전기장을 이용한 분자 및 분자 클러스터 조작에 관한 연구

학위논문(박사)--서울대학교 대학원 :자연과학대학 화학부,2020. 2. 강헌.This dissertation aims to demonstrate how a strong external electrostatic field on the order of 10^8 V/m manipulates molecular properties, such as orientation, structure, dynamics, etc., of small molecules and molecular clusters isolated in cold inert matrices. A combination of the ice film nanocapacitor method and the matrix isolation technique enabled the application of unprecedentedly intense external electric dc fields across the isolated molecules and molecular clusters. Changes in molecular properties driven by external fields were investigated by means of vibrational spectroscopy. Chapter 1 provides a background of molecular-control studies with external forces. A brief history of molecular manipulation using electrostatic, magnetic, and optical fields is introduced, with more detailed examples on molecular control with electrostatic fields in both gas-phase and condensed-phase molecular systems. A concise introduction to the methodology of research in the present dissertation is also given. Detailed experimental methods are described in Chapter 2. The fundamentals and practical aspects of the ice film nanocapacitor method for applying intense external fields, the matrix isolation technique for preparing isolated molecular species, and the reflection–absorption infrared spectroscopy for detecting molecular behaviors are summarized. A description on the instrumentation used in the experiments is provided. Chapter 3 presents the spectroscopic study on the field-driven change in inversion tunneling dynamics of ammonia molecule. An ammonia molecule isolated in the Ar matrix, which undergoes a rapid umbrella inversion tunneling across the barrier of the symmetric double-minimum potential energy surface when undisturbed, reorients into the direction of an strong external field by Stark mixing of inversion states with close energy levels and opposite parities. An external field results in the asymmetrization of the double-minimum potential and thereby the quenching of inversion dynamics. The static infrared spectra recorded at systematically scanned-field strengths, which encrypt such field-induced behavior of ammonia, were decoded with the help of potential energy surface, localization of wavefunctions, and transition selection rule under the external dc field. Chapter 4 reports the experimental measurement of the vibrational Stark sensitivity of small hydrogen-bonded water and ammonia clusters ((D2O)3, (D2O)4, (NH3)3, NH3–HCl, NH3–H2O, and (ND3)3). The vibrational Stark effect manifests the frequency shift as a result of the field-induced manipulation of potential energy surfaces of molecular vibrations. The Stark sensitivity of vibrations of the clusters was found to significantly differ from the corresponding uncomplexed monomer. The clustering