1,721,088 research outputs found
General Linear Scaling Implementation of Polarizable Embedding Schemes
Full text linkA general framework to treat polarizable embedding schemes in the context of QM/MM calculations is presented. Such a framework is completely general, as it allows in principle one to treat any electrostatic distribution and polarization model with minimal modifications and achieves linear scaling in computational cost and memory requirements. The performances and scaling of the new implementation are demonstrated with benchmark calculations on water clusters including up to 1146240 atoms
Second-Order CASSCF Algorithm with the Cholesky Decomposition of the Two-Electron Integrals
Full text linkIn this contribution, we present the implementation of a second-order complete active space-self-consistent field (CASSCF) algorithm in conjunction with the Cholesky decomposition of the two-electron repulsion integrals. The algorithm, called norm-extended optimization, guarantees convergence of the optimization, but it involves the full Hessian and is therefore computationally expensive. Coupling the second-order procedure with the Cholesky decomposition leads to a significant reduction in the computational cost, reduced memory requirements, and an improved parallel performance. As a result, CASSCF calculations of larger molecular systems become possible as a routine task. The performance of the new implementation is illustrated by means of benchmark calculations on molecules of increasing size, with up to about 3000 basis functions and 14 active orbitals
Absorption and Circular Dichroism Spectra of Molecular Aggregates With the Full Cumulant Expansion
No full textThe exciton Hamiltonian of multichromophoric aggregates can be probed by spectroscopic techniques such as linear absorption and circular dichroism. To compare calculated Hamiltonians to experiments, a lineshape theory is needed, which takes into account the coupling of the excitons with inter- and intramolecular vibrations. This coupling is normally introduced in a perturbative way through the cumulant expansion formalism and further approximated by assuming a Markovian exciton dynamics, for example with the modified Redfield theory. Here, we present the implementation of the full cumulant expansion (FCE) formalism ( J. Chem. Phys. 142, 2015, 094106) to efficiently compute absorption and circular dichroism spectra of molecular aggregates beyond the Markov approximation, without restrictions on the form of exciton-phonon coupling. By employing the LH2 system of purple bacteria as a challenging test case, we compare the FCE lineshapes with the Markovian lineshapes obtained with the modified Redfield theory, showing that the latter presents a less satisfying agreement with experiments. The FCE approach instead accurately describes the lineshapes, especially in the vibronic sideband of the B800 peak. We envision that the FCE approach will become a valuable tool for accurately comparing model exciton Hamiltonians with optical spectroscopy experiments
Non covalent interactions in RNA and DNA base pairs: a quantum-mechanical study of the coupling between solvent and electronic density
No full textIt is well-known that a solvent can modify the relative importance of the different constituents (electrostatic and dispersion) of non-covalent interactions, but much less is known about how these solvent-induced modifications specifically couple with the polarization of the electronic
density and electronic correlation. Here we present a quantum mechanical analysis of the effects of the solvent on the non covalent interactions (both stacking and hydrogen bonding) in base pairs using a hierarchy of combinations between a MP2 correlated description for the
base pairs and the polarizable continuum model (PCM) for the solvent. A comparison of the results obtained in these different combinations of increasing accuracy allows us to better analyze the important role played by the coupling between correlated electronic densities and solvent polarization in determining the relative importance of stacking and hydrogen bonding effects
Polarizable force fields and polarizable continuum model: A fluctuating charges/PCM approach. 1. Theory and implementation
No full textWe present a combined fluctuating charges-polarizable continuum model approach to describe molecules in solution. Both static and dynamic approaches are discussed: analytical first and second derivatives are shown as well as an extended lagrangian for molecular dynamics simluations. In particular, we use the polarizable continuum model to provide nonperiodic boundary conditions for molecular dynamics simulations of aqueous solutions. The extended lagrangian method is extensively discussed, with specific reference to the fluctuating charge model, from a numerical point of view by means of several examples, and a rationalization of the behavior found is presented. Several prototypical applications are shown, especially regarding solvation of ions and polar molecules in water. © 2011 American Chemical Society
Embedding effects on charge-transport parameters in molecular organic materials
No full textWe present a generalized version of the tight-binding approach to determine the electronic coupling parameter in charge (hole) transport phenomena in organic materials. The main novelty of this approach is that the “embedding effects” of the environment either a solvent or a crystal packing can be explicitly included in the calculation by considering an embedded dimer. One of the main features shown by the application of the method to both model systems and oligoacene crystals is that the routinely used “energy splitting in a dimer” approximation gives reasonable results even if the transfer units are not equivalent by symmetry but the embedding effects are properly taken into account
Is There a Quadruple Fe-C Bond in FeC(CO)<sub>3</sub>?
Full text linkA recent computational paper (Kalita et al., Phys. Chem. Chem. Phys. 2020, 22, 24178–24180) reports the existence of a quadruple bond between a carbon and an iron atom in the FeC(CO)3 molecule. In this communication, we perform several computations on the same system, using both density functional theory and post-Hartree–Fock methods and find that the results, and in particular the Fe-C bond length and stretching frequency depend strongly on the method used. We ascribe this behavior to a strong multireference character of the FeC(CO)3 ground state, which explains the non-conclusive results obtained with single-reference methods. We therefore conclude that, while the existence of a Fe-C quadruple bond is not disproved, further investigation is required before a conclusion can be drawn
Hybrid QM/classical models: Methodological advances and new applications
Full text linkHybrid methods that combine quantum mechanical descriptions with classical models are very popular in molecular modeling. Such a large diffusion reflects their effectiveness, which over the years has allowed the quantum mechanical description to extend its boundaries to systems
of increasing size and to processes of increasing complexity. Despite this success, research in this field is still very active and a number of advances have been made recently, further extending the range of their applications. In this review, we describe such advances and discuss how
hybrid methods may continue to improve in the future. The various formulations proposed so far are presented here in a coherent way to underline their common methodological aspects. At the same time, the specificities of the different classical models and of their coupling with the quantum mechanical domain are highlighted and discussed, with special attention to the computational and numerical aspects
Perspective: Polarizable continuum models for quantum-mechanical descriptions
Full text linkPolarizable continuum solvation models are nowadays the most popular approach to describe solvent effects in the context of quantum mechanical calculations. Unexpectedly, despite their widespread use in all branches of quantum chemistry and beyond, important aspects of both their theoretical formulation and numerical implementation are still not completely understood. In particular, in this perspective we focus on the numerical issues of their implementation when applied to large systems and on the theoretical framework needed to treat time dependent problems and excited states or to deal with electronic correlation. Possible extensions beyond a purely electrostatic model and generalizations to environments beyond common solvents are also critically presented and discussed. Finally, some possible new theoretical approaches and numerical strategies are suggested to overcome the obstacles which still prevent a full exploitation of these models
General formulation of polarizable embedding models and of their coupling
Full text linkWe propose a general formalism for polarizable embedding models that can be applied to either continuum or atomistic polarizable models. After deriving such a formalism for both variational and non-variational models, we address the problem of coupling two polarizable models among themselves and to a quantum mechanical (QM) description in the spirit of multiscale quantum chemistry. We discuss general, model-independent coupling hypotheses and derive coupled polarization equations for all combinations of variational and non-variational models and discuss the embedding contributions to the analytical derivatives of the energy, with a particular focus on the elements of the Fock or Kohn-Sham matrix. We apply the general formalism to the derivation of the working equations for a three-layered, fully polarizable QM/MM/continuum strategy using the non-variational atomic multipole optimized energetics for biomolecular applications polarizable force field and the domain decomposition conductor-like screening model
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