Relevant bibliographies by topics / Atomic/Molecular Structure and Spectra

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Atomic/Molecular Structure and Spectra'

Author: Grafiati
Published: 4 June 2021
Last updated: 29 January 2023

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Journal articles on the topic "Atomic/Molecular Structure and Spectra"

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Bruley, John, David B. Williams, and Ming-Wei Tseng. "Point-defect distributions in ceramics by spectrum-line profiling." Proceedings, annual meeting, Electron Microscopy Society of America 53 (August 13, 1995): 312–13. http://dx.doi.org/10.1017/s0424820100137938.

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Electron energy-loss spectroscopy is well suited to the study of interfaces because the ionization edges can be used to identify the atomic species present and the near edge fine structures on the edges reveal information on the electronic structure surrounding these atoms. This information can be extracted from regions of sample approaching atomic dimensions. A challenge is to be able to map and interpret spectral features with a level of confidence that will allow explanations of physical properties of interest.The term Spectrum-Line is used here to refer to a linear array of spectra, recorded sequentially along a line traced out by the electron probe and is the 1 dimensional analog of the Spectrum-Image. Processing Spectrum-Lines to generate quantitative profiles can provide a vivid picture of changes in composition, a valence state, or site occupancy across an interface. To aid interpretation and guide further spectrum analysis the near-edge fine structures can be compared to spectra from compounds whose atomic coordinations are well known or modeled using the results of band-structure or molecular orbital calculations of electronic structures.
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Crépin, C., and A. Tramer. "Vibrational structure in atomic emission spectra: Hg atoms in molecular matrices." Journal of Chemical Physics 107, no. 7 (August 15, 1997): 2205–14. http://dx.doi.org/10.1063/1.474600.

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Vijaya Chamundeeswari, S. P., E. James Jebaseelan Samuel, and N. Sundaraganesan. "Molecular structure, vibrational spectra, NMR and UV spectral analysis of sulfamethoxazole." Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 118 (January 2014): 1–10. http://dx.doi.org/10.1016/j.saa.2013.07.063.

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Li, Zhe, Hsin-Yi Tiffany Chen, Koen Schouteden, Thomas Picot, Ting-Wei Liao, Aleksandr Seliverstov, Chris Van Haesendonck, Gianfranco Pacchioni, Ewald Janssens, and Peter Lievens. "Unraveling the atomic structure, ripening behavior, and electronic structure of supported Au20 clusters." Science Advances 6, no. 1 (January 2020): eaay4289. http://dx.doi.org/10.1126/sciadv.aay4289.

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The free-standing Au20 cluster has a unique tetrahedral shape and a large HOMO-LUMO (highest occupied molecular orbital–lowest unoccupied molecular orbital) gap of around 1.8 electron volts. The “magic” Au20 has been intensively used as a model system for understanding the catalytic and optical properties of gold nanoclusters. However, direct real-space ground-state characterization at the atomic scale is still lacking, and obtaining fundamental information about the corresponding structural, electronic, and dynamical properties, is challenging. Here, using cluster-beam deposition and low-temperature scanning tunneling microscopy, atom-resolved topographic images and electronic spectra of supported Au20 clusters are obtained. We demonstrate that individual size-selected Au20 on ultrathin NaCl films maintains its pyramidal structure and large HOMO-LUMO gap. At higher cluster coverages, we find sintering of the clusters via Smoluchowski ripening to Au20n agglomerates. The evolution of the electron density of states deduced from the spectra reveals gap reduction with increasing agglomerate size.
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Samsonowicz, Mariola. "Molecular structure of calcium, magnesium, strontium and barium m-nitrobenzoates." Spectroscopy 24, no. 3-4 (2010): 433–37. http://dx.doi.org/10.1155/2010/501245.

