Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange–correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear–electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an “open teamware” model and an increasingly modular design

Multiscale Modeling of Electrolytes for Energy Storage and Conversion

Fuel cells, redox flow batteries, and secondary ion batteries are under active investigation to fulfill the requirements of efficient and sustainable energy storage and conversion technologies. The discovery of high-performance stable electrolytes that are relatively cheap and versatile is crucial to the commercialization of these electrochemical devices and necessitates a comprehensive understanding of the materials (i.e., from the atomistic to continuum levels). This dissertation is on multiscale modeling and simulations of several electrolytes under consideration in vanadium redox flow batteries (VRFBs), alkaline fuel cells (AFCs), or secondary magnesium batteries. The hydrated structure and associated solvation Gibbs energies were determined for vanadium cations at four oxidation states using first principles based electronic structure calculations and quasi-chemical theory. The effect of sulfuric and trifluoromethanesulfonic (triflic) acids on the local structures of the hydrated vanadium cations was explored by employing hybrid density functional theory (DFT) in conjunction with a continuum solvation model. The results indicate that the hydration structure of vanadium at the oxidation state of three was the most perturbed in acidic media and that the oxo-group of vanadate may be protonated by either acid. Dissipative particle dynamics (DPD) simulations were undertaken and a novel parametrization method developed to study the meso-scale behavior and hydrated morphology of proton and anion exchange membranes (PEMs and AEMs). The results for hydrated Nafion with the absorbed vanadium species indicate that the hydrated cations increase the aggregation of the sulfonate groups and that this effect is a function of both the cation charge and the degree of hydration. It was also observed that the simulated morphology and the size of the water domains in AEMs based on triblock copolymers depend on the hydration level and the anion type. Vibrational frequencies of model clusters were calculated using DFT for two ionic liquid-based electrolytes and their experimental IR and Raman spectra were assigned. Moreover, the hydration of ten acids commonly used in electrolytes was investigated using DFT in order to provide a fundamental understanding of their hydrated acidity and proton transfer

Computer Modelling of an Enzyme Reference Reaction for Empirical Valence Bond Simulation

It is extensively recognized that an enzyme functions through reducing the energy of activation of its elemental reaction and the catalytic effect of an enzyme is as a result of a change in activation free energy obtained relative to a reference reaction in water of the same mechanism. In this study, chorismate mutase which is an enzyme that catalyzes biochemical reactions for chorismate conversion to prephenate has been used as the model enzyme and its catalytic effect was investigated using Empirical Valence Bond method with the employment of Density Functional theory calculation to obtain its reference state reaction. It was found in this study that DFT has been able to produce good activation and reaction free energies compared to experimental values that can serve as a reference to investigate the enzymatic reaction of chorismate mutase and the enzyme’s catalytic effect was well analysed with EVB as the method was able to reproduce the enzyme’s activation and reaction free energies

Software for the frontiers of quantum chemistry : An overview of developments in the Q-Chem 5 package

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange–correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear–electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an “open teamware” model and an increasingly modular design.This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear-electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an "open teamware" model and an increasingly modular design.Peer reviewe

Software for the frontiers of quantum chemistry:An overview of developments in the Q-Chem 5 package

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange–correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear–electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an “open teamware” model and an increasingly modular design

Vibrational spectroscopy by means of first-principles molecular dynamics simulations

Vibrational spectroscopy is one of the most important experimental techniques for the characterization of molecules and materials. Spectroscopic signatures retrieved in experiments are not always easy to explain in terms of the structure and dynamics of the studied samples. Computational studies are a crucial tool for helping to understand and predict experimental results. Molecular dynamics simulations have emerged as an attractive method for the simulation of vibrational spectra because they explicitly treat the vibrational motion present in the compound under study, in particular in large and condensed systems, subject to complex intramolecular and intermolecular interactions. In this context, first-principles molecular dynamics (FPMD) has been proven to provide an accurate realistic description of many compounds. This review article summarizes the field of vibrational spectroscopy by means of FPDM and highlights recent advances made such as the simulation of Infrared, vibrational circular dichroism, Raman, Raman optical activity, sum frequency generation, and nonlinear spectroscopies

Theory of coherent two-dimensional vibrational spectroscopy

Two-dimensional (2D) vibrational spectroscopy has emerged as one of the most important experimental techniques useful to study the molecular structure and dynamics in condensed phases. Theory and computation have also played essential and integral roles in its development through the nonlinear optical response theory and computational methods such as molecular dynamics (MD) simulations and electronic structure calculations. In this article, we present the fundamental theory of coherent 2D vibrational spectroscopy and describe computational approaches to simulate the 2D vibrational spectra. The classical approximation to the quantum mechanical nonlinear response function is invoked from the outset. It is shown that the third-order response function can be evaluated in that classical limit by using equilibrium or non-equilibrium MD simulation trajectories. Another simulation method is based on the assumptions that the molecular vibrations can still be described quantum mechanically and that the relevant molecular response functions are evaluated by the numerical integration of the Schrodinger equation. A few application examples are presented to help the researchers in this and related areas to understand the fundamental principles and to use these methods for their studies with 2D vibrational spectroscopic techniques. In summary, this exposition provides an overview of current theoretical efforts to understand the 2D vibrational spectra and an outlook for future developments. c.Published under license by AIP Publishing

