DOCSLIB.ORG

Electron Paramagnetic Resonance

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Electron Paramagnetic Resonance Ecole Polytechnique Fédérale de Lausanne Section de Physique Travaux Pratiques III Electron Paramagnetic Resonance Responsable : Dr. Arnaud Magrez Superviseur : Felix Blumenschein Lausanne, 6 juin 2017 TP III Electron Paramagnetic Resonance 1 Introduction This TP III experiment is about electron spin resonance (ESR) spectroscopy, in english more often called electron paramagnetic resonance (EPR) and in french résonance param- agnétique électronique (RPE). In EPR spectroscopy we measure the energy differences between the discrete energy states of quasi-free electrons in form of free radicals and paramagnetic centres by measuring their absorption of electro-magnetic radiation. In our present set-up a continuous wave EPR set- up is used. By modulating the magnetic field in combination with the continuous electro- magnetic (EM) microwave (MW) field one can gain insight into the molecular structure, chemical configuration and dynamics of the studied substrate. EPR spectroscopy is used for the detection of free radicals and paramagnetic centres in biology, chemistry and physics. In medicine the application of ESR is rather difficult, as radicals are reactive. 2 Basic ESR theory 1 Electrons have a spin quantum number of s = 2 and corresponding magnetic moment 1 of ms = ± 2 . Without an external field, the spin-orientation is randomly distributed. However, in the presence of an external magnetic field of strength B0, the spin orientates 1 1 itself parallel (− 2 ) or antiparallel ( 2 ) to B0 with corresponding energy E = msgeµBB0, with the Landé g-factor (ge = 2.0023 for free electrons) and the Bohr magneton µB = e¯h = 9.2740 × 10−24 J=T 2me . This splitting of the Energy within an external magnetic field is called Zeeman-Effect and leads to a separation of ∆E = geµBB0 (1) between the lower and upper energy state for free electrons, which is directly linear pro- portional to B0, as depicted in figure 1. According to Planck’s law, a free electron can be transferred between the two levels by emission or absorption of an photon of frequency v and energy ∆E = hv. This leads to the fundamental equation of EPR spectroscopy, the resonance condition hv = geµBB0. (2) ms = +1=2 j"i ∆E = E+1=2 − E−1=2 Energy ms = −1=2 j#i B0 = 0 B0 6= 0 Figure 1: Splitting of the electron spin state in an external magnetic field, Zeeman effect. 1 TP III Electron Paramagnetic Resonance Most of the standard EPR experiments happen in the MW range of 9 GHz to 10 GHz (≈ 33 mm to 30 mm). Regarding the resonance condition, this corresponds to fields of around 0.35 T. In most EPR experiments, the MW frequency is kept constant and the magnetic field is increased between an interval (sweeping) around the expected signal (continuous wave, "CW" EPR). Reaching the resonance condition, the gap-energy ∆E(B0) matches the MW energy hv and the electrons can transit between the two spin states. The Maxwell- Boltzmann distribution predicts a higher population of the lower energy state nlower than the upper energy state nupper, which leads to more absorption than emission: nupper Eupper − Elower ∆E hv = exp − = exp − = exp − , (3) nlower kBT kBT kBT −23 with the Boltzmann constant kB = 1.3806 × 10 J=T. This net resonant absorption due to spin-flip is what we observe in EPR-spectroscopy. An example EPR scan for DPPH is shown in figure 2 on the right in blue, as absorption signal over the swept external magnetic field B0. The basic set-up consists of an electro-magnet for B0 and a MW generator. The MW are guided through wave-guides (metallic, hollow tubes), which allow only single modes. To optimise the EPR absorption, a resonator (cavity) is used. The MW are guided into the resonator where they are reflected from the walls, forming a standing wave. The MW reflected out of the cavity is detected with e.g. a shottky-diode. The dimensions of the cavity therefore have to be adjusted, such that at a certain MW frequency no signal is reflected out of the chamber anymore. Figure 3 shows the reflected signal of the cavity for a frequency sweep. The resonance frequency, where no MW is reflected out of the chamber anymore is visible as the dip in that scan. The adjustment process to find this resonance frequency of the cavity is called matching and tuning. For the EPR spectrum of a sample in the matched and tuned cavity, the MW frequency is kept constant, while B0 is swept. The sample absorbs MW energy at the field corresponding to the resonance condition (eq. 2), B0,res.(hv). The absorption changes the cavity impedance and therefore the coupling condition of the cavity. As the cavity at B0,res.