Representation and display of non-standard peptides using semi-systematic ami...NextMove Software
The document discusses representing non-standard peptides and biopolymers using systematic amino acid and monomer naming conventions. It proposes using semi-systematic naming rules to represent peptides and biopolymers containing modified or non-standard subunits in a way that is comprehensible to scientists. The rules include using D-/L- prefixes to represent stereoconfiguration, retaining widely used 3-letter codes, using modifying prefixes to specify substitutions, representing substitutions through line formulae, and specifying default or optional substitution locants. Standardizing the naming conventions could help ensure unambiguous representation of peptides in databases and registration systems.
Peptide line notations for biologics registration and patent filingsNextMove Software
The document discusses challenges in representing biopolymers like peptides for chemical registration systems. It proposes adopting the IUPAC recommendations for peptide naming using 3-letter amino acid codes and condensed systematic nomenclature. Examples show how this approach can uniquely name peptide drugs and address issues with non-standard amino acids in a way that matches terminology used in scientific literature.
Organic Pedagogical Electronic Network
Aryl Fluorination
This document summarizes aryl fluorination, an important reaction for introducing fluorine groups onto aromatic rings. It notes that two of the top 10 grossing drugs, Lipitor and Reserdal, contain aryl fluorines. The mechanism proceeds through oxidation of an aryl group to a high valent metal species, followed by transmetalation and reductive elimination to introduce the fluorine. Examples are given of stoichiometric and catalytic aryl fluorination reactions using Selectfluor and silver oxide catalysts.
This document summarizes research on the binding mechanism of Cu(II) ions to a poly-histidine peptide found in the venom of an African viper. The peptide contains 9 histidine residues and effectively binds copper, forming thermodynamically stable complexes. Experimental techniques like potentiometric titrations, UV-Vis, and EPR spectroscopy as well as molecular dynamics simulations were used to study the copper binding sites and structure of the complexes. The results show that copper prefers binding to histidine residues separated by one amino acid in the peptide and that more stable complexes form when the peptide adopts an alpha-helical structure.
This chapter reviews the oxidation of methionine residues in model peptides. It discusses how neighboring amino acids can influence the oxidation pattern of methionine. For example, when a hydroxyl radical attacks Thr-Met, the neighboring threonine residue is cleaved. It also notes that the oxidation of peptides and proteins is a complex process that depends on the nature of the oxidizing species and the peptide/protein sequence and structure. Oxidation can lead to chain reactions as oxidation products themselves can initiate further oxidation remote from the initial attack site.
The video analyzes the music video for the song "Hero of War" by Rise Against. It follows the protagonist from being recruited by promises of adventure, through his experiences in war where he is depersonalized and forced to commit violent acts against his will, to the end where he regrets his decision to enlist and has been emotionally and psychologically damaged by the war. The video uses close-up shots and footage to connect the lyrics of disillusionment and trauma to the protagonist's emotional state and deterioration over the course of his military experience.
This document provides an agenda for an EWRT 1C class discussing the short stories "After" and "Living" by John Cheever. It includes 5 discussion questions for each story. It also lists 5 discussion questions about the novel "Room" focusing on characters Ma and Jack. The document concludes with 2 additional discussion questions about "Room" and announces the homework assignment is to post a critical reading of a passage from "Room" through the lens of literary theory.
Our Team Based in Indonesia. This is our Second Assignment for Technology Entrepreneurship Venture Lab 2012.
Team Member:
1. Herman Hermawan
2. Ayub Lin
3. Neni Adiningsih
4. Mandy Marahimin
5. Azhari Patria
6. Titus Wiguno
7. Imanul Hakim
8. Rosanny Sihombing
9. Ratno putro
10. M. Dzulfahmi Yahya
Representation and display of non-standard peptides using semi-systematic ami...NextMove Software
The document discusses representing non-standard peptides and biopolymers using systematic amino acid and monomer naming conventions. It proposes using semi-systematic naming rules to represent peptides and biopolymers containing modified or non-standard subunits in a way that is comprehensible to scientists. The rules include using D-/L- prefixes to represent stereoconfiguration, retaining widely used 3-letter codes, using modifying prefixes to specify substitutions, representing substitutions through line formulae, and specifying default or optional substitution locants. Standardizing the naming conventions could help ensure unambiguous representation of peptides in databases and registration systems.
Peptide line notations for biologics registration and patent filingsNextMove Software
The document discusses challenges in representing biopolymers like peptides for chemical registration systems. It proposes adopting the IUPAC recommendations for peptide naming using 3-letter amino acid codes and condensed systematic nomenclature. Examples show how this approach can uniquely name peptide drugs and address issues with non-standard amino acids in a way that matches terminology used in scientific literature.
