Artificial Bee Colony Optimization of Capping Potentials for Hybrid Quantum Mechanical/Molecular Mechanical Calculations

We present an algorithmic extension of a numerical optimization scheme for analytic capping potentials for use in mixed quantum−classical (quantum mechanical/molecular mechanical, QM/MM) ab initio calculations. Our goal is to minimize bond-cleavage-induced perturbations in the electronic structure, measured by means of a suitable penalty functional. The optimization algorithma variant of the artificial bee colony (ABC) algorithm, which relies on swarm intelligencecouples deterministic (downhill gradient) and stochastic elements to avoid local minimum trapping. The ABC algorithm outperforms the conventional downhill gradient approach, if the penalty hypersurface exhibits wiggles that prevent a straight minimization pathway. We characterize the optimized capping potentials by computing NMR chemical shifts. This approach will increase the accuracy of QM/MM calculations of complex biomolecules

Atomistic Diffusion Pathways of Lithium Ions in Crystalline Lithium Silicides from <i>ab Initio</i> Molecular Dynamics Simulations

The LixSiy class of compounds exhibits a broad variety of crystal structures with high experimentally observed lithium diffusivities. We explore lithium diffusion in a series of LixSiy by means of ab initio molecular dynamics simulations and find a strong variability of diffusion coefficients in the defect-free crystal structures. We explain the microscopic origin of these variations in order to characterize the mobility of lithium ions, both from a local and from a long-range perspective. Our study reveals the existence of important interstitial sites. We identify different types of diffusion pathways in our simulation trajectories and report their energy profiles. It turns out that the diffusive behavior of lithium in these compounds is governed by only a few diffusion paths. We show the connection between diffusion mechanisms and energy barriers and especially highlight the relevance of point defects. We observe considerable structural relaxation within a radius of about 3.5 Å around the diffusion path

Coexistence of Cationic and Anionic Phosphate Moieties in Solids: Unusual but Not Impossible

Phosphoric acid is commonly known either as a neutral molecule or as an anion (phosphate). We theoretically confirm by ab initio molecular dynamics simulations (AIMD) that a cationic form H4PO4+ coexists with the anionic form H2PO4– in the same salt. This paradoxical situation is achieved by partial substitution of Cs+ by H4PO4+ in CsH2PO4. Thus, HnPO4 acts simultaneously as both the positive and the negative ion of the salt. We analyze the dynamical protonation pattern within the unusual hydrogen bond network that is established between the ions. Our AIMD simulations show that a conventional assignment of protonation states of the phosphate groups is not meaningful. Instead, a better description of the protonation situation is achieved by an efficiently fractional assignment of the strongly hydrogen-bonded protons to both its nearest and next-nearest oxygen neighbors

Water Wires in Aqueous Solutions from First-Principles Calculations

We elucidate the concept of water wires in aqueous solutions in view of their structural and dynamical properties by means of first-principles molecular dynamics simulations. We employ a specific set of hydroxyquinoline derivatives (heteroaromatic fluorescent dyes) as probe molecules that provide a well-defined initial and final coordinate for possible water wires by means of their photoacid and photobase functionalities. Besides the geometric structure of the hydrogen bond network connecting these functional sites, we focus on the dependence of the length of the resulting water wire on the initial/final coordinates determined by the chromophore. Special attention is devoted to the persistence of the wires on the picosecond time scale and their capability of shifting the nature of the proton transfer process from a concerted to a stepwise mechanism. Our results shed light on the long debate on whether water wires represent characteristic structural motifs or transient phenomena

Solvation-Dependent Latency of Photoacid Dissociation and Transient IR Signatures of Protonation Dynamics

We elucidate the characteristic proton pathways and the transient infrared signatures of intermediate complexes during the first picoseconds of photoinduced protonation dynamics of a photoacid (<i>N</i>-methyl-6-hydroxyquinolinium) in aqueous solution from first-principles molecular dynamics simulations. Our results indicate that the typical latency time between photoexcitation and proton dissociation ranges from 1 ps to longer time time scales (∼100 ps). The rate-limiting step for the actual dissociation of the proton into the solvent is the solvation structure of the first accepting water molecule. The nature of the proton pathway in water (stepwise or concerted) is not unique but determined by the coordination number of the accepting water molecules along the hydrogen bond chain. We find a characteristic uncommon infrared mode at ∼1300 cm^–1 of the transient photobase-Eigen cation complex immediately after photodissociation that we predict to be observable experimentally in time-resolved IR spectroscopy. A broad continuous absorption band from 1500 to 2000 cm^–1 arises from the acidic proton imminently before dissociation

