Practical Group Theory and Raman Spectroscopy, Part I: Normal Vibrational Modes
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Technical Application Note
Compact Rugged Spectrometers - A Universe of Spectroscopy Systems Technical Application Note Vibrational Spectroscopy: Infrared vs. Raman StellarNet, Inc. Tampa, Fl USA Tony Rizzuto, PhD April 12, 2017 Vibrational spectroscopies are integral in analyzing some of the most fundamentally important processes in physical chemistry: molecular vibrations. While there are many different experimental techniques used to analyze those vibrations, most are variations of the “Big Two,” FTIR and Raman scattering spectroscopies. This article aims to analyze the benefits and drawbacks of each of the “Big Two,” with the hope that it helps one choose the correct technique for one’s research interests. 1. What are the “Big Two?” Fourier Transform Infrared Spectroscopy Raman spectroscopy relies on inelastic (FTIR) is a simple absorption measurement scattering phenomenon that probes the where the detector measures the molecular vibration. Where FTIR will use a absorbance of infrared radiation by the broadband IR source, Raman spectroscopy sample. Each sample will absorb different typically uses a narrow-band, amounts of each frequency resulting in a monochromatic light source in order to “chemical fingerprint” that is the FTIR excite the vibrations of the molecule in your spectrum. sample. 2. Selection Rules: What molecular vibrations are being probed? Imagining a molecular bond vibration with the traditional ball and spring model (Figure 1a) and its resultant harmonic oscillator depiction (Figure 1b) allows us to calculate the selection rules for vibrational transitions to be = 1. However, that does not tell the whole story. In order to truly differentiate FTIR from Raman Spectroscopy, we must think about it on a molecular level. Compact Rugged Spectrometers - A Universe of Spectroscopy Systems Technical Application Note A B Figure 1: A. -
Neutron Vibrational Spectroscopy
Neutron Vibrational Spectroscopy A.J. (Timmy) Ramirez-Cuesta Luke L. Daemen Yongqiang Cheng Spallation Neutron Source Oak Ridge National Laboratory ORNL is managed by UT-Battelle for the US Department of Energy The S(Q,w) Map w=0 Elastic Scattering Diffraction Structural Information 2 "Let there be light" 3 4 How to measure INS (1) Direct Geometry Instrumentation 4000 3500 Direct geometry instruments 3000 ) 1 - m measure Q trajectory is c ( 2500 r e f determined by the angle s n 2000 a r t and energy transfer. y g r 1500 e n Examples: ARCS, CNCS, E HYSPEC, SEQUIOA 1000 500 0 0 10 20 30 Momentum transfer (A-1) ) . U . A ( y t i s n e L t 2 n I Incident neutron beam is 0 10 20 30 40 50 60 70 Energy (meV) s monochromatic t n u o c determining the incident n o r t u Distance energy E1. e N That determines T1. We L1 12000 13000 14000 15000 16000 measure the ToF and we ToF (ms) can work out T2. Resolution is almost constant in units of Ei time 5 VISION: a high throughput spectrometer for neutron vibrational spectroscopy Yongqiang Cheng, Luke Daemen, A.J. (Timmy) Ramirez-Cuesta Spallation Neutron Source, Oak Ridge National Laboratory, Oak Ridge, TN 37931 USA VISION offers users a variety of sample environments How to measure INS (2) Polybenzene nanothreads synthesized at high pressure: single nanothreads VISION is best thought of as and experimental/computational capabilities: the neutron analogue of a Structural inference through modeling of vibrational spectra Indirect Geometry Instrumentation Raman spectrometer. -
Femtosecond Time-Resolved Observation of Butterfly Vibration In
www.nature.com/scientificreports OPEN Femtosecond time-resolved observation of butterfy vibration in electronically excited Received: 7 June 2017 Accepted: 11 October 2017 o-fuorophenol Published: xx xx xxxx Fengzi Ling1,2, Shuai Li1,2, Xinli Song1,2, Yanmei Wang1,2, Jinyou Long1,2 & Bing Zhang 1,2 The butterfy vibration during the hydrogen tunneling process in electronically excited o-fuorophenol has been visualized in real time by femtosecond time-resolved ion yield spectroscopy coupled with time-resolved photoelectron imaging technique. A coherent superposition of out-of-plane C–F butterfy motions is prepared in the frst excited electronic state (S1). As the C–F bond vibrates