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We demonstrate that thermodynamic knowledge acquired by humans can be transferred to computers so that the machine can use it to solve thermodynamic problems and produce explainable solutions with a guarantee of correctness. The actionable knowledge representation system that we have created for this purpose is called KnowTD. It is based on an ontology of thermodynamics that represents knowledge of thermodynamic theory, material properties, and thermodynamic problems. The ontology is coupled with a reasoner that sets up the problem to be solved based on user input, extracts the correct, pertinent equations from the ontology, solves the resulting mathematical problem, and returns the solution to the user, together with an explanation of how it was obtained. KnowTD is presently limited to simple thermodynamic problems, similar to those discussed in an introductory course in Engineering Thermodynamics. This covers the basic theory and working principles of thermodynamics. KnowTD is designed in a modular way and is easily extendable.

Many widely used molecular models of water are built from a single Lennard-Jones site on which three point charges are positioned, one negative and two positive ones. Models from that class, denoted LJ3PC here, are computationally efficient, but it is well known that they cannot represent all relevant properties of water simultaneously with good accuracy. Despite the importance of the LJ3PC water model class, its inherent limitations in simultaneously describing different properties of water have never been studied systematically. This task can only be solved by multicriteria optimization (MCO). However, due to its computational cost, applying MCO to molecular models is a formidable task. We have recently introduced the reduced units method (RUM) to cope with this problem. In the present work, we apply the RUM in a hierarchical scheme to optimize LJ3PC water models taking into account five objectives: the representation of vapor pressure, saturated liquid density, self-diffusion coefficient, shear viscosity, and relative permittivity. Of the six parameters of the LJ3PC models, five were varied; only the H-O-H bond angle, which is usually chosen based on physical arguments, was kept constant. Our hierarchical RUM-based approach yields a Pareto set that contains attractive new water models. Furthermore, the results give an idea of what can be achieved by molecular modeling of water with models from the LJ3PC class.

The inherent extracellular matrix (ECM) originating from a specific tissue impacts the process of vascularization, specifically vascular network formation (VNF) orchestrated by endothelial cells (ECs). The specific contribution toward these processes of ECM from highly disparate organs such as the skin and lungs remains a relatively unexplored area. In this study, we compared VNF and ECM remodeling mediated by microvascular ECs within gel, lung, and combinations thereof (hybrid) ECM hydrogels. Irrespective of the EC source, the skin-derived ECM hydrogel exhibited a higher propensity to drive and support VNF compared to both lung and hybrid ECM hydrogels. There were distinct disparities in the physical properties of the three types of hydrogels, including viscoelastic properties and complex architectural configurations, including fiber diameter, pore area, and numbers among the fibers. The hybrid ECM hydrogel properties were unique and not the sum of the component ECM parts. Furthermore, cellular ECM remodeling responses varied with skin ECM hydrogels promoting matrix metalloproteinase 1 (MMP1) secretion, while hybrid ECM hydrogels exhibited increased MMP9, fibronectin, and collagen IV deposition. Principal component analysis (PCA) indicated that the influence of a gel's mechanical properties on VNF was stronger than the biochemical composition. These data indicate that the organ-specific properties of an ECM dictate its capacity to support VNF, while intriguingly showing that ECs respond to more than just the biochemical constituents of an ECM. The study suggests potential applications in regenerative medicine by strategically selecting ECM origin or combinations to manipulate vascularization, offering promising prospects for enhancing wound healing through pro-regenerative interventions.

MolMod , a web-based database for classical force fields for molecular simulations of fluids [ Mol. Sim. 45 , 10 ( 2019 ), 806-814], was extended to transferable force fields. Eight transferable force fields, including all-atom and united-atom type force fields, were implemented in the MolMod database: OPLS-UA, OPLS-AA, COMPASS, CHARMM, GROMOS, TraPPE, Potoff, and TAMie. These transferable force fields cover a large variety of chemical substance classes. The system is designed such that new transferable force fields can be readily integrated. A graphical user interface was implemented that enables the construction of molecules. The MolMod database compiles the force field for the specified component and force field type and provides the corresponding data and meta data as well as ready-to-use input files for the molecule for different simulation engines. This helps the user to flexibly choose molecular models and integrate them swiftly in their individual workflows, reducing risks of input errors in molecular simulations.

