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In this work, we use density functional theory to investigate the electronic structure of poly(3,4-ethylenedioxythiophene) (PEDOT) oligomers with co-located AlCl4− 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. No self-localisation of positive charges in PEDOT is found, as predicted by the bipolaron model at the hybrid functional level. Instead, our results show distortions that exhibit a single or a double peak in bond length alternations and charge density. Either can occur at different oxidation or anion concentrations. Rather than representing bipolarons or polaron pairs in the original model, these are electron distributions driven by a range of factors. Distortions can span an arbitrary number of nearby anions. We also contribute a novel conductivity hypothesis. Conductivity in conducting polymers has been observed to reduce at anion concentrations above 0.5. We show that at high anion concentrations, the energy of the localised, non-bonding anionic orbitals approaches that of the system HOMO due to Coulombic repulsion between anions. We hypothesize that with nucleic motion in the macropolymer, these orbitals will interfere with the hopping of charge carriers between sites of similar energy, lowering conductivity. [ABSTRACT FROM AUTHOR]

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. Phys. 139, 214103 (2013)] to leverage massive parallelism. Our approach has been implemented in the onetep (Order-N Electronic Total Energy Package) density functional theory framework, which employs a basis of non-orthogonal generalized Wannier functions (NGWFs) to achieve linear scaling with system size while retaining controllable near-complete-basis-set accuracy. For the calculation of Hartree–Fock exchange, we use a resolution-of-identity approach, where an auxiliary basis set of truncated spherical waves is used to fit products of NGWFs. The fact that the electrostatic potential of spherical waves (SWs) is known analytically, combined with the use of a distance-based cutoff for exchange interactions, leads to a calculation cost that scales linearly with the system size. Our new implementation, which we describe in detail, combines distributed memory parallelism (using the message passing interface) with shared memory parallelism (OpenMP threads) to efficiently utilize numbers of central processing unit cores comparable to, or exceeding, the number of atoms in the system. We show how the use of multiple time-memory trade-offs substantially increases performance, enabling our approach to achieve superlinear strong parallel scaling in many cases and excellent, although sublinear, parallel scaling otherwise. We demonstrate that in scenarios with low available memory, which preclude or limit the use of time-memory trade-offs, the performance degradation of our algorithm is graceful. We show that, crucially, linear scaling with system size is maintained in all cases. We demonstrate the practicability of our approach by performing a set of fully converged production calculations with a hybrid functional on large imogolite nanotubes up to over 1400 atoms. We finish with a brief study of how the employed approximations (exchange cutoff and the quality of the SW basis) affect the calculation walltime and the accuracy of the obtained results. [ABSTRACT FROM AUTHOR]

The reactions under which interstitial structures of Pd form are profoundly important and prevalent in catalysis; the formation and stability of Pd hydride structures are well understood, however, interstitial structures of the carbide and nitride are relatively under explored. This work reports a systematic study of the formation and stability of PdCx and PdNx at elevated temperatures and different atmospheres using in situ Pd L3 edge XANES spectroscopy. These studies were further complemented by the application of 14N MAS‐NMR experiments and computational DFT investigations. The experiments confirmed that PdCx was significantly more stable than PdNx; 14N MAS‐NMR provided direct confirmation on the formation of the nitride, however, the XANES studies evidenced very limited stability under the conditions employed. Moreover, the results suggest that the formation of the nitride imparts some structural changes that are not entirely reversible under the conditions used in these experiments. This work provides important insights into the stability of interstitial structures of Pd and the conditions in which they could be employed for directed catalytic processes. [ABSTRACT FROM AUTHOR]

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. We have developed a new hybrid computational method combining DFT and the Poisson–Boltzmann equation (P–BE) capable of simulating experimental electrochemistry under potential control in the presence of a solvent and an electrolyte. The charged electrode is represented quantum-mechanically via linear-scaling DFT, which can model nanoscale systems with thousands of atoms and is neutralized by a counter electrolyte charge via the solution of a modified P–BE. Our approach works with the total free energy of the combined multiscale system in a grand canonical ensemble of electrons subject to a constant electrochemical potential. It is calibrated with respect to the reduction potential of common reference electrodes, such as the standard hydrogen electrode and the Li metal electrode, which is used as a reference electrode in Li-ion batteries. Our new method can be used to predict electrochemical properties under constant potential, and we demonstrate this in exemplar simulations of the differential capacitance of few-layer graphene electrodes and the charging of a graphene electrode coupled to a Li metal electrode at different voltages. [ABSTRACT FROM AUTHOR]