(hv) is now no longer critically coupled, MW is reflected out of the cavity. However, this absorption induced reflection-signal is very small. Therefore, we measure the derivative signal with a Lock-In detector by additional B-field variation coils which induce a sinusoidal field parallel to B0. This corresponds to the red signal on the left in figure 2. Figure 2: EPR spectroscopy signal of DPPH, taken with the MS400. Shown is the absorption signal over the swept external magnetic field B0, on the left as direct Lock-In derivative absorption signal in red and on the right the integrated absorption signal in blue. 2 TP III Electron Paramagnetic Resonance The set-up sensitivity depends strongly on cavity, MW frequency v, MW power P and sample volume V . The quality of the cavity system is defined through the unloaded quality factor Q0 of the microwave cavity and the filling coefficient kf . Q0 indicates how efficiently the microwave energy is stored (reflected) by the cavity and is defined as 2πEstored Q0 = . (4) Edissipated Estored and Edissipated correspond to the energy stored and lost while sweeping once over the resonance frequency. The loss for a perfectly matched and tuned cavity is due to the electrical currents generated in the cavity walls by the MW, which again produce heat. Effectively Q0 is found by measuring the position of the resonance frequency vres. and the width ∆v of the absorption signal at half it’s height in fig. 3, together with formula 4 rewritten as vres. Q0 = . (5) ∆v A high Q0 value is important for a good spin sensitivity. The lowest number of detectable spins Nmin is calculated as k1V Nmin = , (6) 2 1 Q0kf v P 2 with constant k1. A good set-up sensitivity is achieved with a large number of spins and small Nmin. Obviously in equation 6, also higher MW power and lfrequency is of advantage for a good Nmin value. The signal’s size, i.e. the integrated signal intensity, is proportional to the concentration of unpaired electrons. The MW intensity in combination with the electron relaxation time τ has another influence on the signal. The absorbed energy is mostly emitted again in form of phonons, which happens with the rate 1/τ. Too large an MW intensity can lead to an slower relaxation rate compared to the MW excitation rate, i.e. a [ saturation] of the upper level, which -0.5 0.0 Amplitude of the reflected signal [V] 9.30 9.35 9.40 9.45 9.50 Frequency [GHz] Figure 3: Reflected signal for a MW frequency scan to find the resonance position of the cavity. 3 TP III Electron Paramagnetic Resonance again leads to a decrease of the MW absorption. Increasing saturation appears in the EPR spectra as decreasing absorption lines. The theory above is explained for the case of free electrons. In reality however, we look at radicals or paramagnetic centers, the electrons are under the influence of one or more atoms. The influence of the molecule on the electron is visible in the EPR signal, as a change of the g-value, the line-shape, and hyper-fine coupling: g-factor and line shape In the presence of an atom or molecule, the electron possesses, besides its spin s, some orbital momentum L, changing its total angular momentum. This spin-orbit coupling leads to a change of the g-factor away from ge of an unpaired electron. Effectively, the local magnetic field is changed from B0 to Beff = B0(1 − σ). σ is hereby the influence of the magnetic fields from atoms and molecules. By applying this on equation 2, we get hv = geµBB0(1 − σ) ) hv = g · µBB0. (7) σ is the difference of g from the free electrons value ge and is easily determined from the EPR spectrum. Moreover, σ contains information about the substrates’ orbital-structure, as the coupling magnitude depends on the masses. Organic free radicals, with only hydrogen, oxygen, carbon and nitrogen, only have small deviations from ge, while e.g. metals having a more significant influence. For e.g. DPPH, the influence of the molecule is on average zero, leading to an EPR signal for DPPH corresponding to g = 2.0036, which is quasi-free. In general g is a 2nd order tensor with three main or principal components (of the diag- onalised tensor) gx, gy and gz. In the case of an anisotropic electronic structure of the molecule or atomic structure, g is such a tensor. This leads to a signal structure for such anisotropic orbital molecules, which is dependent on their orientation to the direction of B0. By measuring different orientation of the substrate in the external field, additional informations about the substrates structure can be collected. For single crystals, all the molecules are in the same orientation. A molecule with e.g. two different principal compo- nents (e.g. an axial-symmetric crystal with the main-axis gx = gk and gy = gz = g?) will have different signals, depending on the crystals orientation to B0 at Bx or By,z.
