H2O2 and NH 2 OH
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Compact Hyperbolic Tetrahedra with Non-Obtuse Dihedral Angles
Compact hyperbolic tetrahedra with non-obtuse dihedral angles Roland K. W. Roeder ∗ January 7, 2006 Abstract Given a combinatorial description C of a polyhedron having E edges, the space of dihedral angles of all compact hyperbolic polyhe- dra that realize C is generally not a convex subset of RE [9]. If C has five or more faces, Andreev’s Theorem states that the correspond- ing space of dihedral angles AC obtained by restricting to non-obtuse angles is a convex polytope. In this paper we explain why Andreev did not consider tetrahedra, the only polyhedra having fewer than five faces, by demonstrating that the space of dihedral angles of com- pact hyperbolic tetrahedra, after restricting to non-obtuse angles, is non-convex. Our proof provides a simple example of the “method of continuity”, the technique used in classification theorems on polyhe- dra by Alexandrow [4], Andreev [5], and Rivin-Hodgson [19]. 2000 Mathematics Subject Classification. 52B10, 52A55, 51M09. Key Words. Hyperbolic geometry, polyhedra, tetrahedra. Given a combinatorial description C of a polyhedron having E edges, the space of dihedral angles of all compact hyperbolic polyhedra that realize C is generally not a convex subset of RE. This is proved in a nice paper by D´ıaz [9]. However, Andreev’s Theorem [5, 13, 14, 20] shows that by restricting to compact hyperbolic polyhedra with non-obtuse dihedral angles, E the space of dihedral angles is a convex polytope, which we label AC R . It is interesting to note that the statement of Andreev’s Theorem requires⊂ ∗rroeder@fields.utoronto.ca 1 that C have five or more faces, ruling out the tetrahedron which is the only polyhedron having fewer than five faces. -
Using Information Theory to Discover Side Chain Rotamer Classes
Pacific Symposium on Biocomputing 4:278-289 (1999) U S I N G I N F O R M A T I O N T H E O R Y T O D I S C O V E R S I D E C H A I N R O T A M E R C L A S S E S : A N A L Y S I S O F T H E E F F E C T S O F L O C A L B A C K B O N E S T R U C T U R E J A C Q U E L Y N S . F E T R O W G E O R G E B E R G Department of Molecular Biology Department of Computer Science The Scripps Research Institute University at Albany, SUNY La Jolla, CA 92037, USA Albany, NY 12222, USA An understanding of the regularities in the side chain conformations of proteins and how these are related to local backbone structures is important for protein modeling and design. Previous work using regular secondary structures and regular divisions of the backbone dihedral angle data has shown that these rotamers are sensitive to the protein’s local backbone conformation. In this preliminary study, we demonstrate a method for combining a more general backbone structure model with an objective clustering algorithm to investigate the effects of backbone structures on side chain rotamer classes and distributions. For the local structure classification, we use the Structural Building Blocks (SBB) categories, which represent all types of secondary structure, including regular structures, capping structures, and loops. -
Isomerism in Organic Compounds
DEPARTMENT OF ORGANIC CHEMISTRY PHARMACEUTICAL FACULTY SEMMELWEIS UNIVERSITY László Szabó − Gábor Krajsovszky ISOMERISM IN ORGANIC COMPOUNDS Budapest 2017 © László Szabó © Gábor Krajsovszky ISBN 978-963-12-9206-0 Publisher: Dr. Gábor Krajsovszky 2 Acknowledgements The Author is thankful to dr. Ruth Deme assistant lecturer for drawing the structural formulas, as well as to Mrs. Zsuzsanna Petró-Karátson for the typewriting of the text part. The Author is thankful to dr. Péter Tétényi for the translation of the manuscript to English language. Dr. Gábor Krajsovszky 3 ISOMERISM IN ORGANIC COMPOUNDS Isomers are the compounds with the same qualitative and quantitative composition of elements, therefore their relative molecular weights and general formulas are identical, but their structures – including in the 3D arrangement – are different. The