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. The neutralizing effect of the surrounding electrolyte can be incorporated within a hybrid quantum–continuum model based on a modified Poisson–Boltzmann equation, where the concentrations of electrolyte ions are modified to achieve electroneutrality. Among the infinite possible ways of modifying the electrolyte charge, we propose here a physically optimal solution, which minimizes the deviation of concentrations of electrolyte ions from those in open boundary conditions (OBCs). This principle of correspondence of PBCs with OBCs leads to the correct concentration profiles of electrolyte ions, and electroneutrality within the simulation cell and in the bulk electrolyte is maintained simultaneously, as observed in experiments. This approach, which we call the Neutralization by Electrolyte Concentration Shift (NECS), is implemented in our electrolyte model in the Order-N Electronic Total Energy Package (ONETEP) linear-scaling DFT code, which makes use of a bespoke highly parallel Poisson–Boltzmann solver, DL_MG. We further propose another neutralization scheme ("accessible jellium"), which is a simplification of NECS. We demonstrate and compare the different neutralization schemes on several examples. [ABSTRACT FROM AUTHOR]

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. We present a protocol based on molecular dynamics simulations for creating realistic structures of nitrocellulose, particularly focusing on the crystallinity of the systems being created. We will also provide a detailed analysis of the geometric and dynamical parameters used to quantify the degree of crystallinity for the structures created here, with nitration levels varying from 0–14.14 wt% nitrogen content. Paracrystalline cellulose was not created using the protocol designed here, although it was found that the more nitrated a nitrocellulose system, the more the structure tends to paracrystallinity. This is due to a decrease in the number of hydrogen bonds present, and an increase in the size of the functional groups pushing the chains apart and weakening the interactions between the chains of the structure. The structures created are representative of realistic systems, which in the future will be able to be used to build further understanding of long-term storage of nitrocellulose. [ABSTRACT FROM AUTHOR]

Metal oxide supports often play an active part in heterogeneous catalysis by moderating both the structure and the electronic properties of the metallic catalyst particle. In order to provide some fundamental understanding on these effects, we present here a density functional theory (DFT) investigation of the binding of O and CO on Pt nanoparticles supported on titania (anatase) surfaces. These systems are complex, and in order to develop realistic models, here, we needed to perform DFT calculations with up to ∼1000 atoms. By performing full geometry relaxations at each stage, we avoid any effects of "frozen geometry" approximations. In terms of the interaction of the Pt nanoparticles with the support, we find that the surface deformation of the anatase support contributes greatly to the adsorption of each nanoparticle, especially for the anatase (001) facet. We attempt to separate geometric and electronic effects and find a larger contribution to ligand binding energy arising from the former. Overall, we show an average weakening (compared to the isolated nanoparticle) of ∼0.1 eV across atop, bridge and hollow binding sites on supported Pt55 for O and CO, and a preservation of site preference. Stronger effects are seen for O on Pt13, which is heavily deformed by anatase supports. In order to rationalize our results and examine methods for faster characterization of metal catalysts, we make use of electronic descriptors, including the d-band center and an electronic density based descriptor. We expect that the approach followed in this study could be applied to study other supported metal catalysts. [ABSTRACT FROM AUTHOR]

We extend our recently developed quantum-mechanical/molecular mechanics (QM/MM) approach [Dziedzic et al., J. Chem. Phys. 145, 124106 (2016)] to enable in situ optimization of the localized orbitals. The quantum subsystem is described with onetep linear-scaling density functional theory and the classical subsystem – with the AMOEBA polarizable force field. The two subsystems interact via multipolar electrostatics and are fully mutually polarizable. A total energy minimization scheme is employed for the Hamiltonian of the coupled QM/MM system. We demonstrate that, compared to simpler models using fixed basis sets, the additional flexibility offered by in situ optimized basis functions improves the accuracy of the QM/MM interface, but also poses new challenges, making the QM subsystem more prone to overpolarization and unphysical charge transfer due to increased charge penetration. We show how these issues can be efficiently solved by replacing the classical repulsive van der Waals term for QM/MM interactions with an interaction of the electronic density with a fixed, repulsive MM potential that mimics Pauli repulsion, together with a modest increase in the damping of QM/MM polarization. We validate our method, with particular attention paid to the hydrogen bond, in tests on water-ion pairs, the water dimer, first solvation shells of neutral and charged species, and solute-solvent interaction energies. As a proof of principle, we determine suitable repulsive potential parameters for water, K+, and Cl−. The mechanisms we employed to counteract the unphysical overpolarization of the QM subsystem are demonstrated to be adequate, and our approach is robust. We find that the inclusion of explicit polarization in the MM part of QM/MM improves agreement with fully QM calculations. Our model permits the use of minimal size QM regions and, remarkably, yields good energetics across the well-balanced QM/MM interface. [ABSTRACT FROM AUTHOR]

