Vibrational circular dichroism (VCD) is a spectroscopic technique which detects differences in attenuation of left and right circularly polarized light passing through a sample. It is the extension of circular dichroism spectroscopy into the infrared and near infrared ranges. [1]
Because VCD is sensitive to the mutual orientation of distinct groups in a molecule, it provides three-dimensional structural information. Thus, it is a powerful technique as VCD spectra of enantiomers can be simulated using ab initio calculations, thereby allowing the identification of absolute configurations of small molecules in solution from VCD spectra. Among such quantum computations of VCD spectra resulting from the chiral properties of small organic molecules are those based on density functional theory (DFT) and gauge-including atomic orbitals (GIAO). As a simple example of the experimental results that were obtained by VCD are the spectral data obtained within the carbon-hydrogen (C-H) stretching region of 21 amino acids in heavy water solutions. Measurements of vibrational optical activity (VOA) have thus numerous applications, not only for small molecules, but also for large and complex biopolymers such as muscle proteins (myosin, for example) and DNA.
While the fundamental quantity associated with the infrared absorption is the dipole strength, the differential absorption is also proportional to the rotational strength, a quantity which depends on both the electric and magnetic dipole transition moments. Sensitivity of the handedness of a molecule toward circularly polarized light results from the form of the rotational strength. A rigorous theoretical development of VCD was developed concurrently by the late Professor P.J. Stephens, FRS, at the University of Southern California, [2] [3] and the group of Professor A.D. Buckingham, FRS, at Cambridge University in the UK, [4] and first implemented analytically in the Cambridge Analytical Derivative Package (CADPAC) by R.D. Amos. [5] Previous developments by D.P. Craig and T. Thirmachandiman at the Australian National University [6] and Larry A. Nafie and Teresa B. Freedman at Syracuse University [7] though theoretically correct, were not able to be straightforwardly implemented, which prevented their use. Only with the development of the Stephens formalism as implemented in CADPAC did a fast efficient and theoretically rigorous theoretical calculation of the VCD spectra of chiral molecules become feasible. This also stimulated the commercialization of VCD instruments by Biotools, Bruker, Jasco and Thermo-Nicolet (now Thermo-Fisher).
Extensive VCD studies have been reported for both polypeptides and several proteins in solution; [8] [9] [10] several recent reviews were also compiled. [11] [12] [13] [14] An extensive but not comprehensive VCD publications list is also provided in the "References" section. The published reports over the last 22 years have established VCD as a powerful technique with improved results over those previously obtained by visible/UV circular dichroism (CD) or optical rotatory dispersion (ORD) for proteins and nucleic acids.
The effects due to solvent on stabilizing the structures (conformers and zwitterionic species) of amino acids and peptides and the corresponding effects seen in the vibrational circular dichroism (VCD) and Raman optical activity spectra (ROA) have been recently documented by a combined theoretical and experimental work on L-alanine and N-acetyl L-alanine N'-methylamide. [15] [16] Similar effects have also been seen in the nuclear magnetic resonance (NMR) spectra by the Weise and Weisshaar NMR groups at the University of Wisconsin–Madison. [17]
VCD spectra of nucleotides, synthetic polynucleotides and several nucleic acids, including DNA, have been reported and assigned in terms of the type and number of helices present in A-, B-, and Z-DNA.
VCD can be regarded as a relatively recent technique. Although Vibrational Optical Activity and in particular Vibrational Circular Dichroism, has been known for a long time, the first VCD instrument was developed in 1973 [18] and commercial instruments were available only since 1997. [19]
For biopolymers such as proteins and nucleic acids, the difference in absorbance between the levo- and dextro- configurations is five orders of magnitude smaller than the corresponding (unpolarized) absorbance. Therefore, VCD of biopolymers requires the use of very sensitive, specially built instrumentation as well as time-averaging over relatively long intervals of time even with such sensitive VCD spectrometers. Most CD instruments produce left- and right- circularly polarized light which is then either sine-wave or square-wave modulated, with subsequent phase-sensitive detection and lock-in amplification of the detected signal. In the case of FT-VCD, a photo-elastic modulator (PEM) is employed in conjunction with an FTIR interferometer set-up. An example is that of a Bomem model MB-100 FTIR interferometer equipped with additional polarizing optics/ accessories needed for recording VCD spectra. A parallel beam emerges through a side port of the interferometer which passes first through a wire grid linear polarizer and then through an octagonal-shaped ZnSe crystal PEM which modulates the polarized beam at a fixed, lower frequency such as 37.5 kHz. A mechanically stressed crystal such as ZnSe exhibits birefringence when stressed by an adjacent piezoelectric transducer. The linear polarizer is positioned close to, and at 45 degrees, with respect to the ZnSe crystal axis. The polarized radiation focused onto the detector is doubly modulated, both by the PEM and by the interferometer setup. A very low noise detector, such as MCT (HgCdTe), is also selected for the VCD signal phase-sensitive detection. The first dedicated VCD spectrometer brought to market was the ChiralIR from Bomem/BioTools, Inc. in 1997. Today, Thermo-Electron, Bruker, Jasco and BioTools offer either VCD accessories or stand-alone instrumentation. [20] To prevent detector saturation an appropriate, long wave pass filter is placed before the very low noise MCT detector, which allows only radiation below 1750 cm−1 to reach the MCT detector; the latter however measures radiation only down to 750 cm−1. FT-VCD spectra accumulation of the selected sample solution is then carried out, digitized and stored by an in-line computer. Published reviews that compare various VCD methods are also available. [21] [22]
VCD spectra have also been reported in the presence of an applied external magnetic field. [23] This method can enhance the VCD spectral resolution for small molecules. [24] [25] [26] [27] [28]
ROA is a technique complementary to VCD especially useful in the 50–1600 cm−1 spectral region; it is considered as the technique of choice for determining optical activity for photon energies less than 600 cm−1.