Load more

Recommended publications
  • Brief Guide to the Nomenclature of Organic Chemistry
    1 Brief Guide to the Nomenclature of Table 1: Components of the substitutive name Organic Chemistry (4S,5E)-4,6-dichlorohept-5-en-2-one for K.-H. Hellwich (Germany), R. M. Hartshorn (New Zealand), CH3 Cl O A. Yerin (Russia), T. Damhus (Denmark), A. T. Hutton (South 4 2 Africa). E-mail: [email protected] Sponsoring body: Cl 6 CH 5 3 IUPAC Division of Chemical Nomenclature and Structure suffix for principal hept(a) parent (heptane) one Representation. characteristic group en(e) unsaturation ending chloro substituent prefix 1 INTRODUCTION di multiplicative prefix S E stereodescriptors CHEMISTRY The universal adoption of an agreed nomenclature is a key tool for 2 4 5 6 locants ( ) enclosing marks efficient communication in the chemical sciences, in industry and Multiplicative prefixes (Table 2) are used when more than one for regulations associated with import/export or health and safety. fragment of a particular kind is present in a structure. Which kind of REPRESENTATION The International Union of Pure and Applied Chemistry (IUPAC) multiplicative prefix is used depends on the complexity of the provides recommendations on many aspects of nomenclature.1 The APPLIED corresponding fragment – e.g. trichloro, but tris(chloromethyl). basics of organic nomenclature are summarized here, and there are companion documents on the nomenclature of inorganic2 and Table 2: Multiplicative prefixes for simple/complicated entities polymer3 chemistry, with hyperlinks to original documents. An No. Simple Complicated No. Simple Complicated AND overall
    [Show full text]
  • Introduction to NMR Spectroscopy of Proteins
    A brief introduction to NMR spectroscopy of proteins By Flemming M. Poulsen 2002 1 Introduction Nuclear magnetic resonance, NMR, and X-ray crystallography are the only two methods that can be applied to the study of three-dimensional molecular structures of proteins at atomic resolution. NMR spectroscopy is the only method that allows the determination of three-dimensional structures of proteins molecules in the solution phase. In addition NMR spectroscopy is a very useful method for the study of kinetic reactions and properties of proteins at the atomic level. In contrast to most other methods NMR spectroscopy studies chemical properties by studying individual nuclei. This is the power of the methods but sometimes also the weakness. NMR spectroscopy can be applied to structure determination by routine NMR techniques for proteins in the size range between 5 and 25 kDa. For many proteins in this size range structure determination is relatively easy, however there are many examples of structure determinations of proteins, which have failed due to problems of aggregation and dynamics and reduced solubility. It is the purpose of these notes to introduce the reader to descriptions and applications of the methods of NMR spectroscopy most commonly applied in scientific studies of biological macromolecules, in particular proteins. The figures 1,2 and 11 are copied from “Multidímensional NMR in Liquids” by F.J.M de Ven (1995)Wiley-VCH The Figure13 and Table 1 have been copied from “NMR of Proteins and Nucleic acis” K. Wüthrich (1986) Wiley Interscience The Figures 20, 21 and 22 have been copied from J.