The intrinsic sampling method (ISM) is a powerful tool that allows the exploration of interfacial properties from molecular simulations by fitting a function that represents the local boundary between two phases. However, owing to the non-physical nature of an "intrinsic" surface, there remains an ambiguity surrounding the comparison of theoretical properties with the physical world. It is therefore important that the ISM remains internally consistent when reproducing simulated properties which match experiments, such as the surface tension or interfacial density distribution. We show that the current ISM procedure causes an over-fitting of the surface to molecules in the interface region, leading to a biased distribution of curvature at these molecular coordinates. We assert that this biased distribution is a cause of the disparity between predicted interfacial densities upon convolution to a laboratory frame, an artefact which has been known to exist since the development of the ISM. We present an improvement to the fitting procedure of the ISM in an attempt to alleviate the ambiguity surrounding the true nature of an intrinsic surface. Our "surface reconstruction" method is able to amend the shape of the interface so as to reproduce the global curvature distribution at all sampled molecular coordinates. We present the effects that this method has on the ISM predicted structure of a simulated Lennard-Jones fluid air-liquid interface. Additionally, we report an unexpected relationship between surface thermodynamic predictions of our reconstructed ISM surfaces and those of extended capillary wave theory, which is of current interest. [ABSTRACT FROM AUTHOR]

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. We test the interaction entropy and normal mode entropy correction terms to QM- and MM-PBSA. [ABSTRACT FROM AUTHOR]

We present an unexpected finite size effect affecting interfacial molecular simulations that is proportional to the width-to-surface-area ratio of the bulk phase Ll/A. This finite size effect has a significant impact on the variance of surface tension values calculated using the virial summation method. A theoretical derivation of the origin of the effect is proposed, giving a new insight into the importance of optimising system dimensions in interfacial simulations. We demonstrate the consequences of this finite size effect via a new way to estimate the surface energetic and entropic properties of simulated air-liquid interfaces. Our method is based on macroscopic thermodynamic theory and involves comparing the internal energies of systems with varying dimensions. We present the testing of these methods using simulations of the TIP4P/2005 water forcefield and a Lennard-Jones fluid model of argon. Finally, we provide suggestions of additional situations, in which this finite size effect is expected to be significant, as well as possible ways to avoid its impact. [ABSTRACT FROM AUTHOR]

Application of Li-ion batteries in electric vehicles requires improved safety, increased lifetime and high charging rates. One of the most commonly used intercalation anode material for Li-ion batteries, graphite, is vulnerable to Li nucleation, a side reaction which competes with the intercalation process and leads to loss of reversible capacity of the battery, ageing and short-circuits. In this study, we deploy a combined grand canonical large-scale electronic density-functional theory (DFT) and Poisson–Boltzmann electrolyte theory to study the nucleation and growth of Li clusters on the graphite anode in the presence of its surrounding electrolyte environment at different applied voltages with respect to the Li metal reference electrode. We find the voltage below which the nucleation energy becomes negative (corresponding to Li nucleation becoming energetically favourable), the 'potential of zero nucleation energy' (UPZN). We observe a distinct minimum in the plots of UPZN as a function of the size of nucleated clusters. When the applied voltage on the graphite electrode is below the minimum value of UPZN, the nucleated clusters start growing unbounded on graphite electrode. This potential for cluster growth (UPCG) is found to be −0.12 V on the periodic basal plane of unlithiated graphite and −0.08 V on lithiated graphite. The corresponding potential for the zigzag edge termination is −0.06 V on unlithiated graphite and −0.04 V on lithiated graphite. Thus, the nucleation and cluster growth is favored on the zigzag edge termination of the graphite electrode as compared to the periodic basal plane and on the lithiated graphite as compared to the unlithiated graphite. We find that the surrounding environment plays a significant role and that nucleation is more likely to occur in electrolyte environment than that predicted from calculations in vacuum. We observe that the potentials obtained with grand canonical ensemble DFT method in electrolyte are close to experimentally available data. The study has profound implications for the nucleation, growth and control of metal dendrites in a battery cell. [ABSTRACT FROM AUTHOR]

