudios no encuentran evidencia concluyente de una "crisis de mitad de vida" universal, aunque reconocen que esta etapa conlleva
This short document promotes creating presentations using Haiku Deck, an online presentation tool. It encourages the reader to get started making their own Haiku Deck presentation and shares it on SlideShare. In a few words, it advertises the ability to easily create and share online presentations.
True To That is a song by American rapper Logic. The song discusses Logic's journey in the music industry and desire to stay true to himself and his artistry despite pressures from labels and fans. Logic reflects on his rise to fame and promise to continue making music from the heart without compromising his authenticity.
This document discusses natural remedies for treating foot odor. It explains that foot odor is caused by bacteria growing in sweat on the feet. It then provides instructions for using baking soda, a sugar scrub, sage leaves, lavender oil, and black tea to treat foot odor. Baking soda can be mixed with sage leaves and placed in shoes to absorb odor overnight. A sugar, lemon, and coffee scrub can exfoliate feet to remove bacteria. Sage leaves, lavender oil, and black tea soaks have antibacterial properties to reduce foot odor as well.
This document discusses elements of international promotion. It outlines tasks for designing an infographic containing objectives, means, cultural features, law relationships, common mistakes, and support/services. It also defines international promotion. Two case studies are presented: IKEA expanding into China where it targeted young middle class instead of using low prices; and Under Armour being criticized by athletes so promoting benefits to make customers forget mistakes. The conclusion states promotion informs, persuades, and reminds the market of a product to influence feelings, beliefs, or behavior and aims to supplement advertising and personal selling.
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive functioning. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
La auditoría es un proceso cuyo resultado final es la emisión de un informe en el que el auditor opina sobre la situación financiera de una empresa. El auditor evalúa la evidencia obtenida para determinar si los estados financieros representan razonablemente la posición financiera de la empresa. Las Normas de Auditoría Generalmente Aceptadas establecen los requisitos y procedimientos que debe seguir el auditor.
Se presenta a continuación definiciones pertinentes al diseño de losas de concreto armado, principalmente en una dirección. Tipos de losas, características, ventajas y desventajas de las mismas, criterios de selección, cargas usuales, métodos de diseño, detallado del acero de refuerzo, y otros aspectos de suma importancia.
El contenido está descrito principalmente bajo la norma COVENIN de Venezuela.
This document discusses theories of first and second language acquisition. It outlines the typical stages of acquiring a first language, from babbling to using multi-word sentences. It also describes Krashen's theory that there is a distinction between acquiring a language naturally through use and learning a language through formal instruction. The stages of second language acquisition are also outlined, from initial silent periods to advanced fluency. Challenges to achieving fluency in a second language are discussed, such as interference from the first language and fossilization of errors.
The document discusses pericyclic reactions and the Woodward-Hoffmann rules for predicting their stereochemistry. It begins by defining pericyclic reactions as concerted reactions where bonds are formed or broken in a cyclic transition state. It then provides examples of different types of pericyclic reactions, including electrocyclizations, cycloadditions, and sigmatropic rearrangements. The Woodward-Hoffmann theory is explained, showing how it can be used to predict whether a reaction will proceed with antarafacial conrotation or suprafacial disrotation based on whether the reaction is thermally or photochemically induced. Specific examples like cyclobutene formation and the Diels-Alder reaction are analyzed in
This document summarizes a study that introduced mutations to the nuoL gene in Escherichia coli to test the proposed "piston" mechanism of the long alpha-helix (AH) in subunit L of respiratory Complex I. Three types of mutations were made: 1) truncations of the N- and C-termini of subunit L, 2) substitutions of conserved residues in the AH, and 3) insertions/substitutions along the AH to alter its rigidity and geometry. Most mutations had little effect on Complex I function, but insertion of six to seven residues in the AH substantially reduced proton pumping efficiency, questioning the piston model.
Calvin's experiment used radioactive carbon-14 to track the pathway of carbon fixation in photosynthesis. Samples of algae exposed to carbon-14 were taken at intervals and the radioactive compounds identified. Glycerate-3-phosphate was found to be the first labeled compound, indicating it is the initial product of carbon fixation. Analysis of later samples revealed a range of labeled intermediate and final products, elucidating the steps of the Calvin cycle. Calvin's discoveries depended on advances in technology like the discovery of carbon-14 and the development of autoradiography.
The document discusses capillary electrophoresis (CE), including its key terminology, instrumentation, flow dynamics, and factors that affect separation efficiency such as capillary diameter, voltage, and temperature. CE uses narrow capillaries to perform high-efficiency separations of charged molecules. When an electric field is applied, electroosmotic flow and electrophoretic migration move solutes through the capillary at different rates depending on their size and charge. Precise temperature control and optimization of factors like voltage and capillary diameter are important for achieving high resolution separations.