    [Show full text]
  • Chapter 1: Atoms, Molecules and Ions
    Previous Chapter Table of Contents Next Chapter Chapter 1: Atoms, Molecules and Ions Section 1.1: Introduction In this course, we will be studying matter, “the stuff things are made of”. There are many ways to classify matter. For instance, matter can be classified according to the phase, that is, the physical state a material is in. Depending on the pressure and the temperature, matter can exist in one of three phases (solid, liquid, or gas). The chemical structure of a material determines the range of temperatures and pressures under which this material is a solid, a liquid or a gas. Consider water for example. The principal differences between water in the solid, liquid and gas states are simply: 1) the average distance between the water molecules; small in the solid and the liquid and large in the gas and 2) whether the molecules are organized in an orderly three-dimensional array (solid) or not (liquid and gas). Another way to classify matter is to consider whether a substance is pure or not. So, matter can be classified as being either a pure substance or a mixture. A pure substance has unique composition and properties. For example, water is a pure substance (whether from Texas or Idaho, each water molecule always contains 2 atoms of hydrogen for 1 atom of oxygen). Under the same atmospheric pressure and at the same ambient temperature, water always has the same density. We can go a little further and classify mixtures are either homogeneous or heterogeneous. In a homogeneous mixture, for example, as a result of mixing a teaspoon of salt in a glass of water, the composition of the various components and their properties are the same throughout.
    [Show full text]
  • Electron Paramagnetic Resonance of Radicals and Metal Complexes. 2. International Conference of the Polish EPR Association. Wars
    ! U t S - PL — voZ, PL9700944 Warsaw, 9-13 September 1996 ELECTRON PARAMAGNETIC RESONANCE OF RADICALS AND METAL COMPLEXES 2nd International Conference of the Polish EPR Association INSTITUTE OF NUCLEAR CHEMISTRY AND TECHNOLOGY UNIVERSITY OF WARSAW VGL 2 8 Hi 1 2 ORGANIZING COMMITTEE Institute of Nuclear Chemistry and Technology Prof. Andrzej G. Chmielewski, Ph.D., D.Sc. Assoc. Prof. Hanna B. Ambroz, Ph.D., D.Sc. Assoc. Prof. Jacek Michalik, Ph.D., D.Sc. Dr Zbigniew Zimek University of Warsaw Prof. Zbigniew Kqcki, Ph.D., D.Sc. ADDRESS OF ORGANIZING COMMITTEE Institute of Nuclear Chemistry and Technology, Dorodna 16,03-195 Warsaw, Poland phone: (0-4822) 11 23 47; telex: 813027 ichtj pi; fax: (0-4822) 11 15 32; e-mail: [email protected] .waw.pl Abstracts are published in the form as received from the Authors SPONSORS The organizers would like to thank the following sponsors for their financial support: » State Committee of Scientific Research » Stiftung fur Deutsch-Polnische Zusammenarbeit » National Atomic Energy Agency, Warsaw, Poland » Committee of Chemistry, Polish Academy of Sciences, Warsaw, Poland » Committee of Physics, Polish Academy of Sciences, Poznan, Poland » The British Council, Warsaw, Poland » CIECH S.A. » ELEKTRIM S.A. » Broker Analytische Messtechnik, Div. ESR/MINISPEC, Germany 3 CONTENTS CONFERENCE PROGRAM 9 LECTURES 15 RADICALS IN DNA AS SEEN BY ESR SPECTROSCOPY M.C.R. Symons 17 ELECTRON AND HOLE TRANSFER WITHIN DNA AND ITS HYDRATION LAYER M.D. Sevilla, D. Becker, Y. Razskazovskii 18 MODELS FOR PHOTOSYNTHETIC REACTION CENTER: STEADY STATE AND TIME RESOLVED EPR SPECTROSCOPY H. Kurreck, G. Eiger, M. Fuhs, A Wiehe, J.