with respect to the aromatic ring, the nuclear geometry varies periodically, leading to the corresponding variation in the photoionization channel. By virtue of the more favorable ionization probability from the nonplanar minimum via resonance with the Rydberg states, the evolution of the vibrational wave packet is manifested as a superimposed beat in the parent-ion transient. Moreover, time-resolved photoelectron spectra ofer a direct mapping of the oscillating butterfy vibration between the planar geometry and nonplanar minimum. The beats for the photoelectron peaks originating from the planar geometry are out of phase with those from the nonplanar minimum. Our results provide a physically intuitive and complete picture of the oscillatory fow of energy responsible for the coherent vibrational motion on the excited state surface. Ultrafast molecular vibration is one of the fundamental motions that characterize chemical bonding and decide reaction dynamics at the molecular level1–3. Over the past few decades, frequency-resolved spectroscopies such as infrared and Raman spectra4 and resonant two-photon ionization (R2PI) spectroscopy5 have devoted to pro- viding detailed spectroscopic data about molecular vibration. -
Surface-Enhanced Raman Scattering (SERS)
Focal Point Review Applied Spectroscopy 2018, Vol. 72(7) 987–1000 ! The Author(s) 2018 Surface-Enhanced Raman Scattering Reprints and permissions: sagepub.co.uk/journalsPermissions.nav (SERS) in Microbiology: Illumination and DOI: 10.1177/0003702818764672 journals.sagepub.com/home/asp Enhancement of the Microbial World Malama Chisanga, Howbeer Muhamadali, David I. Ellis, and Royston Goodacre Abstract The microbial world forms a huge family of organisms that exhibit the greatest phylogenetic diversity on Earth and thus colonize virtually our entire planet. Due to this diversity and subsequent complex interactions, the vast majority of microorganisms are involved in innumerable natural bioprocesses and contribute an absolutely vital role toward the maintenance of life on Earth, whilst a small minority cause various infectious diseases. The ever-increasing demand for environmental monitoring, sustainable ecosystems, food security, and improved healthcare systems drives the continuous search for inexpensive but reproducible, automated and portable techniques for detection of microbial isolates and understanding their interactions for clinical, environmental, and industrial applications and benefits. Surface-enhanced Raman scattering (SERS) is attracting significant attention for the accurate identification, discrimination and characteriza- tion and functional assessment of microbial cells at the single cell level. In this review, we briefly discuss the technological advances in Raman and Fourier transform infrared (FT-IR) instrumentation and their application for the analysis of clinically and industrially relevant microorganisms, biofilms, and biological warfare agents. In addition, we summarize the current trends and future prospects of integrating Raman/SERS-isotopic labeling and cell sorting technologies in parallel, to link genotype-to-phenotype in order to define community function of unculturable microbial cells in mixed microbial communities which possess admirable traits such as detoxification of pollutants and recycling of essential metals. -
All-Digital Histopathology by Infrared-Optical Hybrid Microscopy
All-digital histopathology by infrared-optical hybrid microscopy Martin Schnella, Shachi Mittala,b, Kianoush Falahkheirkhaha,c, Anirudh Mittala,b, Kevin Yeha,b, Seth Kenkela,d, Andre Kajdacsy-Ballae, P. Scott Carneyf, and Rohit Bhargavaa,b,c,d,g,h,i,1 aBeckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, IL 61801; bDepartment of Bioengineering, University of Illinois at Urbana–Champaign, Urbana, IL 61801; cDepartment of Chemical and Biomolecular Engineering, University of Illinois at Urbana– Champaign, Urbana, IL 61801; dDepartment of Mechanical Science and Engineering, University of Illinois at Urbana–Champaign, Urbana, IL 61801; eDepartment of Pathology, University of Illinois at Chicago, Chicago, IL 60612; fThe Institute of Optics, University of Rochester, Rochester, NY 14620; gCancer Center at Illinois, University of Illinois at Urbana–Champaign, Urbana, IL 61801; hDepartment of Electrical