compounds propyl chloride and propane are not isomers, since their qualitative composition of elements are different. The compounds propane and propene are not isomers, although they are built from the same elements, but with different quanti- tative composition of elements. The compounds propene and cyclohexane are not isomers, although they are built from the same elements, with the same ratio of ele- ments, their relative molecular weights are different. However, the compounds butane and isobutane are isomers, since they have the same general formula, but their 3D arrangement is different. Only one compound or many compounds may have the same general formulas. For example, methane (a linear saturated -
1. Trioxygen Difluoride Reacts with Fluorine to Form A. Dioxygen Trifluoride B
1. Trioxygen difluoride reacts with fluorine to form a. Dioxygen trifluoride b. Dioxygen difluoride c. Oxygen difluoride d. Oxygen & fluorine 2. I2O4 and I2O9 are salt like and a. Are considered as iodine salt b. Are used in table salt c. Are called as iodine – iodates d. None of them 3. Reaction of HClO4 with P2O5 produces a. Chlorine heptaoxide b. Chlorine dioxide c. Dichlorine monoxide d. Chlorine hexaoxide 4. Reaction of bromine vapours with mercuric oxide yields a. Bromine dioxide b. Bromine trioxide c. Bromine monoxide d. All of them 5. Iodine pentaoxide acts as a. An oxidizing agent b. Reducing agent c. Bleaching agent d. Dehydrating agent 6. HClO2 is called a. Hypochlorous acid b. Chlorous acid c. Perchloric acid d. None of them 7. Which compound is used for the quantitative analysis of CO? a. O3F2 b. ClO2 c. Br2O d. I2O5 8. Bleaching powder can be manufactured by a. Hasenclever’s method b. Beckmann’s method c. Both a & b d. None of them 9. Bleaching powder oxidizes NH3 & yields a. Chlorine gas b. Nitrogen gas c. NH4Cl d. None of them 10. Freon is the commercial name of a. fluorochlorcarbons b. Tetrafluoroethylene c. Fluoroethylene d. None of them 11. Halothane is used as a. Disinfectant b. Anaesthetic c. Fungicicle d. Insecticide 12. Which one of the following halides has the highest lattlice energies? a. Iodides b. Chlorides c. Fluorides d. None of them 13. Which one of the following Halogens has the highest oxidizing power? a. F b. Cl c. I d. Br 14. Which one of the following Halogens can oxidize all other halide ions to molecular Halogen? a. -
Chemical Chemical Hazard and Compatibility Information
Chemical Chemical Hazard and Compatibility Information Acetic Acid HAZARDS & STORAGE: Corrosive and combustible liquid. Serious health hazard. Reacts with oxidizing and alkali materials. Keep above freezing point (62 degrees F) to avoid rupture of carboys and glass containers.. INCOMPATIBILITIES: 2-amino-ethanol, Acetaldehyde, Acetic anhydride, Acids, Alcohol, Amines, 2-Amino-ethanol, Ammonia, Ammonium nitrate, 5-Azidotetrazole, Bases, Bromine pentafluoride, Caustics (strong), Chlorosulfonic acid, Chromic Acid, Chromium trioxide, Chlorine trifluoride, Ethylene imine, Ethylene glycol, Ethylene diamine, Hydrogen cyanide, Hydrogen peroxide, Hydrogen sulfide, Hydroxyl compounds, Ketones, Nitric Acid, Oleum, Oxidizers (strong), P(OCN)3, Perchloric acid, Permanganates, Peroxides, Phenols, Phosphorus isocyanate, Phosphorus trichloride, Potassium hydroxide, Potassium permanganate, Potassium-tert-butoxide, Sodium hydroxide, Sodium peroxide, Sulfuric acid, n-Xylene. Acetone HAZARDS & STORAGE: Store in a cool, dry, well ventilated place. INCOMPATIBILITIES: Acids, Bromine trifluoride, Bromine, Bromoform, Carbon, Chloroform, Chromium oxide, Chromium trioxide, Chromyl chloride, Dioxygen difluoride, Fluorine oxide, Hydrogen peroxide, 2-Methyl-1,2-butadiene, NaOBr, Nitric acid, Nitrosyl chloride, Nitrosyl perchlorate, Nitryl perchlorate, NOCl, Oxidizing materials, Permonosulfuric acid, Peroxomonosulfuric acid, Potassium-tert-butoxide, Sulfur dichloride, Sulfuric acid, thio-Diglycol, Thiotrithiazyl perchlorate, Trichloromelamine, 2,4,6-Trichloro-1,3,5-triazine -
Predicting Backbone Cα Angles and Dihedrals from Protein Sequences by Stacked Sparse Auto-Encoder Deep Neural Network
