456 research outputs found

    Harmonic Infrared and Raman Spectra in Molecular Environments Using the Polarizable Embedding Model

    Get PDF
    We present a fully analytic approach to calculate infrared (IR) and Raman spectra of molecules embedded in complex molecular environments modeled using the fragment-based polarizable embedding (PE) model. We provide the theory for the calculation of analytic second-order geometric derivatives of molecular energies and first-order geometric derivatives of electric dipole moments and dipole–dipole polarizabilities within the PE model. The derivatives are implemented using a general open-ended response theory framework, thus allowing for an extension to higher-order derivatives. The embedding-potential parameters used to describe the environment in the PE model are derived through first-principles calculations, thus allowing a wide variety of systems to be modeled, including solvents, proteins, and other large and complex molecular environments. Here, we present proof-of-principle calculations of IR and Raman spectra of acetone in different solvents. This work is an important step toward calculating accurate vibrational spectra of molecules embedded in realistic environments

    Efficient Molecular Dynamics Simulations of Multiple Radical Center Systems Based on the Fragment Molecular Orbital Method

    Get PDF
    The fully analytic energy gradient has been developed and implemented for the restricted open-shell Hartree–Fock (ROHF) method based on the fragment molecular orbital (FMO) theory for systems that have multiple open-shell molecules. The accuracy of the analytic ROHF energy gradient is compared with the corresponding numerical gradient, illustrating the accuracy of the analytic gradient. The ROHF analytic gradient is used to perform molecular dynamics simulations of an unusual open-shell system, liquid oxygen, and mixtures of oxygen and nitrogen. These molecular dynamics simulations provide some insight about how triplet oxygen molecules interact with each other. Timings reveal that the method can calculate the energy gradient for a system containing 4000 atoms in only 6 h. Therefore, it is concluded that the FMO-ROHF method will be useful for investigating systems with multiple open shells

    Universal QM/MM Approaches for General Nanoscale Applications

    Full text link
    Hybrid quantum mechanics/molecular mechanics (QM/MM) hybrid models allow one to address chemical phenomena in complex molecular environments. However, they are tedious to construct and they usually require significant manual preprocessing and expertise. As a result, these models may not be easily transferable to new application areas and the many parameters are not easy to adjust to reference data that are typically scarce. Therefore, it has been difficult to devise automated procedures of controllable accuracy, which makes such type of modelling far from being standardized or of black-box type. Although diverse best-practice protocols have been set up for the construction of individual components of a QM/MM model (e.g., the MM potential, the type of embedding, the choice of the QM region), no automated procedures are available for all steps of the QM/MM model construction. Here, we review the state of the art of QM/MM modeling with a focus on automation. We elaborate on the MM model parametrization, on atom-economical physically-motivated QM region selection, and on embedding schemes that incorporate mutual polarization as critical components of the QM/MM model. In view of the broad scope of the field, we mostly restrict the discussion to methodologies that build de novo models based on first-principles data, on uncertainty quantification, and on error mitigation with a high potential for automation. Ultimately, it is desirable to be able to set up reliable QM/MM models in a fast and efficient automated way without being constrained by some specific chemical or technical limitations.Comment: 54 pages, 3 figures, 1 tabl

    Gradient-Driven Molecule Construction: An Inverse Approach Applied to the Design of Small-Molecule Fixating Catalysts

    Full text link
    Rational design of molecules and materials usually requires extensive screening of molecular structures for the desired property. The inverse approach to deduce a structure for a predefined property would be highly desirable, but is, unfortunately, not well-defined. However, feasible strategies for such an inverse design process may be successfully developed for specific purposes. We discuss options for calculating 'jacket' potentials that fulfill a predefined target requirement - a concept that we recently introduced [T. Weymuth, M. Reiher, MRS Proceediungs, 2013, 1524, DOI:10.1557/opl.2012.1764]. We consider the case of small-molecule activating transition metal catalysts. As a target requirement we choose the vanishing geometry gradients on all atoms of a subsystem consisting of a metal center binding the small molecule to be activated. The jacket potential can be represented within a full quantum model or by a sequence of approximations of which a field of electrostatic point charges is the simplest. In a second step, the jacket potential needs to be replaced by a chemically viable chelate-ligand structure for which the geometry gradients on all of its atoms are also required to vanish. In order to analyze the feasibility of this approach, we dissect a known dinitrogen-fixating catalyst to study possible design strategies that must eventually produce the known catalyst.Comment: 40 pages, 6 tables, 5 figure

