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Vibrational (Infrared and Raman) Spectroscopy And NMR, MRI Dr. Sunil Kumar, Department of Biotechnology Post Graduate College, Sec-11,Chandigarh Introduction • Spectroscopy is an analytical technique which helps determine structure. • It destroys little or no sample. • The amount of light absorbed by the sample is measured as wavelength is varied. 2 Types of Spectroscopy • Infrared (IR) spectroscopy measures the bond vibration frequencies in a molecule and is used to determine the functional group. • Mass spectrometry (MS) fragments the molecule and measures the masses. • Nuclear magnetic resonance (NMR) spectroscopy detects signals from hydrogen atoms and can be used to distinguish isomers. • Ultraviolet (UV) spectroscopy uses electron transitions to determine bonding patterns. => 3 The EM Spectrum The Spectrum and Molecular Effects => Chapter 12 => 5 Infrared Spectroscopy region of infrared that is most useful lies between 2.5-25 mm (4000-400 cm-1) depends on transitions between vibrational energy states :stretching and bending Molecular Excitation Modes Provides a spectroscopic tool for analyzing molecular components in pigments stretching bending scissoring twisting Stretching mode between molecules 1 2 E h ; Phonon energy K m1 m2 m1 m2 k Δf=K·ΔX c Wave number K is spring constant Units K: N/m=kg/s2 Molecular Vibrations Covalent bonds vibrate at only certain allowable frequencies. => Stretching Frequencies • Frequency decreases with increasing atomic weight. • Frequency increases with increasing bond energy. => Vibrational Modes Nonlinear molecule with n atoms usually has 3n 6 fundamental vibrational modes. => How much movement occurs in the vibration of a C-C bond? stretching vibration 154 pm 10 pm For a C-C bond with a bond length of 154 pm, the variation is about 10 pm. bending vibration 4o 10 pm For C-C-C bond angle a change of 4o is typical. This moves a carbon atom about 10 pm. Fingerprint of Molecule • Whole-molecule vibrations and bending vibrations are also quantitized. • No two molecules will give exactly the same IR spectrum (except enantiomers). • Simple stretching: 1600-3500 cm-1. • Complex vibrations: 600-1400 cm-1, called the “fingerprint region.” => IR Stretching Frequencies: What Do they Depend On? Directly on the strength of the bonding between the two atoms ( ~ k) Inversely on the reduced mass of the two atoms (v ~ 1/m) Expect: will increase with increasing bond strength (bond order) and decreasing mass Quantum mechanics: The frequency () depends on the energy gap between vibrational levels E = h= hc/(cm-1) Only the natural frequency will be absorbed The natural frequency (8.67 x 1013 s-1) is absorbed selectively An Infrared Spectrometer => Dipole Moment Must Change during for a vibration to be “IR active”! • In order to interact strongly with the EM radiation, the motion of the molecule must be such that the dipole moment changes. An infrared spectrum consists of a plot of absorbance versus frequency or wavenumber (1/λ) What type of vibrations would occur in pentane? Let’s examine the IR spectrum of pentane. IR spectrum C-H stretching C-H bending Increasing absorption of IR radiation C-C bending Increasing wavelength Increasing wavenumber (energy, frequency) What can we learn from IR spectroscopy? • Atoms vibrate with frequencies in the IR range • Chemical Analysis: • Match spectra to known databases – Identifying an unknown compound, Forensics, etc. • Monitor chemical reactions in-situ • Structural ideas: • Can determine what chemical groups are in a specific compound • Electronic Information: • Measure optical conductivity – Determine if Metal, Insulator, Superconductor, Semiconductor – Band Gaps, Drude model Basic Principles of Vibrational Spectroscopy Inelastic scattering of light at a molecule Sir Chandrashekhara Venkata Raman • November 7, 1888-November 21, 1970 • Won the Noble Prize in 1930 for Physics • Discovered the "Raman Effect" • Besides Discovering the Raman Effect, He studied extensively in X-Ray Diffractions, Acoustics, Optics, Dielectrics, Ultrasonics, Photo electricity, and colloidal particles. Principles of Raman Spectroscopy Molecular excitations are associated with vibrations or rotation of molecules which correlate with low frequency modes. Raman spectroscopy relies on the interaction of monochromatic light produced by a laser (in the infrared to near ultraviolet range) exciting an electron from its molecular bonding configuration with subsequent deexcitation to lower vibrational (rotational) excitation mode. Emitted radiation