Predicting backbone C# angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network Author Lyons, James, Dehzangi, Abdollah, Heffernan, Rhys, Sharma, Alok, Paliwal, Kuldip, Sattar, Abdul, Zhou, Yaoqi, Yang, Yuedong Published 2014 Journal Title Journal of Computational Chemistry DOI https://doi.org/10.1002/jcc.23718 Copyright Statement © 2014 Wiley Periodicals, Inc.. This is the accepted version of the following article: Predicting backbone Ca angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network Journal of Computational Chemistry, Vol. 35(28), 2014, pp. 2040-2046, which has been published in final form at dx.doi.org/10.1002/jcc.23718. Downloaded from http://hdl.handle.net/10072/64247 Griffith Research Online https://research-repository.griffith.edu.au Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network James Lyonsa, Abdollah Dehzangia,b, Rhys Heffernana, Alok Sharmaa,c, Kuldip Paliwala , Abdul Sattara,b, Yaoqi Zhoud*, Yuedong Yang d* aInstitute for Integrated and Intelligent Systems, Griffith University, Brisbane, Australia bNational ICT Australia (NICTA), Brisbane, Australia cSchool of Engineering and Physics, University of the South Pacific, Private Mail Bag, Laucala Campus, Suva, Fiji dInstitute for Glycomics and School of Information and Communication Technique, Griffith University, Parklands Dr. Southport, QLD 4222, Australia *Corresponding authors ([email protected], [email protected]) ABSTRACT Because a nearly constant distance between two neighbouring Cα atoms, local backbone structure of proteins can be represented accurately by the angle between Cαi-1−Cαi−Cαi+1 (θ) and a dihedral angle rotated about the Cαi−Cαi+1 bond (τ). -
Toroidal Diffusions and Protein Structure Evolution
Toroidal diffusions and protein structure evolution Eduardo García-Portugués1;7, Michael Golden2, Michael Sørensen3, Kanti V. Mardia2;4, Thomas Hamelryck5;6, and Jotun Hein2 Abstract This chapter shows how toroidal diffusions are convenient methodological tools for modelling protein evolution in a probabilistic framework. The chapter addresses the construction of ergodic diffusions with stationary distributions equal to well-known directional distributions, which can be regarded as toroidal analogues of the Ornstein–Uhlenbeck process. The important challenges that arise in the estimation of the diffusion parameters require the consideration of tractable approximate likelihoods and, among the several approaches introduced, the one yielding a spe- cific approximation to the transition density of the wrapped normal process is shown to give the best empirical performance on average. This provides the methodological building block for Evolutionary Torus Dynamic Bayesian Network (ETDBN), a hidden Markov model for protein evolution that emits a wrapped normal process and two continuous-time Markov chains per hid- den state. The chapter describes the main features of ETDBN, which allows for both “smooth” conformational changes and “catastrophic” conformational jumps, and several empirical bench- marks. The insights into the relationship between sequence and structure evolution that ETDBN provides are illustrated in a case study. Keywords: Directional statistics; Evolution; Probabilistic model; Protein structure; Stochastic differential equation; Wrapped -
Functional Behavior of Molecular Baskets and Structure-Activity Studies on Trapping Organophosphorus Nerve Agents in Water