Organic Pedagogical Electronic Network
Aryl Fluorination
This document summarizes aryl fluorination, an important reaction for introducing fluorine groups onto aromatic rings. It notes that two of the top 10 grossing drugs, Lipitor and Reserdal, contain aryl fluorines. The mechanism proceeds through oxidation of an aryl group to a high valent metal species, followed by transmetalation and reductive elimination to introduce the fluorine. Examples are given of stoichiometric and catalytic aryl fluorination reactions using Selectfluor and silver oxide catalysts.
This document summarizes research on the binding mechanism of Cu(II) ions to a poly-histidine peptide found in the venom of an African viper. The peptide contains 9 histidine residues and effectively binds copper, forming thermodynamically stable complexes. Experimental techniques like potentiometric titrations, UV-Vis, and EPR spectroscopy as well as molecular dynamics simulations were used to study the copper binding sites and structure of the complexes. The results show that copper prefers binding to histidine residues separated by one amino acid in the peptide and that more stable complexes form when the peptide adopts an alpha-helical structure.
This chapter reviews the oxidation of methionine residues in model peptides. It discusses how neighboring amino acids can influence the oxidation pattern of methionine. For example, when a hydroxyl radical attacks Thr-Met, the neighboring threonine residue is cleaved. It also notes that the oxidation of peptides and proteins is a complex process that depends on the nature of the oxidizing species and the peptide/protein sequence and structure. Oxidation can lead to chain reactions as oxidation products themselves can initiate further oxidation remote from the initial attack site.
The video analyzes the music video for the song "Hero of War" by Rise Against. It follows the protagonist from being recruited by promises of adventure, through his experiences in war where he is depersonalized and forced to commit violent acts against his will, to the end where he regrets his decision to enlist and has been emotionally and psychologically damaged by the war. The video uses close-up shots and footage to connect the lyrics of disillusionment and trauma to the protagonist's emotional state and deterioration over the course of his military experience.
This document provides an agenda for an EWRT 1C class discussing the short stories "After" and "Living" by John Cheever. It includes 5 discussion questions for each story. It also lists 5 discussion questions about the novel "Room" focusing on characters Ma and Jack. The document concludes with 2 additional discussion questions about "Room" and announces the homework assignment is to post a critical reading of a passage from "Room" through the lens of literary theory.
Our Team Based in Indonesia. This is our Second Assignment for Technology Entrepreneurship Venture Lab 2012.
Team Member:
1. Herman Hermawan
2. Ayub Lin
3. Neni Adiningsih
4. Mandy Marahimin
5. Azhari Patria
6. Titus Wiguno
7. Imanul Hakim
8. Rosanny Sihombing
9. Ratno putro
10. M. Dzulfahmi Yahya
Deciphering reaction mechanism with intermediate trappingDaniel Morton
This module provides an overview of a tool used to gain information on a reaction mechanism; reactive intermediate trapping.
A reactive intermediate is a short-lived, high-energy, highly reactive molecule. When generated in a chemical reaction, it will quickly convert into a more stable molecule. When their existence is indicated, reactive intermediates can help explain how a chemical reaction takes place.
Contributed by:
Shuangyu Ma & Yiling Bi (Undergraduate Students)
University of Utah
2014
New insights into the metabolic network of Methylobacterium extorquens AM1Greg Crowther
1. The document summarizes new insights into the metabolic pathways of the methylotrophic bacterium Methylobacterium extorquens AM1.
2. It was previously thought that the direct assimilation pathway dominated metabolism, but new evidence shows that flux through this pathway is insignificant and the long pathway is responsible for all carbon assimilation.
3. Formate dehydrogenase, which was thought to be unnecessary, plays a key role as there are actually four formate dehydrogenase enzymes essential for growth on methanol.
Introduction,Components, and Structure of DNA and RNAAnn Rogon
DNA and RNA are nucleic acids that carry genetic information. DNA usually exists as a double-stranded helix containing deoxyribose, phosphate groups, and four nitrogenous bases (adenine, guanine, cytosine, thymine). RNA is single-stranded and can exist in various structures performing different roles like mRNA, tRNA, rRNA. Both DNA and RNA are made up of nucleotides, which contain a nitrogenous base, a pentose sugar (deoxyribose in DNA and ribose in RNA), and one or more phosphate groups. The base pairs in DNA (adenine-thymine, cytosine-guanine) hold the two strands of the double helix together through hydrogen bonding.
