The Thiocyanate Anion is a Primary Driver of Carbon Dioxide Capture by Ionic Liquids

Carbon dioxide, CO2, capture by room-temperature ionic liquids (RTILs) is a vivid research area featuring both accomplishments and frustrations. This work employs the PM7-MD method to simulate adsorption of CO2 by 1,3-dimethylimidazolium thiocyanate at 300 K. The obtained result evidences that the thiocyanate anion plays a key role in gas capture, whereas the impact of the 1,3-dimethylimidazolium cation is mediocre. Decomposition of the computed wave function on the individual molecular orbitals confirms that CO2-SCN binding extends beyond just expected electrostatic interactions in the ion-molecular system and involves partial sharing of valence orbitals

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

Model Description of Some Molecular Properties by the Modified-Atom-in-Molecule (MAM) Approach

Conclusive evidence is presented whlch shows that the concept of modified atoms in molecule (MAM) is a viable model for a good description of numerous molecular properties. Atomic modification . can be decomposed to isotropic and anisotropic components. The isotropic change caused by molecular formation is given by the electric monopoles of atoms. It is a consequence of the charge drift accompanying chemical bonding. Atomic monopoles reproduce diamagneticshielding of the nuclei rJAd, diamagnetic susceptibility xd and ESCA shifts with an intriguing success. The atomic monopole model is easily extended to include higher local multipoles (i. e. anisotropic contribution), thus yielding satisfactory total molecular multipoles and extramolecular electrostatic potentials. Salient directional properties of covalent bonds are well described by the use of polarized atomic orbitals. It was shown that hybridization is the underlying concept which explains interrelations between steric features and local bond properties. Hybridization rationalizes in a natural and simple way the electron pair (Lewis) bond which is one of the corner stones of chemistry being particularly important for the first row atoms. It was concluded that the high information content of hybrid AOs can be ascribed to the fact that they conform to the local symmetry of the immediate molecular environment. Thus the HAOs are local wavefunctions of the zeroth order which describe atomic angular distortions. Although atoms can not be uniquely defined within molecules, the MAM model has high interpretative power yielding reasonable results. Special attention deserves a picture of charged atoms immersed in the »sea« of mixed electron density, because it is free of any arbitrariness in the slicing of molecular volume of partitioning of overlap charge. Finally, the definition of pseudo-observables is given. It was concluded that atomic monopoles and hybridization indices are pseudo-observables par exceHence. A.pparently there is colour, apparently sweetness, apparently bitterness; actuaUy there are only atoms and the void. Democritus, 420 B. C

Model Description of Some Molecular Properties by the Modified-Atom-in-Molecule (MAM) Approach

Conclusive evidence is presented whlch shows that the concept of modified atoms in molecule (MAM) is a viable model for a good description of numerous molecular properties. Atomic modification . can be decomposed to isotropic and anisotropic components. The isotropic change caused by molecular formation is given by the electric monopoles of atoms. It is a consequence of the charge drift accompanying chemical bonding. Atomic monopoles reproduce diamagneticshielding of the nuclei rJAd, diamagnetic susceptibility xd and ESCA shifts with an intriguing success. The atomic monopole model is easily extended to include higher local multipoles (i. e. anisotropic contribution), thus yielding satisfactory total molecular multipoles and extramolecular electrostatic potentials. Salient directional properties of covalent bonds are well described by the use of polarized atomic orbitals. It was shown that hybridization is the underlying concept which explains interrelations between steric features and local bond properties. Hybridization rationalizes in a natural and simple way the electron pair (Lewis) bond which is one of the corner stones of chemistry being particularly important for the first row atoms. It was concluded that the high information content of hybrid AOs can be ascribed to the fact that they conform to the local symmetry of the immediate molecular environment. Thus the HAOs are local wavefunctions of the zeroth order which describe atomic angular distortions. Although atoms can not be uniquely defined within molecules, the MAM model has high interpretative power yielding reasonable results. Special attention deserves a picture of charged atoms immersed in the »sea« of mixed electron density, because it is free of any arbitrariness in the slicing of molecular volume of partitioning of overlap charge. Finally, the definition of pseudo-observables is given. It was concluded that atomic monopoles and hybridization indices are pseudo-observables par exceHence. A.pparently there is colour, apparently sweetness, apparently bitterness; actuaUy there are only atoms and the void. Democritus, 420 B. C

An overview of nonadiabatic dynamics simulations methods, with focus on the direct approach versus the fitting of potential energy surfaces

We review state-of-the-art nonadiabatic molecular dynamics methods, with focus on the comparison of two general strategies: the "direct" one, in which the potential energy surfaces (PES) and the couplings between electronic states are computed during the integration of the dynamics equations; and the "PES-fitting" one, whereby the PES and couplings are preliminarily computed and represented as functions of the nuclear coordinates. Both quantum wavepacket dynamics (QWD) and classical trajectory approaches are considered, but we concentrate on methods for which the direct strategy is viable: among the QWD ones, we focus on those based on traveling basis functions. We present several topics in which recent progress has been made: quantum decoherence corrections in trajectory methods, the use of quasi-diabatic representations, the sampling of initial conditions and the inclusion of field-molecule interactions and of spin-orbit couplings in the dynamics. Concerning the electronic structure calculations, we discuss the use of ab initio, density functional and semiempirical methods, and their combination with molecular mechanics (QM/MM approaches). Within the semiempirical framework, we provide a concise but updated description of our own method, based on configuration interaction with floating occupation molecular orbitals. We discuss the ability of different approaches to provide observables directly comparable with experimental results and to simulate a variety of photochemical and photophysical processes. In the concluding remarks, we stress how the border between direct and PES-fitting methods is not so sharp, and we briefly discuss recent trends that go beyond this traditional distinction

