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1. Dielectric continuum methods for quantum chemistry

   https://doi.org/10.1002/wcms.1519  

   Herbert, John M. (March 2021, WIREs Computational Molecular Science)

   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 

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2. Variational determination of the two‐electron reduced density matrix: A tutorial review

   https://doi.org/10.1002/wcms.1702  

   Eugene DePrince, III, A. (January 2024, WIREs Computational Molecular Science)

   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 

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3. The electronic structure of genome editors from the first principles

   https://doi.org/10.1088/2516-1075/acb410  

   Nierzwicki, Łukasz; Ahsan, Mohd; Palermo, Giulia (February 2023, Electronic Structure)

   Abstract Ab-initio molecular dynamics enables following the dynamics of biological systems from the first principles, describing the electronic structure and offering the opportunity to “watch” the evolution of biochemical processes with unique resolution, beyond the capabilities of state-of-the-art experimental techniques. This article reports the role of first-principles ( ab-initio ) molecular dynamics (MD) in the CRISPR-Cas9 genome editing revolution, achieving a profound understanding of the enzymatic function and offering valuable insights for enzyme engineering. We introduce the methodologies and explain the use of ab-initio MD simulations to establish the two-metal dependent mechanism of DNA cleavage in the RuvC domain of the Cas9 enzyme, and how a second catalytic domain, HNH, cleaves the target DNA with the aid of a single metal ion. A detailed description of how ab-initio MD is combined with free-energy methods—i.e., thermodynamic integration and metadynamics—to break and form chemical bonds is given, explaining the use of these methods to determine the chemical landscape and establish the catalytic mechanism in CRISPR-Cas9. The critical role of classical methods is also discussed, explaining theory and application of constant pH MD simulations, used to accurately predict the catalytic residues’ protonation states. Overall, first-principles methods are shown to unravel the electronic structure and reveal the catalytic mechanism of the Cas9 enzyme, providing valuable insights that can serve for the design of genome editing tools with improved catalytic efficiency or controllable activity. 

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4. Molecular Dynamics Simulations on Relaxed Reduced-DimensionalPotential Energy Surfaces

   Lui, C. (April 2019, The journal of physical chemistry. A.)

   Molecular dynamics (MD) simulations with full-dimensional potential energy surfaces (PESs) obtained from high-level ab initio calculations are frequently used to model reaction dynamics of small molecules (i.e., molecules with up to 10 atoms). Construction of full-dimensional PESs for larger molecules is, however, not feasible since the number of ab initio calculations required grows rapidly with the increase of dimension. Only a small number of coordinates are often essential for describing the reactivity of even very large systems, and reduced-dimensional PESs with these coordinates can be built for reaction dynamics studies. While analytical methods based on transition-state theory framework are well established for analyzing the reduced-dimensionalPESs, MD simulation algorithms capable of generating trajectories on such surfaces are more rare. In this work, we present a new MD implementation that utilizes the relaxed reduced-dimensional PES for standard micro canonical (NVE) and canonical (NVT) MD simulations.The method is applied to the pyramidal inversion of a NH3molecule. The results from the MD simulations on a reduced, three-dimensional PES are validated against the ab initio MD simulations, as well as MD simulations on full-dimensional PES and experimental data. 

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5. Surface solvation and hindered isomerization at the water/silica interface explored with second harmonic generation

   Purnell, Grace E. Walker (April 2019, Journal of chemical physics)

   Resonantly enhanced second harmonic generation (SHG) spectra of Coumarin 152 (C152) adsorbed at the water-silica interface show that C152 experiences a local dielectric environment slightly more polar than that of bulk water. This result stands in contrast to recently reported time-resolved fluorescence experiments and simulations that suggest a alkane-like permittivity for interfacial water at strongly associating, hydrophilic solid surfaces. Taken together, these results imply that while the static electric field across the aqueous-silica interface may be large, restricted water dynamics lead to apparent nonpolar solvation behavior similar to that experienced by solutes in confinement. Resonance-enhanced SHG spectra and time-resolved fluorescence of C152 adsorbed to aqueous-hydrophobic silica surfaces show that when water’s ability to hydrogen bond with the silica surface is eliminated, a solute’s interfacial solvation and corresponding ability to photoisomerize converge to an intermediate limit similar to that experienced in bulk acetone or methanol. While water structure and dynamics at solid-liquid interfaces have received considerable attention, results presented below show how strong solvent-substrate interactions can create conflicting pictures of solute reactivity across buried interfaces. 

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