    [Show full text]
  • How to Read and Interpret FTIR Spectroscope of Organic Material
    97| Indonesian JournalIndonesian of Science Journal & Technology of Science &,Volum Technologye 4 Issue 4 ( 11,) (20April19 )2019 97-1 18Page 97-118 Indonesian Journal of Science & Technology Journal homepage: http://ejournal.upi.edu/index.php/ijost/ How to Read and Interpret FTIR Spectroscope of Organic Material Asep Bayu Dani Nandiyanto, Rosi Oktiani, Risti Ragadhita Departemen Kimia, Universitas Pendidikan Indonesia, Jl. Dr. Setiabudi no 229 Bandung 40154, Indonesia Correspondence: E-mail: [email protected] A B S T R A C T S A R T I C L E I N F O Article History: Fourier Transform Infrared (FTIR) has been developed as a Received 10 Jan 2019 tool for the simultaneous determination of organic Revised 20 Jan 2019 components, including chemical bond, as well as organic Accepted 31 Aug 2019 Available online 09 Apr 2019 content (e.g., protein, carbohydrate, and lipid). However, ____________________ until now, there is no further documents for describing the Keywords: detailed information in the FTIR peaks. The objective of this FTIR, study was to demonstrate how to read and assess chemical infrared spectrum, organic material, bond and structure of organic material in the FTIR, in which chemical bond, the analysis results were then compared with the literatures. organic structure. The step-by-step method on how to read the FTIR data was also presented, including reviewing simple to the complex organic materials. This study is potential to be used as a standard information on how to read FTIR peaks in the biochemical and organic materials. © 2019Tim Pengembang Jurnal UPI 1. INTRODUCTION analysis is quite rapid, good in accuracy, and relatively sensitive (Jaggi and Vij, 2006).
    [Show full text]
  • Numerical Methods in Electron Magnetic Resonance
    NO0000039 NUMERICAL METHODS IN ELECTRON MAGNETIC RESONANCE ANALYSES AND SIMULATIONS IN QUEST OF STRUCTURAL AND DYNAMICAL PROPERTIES OF FREE RADICALS IN SOLIDS BY ANDERS RASMUS S0RNES Thesis submitted for the degree Doctor scientiarum Department of Physics, University of Oslo 1998 31-18 Preface This thesis encompasses a collection of six theoretical and experimental Electron Magnetic Resonance (EMR) studies of the structure and dynamics of free radicals in solids. Radicals are molecular systems having one or more unpaired electron. Due to their energetically unfavourable open shell configuration, they are highly reactive. Radicals are formed in different ways. They are believed to be present in many chemical reactions as short-lived intermediate products, and they are also produced in interactions of x-radiation with matter, in Compton and photoelectric processes and interactions of their secondary electrons. Longer-lived, quasistable radicals do also exist and these may be used as spin-labels or spin-probes and may be attached to larger molecules and surfaces as measurement probes to examine the environment in their immediate vicinity. EMR is a collective term for a group of spectroscopic techniques inducing and observing transitions between the Zeeman levels of a paramagnetic system, such as a radical situated in an external magnetic field. Whithin the broader concept of EMR, the particular experimental techniques of Electron Paramagnetic Resonance (EPR), ELectron Nuclear DOuble Resonance (ENDOR), Field Swept ENDOR (FSE) and Electron Spin Echo Envelope Modulation (ESEEM) are discussed in this thesis. The focal point of this thesis is the development and use of numerical methods in the analysis, simulation and interpretation of EMR experiments on radicals in solids to uncover the structure, the dynamics and the environment of the system.
    [Show full text]
  • Fourier Transform Infrared (FTIR) Spectroscopy Analysis of Transformer Paper in Mineral Oil-Paper Composite Insulation Under Accelerated Thermal Aging
    energies Article Fourier Transform Infrared (FTIR) Spectroscopy Analysis of Transformer Paper in Mineral Oil-Paper Composite Insulation under Accelerated Thermal Aging Abi Munajad * ID , Cahyo Subroto ID and Suwarno ID School of Electrical Engineering and Informatics, Institut Teknologi Bandung, Bandung 40132, Indonesia; [email protected] (C.S.); [email protected] (S.) * Correspondence: [email protected]; Tel.: +62-857-465-76059 Received: 26 December 2017; Accepted: 29 January 2018; Published: 4 February 2018 Abstract: Mineral oil is the most popular insulating liquid for high voltage transformers due to its function as a cooling liquid and an electrical insulator. Kraft paper has been widely used as transformer solid insulation for a long time already. The degradation process of transformer paper due to thermal aging in mineral oil can change the physical and chemical structure of the cellulose paper. Fourier transform infrared (FTIR) spectroscopy analysis was used to identify changes in the chemical structure of transformer paper aged in mineral oil. FTIR results show that the intensity of the peak absorbance of the O–H functional group decreased with aging but the intensity of the peak absorbance of the C–H and C=O functional groups increased with aging. Changes in the chemical structure of the cellulose paper during thermal aging in mineral oil can be analyzed by an oxidation process of the cellulose paper and the reaction process between the carboxylic acids in the mineral oil and the hydroxyl groups on the cellulose. The correlation between the functional groups and the average number of chain scissions of transformer paper gives initial information that the transformer paper performance can be identified by using a spectroscopic technique as a non-destructive diagnostic technique.