from the deexcitation is shifted in energy (frequency, wavelength) with respect to laser light energy. Challenge is to filter weak Raman transitions from strong Rayleigh scattering transition signals. Raman Principle When a sample is irradiated with monochromatic light (e. g. with laser light using discrete lines between 300 and 1064 nm) Different physical phenomena happen: 1. The main part of the incident light is transmitted without interaction 2. Roughly 10-4 part of the light is elastically scattered with no energy absorption --->Rayleigh line 3. A part of the incident light may be absorbed by electronic transitions and is emitted as ---> Flourescence 4. Only 10-8 of the incident light is inelastically scattered and interacts with the sample . The energy is partly absorbed ---> Raman spectrum Raman spectrometer. Monochromatic light is passed through a concentrated sample. Scattered light (dashed lines) is collected with the aid of a curved mirror. This is then diffracted through a monochromator which allows the identification of frequencies due to both Rayleigh and Raman scattering. Note that the lower mirror reflects transmitted light back through the sample to double the intensity of scattered light. But dominant process is elastic scattering: Rayleigh scattering — — Photon in Photon out No vibration No vibration If incident photon energy E; vibration energy v, then in terms of energy, photon out has energy: E-v Stokes scattering E+v anti-Stokes scattering E Rayleigh scattering Why Raman? • In Raman spectroscopy, by varying the frequency of the radiation, a spectrum can be produced, showing the intensity of the exiting radiation for each frequency. This spectrum will show which frequencies of radiation have been absorbed by the molecule to raise it to higher vibrational energy states. What Exactly Is Being Measured? METHANE When Light hits a sample, It is Excited, and is forced to vibrate and move. It is these vibrations which we are measuring. Stokes vs. Anti Stokes • • • • Atoms are at a certain energy level at any given time. As a laser light hits the atom, it is excited and reaches a higher level of energy, and then is brought back down. If an atom is at a given energy level, it can be excited then fall below the original level. Anti-stokes spectrum are mirror spectrums of Stokes Raman Spectrums Using Stokes/Peaks to Determine Vibrations This is a Raman Spectrum of Methane, along with RS, and IR. Each peak denotes a different vibration. The highest peak implies the strongest vibration. The smallest peak, the last one, shows the weakest of all the vibrations. In short, each vibration implies a different movement: these different movements imply different structures. Advantages of FT-Raman compared to FT-IR • Little or no sample preparation • High sensitivity for symmetric molecules, non polar bondings and homonuclear chains • Only low interferences of water and glass (measurement of aqueous solutions in glass vials) • Raman lines are usually narrower • Low frequency information to 50 cm-1 Nuclear Magnetic Resonance Spectroscopy And Magnetic Resonance Imaging Introduction to NMR Spectroscopy • Nuclear magnetic resonance spectroscopy is a powerful analytical technique used to characterize organic molecules by identifying carbon-hydrogen frameworks within molecules. • Two common types of NMR spectroscopy are used to characterize organic structure: 1H NMR is used to determine the type and number of H atoms in a molecule; 13C NMR is used to determine the type of carbon atoms in the molecule. • The source of energy in NMR is radio waves which have long wavelengths, and thus low energy and frequency. • When low-energy radio waves interact with a molecule, they can change the nuclear spins of some elements, including 1H and 13C. 38 Nuclear Spin • A nucleus with an odd atomic number or an odd mass number has a nuclear spin. • The spinning charged nucleus generates a magnetic field. => External Magnetic Field When placed in an external field, spinning protons act like bar magnets. => Two Energy States The magnetic fields of the spinning nuclei will align either with the external field, or against the field. A photon with the right amount of energy can be absorbed and cause the spinning proton to flip. => The energy difference between these two nuclear spin states corresponds to the low frequency RF region of the electromagnetic spectrum Nuclear Spins in B0 – for 1H and 13C, only two orientations are allowed. Nuclear Spin in B0 – The energy difference between allowed spin states increases linearly with applied field