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The effect of calcium, magnesium, strontium and barium ions on the electronic structure of m-nitrobenzoates was studied. The FT-IR spectra of m-nitrobenzoic acid and its salts were registered, assigned and analyzed. Characteristic shifts and changes in intensities of bands along the metal series were observed. The structures of m-nitrobenzoic acid and its calcium, magnesium, strontium and barium salts were optimized at the B3LYP/LANL2DZ level. Geometric aromaticity indices, atomic charges, dipole moments and energies were also calculated.
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Flambaum, V. V., and V. A. Dzuba. "Search for variation of the fundamental constants in atomic, molecular, and nuclear spectra." Canadian Journal of Physics 87, no. 1 (January 1, 2009): 25–33. http://dx.doi.org/10.1139/p08-072.

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The search for variation of the fundamental constants such as the fine-structure constant α (α = e2/hc) and the ratios of fundamental masses (for example, electron-to-proton mass ratio μ = me/mp) is reviewed. Strong emphasis is given to establishing the relationships between the change in the measured frequencies of atomic, molecular, or nuclear transitions and the corresponding change of the fundamental constants. Transitions in which the sensitivity of the frequency change to the variation of the fine-structure constant is strongly enhanced are discussed and most recent experimental results are presented. Most attention is given to the use of atomic, molecular, and nuclear transitions in the study of quasar absorption spectra and in atomic clock experiments.PACS Nos.: 31.25.Eb, 31.25.Jf
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Benson, Chris S., N. Hładczuk, L. D. Spencer, A. Robb, J. Scott, I. Valtchanov, R. Hopwood, and D. A. Naylor. "The Herschel SPIRE Fourier Transform Spectrometer Spectral Feature Finder – III. Line identification and off-axis spectra." Monthly Notices of the Royal Astronomical Society 496, no. 4 (June 13, 2020): 4906–22. http://dx.doi.org/10.1093/mnras/staa1613.

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ABSTRACT The European Space Agency Herschel Spectral and Photometric Imaging Receiver (SPIRE) Fourier Transform Spectrometer (FTS) Spectral Feature Finder (FF) project is an automated spectral feature fitting routine developed within the SPIRE instrument team to extract all prominent spectral features from all publicly available SPIRE FTS observations. We present the extension of the FF to include the off-axis detectors of the FTS in sparsely sampled single-pointing observations, the results of which have been ingested into the catalogue. We also present the results from an automated routine for identifications of the atomic/molecular transitions that correspond to the spectral features extracted by the FF. We use a template of 307 atomic fine structure and molecular lines that are commonly found in SPIRE FTS spectra for the cross-match. The routine makes use of information provided by the line identification to search for low signal-to-noise ratio features that have been excluded or missed by the iterative FF. In total, the atomic/molecular transitions of 178 942 lines are identified (corresponding to 83 per cent of the entire FF catalogue), and an additional 33 840 spectral lines associated with missing features from SPIRE FTS observations are added to the FF catalogue.
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Drew, Elliot D., and Robert W. Janes. "PDBMD2CD: providing predicted protein circular dichroism spectra from multiple molecular dynamics-generated protein structures." Nucleic Acids Research 48, W1 (April 28, 2020): W17—W24. http://dx.doi.org/10.1093/nar/gkaa296.

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Abstract PDBMD2CD is a new web server capable of predicting circular dichroism (CD) spectra for multiple protein structures derived from molecular dynamics (MD) simulations, enabling predictions from thousands of protein atomic coordinate files (e.g. MD trajectories) and generating spectra for each of these structures provided by the user. Using MD enables exploration of systems that cannot be monitored by direct experimentation. Validation of MD-derived data from these types of trajectories can be difficult via conventional structure-determining techniques such as crystallography or nuclear magnetic resonance spectroscopy. CD is an experimental technique that can provide protein structure information from such conditions. The website utilizes a much faster (minimum ∼1000×) and more accurate approach for calculating CD spectra than its predecessor, PDB2CD (1). As well as improving on the speed and accuracy of current methods, new analysis tools are provided to cluster predictions or compare them against experimental CD spectra. By identifying a subset of the closest predicted CD spectra derived from PDBMD2CD to an experimental spectrum, the associated cluster of structures could be representative of those found under the conditions in which the MD studies were undertaken, thereby offering an analytical insight into the results. PDBMD2CD is freely available at: https://pdbmd2cd.cryst.bbk.ac.uk.
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Zhou, Dapeng, Cuiping Zhai, and Xiaopeng Xuan. "Molecular structure and vibrational spectra of N4-acetylcytosine." Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 112 (August 2013): 139–45. http://dx.doi.org/10.1016/j.saa.2013.04.051.