Functional Behavior of Molecular Baskets and Structure-Activity Studies on Trapping Organophosphorus Nerve Agents in Water DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Yian Ruan Graduate Program in Chemistry The Ohio State University 2014 Dissertation Committee: Jovica D. Badjic, Advisor Christopher M. Hadad Jon R. Parquette Copyright by Yian Ruan 2014 Abstract Molecular recognition is exploited by nature to carry out delicately regulated reactions and form precisely organized structures in living organisms. Enzymes promote reactions by preorganizing substrates and stabilizing transition states in an active site via covalent and non-covalent interactions. Receptor proteins and antibodies can respond selectively to stimuli and trigger subsequent activities. These protein-substrate interactions have been great inspirations for chemists in the design of synthetic receptors as hosts and the study of their molecular recognition properties. Investigation of recognition behaviors can help decipher sub-cellular processes. Moreover, some artificial host-guest complexes have found applications in catalysis, sensing, imaging and drug delivery systems. The Badjic group has developed a family of host molecules called molecular baskets to study the effect of gating on molecular recognition. These baskets possess a cavity formed by a benzene base and phthalimide side walls. Pyridine-based gates close the basket via hydrogen bonds or metal chelation. Tuning the electronic and steric characteristics of gates affects the rate of guests entering and departing the basket. ii With all the knowledge about molecular gating, questions arise as to whether these gates can be applied to other platforms and how the mechanism of gating will be affected. -
Material Safety Data Sheet Ethyl Alcohol 200 Proof MSDS
Material Safety Data Sheet Ethyl alcohol 200 Proof MSDS Section 1: Chemical Product and Company Identification Product Name: Ethyl alcohol 200 Proof Contact Information: Catalog Codes: SLE2248, SLE1357 Sciencelab.com, Inc. 14025 Smith Rd. CAS#: 64-17-5 Houston, Texas 77396 US Sales: 1-800-901-7247 RTECS: KQ6300000 International Sales: 1-281-441-4400 TSCA: TSCA 8(b) inventory: Ethyl alcohol 200 Proof Order Online: ScienceLab.com CI#: Not applicable. CHEMTREC (24HR Emergency Telephone), call: 1-800-424-9300 Synonym: Ethanol; Absolute Ethanol; Alcohol; Ethanol 200 proof; Ethyl Alcohol, Anhydrous; Ethanol, undenatured; International CHEMTREC, call: 1-703-527-3887 Dehydrated Alcohol; Alcohol For non-emergency assistance, call: 1-281-441-4400 Chemical Name: Ethyl Alcohol Chemical Formula: CH3CH2OH Section 2: Composition and Information on Ingredients Composition: Name CAS # % by Weight Ethyl alcohol 200 Proof 64-17-5 100 Toxicological Data on Ingredients: Ethyl alcohol 200 Proof: ORAL (LD50): Acute: 7060 mg/kg [Rat]. 3450 mg/kg [Mouse]. VAPOR (LC50): Acute: 20000 ppm 8 hours [Rat]. 39000 mg/m 4 hours [Mouse]. Section 3: Hazards Identification Potential Acute Health Effects: Hazardous in case of skin contact (irritant), of eye contact (irritant), of inhalation. Slightly hazardous in case of skin contact (permeator), of ingestion. Potential Chronic Health Effects: Slightly hazardous in case of skin contact (sensitizer). CARCINOGENIC EFFECTS: A4 (Not classifiable for human or animal.) by ACGIH. MUTAGENIC EFFECTS: Mutagenic for mammalian somatic cells. Mutagenic for bacteria and/or yeast. TERATOGENIC EFFECTS: Classified PROVEN for human. DEVELOPMENTAL TOXICITY: Classified Development toxin [PROVEN]. Classified Reproductive system/toxin/female, Reproductive system/toxin/male [POSSIBLE]. -
Klein 4A Alkanes+Isomerism
Grossman, CHE 230 4a. Alkanes. Conformational Stereoisomerism. Structural Isomerism. 4a.1 Derivatives of methane. We can replace one of the H atoms in methane with another atom or group. These atoms or groups are called heteroatoms. Examples: Methyl bromide, methyl iodide, methanol, methylamine, methanethiol. Here the central C atom is not quite as perfectly tetrahedral, but for our purposes, it is close enough. If the H atom is replaced with nothing, we have three possibilities. – • We can remove just the H nucleus and leave behind two electrons -- this gives CH3 , with sp3 hybridization. It has the same structure as ammonia, just one fewer proton (and neutron) in the nucleus in the center. + • We can take away the H nucleus and both electrons. This gives us CH3 . The hybridization here? We don't want to waste valuable low-energy s orbital in a hybrid orbital in which there are no electrons. Instead, the valuable s electron is divided equally among the six electrons (three bonds) remaining. Three bonds means three orbitals, one s and two p. That means the third p orbital remains unhybridized. This situation is called sp2 hybridization. Two p orbitals occupy a plane, so in sp2 hybridization, the three hybrid orbitals are coplanar. They point 120° apart, to the corners of a triangle. The unhybridized p orbital is perpendicular to this plane. • What if we take away the H nucleus and one electron? We have a situation in which CH3· (methyl radical) is between sp2 and sp3 hybridization. It's a shallow pyramid. These species are high in energy and don't exist for long. -