Accurate and computationally efficient exchange-correlation functionals are critical to the successful application of linear-scaling density functional theory (DFT). Local and semi-local functionals of the density are naturally compatible with linear-scaling approaches, having a general form which assumes the locality of electronic interactions and which can be efficiently evaluated by numerical quadrature. Presently, the most sophisticated and flexible semi-local functionals are members of the meta-generalized-gradient approximation (meta-GGA) family, and depend upon the kinetic energy density, τ, in addition to the charge density and its gradient. In order to extend the theoretical and computational advantages of τ-dependent meta-GGA functionals to large-scale DFT calculations on thousands of atoms, we have implemented support for τ-dependent meta-GGA functionals in the ONETEP program. In this paper we lay out the theoretical innovations necessary to implement τ-dependent meta-GGA functionals within ONETEP's linear-scaling formalism. We present expressions for the gradient of the τ-dependent exchange-correlation energy, necessary for direct energy minimization. We also derive the forms of the τ-dependent exchange-correlation potential and kinetic energy density in terms of the strictly localized, self-consistently optimized orbitals used by ONETEP. To validate the numerical accuracy of our self-consistent meta-GGA implementation, we performed calculations using the B97M-V and PKZB meta-GGAs on a variety of small molecules. Using only a minimal basis set of self-consistently optimized local orbitals, we obtain energies in excellent agreement with large basis set calculations performed using other codes. Finally, to establish the linear-scaling computational cost and applicability of our approach to large-scale calculations, we present the outcome of self-consistent meta-GGA calculations on amyloid fibrils of increasing size, up to tens of thousands of atoms. [ABSTRACT FROM AUTHOR]

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. The method gives more weight to orbitals that have higher occupancies and treats each fragment as metallic. The resulting HALMO EDA for metallic systems naturally reduces to the insulator version and produces the same results when applied to an insulating system. We present the theory and implementation of our new approach, and we demonstrate it with sample calculations of relevance to industrial materials. This work provides a new EDA paradigm and tool for the study and analysis of interactions in metallic systems within large-scale DFT calculations. [ABSTRACT FROM AUTHOR]

The transition to exascale computing will make possible simulations of unprecedented accuracy and complexity. We focus on materials and molecular modeling (MMM) aspiring to high fidelity, in silico experiments on complex systems of technological interest. This progress will present unprecedented challenges to the software used, especially how to exploit the huge degree of parallelism and the associated problems of creating effective workflows and data management on such platforms. Within the U.K.'s ExCALIBUR computing initiative, our U.K.-led MMM Design and Development Working Group has worked with the broad MMM community to identify high-priority applications that will drive future exascale software developments. We present an overview of selected case studies that pose new methodological challenges on exascale platforms and discuss the requirements, software challenges, and impact of each application area. [ABSTRACT FROM AUTHOR]

The hydration of the actinyl cations, uranyl UO2(super 2+) and plutonyl PuO2(super 2+), has been investigated. Kohn-Sham Density Function Theory calculations using the MAGIC quantuam chemistry code have been performed on the separate uranyl and plutonyl species, and on the complexes AcO2(super 2+).nH2O (AC = U, Pu; N = 4, 5, 6). The results showed that the solvent plays a critical role in the hydration process wherein the solvent molecules were found to behave like actual binding equatorial ligands.

The behavior of lubricants at operational conditions, such as at high pressures, is a topic of great industrial interest. In particular, viscosity and the viscosity-pressure relation are especially important for applications and their determination by computational simulations is very desirable. In this study, we evaluate methods to compute these quantities based on fully atomistic molecular dynamics simulations, which are computationally demanding but also have the potential to be most accurate. We used the 9,10-dimethyloctadecane molecule, main component of PAO-2 base oil as the lubricant for our tests. The methods used for the viscosity simulations are the Green-Kubo equilibrium molecular dynamics (EMD-GK) and nonequilibrium molecular dynamics (NEMD), at pressures of up to 1.0 GPa and various temperatures (40-150 degrees Celsius). We present the theory behind these methods and investigate how the simulation parameters affect the results obtained, to ensure viscosity convergence with respect to the simulation intervals and all other parameters. We show that, by using each method in its regime of applicability, we can achieve good agreement between simulated and measured values. NEMD simulations at high pressures captured zero shear viscosity successfully; while at 40 degrees Celsius, EMD-GK is only applicable to pressures up to 0.3 GPa, where the viscosity is lower. In NEMD, longer and multiply repeated simulations improve the confidence interval of viscosity, which is essential at lower pressures. Another aspect of these methods is the choice of the utilized force field for the atomic interactions. This was investigated by selecting two different commonly used force fields. [ABSTRACT FROM AUTHOR]

