Structural biology , as defined by the Journal of Structural Biology , deals with structural analysis of living material (formed, composed of, and/or maintained and refined by living cells) at every level of organization.
128-468: Early structural biologists throughout the 19th and early 20th centuries were primarily only able to study structures to the limit of the naked eye's visual acuity and through magnifying glasses and light microscopes. In the 20th century, a variety of experimental techniques were developed to examine the 3D structures of biological molecules. The most prominent techniques are X-ray crystallography , nuclear magnetic resonance , and electron microscopy . Through
256-411: A diffraction pattern . These experiments led to the development of X-ray crystallography , and its usage in exploring biological structures. In 1951, Rosalind Franklin and Maurice Wilkins used X-ray diffraction patterns to capture the first image of deoxyribonucleic acid (DNA). Francis Crick and James Watson modeled the double helical structure of DNA using this same technique in 1953 and received
384-468: A gain medium instead of using stimulated emission from atomic or molecular excitations. In an FEL, a bunch of electrons passes through a magnetic structure called an undulator or wiggler to generate radiation, which re-interacts with the electrons to make them emit coherently, exponentially increasing its intensity. As electron kinetic energy and undulator parameters can be adapted as desired, free-electron lasers are tunable and can be built for
512-548: A wiggler , because the Lorentz force of the field forces the electrons in the beam to wiggle transversely, traveling along a sinusoidal path about the axis of the undulator. The transverse acceleration of the electrons across this path results in the release of photons , which are monochromatic but still incoherent, because the electromagnetic waves from randomly distributed electrons interfere constructively and destructively in time. The resulting radiation power scales linearly with
640-461: A branch of molecular biology , biochemistry , and biophysics concerned with the molecular structure of biological macromolecules (especially proteins , made up of amino acids , RNA or DNA , made up of nucleotides , and membranes , made up of lipids ), how they acquire the structures they have, and how alterations in their structures affect their function. This subject is of great interest to biologists because macromolecules carry out most of
768-481: A clear view, a resolution of 0.1–0.3 nm is required. The short pulse durations allow images of X-ray diffraction patterns to be recorded before the molecules are destroyed. The bright, fast X-rays were produced at the Linac Coherent Light Source at SLAC. As of 2014, LCLS was the world's most powerful X-ray FEL. Due to the increased repetition rates of the next-generation X-ray FEL sources, such as
896-421: A design energy by a particle accelerator , usually a linear particle accelerator . Then the beam passes through a periodic arrangement of magnets with alternating poles across the beam path, which creates a side to side magnetic field . The direction of the beam is called the longitudinal direction, while the direction across the beam path is called transverse. This array of magnets is called an undulator or
1024-418: A distance equal to one radiation wavelength. This interaction drives all electrons to begin emitting coherent radiation. Emitted radiation can reinforce itself perfectly whereby wave crests and wave troughs are optimally superimposed on one another. This results in an exponential increase of emitted radiation power, leading to high beam intensities and laser-like properties. Examples of facilities operating on
1152-542: A high-voltage supply. The electron beam must be maintained in a vacuum , which requires the use of numerous vacuum pumps along the beam path. While this equipment is bulky and expensive, free-electron lasers can achieve very high peak powers, and the tunability of FELs makes them highly desirable in many disciplines, including chemistry, structure determination of molecules in biology, medical diagnosis , and nondestructive testing . The Fritz Haber Institute in Berlin completed
1280-441: A higher chemical shift). Unless the local symmetry of such molecular orbitals is very high (leading to "isotropic" shift), the shielding effect will depend on the orientation of the molecule with respect to the external field ( B 0 ). In solid-state NMR spectroscopy, magic angle spinning is required to average out this orientation dependence in order to obtain frequency values at the average or isotropic chemical shifts. This
1408-452: A laser tuned to the resonance of the FEL. Such a temporally coherent seed can be produced by more conventional means, such as by high harmonic generation (HHG) using an optical laser pulse. This results in coherent amplification of the input signal; in effect, the output laser quality is characterized by the seed. While HHG seeds are available at wavelengths down to the extreme ultraviolet, seeding
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#17328733618541536-447: A lower energy when their spins are parallel, not anti-parallel. This parallel spin alignment of distinguishable particles does not violate the Pauli exclusion principle . The lowering of energy for parallel spins has to do with the quark structure of these two nucleons. As a result, the spin ground state for the deuteron (the nucleus of deuterium , the H isotope of hydrogen), which has only
1664-460: A magnetic field and when the RF was of a frequency specific to the identity of the nuclei. When this absorption occurs, the nucleus is described as being in resonance . Different atomic nuclei within a molecule resonate at different (radio) frequencies in the same applied static magnetic field, due to various local magnetic fields. The observation of such magnetic resonance frequencies of the nuclei present in
1792-544: A mid-infrared and terahertz FEL in 2013. The lack of mirror materials that can reflect extreme ultraviolet and x-rays means that X-ray free electron lasers (XFEL) need to work without a resonant cavity . Consequently, in an X-ray FEL (XFEL) the beam is produced by a single pass of radiation through the undulator . This requires that there be enough amplification over a single pass to produce an appropriate beam. Hence, XFELs use long undulator sections that are tens or hundreds of meters long. This allows XFELs to produce
1920-530: A molecule makes it possible to determine essential chemical and structural information about the molecule. The improvements of the NMR method benefited from the development of electromagnetic technology and advanced electronics and their introduction into civilian use. Originally as a research tool it was limited primarily to dynamic nuclear polarization , by the work of Anatole Abragam and Albert Overhauser , and to condensed matter physics , where it produced one of