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Parkinson, W. H. "Commission 14 : Atomic and Molecular Data (Donnees Atomiques et Moleculaires)." Transactions of the International Astronomical Union 21, no. 1 (1991): 105–36. http://dx.doi.org/10.1017/s0251107x00009949.

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Since its creation, the Commission has been keen on activating the cross-discipline interaction between astrophysics and atomic and molecular physics. The need for a variety of atomic and molecular data has become more and more important for the recent past years. This need will certainly increase still more in the next years, due to the creation of new ground based instruments and to the launch of new space missions : they will produce large amounts of high resolution spectra from the X-rays to the infrared and millimeter wavelengths involving many atoms, ions and molecules. At the 1988 Baltimore meeting there was a general consensus that the aim of the Commission is to watch over the atomic and molecular spectral and structure data, together with the energy exchange processes in atomic and molecular physics relevant for astrophysics. In particular, the Commission is concerned by the interactions between photons and atoms (or ions or molecules), including wavelengths and line transition probabilities data, and by the interactions between particles, including atomic, molecular, ionic and electronic collision cross-sections, and by related phenomena, such as line broadening, collisional redistribution of radiation and line polarization. All these informations are essential for the interpretation of astronomical observations, such as spectroscopic diagnosis and theoretical modelling of astrophysical media.
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Dissertations / Theses on the topic "Atomic/Molecular Structure and Spectra"

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Sochi, T. "Atomic and molecular aspects of astronomical spectra." Thesis, University College London (University of London), 2012. http://discovery.ucl.ac.uk/1369696/.

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In the first section of this thesis, we present the atomic part of our investigation. A C2+ atomic target was prepared and used to generate theoretical data required in the investigation of recombination lines that arise from collisions between electrons and ions in thin plasma found in planetary nebulae and other astrophysical objects. The R-matrix method of electron scattering theory was used to describe the C2+ plus electron system. Theoretical data concerning bound and autoionizing states were generated in the intermediate-coupling approximation by R-matrix and Autostructure codes and compared to experimental data. The comparison revealed very good agreement. These theoretical data were then used to generate dielectronic recombination data for C+ which include transition lines, oscillator strengths, radiative transition probabilities, as well as emissivity and dielectronic recombination coefficients. The data were cast in the form of a line list, called SS1, containing 6187 optically-allowed transitions which include many C II lines observed in astronomical spectra. The data were validated by comparison to C+ recombination data obtained from a number of sources in the literature. This line list was used to analyze the spectra from a number of astronomical objects, mainly planetary nebulae, and identify their electron temperature where the observational data were obtained from the literature. The electron temperature investigation was also extended to include free electron energy analysis which uses observational and theoretical data of FF and FB transitions to investigate the long-standing problem of discrepancy between the results of recombination and forbidden lines analysis and its possible connection to the electron distribution (Maxwellian or non-Maxwellian). In the course of this investigation two elaborate methods, one for finding and analyzing resonances (K-matrix method) and the other for analyzing and identifying electron temperature from astronomical spectra (least squares minimization), were employed. A computer program for atomic transition analysis was also developed and used as the main tool for obtaining the line list and analyzing the observational spectra. In the second section of the thesis we present the results of our molecular investigation; the generation of a comprehensive, calculated line list of frequencies and transition probabilities for the singly deuterated isotopologue of H3+, H2D+. The line list, which is the most comprehensive one of its kind in existence, contains over 22 million rotational-vibrational transitions occurring between more than 33 thousand energy levels and covers frequencies up to 18500 cm-1. All energy levels with rotational quantum number, J, up to 20 are considered, making the line list useful for temperatures up to at least 3000 K. About 15% of these levels are fully assigned with approximate rotational and vibrational quantum numbers. The list is calculated using a previously proposed, highly accurate, ab initio model implemented in a high-accuracy computer code based on a two-stage discrete variable representation (DVR) approach. Various consistency checks were carried out to test and validate the results. All these checks confirmed the accuracy of the list. A temperature-dependent partition function, valid over a more extended temperature range than those previously published, and cooling function are presented. Temperature-dependent synthetic spectra for the temperatures T=100, 500, 1000 and 2000 K in the frequency range 0-10000 cm-1 were also generated and presented graphically.
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Harris, M. "Collisional effects in atomic spectra." Thesis, University of Newcastle Upon Tyne, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.352727.