and Computer Engineering, University of Illinois at Urbana–Champaign, Urbana, IL 61801; and iDepartment of Chemistry, University of Illinois at Urbana–Champaign, Urbana, IL 61801 Edited by Christian Huck, University of Innsbruck, Innsbruck, Austria, and accepted by Editorial Board Member John A. Rogers December 20, 2019 (received for review July 19, 2019) Optical microscopy for biomedical samples requires expertise in fidelity imaging in both point-scanning (15) and wide-field (16–19) staining to visualize structure and composition. Midinfrared (mid-IR) modalities, IR pixel sizes are ∼100-fold larger than those easily spectroscopic imaging offers label-free molecular recording and achieved in visible microscopy, and data acquisition speed is still virtual staining by probing fundamental vibrational modes of three to four orders of magnitude slower than in visible imaging molecular components. -
Infrared Spectroscopy: Theory
Online edition for students of organic chemistry lab courses at the University of Colorado, Boulder, Dept of Chem and Biochem. (2002) u Chapter 15 Infrared Spectroscopy: Theory An important tool of the organic chemist is Infrared Spectroscopy, or IR. IR spectra are acquired on a special instrument, called an IR spectrometer. IR is used both to gather information about the structure of a compound and as an analytical tool to assess the purity of a compound. IR spectra are quick and easy to run, and since the teaching labs are fortunate enough to have three of these instruments, students are encouraged to acquire spectra of compounds made in the laboratory throughout the first and second semesters of the lab course. 15.1 The Electromagnetic Spectrum Infrared refers to that part of the electromagnetic spectrum between the visible and microwave regions. Electromagnetic spectrum refers to the seemingly diverse col- lection of radiant energy, from cosmic rays to X-rays to visible light to microwaves, each of which can be considered as a wave or particle traveling at the speed of light. These waves differ from each other in the length and frequency, as illustrated in Figure 15.1. Frequency, ν (nu), is the number of wave cycles that pass through a point in one sec- ond. It is measured in Hz, where 1 Hz = 1 cycle/sec. Wavelength, λ (lambda), is the length of one complete wave cycle. It is often measured in cm (centimeters). Wave- length and frequency are inversely related: c c ν = --- and λ = --- Eq. 1 λ ν where c is the speed of light, 3 x 1010 cm/sec Energy is related to wavelength and frequency by the following for- mulas: Eq. -
Two-Dimensional Infrared Spectroscopy of Vibrational Polaritons
Two-dimensional infrared spectroscopy of vibrational polaritons Bo Xianga, Raphael F. Ribeirob, Adam D. Dunkelbergerc, Jiaxi Wangb, Yingmin Lia, Blake S. Simpkinsc, Jeffrey C. Owrutskyc, Joel Yuen-Zhoub, and Wei Xionga,b,1 aMaterials Science and Engineering Program, University of California, San Diego, La Jolla, CA 92093; bDepartment of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093; and cChemistry Division, Naval Research Laboratory, Washington, DC 20375 Edited by Stephen R. Forrest, University of Michigan, Ann Arbor, MI, and approved March 28, 2018 (received for review December 19, 2017) We report experimental 2D infrared (2D IR) spectra of coherent molecular-cavity system has many dark states in comparison with light–matter excitations––molecular vibrational polaritons. The ap- the few bright modes (3, 17, 18): One type of dark states shares plication of advanced 2D IR spectroscopy to vibrational polaritons molecular components and some small photonic character with challenges and advances our understanding in both fields. First, polaritons as a result of disorder (17). Another type of dark the 2D IR spectra of polaritons differ drastically from free uncoupled states, termed “uncoupled” molecules, consists of molecular vi- excitations and a new interpretation is needed. Second, 2D IR brations which are not coupled to the cavity electric field (e.g., uniquely resolves excitation of hybrid light–matter polaritons and because they may be outside the photonic-mode volume, or unexpected dark states in a state-selective manner, revealing other- because their transition dipole moment is orthogonal to the wise hidden interactions between them. Moreover, 2D IR signals mode polarization). -