Engineering Self-Assembling Peptides to Tune the Coordination Environment of Metalloporphyrins
The document discusses how self-assembling peptides can be designed to control the coordination environment of bound metalloporphyrins and tune their properties. Three peptides were designed with different metal-binding sites: one with a single histidine, one with two histidines, and one with a histidine and methionine. Spectroscopic analysis showed the single histidine and double histidine peptides bound heme in a low-spin state while the histidine-methionine peptide bound it in a high-spin state. Furthermore, the double histidine peptide could reversibly bind oxygen like natural proteins.
Experiment #6 Pre-Case StudyAddress these questions in your es.docxSANSKAR20
Experiment #6 Pre-Case Study
Address these questions in your essay:
1.) Is base-catalyzed racemization the most favorable acid-base reaction for natural amino acids? Determine the most acidic H atom in compound 1 and L-alanine. Are they the same?
2.) The theory relies on crystallization. Are there large solid deposits of amino acids in nature? Are amino acids more or less soluble in water than compound 1? Are crystals of one enantiomer more favorable than crystals of a racemic mixture? (see Klein pg 226-227)
Discuss whether or not you believe the results of this experiment. Do you think this experiment applies to natural amino acids in a prebiotic environment?
Essay Requirements:
1. Minimum of 1-page, double spaced. Maximum of 3 pages (including references).
2. I recommend these search engines for finding relevant chemistry literature:
· Scholar.google.com
· Scifinder (make a login with your UCR email using this link)
3. Provide at least *TWO* citations in Journal of the American Chemical Society format, NOT including the Noorudin paper. At least one citation must be from the scientific literature, the other may be from a religious text, but you must cite a specific chapter and verse.
4. Your essay must include a References Section at the end. You will mark your citations in your essay text by having a superscript number at the end of the sentence, like this.1 Each subsequent citation will also get a number, like here.2 This way, I know where that statement, fact, etc originated from. This is how we cite stuff in science. If you chose a religious text, you will still follow this format. Here I am citing a biblical line about jewelry.3
References
(1) Scepaniak, J. J.; Young, J. A.; Bontchev, R. P.; Smith, J. M. Angew. Chem. Int. Ed. Engl.2009, 48 (17), 3158–3160.
(2) Harman, W. H.; Lin, T.-P.; Peters, J. C. Angew. Chem. Int. Ed. Engl.2014, 53 (4), 1081–1086.
(3) King James Bible, Ezekiel 16:17.
The general format for citations is this:
Author, First; Author, Second. “Article Title (optional)” Abbreviated Journal Name. year, volume, pages.
Refer to this link for more citation details, if needed:
http://libguides.williams.edu/citing/acs
Page 1“Chirality and the Origins of Life” by Young and Hooley
by
Michael C. Young and Richard J. Hooley
Department of Chemistry
University of California, Riverside
NATIONAL CENTER FOR CASE STUDY TEACHING IN SCIENCE
Before Class
1. Read the case scenario provided below.
2. In addition, read the following in advance of class:
a. Noorduin, et al. “Emergence of a Single Solid Chiral State from a Nearly Racemic Amino Acid Derivative.”
J. Am. Chem. Soc. 2008, 130, 1158–1159.
b. Chapter 5 and section 26.1 (“Stereochemistry,” pages143–173 and “Amino Acid Structures,” pages 1045–
1049) of your assigned organic chemistry textbook (McMurry, 8th edition).
c. Th e defi nition of “Ostwald ripening” (from Wikipedia; attached to the end of this worksheet).
3. Answer the pre-case question and be p ...
The document discusses the interpretation of proton nuclear magnetic resonance (NMR) spectroscopy. It explains how NMR works and the information that can be obtained from NMR spectra, including the number of signals indicating different types of hydrogen atoms, peak integration revealing hydrogen ratios, and chemical shifts indicating electronic environments. It also covers spin-spin splitting patterns from neighboring hydrogen atoms. The document uses examples to illustrate concepts like chemically equivalent and non-equivalent protons, diastereotopic and enantiotopic protons, and interpretation of peak area, chemical shifts, and spin-spin splitting. It concludes that NMR spectroscopy is a useful qualitative tool for structural elucidation in pharmaceutical, chemical, and fertilizer industries.
This document discusses different approaches to assessing chemical similarity, including philosophers' and chemists' views, structural similarity using substructures and fingerprints, 3D similarity using fields and shapes, physicochemical properties, quantum chemistry methods, and quantified similarity using numerical representations and comparisons. It notes that while similar structures often have similar activities, there are also many exceptions, and similarity needs to be defined with respect to a particular endpoint.