2048-411: A protein encoded by a protooncogene that is an important drug target in cancer . Similar research has been conducted for HIV targets to treat people with AIDS . Researchers are also developing new antimicrobials for mycobacterial infections using structure-driven drug discovery. Nuclear magnetic resonance Nuclear magnetic resonance ( NMR ) is a physical phenomenon in which nuclei in
2176-462: A proton and a neutron, corresponds to a spin value of 1 , not of zero . On the other hand, because of the Pauli exclusion principle, the tritium isotope of hydrogen must have a pair of anti-parallel spin neutrons (of total spin zero for the neutron spin-pair), plus a proton of spin 1 / 2 . Therefore, the tritium total nuclear spin value is again 1 / 2 , just like
2304-464: A radio frequency pulse, induces an electromagnetic field (emf) in the receiver coil of the NMR spectrometer. This generates an oscillating current and a non-linear induced transverse magnetic field which returns the spin system to equilibrium faster than other mechanisms of relaxation. RD can result in line broadening and measurement of a shorter spin-lattice relaxation time ( T 1 {\displaystyle T_{1}} ). For instance,
2432-541: A range of frequencies centered about the carrier frequency , with the range of excitation ( bandwidth ) being inversely proportional to the pulse duration, i.e. the Fourier transform of a short pulse contains contributions from all the frequencies in the neighborhood of the principal frequency. The restricted range of the NMR frequencies for most light spin- 1 / 2 nuclei made it relatively easy to use short (1 - 100 microsecond) radio frequency pulses to excite
2560-471: A range of frequencies, while another orthogonal coil, designed not to receive radiation from the transmitter, received signals from nuclei that reoriented in solution. As of 2014, low-end refurbished 60 MHz and 90 MHz systems were sold as FT-NMR instruments, and in 2010 the "average workhorse" NMR instrument was configured for 300 MHz. CW spectroscopy is inefficient in comparison with Fourier analysis techniques (see below) since it probes
2688-518: A sample of water in a 400 MHz NMR spectrometer will have T R D {\displaystyle T_{RD}} around 20 ms, whereas its T 1 {\displaystyle T_{1}} is hundreds of milliseconds. This effect is often described using modified Bloch equations that include terms for radiation damping alongside the conventional relaxation terms. The longitudinal relaxation time of radiation damping ( T R D {\displaystyle T_{RD}} )
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#17328733618542816-494: A seeding technique called "High-Gain Harmonic-Generation" that works to X-ray wavelength has been developed. The technique, which can be multiple-staged in an FEL to achieve increasingly shorter wavelengths, utilizes a longitudinal shift of the radiation relative to the electron bunch to avoid the reduced beam quality caused by a previous stage. This longitudinal staging along the beam is called "Fresh-Bunch". This technique
2944-422: A single other intermediate atom, etc. Through-space interactions relate to actual geometric distances and angles, including effects of dipolar coupling and the nuclear Overhauser effect . Free-electron laser A free-electron laser ( FEL ) is a fourth generation light source producing extremely brilliant and short pulses of radiation. An FEL functions much as a laser but employs relativistic electrons as
3072-420: A spectrum that contains many different types of information about the molecules in the sample. In multi-dimensional nuclear magnetic resonance spectroscopy, there are at least two pulses: one leads to the directly detected signal and the others affect the starting magnetization and spin state prior to it. The full analysis involves repeating the sequence with the pulse timings systematically varied in order to probe
3200-406: A static magnetic field. However, in the ordered phases of magnetic materials, very large internal fields are produced at the nuclei of magnetic ions (and of close ligands ), which allow NMR to be performed in zero applied field. Additionally, radio-frequency transitions of nuclear spin I > 1 / 2 with large enough electric quadrupolar coupling to the electric field gradient at
3328-405: A strong constant magnetic field are disturbed by a weak oscillating magnetic field (in the near field ) and respond by producing an electromagnetic signal with a frequency characteristic of the magnetic field at the nucleus. This process occurs near resonance , when the oscillation frequency matches the intrinsic frequency of the nuclei, which depends on the strength of the static magnetic field,
3456-424: A wider frequency range than any other type of laser, currently ranging in wavelength from microwaves , through terahertz radiation and infrared , to the visible spectrum , ultraviolet , and X-ray . The first free-electron laser was developed by John Madey in 1971 at Stanford University using technology developed by Hans Motz and his coworkers, who built an undulator at Stanford in 1953, using
3584-506: Is bioinformatics to look for patterns among the diverse sequences that give rise to particular shapes. Researchers often can deduce aspects of the structure of integral membrane proteins based on the membrane topology predicted by hydrophobicity analysis . See protein structure prediction . Structural biologists have made significant contributions towards understanding the molecular components and mechanisms underlying human diseases. For example, cryo-EM and ssNMR have been used to study
3712-412: Is a key feature of NMR that the resonance frequency of nuclei in a particular sample substance is usually directly proportional to the strength of the applied magnetic field. It is this feature that is exploited in imaging techniques; if a sample is placed in a non-uniform magnetic field then the resonance frequencies of the sample's nuclei depend on where in the field they are located. This effect serves as
3840-450: Is a related technique in which transitions between electronic rather than nuclear spin levels are detected. The basic principles are similar but the instrumentation, data analysis, and detailed theory are significantly different. Moreover, there is a much smaller number of molecules and materials with unpaired electron spins that exhibit ESR (or electron paramagnetic resonance (EPR)) absorption than those that have NMR absorption spectra. On
3968-419: Is associated with a non-zero magnetic dipole moment, μ → {\displaystyle {\vec {\mu }}} , via the relation μ → = γ S → {\displaystyle {\vec {\mu }}=\gamma {\vec {S}}} where γ is the gyromagnetic ratio . Classically, this corresponds to the proportionality between
Structural biology - Misplaced Pages Continue
4096-497: Is clear that to pave the way towards single-particle X-ray FEL imaging at full repetition rates, several challenges have to be overcome before the next resolution revolution can be achieved. New biomarkers for metabolic diseases: taking advantage of the selectivity and sensitivity when combining infrared ion spectroscopy and mass spectrometry scientists can provide a structural fingerprint of small molecules in biological samples, like blood or urine. This new and unique methodology