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McHugh, D. R. "Collisional and radiative studies in atomic spectra." Thesis, University of Newcastle Upon Tyne, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.376224.

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Shannon, I. "Collisional and radiative effects in atomic spectra." Thesis, University of Newcastle Upon Tyne, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.371770.

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Blundell, S. "The theory of nuclear effects in atomic spectra." Thesis, University of Oxford, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.355731.

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Sanchez-Fortún, Stoker Jamie. "Theoretical studies of line mixing in atomic and molecular spectra." Thesis, University of Newcastle Upon Tyne, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.399087.

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Shaw, John A. "Photoabsorption spectra of hydrogen in magnetic fields." W&M ScholarWorks, 1993. https://scholarworks.wm.edu/etd/1539623837.

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Measurements of the absorption spectrum of atomic H in strong magnetic fields have been analyzed. The measurements, performed by the Bielefeld, Germany experimental group, investigated the photoabsorption to levels near the ionization threshold in magnetic fields ranging from 2.7 to 6 Tesla. Taking advantage of a classical scaling law, the photon energy and the magnetic field strength were varied simultaneously in the experiment and the absorption rate vs. B{dollar}\sp{lcub}-1/3{rcub}{dollar} at fixed scaled-energy, {dollar}\varepsilon{dollar} = E/(B/B{dollar}\sb{lcub}\rm o{rcub})\sp{lcub}2/3{rcub}{dollar} was measured. The absorption rate was observed to exhibit sinusoidal fluctuations which we correlate with closed classical orbit of the electron. A Fourier transformation of this signal yields peaks which we interpret as "recurrence strengths" which depend upon the classical action of the closed orbit. Closed-orbit theory gives formulas for these recurrence strengths. as the scaled energy is increased, observed recurrences proliferate, consistent with the change from orderly to chaotic motion of the electron. Bifurcation theory provides organizing principles for understanding this proliferation and for interpreting the data. New "exotic" orbits suddenly appear "out of nowhere" through saddle-node bifurcations. The "main sequence" of orbits is produced from an orbit parallel to B through a sequence of pitchfork and period-doubling bifurcations. Other recurrences are created by period-tripling and higher-order bifurcations of existing orbits. These bifurcations can have generic structure, or sometimes the structures are modified by symmetries of the system. Focusing effects associated with these bifurcations cause some recurrences to be particularly strong.
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Hughes, Alan Nigel. "The structure and spectra of molecular ions." Thesis, University of Newcastle upon Tyne, 2013. http://hdl.handle.net/10443/2217.

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I give a review of the theory of the hydrogen molecular ion H2+ and its isotopomers D2+ and HD+ including the direct analytical solution and the standard adiabatic approximation. I discuss dissociation limits for homonuclear and heteronuclear species; the effect of an external electric field; non adiabatic calculations, relativistic and radiative effects; and spectroscopic measurements of H2+ and D2+ with a comparison of theoretical to experimental values. I give a detailed description of the fast ion-beam spectrometer as used for both laser-beam and microwave spectroscopy and describe the challenges involved in making high resolution spectroscopic measurements. An account is given of theory, experimental details and measurements of transition frequencies and intensities of the forbidden rotational transition (v = 19, N = 1) - (v = 19, N = 0) in the ground electronic state (X2Σg+, also represented as 1sσg) of H2+. Theory has predicted that the transition has measurable intensity due to the Fermi contact hyperfine interaction causing a breaking of electronic g/u symmetry resulting in the mixing of ortho-para states. The measurements were made in both single and double resonance using a fast ion beam/microwave spectrometer at a transition frequency of 14961.7 ± 1.1 MHz, in agreement with the theoretical prediction of 14960 ± 3 MHz. An account is also given of a further search that was conducted for a second forbidden rotational transition (v = 0, N = 1) - (v = 0, N = 0) in the first excited electronic state (2pσu) of H2+. A discussion is given on the possibility of making further observations of forbidden rotational transitions and the experimental difficulties involved; and of adapting the experimental techniques used in order to observe the recently discovered (v = 1, N = 0) in the first excited electronic state (2pσu) of H2+.
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Batchelor, D. R. "Auger electron spectra from bulk elements." Thesis, University of Sussex, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.373904.