This document describes the synthesis and characterization of beta-hydroxy-serotonin (β-OH-5-HT), a derivative of the neurotransmitter serotonin. β-OH-5-HT was successfully synthesized from serotonin using the enzyme tryptophan side chain oxidase type I (TSOI) from Pseudomonas. Structural analysis using NMR and mass spectrometry confirmed the identity of β-OH-5-HT. Interestingly, β-OH-5-HT was found to readily racemize and react with nucleophiles like alcohols and thiols, which is unusual behavior that has not been observed for related compounds. The rapid racemization mechanism of β-OH-5-HT
Quantum Mechanical Calculations on Novel Actinide Chelatin.docxamrit47
Quantum Mechanical Calculations on Novel Actinide Chelating Agents
Aisha Mehmood, Maria Benavides, PhD
Department of Natural Sciences
www.uhd.edu/academic/colleges/sciences/ns/
Abstract: Plutonium is produced in significant amounts as the isotope 239Pu during nuclear reactor operations. The use of actinides such as Pu in energy and weapons production has resulted in major environmental and health concerns. In the event of actinide release it is critical to have the means to treat large number of people in a very short time. Chelation therapy is the approach currently used to treat actinide poisoning because it reduces the deposition of actinides in the internal organs. In order to effectively respond and treat actinide poisoning on a massive scale it is crucial to have access to effective, nontoxic chelating agents that can be orally administered, that are easily produced and safely stored at any location. Specific sequestering agents have been designed and synthesized to bind actinides. Our study focuses on determining the structures and molecular properties of four hydroxypyridinone (HOPO)-based sequestering agents 2,2-Dime-3LI(1,2-HOPO), 3LI-(1,2-HOPO), 4LI(1,2-HOPO) and 5LI(1,2-HOPO) which have been shown to strongly and specifically bind plutonium at physiological pH. Our calculations were carried out using density functional theory (DFT) with the B3LYP functional applied in conjunction with three increasingly larger basis sets (3-21G, 6-31G, and 6-311G) to obtain the equilibrium geometries, vibrational frequencies, and IR spectra for all four ligands. The highest occupied molecular orbital (HOMO) – lowest occupied molecular orbital (LUMO) energy gap values for all four compounds are greater than 4 eV suggesting that the ligands are chemically stable. Two hydrogen bonds are observed in each compound which we suspect contribute to their chemical stability. The four compounds exhibit dipole moments ranging between 3 to 4 Debye which indicates they possess polar character. Our computed vibrational frequencies were found in excellent agreement with the experimental frequencies, suggesting our proposed models are good representations of the actual molecular structures.
Introduction: Over the past years concern for harm caused by radiation in human body has increased. Recent disaster such as Fukushima Daiichi nuclear reactor accident in Japan has raised red flags for radiation safety. Such events are not common; however once the damage has happened, it is large and capable of destroying many lives. Nuclear fissions release significant amount of several different actinides that can enter human body through radiation or radioactive substances. All actinides are radioactive and bind with human internal tissue. Chelation therapy has shown positive results for reducing internal human actinide contamination. Plutonium (Pu) is an alpha emitter that is known to have the greatest retention in the human body among actinides. Our studies focuses ...
Chemistry Notes on Amino acids class 12.pdfHello406957
1. Amino acids are organic compounds that contain amino and carboxyl groups and form proteins through peptide bonds. There are essential and non-essential amino acids.
2. In aqueous solutions, amino acids exist as zwitterions with both positive and negative charges which allows them to react as both acids and bases.
1) The document provides revision materials for organic chemistry concepts like nomenclature, functional groups, and molecular structure and stability for students who feel lost or confused.
2) It explains IUPAC naming rules and gives examples of naming simple organic compounds. Common names are also mentioned.
3) Bond polarity is discussed, noting that most carbon-heteroatom bonds are polarized due to the higher electronegativity of heteroatoms like oxygen, nitrogen, and halogens. Bond dipoles are illustrated for several examples.
