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Molecular Structure: The location of the atoms, groups or ions relative to one another in a molecule, as well as the number, type and location of covalent bonds.

Nanomanipulation of Single RNA Molecules by Optical Tweezers

1Nanoscale Engineering Graduate Program, College of Nanoscale Science and Engineering, University at Albany, State University of New York, 2Nanoscale Science Undergraduate Program, College of Nanoscale Science and Engineering, University at Albany, State University of New York, 3Nanobioscience Constellation, College of Nanoscale Science and Engineering, University at Albany, State University of New York, 4The RNA Institute, University at Albany, State University of New York, 5Department of Biological Sciences, University at Albany, State University of New York

JoVE 51542


Growing Crystals for X-ray Diffraction Analysis

JoVE 10216

Source: Laboratory of Dr. Jimmy Franco - Merrimack College

X-ray crystallography is a method commonly used to determine the spatial arrangement of atoms in a crystalline solid, which allows for the determination of the three-dimensional shape of a molecule or complex. Determining the three-dimensional structure of a compound is of particular importance, since a compound's structure and function are intimately related. Information about a compound's structure is often used to explain its behavior or reactivity. This is one of the most useful techniques for solving the three-dimensional structure of a compound or complex, and in some cases it may be the only viable method for determining the structure. Growing X-ray quality crystals is the key component of X-ray crystallography. The size and quality of the crystal is often highly dependent on the composition of the compound being examined by X-ray crystallography. Typically compounds containing heavier atoms produce a greater diffraction pattern, thus require smaller crystals. Generally, single crystals with well-defined faces are optimal, and typically for organic compounds, the crystals need to be larger than those containing heavy atoms. Without viable crystals, X-ray crystallography is not feasible. Some molecules are inherently more crystalline than others, thu

 Organic Chemistry

Photochemical Initiation Of Radical Polymerization Reactions

JoVE 10461

Source: David C. Powers, Tamara M. Powers, Texas A&M

In this video, we will carry out the photochemically initiated polymerization of styrene to generate polystyrene, which is an important commodity plastic. We will learn the fundamentals of photochemistry and use simple photochemistry to initiate radical polymerization reactions. Specifically, in this module we will examine the photochemistry of benzoyl peroxide and its role as a photo-initiator of styrene polymerization reactions. In the described experiments, we will investigate the role of wavelength, photon absorption, and excited state structure on the efficiency (measured as quantum yield) of photochemical reactions.

 Inorganic Chemistry

Nuclear Magnetic Resonance (NMR) Spectroscopy

JoVE 5680

Source: Laboratory of Dr. Henrik Sundén – Chalmers University of Technology

Nuclear magnetic resonance (NMR) spectroscopy is a vital analysis technique for organic chemists. With the help of NMR, the work in the organic lab has been facilitated tremendously. Not only can it provide information about the structure of a molecule but also determine the content and purity of a sample. Compared with other commonly encountered techniques for organic chemists — such as thermal analysis and mass spectrometry (MS) — NMR is a non-destructive method that is valuable when recovery of the sample is important. One of the most frequently used NMR techniques for an organic chemist is proton (1H) NMR. The protons present in a molecule will behave differently depending on its surrounding chemical environment, making it possible to elucidate its structure. Moreover, it is possible to monitor the completion of a reaction by comparing NMR spectra of the starting material to that of the final product. This video exemplifies how NMR spectroscopy can be used in the everyday work of an organic chemist. The following will be shown: i) preparation of an NMR sample. ii) Using 1H NMR to monitor a reaction. iii) Identifying the product obtained from

 Organic Chemistry

Implementation of a Coherent Anti-Stokes Raman Scattering (CARS) System on a Ti:Sapphire and OPO Laser Based Standard Laser Scanning Microscope

1INSERM U1051, Institut des Neurosciences de Montpellier (INM), Université de Montpellier, 2Université de Nîmes, 3CNRS, IES, UMR 5214, 4Aix-Marseille Université, CNRS, École Centrale Marseille, Institut Fresnel, UMR 7249, 5Montpellier RIO Imaging (MRI)