effect on the Stark sensitivity is discussed in the perspective of anharmonicity, geometric effect, and intermolecular vibrational coupling. As an extreme example of the clustering through hydrogen-bonding, Stark spectra of a crystalline ice were qualitatively interrogated and compared with those of the isolated water monomer. Chapters 5 and 6 demonstrate that a strong electrostatic field enables the dislocation of an acidic proton. In Chapter 5, vibrational Stark spectroscopy was conducted for hydrogen chloride–water (HCl–H2O, HCl–D2O) complexes to examine the field-induced behavior of the proton in hydrated acids. The spectra of the complexes showed an extraordinarily large Stark shift of the proton stretching frequency compared to that of uncomplexed HCl molecule. In the case of HCl–D2O, the vibrational coupling between the proton stretching and the symmetric stretching of D2O was modified by external fields. Spectral analysis aided by a quantum calculation reveals the reversible and asymmetric translocation of the acidic proton along the proton-transfer coordinate in the HCl–water complexes by applied fields. Chapter 6 reports the Stark spectra of HCl complexes with ammonia and methylated amines (methylamine, dimethylamine, and trimethylamine), a prototypical example of proton-transferring molecular system. Not only the proton stretching vibration which is a parallel/anti-parallel motion of proton along the proton-transfer coordinate but also the perpendicular proton bending mode showed exceptionally drastic spectral changes under the influence of external fields. The spectral changes by fields were characteristic of each complex with different degree of proton transfer. The studies on the hydrated acids and the proton-transfer complexes provide the spectroscopic evidence of the large protonic polarizability, a concept which occupies a prominent position in the behavior and spectroscopy of proton in chemistry. Chapter 7 summarizes the dissertation. The significance and prospect of the research presented in this dissertation are briefly addressed in the perspective of intermolecular processes in chemistry and molecular manipulation in quantum technology.본 학위 논문은 10^8 V/m 수준의 강한 외부 정전기장이 저온의 비활성 매트릭스 내에 고립된 분자 및 분자 클러스터의 방향, 구조, 동력학 등의 성질을 어떻게 조작하는지에 대해 다룬다. 얼음 박막 축전법과 매트릭스 고립법을 동시에 이용하여 이전 연구에서는 가할 수 없었던 강한 외부 직류 전기장을 고립된 분자와 분자 클러스터에 가할 수 있었다. 외부 전기장에 의한 분자 특성의 변화는 진동 분광학을 이용해 관측하였다. 1장에서는 외부 힘을 통해 분자를 조작하는 기존 연구들을 소개한다. 정전기장, 자기장, 광학 전기장 등의 외부 힘을 이용한 분자 조작에 관한 간단한 역사를 소개하고, 그 후에는 정전기장을 이용한 연구들에 대해 보다 자세히 다룬다. 본 학위 논문 연구에서 이용된 방법론에 대해서도 간단히 소개한다. 2장에서는 연구에 사용된 실험 방법을 설명한다. 강한 외부 전기장을 걸어주기 위해 얼음 박막 축전법을 사용하였고, 고립된 분자 및 분자 클러스터를 만들기 위해서는 매트릭스 고립법을 사용하였다. 전기장에 의한 분자 및 분자 클러스터의 변화는 반사-흡수 적외선 분광법이 사용되었다. 이 방법들에 대한 원리적, 실용적 측면들을 요약한다. 실험에 사용된 장치에 대해서도 묘사한다. 3장은 암모니아 분자의 반전 터널링 동력학의 전기장에 의한 변화에 대한 분광학적 연구이다. 