    [Show full text]
  • Syllabus Chem 646
    SYLLABUS CHEM 646 Course title and number Physical Organic Chemistry, CHEM 646 Term Fall 2019 Meeting times and location MWF 10:20 am – 11:10 am, Room: CHEM 2121 Course Description and Learning Outcomes Prerequisites: Organic Chemistry I and II or equivalent undergraduate organic chemistry courses. Physical Organic Chemistry (CHEM646) is a graduate/senior-undergrad level course of advanced organic chemistry. Physical organic chemistry refers to a discipline of organic chemistry that focuses on the relationship between chemical structure and property/reactivity, in particular, applying experimental and theoretical tools of physical chemistry to the study of organic molecules and reactions. Specific focal points of study include the bonding and molecular orbital theory of organic molecules, stability of organic species, transition states, and reaction intermediates, rates of organic reactions, and non-covalent aspects of solvation and intermolecular interactions. CHEM646 is designed to prepare students for graduate research on broadly defined organic chemistry. This course will provide the students with theoretical and practical frameworks to understand how organic structures impact the properties of organic molecules and the mechanism for organic reactions. By the end of this course, students should be able to: 1. Gain in-depth understanding of the nature of covalent bonds and non-covalent interactions 2. Use molecule orbital theory to interpret the property and reactivity of organic species. 3. Understand the correlation between the structure and physical/chemical properties of organic molecules, such as stability, acidity, and solubility. 4. Predict the reactivity of organic molecules using thermodynamic and kinetic analyses 5. Probe the mechanism of organic reactions using theoretical and experimental approaches.
    [Show full text]
  • Chapter 12. Decoding Organic Structures: the Functional Groups
    CHAPTER 12. DECODING ORGANIC STRUCTURES: THE FUNCTIONAL GROUPS Functional Groups: The Key To Understanding Organic Molecules Since life on this planet is based on compounds of the element carbon, the study of these compounds, called organic chemistry, is an important area of chemistry.The ability of carbon to form single or multiple covalent bonds with itself to form chains of varying length, and even rings of varying size, leads to great versatility in the size and shape of carbon-based molecules. In this chapter we consider the bonds carbon forms with other elements, further expanding the number and types of possible compounds. The number of compounds formed by carbon is so great that it far exceeds the number of all the compounds formed by all the other elements. Some of these compounds contain thousands of atoms. How are we to begin to understand this myriad of complex molecules? The backbone of any organic compound is its carbon structure, whether in long chains, branched chains, rings, or some combination of these. In nature only a few elements other than carbon are found in most organic compounds: oxygen and nitrogen are the most common of these, along with sulfur and phosphorous. These tend to be found most commonly in only a few arrangements called functional groups. When the structure of an organic compound is drawn, frequently the carbon backbone is indicated only by a structural skeleton, with symbols for the carbon atoms left out. Usually hydrogen atoms attached to carbon atoms are left out, too. Only the atoms and bonds belonging to the functional groups are shown in detail.