This document describes a study that used bioinformatics tools to model the 3D structure of the Hc-Stp1 protein from the parasite Haemonchus contortus. The researchers first identified a homologous protein, Tv-Stp1 from Trichostrongylus vitrinus, to use as a template. They then generated a multiple sequence alignment of Hc-Stp1 and the template protein 3e7a. Secondary structure was predicted using PSIPRED and a homology model of the Hc-Stp1 structure was created using MODELLER. The model was analyzed using Ramachandran plots which showed 3 outliers requiring further investigation before the model could be used as a drug target
The document discusses genome organization in eukaryotes. It describes how DNA is highly condensed and packaged within the nucleus through different levels of organization, from nucleosomes to 30nm fibers and higher-order structures. DNA is wrapped around histone proteins to form nucleosomes, which further condense into 30nm fibers. These fibers compact to form loops, domains, and chromosome territories within the nucleus. The precise structures at higher levels of organization are still being elucidated. Precise packaging is necessary to condense the large eukaryotic genome while allowing access for processes like transcription and replication.
This document discusses a method for predicting stereochemical reaction paths using orbital interactions between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of reacting species. The method involves identifying the HOMO and LUMO regions of the reacting molecules and determining which orientation leads to maximum overlap between the HOMO of one species and LUMO of the other. Several examples of intramolecular reactions are analyzed using this approach. The method is presented as a simple and practical way to interpret and predict favorable reaction stereochemistry.
The halo(gen) effect in para substituted phenyl rings - EuroCup2015Jonas Boström
One key to successfully progress a drug discovery project is to make first-rate decisions (hopefully) based on unambiguous data. This is not trivial since our scientific problems are often very complex and data can be fuzzy. In drug design we try to approach this uncertainty by being rational. It is however sometimes forgotten that our rational approaches may not be that rational after all – decisions may well be based on personal preferences and intuitive biases.... perhaps unconsciously made on biased data
Molecular recognition is the specific interaction between two or more complementary molecules through noncovalent bonding such as hydrogen bonding, metal coordination, hydrophobic forces, etc. This process is crucial in biological systems and modern chemical research. Molecular recognition can be static, involving a 1:1 complex between a host and guest molecule, or dynamic, where binding of the first guest induces a conformational change affecting binding of a second guest. Molecular recognition is important in fields like supramolecular chemistry, self-assembly, and host-guest chemistry. It has applications in areas like sensing, molecular motors, and enzyme mimicry.
Nucleic acids like DNA and RNA contain the genetic information of living organisms. DNA specifically stores and carries genetic information in the form of genes. It has a double helix structure with two strands coiled around each other. Each strand is made up of repeating nucleotide units containing a phosphate, sugar (deoxyribose in DNA), and one of four nitrogenous bases (A, T, C, G). The bases on each strand bond with each other through hydrogen bonds - A pairs with T and C pairs with G. This discovery of DNA's double helix structure was made in 1953 by James Watson and Francis Crick based on experimental evidence from scientists like Rosalind Franklin, Maurice Wilkins, and Erwin Charg
This presentation has been moved. To view this presentation, please visit http://pubs.acs.org/iapps/liveslides/pages/index.htm?mscNo=jz300841u
Determination of Excited-State Energies and Dynamics in the B Band of the Bacterial Reaction Center with 2D Electronic Spectroscopy
This presentation has been moved. To view this presentation, please visit http://pubs.acs.org/iapps/liveslides/pages/index.htm?mscNo=jz3008408
Ultrafast Studies of the Photophysics of Cis and Trans States of the Green Fluorescent Protein Chromophore
This presentation has been moved. To view this presentation, please visit http://pubs.acs.org/iapps/liveslides/pages/index.htm?mscNo=jz300960b
Fast Synthesis of Thiolated Au25 Nanoclusters via ProtectionDeprotection Method
Deciphering reaction mechanism with intermediate trappingDaniel Morton
This module provides an overview of a tool used to gain information on a reaction mechanism; reactive intermediate trapping.
A reactive intermediate is a short-lived, high-energy, highly reactive molecule. When generated in a chemical reaction, it will quickly convert into a more stable molecule. When their existence is indicated, reactive intermediates can help explain how a chemical reaction takes place.
Contributed by:
Shuangyu Ma & Yiling Bi (Undergraduate Students)
University of Utah
2014
New insights into the metabolic network of Methylobacterium extorquens AM1Greg Crowther
1. The document summarizes new insights into the metabolic pathways of the methylotrophic bacterium Methylobacterium extorquens AM1.
2. It was previously thought that the direct assimilation pathway dominated metabolism, but new evidence shows that flux through this pathway is insignificant and the long pathway is responsible for all carbon assimilation.
3. Formate dehydrogenase, which was thought to be unnecessary, plays a key role as there are actually four formate dehydrogenase enzymes essential for growth on methanol.