아르곤 매트릭스 내의 암모니아 분자는 외부 방해가 없을 때 대칭적인 이중-최소점 퍼텐셜 에너지 표면 내에서 매우 빠른 우산-반전 터널링을 일으키는 것으로 알려져 있다. 강한 외부 전기장이 가해지면 반전 상태들의 Stark 섞임이 일어나고, 그로인해 분자가 전기장 방향으로 정렬하게 된다. 정렬된 암모니아 분자는 비대칭적인 이중-최소점 퍼텐셜 에너지 표면을 가지게 되고, 따라서 반전 터널링이 일어나지 않게 된다. 외부 전기장에 의한 이러한 변화들은 전기장 세기를 변화시켜가며 얻은 적외선 스펙트럼에 암호화되어 있으며, 본 연구에서는 퍼텐셜 에너지 표면, 파동함수의 편재화, 전이 선택 규칙 등을 이용하여 이를 해석하였다. 4장에서는 물과 암모니아 분자를 포함하는 수소 결합 클러스터의 진동 Stark 민감도의 실험적 측정에 관해 다룬다. 외부 전기장은 분자 진동의 퍼텐셜 에너지 표면을 조작하여 진동수 이동을 일으키는데, 이를 진동 Stark 효과라고 한다. 분자 클러스터의 진동 Stark 민감도는 클러스터를 이루지 않은 단독 분자의 민감도와 크게 다른 것으로 관찰되었다. 이러한 클러스터 효과를 진동의 비조화성, 구조적 효과, 분자간 진동 짝지음 등의 측면에서 논의한다. 수소 결합을 통한 클러스터링의 극단적 예시로 결정형 얼음의 진동 스펙트럼이 전기장에 의해 어떻게 변하는지를 조사하였으며, 이를 단독 물분자와 비교하였다. 5장과 6장은 강한 외부 전기장이 산성 양성자를 이동시킬 수 있다는 것을 실험적으로 보여주었다. 5장은 염화수소-물(H2O, D2O) 클러스터에 대한 진동 Stark 분광학적 연구이다. 이 클러스터의 양성자 신축 진동수가 외부 전기장에 의해 매우 크게 변화한 것을 관찰하였다. 염화수소-D2O 클러스터의 경우에는 양성자 신축 진동과 D2O의 대칭 신축 진동의 짝지음이 외부 전기장에 의해 변하는 것을 관찰하였다. 양자 계산을 이용해 스펙트럼을 해석한 결과, 외부 전기장이 염화수소- 물 클러스터의 양성자 전달 좌표 상에서 양성자가 가역적, 비대칭적으로 이동하도록 유도한다는 사실을 알 수 있었다. 6장은 염화수소와 암모니아, 메틸화된 아민 분자의 클러스터에 대한 연구이다. 이 클러스터들은 양성자 전달 시스템의 대표적인 예이다. 평행한 방향의 양성자 신축 진동 뿐만 아니라 수직 방향의 양성자 굽힘 진동 역시 외부 전기장에 의해 큰 진동수 변화를 나타냈다. 각 양성자 전달 분자 클러스터는 전기장에 의해 고유한 스펙트럼 변화를 보였다. 수화된 산성 분자와 양성자 전달계에 대한 이러한 연구는 양성자의 거동에 있어서 핵심적인 개념인 큰 양성자 편극도에 대한 실험적 증거를 제공한다. 7장은 본 학위 논문의 요약이다. 본 연구의 중요성과 전망을 분자간 화학적 과정과 양자 기술에서의 분자 조작의 측면에서 서술한다.Chapter 1. Introduction 1 1.1. Manipulation of Molecules with External Fields 2 1.2. Manipulation of Molecules with Homogeneous Electrostatic Fields 4 1.3. Approach and Contents of This Dissertation 6 References 8 Chapter 2. Method 16 2.1. A Combined Technique of Ice Film Nanocapacitor and Matrix Isolation 16 2.2. Reflection-Absorption Infrared Spectroscopy of Matrix-Isolated Molecules under the Influence of External Fields 21 2.3. Instruments 24 References 27 Chapter 3. Electric Field-Control of Inversion Dynamics of Ammonia in an Argon Matrix 31 Abstract 31 3.1. Introduction 32 3.2. Experimental Details 34 3.3. Results and Discusstion 35 3.4. Conclusion 47 References 49 Chapter 4. Experimental Measurement of Vibrational Stark Sensitivity of Small Molecular Clusters: Clustering Effect on Stark Response of Vibrations 52 Abstract 52 4.1. Introduction 53 4.2. Experimental Details 55 4.3. Results and Discussion 56 4.4. Conclusion 70 References 71 Chapter 5. Spectroscopic Evidence of Large Protonic Polarizability of Hydrogen Chloride-Water Complexes 77 Abstract 77 Main Text 78 References 88 Supporting Information 92 Chapter 6. Vibrational Stark Spectroscopy on Proton Vibrations in Proton-Transfer Complexes of Hydrogen Chloride with Ammonia and Methylated Amines 103 Abstract 103 6.1. Introduction 104 6.2. Experimental Details 107 6.3. Results 108 6.4. Discussion 115 6.5. Conclusion 121 References 122 Chapter 7. Summary 126 List of Publications 128 Abstract in Korean (국문 초록) 131 Acknowledgement (감사의 글) 135Docto

