published_or_final_version / abstract / Physics / Doctoral / Doctor of Philosophy

The focus of this research is to combine both computational as well as experimental methods to study the non-covalent interaction between a selected set of proteins with small molecules. Experimentally, a mass spectrometric technique, recently known as electrospray mass spectrometry together with the computational aspect of this research, in the area of molecular modeling and quantum mechanics would be exercised.Due to the soft ionization nature of this process, electrospray (ES) mass spectrometry (MS) has been employed to study a broad class of large proteins and their non-covalent interaction with small structures, making it possible for the mass of these complexes to _be determined with an error of less than 0.1%. For this research, a set of proteins known as histones and a class of structures known as crown ethers were chosen. The ES technique allows the proteins to be prepared in an acidic medium that protonates the basic amino acids that have been exposed by the solvent. This process leaves the protein with a lot of positive charges thereby making the analysis with a single quadrupole mass spectrometer, Extrel ELQ 400 possible. The non-covalent complexation between the histones and the crown ethers is stabilized by hydrogen bonding therefore the positive charges of the protein remain unchanged. This bonding is made possible by the ability of crown ethers to bind ammonium ion or protonated amino groups. The mass of the protein which is divided by the number of its positive charges can be determined by a new kind of linear plot constructed from the ES data. The ion currents from the electrospray ionization technique is a representation of the non-covalent complexation of the histones and the crown ethers which can be observed in the mass spectra. Other information such as, the binding constants, can be obtained from the mass spectra. / Department of Chemistry

自由電子雷射器和傅裡葉變換質譜儀的組合使之成為一種研究生物分子和一些水和離子的溶解動力學的有力工具。而理論方法作為實驗的輔助手段常用于判斷一些分子的結構。在本論文中，我運用密度泛函理論和第一性分子動力學方法研究了陽離子化的氨基酸和一些水合陰離子的實驗紅外多光子吸收譜。 / 第二章研究了氫離子和鹼金屬離子化的天冬醯胺酸的紅外多光子吸收譜。以前有文獻用簡諧近似的方法研究過這個團簇，不過這種方法忽略了分子的動力學和非諧效應。我用第一性分子動力學方法重新研究了這個體系，結果顯示這種陽離子化的氨基酸的分子結構非常柔軟，在有限溫度下可以通過二面角的轉動和離子與氨基酸中的氧和氮原子距離的振動可以相互的轉化。而這些構型的相互轉化可以解釋實驗紅外吸收峰的展寬和相對強度變化趨勢。 / 第三章研究了水合碳酸氫根陰離子的紅外多光子吸收譜。以前的文獻指出，對於這種團簇，僅通過對比實驗和簡諧近似的紅外譜圖不能夠判斷是否只有一種異構體存在。應用第一性分子動力學方法，我發現簡諧近似紅外譜和實驗譜的不吻合之處，特別是水分子個數小於等於5時，水分子中氫原子的左右搖擺振動和來回搖擺振動吸收峰在實驗譜中的缺失。通過計算一系列異構體的熱能，我發現一些含量較少的異構體仍然對吸收峰有比較大的貢獻，考慮了這些結構的貢獻我們就可以理解為什麼隨著團簇尺寸的增加，一些吸收峰的強度有一定的變化趨勢。 / 最後兩章研究了水合磷酸二氫根的紅外多光子吸收譜。這是第一次我們和實驗組合作成果。在這個專案裡，我負責分析和全部的理論計算。對於這種團簇，實驗上測量了紅外譜的低頻和高頻區(n=1-4)。有趣的是，特別是體系只包含一個水分子時，兩個穩定的異構體均不能單獨解釋低頻和高頻的實驗結果。基於分子動力學的研究發現，有一個過渡態的吸收峰出現在了高頻區。其原因是氫原子的零點能和隧穿效應。與n=1類似,對於存在多個水分子的體系，實驗譜也揭示了低溫下的異構體效應，而這個效應使得簡諧效應完全失效。 / The combination of the FEL with FTICR makes it a powerful tool in researching the biochemical molecules and solvation dynamics of small hydrated ions. And theoretical methods are often employed in the determination of the molecular structures as auxiliary tools. In this thesis, density functional theory and ab initio molecular dynamics method have been applied to study the experimental infrared multiphoton dissociation (IRMPD) processes for cationized amino acids and hydrated anions. / The second Chapter is the AIMD simulated IR spectra for Asparagine cationized by H⁺, Li⁺, Na⁺, K⁺, and Cs⁺. The previous work simulated these type clusters with harmonic approximation in which the dynamics and anharmonicity effects were missed. My result shows that M⁺(Asn) complexes are very flexible and they could convert into each other at finite temperatures by torsional rotation and stretching the distances between the ion and N, O atoms in Asn. The broaden features and shift of the relative intensities of the vibrational profiles for these conformers are dependent on the structural flexibility of the complexes. / The third Chapter is the IRMPD spectra of the hydrated bicarbonate anion clusters for n=1-7. For some clusters, as mentions in the former harmonic results, comparing the experimental and calculated spectra does not always identify a single isomer as being responsible for the spectrum. By using AIMD technique, I found discrepancies between the harmonic and experimental spectra, especially for the absence of water wagging and rocking mode in the experimental result for n=1-5. By calculating the thermal energies of various isomers of each cluster, I found that the less dominate conformer also shows its large contributions to the vibrational profiles and this could explain the peak intensity trend as the cluster size increase. / The vibrational spectra for (HO)₂PO₂⁻(H₂O)n=1-4, 6, and 8 are presented in the last two chapters. It is the first time we collaborate with experiment group. In these works, I have done all the theoretical simulations. For these clusters, both the low and high (n=1-4) frequency regions of IRMPD spectra are measured. Interestingly for n=1, both the two stable isomer cannot alone represent both the low and high frequency profiles. Base on the AIMD simulations, I found that the existence of an unstable transient state shows it absorption profile in the high frequency region due to the zero point energy and tunneling effect of hydrogen atom. Similar to n=1, the IRMPD spectra of larger clusters (n>1) also show evidence for isomerization at cryogenic temperatures which leads to a complete breakdown of the harmonic approximation. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Sun, Shoutian. / Thesis (Ph.D.) Chinese University of Hong Kong, 2014. / Includes bibliographical references. / Abstracts also in Chinese. / Sun, Shoutian.