Infrared spectroscopy is the measurement of the interaction of infrared radiation with matter by absorption, emission, or reflection. It is used to study and identify chemical substances or functional groups in solid, liquid, or gaseous forms. It can be used to characterize new materials or identify and verify known and unknown samples. The method or technique of infrared spectroscopy is conducted with an instrument called an infrared spectrometer which produces an infrared spectrum. An IR spectrum can be visualized in a graph of infrared light absorbance on the vertical axis vs. frequency, wavenumber or wavelength on the horizontal axis. Typical units of wavenumber used in IR spectra are reciprocal centimeters, with the symbol cm−1. Units of IR wavelength are commonly given in micrometers, symbol μm, which are related to the wavenumber in a reciprocal way. A common laboratory instrument that uses this technique is a Fourier transform infrared (FTIR) spectrometer. Two-dimensional IR is also possible as discussed below.
Spectroscopy is the general field of study that measures and interprets the electromagnetic spectra that result from the interaction between electromagnetic radiation and matter as a function of the wavelength or frequency of the radiation. Matter waves and acoustic waves can also be considered forms of radiative energy, and recently gravitational waves have been associated with a spectral signature in the context of the Laser Interferometer Gravitational-Wave Observatory (LIGO)
Protein folding is the physical process by which a protein chain is translated to its native three-dimensional structure, typically a "folded" conformation by which the protein becomes biologically functional. Via an expeditious and reproducible process, a polypeptide folds into its characteristic three-dimensional structure from a random coil. Each protein exists first as an unfolded polypeptide or random coil after being translated from a sequence of mRNA to a linear chain of amino acids. At this stage the polypeptide lacks any stable (long-lasting) three-dimensional structure. As the polypeptide chain is being synthesized by a ribosome, the linear chain begins to fold into its three-dimensional structure.
Raman spectroscopy is a spectroscopic technique typically used to determine vibrational modes of molecules, although rotational and other low-frequency modes of systems may also be observed. Raman spectroscopy is commonly used in chemistry to provide a structural fingerprint by which molecules can be identified.
Circular dichroism (CD) is dichroism involving circularly polarized light, i.e., the differential absorption of left- and right-handed light. Left-hand circular (LHC) and right-hand circular (RHC) polarized light represent two possible spin angular momentum states for a photon, and so circular dichroism is also referred to as dichroism for spin angular momentum. This phenomenon was discovered by Jean-Baptiste Biot, Augustin Fresnel, and Aimé Cotton in the first half of the 19th century. Circular dichroism and circular birefringence are manifestations of optical activity. It is exhibited in the absorption bands of optically active chiral molecules. CD spectroscopy has a wide range of applications in many different fields. Most notably, UV CD is used to investigate the secondary structure of proteins. UV/Vis CD is used to investigate charge-transfer transitions. Near-infrared CD is used to investigate geometric and electronic structure by probing metal d→d transitions. Vibrational circular dichroism, which uses light from the infrared energy region, is used for structural studies of small organic molecules, and most recently proteins and DNA.
Magnetic circular dichroism (MCD) is the differential absorption of left and right circularly polarized light, induced in a sample by a strong magnetic field oriented parallel to the direction of light propagation. MCD measurements can detect transitions which are too weak to be seen in conventional optical absorption spectra, and it can be used to distinguish between overlapping transitions. Paramagnetic systems are common analytes, as their near-degenerate magnetic sublevels provide strong MCD intensity that varies with both field strength and sample temperature. The MCD signal also provides insight into the symmetry of the electronic levels of the studied systems, such as metal ion sites.
