전해질 수용액의 물분자 재배향 동역학에 작용하는 협동수화효과에 관한 연구

학위논문 (박사) -- 서울대학교 대학원 : 자연과학대학 물리·천문학부(물리학전공), 2021. 2. 박건식.This thesis describes the structure and reorientation dynamics of water in MgCl2 aqueous electrolyte solution by using ab-initio MD simulation and dielectric relaxation spectroscopy method. By using MgCl2, which has strong hydration effect, as a system solute, ion hydration and its cooperativity were investigated. Unlike bulk water, MgCl2 has considerable influences on the hydrogen bond network of water, as confirmed by the analysis of the radial distribution function, hydrogen bond kinetics, and vibrational density of state. Through this, we found the strong interaction with Mg ions bounds the water in the first hydration shell. Also, the weakening of water-water interaction can be found beyond the first hydration shell. In addition, in this thesis, water molecules' reorientation dynamics were characterized using a cooperative ion hydration model to quantify the cooperative hydration effect. This hydration model showed that the cation-anion mixture effect appears in the reorientation dynamics of water. We have found that water molecules in the second shell of Mg2+ and the first shell of Cl− show retarded reorientation dynamics compared with bulk-like behavior because of cooperative ion hydration. Finally, through a comparison of macroscopic DRS measurement and MD simulation, we have found that the existing additive concept fails to describe the hydration number changing with the concentration. However, the model considering the cooperative effect of Mg2+ and Cl- can accurately describe the hydration number changing with the concentration. These results can indicate that the cooperative effect in the short-range could be an essential factor in determining macroscopic solvent properties.본 연구에서는 ab-initio 전산 모사와 유전체 분광학의 방법으로 염화마그네슘 전해질 수용액의 구조 및 물 분자의 재배향 동역학을 연구하였다. 또한 이온 수화 현상과 여기서 나타나는 협동 수화 효과를 효과적으로 관찰하기 위해 수화 효과가 강한 MgCl2 수용액을 모델 시스템으로 사용했다. 순수한 물과는 다르게 염화마그네슘은 수용액 상태의 물의 수소 결합 네트워크에 영향을 미치며, 이 영향은 방사 방향 분포 함수 (Radial distribution function), 수소결합 동역학, 진동 모드의 상태 밀도 함수 (vibrational density of states) 등을 통해 확인되었다. 이를 통하여 마그네슘 이온의 제 1 수화 껍질 영역에 물과 마그네슘의 강한 상호작용으로 인해 억류 수(bound water)가 생길 뿐 아니라, 그 너머의 물에 대하여 수소 결합 네트워크의 결속이 약해지는 것을 확인할 수 있었다. 또한 본 연구에서는 이온의 수화 과정 속에서 나타나는 협동 효과를 정량화 할 수 있는 협동 수화 모형을 이용하여 물 분자의 재배향 동역학의 특성을 규명하였다. 위 수화 모형을 통해서 전해질 수용액에서 나타나는 협동 수화 효과는 마그네슘 이온의 제 2 수화 껍질과 염소 이온의 제 1 수화 껍질에 동시에 속하는 물분자에서 주로 나타나며 그 결과로 물의 재배향 동역학이 느려짐을 확인하였다. 마지막으로 거시적인 유전체 분광학 측정과 분자 수준의 전산 모사의 결과 비교를 통하여, 이온의 수화 현상을 가법 효과로 (additive effect) 고려했을 때 농도에 따라 변화하는 수화 수 (hydration number) 를 설명할 수 없으나, 협동 수화 효과를 고려한 모형으로는 정확하게 설명할 수 있음을 확인했다. 이는 미시 영역에서 나타나는 협동 수화 효과가 거시 영역의 수용액의 성질을 결정하는데 중요한 요소가 될 수 있음을 의미한다.Contents Abstract i Chapter 1 Introduction 1 1.1 Water 1 1.2 Aqueous Electrolyte Solution 4 1.2.1 Ion hydration 4 1.2.2 Effect of ions on the water structure 7 1.3 Reorientation dynamics of water 14 1.4 Outlook 16 Chapter 2 Method & Materials 17 2.1 Molecular dynamics simulation 17 2.1.1 General principles 17 2.1.2 Classical molecular dynamics simulation 20 2.1.3 Ab-initio molecular dynamics simulation 29 2.1.4 Sample system (MgCl2) & Simulation details 35 2.2 Dielectric relaxation spectroscopy 42 2.2.1 Theoretical background 42 2.2.2 Experimental techniques 53 Chapter 3 Solvation structure 62 3.1 Pair-correlation function 62 3.2 Solvation structure around ion 64 3.3 Influence of ion on the structural properties of water 69 Chapter 4 Effect of ion on the water dynamics 77 4.1 Hydration-shell vibrational density of states 77 4.2 Hydrogen bond kinetics 82 4.3 Water reorientation dynamics 86 Chapter 5 Cooperative effect on ion hydration 89 5.1 Cooperative hydration model 89 5.2 Reorientation dynamics in different water subpopulation 95 5.3 Dielectric relaxation spectroscopy of ion solution 101 5.4 Cooperativity in ion hydration 104 Chapter 6 Summary and Conclusions 107 Bibliography 109 Appendix A Calculation of time correlation function 118 Appendix B Connection between single-water molecule reorientational dynamics and DRS measurements 123 Appendix C Water exchange between different subpopulations 127 Appendix D Reorientation time correlation function analysis from classical MD 133 Appendix E Information on DRS of MgCl2 aqueous solution 135 초록 140Docto

