Seamless integration of GEM, a density based-force field, for QM/MM simulations via LICHEM, Psi4, and Tinker-HP.

Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations have become an essential tool in computational chemistry, particularly for analyzing complex biological and condensed phase systems. Building on this foundation, our work presents a novel implementation of the Gaussian Electrostatic Model (GEM), a polarizable density-based force field, within the QM/MM framework. This advancement provides seamless integration, enabling efficient and optimized QM/GEM calculations in a single step using the LICHEM Code.

Impact of an Ionic Liquid Solution on Horseradish Peroxidase Activity.

Horseradish peroxidase (HRP) is an enzyme that oxidizes pollutants from wastewater. A previous report indicated that peroxidases can have an enhancement in initial enzymatic activity in an aqueous solution of 0.26 M 1-ethyl-3-methylimidazolium ethyl sulfate ([EMIm][EtSO]) at neutral pH.

Relative cooperativity in neutral and charged molecular clusters using QM/MM calculations.

QM/MM methods have been used to study electronic structure properties and chemical reactivity in complex molecular systems where direct electronic structure calculations are not feasible. In our previous work, we showed that non-polarizable force fields, by design, describe intermolecular interactions through pairwise interactions, overlooking many-body interactions involving three or more particles. In contrast, polarizable force fields account partially for many-body effects through polarization, but still handle van der Waals and permanent electrostatic interactions pairwise.

Cooperativity and Frustration Effects (or Lack Thereof) in Polarizable and Non-polarizable Force Fields.

Understanding cooperativity and frustration is crucial for studying biological processes such as molecular recognition and protein aggregation. Force fields have been extensively utilized to explore cooperativity in the formation of protein secondary structures and self-assembled systems. Multiple studies have demonstrated that polarizable force fields provide more accurate descriptions of this phenomenon compared to fixed-charge pairwise nonpolarizable force fields, thanks to the incorporation of polarization effects.

Polarizable MD and QM/MM investigation of acrylamide-based leads to target the main protease of SARS-CoV-2.

The main protease (Mpro) of SARS-CoV-2 is an essential enzyme for the replication of the virus causing the COVID-19 pandemic. Because there is no known homologue in humans, it has been proposed as a primary target for antiviral drug development. Here, we explore the potential of five acrylamide-based molecules as possible covalent inhibitors, leading to target MPro by docking, followed by polarizable molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) calculations.

Electronic Structure Effects Related to the Origin of the Remarkable Near-Infrared Absorption of ' Light Harvesting 1-Reaction Center Complex.

Various photosynthetic organisms have evolved to absorb light in different regions of the visible light spectrum, thus adapting to the various lighting conditions available on Earth. While most of these autotrophic organisms absorb wavelengths around the 700-800 nm region, some are capable of red-shifted absorptions above this range, but none as remarkably as whose main absorption is observed at 1015 nm, approximately 220 nm (0.34 eV) lower in energy than their main constituent pigments, BChl-, whose main absorption is observed at 795 nm.

Structural and electronic analysis of the octarepeat region of prion protein with four Cu by polarizable MD and QM/MM simulations.

Prions have been linked to neurodegenerative diseases that affect various species of mammals including humans. The prion protein, located mainly in neurons, is believed to play the role of metal ion transporter. High levels of copper ions have been related to structural changes.

Development and application of quantum mechanics/molecular mechanics methods with advanced polarizable potentials.

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.

Origin of cooperativity in hydrogen bonding.

The origin of non-additivity in hydrogen bonds (H-bonds), usually termed as H-bond cooperativity, is investigated in H-bonded linear chains. It is shown that H-bond cooperativity originates solely from classical electrostatics. The latter is corroborated by comparing the H-bond cooperativity in infinitely-long H-bonded hydrogen cyanide, 4-pyridone and formamide chains, assessed using density functional theory (DFT), against the strengthening of the dipole-dipole interaction upon the formation of an infinite chain of effective point-dipoles.

On cooperative effects and aggregation of GNNQQNY and NNQQNY peptides.

Some health disturbances like neurodegenerative diseases are associated to the presence of amyloids. GNNQQNY and NNQQNY peptides are considered as prototypical examples for studying the formation of amyloids. These exhibit quite different aggregation behaviors despite they solely differ in size by one residue.