Both Zundel and Eigen Isomers Contribute to the IR Spectrum of the Gas-Phase H₉O₄ ⁺ Cluster

The “Eigen cation”, H₃O⁺(H₂O)₃, is the most prevalent protonated water structure in the liquid phase and the most stable gas-phase isomer of the H⁺(H₂O)₄ cluster. Nevertheless, its 50 K argon predissociation vibrational spectrum contains unexplainable low frequency peak(s). We have simulated the IR spectra of 10 gas-phase H⁺(H₂O)₄ isomers, that include zero to three argon ligands, using dipole autocorrelation functions from ab initio molecular dynamics with the CP2K software. We have also tested the effect of elevated temperature and dispersion correction. The Eigen isomers describe well the high frequency portion of the spectrum but do not agree with experiment below 2000 cm^–1. Most notably, they completely lack the “proton transfer bands” observed at 1050 and 1750 cm^–1, which characterize Zundel-type (H₅O₂ ⁺) isomers. In contrast, linear isomers with a Zundel core, although not the lowest in energy, show very good agreement with experiment, particularly at low frequencies. Peak assignments made with partial velocity autocorrelation functions verify that the 1750 cm^–1 band does not originate with the Eigen isomer but is rather due to coupled proton transfer/water bend in the Zundel isomer

Both Zundel and Eigen Isomers Contribute to the IR Spectrum of the Gas-Phase H₉O₄ ⁺ Cluster

The “Eigen cation”, H₃O⁺(H₂O)₃, is the most prevalent protonated water structure in the liquid phase and the most stable gas-phase isomer of the H⁺(H₂O)₄ cluster. Nevertheless, its 50 K argon predissociation vibrational spectrum contains unexplainable low frequency peak(s). We have simulated the IR spectra of 10 gas-phase H⁺(H₂O)₄ isomers, that include zero to three argon ligands, using dipole autocorrelation functions from ab initio molecular dynamics with the CP2K software. We have also tested the effect of elevated temperature and dispersion correction. The Eigen isomers describe well the high frequency portion of the spectrum but do not agree with experiment below 2000 cm^–1. Most notably, they completely lack the “proton transfer bands” observed at 1050 and 1750 cm^–1, which characterize Zundel-type (H₅O₂ ⁺) isomers. In contrast, linear isomers with a Zundel core, although not the lowest in energy, show very good agreement with experiment, particularly at low frequencies. Peak assignments made with partial velocity autocorrelation functions verify that the 1750 cm^–1 band does not originate with the Eigen isomer but is rather due to coupled proton transfer/water bend in the Zundel isomer

Molecular Dynamics Insights into Water–Parylene C Interface: Relevance of Oxygen Plasma Treatment for Biocompatibility

Solid–water interfaces play a vital role in biomaterials science because they provide a natural playground for most biochemical reactions and physiological processes. In the study, fully atomistic molecular dynamics simulations were performed to investigate interactions between water molecules and several surfaces modeling for unmodified and modified parylene C surfaces. The introduction of −OH, −CHO, and −COOH to the surface and alterations in their coverage significantly influence the energetics of interactions between water molecules and the polymer surface. The theoretical studies were complemented with experimental measurements of contact angle, surface free energy, and imaging of osteoblast cells adhesion. Both MD simulations and experiments demonstrate that the optimal interface, in terms of biocompatibility, is obtained when 60% of native −Cl groups of parylene C surface is exchanged for −OH groups. By exploring idealized models of bare and functionalized parylene C, we obtained a unique insight into molecular interactions at the water–polymer interface. The calculated values of interaction energy components (electrostatic and dispersive) correspond well with the experimentally determined values of surface free energy components (polar and dispersive), revealing their optimal ratio for cells adhesion. The results are discussed in the context of controllable tuning and functionalization of implant polymeric coating toward improved biocompatibility

How To Minimize Artifacts in Atomistic Simulations of Membrane Proteins, Whose Crystal Structure Is Heavily Engineered: β₂‑Adrenergic Receptor in the Spotlight

Atomistic molecular dynamics (MD) simulations are used extensively to elucidate membrane protein properties. These simulations are based on three-dimensional protein structures that in turn are often based on crystallography. The protein structures resolved in crystallographic studies typically do not correspond to pristine proteins, however. Instead the crystallized proteins are commonly engineered, including structural modifications (mutations, replacement of protein sequences by antibodies, bound ligands, etc.) whose impact on protein structure and dynamics is largely unknown. Here we explore this issue through atomistic MD simulations (∼5 μs in total), focusing on the β₂-adrenergic receptor (β₂AR) that is one of the most studied members of the G-protein coupled receptor superfamily. Starting from an inactive-state crystal structure of β₂AR, we remove the many modifications in β₂AR systematically one at a time, in six consecutive steps. After each step, we equilibrate the system and simulate it quite extensively. The results of this step-by-step approach highlight that the structural modifications used in crystallization can affect ligand and G-protein binding sites, packing at the transmembrane-helix interface region, and the dynamics of connecting loops in β₂AR. When the results of the systematic step-by-step approach are compared to an all-at-once technique where all modifications done on β₂AR are removed instantaneously at the same time, it turns out that the step-by-step method provides results that are superior in terms of maintaining protein structural stability. The results provide compelling evidence that for membrane proteins whose 3D structure is based on structural engineering, the preparation of protein structure for atomistic MD simulations is a delicate and sensitive process. The results show that most valid results are found when the structural modifications are reverted slowly, one at a time

nmrlipids.blogspot.fi — on October 25th 2015

<p>Snapshot of the blog nmrlipids.blogspot.fi on October 25th 2015.</p> <p> </p> <p>The NMRlipids project is an open scientific collaboration to understand the atomistic resolution structures of lipid bilayers through classical molecular dynamics simulations. The project is progressed through the comments in the blog and using the GitHub organization (see links). The main results are also published in traditional peer reviewed scientific journals.</p