Hydration of Heavy Alkaline-Earth Cations Studied by Molecular Dynamics Simulations and X-ray Absorption Spectroscopy

The physicochemical properties of the three heaviest alkaline-earth cations, Sr2+, Ba2+, and Ra2+ in water have been studied by means of classical molecular dynamics (MD) simulations. A specific set of cation-water intermolecular potentials based on ab initio potential energy surfaces has been built on the basis of the hydrated ion concept. The polarizable and flexible model of water MCDHO2 was adopted. The theoretical-experimental comparison of structural, dynamical, energetic, and spectroscopical properties of Sr2+ and Ba2+ aqueous solutions is satisfactory, which supports the methodology developed. This good behavior allows a reasonable reliability for the predicted Ra2+ physicochemical data not experimentally determined yet. Simulated extended X-ray absorption fine-structure (EXAFS) and X-ray absorption near-edge spectroscopy spectra have been computed from the snapshots of the MD simulations and compared with the experimental information available for Sr2+ and Ba2+. For the Ra2+ case, the Ra L3-edge EXAFS spectrum is proposed. Structural and dynamical properties of the aqua ions for the three cations have been obtained and analyzed. Along the [M(H2O)n]m+ series, the M-O distance for the first-hydration shell is 2.57, 2.81, and 2.93 Å for Sr2+, Ba2+, and Ra2+, respectively. The hydration number also increases when one is going down along the group: 8.1, 9.4, and 9.8 for Sr2+, Ba2+, and Ra2+, respectively. Whereas [Sr(H2O)8]2+ is a typical aqua ion with a well-defined structure, the Ba2+ and Ra2+ hydration provides a picture exhibiting an average between the ennea- and the deca-hydration. These results show a similar chemical behavior of Ba2+ and Ra2+ aqueous solutions and support experimental studies on the removal of Ra-226 of aquifers by different techniques, where Ra2+ is replaced by Ba2+. A comparison of the heavy alkaline ions, Rb+ and Cs+, with the heavy alkaline-earth ions is made.Universidad de Sevilla US-126447

Hydrogen-bond structure and low-frequency dynamics of electrolyte solutions: Hydration numbers from ab Initio water reorientation dynamics and dielectric relaxation spectroscopy

We present an atomistic simulation scheme for the determination of the hydration number (h) of aqueous electrolyte solutions based on the calculation of the water dipole reorientation dynamics. In this methodology, the time evolution of an aqueous electrolyte solution generated from ab initio molecular dynamics simulations is used to compute the reorientation time of different water subpopulations. The value of h is determined by considering whether the reorientation time of the water subpopulations is retarded with respect to bulk-like behavior. The application of this computational protocol to magnesium chloride (MgCl2 ) solutions at different concentrations (0.6-2.8 mol kg-1 ) gives h values in excellent agreement with experimental hydration numbers obtained using GHz-to-THz dielectric relaxation spectroscopy. This methodology is attractive because it is based on a well-defined criterion for the definition of hydration number and provides a link with the molecular-level processes responsible for affecting bulk solution behavior. Analysis of the ab initio molecular dynamics trajectories using radial distribution functions, hydrogen bonding statistics, vibrational density of states, water-water hydrogen bonding lifetimes, and water dipole reorientation reveals that MgCl2 has a considerable influence on the hydrogen bond network compared with bulk water. These effects have been assigned to the specific strong Mg-water interaction rather than the Cl-water interaction