This document summarizes femtosecond-resolved experiments on the primary photochemistry of 9-nitroanthracene. The experiments observed the ultrafast decay of the initially excited singlet state through time-resolved fluorescence, and detected the accumulation of the anthryloxy radical and formation of the relaxed phosphorescent T1 state through transient absorption experiments. The experiments provide timescales for the formation of the primary photoproducts, the anthryloxy radical and the T1 state, which both occur within a few picoseconds. Calculations were also performed to understand the molecular orbitals responsible for intersystem crossing between the singlet and triplet manifolds.
1) The document discusses various methods of substrate control in organic reactions, focusing on how substrate conformation can influence diastereoselectivity. Allylic 1,3-strain (A1,3 strain), where substituents on the first and third carbons interact sterically, is a key concept.
2) Reactions like epoxidation and hydroboration are often highly diastereoselective when the substrate adopts a conformation that positions the smallest substituent syn to the reactive double bond to minimize A1,3 strain. The reagent then approaches from the least hindered face.
3) Directed reactions use hydrogen bonding or coordination to deliver the reagent to one
This document outlines a graduate student's thesis work on multi-scale modeling of micro-coronas. There are wide variations in both time and length scales involved in plasma modeling, from picoseconds to hours/days and from molecular to macroscopic scales. A multi-scale modeling technique of domain decomposition is proposed, using microscopic models locally where needed and macroscopic models for the rest. The goals are to develop a modeling tool that can span micro- to macro-scales and simulate plasmas in complex geometries. Challenges include bridging between scales and incorporating particle and fluid models.
The document discusses 1,3-dipolar cycloaddition reactions, which involve a 1,3-dipole reacting with a dipolarophile to form a 5-membered heterocyclic ring. Key points include:
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- The reaction typically proceeds by a concerted pericyclic mechanism through a six-electron transition state, though some exceptions involve a stepwise mechanism.
- Frontier molecular orbital theory can be used to classify dipoles as HOMO-controlled, LUMO-controlled, or ambiphilic based
The document discusses 1,3-dipolar cycloaddition reactions, which involve a 1,3-dipole reacting with a dipolarophile to form a 5-membered heterocyclic ring. Key points include:
- 1,3-dipoles are classified into three types based on their electronic structure. Common examples are azides, nitrones, and carbonyl ylides.
- The reaction typically proceeds by a concerted pericyclic mechanism through a six-electron transition state, though some exceptions involve a stepwise mechanism.
- Frontier molecular orbital theory can be used to classify dipoles as HOMO-controlled, LUMO-controlled, or ambiphilic based
The document discusses standard conditions, standard states of elements, and standard enthalpy changes of formation and combustion. It defines standard enthalpy change of formation as the energy exchanged when 1 mole of a compound is formed from its elements in their standard states. It also defines standard enthalpy change of combustion as the energy given off when 1 mole of a compound undergoes complete combustion. Hess's law and Born-Haber cycles are introduced to calculate enthalpy changes from other known values using the principle that total energy change is independent of reaction path.
This document summarizes a study of the magnetic properties of the sodium iron phosphite compound NaFe3(HPO3)2(H2PO3)6. Key findings include:
1) The compound develops ferrimagnetic order below 9.5 K and exhibits a 1/3 magnetization plateau that extends to 8T, with linear increase in magnetization above this field until saturation at 27T.
2) There are two nonequivalent iron sites revealed by Mossbauer spectroscopy with a 2:1 ratio.
3) High-frequency ESR and other measurements indicate weak magnetic anisotropy and short-range spin order above the ordering temperature.
4) DFT calculations show the
The document summarizes a study that investigated how the photoluminescence quantum yield of lead selenide quantum dots is affected by increasing excitation energy. Three samples of PbSe quantum dots were synthesized with different diameters and characterized. It was found that the quantum yield decreased as the excitation energy increased, likely due to the formation of multi-exciton states within single quantum dots that lead to non-radiative Auger processes. The quantum yield was measured using an integrating sphere method and by analyzing absorption and emission spectra of the samples excited at different wavelengths. The results supported the expectation that higher excitation energies reduce quantum yield.
1) Electrogenic pumps like the Na+/K+ ATPase transport ions across membranes using energy from ATP hydrolysis. This leads to a net movement of charge across the membrane.
2) Early models assumed passive ion diffusion established ion gradients, but problems arose. Equations were developed but inconsistencies emerged when applying them to plant cells.
3) The mechanism of the Na+/K+ ATPase involves ions binding deep within the protein and moving through access channels to binding sites. Transient currents from external ions like K+ and Na+ moving through these channels have been measured.
This document provides information about electrophoresis. It discusses different types of electrophoretic techniques including slab electrophoresis, capillary electrophoresis, capillary zone electrophoresis, capillary gel electrophoresis, capillary isotachophoresis, and micellar electrokinetic chromatography. It also covers principles, instrumentation, applications in areas like DNA analysis and vaccine analysis.
Organic chemistry has two main divisions. One division deals with aliphatic (fatty) compounds, the first compounds you encountered in Organic Chemistry I. The second division includes the aromatic (fragrant) compounds, of which benzene is a typical example.
