How Water's Properties Are Encoded in Its Molecular Structure and Energies.

How are water's material properties encoded within the structure of the water molecule? This is pertinent to understanding Earth's living systems, its materials, its geochemistry and geophysics, and a broad spectrum of its industrial chemistry. Water has distinctive liquid and solid properties: It is highly cohesive. It has volumetric anomalies-water's solid (ice) floats on its liquid; pressure can melt the solid rather than freezing the liquid; heating can shrink the liquid. It has more solid phases than other materials. Its supercooled liquid has divergent thermodynamic response functions. Its glassy state is neither fragile nor strong. Its component ions-hydroxide and protons-diffuse much faster than other ions. Aqueous solvation of ions or oils entails large entropies and heat capacities. We review how these properties are encoded within water's molecular structure and energies, as understood from theories, simulations, and experiments. Like simpler liquids, water molecules are nearly spherical and interact with each other through van der Waals forces. Unlike simpler liquids, water's orientation-dependent hydrogen bonding leads to open tetrahedral cage-like structuring that contributes to its remarkable volumetric and thermal properties

Simulaciones de sistemas acuosos: de la fase gas a la fase condensada

Tesis doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Química. Fecha de lectura: 21-11-2017La presente tesis está dedicada a la simulación de sistemas acuosos desde la fase gas hasta la fase condensada. En la misma, se utilizaron enfoques y métodos complementarios para estudiar sistemas acuosos homogéneos y heterogéneos. En particular, se ofrece un análisis detallado de las propiedades estructurales, termodinámicas, espectroscópicas y de transporte en distintas condiciones termodinámicas para estos sistemas. A lo largo de todo el trabajo, las comparaciones entre el experimento y la teoría se establecieron sobre la base de la naturaleza de la interacción entre diferentes sistemas: Agua-Agua, Ion-Agua y hospedador-huésped (agua). Así, el presente trabajo se ha dividido en tres partes principales. En la primera parte, se realizaron simulaciones de dinámica molecular clásica en función de la temperatura para estudiar y determinar las propiedades estructurales y de transporte (tanto individuales como colectivas) del agua líquida. Hasta la fecha, la estimación de viscosidades a partir de simulaciones representa un problema computacional desafiante ya que se requieren tiempos de simulación largos para alcanzar precisión estadística, por lo que aquí se compararon varias estrategias de simulación y también se validan diversos potenciales de interacción disponibles en la literatura. En la segunda parte, se utilizaron cálculos de estructura electrónica de última generación para diseñar, desde un enfoque bottom-up, superficies de energías de potencial analíticas de alta precisión. Dichos modelos de interacción transferibles, son los primeros potenciales de ion-agua polarizables completamente ab-initio para el estudio de electrolitos en diferentes entornos acuosos, por ejemplo, desde la microsolvatación de monohidratos a polihidratos, así como soluciones a dilución infinita, y propiedades interfaciales. En una colaboración con dos grupos experimentales (EEUU y UE), predecimos y validamos la dependencia de la temperatura en el mecanismo de predisociación de un ion en contacto con dos moléculas de agua mediante simulaciones de dinámica molecular mixtas clásico-cuánticas. Finalmente en la tercera parte, estudiamos la encapsulación de átomos y moléculas dentro de las cavidades del clatrato hidrato sI. Estas investigaciones estuvieron motivadas por la disponibilidad de mediciones experimentales a partir de difracción de rayos X y espectros IR, así como de transiciones de fase observadas en el bulk. Para ello, se tomaron como sistemas de referencia el hidrato clatrato de dióxido de carbono, y los hidrato clatrato de gases nobles. En particular se llevaron a cabo cálculos cuánticos con el método de “Multiconfigurational Time Dependent Hartree” para las dos cavidades de clatrato CO2@sI, y por primera vez se presentan resultados sobre los estados traslacionales-rotacionales-vibracionales de dicho sistema. Además, se comprobó el rendimiento de diferentes modelos de interacción analítica, así como cálculos de estructura electrónica para describir la orientación rotacional y la anisotropía angular dentro de ambas cavidades. De igual manera, se llevaron a cabo simulaciones clásicas de “parallel-tempering Monte Carlo” en el ensamble isobárico-isotérmico (NPT) para agregados tipo clatratos con gases nobles de tamaño seleccionado y se presentó un análisis detallado de sus diagramas de fase en temperatura y presión, así como cambios estructurales en un amplio rango de presiones y temperatura.The present thesis is devoted to the simulations of aqueous systems from the gas to the condensed phase. Here we used complementary approaches and methods to study both homogeneous and heterogeneous aqueous systems. In particular, we provided a detailed analysis on their, structural, thermodynamical, spectroscopical and transport properties at different thermodynamic conditions. Along the whole work, comparisons between experiment and theory were established based on the nature of the interactions between different systems. It was divided into three main parts corresponding to: water-water, ion-water and guest-host(water network). In the first part, classical molecular dynamic simulations were performed as a function of temperature, to study and determine the structural and transport properties (both single and collective) of liquid water. Nowadays, the estimation of viscosities from simulations is a challenging computational problem, as long simulation times are required to reach statistical accuracy. So several simulation strategies were compared being able to validate interaction model potentials available in the literature. In the second part, state-of-the-art electronic structure calculations were employed to design, from a bottom-up approach, highly accurate analytical potential energy surfaces. Such transferable interaction models are the first fully ab-initio polarizable ion-water potentials for studying electrolytes at different aqueous environments i.e. from the microsolvation of monohydrates, to polyhydrates, as well as solutions at infinite dilution, and interfacial properties. In a collaboration with two experimental groups (USA and EU) we predict and validate the temperature dependence vibrational predissociation mechanism of an ion in contact with two water molecules by means of mixed quantum-classical molecular dynamic simulations. Finally in the third part, we studied the encapsulation of atoms and molecules within the cavities of sI type clathrate hydrates. These investigations were motivated by available experimental measurements from X-ray diffraction and IR spectra, as well as observed phase transitions in the bulk. For such, we took as reference systems the carbon dioxide clathrate hydrate and the rare gases (Rg) clathrate hydrates. In particular, we performed quantum multi-configuration time-dependent Hartree calculations for the two cages of the sI CO2 clathrate hydrate, and we reported for the first time results on the translational, rotational and vibrational states. Additionally, we tested the performance of different analytical interaction models, as well as electronic structure calculations for describing the rotational orientations and angular anisotropy of the CO2 within both cages. Moreover, classical parallel-tempering Monte Carlo simulations in the isobaric-isothermic (NPT) ensemble were carried out for size-selected Rg clathrate-like clusters and we presented a detailed analysis of their temperature-pressure phase diagrams, as well as structural changes in a wide range of temperatures and pressuresEste trabajo de investigación ha sido posible gracias a la concesión de una beca predoctoral BES2012-054209 enmarcada en el subprograma de ayudas de formación de personal investigador (FPI) del gobierno español, a través del Ministerio de Economía, Industria y Competitividad, y asociada al proyecto de investigación FIS2014-51933-P del CSIC