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This dissertation describes the first high-precision observation of the infrared spectrum of the helium hydride molecular ion HeH⁺. The frequencies of five vibrational-rotational transitions in the range 1700-1900 cm⁻¹ in the X¹Σ⁺ ground electronic state of ⁴HeH⁺ have been measured to ±0.002 cm⁻¹ (±1 ppm). The Doppler tuned ion beam laser spectroscopic method was used in making the measurements: In a region of constant electrostatic potential, an HeH⁺ ion beam of several keV energy is intercepted at a small angle by a beam from a carbon monoxide infrared gas laser. The energy of the ion beam is adjusted to Doppler-shift an ion transition into resonance with a nearby laser line. On resonance the laser light stimulates transitions to take place. If the resonating states differ in population, the laser-induced transitions produce a net population transfer. The occurrence of population transfer is detected by monitoring the transmission of the ion beam through a gas target downstream from the laser beam interaction region. The transmission through the target is dependent upon the ion beam vibrational-state population distribution and therefore is sensitive to changes in the population distribution, because the cross-section for charge-exchange neutralization of an incident ion is dependent upon the vibrational state of the ion. The current interest in molecular ions in general, and in HeH⁺ in particular, is explained. The existing theory of the structure of HeH⁺ is summarized and a comprehensive listing of theoretical treatments of the structure of HeH⁺ is given. The meager previous experimental work on HeH⁺ is reviewed. The principles of the Doppler tuned ion beam laser resonance method are discussed and the experimental apparatus used is described in detail. The acquisition and analysis of the data is described and the results are compared with the best existing theoretical predictions of the transition frequencies. The present experimental values (given by D. E. Tolliver, G. A. Kyrala, and W. H. Wing, Phys. Rev. Lett. 43, 1719) for the measured transitions are (with the corresponding values calculated by D. L. Bishop and L. M. Cheung, J. Mol. Spectrosc. 75, 462, given in parentheses): (v,J)=(1,11)↔(0,12), 1855.905 cm⁻¹ (1856.152 cm⁻¹); (1,12)↔(0,13), 1751.971 cm⁻¹ (1752.198 cm⁻¹); (2,8)↔(1,9), 1896.992 cm⁻¹ (1897.139 cm⁻¹); (2,9)↔(1,10), 1802.349 cm⁻¹ (1802.492 cm⁻¹); and (2,10)↔(1,11), 1705.543 cm⁻¹ (1705.684 cm⁻¹). It is seen that the present experimental values deviate from the theory by typically 0.2 cm⁻¹, and are two orders of magnitude more precise than the theoretical values.

