Free energy calculations of small molecules in dense amorphous polymers. Effect on the initial guess configuration in molecular dynamics studies

The excess free energy of small molecules in the amorphous polymers poly(ethylene) and poly(dimethylsiloxane) was calculated, using the test-particle-insertion method. The method was applied to polymer configurations obtained from molecular dynamics simulations with differently prepared initial guess configurations. It was found that the calculated solubility coefficients strongly depend on the quality of the initial guess configuration. Slow compression of dilute systems, during which process only the repulsive parts of the nonbonded Lennard-Jones potentials are taken into account, yields polymer melts which are better relaxed, and which offer lower solubilities for guest molecules compared with polymer melts generated at the experimental density or prepared by compressing boxes with soft-core nonbonded potentials. For the last two methods initial stresses relax by straining the internal modes (bond angles, torsion angles) of the chain

Validation of the 53A6 GROMOS force field

The quality of biomolecular dynamics simulations relies critically on the force field that is used to describe the interactions between particles in the system. Force fields, which are generally parameterized using experimental data on small molecules, can only prove themselves in realistic simulations of relevant biomolecular systems. In this work, we begin the validation of the new 53A6 GROMOS parameter set by examining three test cases. Simulations of the well-studied 129 residue protein hen egg-white lysozyme, of the DNA dodecamer d(CGCGAATTCGCG)2, and a proteinogenic β3-dodecapeptide were performed and analysed. It was found that the new parameter set performs as well as the previous parameter sets in terms of protein (45A3) and DNA (45A4) stability and that it is better at describing the folding-unfolding balance of the peptide. The latter is a property that is directly associated with the free enthalpy of hydration, to which the 53A6 parameter set was parameterize

Water-Mediated Ion Pairing: Occurrence and Relevance

We present an overview of the studies of ion pairing in aqueous media of the past decade. In these studies, interactions between ions, and between ions and water, are investigated with relatively novel approaches, including dielectric relaxation spectroscopy, far-infrared (terahertz) absorption spectroscopy, femtosecond mid-infrared spectroscopy, and X-ray spectroscopy and scattering, as well as molecular dynamics simulation methods. With these methods, it is found that ion pairing is not a rare phenomenon only occurring for very particular, strongly interacting cations and anions. Instead, for many salt solutions and their interfaces, the measured and calculated structure and dynamics reveal the presence of a distinct concentration of contact ion pairs (CIPs), solvent shared ion pairs (SIPs), and solvent-separated ion pairs (2SIPs). We discuss the importance of specific ion-pairing interactions between cations like Li+ and Na+ and anionic carboxylate and phosphate groups for the structure and functioning of large (bio)molecular systems

Lack of Conventional Acinar Cells in Parotid Salivary Gland of Patient Taking an Anti-PD-L1 Immune Checkpoint Inhibitor

Background: Salivary glands (SGs) can be damaged by immune checkpoint inhibitor (ICI) therapy. In patients with ICI-induced SG dysfunction, 60% progress to fulfill classification criteria for primary Sjogren's syndrome (pSS), owing to immune foci in SGs and/or anti-SSA autoantibody positivity. We report the SG tissue analysis of a patient with SG dysfunction after treatment with a programmed death ligand-1 (PD-L1) inhibitor, compared to that of a dry mouth ("sicca") control and pSS patient. Case presentation: The patient received the PD-L1 inhibitor durvalumab (10 mg/kg, every 2 weeks by intravenous infusion) as adjuvant treatment for stage 3 non-small cell lung carcinoma, following concurrent chemo radiotherapy. At 43 weeks after 21 cycles of Durvalumab, the patient was not capable of producing unstimulated or stimulated parotid gland saliva, and a biopsy was taken. Immunohistochemical analysis showed no classical AQP5(+) CK7(-) acinar cell clusters (CK7 marks intercalated ducts, IDs). In contrast, the parenchyma was dominated by hybrid epithelial "structures" with ID-like morphology, containing a mixture of AQP5(+)CK7(-), AQP5(-)CK7(+), and AQP5(+)CK7(+) cells (30 structures/mm(2)). These structures were present at lower frequencies in sicca control (2/mm(2)) and pSS (10/mm(2)) tissue. Hybrid structures contained proliferating (Ki67(+)) cells and senescent (p16(+)) cells. Striated ducts showed no abnormal morphology post PD-L1 treatment, in contrast to pSS tissue. PD-L1 expression was detected in the SG parenchyma following anti-PD-L1 therapy. The SG post-PD-L1 therapy further demonstrated focal lymphocytic sialadentitis, harboring disperse, and focal CD4(+) T cell-rich infiltrates. CD8(+) T cells were also present. In this patient, these CD4(+) and CD8(+) T cells were observed in-between and inside hybrid structures. CD20(+) B-cells were infrequently detected following PD-L1 blockade, in contrast to their preponderance in pSS SG tissue. Conclusion: This patient lacked conventional SG acinar cells following anti-PD-L1 therapy and demonstrated presence of hybrid intercalated duct-like structures. Understanding which mechanisms and dynamics underpinning this aberrant parenchyma may be crucial to understand how SG dysfunction post ICI therapy, and potentially other affected organs. Furthermore, although the patient treated with anti-PD-L1 antibody examined here fulfills the criteria for pSS and demonstrated focal lymphocytic sialadentitis, the further histopathological characteristics do not resemble pSS

Modelling molecule-surface interactions-an automated quantum-classical approach using a genetic algorithm

We present an automated and efficient method to develop force fields for molecule-surface interactions. A genetic algorithm (GA) is used to parameterise a classical force field so that the classical adsorption energy landscape of a molecule on a surface matches the corresponding landscape from density functional theory (DFT) calculations. The procedure performs a sophisticated search in the parameter phase space and converges very quickly. The method is capable of fitting a significant number of structures and corresponding adsorption energies. Water on a ZnO(0001) surface was chosen as a benchmark system but the method is implemented in a flexible way and can be applied to any system of interest. In the present case, pairwise Lennard Jones (LJ) and Coulomb potentials are used to describe the molecule-surface interactions. In the course of the fitting procedure, the LJ parameters are refined in order to reproduce the adsorption energy landscape. The classical model is capable of describing a wide range of energies, which is essential for a realistic description of a fluid-solid interface

Data of the publication: Bottom-up Informed and Iteratively Optimized Coarse-Grained Non-Markovian Water Models With Accurate Dynamics.

Atomistic and coarse-grained models, memory kernels, structural and dynamic properties. Jupyter notebook files for reproducing the figures in the publication.V1.

Addressing the temperature transferability of structure based coarse graining models

We present a novel idea to improve the temperature transferability of structure based coarse graining models.</p