Constantes de acidez y potenciales red-ox de compuestos derivados de los carboranos mediante cálculos de estructura electrónica

[Abstract] Carboranes, clusters composed of boron, carbon and hydrogens, show unique physical and chemical properties having application on cancer treatments. Computational Chemistry, a tool to assist in solving chemical problems, has been used to calculate structure, acidity constants and one-electron reduction potentials of carboxyl functionalized carboranes. Those physico-chemical properties as well as geometry, electronic parameters and IR spectra have been calculated for 1,2-closo-dicarbadodecaborane-1,2-dicarboxylic acid, 1,7-closo-dicarbadodecaborane-1,7-dicarboxylic acid, 1,12-closo-dicarbadodecabo-rane-1,12-dicarboxylic acid, benzoic acid, phthalic, isophthalic and terephthalic acids and that of their corresponding anions after the first and the second deprotonation - the latter four acids for comparison purposes. Density functional theory (DFT) was used with 6-31++G(d,p) as basis set, and the solvation model based on density (SMD) to simulate the solvent, water. Structure and characteristics of the most stable species, in terms of Gibbs free energy, were obtained after the corresponding conformational study (PES), which showed that, except for ortho-derivatives, all conformers have similar energy. Selected geometric parameters (distances and angles) and electronic parameters (dipole moments and Mulliken atomic charges) including frontier molecular orbitals, are reported. Similar behaviour is observed when comparing phthalic acids and carborane dicarboxylic acids. Acidity constants were calculated using six different methods, some of them involving a thermodynamic cycle with calculation in the gas phase and in water. No real improvement was found using a more complete basis set. Best results were obtained using a thermodynamic cycle with calculation in the gas phase and in water taking into account empirical values for the solvation energy of water and hydronium ion. Carborane dicarboxylic acids are more acidic, ca. 4 pK units, than phthalic acids. On the other hand, one-electron reduction potentials were calculated using two methods, one involving a thermodynamic cycle also. Selected values are reported. Loss of CO2 by the dianion of p-carborane dicarboxylic acid upon one-electron oxidation should be highlighted.[Resumo] Os carboranos, clústeres compostos de boro, carbono e hidróxenos, amosan propiedades físicas e químicas únicas que teñen aplicación en tratamentos contra o cancro. A Química Computacional, unha ferramenta de gran axuda para resolver problemas químicos, utilizouse para calcular a estrutura, as constantes de acidez e os potenciais de redución monoelectrónicos de carboranos funcionalizados con carboxilo. Calculáronse as propiedades fisicoquímicas, así como a xeometría, os parámetros electrónicos e os espectros IR para o ácido 1,2-closo-dicarbadodecaborano-1,2-dicarboxílico, ácido 1,7-closo-dicarbadodecaborano-1,7-dicarboxílico, ácido 1,12-closo-dicarbadodecaborano-1,12-dicarboxílico, ácido benzoico, ácido ftálico, ácido isoftálico e ácido tereftálico e os dos seus correspondentes anións despois da primeira e segunda desprotonación, estes últimos catro ácidos para propósitos de comparación. A teoría funcional de densidade (DFT) usouse co 6-31++G(d,p) como función base, e o modelo de solvatación baseado na densidade (SMD) para simular o disolvente, auga. A estrutura e as características das especies máis estables, en termos de enerxía libre de Gibbs, obtivéronse despois do correspondente estudo conformacional (PES), que amosou que, a excepción dos orto-derivados, todos os confórmeros teñen una enerxía similar. Infórmase sobre parámetros xeométricos seleccionados (distancias e ángulos) e parámetros electrónicos (momentos dipolares e cargas atómicas de Mulliken), incluídos os orbitais moleculares de fronteira. Obsérvase un comportamento similar cando se comparan os ácidos ftálicos e os ácidos dicarboxílicos de carborano. As constantes de acidez calculáronse utilizando seis métodos diferentes, algún dos cales implican un ciclo termodinámico con cálculo na fase gaseosa e en auga. Non se atopou una mellora real empregando unha función base máis completa. Os mellores resultados obtivéronse usando un ciclo termodinámico con cálculo na fase gaseosa e en auga, tendo en conta os valores empíricos para a enerxía de solvatación da auga e o ión hidronio. Os ácidos dicarboxílicos de carboranos son máis ácidos, aprox. 4 unidades de pK, que os ácidos ftálicos. Por outro lado, os potenciais de redución monoelectrónicos calculáronse utilizando dous métodos, un que tamén involucra un ciclo termodinámico. Os valores seleccionados infórmanse. Debe resaltarse a perda de CO2 polo dianión do ácido p-carborano dicarboxílico tras a oxidación dun electrón.[Resumen] Los carboranos, clústeres compuestos de boro, carbono e hidrógenos, muestran propiedades físicas y químicas únicas que tienen aplicación en tratamientos contra el cáncer. La Química Computacional, una herramienta de gran ayuda para resolver problemas químicos, se ha utilizado para calcular la estructura, las constantes de acidez y los potenciales de reducción monoelectrónicos de carboranos funcionalizados con grupos carboxilo. Se han calculado las propiedades fisicoquímicas, así como la geometría, los parámetros electrónicos y los espectros IR para el ácido 1,2-closo-dicarbadodecaborano-1,2-dicarboxílico, ácido 1,7-closo-dicarbadodecaborano-1,7-dicarboxílico, ácido 1,12-closo-dicarbadodecaborano-1,12-dicarboxílico, ácido benzoico, ácido ftálico, ácido isoftálico y ácido tereftálico y los de sus correspondientes aniones después de la primera y la segunda desprotonación, estos últimos cuatro ácidos para propósitos de comparación. La teoría funcional de densidad (DFT) se usó con 6-31++G(d,p) como función base, y el modelo de solvatación basado en la densidad (SMD) para simular el disolvente, agua. La estructura y las características de las especies más estables, en términos de energía libre de Gibbs, se obtuvieron después del correspondiente estudio conformacional (PES), que mostró que, a excepción de los orto-derivados, todos los confórmeros tienen una energía similar. Se informa sobre parámetros geométricos seleccionados (distancias y ángulos) y parámetros electrónicos (momentos dipolares y cargas atómicas de Mulliken), incluidos los orbitales moleculares de frontera. Se observa un comportamiento similar cuando se comparan los ácidos ftálicos y los ácidos dicarboxílicos de carborano. Las constantes de acidez se calcularon utilizando seis métodos diferentes, algunos de los cuales implican un ciclo termodinámico con cálculo en la fase gaseosa y en agua. No se encontró una mejora real usando una función base más completa. Los mejores resultados se obtuvieron utilizando un ciclo termodinámico con cálculo en la fase gaseosa y en agua, teniendo en cuenta los valores empíricos para la energía de solvatación del agua y el ion hidronio. Los ácidos dicarboxílicos de carboranos son más ácidos, aprox. 4 unidades de pK, que los ácidos ftálicos. Por otro lado, los potenciales de reducción monoelectrónicos se calcularon utilizando dos métodos, uno que también involucra un ciclo termodinámico. Los valores seleccionados se informan. Debe resaltarse la pérdida de CO2 por el dianión del ácido p-carborano dicarboxílico tras la oxidación de un electrón.Traballo fin de grao (UDC.CIE). Química. Curso 2017/201