4224-502: Is commonly used to analyze the dynamic movements of biological molecules. In 1975, the first simulation of a biological folding process using MD was published in Nature. Recently, protein structure prediction was significantly improved by a new machine learning method called AlphaFold . Some claim that computational approaches are starting to lead the field of structural biology research. Biomolecules are too small to see in detail even with
4352-468: Is generating exciting new possibilities to better understand metabolic diseases and develop novel diagnostic and therapeutic strategies. Research by Glenn Edwards and colleagues at Vanderbilt University 's FEL Center in 1994 found that soft tissues including skin, cornea , and brain tissue could be cut, or ablated , using infrared FEL wavelengths around 6.45 micrometres with minimal collateral damage to adjacent tissue. This led to surgeries on humans,
4480-406: Is given by the equation [1]. T R D = 2 γ μ 0 η Q M 0 {\displaystyle T_{RD}={\frac {2}{\gamma \mu _{0}\eta QM_{0}}}} [1] where γ {\displaystyle \gamma } is the gyromagnetic ratio , μ 0 {\displaystyle \mu _{0}}
4608-559: Is in the initial, equilibrium (mixed) state. The precessing nuclei can also fall out of alignment with each other and gradually stop producing a signal. This is called T 2 or transverse relaxation . Because of the difference in the actual relaxation mechanisms involved (for example, intermolecular versus intramolecular magnetic dipole-dipole interactions), T 1 is usually (except in rare cases) longer than T 2 (that is, slower spin-lattice relaxation, for example because of smaller dipole-dipole interaction effects). In practice,
4736-420: Is influenced significantly by system parameters. It is notably more prominent in systems where the NMR probe possesses a high quality factor ( Q {\displaystyle Q} ) and a high filling factor , resulting in a strong coupling between the probe coil and the sample. The phenomenon is also impacted by the concentration of the nuclei within the sample and their magnetic moments, which can intensify
4864-662: Is not feasible at x-ray wavelengths due to the lack of conventional x-ray lasers. In late 2010, in Italy, the seeded-FEL source FERMI@Elettra started commissioning, at the Trieste Synchrotron Laboratory . FERMI@Elettra is a single-pass FEL user-facility covering the wavelength range from 100 nm (12 eV) to 10 nm (124 eV), located next to the third-generation synchrotron radiation facility ELETTRA in Trieste, Italy. In 2001, at Brookhaven national laboratory ,
4992-438: Is one of the techniques that has been used to design quantum automata, and also build elementary quantum computers . In the first few decades of nuclear magnetic resonance, spectrometers used a technique known as continuous-wave (CW) spectroscopy, where the transverse spin magnetization generated by a weak oscillating magnetic field is recorded as a function of the oscillation frequency or static field strength B 0 . When
5120-720: Is the Bohr frequency Δ E / ℏ {\displaystyle \Delta {E}/\hbar } of the S x {\displaystyle S_{x}} and S y {\displaystyle S_{y}} expectation values. Precession of non-equilibrium magnetization in the applied magnetic field B 0 occurs with the Larmor frequency ω L = 2 π ν L = − γ B 0 , {\displaystyle \omega _{L}=2\pi \nu _{L}=-\gamma B_{0},} without change in
5248-405: Is the elementary charge . Expressed in practical units, the dimensionless undulator parameter is K = 0.934 ⋅ B 0 [T] ⋅ λ u [cm] {\displaystyle K=0.934\cdot B_{0}\,{\text{[T]}}\cdot \lambda _{u}\,{\text{[cm]}}} . In most cases, the theory of classical electromagnetism adequately accounts for
Structural biology - Misplaced Pages Continue
5376-400: Is the magnetic permeability , M 0 {\displaystyle M_{0}} is the equilibrium magnetization per unit volume, Q {\displaystyle Q} is the filling factor of the probe which is the ratio of the probe coil volume to the sample volume enclosed, Q = ω L R {\displaystyle Q={\frac {\omega L}{R}}}
5504-460: Is the magnitude of the field. This means that the spin magnetization, which is proportional to the sum of the spin vectors of nuclei in magnetically equivalent sites (the expectation value of the spin vector in quantum mechanics), moves on a cone around the B field. This is analogous to the precessional motion of the axis of a tilted spinning top around the gravitational field. In quantum mechanics, ω {\displaystyle \omega }
5632-431: Is the precession of the spin magnetization around the magnetic field at the nucleus, with the angular frequency ω = − γ B {\displaystyle \omega =-\gamma B} where ω = 2 π ν {\displaystyle \omega =2\pi \nu } relates to the oscillation frequency ν {\displaystyle \nu } and B
5760-697: Is the quality factor of the probe, and , L {\displaystyle L} , and R {\displaystyle R} are the resonance frequency, inductance, and resistance of the coil, respectively. The quantification of line broadening due to radiation damping can be determined by measuring the Δ v 1 2 {\displaystyle \Delta v_{\frac {1}{2}}} and use equation [2]. T R D − 1 = π 0.8384 Δ v 1 2 {\displaystyle T_{RD}^{-1}={\frac {\pi }{0.8384}}\Delta v_{\frac {1}{2}}} [2] Radiation damping in NMR
5888-438: Is the undulator wavelength (the spatial period of the magnetic field), γ {\displaystyle \gamma } is the relativistic Lorentz factor and the proportionality constant depends on the undulator geometry and is of the order of 1. This formula can be understood as a combination of two relativistic effects. Imagine you are sitting on an electron passing through the undulator. Due to Lorentz contraction
6016-612: Is therefore S z = mħ . The z -component of the magnetic moment is simply: μ z = γ S z = γ m ℏ . {\displaystyle \mu _{z}=\gamma S_{z}=\gamma m\hbar .} Consider nuclei with a spin of one-half, like H , C or F . Each nucleus has two linearly independent spin states, with m = 1 / 2 or m = − 1 / 2 (also referred to as spin-up and spin-down, or sometimes α and β spin states, respectively) for
6144-626: Is unnecessary in conventional NMR investigations of molecules in solution, since rapid "molecular tumbling" averages out the chemical shift anisotropy (CSA). In this case, the "average" chemical shift (ACS) or isotropic chemical shift is often simply referred to as the chemical shift. In 1949, Suryan first suggested that the interaction between a radiofrequency coil and a sample's bulk magnetization could explain why experimental observations of relaxation times differed from theoretical predictions. Building on this idea, Bloembergen and Pound further developed Suryan's hypothesis by mathematically integrating
6272-480: The European XFEL , the expected number of diffraction patterns is also expected to increase by a substantial amount. The increase in the number of diffraction patterns will place a large strain on existing analysis methods. To combat this, several methods have been researched to sort the huge amount of data that typical X-ray FEL experiments will generate. While the various methods have been shown to be effective, it
