skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

Attention:

The NSF Public Access Repository (PAR) system and access will be unavailable from 11:00 PM ET on Friday, November 14 until 2:00 AM ET on Saturday, November 15 due to maintenance. We apologize for the inconvenience.


Title: Dielectric continuum methods for quantum chemistry
Abstract This review describes the theory and implementation of implicit solvation models based on continuum electrostatics. Within quantum chemistry this formalism is sometimes synonymous with the polarizable continuum model, a particular boundary‐element approach to the problem defined by the Poisson or Poisson–Boltzmann equation, but that moniker belies the diversity of available methods. This work reviews the current state‐of‐the art, with emphasis on theory and methods rather than applications. The basics of continuum electrostatics are described, including the nonequilibrium polarization response upon excitation or ionization of the solute. Nonelectrostatic interactions, which must be included in the model in order to obtain accurate solvation energies, are also described. Numerical techniques for implementing the equations are discussed, including linear‐scaling algorithms that can be used in classical or mixed quantum/classical biomolecular electrostatics calculations. Anisotropic models that can describe interfacial solvation are briefly described. This article is categorized under:Electronic Structure Theory > Ab Initio Electronic Structure MethodsMolecular and Statistical Mechanics > Free Energy Methods  more » « less
Award ID(s):
1955282 1665322
PAR ID:
10387064
Author(s) / Creator(s):
 
Publisher / Repository:
Wiley Blackwell (John Wiley & Sons)
Date Published:
Journal Name:
WIREs Computational Molecular Science
Volume:
11
Issue:
4
ISSN:
1759-0876
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract Reliable simulations of molecules in condensed phase require the combination of an accurate quantum mechanical method for the core region, and a realistic model to describe the interaction with the environment. Additionally, this combination should not significantly increase the computational cost of the calculation compared to the corresponding in vacuo case. In this review, we describe the combination of methods based on coupled cluster (CC) theory with polarizable classical models for the environment. We use the polarizable continuum model (PCM) of solvation to discuss the equations, but we also show how the same theoretical framework can be extended to polarizable force fields. The theory is developed within the perturbation theory energy and singles‐T density (PTES) scheme, where the environmental response is computed with the CC single excitation amplitudes as an approximation for the full one‐particle reduced density. The CC‐PTES combination provides the best compromise between accuracy and computational effort for CC calculations in condensed phase, because it includes the response of the environment to the correlation density at the same computational cost of in vacuo CC. We discuss a number of numerical applications for ground and excited state properties, based on the implementation of CC‐PTES with single and double excitations (CCSD‐PTES), which show the reliability and computational efficiency of the method in reproducing experimental or full‐CC data. This article is characterized under:Electronic Structure Theory > Ab Initio Electronic Structure MethodsElectronic Structure Theory > Combined QM/MM MethodsSoftware > Quantum Chemistry 
    more » « less
  2. Abstract The Chronus Quantum (ChronusQ) software package is an open source (under the GNU General Public License v2) software infrastructure which targets the solution of challenging problems that arise in ab initio electronic structure theory. Special emphasis is placed on the consistent treatment of time dependence and spin in the electronic wave function, as well as the inclusion of relativistic effects in said treatments. In addition, ChronusQ provides support for the inclusion of uniform finite magnetic fields as external perturbations through the use of gauge‐including atomic orbitals. ChronusQ is a parallel electronic structure code written in modern C++ which utilizes both message passing implementation and shared memory (OpenMP) parallelism. In addition to the examination of the current state of code base itself, a discussion regarding ongoing developments and developer contributions will also be provided. This article is categorized under:Software > Quantum ChemistryElectronic Structure Theory > Ab Initio Electronic Structure MethodsElectronic Structure Theory > Density Functional Theory 
    more » « less
  3. Abstract Flavins have emerged as central to electron bifurcation, signaling, and countless enzymatic reactions. In bifurcation, two electrons acquired as a pair are separated in coupled transfers wherein the energy of both is concentrated on one of the two. This enables organisms to drive demanding reactions based on abundant low‐grade chemical fuel. To enable incorporation of this and other flavin capabilities into designed materials and devices, it is essential to understand fundamental principles of flavin electronic structure that make flavins so reactive and tunable by interactions with protein. Emerging computational tools can now replicate spectra of flavins and are gaining capacity to explain reactivity at atomistic resolution, based on electronic structures. Such fundamental understanding can moreover be transferrable to other chemical systems. A variety of computational innovations have been critical in reproducing experimental properties of flavins including their electronic spectra, vibrational signatures, and nuclear magnetic resonance (NMR) chemical shifts. A computational toolbox for understanding flavin reactivity moreover must be able to treat all five oxidation and protonation states, in addition to excited states that participate in flavoprotein's light‐driven reactions. Therefore, we compare emerging hybrid strategies and their successes in replicating effects of hydrogen bonding, the surrounding dielectric, and local electrostatics. These contribute to the protein's ability to modulate flavin reactivity, so we conclude with a survey of methods for incorporating the effects of the protein residues explicitly, as well as local dynamics. Computation is poised to elucidate the factors that affect a bound flavin's ability to mediate stunningly diverse reactions, and make life possible. This article is categorized under:Structure and Mechanism > Computational Biochemistry and BiophysicsElectronic Structure Theory > Combined QM/MM MethodsTheoretical and Physical Chemistry > Spectroscopy 
    more » « less
  4. Abstract The two‐electron reduced density matrix (2RDM) carries enough information to evaluate the electronic energy of a many‐electron system. The variational 2RDM (v2RDM) approach seeks to determine the 2RDM directly, without knowledge of the wave function, by minimizing this energy with respect to variations in the elements of the 2RDM, while also enforcing knownN‐representability conditions. In this tutorial review, we provide an overview of the theoretical underpinnings of the v2RDM approach and theN‐representability constraints that are typically applied to the 2RDM. We also discuss the semidefinite programming (SDP) techniques used in v2RDM computations and provide enough Python code to develop a working v2RDM code that interfaces to thelibSDPlibrary of SDP solvers. This article is categorized under:Electronic Structure Theory > Ab Initio Electronic Structure MethodsSoftware > Quantum Chemistry 
    more » « less
  5. Abstract Quantum mechanics/molecular mechanics (QM/MM) simulations are a popular approach to study various features of large systems. A common application of QM/MM calculations is in the investigation of reaction mechanisms in condensed‐phase and biological systems. The combination of QM and MM methods to represent a system gives rise to several challenges that need to be addressed. The increase in computational speed has allowed the expanded use of more complicated and accurate methods for both QM and MM simulations. Here, we review some approaches that address several common challenges encountered in QM/MM simulations with advanced polarizable potentials, from methods to account for boundary across covalent bonds and long‐range effects, to polarization and advanced embedding potentials. This article is categorized under:Electronic Structure Theory > Combined QM/MM MethodsMolecular and Statistical Mechanics > Molecular InteractionsSoftware > Simulation Methods 
    more » « less