Bridging the size gap between experiment and theory: large-scale DFT calculations on realistic sized Pd particles for acetylene hydrogenation.

Metal nanoparticles, often supported on metal oxide promoters, are a cornerstone of heterogeneous catalysis. Experimentally, size effects are well-established and are manifested through changes to catalyst selectivity, activity and durability. Density Functional Theory (DFT) calculations have provided an attractive way to study these effects and rationalise the change in nanoparticle properties.

Conformational Analysis of 1,3-Difluorinated Alkanes.

Fluorine substitution can have a profound impact on molecular conformation. Here, we present a detailed conformational analysis of how the 1,3-difluoropropylene motif (-CHF-CH-CHF-) determines the conformational profiles of 1,3-difluoropropane, - and -2,4-difluoropentane, and - and -3,5-difluoroheptane. It is shown that the 1,3-difluoropropylene motif strongly influences alkane chain conformation, with a significant dependence on the polarity of the medium.

An Electronic Structure Investigation of PEDOT with AlCl Anions-A Promising Redox Combination for Energy Storage Applications.

In this work, we use density functional theory to investigate the electronic structure of poly(3,4-ethylenedioxythiophene) (PEDOT) oligomers with co-located AlCl anions, a promising combination for energy storage. The 1980s bipolaron model remains the dominant interpretation of the electronic structure of PEDOT despite recent theoretical progress that has provided new definitions of bipolarons and polarons. By considering the influence of oligomer length, oxidation or anion concentration and spin state, we find no evidence for many of the assertions of the 1980s bipolaron model and so further contribute to a new understanding.

Calculating shear viscosity with confined non-equilibrium molecular dynamics: a case study on hematite - PAO-2 lubricant.

The behaviour of confined lubricants at the atomic scale as affected by the interactions at the surface-lubricant interface is relevant in a range of technological applications in areas such as the automotive industry. In this paper, by performing fully atomistic molecular dynamics, we investigate the regime where the viscosity starts to deviate from the bulk behaviour, a topic of great practical and scientific relevance. The simulations consist of setting up a shear flow by confining the lubricant between iron oxide surfaces.

A Workflow for Identifying Viable Crystal Structures with Partially Occupied Sites Applied to the Solid Electrolyte Cubic LiLaZrO.

To date, experimental and theoretical works have been unable to uncover the ground-state configuration of the solid electrolyte cubic LiLaZrO (-LLZO). Computational studies rely on an initial low-energy structure as a reference point. Here, we present a methodology for identifying energetically favorable configurations of -LLZO for a crystallographically predicted structure.

Does a Machine-Learned Potential Perform Better Than an Optimally Tuned Traditional Force Field? A Case Study on Fluorohydrins.

We present a comparative study that evaluates the performance of a machine learning potential (ANI-2x), a conventional force field (GAFF), and an optimally tuned GAFF-like force field in the modeling of a set of 10 γ-fluorohydrins that exhibit a complex interplay between intra- and intermolecular interactions in determining conformer stability. To benchmark the performance of each molecular model, we evaluated their energetic, geometric, and sampling accuracies relative to quantum-mechanical data. This benchmark involved conformational analysis both in the gas phase and chloroform solution.

Computing Viscosities of Mixtures of Ester-Based Lubricants at Different Temperatures.

Synthetic esters are used as lubricants for applications at high temperatures, but their development can be a trial and error process. In this context, molecular dynamics simulations could be used as a tool to investigate the properties of new lubricants, in particular viscosity. We employ nonequilibrium molecular dynamics (NEMD) simulations to predict bulk Newtonian viscosities of a set of mixtures of two esters, di(2-ethylhexyl) sebacate (DEHS) and di(2-ethylhexyl) adipate (DEHA) at 293 and 343 K as well as equilibrium molecular dynamics (EMD) and NEMD at 393 K and compare these to experimental measurements.

Atomistic simulations on the carbidisation processes in Pd nanoparticles.

The formation of interstitial PdC nanoparticles (NPs) is investigated through DFT calculations. Insights on the mechanisms of carbidisation are obtained whilst the material's behaviour under conditions of increasing C-concentration is examined. Incorporation of C atoms in the Pd octahedral interstitial sites is occurring through the [111] facet with an activation energy barrier of 19.

Using molecular dynamics to simulate realistic structures of nitrocellulose of different nitration levels.

Nitrocellulose is a reactive derivative of cellulose, one of the most commonly occurring natural materials. Nitration of cellulose decreases the stability of the structure, meaning less is understood about its structure and reactions. Although cellulose is often found in fully crystalline forms, nitrocellulose is more commonly paracrystalline, or amorphous.

BRD4: quantum mechanical protein-ligand binding free energies using the full-protein DFT-based QM-PBSA method.

Fully quantum mechanical approaches to calculating protein-ligand free energies of binding have the potential to reduce empiricism and explicitly account for all physical interactions responsible for protein-ligand binding. In this study, we show a realistic test of the linear-scaling DFT-based QM-PBSA method to estimate quantum mechanical protein-ligand binding free energies for a set of ligands binding to the pharmaceutical drug-target bromodomain containing protein 4 (BRD4). We show that quantum mechanical QM-PBSA is a significant improvement over traditional MM-PBSA in terms of accuracy against experiment and ligand rank ordering and that the quantum and classical binding energies are converged to a similar degree.

Corrigendum to "Atomistic level characterisation of ssDNA translocation through the proteins CsgG and CsgF for nanopore sequencing" [Comput. Struct. Biotechnol. J. 19 (2021) 6417-6430].