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Zahidi, Assou. "Etudes structurales et dynamiques de complexes macrocycliques par rmn heteronucleaire." Université Louis Pasteur (Strasbourg) (1971-2008), 1986. http://www.theses.fr/1986STR13171.

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Etude de la complexation de cations et d'anions par des ligands synthetiques a l'aide de la rmn heteronucleaire (**(6)li, **(7)li, **(13)c, **(14)n, **(15)n, **(19)f, **(31)p, **(35)cl et **(109)ag) et de mesures d'effet overhauser homo- et heteronuclaires
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Books on the topic "Atomic/Molecular Structure and Spectra"

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European, Conference on Atomic and Molecular Physics (2nd 1985 Free University Amsterdam). Second European Conference on Atomic and Molecular Physics, April 15-19, 1985, Free University, Amsterdam, the Netherlands: Book of abstracts. Geneva: European Physical Society, 1985.

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European Conference on Atomic and Molecular Physics (3rd 1989 Université de Bordeaux. Third European Conference on Atomic and Molecular Physics, April 3-7, 1989, Université de Bordeaux I: Book of abstracts. Edited by Salin A and European Physical Society. Division of Atomic and Molecular Physics. Geneva: The Division, The Society, 1989.

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Jürgen, Popp, and SpringerLink (Online service), eds. Challenges in Molecular Structure Determination. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012.

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Moog, Richard Samuel. Physical chemistry, a guided inquiry: Atoms, molecules, and spectroscopy. Boston, Mass: Houghton Mifflin, 2004.

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service), SpringerLink (Online, ed. Molecular Conformation and Organic Photochemistry: Time-resolved Photoionization Studies. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012.

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Ratcliff, Laura. Optical Absorption Spectra Calculated Using Linear-Scaling Density-Functional Theory. Heidelberg: Springer International Publishing, 2013.

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Kalmykov, Yuri P. Recent Advances in Broadband Dielectric Spectroscopy. Dordrecht: Springer Netherlands, 2013.

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service), SpringerLink (Online, ed. Visualization of Hydrogen-Bond Dynamics: Water-Based Model Systems on a Cu(110) Surface. Tokyo: Springer Japan, 2012.

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T, Maitra Neepa, Nogueira Fernando M. S, Gross E. K. U, Rubio Angel, and SpringerLink (Online service), eds. Fundamentals of Time-Dependent Density Functional Theory. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012.

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Batsanov, Stepan S. Introduction to Structural Chemistry. Dordrecht: Springer Netherlands, 2012.

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Book chapters on the topic "Atomic/Molecular Structure and Spectra"

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Micsonai, András, Éva Bulyáki, and József Kardos. "BeStSel: From Secondary Structure Analysis to Protein Fold Prediction by Circular Dichroism Spectroscopy." In Methods in Molecular Biology, 175–89. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0892-0_11.