6400-552: The HIV envelope allows the virus to evade human immune responses. Structural biology is also an important component of drug discovery . Scientists can identify targets using genomics, study those targets using structural biology, and develop drugs that are suited for those targets. Specifically, ligand- NMR , mass spectrometry , and X-ray crystallography are commonly used techniques in the drug discovery process. For example, researchers have used structural biology to better understand Met ,
6528-527: The Maxwell–Bloch equations , a process through which they introduced the concept of "radiation damping." Radiation damping (RD) in Nuclear Magnetic Resonance (NMR) is an intrinsic phenomenon observed in many high-field NMR experiments, especially relevant in systems with high concentrations of nuclei like protons or fluorine. RD occurs when transverse bulk magnetization from the sample, following
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#17328733618546656-450: The Office of Naval Research announced it had awarded Raytheon a contract to develop a 100 kW experimental FEL. On March 18, 2010 Boeing Directed Energy Systems announced the completion of an initial design for U.S. Naval use. A prototype FEL system was demonstrated, with a full-power prototype scheduled by 2018. The FEL prize is given to a person who has contributed significantly to
6784-404: The square root of the number of spectra added (see random walk ). Hence the overall signal-to-noise ratio increases as the square-root of the number of spectra measured. However, monitoring an NMR signal at a single frequency as a function of time may be better suited for kinetic studies than pulsed Fourier-transform NMR spectrosocopy. Most applications of NMR involve full NMR spectra, that is,
6912-412: The wiggler magnetic configuration. Madey used a 43 MeV electron beam and 5 m long wiggler to amplify a signal. To create an FEL, an electron gun is used. A beam of electrons is generated by a short laser pulse illuminating a photocathode located inside a microwave cavity and accelerated to almost the speed of light in a device called a photoinjector . The beam is further accelerated to
7040-404: The z -axis is chosen to be along B 0 , and the above expression reduces to: E = − μ z B 0 , {\displaystyle E=-\mu _{\mathrm {z} }B_{0}\,,} or alternatively: E = − γ m ℏ B 0 . {\displaystyle E=-\gamma m\hbar B_{0}\,.} As a result,
7168-474: The 2020s zero- to ultralow-field nuclear magnetic resonance ( ZULF NMR ), a form of spectroscopy that provides abundant analytical results without the need for large magnetic fields , was developed. It is combined with a special technique that makes it possible to hyperpolarize atomic nuclei . All nucleons, that is neutrons and protons , composing any atomic nucleus , have the intrinsic quantum property of spin , an intrinsic angular momentum analogous to
7296-496: The NMR frequency of the spins. This oscillating magnetization vector induces a voltage in a nearby pickup coil, creating an electrical signal oscillating at the NMR frequency. This signal is known as the free induction decay (FID), and it contains the sum of the NMR responses from all the excited spins. In order to obtain the frequency-domain NMR spectrum (NMR absorption intensity vs. NMR frequency) this time-domain signal (intensity vs. time) must be Fourier transformed. Fortunately,
7424-406: The NMR response at individual frequencies or field strengths in succession. Since the NMR signal is intrinsically weak, the observed spectrum suffers from a poor signal-to-noise ratio . This can be mitigated by signal averaging, i.e. adding the spectra from repeated measurements. While the NMR signal is the same in each scan and so adds linearly, the random noise adds more slowly – proportional to
7552-626: The Nobel Prize in Medicine along with Wilkins in 1962. Pepsin crystals were the first proteins to be crystallized for use in X-ray diffraction, by Theodore Svedberg who received the 1962 Nobel Prize in Chemistry. The first tertiary protein structure , that of myoglobin , was published in 1958 by John Kendrew . During this time, modeling of protein structures was done using balsa wood or wire models. With
7680-550: The RF inhomogeneity of the resonant pulse). In the corresponding FT-NMR spectrum—meaning the Fourier transform of the free induction decay — the width of the NMR signal in frequency units is inversely related to the T 2 * time. Thus, a nucleus with a long T 2 * relaxation time gives rise to a very sharp NMR peak in the FT-NMR spectrum for a very homogeneous ( "well-shimmed" ) static magnetic field, whereas nuclei with shorter T 2 * values give rise to broad FT-NMR peaks even when
7808-450: The SASE FEL principle include the: In 2022, an upgrade to Stanford University ’s Linac Coherent Light Source (LCLS-II) used temperatures around −271 °C to produce 10 pulses/second of near light-speed electrons, using superconducting niobium cavities. One problem with SASE FELs is the lack of temporal coherence due to a noisy startup process. To avoid this, one can "seed" an FEL with
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#17328733618547936-412: The above that all nuclei of the same nuclide (and hence the same γ ) would resonate at exactly the same frequency but this is not the case. The most important perturbation of the NMR frequency for applications of NMR is the "shielding" effect of the shells of electrons surrounding the nucleus. Electrons, similar to the nucleus, are also charged and rotate with a spin to produce a magnetic field opposite to
8064-424: The added benefit of minimal collateral damage. A review of FELs for medical uses is given in the 1st edition of Tunable Laser Applications. Several small, clinical lasers tunable in the 6 to 7 micrometre range with pulse structure and energy to give minimal collateral damage in soft tissue have been created. At Vanderbilt, there exists a Raman shifted system pumped by an Alexandrite laser. Rox Anderson proposed
8192-434: The advancement of the field of free-electron lasers. In addition, it gives the international FEL community the opportunity to recognize its members for their outstanding achievements. The prize winners are announced at the FEL conference, which currently takes place every two years. The Young Scientist FEL Award (or "Young Investigator FEL Prize") is intended to honor outstanding contributions to FEL science and technology from
8320-515: The aggregation of amyloid fibrils, which are associated with Alzheimer's disease , Parkinson's disease , and type II diabetes . In addition to amyloid proteins, scientists have used cryo-EM to produce high resolution models of tau filaments in the brain of Alzheimer's patients which may help develop better treatments in the future. Structural biology tools can also be used to explain interactions between pathogens and hosts. For example, structural biology tools have enabled virologists to understand how