Mapping Free Energy Pathways for ATP Hydrolysis in the E. coli ABC Transporter HlyB by the String Method

HlyB functions as an adenosine triphosphate (ATP)-binding cassette (ABC) transporter that enables bacteria to secrete toxins at the expense of ATP hydrolysis. Our previous work, based on potential energy profiles from combined quantum mechanical and molecular mechanical (QM/MM) calculations, has suggested that the highly conserved H-loop His residue H662 in the nucleotide binding domain (NBD) of E. coli HlyB may catalyze the hydrolysis of ATP through proton relay. To further test this hypothesis when entropic contributions are taken into account, we obtained QM/MM minimum free energy paths (MFEPs) for the HlyB reaction, making use of the string method in collective variables. The free energy profiles along the MFEPs confirm the direct participation of H662 in catalysis. The MFEP simulations of HlyB also reveal an intimate coupling between the chemical steps and a local protein conformational change involving the signature-loop residue S607, which may serve a catalytic role similar to an Arg-finger motif in many ATPases and GTPases in stabilizing the phosphoryl-transfer transition state

An Effective Fragment Method for Modeling Solvent Effects in Quantum Mechanical Calculations

An effective fragment model is developed to treat solvent effects on chemical properties andreactions. The solvent, which might consist of discrete water molecules, protein, or othermaterial, is treated explicitly using a model potential that incorporates electrostatics,polarization, and exchange repulsion effects. The solute, which one can most generally envision as including some number of solvent molecules as well, is treated in a fully ab initio manner, using an appropriate level of electronic structure theory. In addition to the fragment model itself, formulae are presented that permit the determination of analytic energy gradients and, therefore, numerically determined energy second derivatives (hessians) for the complete system. Initial tests of the model for the water dimer and water‐formamide are in good agreement with fully abinitio calculations

The Molecular Electrostatic Potential as a Determinant of Receptor-Drug Recognition

The validity of the concept of the molecular electrostatic . potential and its applicability in rationalizing drug-receptor interactions are discussed on hand of examples covering the qualitative aspects. The computational methods are briefly reviewed with respect to economy and quality of results