Molecular dynamics (MD) simulations are highly attractive for studying the influence of interfacial effects, such as the enrichment of components, on the mass transfer through the interface. In a recent work, we have presented a steady-state MD simulation method for investigating this phenomenon and tested it using model mixtures with and without interfacial enrichment. The present study extends this work by introducing a non-stationary MD simulation method. A rectangular simulation box that contains a mixture of two components 1 + 2 with a vapor phase in the middle and two liquid phases on both sides is used. Starting from a vapor-liquid equilibrium state, a non-stationary molar flux of component 2 is induced by inserting particles of component 2 into the center of the vapor phase in a pulse-like manner. During the isothermal relaxation process, particles of component 2 pass through the vapor phase, cross the vapor-liquid interface, and enter the liquid phase. The system thereby relaxes into a new vapor-liquid equilibrium state. During the relaxation process, spatially resolved responses for the component densities, fluxes, and pressure are sampled. To reduce the noise and provide measures for the uncertainty of the observables, a set of replicas of simulations is carried out. The new simulation method was applied to study mass transfer in two binary Lennard-Jones mixtures: one that exhibits a strong enrichment of the low-boiling component 2 at the vapor-liquid interface and one that shows no enrichment. Even though both mixtures have similar transport coefficients in the bulk phases, the results for mass transfer differ significantly, indicating that the interfacial enrichment influences the mass transfer.

The prediction of thermophysical properties at extreme conditions is an important application of molecular simulations. The quality of these predictions primarily depends on the quality of the employed force field. In this work, a systematic comparison of classical transferable force fields for the prediction of different thermophysical properties of alkanes at extreme conditions, as they are encountered in tribological applications, was carried out using molecular dynamics simulations. Nine transferable force fields from three different classes were considered (all-atom, united-atom, and coarse-grained force fields). Three linear alkanes ( n -decane, n -icosane, and n -triacontane) and two branched alkanes (1-decene trimer and squalane) were studied. Simulations were carried out in a pressure range between 0.1 and 400 MPa at 373.15 K. For each state point, density, viscosity, and self-diffusion coefficient were sampled, and the results were compared to experimental data. The Potoff force field yielded the best results.

Compatibility between the rubber material of radial shaft seals and the lubricants to be sealed is an important requirement that customers demand of their lubricant suppliers. Among other effects that may result from incompatibility, the penetration of lubricant components into the rubber (swelling) can impair the seal's functionality due to changes in its geometry and mechanical behavior. Typically, the penetration of a lubricant into an elastomer is evaluated after an immersion test using volumetric, gravimetric, and extraction measurements. Due to the small changes that need to be detected, such methods may not be sufficient to obtain meaningful results. In this contribution, we use magnetic resonance imaging (MRI) to investigate swelling on special tribometer samples as well as a radial shaft seal that were previously used in component tests. Several combinations of rubbers and lubricants that have proven to be compatible were tested in addition to combinations with expected incompatibilities in real applications. The results indicate that MRI measurements can be used to quantify the penetration depth and potentially also the velocity with which the lubricant diffuses into the rubber, thereby yielding detailed insights into the swelling process of the seal., Competing Interests: The authors declare no competing financial interest., (© 2022 The Authors. Published by American Chemical Society.)

Analysis of a fast-flowing liquid with NMR spectroscopy is challenging because short residence times in the magnetic field of the spectrometer result in inefficient polarization buildup and thus poor signal intensity. This is particularly problematic for benchtop NMR spectrometers because of their compact design. Therefore, in the present work, different methods to counteract this prepolarization problem in benchtop NMR spectroscopy were studied experimentally. The tests were carried out with an equimolar acetonitrile + water mixture flowing through a capillary with a 0.25 mm inner diameter at flow rates up to 2.00 mL min -1 , corresponding to mean velocities of up to 0.7 m s -1 . Established approaches gave only poor results at high flow rates, namely, using a prepolarization magnet, using a loopy flow cell, and using a T 1 relaxation agent. To overcome this, signal enhancement by Overhauser dynamic nuclear polarization (ODNP) was used, which is based on polarization transfer from unpaired electron spins to nuclear spins and happens on very short time scales, resulting in high signal enhancements, also in fast-flowing liquids. A corresponding setup was developed and used for the studies: the line leading to the 1 T benchtop NMR spectrometer first passes through a fixed bed with a radical matrix placed in a Halbach magnet equipped with a microwave cavity to facilitate the spin transfer. With this ODNP setup, excellent results were obtained even for the highest studied flow rates. This shows that ODNP is an enabler for fast-flow benchtop NMR spectroscopy.