The uranium hexafluoride and plutonium hexafluoride monomer and dimer were investigated using the relativistic density functional approach. Optimization of the U-F distance in the UF6 monomer was carried out at different levels of theory. Atomization energies were derived at all levels and were increased by relativistic effects. A weak interaction between the two monomers in the UF6 dimer was observed at LDAX and BLYP levels, suggesting that the dimer is not stable enough to exist during the key reaction.

We present a novel quantum mechanical/molecular mechanics (QM/MM) approach in which a quantum subsystem is coupled to a classical subsystem described by the AMOEBA polarizable force field. Our approach permits mutual polarization between the QM and MM subsystems, effected through multipolar electrostatics. Self-consistency is achieved for both the QM and MM subsystems through a total energy minimization scheme. We provide an expression for the Hamiltonian of the coupled QM/MM system, which we minimize using gradient methods. The QM subsystem is described by the ONETEP linear-scaling DFT approach, which makes use of strictly localized orbitals expressed in a set of periodic sinc basis functions equivalent to plane waves. The MM subsystem is described by the multipolar, polarizable force field AMOEBA, as implemented in TINKER. Distributed multipole analysis is used to obtain, on the fly, a classical representation of theQMsubsystem in terms of atom-centered multipoles. This auxiliary representation is used for all polarization interactions between QM and MM, allowing us to treat them on the same footing as in AMOEBA.We validate our method in tests of solute-solvent interaction energies, for neutral and charged molecules, demonstrating the simultaneous optimization of the quantum and classical degrees of freedom. Encouragingly, we find that the inclusion of explicit polarization in the MM part of QM/MM improves the agreement with fully QM calculations. [ABSTRACT FROM AUTHOR]

Recently developed density functionals have good accuracy for both thermochemistry (TC) and non-covalent interactions (NC) if very large atomic orbital basis sets are used. To approach the basis set limit with potentially lower computational cost, a new self-consistent field (SCF) scheme is presented that employs minimal adaptive basis (MAB) functions. The MAB functions are optimized on each atomic site by minimizing a surrogate function. High accuracy is obtained by applying a perturbative correction (PC) to the MAB calculation, similar to dual basis approaches. Compared to exact SCF results, using this MAB-SCF (PC) approach with the same large target basis set produces <0.15 kcal/mol root-mean-square deviations for most of the tested TC datasets, and <0.1 kcal/mol for most of the NC datasets. The performance of density functionals near the basis set limit can be even better reproduced. With further improvement to its implementation, MAB-SCF (PC) is a promising lower-cost substitute for conventional large-basis calculations as a method to approach the basis set limit of modern density functionals. [ABSTRACT FROM AUTHOR]

Lithium metal plating is a critical safety issue in Li-ion cells with graphite anodes, and contributes significantly to ageing, drastically limiting the lifetime and inducing capacity loss. Nonetheless, the nucleation mechanism of metallic Li on graphite anodes is still poorly understood. But in-depth understanding is needed to rationally design mitigation measures. In this work, we conducted First-Principles studies to elucidate the Li nucleation mechanism on graphite surfaces. These large-scale density-functional-theory (DFT) calculations indicate that nano-particulate Li forms much more readily than classical nucleation theory predicts. Further, our calculations indicate a crucial role of topological surface states near the zigzag edge, lowering the nucleation barrier by a further 1.32 eV relative to nucleation on the basal plane. Li nucleation, therefore, is likely to initiate at or near the zigzag edges of graphitic particles. Finally, we suggest that chemical doping with a view to reducing the effect of the topological surface states might be a potential mitigation strategy to increase nucleation barriers and reduce the propensity to plate Li near the zigzag edge. [ABSTRACT FROM AUTHOR]