Solar and Stellar Photospheric Abundances

The determination of photospheric abundances in late-type stars from spectroscopic observations is a well-established field, built on solid theoretical foundations. Improving those foundations to refine the accuracy of the inferred abundances has proven challenging, but progress has been made. In parallel, developments on instrumentation, chiefly regarding multi-object spectroscopy, have been spectacular, and a number of projects are collecting large numbers of observations for stars across the Milky Way and nearby galaxies, promising important advances in our understanding of galaxy formation and evolution. After providing a brief description of the basic physics and input data involved in the analysis of stellar spectra, a review is made of the analysis steps, and the available tools to cope with large observational efforts. The paper closes with a quick overview of relevant ongoing and planned spectroscopic surveys, and highlights of recent research on photospheric abundances.Comment: Invited review to appear in Living Reviews in Solar Physics. 39 pages, 7 figure

Development of innovative analytical methods based on spectroscopic techniques and multivariate statistical analysis for quality control in the food and pharmaceutical fields.

The increasing demand on quality assurance and ever more stringent regulations in food and pharmaceutical fields are promoting the need for analytical techniques enabling to provide reliable and accurate results. However, traditional analytical methods are labor-intensive, time-consuming, expensive and they usually require skilled personnel for performing the analysis. For these reasons, in the last decades, quality control protocols based on the employment of spectroscopic methods have been developed for many different application fields, including pharmaceutical and food ones. Vibrational spectroscopic techniques can be an adequate alternative for acquiring both chemical and physical information related to homogenous and heterogenous matrices of interest. Moreover, the significant development of powerful data-driven methodologies allowed to develop algorithms for the optimal extraction and processing of the complex spectroscopic signals allowing to apply combined approaches for quantitative and qualitative purposes. The present Doctoral Thesis has been focused on the development of ad-hoc analytical strategies based on the application of spectroscopic techniques coupled with multivariate data analysis approaches for providing alternative analytical protocols for quality control in food and pharmaceutical sectors. Regarding applications in food sector, excitation-emission Fluorescence Spectroscopy, Near Infrared Spectroscopy (NIRS) and NIR Hyperspectral Imaging (HSI) have been tested for solving analytical issues of independent case-studies. Unsupervised approaches based on Principal Component Analysis (PCA) and Parallel Factor Analysis (PARAFAC) have been applied on fluorescence data for characterizing green tea samples, while quantitative predictive approaches as Partial Least Squares regression have been used to correlate NIR spectra with quality parameters of extra-virgin olive oil samples. HSI was applied to study dynamic chemical processes which occur during cheese ripening with the aim to map chemical and sensory changes over time. The rapid technical progress in terms of spectroscopic instrumentations has led to have more flexible portable systems suitable for performing measurements directly in the field or in a manufacturing plant. Within this scenario, NIR spectroscopy proved to be one of the most powerful Process Analytical Technologies (PAT) for monitoring and controlling complex manufacturing processes. In this thesis, two applications based on the implementation of miniaturized NIR sensors have been performed for the real-time powder blending monitoring of pharmaceutical and food formulation, respectively. The main challenges in blending monitoring are related to the assessment of the homogeneity of multicomponent formulations, which is crucial to ensure the safety and effectiveness of a solid pharmaceutical formulation or the quality of a food product. In the third chapter of this thesis, tailor made qualitative chemometric strategies for obtaining a global understanding of blending processes and to optimize the endpoint detection are presented

Influence of subunit structure on the oligomerization state of light harvesting complexes: a free energy calculation study

Light harvesting complexes 2 (LH2) from Rhodospirillum (Rs.) molischianum and Rhodopseudomonas (Rps.) acidophila form ring complexes out of eight or nine identical subunits, respectively. Here, we investigate computationally what factors govern the different ring sizes. Starting from the crystal structure geometries, we embed two subunits of each species into their native lipid-bilayer/water environment. Using molecular dynamics simulations with umbrella sampling and steered molecular dynamics, we probe the free energy profiles along two reaction coordinates, the angle and the distance between two subunits. We find that two subunits prefer to arrange at distinctly different angles, depending on the species, at about 42.5 deg for Rs. molischianum and at about 38.5 deg for Rps. acidophila, which is likely to be an important factor contributing to the assembly into different ring sizes. Our calculations suggest a key role of surface contacts within the transmembrane domain in constraining these angles, whereas the strongest interactions stabilizing the subunit dimers are found in the C-, and to a lesser extent, N-terminal domains. The presented computational approach provides a promising starting point to investigate the factors contributing to the assembly of protein complexes, in particular if combined with modeling of genetic variants.Comment: 28 pages, 7 figures, LaTeX2e - requires elsart.cls (included), submitted to Chemical Physic

Assessment of Multi-Scale Approaches for ComputingUV–Vis Spectra in Condensed Phases: Toward an Effective yetReliable Integration of Variational and Perturbative QM/MM Approaches

Computational simulation of UV/vis spectra in condensed phases can be performed starting from converged molecular dynamics (MD) simulations and then performing quantum mechanical/molecular mechanical (QM/MM) computations for a statistically significant number of snapshots. However, the need of variational solutions (e.g., ONIOM/EE) for a huge number of snapshots makes unpractical the use of state-of-the-art QM Hamiltonians. On the other hand, the effectivity of perturbative approaches (e.g., perturbed matrix method, PMM) comes at the price of poor convergence for configurations strongly different from the reference one. In this paper we introduce an integrated strategy based on a cluster analysis of the MD snapshots. Next, a representative configuration for each cluster is treated at the ONIOM/EE level, whereas local fluctuations within each cluster are described at the PMM level. Some representative systems (uracil in dimethylformamide and in water and tyrosine zwitterion in water) are analyzed to show t..