Nomenclature and Conformations of Alkanes and Cycloalkanes1 on The
Andrew Rosen Chapter 4 - Nomenclature and Conformations of Alkanes and Cycloalkanes1 4.1 - Introduction to Alkanes and Cycloalkanes - Alkanes are hydrocarbons with all carbon-carbon single bonds - Alkenes are hydrocarbons with a carbon-carbon double bond - Alkynes are hydrocarbons with a carbon-carbon triple bond - Cycloalkanes are alkanes in which all or some of the carbon atoms are arranged in a ring - Alkanes have the general formula of CnH2n+2 - Cycloalkanes with a single ring have the formula CnH2n 4.2 - Shapes of Alkanes - An unbranched chain means that each carbon atom is bonded to no more than two other carbon atoms and that there are only primary and secondary carbon atoms 4.3 - IUPAC Nomenclature of Alkanes, Alkyl Halides, and Alcohols - Endings of alkane names end in −ane, and the standard prexes apply to how many carbon atoms there are (meth-, eth-, prop-, but-, pent-, etc.) - An alkyl group has one hydrogen removed from an alkane, and the names have a sux of −yl Rules for naming branched-chain alkanes: 1) Locate the longest continuous chain of carbon atoms. This chain determines the parent (prex) name for the alkane. Always start numbering from the end of a chain 2) Number the longest chain begining with the end of the chain nearer the substitutent 3) Use the numbers obtained by application of Rule 2 to designate the location of the substitutent group 4) When two or more substitutents are present, give each substituent a number corresponding to its location on the longest chain. Name them in alphabetical order 5) When two -
Unit-2 Conformational Isomerism
UNIT-2 CONFORMATIONAL ISOMERISM In chemistry, conformational isomerism is a form of stereoisomerism in which the isomers can be interconverted exclusively by rotations about formally single bonds. Such isomers are generally referred to as conformational isomers or conformers and specifically as rotamers when the rotation leading to different conformations is restricted (hindered) rotation, in the sense that there exists a rotational energy barrier that needs to be overcome to convert one conformer to another. Conformational isomers are thus distinct from the other classes of stereoisomers for which interconversion necessarily involves breaking and reforming of chemical bonds. The rotational barrier, or barrier to rotation, is the activation energy required to interconvert rotamers. Conformers of butane, shown in Newman projection. The two gauche as well as the anti form are staggered conformations Types of conformational isomerism Butane has three rotamers: two gauche conformers, which are enantiomeric and an anti conformer, where the four carbon centres are coplanar. The three eclipsed conformations with dihedral angles of 0°,120° and 240° are not considered to be rotamers, but are instead transition states. Some important examples of conformational isomerism include: 1. Linear alkane conformations with staggered, eclipsed and gauche conformers, and 2. Ring conformation o Cyclohexane conformations with chair and boat conformers. o Carbohydrate conformation 3. Atropisomerism- due to restricted rotation about a bond, a molecule can become chiral 4. Folding of molecules, where some shapes are stable and functional, but others are not. Conformations of Ethane While there are an infinite number of conformations about any sigma bond, in ethane two particular conformers are noteworthy and have special names.