Infrared Spectroscopy: Fundamentals and Applications
Contents Series Preface ix Preface xi Acronyms, Abbreviations and Symbols xiii About the Author xvii 1 Introduction 1 1.1 Electromagnetic Radiation 2 1.2 Infrared Absorptions 5 1.3 Normal Modes of Vibration 6 1.4 Complicating Factors 11 1.4.1 Overtone and Combination Bands 11 1.4.2 Fermi Resonance 12 1.4.3 Coupling 12 1.4.4 Vibration–Rotation Bands 12 References 13 2 Experimental Methods 15 2.1 Introduction 15 2.2 Dispersive Infrared Spectrometers 16 2.3 Fourier-Transform Infrared Spectrometers 18 2.3.1 Michelson Interferometers 18 2.3.2 Sources and Detectors 19 2.3.3 Fourier-Transformation 20 2.3.4 Moving Mirrors 21 2.3.5 Signal-Averaging 22 vi Infrared Spectroscopy: Fundamentals and Applications 2.3.6 Advantages 23 2.3.7 Computers 23 2.3.8 Spectra 24 2.4 Transmission Methods 25 2.4.1 Liquids and Solutions 25 2.4.2 Solids 28 2.4.3 Gases 31 2.4.4 Pathlength Calibration 32 2.5 Reflectance Methods 33 2.5.1 Attenuated Total Reflectance Spectroscopy 33 2.5.2 Specular Reflectance Spectroscopy 35 2.5.3 Diffuse Reflectance Spectroscopy 36 2.5.4 Photoacoustic Spectroscopy 37 2.6 Microsampling Methods 38 2.7 Chromatography–Infrared Spectroscopy 41 2.8 Thermal Analysis–Infrared Spectroscopy 42 2.9 Other Techniques 43 References 44 3 Spectral Analysis 45 3.1 Introduction 45 3.2 Group Frequencies 46 3.2.1 Mid-Infrared Region 46 3.2.2 Near-Infrared Region 47 3.2.3 Far-Infrared Region 48 3.3 Identification 48 3.4 Hydrogen Bonding 49 3.5 Spectrum Manipulation 51 3.5.1 Baseline Correction 51 3.5.2 Smoothing 51 3.5.3 Difference Spectra 52 3.5.4 Derivatives -
Infrared Spectroscopy
23 chapter Infrared Spectroscopy Randy L. Wehling Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68583-0919, USA [email protected] 23.1 Introduction 409 23.3.2 Applications of Mid-IR 23.2 Principles of IR Spectroscopy 409 Spectroscopy 411 23.2.1 The IR Region of the Electromagnetic 23.3.2.1 Absorption Bands of Organic Spectrum 409 Functional Groups 411 23.2.2 Molecular Vibrations 409 23.3.2.2 Presentation of Mid-IR 23.2.3 Factors Affecting the Frequency Spectra 411 of Vibration 409 23.3.2.3 Qualitative Applications 412 23.3 Mid-IR Spectroscopy 410 23.3.2.4 Quantitative Applications 412 23.3.1 Instrumentation 410 23.3.3 Raman Spectroscopy 412 23.3.1.1 Dispersive Instruments 410 23.4 Near-Infrared Spectroscopy 413 23.3.1.2 Fourier Transform 23.4.1 Principles 413 Instruments 410 23.4.1.1 Principles of Diffuse Reflection 23.3.1.3 Sample Handling Measurements 413 Techniques 411 S.S. Nielsen, Food Analysis, Food Science Texts Series, DOI 10.1007/978-1-4419-1478-1_23, 407 °c Springer Science+Business Media, LLC 2010 408 Part IV • Spectroscopy 23.4.1.2 Absorption Bands in the NIR 23.4.4 Qualitative Analysis by NIR Region 414 Spectroscopy 417 23.4.2 Instrumentation 415 23.4.5 Applications of NIR Spectroscopy 23.4.3 Quantitative Methods Using NIR to Food Analysis 417 Spectroscopy 416 23.5 Summary 418 23.4.3.1 Calibration Methods 23.6 Study Questions 418 Using Multiple Linear 23.7 References 419 Regression 417 23.4.3.2 Calibration Development Using Full Spectrum Methods 417 Chapter 23 • Infrared Spectroscopy 409 23.1 INTRODUCTION Infrared (IR) spectroscopy refers to measurement of the absorption of different frequencies of IR radia- tion by foods or other solids, liquids, or gases. -
Complementary Vibrational Spectroscopy
Complementary Vibrational Spectroscopy Kazuki Hashimoto1,2, Venkata Ramaiah Badarla3, Akira Kawai1 and Takuro Ideguchi*3,4 1 Department of Physics, The University of Tokyo, Tokyo 113-0033, Japan 2 Aeronautical Technology Directorate, Japan Aerospace Exploration Agency, Tokyo 181-0015, Japan 3 Institute for Photon Science and Technology, The University of Tokyo, Tokyo 113-0033, Japan 4 PRESTO, Japan Science and Technology Agency, Saitama 332-0012, Japan *[email protected] Vibrational spectroscopy, comprised of infrared absorption and Raman scattering spectroscopy, is widely used for label-free optical sensing and imaging in various scientific and industrial fields. The group theory states that the two molecular spectroscopy methods are sensitive to vibrations categorized in different point groups and provide complementary vibrational spectra. Therefore, complete vibrational information cannot be acquired by a single spectroscopic device, which has impeded the full potential of vibrational spectroscopy. Here, we demonstrate simultaneous infrared absorption and Raman scattering spectroscopy that allows us to measure the complete broadband vibrational spectra in the molecular fingerprint region with a single instrument based on an ultrashort pulsed laser. The system is based on dual-modal Fourier-transform spectroscopy enabled by efficient use of nonlinear optical effects. Our proof-of-concept experiment demonstrates rapid, broadband and high spectral resolution measurements of complementary spectra of organic liquids for -