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Abstract Far-UV circular dichroism (CD) spectroscopy is a classical method for the study of the secondary structure of polypeptides in solution. It has been the general view that the α-helix content can be estimated accurately from the CD spectra. However, the technique was less reliable to estimate the β-sheet contents as a consequence of the structural variety of the β-sheets, which is reflected in a large spectral diversity of the CD spectra of proteins containing this secondary structure component. By taking into account the parallel or antiparallel orientation and the twist of the β-sheets, the Beta Structure Selection (BeStSel) method provides an improved β-structure determination and its performance is more accurate for any of the secondary structure types compared to previous CD spectrum analysis algorithms. Moreover, BeStSel provides extra information on the orientation and twist of the β-sheets which is sufficient for the prediction of the protein fold. The advantage of CD spectroscopy is that it is a fast and inexpensive technique with easy data processing which can be used in a wide protein concentration range and under various buffer conditions. It is especially useful when the atomic resolution structure is not available, such as the case of protein aggregates, membrane proteins or natively disordered chains, for studying conformational transitions, testing the effect of the environmental conditions on the protein structure, for verifying the correct fold of recombinant proteins in every scientific fields working on proteins from basic protein science to biotechnology and pharmaceutical industry. Here, we provide a brief step-by-step guide to record the CD spectra of proteins and their analysis with the BeStSel method.
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Gramaccioli, C. M. "Atomic Displacement Parameters, Vibrational Spectra and Thermodynamic Functions for Crystals: A Strong Connection." In Implications of Molecular and Materials Structure for New Technologies, 59–70. Dordrecht: Springer Netherlands, 1999. http://dx.doi.org/10.1007/978-94-011-4653-1_5.

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Pal’chikov, Vitalij G., and Vjatcheslav P. Shevelko. "Atomic Structure and Spectra." In Reference Data on Multicharged Ions, 3–73. Berlin, Heidelberg: Springer Berlin Heidelberg, 1995. http://dx.doi.org/10.1007/978-3-642-57789-5_2.

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Shevelko, Viatcheslav P. "Atomic Structure and Spectra." In Atoms and Their Spectroscopic Properties, 3–39. Berlin, Heidelberg: Springer Berlin Heidelberg, 1997. http://dx.doi.org/10.1007/978-3-662-03434-7_2.

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Beyer, Heinrich F., H. Jürgen Kluge, and Viatcheslav P. Shevelko. "Atomic Structure and Spectra." In X-Ray Radiation of Highly Charged Ions, 61–84. Berlin, Heidelberg: Springer Berlin Heidelberg, 1997. http://dx.doi.org/10.1007/978-3-662-03495-8_3.

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Svanberg, Sune. "Atomic Structure." In Atomic and Molecular Spectroscopy, 5–30. Berlin, Heidelberg: Springer Berlin Heidelberg, 2001. http://dx.doi.org/10.1007/978-3-642-98107-4_2.

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Svanberg, Sune. "Atomic Structure." In Atomic and Molecular Spectroscopy, 5–30. Berlin, Heidelberg: Springer Berlin Heidelberg, 2004. http://dx.doi.org/10.1007/978-3-642-18520-5_2.

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Svanberg, Sune. "Atomic Structure." In Atomic and Molecular Spectroscopy, 4–28. Berlin, Heidelberg: Springer Berlin Heidelberg, 1992. http://dx.doi.org/10.1007/978-3-642-97398-7_2.

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Svanberg, Sune. "Atomic Structure." In Atomic and Molecular Spectroscopy, 4–28. Berlin, Heidelberg: Springer Berlin Heidelberg, 1991. http://dx.doi.org/10.1007/978-3-642-97258-4_2.

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Svanberg, Sune. "Atomic Structure." In Atomic and Molecular Spectroscopy, 15–43. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-031-04776-3_2.

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Conference papers on the topic "Atomic/Molecular Structure and Spectra"

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Kitani, Takumu, and Tatiana Zolotoukhina. "MD Evaluation of the IR Spectra of DNA Bases in the Process of Transport Through Graphene Nanopore." In ASME 2015 International Technical Conference and Exhibition on Packaging and Integration of Electronic and Photonic Microsystems collocated with the ASME 2015 13th International Conference on Nanochannels, Microchannels, and Minichannels. American Society of Mechanical Engineers, 2015. http://dx.doi.org/10.1115/ipack2015-48298.