Introduction,Components, and Structure of DNA and RNAAnn Rogon
DNA and RNA are nucleic acids that carry genetic information. DNA usually exists as a double-stranded helix containing deoxyribose, phosphate groups, and four nitrogenous bases (adenine, guanine, cytosine, thymine). RNA is single-stranded and can exist in various structures performing different roles like mRNA, tRNA, rRNA. Both DNA and RNA are made up of nucleotides, which contain a nitrogenous base, a pentose sugar (deoxyribose in DNA and ribose in RNA), and one or more phosphate groups. The base pairs in DNA (adenine-thymine, cytosine-guanine) hold the two strands of the double helix together through hydrogen bonding.
Engineering Self-Assembling Peptides to Tune the Coordination Environment of Metalloporphyrins
The document discusses how self-assembling peptides can be designed to control the coordination environment of bound metalloporphyrins and tune their properties. Three peptides were designed with different metal-binding sites: one with a single histidine, one with two histidines, and one with a histidine and methionine. Spectroscopic analysis showed the single histidine and double histidine peptides bound heme in a low-spin state while the histidine-methionine peptide bound it in a high-spin state. Furthermore, the double histidine peptide could reversibly bind oxygen like natural proteins.
Experiment #6 Pre-Case StudyAddress these questions in your es.docxSANSKAR20
Experiment #6 Pre-Case Study
Address these questions in your essay:
1.) Is base-catalyzed racemization the most favorable acid-base reaction for natural amino acids? Determine the most acidic H atom in compound 1 and L-alanine. Are they the same?
2.) The theory relies on crystallization. Are there large solid deposits of amino acids in nature? Are amino acids more or less soluble in water than compound 1? Are crystals of one enantiomer more favorable than crystals of a racemic mixture? (see Klein pg 226-227)
Discuss whether or not you believe the results of this experiment. Do you think this experiment applies to natural amino acids in a prebiotic environment?
Essay Requirements:
1. Minimum of 1-page, double spaced. Maximum of 3 pages (including references).
2. I recommend these search engines for finding relevant chemistry literature:
· Scholar.google.com
· Scifinder (make a login with your UCR email using this link)
3. Provide at least *TWO* citations in Journal of the American Chemical Society format, NOT including the Noorudin paper. At least one citation must be from the scientific literature, the other may be from a religious text, but you must cite a specific chapter and verse.
4. Your essay must include a References Section at the end. You will mark your citations in your essay text by having a superscript number at the end of the sentence, like this.1 Each subsequent citation will also get a number, like here.2 This way, I know where that statement, fact, etc originated from. This is how we cite stuff in science. If you chose a religious text, you will still follow this format. Here I am citing a biblical line about jewelry.3
References
(1) Scepaniak, J. J.; Young, J. A.; Bontchev, R. P.; Smith, J. M. Angew. Chem. Int. Ed. Engl.2009, 48 (17), 3158–3160.
(2) Harman, W. H.; Lin, T.-P.; Peters, J. C. Angew. Chem. Int. Ed. Engl.2014, 53 (4), 1081–1086.
(3) King James Bible, Ezekiel 16:17.
The general format for citations is this:
Author, First; Author, Second. “Article Title (optional)” Abbreviated Journal Name. year, volume, pages.
Refer to this link for more citation details, if needed:
http://libguides.williams.edu/citing/acs
Page 1“Chirality and the Origins of Life” by Young and Hooley
by
Michael C. Young and Richard J. Hooley
Department of Chemistry
University of California, Riverside
NATIONAL CENTER FOR CASE STUDY TEACHING IN SCIENCE
Before Class
1. Read the case scenario provided below.
2. In addition, read the following in advance of class:
a. Noorduin, et al. “Emergence of a Single Solid Chiral State from a Nearly Racemic Amino Acid Derivative.”
J. Am. Chem. Soc. 2008, 130, 1158–1159.
b. Chapter 5 and section 26.1 (“Stereochemistry,” pages143–173 and “Amino Acid Structures,” pages 1045–
1049) of your assigned organic chemistry textbook (McMurry, 8th edition).
c. Th e defi nition of “Ostwald ripening” (from Wikipedia; attached to the end of this worksheet).
3. Answer the pre-case question and be p ...
The document discusses the interpretation of proton nuclear magnetic resonance (NMR) spectroscopy. It explains how NMR works and the information that can be obtained from NMR spectra, including the number of signals indicating different types of hydrogen atoms, peak integration revealing hydrogen ratios, and chemical shifts indicating electronic environments. It also covers spin-spin splitting patterns from neighboring hydrogen atoms. The document uses examples to illustrate concepts like chemically equivalent and non-equivalent protons, diastereotopic and enantiotopic protons, and interpretation of peak area, chemical shifts, and spin-spin splitting. It concludes that NMR spectroscopy is a useful qualitative tool for structural elucidation in pharmaceutical, chemical, and fertilizer industries.