8448-430: The angular momentum and the magnetic dipole moment of a spinning charged sphere, both of which are vectors parallel to the rotation axis whose length increases proportional to the spinning frequency. It is the magnetic moment and its interaction with magnetic fields that allows the observation of NMR signal associated with transitions between nuclear spin levels during resonant RF irradiation or caused by Larmor precession of
8576-413: The applied magnetic field. In general, this electronic shielding reduces the magnetic field at the nucleus (which is what determines the NMR frequency). As a result, the frequency required to achieve resonance is also reduced. This shift in the NMR frequency due to the electronic molecular orbital coupling to the external magnetic field is called chemical shift , and it explains why NMR is able to probe
8704-569: The average magnetic moment after resonant irradiation. Nuclides with even numbers of both protons and neutrons have zero nuclear magnetic dipole moment and hence do not exhibit NMR signal. For instance, O is an example of a nuclide that produces no NMR signal, whereas C , P , Cl and Cl are nuclides that do exhibit NMR spectra. The last two nuclei have spin S > 1 / 2 and are therefore quadrupolar nuclei. Electron spin resonance (ESR)
8832-660: The basis of magnetic resonance imaging . The principle of NMR usually involves three sequential steps: The two magnetic fields are usually chosen to be perpendicular to each other as this maximizes the NMR signal strength. The frequencies of the time-signal response by the total magnetization ( M ) of the nuclear spins are analyzed in NMR spectroscopy and magnetic resonance imaging. Both use applied magnetic fields ( B 0 ) of great strength, usually produced by large currents in superconducting coils, in order to achieve dispersion of response frequencies and of very high homogeneity and stability in order to deliver spectral resolution ,
8960-402: The behavior of free electron lasers. For sufficiently short wavelengths, quantum effects of electron recoil and shot noise may have to be considered. Free-electron lasers require the use of an electron accelerator with its associated shielding, as accelerated electrons can be a radiation hazard if not properly contained. These accelerators are typically powered by klystrons , which require
9088-413: The brightest X-ray pulses of any human-made x-ray source. The intense pulses from the X-ray laser lies in the principle of self-amplified spontaneous emission (SASE), which leads to microbunching. Initially all electrons are distributed evenly and emit only incoherent spontaneous radiation. Through the interaction of this radiation and the electrons' oscillations , they drift into microbunches separated by
9216-421: The bunched electrons is in phase, and the fields add together coherently . The radiation intensity grows, causing additional microbunching of the electrons, which continue to radiate in phase with each other. This process continues until the electrons are completely microbunched and the radiation reaches a saturated power several orders of magnitude higher than that of the undulator radiation. The wavelength of
9344-407: The chemical environment, and the magnetic properties of the isotope involved; in practical applications with static magnetic fields up to ca. 20 tesla , the frequency is similar to VHF and UHF television broadcasts (60–1000 MHz). NMR results from specific magnetic properties of certain atomic nuclei. High-resolution nuclear magnetic resonance spectroscopy is widely used to determine
9472-484: The chemical structure of molecules, which depends on the electron density distribution in the corresponding molecular orbitals. If a nucleus in a specific chemical group is shielded to a higher degree by a higher electron density of its surrounding molecular orbitals, then its NMR frequency will be shifted "upfield" (that is, a lower chemical shift), whereas if it is less shielded by such surrounding electron density, then its NMR frequency will be shifted "downfield" (that is,
9600-564: The classical angular momentum of a spinning sphere. The overall spin of the nucleus is determined by the spin quantum number S . If the numbers of both the protons and neutrons in a given nuclide are even then S = 0 , i.e. there is no overall spin. Then, just as electrons pair up in nondegenerate atomic orbitals , so do even numbers of protons or even numbers of neutrons (both of which are also spin- 1 / 2 particles and hence fermions ), giving zero overall spin. However, an unpaired proton and unpaired neutron will have
9728-430: The constant magnetic field B 0 ("90° pulse"), while after a twice longer time, the initial magnetization has been inverted ("180° pulse"). It is the transverse magnetization generated by a resonant oscillating field which is usually detected in NMR, during application of the relatively weak RF field in old-fashioned continuous-wave NMR, or after the relatively strong RF pulse in modern pulsed NMR. It might appear from
9856-536: The decoherence that is not refocused by the 180° pulse. In simple cases, an exponential decay is measured which is described by the T 2 time. NMR spectroscopy is one of the principal techniques used to obtain physical, chemical, electronic and structural information about molecules due to the chemical shift of the resonance frequencies of the nuclear spins in the sample. Peak splittings due to J- or dipolar couplings between nuclei are also useful. NMR spectroscopy can provide detailed and quantitative information on
9984-587: The details of which are described by chemical shifts , the Zeeman effect , and Knight shifts (in metals). The information provided by NMR can also be increased using hyperpolarization , and/or using two-dimensional, three-dimensional and higher-dimensional techniques. NMR phenomena are also utilized in low-field NMR , NMR spectroscopy and MRI in the Earth's magnetic field (referred to as Earth's field NMR ), and in several types of magnetometers . Nuclear magnetic resonance
10112-407: The detection of the kinds of nuclear–nuclear interactions that allowed for the magnetization transfer. Interactions that can be detected are usually classified into two kinds. There are through-bond and through-space interactions. Through-bond interactions relate to structural connectivity of the atoms and provide information about which ones are directly connected to each other, connected by way of
10240-551: The development of Fourier transform (FT) NMR coincided with the development of digital computers and the digital fast Fourier transform (FFT). Fourier methods can be applied to many types of spectroscopy. Richard R. Ernst was one of the pioneers of pulsed NMR and won a Nobel Prize in chemistry in 1991 for his work on Fourier Transform NMR and his development of multi-dimensional NMR spectroscopy. The use of pulses of different durations, frequencies, or shapes in specifically designed patterns or pulse sequences allows production of