Coulomb Screening and Coherent Phonon in Methylammonium Lead Iodide PerovskitesLexi Cao
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Commentary: The number of Electrons in the Nernst Equation: Energetic Conside...crimsonpublishersOJCHD
The document discusses the Nernst equation and its role in describing the transmembrane potential of cells. It summarizes the conventional view that the sodium-potassium pump maintains ion concentration gradients that give rise to the negative intracellular potential. However, it argues that this view is energetically costly and proposes an alternative mechanism. Specifically, it suggests that electrons from oxidative phosphorylation in mitochondria directly contribute to the intracellular negative charge, without requiring ion pumping, providing a more energetically favorable explanation of the Nernst equation and cell potentials.
This document provides an overview of a university course on organic synthesis. It covers topics like pericyclic reactions, electrocyclizations, sigmatropic rearrangements, and the Woodward-Hoffmann rules for predicting stereochemistry. Examples are given of reaction mechanisms and how the rules explain stereochemical outcomes. The document also lists additional reading materials and notes that attending all lectures is essential since not all material is covered in the handout.
This study investigated the electrochemical oxidation of catechols in the presence of 4-amino-3-thio-1,2,4-triazole (3) using cyclic voltammetry and controlled-potential coulometry. Results showed that catechols reacted with compound 3 via an intramolecular cyclization reaction to form 1,2,4-triazino[5,4-b]-1,3,4-thiadiazine derivatives. The observed homogeneous rate constants for the Michael addition reaction were estimated by comparing experimental voltammograms to digitally simulated responses. The oxidation mechanism was proposed to follow an electron transfer-chemical reaction-electron transfer-chemical reaction pathway based on diagnostic criteria for
1. Pericyclic reactions involve concerted bonding changes through a cyclic transition state involving pi and sigma orbitals.
2. They include electrocyclic reactions, cycloadditions, and sigmatropic shifts.
3. Frontier molecular orbital theory is used to predict the stereochemistry of pericyclic reactions based on the symmetry of the highest occupied molecular orbital.
Similar to Molecular dynamics-of-ions-in-two-forms-of-an-electroactive-polymer (20)
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In the rapidly evolving landscape of technologies, XML continues to play a vital role in structuring, storing, and transporting data across diverse systems. The recent advancements in artificial intelligence (AI) present new methodologies for enhancing XML development workflows, introducing efficiency, automation, and intelligent capabilities. This presentation will outline the scope and perspective of utilizing AI in XML development. The potential benefits and the possible pitfalls will be highlighted, providing a balanced view of the subject.
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1. INTERDISCIPLINARY TRANSPORT PHENOMENA
Molecular Dynamics of Ions in Two Forms
of an Electroactive Polymer
D. A. Morton-Blake and Darren Leith
School of Chemistry, Trinity College, Dublin, Ireland
Molecular dynamics (MD) are performed in all-atom simulations of two polymer species
based on polythiophene. In one case the amphiphilic polymer forms a monolayer inter-
face between a vacuum and an aqueous layer containing ions. The electroactive nature
of the polymer is invoked by conferring a negative charge on it to compensate for charge
imbalance in the Na+
and Cl−
concentrations of the aqueous layer. The effects of hydro-
static pressure and charge imbalance on the stability of the monolayer are investigated.
In another simulation a polythiophene oligomer is wound into a helix where it serves
as an ion channel between two aqueous regions on both sides of a phospholipid bilayer
membrane.
Key words: molecular dynamics; electroactive polymer; charged monolayer; helical ion
channel
Introduction
Polythiophene chains can minimize their
steric repulsion in one of two ways. The most
common one is the anti conformation1
in which
successive sulfur atoms along the chain point
“up” and “down,” as shown in Figure 1.
The same polymer in a helical conformation
is shown in Figure 2. It is generated by twisting
the entire chain to the right of each inter-ring
bond in turn, by the same torsional angle.
The backbones of these polymers are π con-
jugated, and because this property confers on
them a reduced band gap compared with all-σ
systems, they can undergo redox changes that
permit them to acquire overall positive or neg-
ative charge, which is located principally in the
thiophene rings.
The properties of this kind of polymer are
also influenced by substituting the H atoms
on the “3” position of the thiophene rings by
various groups; alkyl substitution renders the
polymer soluble in largely nonpolar solvents,
Address for correspondence: D. A. Morton-Blake, School of Chemistry,
Trinity College, Dublin 2, Ireland. Voice: 353 1 8961943; fax: 353 1
671826. tblake@tcd.ie
whereas oxygen-containing substituents would
favor a protic environment. These properties
will be exploited in the molecular dynamics
(MD) investigations described here.
Part 1: Amphiphilic Polymer
Monolayer
Consider the substitution of the “3” posi-
tions of successive thiophene rings alternately
with an alkyl side chain, which is here the hy-
drophobic group octyl (C8H17), and with the
hydrophilic chain -(CH2-O-CH2)4-CH2-OH.