This document discusses different approaches to assessing chemical similarity, including philosophers' and chemists' views, structural similarity using substructures and fingerprints, 3D similarity using fields and shapes, physicochemical properties, quantum chemistry methods, and quantified similarity using numerical representations and comparisons. It notes that while similar structures often have similar activities, there are also many exceptions, and similarity needs to be defined with respect to a particular endpoint.
This document describes the synthesis and characterization of beta-hydroxy-serotonin (β-OH-5-HT), a derivative of the neurotransmitter serotonin. β-OH-5-HT was successfully synthesized from serotonin using the enzyme tryptophan side chain oxidase type I (TSOI) from Pseudomonas. Structural analysis using NMR and mass spectrometry confirmed the identity of β-OH-5-HT. Interestingly, β-OH-5-HT was found to readily racemize and react with nucleophiles like alcohols and thiols, which is unusual behavior that has not been observed for related compounds. The rapid racemization mechanism of β-OH-5-HT
Quantum Mechanical Calculations on Novel Actinide Chelatin.docxamrit47
Quantum Mechanical Calculations on Novel Actinide Chelating Agents
Aisha Mehmood, Maria Benavides, PhD
Department of Natural Sciences
www.uhd.edu/academic/colleges/sciences/ns/
Abstract: Plutonium is produced in significant amounts as the isotope 239Pu during nuclear reactor operations. The use of actinides such as Pu in energy and weapons production has resulted in major environmental and health concerns. In the event of actinide release it is critical to have the means to treat large number of people in a very short time. Chelation therapy is the approach currently used to treat actinide poisoning because it reduces the deposition of actinides in the internal organs. In order to effectively respond and treat actinide poisoning on a massive scale it is crucial to have access to effective, nontoxic chelating agents that can be orally administered, that are easily produced and safely stored at any location. Specific sequestering agents have been designed and synthesized to bind actinides. Our study focuses on determining the structures and molecular properties of four hydroxypyridinone (HOPO)-based sequestering agents 2,2-Dime-3LI(1,2-HOPO), 3LI-(1,2-HOPO), 4LI(1,2-HOPO) and 5LI(1,2-HOPO) which have been shown to strongly and specifically bind plutonium at physiological pH. Our calculations were carried out using density functional theory (DFT) with the B3LYP functional applied in conjunction with three increasingly larger basis sets (3-21G, 6-31G, and 6-311G) to obtain the equilibrium geometries, vibrational frequencies, and IR spectra for all four ligands. The highest occupied molecular orbital (HOMO) – lowest occupied molecular orbital (LUMO) energy gap values for all four compounds are greater than 4 eV suggesting that the ligands are chemically stable. Two hydrogen bonds are observed in each compound which we suspect contribute to their chemical stability. The four compounds exhibit dipole moments ranging between 3 to 4 Debye which indicates they possess polar character. Our computed vibrational frequencies were found in excellent agreement with the experimental frequencies, suggesting our proposed models are good representations of the actual molecular structures.
Introduction: Over the past years concern for harm caused by radiation in human body has increased. Recent disaster such as Fukushima Daiichi nuclear reactor accident in Japan has raised red flags for radiation safety. Such events are not common; however once the damage has happened, it is large and capable of destroying many lives. Nuclear fissions release significant amount of several different actinides that can enter human body through radiation or radioactive substances. All actinides are radioactive and bind with human internal tissue. Chelation therapy has shown positive results for reducing internal human actinide contamination. Plutonium (Pu) is an alpha emitter that is known to have the greatest retention in the human body among actinides. Our studies focuses ...
Chemistry Notes on Amino acids class 12.pdfHello406957
1. Amino acids are organic compounds that contain amino and carboxyl groups and form proteins through peptide bonds. There are essential and non-essential amino acids.
2. In aqueous solutions, amino acids exist as zwitterions with both positive and negative charges which allows them to react as both acids and bases.
1) The document provides revision materials for organic chemistry concepts like nomenclature, functional groups, and molecular structure and stability for students who feel lost or confused.
2) It explains IUPAC naming rules and gives examples of naming simple organic compounds. Common names are also mentioned.
3) Bond polarity is discussed, noting that most carbon-heteroatom bonds are polarized due to the higher electronegativity of heteroatoms like oxygen, nitrogen, and halogens. Bond dipoles are illustrated for several examples.