10368-442: The development of more coherent electron sources, aberration correction for electron microscopes, and reconstruction software that enabled the successful implementation of high resolution cryo-electron microscopy, thereby permitting the study of individual proteins and molecular complexes in three-dimensions at angstrom resolution. With the development of these three techniques, the field of structural biology expanded and also became
10496-655: The development of nuclear magnetic resonance (NMR). Currently, solid-state NMR is widely used in the field of structural biology to determine the structure and dynamic nature of proteins ( protein NMR ). In 1990, Richard Henderson produced the first three-dimensional, high resolution image of bacteriorhodopsin using cryogenic electron microscopy (cryo-EM). Since then, cryo-EM has emerged as an increasingly popular technique to determine three-dimensional, high resolution structures of biological images. More recently, computational methods have been developed to model and study biological structures. For example, molecular dynamics (MD)
10624-466: The different nuclear spin states have different energies in a non-zero magnetic field. In less formal language, we can talk about the two spin states of a spin 1 / 2 as being aligned either with or against the magnetic field. If γ is positive (true for most isotopes used in NMR) then m = 1 / 2 ("spin up") is the lower energy state. The energy difference between
10752-399: The discovery of X-rays and its applications to protein crystals, structural biology was revolutionized, as now scientists could obtain the three-dimensional structures of biological molecules in atomic detail. Likewise, NMR spectroscopy allowed information about protein structure and dynamics to be obtained. Finally, in the 21st century, electron microscopy also saw a drastic revolution with
10880-400: The effect of the same couplings by Magic Angle Spinning techniques. The most commonly used nuclei are H and C , although isotopes of many other elements, such as F , P , and Si , can be studied by high-field NMR spectroscopy as well. In order to interact with the magnetic field in the spectrometer,
11008-586: The effects of radiation damping. The strength of the magnetic field is inversely proportional to the lifetime of RD. The impact of radiation damping on NMR signals is multifaceted. It can accelerate the decay of the NMR signal faster than intrinsic relaxation processes would suggest. This acceleration can complicate the interpretation of NMR spectra by causing broadening of spectral lines, distorting multiplet structures, and introducing artifacts, especially in high-resolution NMR scenarios. Such effects make it challenging to obtain clear and accurate data without considering
11136-415: The entire NMR spectrum. Applying such a pulse to a set of nuclear spins simultaneously excites all the single-quantum NMR transitions. In terms of the net magnetization vector, this corresponds to tilting the magnetization vector away from its equilibrium position (aligned along the external magnetic field). The out-of-equilibrium magnetization vector then precesses about the external magnetic field vector at
11264-629: The external magnetic field. The energy of a magnetic dipole moment μ → {\displaystyle {\vec {\mu }}} in a magnetic field B 0 is given by: E = − μ → ⋅ B 0 = − μ x B 0 x − μ y B 0 y − μ z B 0 z . {\displaystyle E=-{\vec {\mu }}\cdot \mathbf {B} _{0}=-\mu _{x}B_{0x}-\mu _{y}B_{0y}-\mu _{z}B_{0z}.} Usually
11392-419: The fields induced by radiation damping. These approaches aim to control and limit the disruptive effects of radiation damping during NMR experiments and all approaches are successful in eliminating RD to a fairly large extent. Overall, understanding and managing radiation damping is crucial for obtaining high-quality NMR data, especially in modern high-field spectrometers where the effects can be significant due to
11520-529: The first demonstrations of the validity of the BCS theory of superconductivity by the observation by Charles Slichter of the Hebel-Slichter effect. It soon showed its potential in organic chemistry , where NMR has become indispensable, and by the 1990s improvement in the sensitivity and resolution of NMR spectroscopy resulted in its broad use in analytical chemistry , biochemistry and materials science . In
11648-420: The first ever using a free-electron laser. Starting in 1999, Copeland and Konrad performed three surgeries in which they resected meningioma brain tumors . Beginning in 2000, Joos and Mawn performed five surgeries that cut a window in the sheath of the optic nerve , to test the efficacy for optic nerve sheath fenestration . These eight surgeries produced results consistent with the standard of care and with
11776-474: The functional groups, topology, dynamics and three-dimensional structure of molecules in solution and the solid state. Since the area under an NMR peak is usually proportional to the number of spins involved, peak integrals can be used to determine composition quantitatively. Structure and molecular dynamics can be studied (with or without "magic angle" spinning (MAS)) by NMR of quadrupolar nuclei (that is, with spin S > 1 / 2 ) even in
11904-547: The functions of cells , and it is only by coiling into specific three-dimensional shapes that they are able to perform these functions. This architecture, the " tertiary structure " of molecules, depends in a complicated way on each molecule's basic composition, or " primary structure ." At lower resolutions, tools such as FIB-SEM tomography have allowed for greater understanding of cells and their organelles in 3-dimensions, and how each hierarchical level of various extracellular matrices contributes to function (for example in bone). In
12032-458: The increased sensitivity and resolution. The process of population relaxation refers to nuclear spins that return to thermodynamic equilibrium in the magnet. This process is also called T 1 , " spin-lattice " or "longitudinal magnetic" relaxation, where T 1 refers to the mean time for an individual nucleus to return to its thermal equilibrium state of the spins. After the nuclear spin population has relaxed, it can be probed again, since it
12160-467: The influence of radiation damping. To mitigate these effects, various strategies are employed in NMR spectroscopy. These methods majorly stem from hardware or software. Hardware modifications including RF feed-circuit and Q-factor switches reduce the feedback loop between the sample magnetization and the electromagnetic field induced by the coil and function successfully. Other approaches such as designing selective pulse sequences also effectively manage
12288-435: The intensity of the NMR signal as a function of frequency. Early attempts to acquire the NMR spectrum more efficiently than simple CW methods involved illuminating the target simultaneously with more than one frequency. A revolution in NMR occurred when short radio-frequency pulses began to be used, with a frequency centered at the middle of the NMR spectrum. In simple terms, a short pulse of a given "carrier" frequency "contains"