strength. – Values shown here are for 1H nuclei. Nuclear Magnetic Resonance • If the precessing nucleus is irradiated with electromagnetic radiation of the same frequency as the rate of precession, – the two frequencies couple – energy is absorbed – the nuclear spin is flipped from spin state +1/2 (with the applied field) to -1/2 (against the applied field). Nuclear Magnetic Resonance – (a) Precession and (b) after absorption of electromagnetic radiation. Nuclear Magnetic Resonance • Resonance: In NMR spectroscopy, resonance is the absorption of energy by a precessing nucleus and the resulting “flip” of its nuclear spin from a lower energy state to a higher energy state. • The precessing spins induce an oscillating magnetic field that is recorded as a signal by the instrument. – Signal: A recording in an NMR spectrum of a nuclear magnetic resonance. In order to undergo an NMR transition at a particular value of v, a specific set of circumstances called the resonance condition needs to exist The resonance condition. Exposure of the nucleus to radio frequency radiation sets up a magnetic field (of field strength B1, shown in grey) which has a frequency of oscillation. The resonance condition occurs when this frequency equals the Larmor frequency of the spin magnetic moment. Transition between spin states only occurs at the resonance condition. Nuclear Magnetic Resonance – If we were dealing with 1H nuclei isolated from all other atoms and electrons, any combination of applied field and radiation that produces a signal for one 1H would produce a signal for all 1H. The same is true of 13C nuclei. – Hydrogens in organic molecules, however, are not isolated from all other atoms. They are surrounded by electrons, which are caused to circulate by the presence of the applied field. – The circulation of electrons around a nucleus in an applied field is called diamagnetic current and the nuclear shielding resulting from it is called diamagnetic shielding. E and Magnet Strength • Energy difference is proportional to the magnetic field strength. • E = h = h B0 2 • Gyromagnetic ratio, , is a constant for each nucleus (26,753 s-1gauss-1 for H). • In a 14,092 gauss field, a 60 MHz photon is required to flip a proton. • Low energy, radio frequency. => Nuclear Magnetic Resonance Spectroscopy Introduction to NMR Spectroscopy • Protons in different environments absorb at slightly different frequencies, so they are distinguishable by NMR. • The frequency at which a particular proton absorbs is determined by its electronic environment. • The size of the magnetic field generated by the electrons around a proton determines where it absorbs. • Modern NMR spectrometers use a constant magnetic field strength B0, and then a narrow range of frequencies is applied to achieve the resonance of all protons. • Only nuclei that contain odd mass numbers (such as 1H, 13C, 19F and 31P) or odd atomic numbers (such as 2H and 14N) give rise to NMR signals. Magnetic Shielding • If all protons absorbed the same amount of energy in a given magnetic field, not much information could be obtained. • But protons are surrounded by electrons that shield them from the external field. • Circulating electrons create an induced magnetic field that opposes the external magnetic field. => Shielded Protons Magnetic field strength must be increased for a shielded proton to flip at the same frequency. => Protons in a Molecule Depending on their chemical environment, protons in a molecule are shielded by different amounts. => Nuclear Magnetic Resonance Spectroscopy 1H NMR—The Spectrum • An NMR spectrum is a plot of the intensity of a peak against its chemical shift, measured in parts per million (ppm). 54 Nuclear Magnetic Resonance Spectroscopy 1H NMR—The Spectrum • • • • NMR absorptions generally appear as sharp peaks. Increasing chemical shift is plotted from left to right. Most protons absorb between 0-10 ppm. The terms “upfield” and “downfield” describe the relative location of peaks. Upfield means to the right. Downfield means to the left. • NMR absorptions are measured relative to the position of a reference peak at 0 ppm on the d scale due to tetramethylsilane (TMS). TMS is a volatile inert compound that gives a single peak upfield from typical NMR absorptions. 55 Nuclear Magnetic Resonance Spectroscopy 1H NMR—The Spectrum • The chemical shift of the x axis gives the position of an NMR signal, measured in ppm, according to the following equation: • • By reporting the NMR absorption as a fraction of the NMR operating frequency, we get units, ppm, that are independent of the spectrometer. Four different features of a 1H NMR spectrum provide information about a compound’s structure: a. Number of signals b. Position of signals c. Intensity of signals. 