[This corrects the article DOI: 10.1016/j.csbj.

Energy decomposition analysis method for metallic systems.

In this work, we present the first extension of an energy decomposition analysis (EDA) method to metallic systems. We extend the theory of our Hybrid Absolutely Localized Molecular Orbitals (HALMO) EDA to take into account that molecular orbitals in metallic systems are partially occupied, which is done by weighted orthogonalization (WO) of the molecular orbitals using their associated fractional occupancies as weights in the construction of the projection operators. These operators are needed for the self-consistent field for molecular interaction (SCF MI) computation of the polarization-energy contribution to the interaction.

Atomistic level characterisation of ssDNA translocation through the proteins CsgG and CsgF for nanopore sequencing.

Two proteins of the membrane protein complex, CsgG and CsgF, are studied as proteinaceous nanopores for DNA sequencing. It is highly desirable to control the DNA as it moves through the pores, this requires characterisation of DNA translocation and subsequent optimization of the pores. In order to inform protein engineering to improve the pores, we have conducted a series of molecular dynamics simulations to characterise the mechanical strength and conformational dynamics of CsgG and the CsgG-CsgF complex and how these impact ssDNA, water and ion movement.

Massively parallel linear-scaling Hartree-Fock exchange and hybrid exchange-correlation functionals with plane wave basis set accuracy.

We extend our linear-scaling approach for the calculation of Hartree-Fock exchange energy using localized in situ optimized orbitals [Dziedzic et al., J. Chem.

Generation of Quantum Configurational Ensembles Using Approximate Potentials.

Conformational analysis is of paramount importance in drug design: it is crucial to determine pharmacological properties, understand molecular recognition processes, and characterize the conformations of ligands when unbound. Molecular Mechanics (MM) simulation methods, such as Monte Carlo (MC) and molecular dynamics (MD), are usually employed to generate ensembles of structures due to their ability to extensively sample the conformational space of molecules. The accuracy of these MM-based schemes strongly depends on the functional form of the force field (FF) and its parametrization, components that often hinder their performance.

Electrochemistry from first-principles in the grand canonical ensemble.

Progress in electrochemical technologies, such as automotive batteries, supercapacitors, and fuel cells, depends greatly on developing improved charged interfaces between electrodes and electrolytes. The rational development of such interfaces can benefit from the atomistic understanding of the materials involved by first-principles quantum mechanical simulations with Density Functional Theory (DFT). However, such simulations are typically performed on the electrode surface in the absence of its electrolyte environment and at constant charge.

Protein-ligand free energies of binding from full-protein DFT calculations: convergence and choice of exchange-correlation functional.

The accurate prediction of protein-ligand binding free energies with tractable computational methods has the potential to revolutionize drug discovery. Modeling the protein-ligand interaction at a quantum mechanical level, instead of relying on empirical classical-mechanics methods, is an important step toward this goal. In this study, we explore the QM-PBSA method to calculate the free energies of binding of seven ligands to the T4-lysozyme L99A/M102Q mutant using linear-scaling density functional theory on the whole protein-ligand complex.

Analysis of DNA interactions and GC content with energy decomposition in large-scale quantum mechanical calculations.

GC content is a contributing factor to the stability of nucleic acids due to hydrogen bonding. More hydrogen bonding generally results in greater stability. Empirical evidence, however, has suggested that the GC content of a nucleic acid is a poor predictor of its stability, implying that there are sequence-dependent interactions besides what its GC content indicates.

ParaMol: A Package for Automatic Parameterization of Molecular Mechanics Force Fields.

The ensemble of structures generated by molecular mechanics (MM) simulations is determined by the functional form of the force field employed and its parameterization. For a given functional form, the quality of the parameterization is crucial and will determine how accurately we can compute observable properties from simulations. While accurate force field parameterizations are available for biomolecules, such as proteins or DNA, the parameterization of new molecules, such as drug candidates, is particularly challenging as these may involve functional groups and interactions for which accurate parameters may not be available.

Translocation of flexible and tensioned ssDNA through designed hydrophobic nanopores with two constrictions.

Protein-inspired nanopores with hydrophobic constriction regions have previously been shown to offer some promise for DNA sequencing. Here we explore a series of pores with two hydrophobic constrictions. The impact of nanopore radius, the nature of residues that define the constriction region and the flexibility of the ssDNA is explored.

Strain effects in core-shell PtCo nanoparticles: a comparison of experimental observations and computational modelling.

Strain in Pt nanoalloys induced by the secondary metal has long been suggested as a major contributor to the modification of catalytic properties. Here, we investigate strain in PtCo nanoparticles using a combination of computational modelling and microscopy experiments. We have used a combination of molecular dynamics (MD) and large-scale density functional theory (DFT) for our models, alongside experimental work using annular dark field scanning transmission electron microscopy (ADF-STEM).

Electronic structure calculations in electrolyte solutions: Methods for neutralization of extended charged interfaces.

Density functional theory (DFT) is often used for simulating extended materials such as infinite crystals or surfaces, under periodic boundary conditions (PBCs). In such calculations, when the simulation cell has non-zero charge, electrical neutrality has to be imposed, and this is often done via a uniform background charge of opposite sign ("jellium"). This artificial neutralization does not occur in reality, where a different mechanism is followed as in the example of a charged electrode in electrolyte solution, where the surrounding electrolyte screens the local charge at the interface.