UvA-DARE (Digital Academic Repository) Ultrasensitive nonlinear vibrational spectroscopy of complex molecular systems Selig, O. Publication date 2017 Document Version Other version License Other Link to publication Citation for published version (APA): Selig, O. (2017). Ultrasensitive nonlinear vibrational spectroscopy of complex molecular systems. General rights It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible. UvA-DARE is a service provided by the library of the University of Amsterdam (https://dare.uva.nl) Download date:27 Sep 2021 BIBLIOGRAPHY 1 H.E. Roscoe. Spectrum Analysis: Six Lectures, Delivered in 1868, Before the Society of Apothecaries of London. Macmillan and Company, 1873. 2 H. Kayser and H.M. Konen. Handbuch der Spectroscopie. Number v. 5 in Handbuch der Spectroscopie. S. Hirzel, 1910. 3 I. Newton. Opticks: Or, A Treatise Of The Reflexions, Refractions, Inflexions and Colours Of Light: Also Two Treatises Of The Species and Magnitude Of Curvilinear Figures. Smith and Walford, 1704. 4 William Hyde Wollaston. A method of examining refractive and dispersive powers, by prismatic reflection. Philosophical Transactions of the Royal Society of London, 92:365–380, 1802. 5 S.J. Lewis. Spectroscopy in Science and Industry. Blackie and Son, 1933. 6 G. Kirchhoff and R. Bunsen. Chemische analyse durch spectralbeobachtungen. Annalen der Physik, 186(6):161–189, 1860. 7 G. Kirchhoff and R. Bunsen. Xlii. chemical analysis by spectrum-observations. Philosophical Magazine Series 4, 22(148):329–349, 1861. 8 W.M. Sears. Helium: The Disappearing Element. SpringerBriefs in Earth Sciences. Springer International Publishing, 2015. 9 Samuel Krimm and Jagdeesh Bandekar. Vibrational spectroscopy and conformation of peptides, polypeptides, and proteins. Advances in protein chemistry, 38:181–364, 1986. 10 William Herschel. Experiments on the refrangibility of the invisible rays of the sun. by william herschel, ll. d. f. r. s. Philosophical Transactions of the Royal Society of London, 90:284–292, 1800. 11 Captain Abney and Lieut-Colonel Festing. On the influence of the atomic grouping in the molecules of organic bodies on their absorption in the infra-red region of the spectrum. Philosophical Transactions of the Royal Society of London, 172:887–918, 1881. 12 W.W. Coblentz. Investigations of Infra-red Spectra. Carnegie Institution of Washington publication. Carnegie institution of Washington, 1905. 13 F.W. Rose Jr. Infrared absorption of nineteen hydrocarbons including ten of high molecular weight. Journal of Research, National Bureau of Standards, 19:143–161, 1937. 14 F.W. Rose. Quantitative analysis, with respect to the component structural groups, of the infrared (1 to 2 mu) molal absorptive indices of 55 hydrocarbons. J Res Natl Bur Stand, 20:129, 1938. 15 G.M. Cooper and R.E. Hausman. The Cell: A Molecular Approach. ASM Press, 2007. 16 Timo Partonen. Circadian clock proteins in mood regulation. Frontiers in psychiatry, 5, 2014. 17 Miyuki Kabayama, Kazuto Sakoori, Kazuyuki Yamada, Veravej G. Ornthanalai, Maya Ota, Naoko Morimura, Kei-ichi Katayama, Niall P. Murphy, and Jun Aruga. Rines e3 ubiquitin ligase regulates mao-a levels and emotional responses. The Journal of Neuroscience, 33(32):12940–12953, 2013. 18 Jeremy M. Berg, John L. Tymoczko, and Lubert Stryer. Protein structure and function. 2002. 19 Julie S. Valastyan and Susan Lindquist. Mechanisms of protein-folding diseases at a glance. Disease Models and Mechanisms, 7(1):9–14, 2014. 20 Sandra Vidak and Roland Foisner. Molecular insights into the premature aging disease progeria. Histochemistry and cell biology, 145(4):401–417, 2016. 21 Andreas Barth. Infrared spectroscopy of proteins. Biochimica et Biophysica Acta (BBA)-Bioenergetics, 1767(9):1073–1101, 2007. 165 166 BIBLIOGRAPHY 22 Joachim A. Hering, Peter R. Innocent, and Parvez I. Haris. Automatic amide I frequency selection for rapid quantification of protein secondary structure from fourier transform infrared spectra of proteins. Proteomics, 2(7):839–849, 2002. 23 Erik Goormaghtigh, Jean-Marie Ruysschaert, and Vincent Raussens. Evaluation of the information content in infrared spectra for protein secondary structure determination. Biophysical journal, 90(8):2946–2957, 2006. 24 Lauren P DeFlores, Ziad Ganim, Rebecca A. Nicodemus, and Andrei Tokmakoff. Amide I’- II’ 2D IR spectroscopy provides enhanced protein secondary structural sensitivity. Journal of the American Chemical Society, 131(9):3385–3391, 2009. 