Because these “3” positions alternate along the
backbone, the side groups that they bear also al-
ternate “up” and “down,” as shown in Figure 3.
The result2
is an amphiphilic polymer with the
ability to form monolayers on a water surface;
the hydrophilic oxanoyl chains enter the aque-
ous layer, whereas the hydrophobic alkyl chains
are directed almost normal to the water sur-
face into the vacuum. We previously3
applied
MD to simulate a stable, ordered film of a self-
assembled stable monolayer interface of these
polymers at a water surface.
In a quest for materials for novel nanoscale
devices, we wish to characterize the stability of
Interdisciplinary Transport Phenomena: Ann. N.Y. Acad. Sci. 1161: 105–116 (2009).
doi: 10.1111/j.1749-6632.2009.04095.x C⃝ 2009 New York Academy of Sciences.
105
2. 106 Annals of the New York Academy of Sciences
Figure 1. An anti sequence of a polythiophene chain backbone.
Figure 2. Polythiophene in a syn conformation,
resulting in a helical chain. (In color in Annals online.)
the monolayer film to the application of hy-
drostatic pressure and when the electroactive
character of the polythiophene backbone is ex-
ploited by allowing it to assume an overall elec-
tric charge. (The charge will be compensated
by unbalancing concentrations of the Na+
and
Cl−
solutes in the water layer.)
Computation
The code used for the MD was DL_POLY,4
which was run with periodic boundary condi-
tions (forming Ewald coulombic sums along the
membrane surface) usually for 105
time steps (1
time step = 0.001 ps) in a Hoover thermostat
at 300 K at a series of constant pressures. Us-
Figure 3. The amphiphilic polymer poly(3-octyl
3′
-oxanoyl bithiophene). The red and yellow atoms
are, respectively, oxygen and sulfur. (In color in
Annals online.)
ing code written for parallel processors, such
an MD run took 90 h of CPU time on a com-
puter cluster of two nodes, both consisting of
two processors. The atomistic potentials used
were intramolecular (bond and bond angle) and
nonbonding (intermolecular), which were as-
signed according to the DREIDING generic
formulation5
—except for those involving the
water molecule, for which the SPC potentials
of Berendsen et al. were used,6
and those for
the Na+
and Cl−
ions, which were described
3. Morton-Blake & Leith: Molecular Dynamics of Ions in a Polymer 107
by the potentials of Rasaiah et al.7
The potential
parameters for the interactions between water
and the other atoms, and between the ions and
other atoms, were obtained by the commonly
used geometric-mean rule. Torsional potentials
in the polythiophene main chain were assigned
as described in our previous work.8
The partial atomic charges on the thiophene
rings were taken from DFT calculations on neu-
tral and charged oligothiophenes,9
and those
of the oxidized polymer main chain were as-
signed by distributing the additional charge
evenly over the five atoms of each thiophene
ring in the polymer chains. The atoms of the
hydrophobic octyl side chains were assumed
to have no net charges, and those on the
hydrophilic oxanoyl chains were taken from
the work of Udier-Blagovi´c et al.10
on model
compounds.
Monolayer Molecular Model
The unit cell constituting the MD simulation
box contained chains of poly(3-octyl 3′
-oxanoyl
bithiophene), whose primary structure was de-
scribed in the introduction and a fragment of
which is illustrated in Figure 3. The structural
repeat unit of the cell’s polymer component
consisted of two such chains with a mutual
displacement of half a bithiophene unit along
the polymer backbone. In this way steric en-
ergy was minimized because the side groups
of each chain corresponded with the gaps be-
tween those of the adjacent one when viewed
in the sense of Figure 3. The MD simulation
box was a two-dimensional unit cell in the ab
plane, consisting of six pairs of chains. The box
therefore contained a total of 12 chains along
the b axis, and 6 substituted bithiophenes along
a, making a total of 72 bithiophene units. The
polymer constituted the interface between the
vacuum and an aqueous layer, which was po-
sitioned to overlay the oxanoyl side chains. It
consisted usually of 2222 water molecules and
a total of about 290 ions from the NaCl elec-
trolyte, resulting in a 11% NaCl solution.
Results of Monolayer Investigation
Pressure
We have shown that application of lateral
pressure, which is equivalent to compressing
the monolayer by a piston in the interfacial
plane, as in a Langmuir trough, first disor-
ders and then ruptures the monolayer with in-
creasing pressure.3
Hydrostatic pressure, on the
other hand, which we describe here, is applied
isotropically to the complete system.