    [Show full text]
  • Organic and Biological Chemistry
    CHAPTER 23 Organic and Biological Chemistry CONTENTS HO H 23.1 ▶ Organic Molecules and Their C Structures: Alkanes H H C 23.2 ▶ Families of Organic Compounds: HO O O C C Functional Groups 23.3 ▶ Naming Organic Compounds H CC 23.4 ▶ Carbohydrates:HO A Biological Example HO OH of Isomers H 23.5 ▶ Valence Bond TCheory and Orbital OverlapH Pictures H C 23.6 ▶ Lipids:HO A Biological EOxample ofO Cis–Trans IsomerismC C 23.7 ▶ Formal Charge and Resonance in Organic CompoundsH CC 23.8 ▶ Conjugated SystemsHO OH 23.9 ▶ Proteins: A Biological Example of Conjugation 23.10 ▶ Aromatic Compounds and Molecular Ascorbic acid, also known as vitamin C, is an essential nutrient in the human diet Orbital Theory because it is not synthesized in our body. We can eat citrus fruits or take pills that contain vitamin C to maintain health. 23.11 ▶ Nucleic Acids: A Biological Example of Aromaticity ? Which Is Better, Natural or Synthetic? The answer to this question can be found in the INQUIRY ▶▶▶ on page 1021. STUDY GUIDE M23_MCMU3170_07_SE_C23.indd 978 27/11/14 2:11 AM f the ultimate goal of chemistry is to understand the world around us on a molecular level, then a knowledge of biochemistry—the chemistry of living organisms—is a central part Iof that goal. Biochemistry, in turn, is a branch of organic chemistry, a term originally used to mean the study of compounds from living organisms while inorganic chemistry was used for the study of compounds from nonliving sources. Today, however, we know that there are no fundamental differences between organic and inorganic compounds; the same principles apply to both.
    [Show full text]
  • 1.2 Classical Theories of Chemical Bonding 3
    01_BRCLoudon_pgs5-1.qxd 12/8/08 11:48 AM Page 3 1.2 CLASSICAL THEORIES OF CHEMICAL BONDING 3 simply memorizing them. We’ll consider some of the organic chemistry that is industrially im- portant. Finally, we’ll examine some of the beautiful applications of organic chemistry in bi- ology, such as how nature does organic chemistry and how the biological world has inspired a great deal of the research in organic chemistry. 1.2 CLASSICAL THEORIES OF CHEMICAL BONDING To understand organic chemistry, it is necessary to have some understanding of the chemical bond—the forces that hold atoms together within molecules. First, we’ll review some of the older, or “classical,” ideas of chemical bonding—ideas that, despite their age, remain useful today. Then, in the last part of this chapter, we’ll consider more modern ways of describing the chemical bond. A. Electrons in Atoms Chemistry happens because of the behavior of electrons in atoms and molecules. The basis of this behavior is the arrangement of electrons within atoms, an arrangement suggested by the periodic table. Consequently, let’s first review the organization of the periodic table (see page facing inside back cover). The shaded elements are of greatest importance in organic chem- istry; knowing their atomic numbers and relative positions will be valuable later on. For the moment, however, consider the following details of the periodic table because they were im- portant in the development of the concepts of bonding. A neutral atom of each element contains a number of both protons and electrons equal to its atomic number.
    [Show full text]
  • How Mathematical Trees Can Be Used to Produce Molecular Formulas Systematically
    Chin-yah Yeh*, The Journal of the Utah Academy of Sciences, Arts, & Letters, 2012. *[email protected] Romancing Mathematics with Chemistry—How Mathematical Trees Can Be Used to Synthesize Molecular Structures Chin-yah Yeh Utah Valley University Abstract Structures of chemical compounds can be synthesized and categorized through mathematical means. Organic compounds are suitable targets because of their simple valences. Acyclic organic compounds made of hydrogen and second-row elements C, N, O, and F are presented as an example. In five categories of organic compounds, chemical structures can be generated exclusively and exhaustively using ab initio methods. It is shown that mathematical variables can serve as chemical symbols and mathematical equations are chemical structure generators. I. BACKGROUND Chemists have a long tradition of using atomic valences to find molecular structures graphically. Chemistry relies on this simple procedure to make progress; however, drawing does not generate structures systematically, i.e., there is no guaranteed completeness or uniqueness. Are all structures generated? Is a structure generated more than once? Take butane molecules (C4H10) for instance. It can be seen (Fig. 1) that one straight-chain and one branched structure suffice. But as molecular size gets bigger, finding structures exhaustively and uniquely can become a daunting job. This paper deals with how we generate chemical structures from first principles. Compared with the empirical method that relies on computers,1 structural generation through first principle has a long and winding past. Fig. 1. Structures for butanes About the time Darwin published his Origin of Species, two mathematicians endeavored in structuring chemical compounds.
    [Show full text]