Direct Observation of Early-stage Quantum Dot Growth Mechanisms with High-temperature Ab Initio Molecular Dynamics

Colloidal quantum dots (QDs) exhibit highly desirable size- and shape-dependent properties for applications from electronic devices to imaging. Indium phosphide QDs have emerged as a primary candidate to replace the more toxic CdSe QDs, but production of InP QDs with the desired properties lags behind other QD materials due to a poor understanding of how to tune the growth process. Using high-temperature ab initio molecular dynamics (AIMD) simulations, we report the first direct observation of the early stage intermediates and subsequent formation of an InP cluster from separated indium and phosphorus precursors. In our simulations, indium agglomeration precedes formation of In-P bonds. We observe a predominantly intercomplex pathway in which In-P bonds form between one set of precursor copies while the carboxylate ligand of a second indium precursor in the agglomerated indium abstracts a ligand from the phosphorus precursor. This process produces an indium-rich cluster with structural properties comparable to those in bulk zinc-blende InP crystals. Minimum energy pathway characterization of the AIMD-sampled reaction events confirms these observations and identifies that In-carboxylate dissociation energetics solely determine the barrier along the In-P bond formation pathway, which is lower for intercomplex (13 kcal/mol) than intracomplex (21 kcal/mol) mechanisms. The phosphorus precursor chemistry, on the other hand, controls the thermodynamics of the reaction. Our observations of the differing roles of precursors in controlling QD formation strongly suggests that the challenges thus far encountered in InP QD synthesis optimization may be attributed to an overlooked need for a cooperative tuning strategy that simultaneously addresses the chemistry of both indium and phosphorus precursors.Comment: 40 pages, 9 figures, submitted for publicatio

Local Structure in Terms of Nearest-Neighbor Approach in 1-Butyl-3-methylimidazolium-Based Ionic Liquids: MD Simulations

Description of the local microscopic structure in ionic liquids (ILs) is a prerequisite to obtain a comprehensive understanding of the influence of the nature of ions on the properties of ILs. The local structure is mainly determined by the spatial arrangement of the nearest neighboring ions. Therefore, the main interaction patterns in ILs, such as cation–anion H-bond-like motifs, cation–cation alkyl tail aggregation, and ring stacking, were considered within the framework of the nearest-neighbor approach with respect to each particular interaction site. We employed classical molecular dynamics (MD) simulations to study in detail the spatial, radial, and orientational relative distribution of ions in a set of imidazolium-based ILs, in which the 1-butyl-3-methylimidazolium (C₄mim⁺) cation is coupled with the acetate (OAc^–), chloride (Cl^–), tetrafluoroborate (BF₄^–), hexafluorophosphate (PF₆^–), trifluoromethanesulfonate (TfO^–), or bis­(trifluoromethanesulfonyl)­amide (TFSA^–) anion. It was established that several structural properties are strongly anion-specific, while some can be treated as universally applicable to ILs, regardless of the nature of the anion. Namely, strongly basic anions, such as OAc^– and Cl^–, prefer to be located in the imidazolium ring plane next to the C–H^2/4–5 sites. By contrast, the other four bulky and weakly coordinating anions tend to occupy positions above/below the plane. Similarly, the H-bond-like interactions involving the H² site are found to be particularly enhanced in comparison with the ones at H^4–5 in the case of asymmetric and/or more basic anions (C₄mimOAc, C₄mimCl, C₄mimTfO, and C₄mimTFSA), in accordance with recent spectroscopic and theoretical findings. Other IL-specific details related to the multiple H-bond-like binding and cation stacking issues are also discussed in this paper. The secondary H-bonding of anions with the alkyl hydrogen atoms of cations as well as the cation–cation alkyl chain aggregation turned out to be poorly sensitive to the nature of the anion