The wetting of surfaces is strongly influenced by adsorbate layers. Therefore, in this work, sessile drops and their interaction with adsorbate layers on surfaces were investigated by molecular dynamics simulations. Binary fluid model mixtures were considered. The two components of the fluid mixture have the same pure component parameters, but one component has a stronger and the other a weaker affinity to the surface. Furthermore, the unlike interactions between both components were varied. All interactions were described by the Lennard-Jones truncated and shifted potential with a cutoff radius of 2.5σ. The simulations were carried out at constant temperature for mixtures of different compositions. The parameters were varied systematically and chosen such that cases with partial wetting as well as cases with total wetting were obtained and the relation between the varied molecular parameters and the phenomenological behavior was elucidated. Data on the contact angle as well as on the mole fraction and thickness of the adsorbate layer were obtained, accompanied by information on liquid and gaseous bulk phases and the corresponding phase equilibrium. Also, the influence of the adsorbate layer on the wetting was studied: for a sufficiently thick adsorbate layer, the wall's influence on the wetting vanishes, which is then only determined by the adsorbate layer.

Nuclear magnetic resonance (NMR) spectroscopy is a powerful tool for elucidating the structure of unknown components and the composition of liquid mixtures. However, these tasks are often tedious and challenging, especially if complex samples are considered. In this work, we introduce automated methods for the identification and quantification of structural groups in pure components and mixtures from NMR spectra using support vector classification. As input, a 1 H NMR spectrum and a 13 C NMR spectrum of the liquid sample (pure component or mixture) that is to be analyzed is needed. The first method, called group-identification method, yields qualitative information on the structural groups in the sample. The second method, called group-assignment method, provides the basis for a quantitative analysis of the sample by identifying the structural groups and assigning them to signals in the 13 C NMR spectrum of the sample; quantitative information can then be obtained with readily available tools by simple integration. We demonstrate that both methods, after being trained to NMR spectra of nearly 1000 pure components, yield excellent predictions for pure components that were not part of the training set as well as mixtures. The structural group-specific information obtained with the presented methods can, e.g., be used in combination with thermodynamic group-contribution methods to predict fluid properties of unknown samples.

Multicriteria optimization (MCO) is used to parametrize molecular models of water. The set of the best possible compromises between different objectives, the Pareto set, is determined. Calculating Pareto sets for optimization problems involving molecular simulations is computationally expensive. Therefore, we use a novel, highly efficient method, which is based on the fact that numerical results from molecular simulations can be interpreted as dimensionless numbers. Hence, they carry information on an entire class of models in physical units. This approach was applied here for the MCO of water models of the "one-center Lennard-Jones + point charge" type, in which the objectives were the quality of the description of the vapor pressure, liquid density, and enthalpy of vaporization. The results were compared to models from the literature. Significant improvements were observed. The new optimization method for the development of molecular models is efficient, robust, and broadly applicable.

A united atom force field for the homologous series of the poly(oxymethylene) dimethyl ethers (OME n ), H 3 C-O-(CH 2 O) n -CH 3 , is presented. OME n are oxygenates and promising new synthetic fuels and solvents. The molecular geometry of the OME n , the internal degrees of freedom, and their electrostatic properties were obtained from quantum mechanical calculations. To model repulsion and dispersion, Lennard-Jones parameters were fitted to the experimental liquid densities and vapor pressures of pure OME n ( n = 1-4). The critical properties of OME n ( n = 1-4) were determined from the simulation data. Additionally, the shear viscosity of pure liquid OME n is evaluated and compared with literature data. Finally, the solubility of CO 2 in OME2, OME3, and OME4 is predicted using a literature model for CO 2 and the Lorentz-Berthelot combining rules. The results agree well with experimental data from the literature.

Activity coefficients, which are a measure of the nonideality of liquid mixtures, are a key property in chemical engineering with relevance to modeling chemical and phase equilibria as well as transport processes. Although experimental data on thousands of binary mixtures are available, prediction methods are needed to calculate the activity coefficients in many relevant mixtures that have not been explored to date. In this report, we propose a probabilistic matrix factorization model for predicting the activity coefficients in arbitrary binary mixtures. Although no physical descriptors for the considered components were used, our method outperforms the state-of-the-art method that has been refined over three decades while requiring much less training effort. This opens perspectives to novel methods for predicting physicochemical properties of binary mixtures with the potential to revolutionize modeling and simulation in chemical engineering.