A Coupled Molecular Dynamics/Kinetic Monte Carlo Approach for Protonation Dynamics in Extended Systems

We propose a multiscale simulation scheme that combines first-principles Molecular Dynamics (MD) and kinetic Monte Carlo (kMC) simulations to describe ion transport processes. On the one hand, the molecular dynamics trajectory provides an accurate atomistic structure and its temporal evolution, and on the other hand, the Monte Carlo part models the long-time motion of the acidic protons. Our hybrid approach defines a coupling scheme between the MD and kMC simulations that allows the kMC topology to adapt continuously to the propagating atomistic microstructure of the system. On the example of a fuel cell membrane material, we validate our model by comparing its results with those of the pure MD simulation. We show that the hybrid scheme with an evolving topology results in a better description of proton diffusion than a conventional approach with a static kMC transfer rate matrix. Furthermore, we show that our approach can incorporate additional dynamical features such as the coupling of the rotation of a side group in the molecular building blocks. In the present implementation, we focus on ion conduction, but it is straightforward to generalize our approach to other transport phenomena such as electronic conduction or spin diffusion

Perfluoroalkane Force Field for Lipid Membrane Environments

In this work, we present atomic parameters of perfluoroalkanes for use within the CHARMM force field. Perfluorinated alkanes represent a special class of molecules. On the one hand, they are considerably more hydrophobic than lipids, but on the other hand, they are not lipophilic either. Instead, they represent an independent class of philicity, enabling a whole portfolio of applications within both materials science and biochemistry. We performed a thorough parametrization of all bonded and nonbonded parameters with a particular focus on van der Waals parameters. Here, the general framework of the CHARMM and CGenFF force fields has been followed. The van der Waals parameters have been fitted to experimental densities over a wide range of temperatures and pressures. This newly parametrized class of molecules will open the gate for a variety of simulations of biologically relevant systems within the CHARMM force field. A particular perspective for the present work is the influence of polyphilic transmembrane molecules on membrane properties, aggregation phenomena, and transmembrane channels

Molecular Mechanisms of Additive Fortification in Model Epoxy Resins: A Solid State NMR Study

The bulk properties of polymers are often adjusted via addition of a complex blend of compounds collectively known as additives, where so-called molecular fortifiers (or antiplasticizers) may improve the mechanical properties. In the present work, insight into molecular mechanisms of additive-fortification in model epoxy resins was obtained from multinuclear solid-state NMR analysis. In particular, we have demonstrated a “free molecule”-type behavior of DMSO-d6 in DMSO-fortified resins similar to common inclusion compounds thereby revealing mere filling of free volume. In case of DMMP-fortified resins, however, chemical modification during postcure of the epoxy resin is observed yielding methyl methylphosphonate (MMP) and salt formation, where dynamic heterogeneities of MMP-d3 suggest a rather complex mechanism of fortification. The interpretation of NMR data was further supported by ab initio calculations

Triazolium-Based Ionic Liquids: A Novel Class of Cellulose Solvents

We present first results on triazolium-based ionic liquids (ILs) as a novel class of nonderivatizing solvents for cellulose. Despite their chemical similarity to imidazolium cations, the 1,2,3-triazolium cation lacks the isolated ring proton, leading to reduced formation of N-heterocyclic carbenes (NHCs) and therefore to lower reactivity and less unwanted side reactions. We synthesized six ILs based on 1,2,3-triazolium and 1,2,4-triazolium cations. The acetates are room-temperature ionic liquids and dissolve a similar amount of cellulose as the corresponding imidazolium salt. From NMR spectroscopy of the solution, we rule out polymer degradation. The cellulose solubility rises with increasing anion basicity, while being almost independent of the cation. We perform molecular dynamics simulations and compute enthalpies of solvation, which quantitatively fit the experimental solubilities. Trajectory analysis reveals strong hydrogen bonds between acetate anions and cellulose hydroxyl groups, while the cations do not form strong hydrogen bonds with cellulose. Thus, the simulations provide an atomistic explanation of our experimental observations