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. By leveraging modern high-performance computing we perform over 2900 full-protein (2600 atoms) DFT calculations providing new insights into the convergence, precision and reproducibility of the QM-PBSA method. We find that even at moderate sampling over 50 snapshots, the convergence of QM-PBSA is similar to traditional MM-PBSA and that the DFT-based energy evaluations are very reproducible. We show that in the QM-PBSA framework, the physically-motivated GGA exchange–correlation functional PBE outperforms the more modern, dispersion-including non-local and meta-GGA-nonlocal functionals VV10 and B97M-rV. Different empirical dispersion corrections perform similarly well but the three-body dispersion term, as included in Grimme's D3 dispersion, is significant and improves results slightly. Inclusion of an entropy correction term sampled over less than 25 snapshots is detrimental while an entropy correction sampled over the same 50 or 100 snapshots as the enthalpies improves the accuracy of the QM-PBSA method. As full-protein DFT calculations can now be performed on modest computational resources our study demonstrates that they can be a useful addition to the toolbox of free energy calculations. [ABSTRACT FROM AUTHOR]

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. To examine how much such sequence-dependent interactions affect the interaction energies of double-stranded DNA (dsDNA) molecules, dsDNA molecules of different sequences are generated and examined in silico for variabilities in the interaction energies within each group of dsDNA molecules of the same GC content. Since the amount of hydrogen bonding depends on the GC content, holding the GC content fixed when examining the differences in interaction energies allows sequence-dependent interactions to be isolated. The nature of sequence-dependent interactions is then dissected using energy decomposition analysis (EDA). By using EDA, the components of the interactions that depend on the neighboring base pairs help explain some of the variability in the interaction energies of the dsDNA molecules despite having the same GC content. This work provides a new paradigm and tool for the study and analysis of the distributions of interaction components in dsDNA with the same GC content using EDA within large-scale quantum chemistry calculations. [ABSTRACT FROM AUTHOR]

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). We have performed extensive validation of the interatomic potential against DFT using a Pt568Co18 nanoparticle. Modelling gives access to 3 dimensional structures that can be compared to the 2D ADF-STEM images, which we use to build an understanding of nanoparticle structure and composition. Strain has been measured for PtCo and pure Pt nanoparticles, with MD annealed models compared to ADF-STEM images. Our analysis was performed on a layer by layer basis, where distinct trends between the Pt and PtCo alloy nanoparticles are observed. To our knowledge, we show for the first time a way in which detailed atomistic simulations can be used to augment and help interpret the results of ADF-STEM strain mapping experiments, which will enhance their use in characterisation towards the development of improved catalysts. [ABSTRACT FROM AUTHOR]

A new method for finite-temperature density functional theory calculations which significantly increases the number of atoms that can be simulated in metallic systems is presented. A self-consistent, direct minimization technique is used to obtain the Helmholtz free energy of the electronic system, described in terms of a set of non-orthogonal, localized functions which are optimized in situ using a periodic-sinc basis set, equivalent to plane waves. Most parts of the calculation, including the demanding operation of building the Hamiltonian matrix, have a computational cost that scales linearly with the number of atoms in the system. Also, this approach ensures that the Hamiltonian matrix has a minimal size, which reduces the computational overhead due to diagonalization, a cubic-scaling operation that is still required. Large basis set accuracy is retained via the optimization of the localized functions. This method allows accurate simulations of entire metallic nanostructures, demonstrated with calculations on a supercell of bulk copper with 500 atoms and on gold nanoparticles with up to 2057 atoms. [ABSTRACT FROM AUTHOR]

The interface between the electrolyte and graphite anodes plays an important role for lithium (Li) intercalation and has significant impact on the charging/discharging performance of Lithium-Ion Batteries (LIBs). However, atomistic understanding of interface effects that would allow the interface to be rationally optimized for application needs is largely missing. Here we comprehensively study the energetics of Li intercalation near the main non-basal surfaces of graphite, namely the armchair and zigzag edges. We find that edge sites at both surfaces bind Li more strongly than in the bulk of graphite. Therefore, lithiation of these sites is expected to proceed at higher voltages than in the bulk. Furthermore, this effect is significantly more pronounced at the zigzag edge compared to the armchair edge due to its unique electronic structure. The "peculiar" topologically stabilized electronic surface state found at zigzag edges strongly interacts with Li, thereby changing Li diffusion behavior at the surface as well. Finally, we investigate boron (B)/nitrogen (N) doping as a promising strategy to tune the Li intercalation behavior at both edge systems, which could lead to enhanced intercalation kinetics in B/N doped graphite anodes. [ABSTRACT FROM AUTHOR]