Liquid lubricants play an important role in contact processes; for example, they reduce friction and cool the contact zone. To gain better understanding of the influence of lubrication on the nanoscale, both dry and lubricated scratching processes in a model system are compared in the present work using molecular dynamics simulations. The entire range between total dewetting and total wetting is investigated by tuning the solid-fluid interaction energy. The investigated scratching process consists of three sequential movements: A cylindrical indenter penetrates an initially flat substrate, then scratches in the lateral direction, and is finally retracted out of the contact with the substrate. The indenter is fully submersed in the fluid in the lubricated cases. The substrate, the indenter, and the fluid are described by suitably parametrized Lennard-Jones model potentials. The presence of the lubricant is found to have a significant influence on the friction and on the energy balance of the process. The thermodynamic properties of the lubricant are evaluated in detail. A correlation of the simulation results for the profiles of the temperature, density, and pressure of the fluid in the vicinity of the chip is developed. The work done by the indenter is found to mainly dissipate and thereby heat up the substrate and eventually the fluid. Only a minor part of the work causes plastic deformation of the substrate.

Literature data on the thermophysical properties of the Lennard-Jones fluid, which were sampled with molecular dynamics and Monte Carlo simulations, were reviewed and assessed. The literature data were complemented by simulation data from the present work that were taken in regions in which previously only sparse data were available. Data on homogeneous state points (for given temperature T and density ρ: pressure p , thermal expansion coefficient α, isothermal compressibility β, thermal pressure coefficient γ, internal energy u , isochoric heat capacity c v , isobaric heat capacity c p , Grüneisen parameter Γ, Joule-Thomson coefficient μ JT , speed of sound w , Helmholtz energy a , and chemical potential) were considered, as well as data on the vapor-liquid equilibrium (for given T : vapor pressure p s , saturated liquid and vapor densities ρ' and ρ″, respectively, enthalpy of vaporization Δ h v , and as well as surface tension γ). The entire set of available data, which contains about 35 000 data points, was digitalized and included in a database, which is made available in the Supporting Information of this paper. Different consistency tests were applied to assess the accuracy and precision of the data. The data on homogeneous states were evaluated pointwise using data from their respective vicinity and equations of state. Approximately 10% of all homogeneous bulk data were discarded as outliers. The vapor-liquid equilibrium data were assessed by tests based on the compressibility factor, the Clausius-Clapeyron equation, and by an outlier test. Seven particularly reliable vapor-liquid equilibrium data sets were identified. The mutual agreement of these data sets is approximately ±1% for the vapor pressure, ±0.2% for the saturated liquid density, ±1% for the saturated vapor density, and ±0.75% for the enthalpy of vaporization-excluding the region close to the critical point.

Thermodynamic properties are often modeled by classical force fields which describe the interactions on the atomistic scale. Molecular simulations are used for retrieving thermodynamic data from such models, and many simulation techniques and computer codes are available for that purpose. In the present round robin study, the following fundamental question is addressed: Will different user groups working with different simulation codes obtain coinciding results within the statistical uncertainty of their data? A set of 24 simple simulation tasks is defined and solved by five user groups working with eight molecular simulation codes: DL_POLY, GROMACS, IMC, LAMMPS, ms2, NAMD, Tinker, and TOWHEE. Each task consists of the definition of (1) a pure fluid that is described by a force field and (2) the conditions under which that property is to be determined. The fluids are four simple alkanes: ethane, propane, n-butane, and iso-butane. All force fields consider internal degrees of freedom: OPLS, TraPPE, and a modified OPLS version with bond stretching vibrations. Density and potential energy are determined as a function of temperature and pressure on a grid which is specified such that all states are liquid. The user groups worked independently and reported their results to a central instance. The full set of results was disclosed to all user groups only at the end of the study. During the study, the central instance gave only qualitative feedback. The results reveal the challenges of carrying out molecular simulations. Several iterations were needed to eliminate gross errors. For most simulation tasks, the remaining deviations between the results of the different groups are acceptable from a practical standpoint, but they are often outside of the statistical errors of the individual simulation data. However, there are also cases where the deviations are unacceptable. This study highlights similarities between computer experiments and laboratory experiments, which are both subject not only to statistical error but also to systematic error.