56 d. Spin-spin splitting of signals. NMR Signals • The number of signals shows how many different kinds of protons are present. • The location of the signals shows how shielded or deshielded the proton is. • The intensity of the signal shows the number of protons of that type. • Signal splitting shows the number of protons on adjacent atoms. => Nuclear Magnetic Resonance Spectroscopy 1H NMR—Number of Signals • The number of NMR signals equals the number of different types of protons in a compound. • Protons in different environments give different NMR signals. • Equivalent protons give the same NMR signal. • To determine equivalent protons in cycloalkanes and alkenes, always draw all bonds to hydrogen. 58 Nuclear Magnetic Resonance Spectroscopy 1H NMR—Position of Signals • In the vicinity of the nucleus, the magnetic field generated by the circulating electron decreases the external magnetic field that the proton “feels”. • Since the electron experiences a lower magnetic field strength, it needs a lower frequency to achieve resonance. Lower frequency is to the right in an NMR spectrum, toward a lower chemical shift, so shielding shifts the absorption upfield. 59 Nuclear Magnetic Resonance Spectroscopy 1H NMR—Position of Signals • The less shielded the nucleus becomes, the more of the applied magnetic field (B0) it feels. • This deshielded nucleus experiences a higher magnetic field strength, to it needs a higher frequency to achieve resonance. • Higher frequency is to the left in an NMR spectrum, toward higher chemical shift—so deshielding shifts an absorption downfield. • Protons near electronegative atoms are deshielded, so they absorb downfield. 60 Nuclear Magnetic Resonance Spectroscopy 1H NMR—Position of Signals 61 Chemical Shift • Chemical shift depends on the (1) electronegativity of nearby atoms, (2) hybridization of adjacent atoms, and (3) diamagnetic effects from adjacent pi bonds. • Electronegativity Electron eg- Chemical CH3 -X ativity of X Shift () CH3 F CH3 OH CH3 Cl CH3 Br CH3 I 4.0 3.5 3.1 2.8 2.5 4.26 3.47 3.05 2.68 2.16 (CH3 ) 4 C (CH3 ) 4 Si 2.1 1.8 0.86 0.00 Nuclear Magnetic Resonance Spectroscopy 1H NMR—Chemical Shift Values • In a magnetic field, the six electrons in benzene circulate around the ring creating a ring current. • The magnetic field induced by these moving electrons reinforces the applied magnetic field in the vicinity of the protons. • The protons thus feel a stronger magnetic field and a higher frequency is needed for resonance. Thus they are deshielded and absorb downfield. 64 Nuclear Magnetic Resonance Spectroscopy 1H NMR—Chemical Shift Values • In a magnetic field, the loosely held electrons of the double bond create a magnetic field that reinforces the applied field in the vicinity of the protons. • The protons now feel a stronger magnetic field, and require a higher frequency for resonance. Thus the protons are deshielded and the absorption is downfield. 65 Nuclear Magnetic Resonance Spectroscopy 1H NMR—Chemical Shift Values • In a magnetic field, the electrons of a carbon-carbon triple bond are induced to circulate, but in this case the induced magnetic field opposes the applied magnetic field (B0). • Thus, the proton feels a weaker magnetic field, so a lower frequency is needed for resonance. The nucleus is shielded and the absorption is upfield. 66 Nuclear Magnetic Resonance Spectroscopy 1H NMR—Chemical Shift Values 67 Nuclear Magnetic Resonance Spectroscopy 1H NMR—Intensity of Signals • The area under an NMR signal is proportional to the number of absorbing protons. • An NMR spectrometer automatically integrates the area under the peaks, and prints out a stepped curve (integral) on the spectrum. • The height of each step is proportional to the area under the peak, which in turn is proportional to the number of absorbing protons. • Modern NMR spectrometers automatically calculate and plot the value of each integral in arbitrary units. • The ratio of integrals to one another gives the ratio of absorbing protons in a spectrum. Note that this gives a ratio, and not the absolute number, of absorbing protons. 