Atomistic simulation studies of the cement paste components

230 p.El cemento y sus derivados, como los morteros o el hormigón, son generalmente considerados materiales de bajo nivel tecnológico. A pesar de ser el material manufacturado más empleado en el mundo, otros como los plásticos, los metales, el algodón, la lana, la madera e incluso las piedras, se valoran más en el día a día. De hecho, el cemento es comúnmente considerado como una pasta gris, con la única característica de endurecerse cuando se seca, y que se empleada para construir edificios. Probablemente, el hecho de que sea barato, disponible, común y haya sido empleado satisfactoriamente durante siglos, contribuye a su percepción como material de bajo perfíl tecnológico. Sin embargo, esa visión se aleja de la realidad. La pasta de cemento es un compuesto complejo y heterogéneo, con diferentes características a diferentes escalas de tamaño. El mecanismo por el cual el clínker al entrar en contacto con el agua se convierte en una pasta endurecida incluye cientos de reacciones químicas y procesos físicos. El componente principal de la pasta de cemento, el gel C-S-H, es una fase amorfa con una determinada porosidad intrínseca, y su nanoestructura aún se desconoce. Curiosamente, el gel C-S-H presenta claras similitudes con otros sistemas de interés tecnológico. Por ejemplo, la estructura del gel es habitualmente descrita en términos de minerales naturales tobermorita y jennita. Estos minerales presentan una estructura laminar similar al de las arcillas montmorillonita-esmectita, que son utilizadas con objetivos catalíticos, como parte de los nano- y bio-composites, o como absorbentes de residuos contaminantes. La morfología del gel C-S-H en la microescala se parece también a la de la hidroxiapatita, que es el principal componente de los huesos. Tal semejanza proviene de su composición análoga: silicato-calcico-hidratado (C-S-H) en la matriz de cemento, y fosfato-calcico-hidratado (C-P-H) en hidroxiapatita. De hecho, tanto el gel C-S-H como la hidroxiapatita sufren un proceso de descalcificación, conocida como lixiviación de calcio en el cemento y osteoporosis en los huesos. Pero hay analogías adicionales con otros sistemas biológicos. La posición y el papel del agua en el gel C-S-H y en ciertas proteínas cristalinas son similares. Las moléculas de agua pueden estar en diferentes posiciones y asociadas con fuerzas diferentes, actuando como una parte estructural o como una solución en los poros. Estos ejemplos ilustran porque el interés de la estructura y las propiedades del gel C-S-H son comparables a los de otros materiales. La investigación en cemento incluye muchos aspectos diferentes, desde la reducción de los gases de efecto invernadero emitidos durante el proceso de fabricación, a la investigación de la nanoestructura del material, incluyendo el desarrollo de nuevos cementos que utilizan desechos como materias primas, o la modificación y mejora de las propiedades del cemento Portland ordinario. Debido a su naturaleza heterogénea, la pasta de cemento es un material multiescalar. El cemento presenta diferentes rasgos y características a escalas nano-, micro- y macro-, y su comportamiento en dichas escalas dista de ser el mismo, Además, la investigación del cemento es un campo multidisciplinar en el que están implicados ingenieros, químicos, físicos y geólogos. Ese ambiente cooperativo, así como la naturaleza de multiescalar de los problemas a estudiar, implican el uso de numerosas técnicas experimentales en la investigación del material. La evolución de las técnicas experimentales en los últimos años nos permite estudiar la pasta de cemento a escalas cada vez más pequeñas, con la apertura al cemento de un campo como la nanotecnología. En nanotecnología, los métodos de simulación atomística han demostrado ser un instrumento numérico indispensable. Estos métodos nos permiten estudiar la nanoescala de un material o molécula con gran detalle. Sin embargo, los métodos de simulación atomística apenas se han aplicado en la investigación de aspectos relacionados con el cemento. La misma complejidad que dificulta las investigaciones experimentales de los materiales en base cemento en la nanoescala, como su naturaleza amorfa y heterogénea, es un problema en la simulación atomística, ya que la posición exacta de los átomos es información necesaria para los cálculos. No obstante este problema ha sido parcialmente solucionado por el incremento de la capacidad computacional y el desarrollo de nuevas técnicas y métodos de cálculo. En esta Tesis, se han empleado métodos de simulación atomísticos para estudiar diversos aspectos de los componentes de pasta de cemento, como son sus propiedades elásticas, reactividad, estructura y formación, prestando una atención especial al gel C-S-H

Elastic and thermodynamic properties of the major clinker phases of Portland cement: Insights from first principles calculations