Electrolyte Solutions
An optimum statistical analysis of the be-
havior of the ions in the NaCl solution would
require many ions to be present in the aqueous
layer. We therefore worked with a mole fraction
of 11% NaCl in water, which is the maximum
concentration achievable under normal con-
ditions. Using the electroactive facility of the
polymer to acquire an overall electric charge
(although the electrochemical species that pro-
mote this charge were not explicitly included in
the simulation), we compensated the polymer
charge by removing the equality of the concen-
trations of the Na+
and Cl−
ions in the aque-
ous layer. We must also decide on the range of
charges to confer on the polymer and the com-
pensating electrolyte solutions. An upper limit
of such a range would normally be the max-
imum charge that oxidized electroactive poly-
mer can acquire by the transfer of electronic
charge by a redox mechanism. For heteroaro-
matic ring polymers this value is that of a chain
in which approximately half the rings acquire
a unit electron charge.11
Because there are 144
thiophene rings in our MD box and only about
145 ions in all, compensating such a large poly-
mer charge by unbalancing the concentrations
of the Na+
and Cl−
ions would be unrealistic.
Because in any case such a charge would de-
stroy the monolayer, we must use much lower
degrees of polymer oxidation or reduction. To
examine the effect on the monolayer, we there-
fore performed a series of calculations in which
4. 108 Annals of the New York Academy of Sciences
Figure 4. View of the polymer monolayer on the aqueous layer along a direction parallel to the interface,
which is also the direction of the polythiophene chains. The sulfur atoms (yellow) of the thiophene rings trace
the polymer backbone. (In color in Annals online.)
the Na+
and Cl−
ion concentrations were un-
balanced up to a maximum of 30%.
Results
Hydrostatic Pressure
Figure 4 shows the monolayer system on
an 11% aqueous NaCl solution after dynam-
ics periods of 100 ps at hydrostatic pressures
of from atmospheric to 1000 bar. In these
atomic plots the system is viewed along the
interface parallel to the directions of the poly-
mer chains. The thiophene rings in the polymer
backbone can be identified by the yellow sulfur
atoms. During the 100-ps period at 1-bar pres-
sure, order is retained in the main chains of
the polymer (though not in the side chains).
The packing of the polymers had been de-
fined in the initial (input) structure with ad-
jacent chains displaced by half a bithiophene
unit in accordance with the structures of bulk
lattice poly(alkylthiophene)s12
; in this way thio-
phene rings in adjacent chains formed a stag-
gered stacked relationship. A detailed exami-
nation of the postdynamics equilibrium struc-
tures at 1-bar pressure, however, showed that
the chains had been displaced into positions in
which the thiophene rings now showed near-
eclipsed stacking. Energy was reduced by a slight
up–down slipping of alternate chains along the
c axis (normal to the interface).
Water molecules and Na+
and Cl−
ions ap-
pear in the space of the oxanoyl side chains but
do not venture into the region occupied by the
polymer backbone. At a pressure of 10 bars sev-
eral polymer chains are displaced significantly
“upward” (into the vacuum layer) or “down-
ward” (into the aqueous layer) from their for-
mer surface positions. Because the monolayer
“seal” is broken, water molecules and the ions
can seep into the region that was formerly as-
sociated with the interface.
Because the pressures were imposed instan-
taneously at the outset of the dynamics rather
than successively, the higher pressures of 100
and 1000 bars preclude the “slipping” of the
polymer chains out of the interface region in
the manner that occurs at 10 bars. As a result,
although individual thiophene rings twist out of
their former planes normal to the interface, the
high pressures immobilize the chains in the in-
terface, sealing the region of the polymer back-
bone from invasion by water molecules and
ions, which can reach only the region of the
oxanoyl chains.
The radial distribution function (RDF) plots
in Figure 5 indicate the probabilities of finding
a specified pair of atom types at various sepa-
rations. Because one sulfur atom is present in
each thiophene ring in the polymer main chain,
the function gSS(r) in part A of the figure can
demonstrate the degree to which adjacent thio-
phene rings twist around their interconnecting
5. Morton-Blake & Leith: Molecular Dynamics of Ions in a Polymer 109
Figure 5. RDFs for the atom pairs (A) S . . . S and (B) S . . . O (where O is an oxygen atom in water) at
four values of hydrostatic pressure. (In color in Annals online.)
bonds. In a polythiophene chain in which the
thiophene rings are coplanar and adjacent rings
are in an anti conformation (i.e., trans in the
S−C−C−S link) the smallest S . . . S separa-
tion is that between S atoms in adjoining rings,
which is 4.31 A˚ . At a pressure of 1 bar Figure 5A
shows that the sharpest peak is a narrow one
at r = 4.18 A˚ , indicating a twist from trans
of about 45◦
around inter-ring bonds, which
would bring the S atoms closer. The peak height
increases with the application of greater pres-
sure, the maximum shifting to r = 4.3 A˚ , imply-
ing that the pressure induces greater uniformity
on the main-chain torsions. An examination of
individual chains showed that the torsional an-
gles of successive thiophene rings alternated in
a rather regular manner. From the foregoing we
can infer a result that was not obvious from the
atomic plots in Figure 2, namely, that although
hydrostatic pressure reduces the positional order
of the polymer chains their conformational order
is increased by the pressure.