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Development of the 1D and 2D IR spectroscopy of small organic molecules and clusters opens yet another way of possible identification of small organic molecules in the state of motion in the graphene nanopore scanning device. With the advantage of obtaining qualitative and at least semi-quantitative information of specimens real-time and non-invasively, vibrational spectroscopy techniques, infrared (IR) and Raman have become more and more important in the analysis of biomolecular samples. At present, the sensitivity and spatial resolution of these techniques stands at the challenge of the detection and analysis of biosamples at very low concentration (single molecule) and high spatial resolution (nanometer/sub-nanometer scale). Spectral analysis requires theoretical assignment of vibrational modes to each biomolecule. We considered vibrational spectra of DNA nucleobase at the time when they are translocated through the graphene nanopore. The Fourier transform of the density of states (DOS) of each base was calculated and the spectra of the base molecules and C atoms of graphene pore edge were obtained. Translocation rate was fixed to have maximum interaction of the base with 1.5 nm pore and single orientation of nucleobases was evaluated relative to molecular plane. Whether interaction of nucleobase and nanopore is able to enhance the signal is still remains unanswered. But we have shown that the spectra of each nucleobase are different and can be considered the fingerprint of the particular molecule. The interaction forces between pore and base are structure dependent and time-limited by translocation time. In such case, transient correlation functions were utilized for the DOSes of the individual bases and forces on each atom of the particular base were sorted by intensity. The spectra of individual atoms in the bases as well as of whole molecule were compared and frequencies of most intense peaks were related to particular atoms. Molecular dynamics method is used for the DNA base and graphene nanopore calculations with the MM2/MM3 potentials for the base and REBO graphene potential. Interaction potential between the bases can simultaneously give additional information for the electronic transport calculations with possible tra and graphene are of the MM2/MM3 part of the Van der Waals interaction only has been considered. Possibility of base identification by spectral signature is confirmed. Calculated spectra are compared with results of the existing IR measurements for nucleobases.
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Bešlo, D., M. Molnar, D. Agić, S. Roca, and B. Lučić. "THE PREDICTION ACCURACY OF 1H AND 13C NMR CHEMICAL SHIFTS OF COUMARIN DERIVATIVES BY CHEMO/BIOINFORMATICS METHODS." In 1st INTERNATIONAL Conference on Chemo and BioInformatics. Institute for Information Technologies, University of Kragujevac, 2021. http://dx.doi.org/10.46793/iccbi21.422b.

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In plant biochemistry and physiology, coumarins are known as antioxidants, enzyme inhibitors and precursors of toxic substances. Nuclear magnetic resonance (NMR) spectra are primary sources of molecular structural data. NMR provides detailed information about the local environment of the atom which can be used to determine the atomic connectivity, stereochemistry, and molecular conformation. For many years the molecular structure has been determined by NMR spectroscopy and chemical shifts are determined manually with the help of computer programs. However, recent progress in computational chemistry and chemo/bioinformatics opened the possibility for the prediction of chemical shifts (especially those of 1H and 13C nuclei) of new chemicals. We analyzed the accuracy of three available chemoinformatics methods developed for the prediction of 1H and 13C chemical shifts based on deep neural networks CASCADE [1], an older prediction method based on classical neural networks NMRshiftDB [2,3], and group-contribution method in ChemDraw [4]. The mean absolute errors (MAEs) in the prediction of NMR shifts of four newly synthesized coumarins [5] by CASCADE, NMRshiftDB and ChemDraw are (respectively) 0.39, 0.65 and 0.32 ppm for 1H, and 1.5, 6.5 and 2.3 ppm for 13C atoms, shoving relatively big differences between these prediction methods.
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Drewsen, Michael. "High-resolution direct optical frequency comb Raman spectroscopy of single ions: from atomic fine structures to rotational spectra of molecular ions." In Optical, Opto-Atomic, and Entanglement-Enhanced Precision Metrology II, edited by Selim M. Shahriar and Jacob Scheuer. SPIE, 2020. http://dx.doi.org/10.1117/12.2552656.

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Rehn, Victor. "Surface Analysis Using Time-Resolved Techniques in Extreme-Ultraviolet Free-Electron-Laser Radiation." In Free-Electron Laser Applications in the Ultraviolet. Washington, D.C.: Optica Publishing Group, 1988. http://dx.doi.org/10.1364/fel.1988.thc5.