The Possible Role of Molecular Vibration in Intracellular Signalling
https://www.scientificarchives.com/journal/journal-of-cellular-signaling Journal of Cellular Signaling Review Article The Possible Role of Molecular Vibration in Intracellular Signalling Werner Jaross* Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Technische Universitaet Dresden, Fetscherstrasse 74, 01307, Dresden, Germany *Correspondence should be addressed to Werner Jaross; [email protected] Received date: July 03, 2020, Accepted date: October 27, 2020 Copyright: © 2020 Jaross W. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Abstract The exchange of information within the cell is extremely complex. Besides the well-studied chemical signalling, physical signalling is required to fulfil spatial and temporal aspects. The Golgi apparatus and the microtubule skeleton system are the decisive structures for numerous intracellular transport tasks . Close communication between the Golgi apparatus and the cell periphery is an absolute prerequisite for the well-directed positioning of structural elements. The majority of the substances that influence the cell from the membrane transmit the information to the intracellular destination via signal transduction pathways. It is discussed in detail that the transmission of information in both systems is based on emission and resonance of electromagnetic patterns in the infrared frequency range generated by the vibrations of the respective molecules. This radiation with fingerprint patterns must be coherent to activate enzymes. Coherence could be achieved by the chemical reactions of the molecules to be replaced or in the signal transduction pathways, by the phosphorylation of the transduction proteins. -
Coherence in Molecular Photoionization
Coherence in Molecular Photoionization PhD thesis David Ayuso Molinero Supervisors: ○ Alicia Palacios Cañas ○ Fernando Martín García arXiv:1705.06276v1 [physics.chem-ph] 17 May 2017 December 2015 Coherence in Molecular Photoionization PhD thesis David Ayuso Abstract We present a theoretical study of light-induced phenomena in gas-phase molecu- les, exploring the physical phenomena arising in two distinct contexts: using syn- chrotron radiation and ultrashort laser pulses. This work has been done in close collaboration with Piero Decleva (Universit`adegli Studi di Trieste). We first present our work on inner-shell photoionization of diatomic (CO) and small polyatomic (CF4, BF3) molecules at high photoelectron energies performed in collaboration with the experimental the groups of Edwin Kukk (Turku Univer- sity), Catalin Miron (Synchrotron SOLEIL), Kiyosi Ueda (Synchrotron SPring-8) and Thomas Darrah Thomas (Oregon State University). The combination of state-of-the-art Density Functional Theory (DFT)-like calculations, capable to describe photoionization accounting for the nuclear degrees of freedom, together with high-resolution third-generation synchrotron facilities, has enabled the inves- tigation of non-Franck-Condon effects observable in vibrationally resolved pho- toionization measurements. We demonstrate that the nuclear response to in- tramolecular electron diffraction is observable and can be used to obtain struc- tural information. As a proof-of-principle, by using the DFT calculations as an analysis tool to fit the experimental data, we have accurately determined the equi- librium distance of the CO molecule and the bond contraction that takes place upon C 1s ionization. This is a surplus of photoelectron spectroscopy with res- pect to more conventional spectroscopic techniques, which usually can only pro- vide structural information of neutral molecular species.