Machine Learning methodology for the study of a disulfide exchange reaction

Die Thiol-Disulfid-Austauschreaktion ist eine nukleophile Substitution, die in einer großen Klasse von Proteinen stattfindet. Sie spielt eine wichtige Rolle für die dritt- und viertdimensionale Struktur von Proteinen und die Katalyse biologischer Reaktionen. Außerdem kann der Thiol-Disulfid-Austausch die Aktivität bestimmter Proteine regulieren. In dieser Arbeit werden die strukturellen und Umgebungsfaktoren, die diese Reaktion beeinflussen, diskutiert. Aufgrund ihrer Recheneffizienz hat sich die Density-Functional based Tight-binding (DFTB) Methode als beliebte und zuverlässige quantenmechanische Methode für Anwendungen in kondensierter Phase positioniert. Mit DFTB ist es möglich die freie Energiefläche komplexer Reaktionen zu erzeugen, da der Phasenraum usreichen abgetastet werden kann. Diese Einsparungen bei den Rechenkosten können jedoch auf Kosten einer geringeren Genauigkeit gehen. Beim Thiol-Disulfid-Austausch zum Beispiel weisen die Übergangszustände eine fehlerhate Struktur und Energie auf. Die Literaturrecherche zeigt, dass für eine korrekte Beschreibung dieser Reaktion sehr genaue ab initio Methoden verwendet werden müssen. Daher bestand die Motivation dieser Arbeit darin, die DFTB-Fehler mit einem maschinellen Lernansatz zu korrigieren. Um dies zu erreichen, haben wir ein neuronales Netzwerk vom Typ Behler-Parrinello verwendet, das die Energiewertdifferenzen zwischen der ab initio und DFTB Methode füreine gegebene Molekülstruktur erlernt. Die maschinell erlernte Energiekorrektur wurde dann in die DFTB+ Software implementiert. Mit diesem neuen Ansatz konnten wir hybride Quantum Mechanics/Molecular Mechanics (QM/MM)-Simulationen des Thiol-Disulfid-Austauschs mit Coupled Cluster und B3LYP-Genauigkeit mit einem Rechenaufwand durchführen, der mit DFTB vergleichbar ist. Dieser Korrekturalgorithmus ist auch in einer Pipeline mit grafischer Schnittstelle implementiert, die dem Benutzer hilft, Trainingsdaten zu generieren und zu arrangieren sowie das maschinelle Lernmodell in DFTB+ zu exportieren, um es in QM/MM-Simulationen weiter zu verwenden. Die Einführung dieser Pipeline soll die Anwendungsmöglichkeiten des Codes für neuronale Netze erweitern, indem das Wissen über Quantenmodellierung gegenüber einem Programmierhintergrund bevorzugt wird. Darüber hinaus stellen wir erste Arbeiten an einem maschinell erlernten Kraftfeld zur Beschreibung der Disulfid-Austauschreaktion unter Verwendung von Coupled Cluster-Referenzdaten vor

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

Determination of Noncovalent Intermolecular Interaction Energy from Electron Densities

Noncovalent intermolecular interactions, widely found in molecular clusters and bio-molecules, play a key role in many important processes, such as phase changes, folding of proteins and molecular recognition. However, accurate calculation of interaction energies is a very difficult task because the interactions are normally very weak. Rigorous expressions for the electrostatic and polarization interaction energies between two molecules A and B, in term of the electronic densities, have been programmed: (see formula in document). Z is atomic charge, ρ0 is the electron density of the isolated molecule and Δρind is the electron density change of the molecule caused by polarization. With some approximations, procedures for electrostatic and polarization energy calculations were developed that involve numerical integration. Electrostatic and polarization energies for several bimolecular systems, some of which are hydrogen bonded, were calculated and the results were compared to other theoretical and experimental data. A second method for the computing of intermolecular interaction energies has also been developed. It involves a “supermolecule” calculation for the entire system, followed by a partitioning of the overall electric density into the two interacting components and then application of eq. (1) to find the interaction energy. In this approach, according to Feynman’s explanation to intermolecular interactions, all contributions are treated in a unified manner. The advantages of this method are that it avoids treating the supersystem and subsystems separately and no basis set superposition error (BSSE) correction is needed. Interaction energies for several hydrogen-bonded systems are calculated by this method. Compared with the result from experiment and high level ab initio calculation, the results are quite reliable

An Integrated Effective Fragment—Polarizable Continuum Approach to Solvation: Theory and Application to Glycine

A new discrete/continuum solvation model has been developed by combining the effective fragment potential (EFP) for the discrete part and the polarizable continuum model (PCM) for the continuum part. The usefulness of this model is demonstrated by applying it to the calculation of the relative energies of the neutral and zwitterionic forms of glycine. These calculations were performed by treating glycine with ab initiowave functions. Water clusters were treated with bothab initio and EFP methods for comparison purposes, and the effect of the continuum was accounted for by the PCM model. The energy barrier connecting the zwitterionic and neutral three-water clusters was also examined. The computationally efficient EFP/PCM model gives results that are in close agreement with the much more expensive full ab initio/PCM calculation. The use of methods that account for electron correlation is necessary to obtain accurate relative energies for the isomers of glycine