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When a short pulse of high-intensity free-electron-laser (FEL) radiation strikes a surface, the resulting electronic excitations may stimulate the emission or ejection of any of several particles: ionic or neutral atomic or molecular particles, electrons, or photons. Using high-speed pulse-timing techniques, a variety of information may be obtained. It is possible to determine the kinetic-energy spectra of massive particles; to identify massive particles via their charge-to-mass ratios or via their laser-induced fluorescence; and to determine the angular distributions and coincidences of emitted particles. From such information (and its spectral dependence), details of the surface structure and the emission process can be learned. Examples relevant to semiconductor surface studies are discussed.
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Luo, Tengfei, and John R. Lloyd. "Ab-Initio Molecular Dynamics Study of Nano-Scale Thermal Energy Transport." In ASME 2007 2nd Energy Nanotechnology International Conference. ASMEDC, 2007. http://dx.doi.org/10.1115/enic2007-45033.

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Ab-initio molecular dynamics (MD) which employs density functional theory (DFT) is used to study thermal energy transport phenomena in nano-scale structures. Thermal equilibration in multiple thin layer structures with thicknesses less than 1 nanometer per layer is simulated. Different types of layer combinations are investigated. Periodic boundary conditions in all directions are used in all cases. Two neighboring layers are first set to different temperatures using Nose-Hoover thermostats, and then the process of energy equilibration is simulated with a “free run” (without any thermostat controlling the temperatures). The temperature evolutions in the two neighboring layers are computed. The atomic vibration power spectra are calculated and used to explain the phenomena observed in the simulation.
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Wiese, Wolfgang L. "The NIST atomic spectra database." In Second international conference on atomic and molecular data and their applications. AIP, 2000. http://dx.doi.org/10.1063/1.1336287.

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DiMauro, Louis. "Attosecond Probing of Atomic & Molecular Structure." In Laser Science. Washington, D.C.: OSA, 2014. http://dx.doi.org/10.1364/ls.2014.lw5h.1.

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Lipatov, Evgeniy I., Alexander G. Burachenko, Sergey M. Avdeev, Victor F. Tarasenko, and Michael A. Bublik. "Identification of natural and synthetic diamonds by cathodoluminescence spectra." In XIII International Conference on Atomic and Molecular Pulsed Lasers, edited by Andrei M. Kabanov and Victor F. Tarasenko. SPIE, 2018. http://dx.doi.org/10.1117/12.2302979.

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Pate, Brooks, Lorenzo Spada, Nathan Seifert, and Luca Evangelisti. "ROTATIONAL SPECTRUM AND CARBON ATOM STRUCTURE OF DIHYDROARTEMISINIC ACID." In 71st International Symposium on Molecular Spectroscopy. Urbana, Illinois: University of Illinois at Urbana-Champaign, 2016. http://dx.doi.org/10.15278/isms.2016.wk04.

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Kazaryan, Mishik A., Sergey Rasmagin, Vitaly Krasovskii, Igor Novikov, and Vitaly Kryshtob. "Changes in optical spectra of silver nanoparticles doped europium ions." In XIII International Conference on Atomic and Molecular Pulsed Lasers, edited by Andrei M. Kabanov and Victor F. Tarasenko. SPIE, 2018. http://dx.doi.org/10.1117/12.2302987.

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Reports on the topic "Atomic/Molecular Structure and Spectra"

1

Langhoff, P. W., J. A. Boatz, R. J. Hinde, and J. A. Sheehy. Atomic Spectral Methods for Molecular Electronic Structure Calculations. Fort Belvoir, VA: Defense Technical Information Center, June 2004. http://dx.doi.org/10.21236/ada429238.

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2

Surdoval, Wayne A., David A. Berry, and Travis R. Shultz. New Equations for Calculating Principal and Fine-Structure Atomic Spectra for Single and Multi-Electron Atoms. Office of Scientific and Technical Information (OSTI), March 2018. http://dx.doi.org/10.2172/1427018.

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Koffas, Telly Stelianos. Characterization of the molecular structure and mechanical properties of polymer surfaces and protein/polymer interfaces by sum frequency generation vibrational spectroscopy and atomic force microscopy. Office of Scientific and Technical Information (OSTI), January 2004. http://dx.doi.org/10.2172/825532.

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