25 Sander Woutersen and Peter Hamm. Structure determination of trialanine in water using polarization sensitive two-dimensional vibrational spectroscopy. The Journal of Physical Chemistry B, 104(47):11316– 11320, November 2000. 26 Igor V. Rubtsov. Relaxation-assisted two-dimensional infrared (RA 2DIR) method: Accessing distances over 10 å and measuring bond connectivity patterns. Accounts of chemical research, 42(9):1385–1394, 2009. 27 Yung Sam Kim, Liu Liu, Paul H. Axelsen, and Robin M. Hochstrasser. 2D IR provides evidence for mobile water molecules in β-amyloid fibrils. Proceedings of the National Academy of Sciences, 106(42):17751–17756, 2009. 28 Satoshi Fukuchi, Kazuo Hosoda, Keiichi Homma, Takashi Gojobori, and Ken Nishikawa. Binary classification of protein molecules into intrinsically disordered and ordered segments. BMC structural biology, 11(1):29, 2011. 29 Zhirong Liu and Yongqi Huang. Advantages of proteins being disordered. Protein Science, 23(5):539– 550, 2014. 30 Vladimir N. Uversky, Vrushank Dave, Lilia M. Iakoucheva, Prerna Malaney, Steven J. Metallo, Ravi Ramesh Pathak, and Andreas C. Joerger. Pathological unfoldomics of uncontrolled chaos: Intrinsically disordered proteins and human diseases. Chemical Reviews, 114(13):6844–6879, 2014. PMID: 24830552. 31 Vladimir N. Uversky. Targeting intrinsically disordered proteins in neurodegenerative and protein dysfunction diseases: another illustration of the d2 concept. Expert review of proteomics, 7(4):543–564, 2010. 32 Tod D. Romo and Alan Grossfield. How fast is your camera? timescales for molecular motion and their role in restraining molecular dynamics. Biophysical journal, 106(12):2549–2551, 2014. 33 Stefan Roberts, Michael Dzuricky, and Ashutosh Chilkoti. Elastin-like polypeptides as models of intrinsically disordered proteins. FEBS letters, 589(19PartA):2477–2486, 2015. 34 Thomas Buergi and Alfons Baiker. Attenuated total reflection infrared spectroscopy of solid catalysts functioning in the presence of liquid-phase reactants. Advances in Catalysis, 50:227–283, 2006. 35 Martin Fleischmann, Patrick J. Hendra, and A.J. McQuillan. Raman spectra of pyridine adsorbed at a silver electrode. Chemical Physics Letters, 26(2):163–166, 1974. 36 A. Hartstein, J.R. Kirtley, and J.C. Tsang. Enhancement of the infrared absorption from molecular monolayers with thin metal overlayers. Physical Review Letters, 45(3):201, 1980. 37 Lisa V. Brown, Ke Zhao, Nicholas King, Heidar Sobhani, Peter Nordlander, and Naomi J. Halas. Surface-enhanced infrared absorption using individual cross antennas tailored to chemical moieties. Journal of the American Chemical Society, 135(9):3688–3695, March 2013. 38 Lisa V. Brown, Ke Zhao, Nancy J. Halas, and Peter J. Nordlander. Cross antennas for surface- enhanced infrared absorption (seira) spectroscopy of chemical moieties, March 13 2014. US Patent App. 14/209,310. 39 Ronen Adato and Hatice Altug. In-situ ultra-sensitive infrared absorption spectroscopy of biomolecule interactions in real time with plasmonic nanoantennas. Nature communications, 4, 2013. 40 J.D. Jackson. Classical electrodynamics. Wiley, 1975. 41 E. Hecht. Optics. Pearson education. Addison-Wesley, 2002. BIBLIOGRAPHY 167 42 D.J. Griffiths. Introduction to Electrodynamics. Prentice Hall, 1999. 43 Craig F. Bohren and Donald R. Huffman. Classical Theories of Optical Constants, pages 226–267. Wiley- VCH Verlag GmbH, 2007. 44 H. A. Lorentz. The Theory of Electrons: And Its Applications to the Phenomena of Light and Radiant Heat. CreateSpace Independent Publishing Platform, 2 2014. 45 Neil W. Ashcroft. Solid State Physics. Thomson Press (India) Ltd, 1 edition, 12 2003. 46 Ellen J. Zeman and George C. Schatz. An accurate electromagnetic theory study of surface enhancement factors for silver, gold, copper, lithium, sodium, aluminum, gallium, indium, zinc, and cadmium. The Journal of Physical Chemistry, 91(3):634–643, 1987. 47 P. G. Etchegoin, E. C. Le Ru, and M. Meyer. An analytic model for the optical properties of gold. The Journal of Chemical Physics, 125(16), 2006. 48 Stefan Alexander Maier. Plasmonics: Fundamentals and Applications. Springer, softcover reprint of hardcover 1st ed. 2007 edition, 12 2010. 49 Paolo Biagioni, Jer-Shing Huang, and Bert Hecht. Nanoantennas for visible and infrared radiation. Reports On Progress In Physics, 75(2):024402, February