Peptide-Cation Systems: Conformational Search, Benchmark Evaluation, and Force Field Parameter Adjustment Using Regularized Linear Regression

Metal cations often play an important role in shaping the three-dimensional structure of peptides. As an example, the model system AcPheAla5LysH+ is investigated in order to fully understand the forces that stabilize its helical structure. In particular, the question of whether the local fixation of the positive charge at the peptide's C-terminus is a prerequisite for forming helices is addressed by replacing the protonated lysine residue by alanine and a sodium cation. The combination of gas-phase cold-ion vibrational spectroscopy with molecular simulations based on density-functional theory (DFT) revealed that the charge localization at the C-terminus is imperative for helix formation in the gas phase as this stabilizes the structure through a cation-helix dipole interaction. For sodiated AcPheAla6, globular rather than helical structures were found caused by the strong cation-backbone and cation-pi interactions. Interestingly, the global minimum-energy structure from simulation is not present in the experiment where the system remains kinetically trapped in a solution-state structure. Thereby calculated energies and IR spectra that are sufficiently accurate relied on DFT with computationally costly hybrid functionals, while for the structure search low-computational-cost force field (FF) models are crucial. This inspired a study where the goodness of commonly applied levels of theory, i.e. FFs, semi-empirical methods, density-functional approximations, composite methods, and wavefunction-based methods are being evaluated with respect to benchmark-grade coupled-cluster calculations. Acetylhistidine - either bare or in presence of a zinc cation - thereby serves as a molecular benchmark system. Neither FFs nor semi-empirical methods are reliable enough for a description of these systems within "chemical accuracy" of 1 kcal/mol. Accurate energetic description within chemical accuracy is achieved for all systems using the meta-GGA SCAN or computationally more demanding hybrid functionals. The double-hybrid functional B3LYP+XYG3 is best resembling the benchmark method DLPNO-CCSD(T). Despite poor energetic performances of conventional FFs for peptides in the gas phase, their low computational costs still render them appealing tools for large-scale structure searches. Consequently, a machine learning approach is presented where the torsional parameters and (if desired) van der Waals parameters in the potential-energy function of a particular FF are adjusted by fitting it against DFT energies using regularized regression models like LASSO or Ridge regression. For the peptide AcAla2NMe, this resulted in a significant improvement when comparing to standard OPLS-AA parameters. For more challenging peptide-cation systems, e.g. AcAla2NMe + Na+, this approach does not give satisfying results, which is caused by the formulation of the potential energy of the FF itself: While derived empirical partial charges using Hirshfeld partitioning or the electrostatic potential (ESP) decrease the accuracy, part of the energetic discrepancy can be "compensated" due to the flexibility of the torsional contributions in terms of the energetic description