In a regular planar polythiophene chain the
separation of S atoms in next-nearest-neighbor
rings is 7.76 A˚ . The second narrow g(r) peak in
Figure 5A is at r = 7.7 A˚ , a distance that does
not change significantly with pressure. How-
ever, 7.7 A˚ is also the separation of S atoms in
the near-eclipsed stacked columns of thiophene
rings, and the broader RDF peaks in this region
arise from the buckling of the main-chain di-
rections, which widens the range of separation
of the S atoms in pairs of adjacent chains.
Figure 6. The distribution of torsional angles
S−C−C−S around the inter–thiophene ring C−C
bonds in the amphiphilic polymer at the hydrostatic
pressures shown (anti, 180◦
; syn, 0◦
). The links are
in largely gauche conformations, but there is a sub-
stantial trans population (±180◦
) particularly at high
pressures.
The principal g(r) peak for the atom pair S . . .
O in Figure 5B, where O is the oxygen atom in
the water molecules, decreases markedly with
increasing applied pressure, showing that be-
cause of the denser packing of the alkanoyl side
chains at high pressures, water molecules are
denied access to the polymer backbone of the
solvent.
Figure 6 shows the distribution of torsional
angles ϕ in the polythiophene backbone. The
traces confirm our preceding conclusions
from the atom plots and the RDF curves,
that although the anti conformation of the
bithiophene unit (trans S−C−C−S, ϕ = 180◦
)
is common, most of them are in equally
6. 110 Annals of the New York Academy of Sciences
Figure 7. The surface of an 11% NaCl aqueous solution in which the monolayer bears a series of
negative charges compensated by appropriate values of excess Na+
in the electrolyte. (In color in Annals
online.)
weighted gauche conformations g+ and g− with
ϕ ≈ ±120◦
.
Charged Polymer
We have already described that redox pro-
cesses can confer overall charges on such poly-
mers as polythiophene to the extent of imposing
a unit charge (on average) on every two thio-
phene rings along the chain. However, that con-
dition would be for a bulk electrolytic medium
in which the coulombic energy is lowered by the
close approach of counterions to the charged
chain sites. We have yet to see whether the
Na+
or Cl−
ions could penetrate the region
of densely packed oxanoyl chains of the mono-
layer sufficiently readily to access the oppositely
charged thiophene rings.
A series of monolayers were simulated in
which the charge balance of the 290-ion
Na+
/Cl−
ion system in the aqueous layer (con-
stituting an 11% NaCl solution) was gradually
decoupled by converting the requisite num-
ber of Cl−
ions into Na+
ions. Distribution
of the compensating negative charge evenly on
the thiophene rings produced charged polymer
monolayers on NaCl solutions that had excess
negative charge varying from 1% to 30% of the
total ion concentration.
Figure 7 shows the structure at the water–
polymer interface after 50,000 time steps (50 ps)
for a series of systems with the charge excess
percentage in the aqueous layer indicated. The
figures show that the monolayer structure is
well preserved up to 14% excess but that it de-
teriorates markedly at higher polymer charge.
An examination of the interface region shows
7. Morton-Blake & Leith: Molecular Dynamics of Ions in a Polymer 111
Figure 8. RDF traces for atom pairs (A) S, O (where O is a water oxygen atom) and (B) S, Na+
in systems
of different excess charges. (In color in Annals online.)
that at 6% excess charge Na+
ions are attracted
into the interface region and begin to occupy
sites between the polymer’s stacked (negatively
charged) thiophene rings. The fact that no
uncharged water molecules make it into this re-
gion for the neutral polymer (at least in the time
scale of the MD) and that it is observed to occur
only when there is an Na+
/Cl−
charge imbal-
ance in the aqueous layer demonstrates the ef-
fectiveness of the electric field arising from the
coulombic charge on the polymer main chain
in attracting the Na+
ions and water molecules
of hydration.
Because of the short intervals characterizing
MD runs, it is difficult to specify the critical
charge excess that ruptures the monolayer. In-
terfaces that have achieved stability after 105
time steps (0.1 ns) might be found to destabi-
lize in laboratory intervals that are inaccessible
to MD. But it is apparent from the results pre-
sented here that a polymer monolayer with no
overall charge is more stable than a charged
monolayer. Investigations have been cited of
electroactive polymer films that have been sub-
jected to a maximum oxidation that confers a
unit charge on every three rings.13
A mono-
layer instability setting in (as suggested by our
results, say) 10% charge excess implies an ex-
cess of 30 Na+
in 290 ions. This requires that
the compensating charge of −30e is distributed
over the 144 thiophene rings of the polymer.
On average, then, one unit negative charge
would be distributed over about five thiophene
rings. This might well be possible in a polymer
film or poly(3-alkylthiophene) solution, where
we have shown9
that counterions can access
the charged rings and lower the electrostatic
energy by forming ion pairs with the oppo-
sitely charged site on the polymer. However,
in a system such as the one considered here
the acquisition of one charge per three rings
would correspond to 48 charges spread over
144 thiophene rings and a charge imbalance of
16.5% between the polymer and the 290 ions in
solution.