12416-481: The invention of modeling software such as CCP4 in the late 1970s, modeling is now done with computer assistance. Recent developments in the field have included the generation of X-ray free electron lasers , allowing analysis of the dynamics and motion of biological molecules, and the use of structural biology in assisting synthetic biology . In the late 1930s and early 1940s, the combination of work done by Isidor Rabi , Felix Bloch , and Edward Mills Purcell led to
12544-423: The magnet is shimmed well. Both T 1 and T 2 depend on the rate of molecular motions as well as the gyromagnetic ratios of both the resonating and their strongly interacting, next-neighbor nuclei that are not at resonance. A Hahn echo decay experiment can be used to measure the dephasing time, as shown in the animation. The size of the echo is recorded for different spacings of the two pulses. This reveals
12672-406: The medical application of the free-electron laser in melting fats without harming the overlying skin. At infrared wavelengths , water in tissue was heated by the laser, but at wavelengths corresponding to 915, 1210 and 1720 nm , subsurface lipids were differentially heated more strongly than water. The possible applications of this selective photothermolysis (heating tissues using light) include
12800-535: The most advanced light microscopes . The methods that structural biologists use to determine their structures generally involve measurements on vast numbers of identical molecules at the same time. These methods include: Most often researchers use them to study the " native states " of macromolecules. But variations on these methods are also used to watch nascent or denatured molecules assume or reassume their native states. See protein folding . A third approach that structural biologists take to understanding structure
12928-520: The nucleus may also be excited in zero applied magnetic field ( nuclear quadrupole resonance ). In the dominant chemistry application, the use of higher fields improves the sensitivity of the method (signal-to-noise ratio scales approximately as the power of 3 / 2 with the magnetic field strength) and the spectral resolution. Commercial NMR spectrometers employing liquid helium cooled superconducting magnets with fields of up to 28 Tesla have been developed and are widely used. It
13056-405: The nucleus must have an intrinsic angular momentum and nuclear magnetic dipole moment . This occurs when an isotope has a nonzero nuclear spin , meaning an odd number of protons and/or neutrons (see Isotope ). Nuclides with even numbers of both have a total spin of zero and are therefore not NMR-active. In its application to molecules the NMR effect can be observed only in the presence of
13184-445: The number of electrons. Mirrors at each end of the undulator create an optical cavity , causing the radiation to form standing waves , or alternately an external excitation laser is provided. The radiation becomes sufficiently strong that the transverse electric field of the radiation beam interacts with the transverse electron current created by the sinusoidal wiggling motion, causing some electrons to gain and others to lose energy to
13312-404: The optical field via the ponderomotive force . This energy modulation evolves into electron density (current) modulations with a period of one optical wavelength. The electrons are thus longitudinally clumped into microbunches , separated by one optical wavelength along the axis. Whereas an undulator alone would cause the electrons to radiate independently (incoherently), the radiation emitted by
13440-439: The oscillation frequency matches the nuclear resonance frequency, the transverse magnetization is maximized and a peak is observed in the spectrum. Although NMR spectra could be, and have been, obtained using a fixed constant magnetic field and sweeping the frequency of the oscillating magnetic field, it was more convenient to use a fixed frequency source and vary the current (and hence magnetic field) in an electromagnet to observe
13568-647: The oscillations of the spin system are point by point in the time domain. Multidimensional Fourier transformation of the multidimensional time signal yields the multidimensional spectrum. In two-dimensional nuclear magnetic resonance spectroscopy (2D-NMR), there will be one systematically varied time period in the sequence of pulses, which will modulate the intensity or phase of the detected signals. In 3D-NMR, two time periods will be varied independently, and in 4D-NMR, three will be varied. There are many such experiments. In some, fixed time intervals allow (among other things) magnetization transfer between nuclei and, therefore,
13696-406: The other hand, ESR has much higher signal per spin than NMR does. Nuclear spin is an intrinsic angular momentum that is quantized. This means that the magnitude of this angular momentum is quantized (i.e. S can only take on a restricted range of values), and also that the x, y, and z-components of the angular momentum are quantized, being restricted to integer or half-integer multiples of ħ ,
13824-457: The past few years it has also become possible to predict highly accurate physical molecular models to complement the experimental study of biological structures. Computational techniques such as molecular dynamics simulations can be used in conjunction with empirical structure determination strategies to extend and study protein structure, conformation and function. In 1912 Max Von Laue directed X-rays at crystallized copper sulfate generating
13952-544: The populations of the energy levels because energy is constant (time-independent Hamiltonian). A perturbation of nuclear spin orientations from equilibrium will occur only when an oscillating magnetic field is applied whose frequency ν rf sufficiently closely matches the Larmor precession frequency ν L of the nuclear magnetization. The populations of the spin-up and -down energy levels then undergo Rabi oscillations , which are analyzed most easily in terms of precession of
14080-453: The presence of magnetic " dipole -dipole" interaction broadening (or simply, dipolar broadening), which is always much smaller than the quadrupolar interaction strength because it is a magnetic vs. an electric interaction effect. Additional structural and chemical information may be obtained by performing double-quantum NMR experiments for pairs of spins or quadrupolar nuclei such as H . Furthermore, nuclear magnetic resonance
14208-454: The radiation emitted can be readily tuned by adjusting the energy of the electron beam or the magnetic-field strength of the undulators. FELs are relativistic machines. The wavelength of the emitted radiation, λ r {\displaystyle \lambda _{r}} , is given by or when the wiggler strength parameter K , discussed below, is small where λ u {\displaystyle \lambda _{u}}
14336-480: The reduced Planck constant . The integer or half-integer quantum number associated with the spin component along the z-axis or the applied magnetic field is known as the magnetic quantum number , m , and can take values from + S to − S , in integer steps. Hence for any given nucleus, there are a total of 2 S + 1 angular momentum states. The z -component of the angular momentum vector ( S → {\displaystyle {\vec {S}}} )