This document describes a study that used bioinformatics tools to model the 3D structure of the Hc-Stp1 protein from the parasite Haemonchus contortus. The researchers first identified a homologous protein, Tv-Stp1 from Trichostrongylus vitrinus, to use as a template. They then generated a multiple sequence alignment of Hc-Stp1 and the template protein 3e7a. Secondary structure was predicted using PSIPRED and a homology model of the Hc-Stp1 structure was created using MODELLER. The model was analyzed using Ramachandran plots which showed 3 outliers requiring further investigation before the model could be used as a drug target
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One key to successfully progress a drug discovery project is to make first-rate decisions (hopefully) based on unambiguous data. This is not trivial since our scientific problems are often very complex and data can be fuzzy. In drug design we try to approach this uncertainty by being rational. It is however sometimes forgotten that our rational approaches may not be that rational after all – decisions may well be based on personal preferences and intuitive biases.... perhaps unconsciously made on biased data
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JPCL jz300207k Himansu Presentation
1. The Strength of NH---S Hydrogen Bonds
in Methionine Residues Revealed by Gas
Phase IR/UV Spectroscopy
Himansu S. Biswal*#†, Eric Gloaguen#, Yohan
Loquais#, Benjamin Tardivel# and Michel Mons*#
# CEA, Laboratoire Francis
Perrin, DSM/IRAMIS/SPAM, Bât 522, 91191 Gif-sur-
Yvette, France
# CNRS, Laboratoire Francis Perrin, URA 2453, 91191
Gif-sur-Yvette, France.
† National Institute of Science Education and Research,
Sachivalaya Marg, Bhubaneswar - 751 005, India.
J. Phys. Chem. Lett. 2012, 3, 755 -759 1
2. Motivation
Studies on intermolecular complexes suggest “sulfur” is a potential H-
bond acceptor as “Oxygen”.1
The intramolecular H-bonds frequently observed in proteins such as
Namide-H···S hydrogen bonds linking the sulfur atom of methionine to
backbone NamideH groups has not yet been received much attention.
Open Question
How strong is the Namide-H···S H-bond?
Does it compete with other intramolecular H-bonds found in peptides
and proteins?
How does it control the peptide structure and conformational space?
1Biswal,H. S. et al. J. Phys. Chem. A, 2009, 113, 12763; ibid, 2010, 114, 5497; J. Chem. Phys.
2011, 135, 134306.
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3. Model Peptide and H-bond Pattern
O H O
N H
H3C N N
H
H O
S
H3C
Ac-Phe-Met-NH2 (FM)
CH3
S
O H O
N H
H3C N N
H
H O
Ac-Met-Phe-NH2 (MF)
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4. Experimental Strategy
Pulsed valve
• Laser desorption: hot species in the
gas phase
• Cooling in the supersonic expansion :
Sample molecules are trapped in one or more
(Peptide + graphite) conformations
Vacuum chamber
• Recognition of H-bond network by
IR and UV spectroscopy
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5. IR Spectra and Structure Assignment
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6. Evidence of strong NH---S H-Bonds
The „sulfur‟ atom of Methionine forms both intra and
inter-residue N-H---S H-bond.
intra-residue It is observed from Protein Data Bank 24% Methionine
residues displays such local folding pattern.
inter-residue
Stabilization Energy = 10 kJ/mol
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7. Comparison with Protein Structures
Protein with
-Met - Phe – Sequence
… comparable with
isolated structure
Ramachandran Angles
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8. Conclusions
The sulfur atom of methionine is found to be an H-bond Authors
acceptor as strong as the oxygen atom of backbone
carbonyl groups, despite its less electronegativity
(generally considered as a weaker H-bond acceptor).
The close similarity of local folding of the model
dipeptides and those of proteins suggest that the strong
N-H•••S H-bonds acting in dipeptides also occur in Himansu S. Biswal Eric Gloaguen
proteins. This observation also suggests that they take
part in the local shaping of the protein chain, like the
classical N-H•••O interactions, and illustrates the
relevance of such gas phase data to biochemical issues.
The concept of „Sulfur Center Hydrogen Bonds‟
(SCHBs) needs a proper attention while designing new
generation force field for protein structure simulation. Michel Mons
Acknowledgments
This work was financially supported by the French
National Research Agency (ANR) (Grant ANR-08-BLAN-
0158-01) and the “Triangle de la Physique” Foundation
(Grant 2008-053T-SERPBIO).
Yohan Loquais Benjamin Tardivel
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