Because the monolayer starts to break down
at 11% charge excess, such an imbalance would
be fatal to the structure of the monolayer. We
have mentioned the entry of Na+
ions and a
few H2O molecules of hydration into the inter-
face region for monomer/aqueous-electrolyte
systems shown in Figure 7 with the Na+
con-
centration exceeding that of the Cl−
ions. More
details of this event are presented in Figure 8,
which shows the RDF functions between the
S atoms of the thiophene ring and the Na+
ions in part A of the figure and between S
and the water oxygen atoms in part B. Al-
though the penetration of both species into
the interface region occurs, a comparison of
the amplitude of the g(r) scale between parts
A and B of the figure confirms the results
from the atom plots, that the electric field of
the charged polymer attracts the Na+
ions
more strongly than the water atoms, the lat-
ter probably arriving in the interface through
participation in the solvent sheaths of the
Na+
ions.
8. 112 Annals of the New York Academy of Sciences
Figure 9. Phospholipid dipalmitoyl-phosphatidyl
choline (DPPC).
Part 2: Amphiphilic Polymer Ion
Channel
Molecular Model
The transport of ions across a cellular mem-
brane is central to the functioning of a liv-
ing cell. Recognizing the advances being made
in nanoscience, we consider the possibility of
a synthetic channel that conducts ions across
a conventional bilayer membrane consisting
of the amphiphilic phospholipid zwitterion di-
palmitoyl phosphatidyl choline (DPPC), whose
molecular structure is shown in Figure 9. The
polar head group consists of a trimethylammo-
nium cation, a negatively charged phosphate
anion, and two hydrophobic C14 alkyl chain
tails. The artificial transporter is a short length
of a polythiophene derivative that is twisted into
a helical conformation. The resulting rather
rigid channel possesses the electroactive prop-
erty of being capable of maintaining a charge of
either sign. The DPPC phospholipid molecules
were assembled with their alkyl chains perpen-
dicular to a two-dimensional ab plane, defining
a structural cell with periodic boundary con-
ditions in the plane of the membrane. A “ba-
sic” cell contained two DPPC molecules, whose
relative orientations were varied to minimize
packing forces, which occurred when the car-
bon planes of the (four) alkyl chains were almost
parallel. The structural cell was then assembled
into a 4 × 6 supercell, which contained a to-
tal of 96 phospholipid molecules placed end to
end to form a bilayer, leaving a gap of 0.75
A˚ between the closest hydrogen atoms in the
terminal methyl groups in the two monolay-
ers. The two aqueous layers, each of depth
32.3 A˚ , consisting of 4000 water molecules di-
vided equally between the layers, were sepa-
rated by two lengths of phospholipid chain,
each 17.93 A˚ . If we include the tip-to-tip gap
between the alkyl chains, the aqueous regions
were thus separated by distance of 36.5 A˚ . Na+
and Cl−
ions were then created in the aque-
ous layers by replacing water molecules with
ions at regular separations that were consistent
with the required NaCl concentrations, which
were around 0.015 M. Ionic imbalances could
be created by varying the relative sodium and
chloride concentrations in such a way that the
n(Na+
):n(Cl−
) ratio in one layer was precisely
matched by its inverse n(Cl−
):n(Na+
) ratio in
the other to preserve overall charge neutrality.
Ion Transporter Channel
We simulated a substitutional derivative of
an oligothiophene chain, which in Figure 10
is shown in the planar all-anti conformation.
When the entire chain to the right of the inter-
ring bond labeled a is twisted by 175◦
about a,
and the process repeated in turn around each
inter-ring bond to the right along the chain, a
tight helical conformation is generated. The ex-
ternal and internal diameters of the helix are,
respectively, 21.0 and 11.5 A˚ , and the screw
axes have close to 11 thiophene rings per turn.
Such helices of polythiophene and polypyrrole
have been observed in the solid phase and in
solution and have been structurally character-
ized.14
For the helical chain to function as an
ion channel it must span the 35.9-A˚ thickness
of the membrane between the two aqueous lay-
ers. For this purpose an oligothiophene chain
consisting of 94 thiophene rings was simulated.
Also, the chain must be capable of hydrophilic
association with the aqueous layers above and
below the phospholipid membrane as well as
lipophilic association with the membrane bi-
layer itself. For this reason hydrogen atoms in
the thiophene “3” positions on the 11 rings at
each end of the chain are substituted by polar
9. Morton-Blake & Leith: Molecular Dynamics of Ions in a Polymer 113
Figure 10. The terminal portion of the substituted oligothiophene chain showing the polar
(left) and nonpolar (right) rings.