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The nearby excited states of Fe('2+) in MgO have been observed by Raman spectroscopy for the first time. We observed an A(,1g) impurity mode (185 cm('-1)) and an electronic transition at 110.5 (+OR-) .8 cm('-1) which we associate with the first excited states of the ferrous ion, (GAMMA)(,3g) and (GAMMA)(,4g), previously observed by far infra-red optical absorption. / Crystal field theory and group theory are used to characterize the energy levels and the wavefunctions of the ferrous ion. The observed reduction in the spin-orbit splitting of the energy levels is accounted for by solving the Jahn-Teller Hamiltonian in the approximation of the cluster model. / Uniaxial stress applied to the MgO:Fe('2+) samples produced a shift in the observed electronic transitions. The stress Hamiltonian is solved from which is extracted the experimental value of the strain coupling coefficient to E(,g) deformation (V(,2) = 7140 (+OR-) 1800 cm('-1)) which led, ultimately, to the Jahn-Teller coupling coefficients and to the Jahn-Teller energies ((E(,JT))(,E) = 80 cm('-1) and 3/2(E(,JT))(,T) = 150('-1)) pertinent to the ferrous ion in MgO.

This research is directed at developing the interplay of experimental and computational methods in the area of biochemical mass spectrometry. The experimental method is that of electrospray ionization mass spectrometry (ESI-MS). The computational methods employed are those of semi-empirical quantum mechanics and molecular modeling.The use of Electrospray Mass Spectrometry was developed to investigate whole proteins and the non-covalent complexes that may be formed with small molecules. This method provides the soft ionization needed to accurately determine a noncovalently bound complex's mass with an error of less than 0.1 %. An original design electrospray ionization source (ESI) and a syringe pump have been built to fulfill the goals of the research. The ESI source design has been published in The Journal of the American Society for Mass Spectrometry, (1993, 4, 964-967).In this work the protein selected was cytochrome c and its variants from different species. The small molecules chosen were a broad class of structures known as crown ethers. With the ESI technique the proteins are prepared in an acidic solution that fully protonates the solvent-exposed basic amino acid residues. This provides the protein with many positive charges which makes the analysis by ESI mass spectrometry possible with a single quadrupole instrument, an Extrel ELQ 400. The mass of the protein is divided by the number of positive charges. The small molecules, the crown ethers, were chosen due to their ability to bind ammonium ion and protonated amino groups. This binding is non-covalent, hydrogen bonds stabilize the complex formation. Because this complex is non-covalent in nature the charge of proteins does not change. To aid in the interpretation of our electrospray mass spectra we have originated a new kind of linear plot for use with ESI data. It was found that in using the ESI technique that ion currents representing non-covalent complexes of cytochrome c and crown ethers could be observed in the mass spectra. The measurements of the total ion counts of peaks in the mass spectra allowed binding constants to be calculated. This had not been reported before in the literature.The accurate weight determination and the characteristic charge distribution in the ESI mass spectrum provides data suitable for computer modeling. The nature of the protein's positive charges in ESI had not been well defined. The experimentally determined binding constants allowed comparison to results from computational chemistry and molecular modeling. This result shows that the binding occurs at specific, protonated amino acid residues. The calculations performed yielding the Heats of Formation (OH f) for protonated amino acids complexed with crown ethers indicates that the OH binding of crowns increases from histidine, to arginine, to lysine. The use of a 3D model of cytochrome c from crystallographic data provided in the Brookhaven Protein Database and the SYBYL molecular modeling program allows a structural correlation to be made between the 3D model of the protein and protein/crown ether complex. The stoichiometric ratios of bound crown ether to protein determined from experiment, along with the computational results, have been used to rationalize a protein molecular model that allows predictions to be made about the potential for binding of other small molecules. / Department of Chemistry

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