Portland based cement is one of the most popular materials used in the civil and construction applications. Reliable computational methods to provide an insight into the underlying mechanics of the major phases of this material are of great interest for cement design. The present work investigated the performance of density functional theory (DFT) calculations using the PBE-D2 method to predict the mechanical, thermodynamic properties of four major phases namely Alite C3S, Belite C2S, tricalcium aluminate C3A and tetracalcium aluminoferrite C4AF. The calculated elastic properties were in a good agreement with available experimental data. In addition, a deeper insight into the electron density of state, spin-polarization, atomic charge, as well as free energy and entropy properties were also presented. Further development is necessary to improve the established DFT models for predicting the mechanical properties of the ferrite phase of Portland clinker.publishedVersio

Pre-mRNA Splicing: An Evolutionary Computational Journey from Ribozymes to Spliceosome

The intron\u2013exon organization of the genes is nowadays taken for granted and constitutes a fully established theory. DNA protein-coding sequences (exons) are not contiguous but rather separated by silent intervening fragments (introns), which must be removed in a process called pre-mRNA splicing. However, this fragmented composition of the eukaryotic genome has ancient origins. It appears that, during the initial stages of eukaryotic evolution, group II introns, i.e. self-splicing catalytic ribozymes, invaded the eukaryotic genome via the endosymbiosis of an alpha-proteobacterium in an archaeal host. At a later time, they split into the inert spliceosomal introns and the catalytically active small nuclear (sn)RNAs, which, together with additional splicing factors, gave rise to the eukaryotic spliceosome. This marked the transition from the autocatalytic splicing, mediated by ribozymes (RNA filaments endowed with an intrinsic catalytic activity) to splicing mediated by a protein-RNA machinery, the spliceosome. In the present thesis, the evolutionary relationship between group II introns and the spliceosome is retraced from a computational perspective by means of classical molecular dynamics simulations (MD), quantum mechanics calculations (QM) and combined quantum-classical simulations (QM/MM). The splicing process of these two different \u2013 but mechanistically related \u2013 large and sophisticated biomolecules is investigated with the aim of deciphering the reactivity and the structural properties from a computational point of view, with a focus on the role played by the Mg2+ ions as splicing cofactors. In Chapter 2, the importance of Mg2+ ions in the RNA biology is introduced. Not only they participate to the catalysis, but also represent essential structural and functional elements for RNA filaments. Moreover, the structural and molecular biology of group II intron ribozymes and the spliceosome machinery are widely discussed with a focus on their evolutionary links. Chapter 3 consists of a brief review of all the computational techniques employed in this thesis, from classical MD to QM and QM/MM simulations and enhanced sampling methods aimed at reconstructing the free energy of a process. Chapter 4 is entirely dedicated to the splicing mechanism promoted by group II intron ribozymes, representing the starting point of the evolutionary journey. In this chapter, a QM/MM study of the molecular mechanism of group II introns first-step hydrolytic splicing is presented, unveiling an RNA-adapted Steitz and Steitz\u2019s two-Mg2+-ion dissociative catalysis which differs from the one observed in protein enzymes. Chapter 5 is focused on Mg2+ ions, which are the natural cofactors of splicing, both in group II introns and in the spliceosome. Mg2+/RNA interplay is here addressed using a group II intron as a prototype of a large RNA molecule binding Mg2+. The performances of five different force fields currently used to describe Mg2+ in MD simulations are benchmarked, showing strengths and drawbacks. Moreover, the non-trivial electronic effects induced by Mg2+ on its ligands, such as charge transfer and polarization, are also characterized using 16 recurrent binding motifs. Overall, the study offers some guidelines on Mg2+ force fields for users and developers. Chapter 6 represents the final stop of the evolutionary journey. Here, an exquisite cryo-EM model of the ILS spliceosomal complex solved at 3.6 \uc5 resolution is used for a long-time scale MD study. This provides precious insights on the main proteins and snRNAs involved in the pre-mRNA splicing in eukaryotes as well as on the catalytic site. Unprecedentedly, the structural and dynamical properties of the spliceosome machinery are investigated at the atomistic level, with a particular emphasis on protein/RNA interplay through the characterization of their principal motions, among which the intron lariat/U2 snRNA helix unwinding