Figure 11. The 94-ring oligothiophene helix ion channel, lateral and axial views (A) and (B). The black,
white, yellow, and red atoms are, respectively, those of carbon, hydrogen, oxygen, and sulfur. (In color in
Annals online.)
hydroxyl groups, and each terminal ring in ad-
dition is “capped” with a carboxylic acid group,
COOH. In this way the “first” and “last” com-
plete turn in the helix, both of which contacted
the aqueous electrolyte layers, were rendered
hydrophilic. The remaining 72 rings of the he-
lix, which were embedded in the membrane’s
nonpolar phospholipid tails, were made hy-
drophobic by substituting in the “3” positions
with methyl groups. The resulting chain is illus-
trated in Figure 11, where the atoms are iden-
tified by the colors in the figure caption and
Figure 12 shows the predynamics extent of the
helix channel bridging the aqueous layers on
both sides of the DPPC membrane. The single
turn of the coil in each layer has been rendered
hydrophilic by the substitution of hydroxyl and
carboxylic groups, whereas the remaining coils,
10. 114 Annals of the New York Academy of Sciences
Figure 12. The polythiophene helix of Figure 11
embedded in a DPPC bilayer and two layers of aque-
ous NaCl solution prior to the MD; (A) side and (B)
axial view. (In color in Annals online.)
which are embedded in the bilayer membrane,
are made hydrophobic by methyl groups.
The bridged membrane structure, relaxed
by the MD, is shown in Figure 13. In part B,
the phospholipid molecules have been removed
to show the helix, which is still anchored to
the aqueous layers and to the membrane by
its hydrophilic and hydrophobic moieties. Al-
though the chain exhibits distortions compared
to Figure 11, their dynamic nature retains a
channel whose diameter averages 6–7 A˚ .
Because the aim is to study the migration of
ions along the transporter channel, we placed
the ions in the two aqueous layers near each
end of the helix channel bridging the layers
to avoid prohibitively long MD run times. Al-
though charge neutrality was preserved by cre-
ating equal numbers of Na+
and Cl−
ions over-
all, a charge imbalance between the aqueous
layers was sometimes created by allowing the
composition of the ion mixture to vary at each
end of the channel.
DPPC molecules have been removed to ex-
pose the oligothiophene helix bridging the two
layers. The helix channel is revealed by the yel-
low sulfur atoms in the thiophene rings. Blue
and green atoms show Na+
and Cl−
ions, re-
spectively, in the aqueous layers.
The migration of the ions was monitored
by RDF functions for which the atom pairs
selected were (Na+
, S) and (Cl−
, S) for, as is
clear from Figure 11, sulfur is a unique atom
species to the interior of the channel. By 105
time steps (100 ps) the ions in the channel have
reached a steady-state concentration and the
rather scattered (because of the paucity of Na+
and Cl−
ions) RDF traces in Figure 14 show the
progress of the three migrating species—Na+
,
Cl−
, and the water molecules—along the chan-
nel. Not surprisingly, because the thiophene
S atom bears partial charges of +0.26e, the
strongest peaks are those for the Cl−
ions, which
show temporary halting sites (or slowdown re-
gions) at roughly evenly spaced intervals of 3.6,
5.2, 7.2, 8.4, and 10.2 A˚ , whereas those for the
Na+
ion are less well defined with a principal
Na+
–S distance of 6 A˚ . The water molecules,
although polar, do not show well-defined asso-
ciations with the channel atoms.
Conclusions
The two structural modifications of polythio-
phene described in this work demonstrate the
wide properties of this electroactive polymer.
We have shown that the amphiphilic properties
of both 3-octyl 3′
-oxanoyl and the derivatized
helical 3-methyl polythiophene species can
be deployed to perform nanoscale activities,
11. Morton-Blake & Leith: Molecular Dynamics of Ions in a Polymer 115
Figure 13. (A) The phospholipid bilayer membrane separates the two aqueous layers
(red O atoms). In (B) DPPC molecules have been removed to expose the oligothiophene
helix bridging the two layers. The helix channel is revealed by the yellow sulfur atoms in the
thiophene rings. Blue and green atoms show Na+
and Cl−
ions, respectively, in the aqueous
layers. (In color in Annals online.)
provided that the excess charge is less than
about 12%. However, the stabilizing effect of
hydrostatic pressure provides hope that even
a charged monolayer film may be preserved.
The charged monolayer formed by the alkyl–
oxanoyl polymer opens up the possibility that
the material might be used in multilayers as
a molecular membrane separating protic and
nonprotic liquid layers such as water and chlo-
roform, which we are currently investigating.
The polymer’s ability to occlude ions from the
layers could confer novel properties on the re-
sulting mono- and multilayer systems.
To our knowledge, the use of the helical poly-
mer to form an ion transporter between two
nanoscale aqueous electrolyte regions as de-
scribed in the second part of the work has not
hitherto been proposed, but a simple channel
Figure 14. RDF traces expressing the associa-
tions of the three migrating species along the poly-
thiophene helix channel. (In color in Annals online.)
of this kind might be a valuable for practical in-
vestigations into the migration of ions, solvent
molecules, and other dissolved species bridging
electrolyte systems.
12. 116 Annals of the New York Academy of Sciences
Acknowledgment
We acknowledge support from Instit´ud um
Theicneola´ıcht Eolais agus Riomhfhorbairt
(IITAC).
Conflicts of Interest
The authors declare no conflicts of interest.
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