14464-543: The resonant absorption signals. This is the origin of the counterintuitive, but still common, "high field" and "low field" terminology for low frequency and high frequency regions, respectively, of the NMR spectrum. As of 1996, CW instruments were still used for routine work because the older instruments were cheaper to maintain and operate, often operating at 60 MHz with correspondingly weaker (non-superconducting) electromagnets cooled with water rather than liquid helium. One radio coil operated continuously, sweeping through
14592-404: The second γ {\displaystyle \gamma } factor to the above formula. In an X-ray FEL the typical undulator wavelength of 1 cm is transformed to X-ray wavelengths on the order of 1 nm by γ {\displaystyle \gamma } ≈ 2000, i.e. the electrons have to travel with the speed of 0.9999998 c . K , a dimensionless parameter, defines
14720-519: The seeding limitation for x-ray wavelengths by self-seeding the laser with its own beam after being filtered through a diamond monochromator . The resulting intensity and monochromaticity of the beam were unprecedented and allowed new experiments to be conducted involving manipulating atoms and imaging molecules. Other labs around the world are incorporating the technique into their equipment. Researchers have explored X-ray free-electron lasers as an alternative to synchrotron light sources that have been
14848-616: The selective destruction of sebum lipids to treat acne , as well as targeting other lipids associated with cellulite and body fat as well as fatty plaques that form in arteries which can help treat atherosclerosis and heart disease . FEL technology is being evaluated by the US Navy as a candidate for an anti-aircraft and anti- missile directed-energy weapon . The Thomas Jefferson National Accelerator Facility 's FEL has demonstrated over 14 kW power output. Compact multi-megawatt class FEL weapons are undergoing research. On June 9, 2009
14976-549: The simpler, abundant hydrogen isotope, H nucleus (the proton ). The NMR absorption frequency for tritium is also similar to that of H. In many other cases of non-radioactive nuclei, the overall spin is also non-zero and may have a contribution from the orbital angular momentum of the unpaired nucleon . For example, the Al nucleus has an overall spin value S = 5 / 2 . A non-zero spin S → {\displaystyle {\vec {S}}}
15104-470: The spin magnetization around the effective magnetic field in a reference frame rotating with the frequency ν rf . The stronger the oscillating field, the faster the Rabi oscillations or the precession around the effective field in the rotating frame. After a certain time on the order of 2–1000 microseconds, a resonant RF pulse flips the spin magnetization to the transverse plane, i.e. it makes an angle of 90° with
15232-510: The structure of organic molecules in solution and study molecular physics and crystals as well as non-crystalline materials. NMR is also routinely used in advanced medical imaging techniques, such as in magnetic resonance imaging (MRI). The original application of NMR to condensed matter physics is nowadays mostly devoted to strongly correlated electron systems. It reveals large many-body couplings by fast broadband detection and should not be confused with solid state NMR, which aims at removing
15360-401: The two states is: Δ E = γ ℏ B 0 , {\displaystyle \Delta {E}=\gamma \hbar B_{0}\,,} and this results in a small population bias favoring the lower energy state in thermal equilibrium. With more spins pointing up than down, a net spin magnetization along the magnetic field B 0 results. A central concept in NMR
15488-414: The undulator is shortened by a γ {\displaystyle \gamma } factor and the electron experiences much shorter undulator wavelength λ u / γ {\displaystyle \lambda _{u}/\gamma } . However, the radiation emitted at this wavelength is observed in the laboratory frame of reference and the relativistic Doppler effect brings
15616-400: The value of T 2 *, which is the actually observed decay time of the observed NMR signal, or free induction decay (to 1 / e of the initial amplitude immediately after the resonant RF pulse), also depends on the static magnetic field inhomogeneity, which may be quite significant. (There is also a smaller but significant contribution to the observed FID shortening from
15744-406: The wiggler strength as the relationship between the length of a period and the radius of bend, where ρ {\displaystyle \rho } is the bending radius, B 0 {\displaystyle B_{0}} is the applied magnetic field, m e {\displaystyle m_{e}} is the electron mass, and e {\displaystyle e}
15872-412: The workhorses of protein crystallography and cell biology . Exceptionally bright and fast X-rays can image proteins using x-ray crystallography . This technique allows first-time imaging of proteins that do not stack in a way that allows imaging by conventional techniques, 25% of the total number of proteins. Resolutions of 0.8 nm have been achieved with pulse durations of 30 femtoseconds . To get
16000-414: The z-component of spin. In the absence of a magnetic field, these states are degenerate; that is, they have the same energy. Hence the number of nuclei in these two states will be essentially equal at thermal equilibrium . If a nucleus with spin is placed in a magnetic field, however, the two states no longer have the same energy as a result of the interaction between the nuclear magnetic dipole moment and
16128-664: Was accepted on July 24, 1951. Varian Associates developed the first NMR unit called NMR HR-30 in 1952. Purcell had worked on the development of radar during World War II at the Massachusetts Institute of Technology 's Radiation Laboratory . His work during that project on the production and detection of radio frequency power and on the absorption of such RF power by matter laid the foundation for his discovery of NMR in bulk matter. Rabi, Bloch, and Purcell observed that magnetic nuclei, like H and P , could absorb RF energy when placed in
16256-598: Was demonstrated at x-ray wavelength at Trieste Synchrotron Laboratory . A similar staging approach, named "Fresh-Slice", was demonstrated at the Paul Scherrer Institut , also at X-ray wavelengths. In the Fresh Slice the short X-ray pulse produced at the first stage is moved to a fresh part of the electron bunch by a transverse tilt of the bunch. In 2012, scientists working on the LCLS found an alternative solution to
16384-690: Was first described and measured in molecular beams by Isidor Rabi in 1938, by extending the Stern–Gerlach experiment , and in 1944, Rabi was awarded the Nobel Prize in Physics for this work. In 1946, Felix Bloch and Edward Mills Purcell expanded the technique for use on liquids and solids, for which they shared the Nobel Prize in Physics in 1952. Russell H. Varian filed the "Method and means for correlating nuclear properties of atoms and magnetic fields", U.S. patent 2,561,490 on October 21, 1948 and
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