Molecular Dynamics Methods applied to flexible macromolecules

Cement-based materials, such as concrete or mortars, are usually considered materials with low technological level. Although they are the most employed human made materials in the world, others such as wood, plastics, metals and even stones are usually more valued in the everyday life: probably the fact that cement is cheap, readily available, common, and has been employed successfully for centuries, contributes to its low technology perception. However, this vision is far from the reality: the cement paste is a complex multicomponent and heterogeneous composite system, with different structural features at different length scales. The mechanism in which the clinker in contact with water becomes a hardened paste comprises hundreds of chemical reactions and physical processes. Understanding the molecular details of cement hydration processes is of fundamental importance due to the technological and economical impact of these materials. Several aspects need to be considered, and a realistic approach should be limited to a few specific features. Many efforts have been devoted over the last 40 years to develop mathematical models for understanding and predicting highly complex cement hydration kinetics, microstructure development and the implications of these for the changing physical-chemical properties of cement paste and concrete. An accurate hydration simulation approach would enable scientists and engineers not only to predict the performance of concrete, but also to design new cementitious materials. Despite significant effort and progress, the ability to perform such a complete simulation has not yet been developed, mainly because cement hydration is one of the more complex phenomena in engineering/materials science. The main objective of this PhD thesis is to analyse the influence of superplasticizers on the microevolution of cement suspensions during early hydration based of Molecular Dynamics (MD) approaches. To this purpose we implemented a MD protocol for the study of the behavior of polycarboxylate-ether-based superplasticizers (PCEs) in the presence of selected cement surfaces, tricalcium aluminate (C3A) and tricalcium silicate (C3S), water molecules and calcium hydroxide. The final goal of the project, which was carried in collaboration with the group of Prof. G. Artioli - Università degli Studi di Padova, Dipartimento di Geoscienze, was to clarify structure-properties relationships, in order to design new products with enhanced properties. In fact, the rheology of cement pastes can be controlled by the use of superplasticizers that, by adsorbing on the surfaces of cement particles, enhance their workability. The protocol was made up of the following steps: i) building of the cement surfaces, ii) parameterization of force field, iii) setting of the simulation and evaluation of physical observables. Some methodological knowledges acquired were employed on side-applications, for example the evaluation of electrostatic interactions of other organic molecules, in particular partial charges of amino acids (AA) and nonstandard amino acids (Non-AA), present in the human Connexin protein. To be precise, following the earlier approach of Bayly et al [Bayly1993], we obtained the charge set by fitting to the electrostatic potentials of Non-AA calculated using ab-initio methods. This effort was carried out in collaboration with the group of F. Mammano - Università degli Studi di Padova, Dipartimento di Fisica e Astronomia [Zonta2014]. Finally, in a joint effort with Dott.ssa L. Orian, Dott. M. Torsello and P. Calligari, of my research group, simulate complete simulation was carried out of the Connexin 26 hemichannel (Cx26) behaviour in the presence of post-translational modifications (PTMs) and Ca2+. The contribution to this joint project described in this thesis, was aimed to i) the analysis of the structure of the channel and ii) the preservation of salt bridges between Glu47, Arg75 and gamma-Glu47, Arg75 in the presence/asbsence of Ca2+. Lastly, preliminary results based on a collaboration with Stazione Sperimentale del Vetro (SSV) of Murano (Ve) for the project: "Computational methods for the modeling of equilibrium properties of glassy materials", is presented. The goal of this work was the elaboration, optimization and validation of a model of the type of ideal solutions for the thermodynamic properties of glasses and the inclusion in integrated software platforms. This work is organised as follows. In chapter 1, a brief overview is presented of the atomistic simulation methods used during the Thesis, because several levels of theory were selected depending on their capabilities to solve punctual problems: ab initio, Molecular Mechanics, and Molecular Dynamics. In chapter 2, an introduction to cement chemistry and the necessary basis is given in order to follow the results and discussions of the systems presented in this Thesis. It covers a description of clinker phases, superplasticizers, the hydration process, the cement paste structure and computational methods applied in cement research. In chapter 3, the results of four MD simulations are discussed for a system consisting of PCE-(23-7-1), a comb-shaped polymer unit model superplasticizer of methyl-polyethylene glycole methacrylate and methacrylic acids (seven back bone units, one side-chain unit and twenty three polyethylene-oxide units in the side chain), the C3A and C3S surfaces, explicit molecules of water, Ca2+ and OH- ions (pore solution): from the MD trajectories were calculated conformational properties. In chapter 4, the results are discussed of partial charges parametrization of Non-AA, the structural channel analysis and salt-bridges analysis of Cx26 protein. In chapter 5, the thermodynamic model is presented for calculating the composition of glasses, the interpolation for temperature dependence of thermodynamic properties and the validation of model with a simple binary oxide system Na2O-SiO2