    Developments in multiscale ONIOM and fragment methods for complex chemical systems

    Get PDF
    Multiskalenprobleme werden in der Computerchemie immer allgegenwärtiger und bestimmte Klassen solcher Probleme entziehen sich einer effizienten Beschreibung mit den verfügbaren Berechnungsansätzen. In dieser Arbeit wurden effiziente Erweiterungen der Multilayer-Methode ONIOM und von Fragmentmethoden als Lösungsansätze für derartige Probleme entwickelt. Dabei wurde die Kombination von ONIOM und Fragmentmethoden im Rahmen der Multi-Centre Generalised ONIOM entwickelt sowie die eine Multilayer-Variante der Fragment Combinatio Ranges. Außerdem wurden Schemata für elektronische Einbettung derartiger Multilayer-Systeme entwickelt. Der zweite Teil der Arbeit beschreibt die Implementierung im Haskell-Programm "Spicy" und demonstriert Anwendungen derartiger Multiskalen-Methoden

    A simplified charge projection scheme for long-range electrostatics in ab initio QM/MM calculations

    Get PDF
    In a previous work [Pan et al., Molecules 23, 2500 (2018)], a charge projection scheme was reported, where outer molecular mechanical (MM) charges [>10 Ă… from the quantum mechanical (QM) region] were projected onto the electrostatic potential (ESP) grid of the QM region to accurately and efficiently capture long-range electrostatics in ab initio QM/MM calculations. Here, a further simplification to the model is proposed, where the outer MM charges are projected onto inner MM atom positions (instead of ESP grid positions). This enables a representation of the long-range MM electrostatic potential via augmentary charges (AC) on inner MM atoms. Combined with the long-range electrostatic correction function from Cisneros et al. [J. Chem. Phys. 143, 044103 (2015)] to smoothly switch between inner and outer MM regions, this new QM/MM-AC electrostatic model yields accurate and continuous ab initio QM/MM electrostatic energies with a 10 Ă… cutoff between inner and outer MM regions. This model enables efficient QM/MM cluster calculations with a large number of MM atoms as well as QM/MM calculations with periodic boundary conditions

    Electronic Structure Methods for Large Molecular Systems and Materials in Strong Magnetic Fields

    Get PDF
    The high-rank polynomial scaling of modern electronic structure methods can present significant limitations on the size of molecular systems that can be accurately studied. This issue is further exasperated when using non-perturbative approaches for studying systems within arbitrary strength magnetic fields due to the requirements for complex algebra and reduced permutational symmetry. One such attempt at overcoming this issue is the concept of fragmentation, which has shown promise in recent years for accurately determining the electronic structure of systems that can be sensibly fragmented into smaller subunits. The main aim in this work is to combine the concepts of one such method, the embedding fragment method (EFM), with recent advances in non-perturbative treatment of external fields, enabling the study of increasingly large or complex systems. The implementation of this approach is presented for systems in strong magnetic fields. The method is applied to determine energetic, structural and magnetic response properties of systems beyond the scope of more conventional methods. The EFM is shown to provide an accurate electronic structure approximation when studying systems within extremely strong magnetic fields, with errors generally 70000 Tesla. Its application to large water clusters is presented showing how external magnetic fields strengthen intermolecular interactions, as has previously been demonstrated through experiment, but that the origin of this strengthening is not as straightforward as the altering of the hydrogen bonding present at zero field, a rational often considered alongside experimental results. Also demonstrated is how this approach can be used to accurately model solvation effects when calculating magnetic properties of solute molecules. In this work the calculation of nuclear magnetic resonance chemical shifts is considered, using the EFM and comparing to both gas phase calculations and calculations including solvent effects using the polarisable continuum method. To aid in the interpretation of results, two additional tool sets have been development. The first is a suite of tools to analyse the complex current vector field induced by exposing a molecule to an external field. The second is a new molecular viewer software package, improving the ability to analyse the effects of external magnetic fields on molecular systems

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

    Get PDF
    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
    • …
    corecore