Rotational spectroscopy is concerned with the measurement of the energies of transitions between quantized rotational states of molecules in the gas phase. The spectra of polar molecules can be measured in absorption or emission by microwave spectroscopy or by far infrared spectroscopy. The rotational spectra of non-polar molecules cannot be observed by those methods, but can be observed and measured by Raman spectroscopy. Rotational spectroscopy is sometimes referred to as pure rotational spectroscopy to distinguish it from rotational-vibrational spectroscopy where changes in rotational energy occur together with changes in vibrational energy, and also from ro-vibronic spectroscopy where rotational, vibrational and electronic energy changes occur simultaneously.
Raman scattering or the Raman effect is the inelastic scattering of photons by matter, meaning that there is both an exchange of energy and a change in the light's direction. Typically this effect involves vibrational energy being gained by a molecule as incident photons from a visible laser are shifted to lower energy. This is called normal Stokes Raman scattering. The effect is exploited by chemists and physicists to gain information about materials for a variety of purposes by performing various forms of Raman spectroscopy. Many other variants of Raman spectroscopy allow rotational energy to be examined and electronic energy levels may be examined if an X-ray source is used in addition to other possibilities. More complex techniques involving pulsed lasers, multiple laser beams and so on are known.
Resonance Raman spectroscopy is a Raman spectroscopy technique in which the incident photon energy is close in energy to an electronic transition of a compound or material under examination. The frequency coincidence can lead to greatly enhanced intensity of the Raman scattering, which facilitates the study of chemical compounds present at low concentrations.
Raman optical activity (ROA) is a vibrational spectroscopic technique that is reliant on the difference in intensity of Raman scattered right and left circularly polarised light due to molecular chirality.
Jaguar is a computer software package used for ab initio quantum chemistry calculations for both gas and solution phases. It is commercial software marketed by the company Schrödinger. The program was originated in research groups of Richard Friesner and William Goddard and was initially called PS-GVB.
Molecular biophysics is a rapidly evolving interdisciplinary area of research that combines concepts in physics, chemistry, engineering, mathematics and biology. It seeks to understand biomolecular systems and explain biological function in terms of molecular structure, structural organization, and dynamic behaviour at various levels of complexity. This discipline covers topics such as the measurement of molecular forces, molecular associations, allosteric interactions, Brownian motion, and cable theory. Additional areas of study can be found on Outline of Biophysics. The discipline has required development of specialized equipment and procedures capable of imaging and manipulating minute living structures, as well as novel experimental approaches.
Amyand David Buckingham born in Pymble, Sydney, New South Wales, Australia was a chemist, with primary expertise in chemical physics.
Chemical imaging is the analytical capability to create a visual image of components distribution from simultaneous measurement of spectra and spatial, time information. Hyperspectral imaging measures contiguous spectral bands, as opposed to multispectral imaging which measures spaced spectral bands.
Two-dimensional infrared spectroscopy is a nonlinear infrared spectroscopy technique that has the ability to correlate vibrational modes in condensed-phase systems. This technique provides information beyond linear infrared spectra, by spreading the vibrational information along multiple axes, yielding a frequency correlation spectrum. A frequency correlation spectrum can offer structural information such as vibrational mode coupling, anharmonicities, along with chemical dynamics such as energy transfer rates and molecular dynamics with femtosecond time resolution. 2DIR experiments have only become possible with the development of ultrafast lasers and the ability to generate femtosecond infrared pulses.
Richard C. Lord (1910–1989) was an American chemist best known for his work in the field of spectroscopy.
Molecular models of DNA structures are representations of the molecular geometry and topology of deoxyribonucleic acid (DNA) molecules using one of several means, with the aim of simplifying and presenting the essential, physical and chemical, properties of DNA molecular structures either in vivo or in vitro. These representations include closely packed spheres made of plastic, metal wires for skeletal models, graphic computations and animations by computers, artistic rendering. Computer molecular models also allow animations and molecular dynamics simulations that are very important for understanding how DNA functions in vivo.
Laurence David Barron has been Gardiner Professor of Chemistry at the University of Glasgow since 1998. He is a chemist who has conducted pioneering research into the properties of chiral molecules — defined by Lord Kelvin as those that cannot be superimposed onto their mirror image. By extending this definition of chirality to include moving particles and processes that vary with time, he has made a fundamental theoretical contribution to the field. Chiral molecules such as amino acids, sugars, proteins, and nucleic acids play a central role in the chemistry of life, and many drug molecules are chiral. Laurence’s work on Raman optical activity — a spectroscopic technique capable of determining the three-dimensional structures of chiral molecules, which he predicted, observed, and applied to problems at the forefront of chemistry and structural biology — has led to its development as a powerful analytical tool used in academic and industrial laboratories worldwide. His much-cited book, Molecular Light Scattering and Optical Activity, has contributed to the growing impact of chirality on many areas of modern science.
The following outline is provided as an overview of and topical guide to biophysics:
Two-photon circular dichroism (TPCD), the nonlinear counterpart of electronic circular dichroism (ECD), is defined as the differences between the two-photon absorption (TPA) cross-sections obtained using left circular polarized light and right circular polarized light.
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