68 Nuclear Magnetic Resonance Spectroscopy 1H NMR—Spin-Spin Splitting • Consider the spectrum below: 69 Spin-Spin Splitting in 1H NMR Spectra • Peaks are often split into multiple peaks due to magnetic interactions between nonequivalent protons on adjacent carbons, The process is called spin-spin splitting • The splitting is into one more peak than the number of H’s on the adjacent carbon(s), This is the “n+1 rule” • The relative intensities are in proportion of a binomial distribution given by Pascal’s Triangle • The set of peaks is a multiplet (2 = doublet, 3 = triplet, 4 = quartet, 5=pentet, 6=hextet, 7=heptet…..) 1 1 1 1 2 1 1 3 3 1 1 4 6 4 1 1 5 10 10 5 1 1 6 15 20 15 6 1 singlet doublet triplet quartet pentet hextet heptet Rules for Spin-Spin Splitting • Equivalent protons do not split each other • Protons that are farther than two carbon atoms apart do not split each other Origins of Signal Splitting • Signal coupling: An interaction in which the nuclear spins of adjacent atoms influence each other and lead to the splitting of NMR signals. • Coupling constant (J): The separation on an NMR spectrum (in hertz) between adjacent peaks in a multiplet. – A quantitative measure of the spin-spin coupling with adjacent nuclei. Origins of Signal Splitting • Illustration of spin-spin coupling that gives rise to signal splitting in 1H-NMR spectra. The Origin of 1H NMR—Spin-Spin Splitting Let us now consider how a triplet arises: • When placed in an applied magnetic field (B0), the adjacent protons Ha and Hb can each be aligned with () or against () B0. • Thus, the absorbing proton feels three slightly different magnetic fields—one slightly larger than B0(ab). one slightly smaller than B0(ab) and one the same strength as B0 (ab). 74 The Origin of 1H NMR—Spin-Spin Splitting • Because the absorbing proton feels three different magnetic fields, it absorbs at three different frequencies in the NMR spectrum, thus splitting a single absorption into a triplet. • Because there are two different ways to align one proton with B0, and one proton against B0—that is, ab and ab—the middle peak of the triplet is twice as intense as the two outer peaks, making the ratio of the areas under the three peaks 1:2:1. • Two adjacent protons split an NMR signal into a triplet. • When two protons split each other, they are said to be coupled. • The spacing between peaks in a split NMR signal, measured by the J value, is equal for coupled protons. 75 The Origin of 1H NMR—Spin-Spin Splitting 76 Nuclear Magnetic Resonance Spectroscopy 1H NMR—Structure Determination 77 Nuclear Magnetic Resonance Spectroscopy 1H NMR—Structure Determination 78 Nuclear Magnetic Resonance Spectroscopy 1H NMR—Structure Determination 79 Nuclear Magnetic Resonance Spectroscopy 1H NMR—Structure Determination 80 Magnetic Resonance Imaging (MRI) Introduction • What is MRI? – Magnetic resonance imaging (MRI) is a spectroscopic imaging technique used in medical settings to produce images of the inside of the human body. – MRI is based on the principles of nuclear magnetic resonance (NMR), which is a spectroscopic technique used to obtain microscopic chemical and physical data about molecules – In 1977 the first MRI exam was performed on a human being. It took 5 hours to produce one image. Introduction • How Does it Work? – The magnetic resonance imaging is accomplished through the absorption and emission of energy of the radio frequency (RF) range of the electromagnetic spectrum. The Components: • A magnet which produces a very powerful uniform magnetic field. • Gradient Magnets which are much lower in strength. • Equipment to transmit radio frequency (RF). • A very powerful computer system, which translates the signals transmitted by the coils. The Magnet • The most important component of the MRI scanner is the magnet: – The magnets currently used in scanners today are in the .5tesla to 2.0-tesla range (5,000 to 20,000-gauss). Higher values are used for research. – Earth magnetic field: 0.5-gauss The Magnet (cont.) • There are three types of magnets used in MRI systems: – Resistive magnets – Permanent magnets – Super conducting magnets (the most commonly used type in MRI scanners). • In addition to the main magnet, the MRI machine also contains three gradient magnets. These magnets have a much lower magnetic field and are used to create a variable field. The Technology • How Does It All Work? • Spin: – The atoms that compose the human body have a property known as spin (a fundamental property of all atoms in nature like mass or charge). – Spin can be thought of as a small magnetic field and can be given a + or – sign and a mathematical value of multiples of ½. – Components of an atom such as protons, electrons and neutrons all have spin. The Technology (cont.) • Spin (cont.): – Protons and neutron spins are known as nuclear spins. – An unpaired component has a spin of ½ and two