JoVE 54262


Lewis Acid-Base Interaction in Ph3P-BH3

JoVE 10316

Source: Tamara M. Powers, Department of Chemistry, Texas A&M University 

One of the goals of chemistry is to use models that account for trends and provide insights into the properties of reactants that contribute to reactivity. Substances have been classified as acids and bases since the time of the ancient Greeks, but the definition of acids and bases has been modified and expanded over the years.1 The ancient Greeks would characterize substances by taste, and defined acids as those that were sour-tasting, such as lemon juice and vinegar. The term "acid" is derived from the Latin term for "sour-tasting." Bases were characterized by their ability to counteract or neutralize acids. The first bases characterized were those of ashes from a fire, which were mixed with fats to make soap. In fact, the term "alkaline" is derived from the Arabic word for "roasting." Indeed, it has been known since ancient times that acids and bases can be combined to give a salt and water. The first widely-used description of an acid is that of the Swedish chemist, Svante Arrhenius, who in 1894 defined acids as substances which dissociate in water to give hydronium ions, and bases as substances which dissociate in water to give

 Inorganic Chemistry

Introduction to Mass Spectrometry

JoVE 5634

Source: Laboratory of Dr. Khuloud Al-Jamal - King's College London

Mass spectrometry is an analytical chemistry technique that enables the identification of unknown compounds within a sample, the quantification of known materials, the determination of the structure, and chemical properties of different molecules.

A mass spectrometer is composed of an ionization source, an analyzer, and a detector. The process involves the ionization of chemical compounds to generate ions. When using inductively coupled plasma (ICP), samples containing elements of interest are introduced into argon plasma as aerosol droplets. The plasma dries the aerosol, dissociates the molecules, and then removes an electron from the components to be detected by the mass spectrometer. Other ionization methods such as electrospray ionization (ESI) and matrix assisted laser desorption ionization (MALDI) are used to analyze biological samples. Following the ionization procedure, ions are separated in the mass spectrometer according to their mass-to-charge ratio (m/z), and the relative abundance of each ion type is measured. Finally, the detector commonly consists in an electron multiplier where the collision of ions with a charged anode leads to a cascade of increasing number of electrons, which can b

 Analytical Chemistry

Glycan Profiling of Plant Cell Wall Polymers using Microarrays

1Australian Centre of Excellence in Plant Cell Walls, School of Botany, University of Melbourne, 2Plant Cell Biology Research Centre, School of Botany, University of Melbourne, 3CSIRO Plant Industry, Black Mountain Laboratories, 4Department of Plant Biology and Biotechnology, University of Copenhagen

JoVE 4238


Raman Spectroscopy for Chemical Analysis

JoVE 5701

Source: Laboratory of Dr. Ryoichi Ishihara — Delft University of Technology

Raman spectroscopy is a technique for analyzing vibrational and other low frequency modes in a system. In chemistry it is used to identify molecules by their Raman fingerprint. In solid-state physics it is used to characterize materials, and more specifically to investigate their crystal structure or crystallinity. Compared to other techniques for investigating the crystal structure (e.g. transmission electron microscope and x-ray diffraction) Raman micro-spectroscopy is non-destructive, generally requires no sample preparation, and can be performed on small sample volumes. For performing Raman spectroscopy a monochromatic laser is shone on a sample. If required the sample can be coated by a transparent layer which is not Raman active (e.g., SiO2) or placed in DI water. The electromagnetic radiation (typically in the near infrared, visible, or near ultraviolet range) emitted from the sample is collected, the laser wavelength is filtered out (e.g., by a notch or bandpass filter), and the resulting light is sent through a monochromator (e.g., a grating) to a CCD detector. Using this, the inelastic scattered light, originating from Raman scattering, can be captured and used to construct the Raman spectrum o

 Analytical Chemistry

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