particles with opposite spins cancel one another. – In NMR it is the unpaired nuclear spins that produce a signal in a magnetic field. The Technology (cont.) • Human body is mainly composed of fat and water, which makes the human body composed of about 63% hydrogen. • Why Are Protons Important to MRI? – positively charged – spin about a central axis – a moving (spinning) charge creates a magnetic field. – the straight arrow (vector) indicates the direction of the magnetic field. The Technology (cont.) • When placed in a large magnetic field, hydrogen atoms have a strong tendency to align in the direction of the magnetic filed • Inside the bore of the scanner, the magnetic field runs down the center of the tube in which the patient is placed, so the hydrogen protons will line up in either the direction of the feet or the head. • The majority will cancel each other, but the net number of protons is sufficient to produce an image. The Technology (cont.) • Energy Absorption: – The MRI machine applies radio frequency (RF) pulse that is specific to hydrogen. – The RF pulses are applied through a coil that is specific to the part of the body being scanned. RF Coil as the Receiver • After excitation, the magnetization flips to being partially or completely “flipped”. • The M-vector now precesses around the Bofield at the Larmor frequency. • A coil placed near the object can detect this magnetization Behavior when radio excitation is stopped • If we stop this RF excitation, it returns to equilibrium ( M z M 0 1 e t / T1 ) T1 = spin-lattice relaxation time T1 is one source of clinical info we take advantage of in MRI. The Technology (Cont.) Resonance (cont.) The gradient magnets are rapidly turned on and off which alters the main magnetic field. – The pulse directed to a specific area of the body causes the protons to absorb energy and spin in different direction, which is known as resonance Frequency (Hz) of energy absorption depends on strength of external magnetic field. The Technology (cont.) Larmor Equation = 2 0 For hydrogen at 1.5T: 0 2.675x108 s1T 1.5T 63.864MHz 0 0 • The resonance frequency, 0, is referred to as the Larmor frequency. Relaxation and Receiving Receive Radio Frequency Field • receiving coil: measure net magnetization (M) • readout interval (~10-100 ms) • relaxation: after RF field turned on and off, magnetization returns to normal longitudinal magnetization T1 signal recovers transverse magnetization T2 signal decays Source: Robert Cox’s web slides T1 and TR T1 = recovery of longitudinal (B0) magnetization • used in anatomical images • ~500-1000 msec (longer with bigger B0) TR (repetition time) = time to wait after excitation before sampling T1 Source: Mark Cohen’s web slides The Technology (cont.) • Imaging: – When the RF pulse is turned off the hydrogen protons slowly return to their natural alignment within the magnetic field and release their excess stored energy. This is known as relaxation. • What happens to the released energy? – Released as heat OR – Exchanged and absorbed by other protons OR – Released as Radio Waves. The Technology (cont.) • Measuring the MR Signal: – the moving proton vector induces a signal in the RF antenna – The signal is picked up by a coil and sent to the computer system. the received signal is sinusoidal in nature – The computer receives mathematical data, which is converted through the use of a Fourier transform into an image. The Image Physics of MRI It is an interplay of • Magnetism • Resonance Recap: What Does the Image Represent? • For every unit volume of tissue, there is a number of cells, these cells contain water molecules, each water molecule contain one oxygen and two hydrogen atoms. • Each hydrogen atom contains one proton in its nucleus. Different tissues thus produce different images based on the amount of their hydrogen atoms producing a signal Summary: Magnetic Resonance Principles • Some atomic nuclei have a property called “spin” • Spin gives the nuclei a magnetic moment • These moments are randomly oriented • When the spins are placed in a magnetic field, they align either with or against the field. Summary: Magnetic Resonance Principles • The two states are not equal in energy and therefore not equally populated. • This results in a net polarization or longitudinal magnetization • Transverse magnetization can be created by “flipping” the spins with a magnetic field applied in the rotating frame of reference (i.e an RF pulse) • After the “flip” the spins return to the equilibrium condition through the T1 and T2 relaxation mechanisms measured by the RF coil.