Self-assembled monolayers (SAM) of dodecyltrichlorosilane (DTS) and octadecyltrichlorosilane (OTS) on silica are studied by molecular dynamics simulations at 298 K and 1 bar. The coverage (number of alkylsilane molecules per surface area) is systematically varied. The results yield insight into the properties of the alkylsilane SAMs, which complement experimental studies from the literature. Relationships are reported between thickness, tilt angle, and coverage of alkylsilane SAMs, which also hold for alkylsilanes other than DTS and OTS. They are interpreted based on the information on molecular ordering in the SAMs taken form the simulation data. System size and simulation time are much larger than in most former simulation works on the topic. This reduces the influence of the initial configuration as well as the periodic boundary conditions and hence minimizes the risk of artificial ordering. At the same time, more reliable statistics for the calculated properties can be provided. The evaluation of experimental data in the field is often based on strongly simplified models. The present simulation results suggest that some of these lead to errors, concerning the interpretation of experimental results, which could be avoided by introducing more realistic models.

Molecular dynamics simulations are used for studying the contact angle of nanoscale sessile drops on a planar solid wall in a system interacting via the truncated and shifted Lennard-Jones potential. The entire range between total wetting and dewetting is investigated by varying the solid-fluid dispersive interaction energy. The temperature is varied between the triple point and the critical temperature. A correlation is obtained for the contact angle in dependence of the temperature and the dispersive interaction energy. Size effects are studied by varying the number of fluid particles at otherwise constant conditions, using up to 150,000 particles. For particle numbers below 10,000, a decrease of the contact angle is found. This is attributed to a dependence of the solid-liquid surface tension on the droplet size. A convergence to a constant contact angle is observed for larger system sizes. The influence of the wall model is studied by varying the density of the wall. The effective solid-fluid dispersive interaction energy at a contact angle of θ = 90° is found to be independent of temperature and to decrease linearly with the solid density. A correlation is developed that describes the contact angle as a function of the dispersive interaction, the temperature, and the solid density. The density profile of the sessile drop and the surrounding vapor phase is described by a correlation combining a sigmoidal function and an oscillation term.

The molecular dynamics simulation code ls1 mardyn is presented. It is a highly scalable code, optimized for massively parallel execution on supercomputing architectures and currently holds the world record for the largest molecular simulation with over four trillion particles. It enables the application of pair potentials to length and time scales that were previously out of scope for molecular dynamics simulation. With an efficient dynamic load balancing scheme, it delivers high scalability even for challenging heterogeneous configurations. Presently, multicenter rigid potential models based on Lennard-Jones sites, point charges, and higher-order polarities are supported. Due to its modular design, ls1 mardyn can be extended to new physical models, methods, and algorithms, allowing future users to tailor it to suit their respective needs. Possible applications include scenarios with complex geometries, such as fluids at interfaces, as well as nonequilibrium molecular dynamics simulation of heat and mass transfer.

Adsorption of native as well as mono-, di-, and tri-PEGylated lysozyme on Toyopearl PPG-600M, a mildly hydrophobic resin is studied by isothermal titration calorimetry and by independent adsorption equilibrium measurements in sodium phosphate buffer at pH 7.0 and 25 °C. For PEGylation two different PEG sizes are used (5 and 10 kDa) which leads to six different forms of PEGylated lysozyme all of which are systematically studied. Additionally, the adsorption of five pure PEGs is explored. The ammonium sulfate concentration is varied from 600 to 1200 mM. The molar enthalpy of adsorption Δh(p)(ads) is determined from the calorimetric and the adsorption equilibrium data. It is found to be endothermic in all experiments. The comparison of the adsorption of different PEGylated forms shows that the adsorption of PEGylated lysozyme is driven by the adsorption of the PEG chain. The results provide insight into the adsorption mechanisms of polymer-modified proteins on hydrophobic chromatographic resins.

New Lennard-Jones plus point charge models are developed for alkaline-earth cations. The cation parameters are adjusted to the reduced liquid solution density of aqueous alkaline-earth halide salt solutions at a temperature of 293.15 K and a pressure of 1 bar. This strategy is analogous to the one that was recently used for developing models for alkali and halide ions so that both model families are compatible. The force fields yield the reduced liquid solution density of aqueous alkaline-earth halide solutions in good agreement with experimental data over a wide range of salinity. Structural microscopic properties (i.e. radial distribution function and hydration number) are predicted in good agreement with experimental and quantum chemical data. The same holds for dynamic properties (i.e., hydration dynamics, self-diffusion coefficient and electric conductivity). Finally, the enthalpy of hydration of the salts in aqueous solution was favorably assessed.

The conformation transition of poly(N-isopropylacrylamide) hydrogel as a function of the methanol mole fraction in water/methanol mixtures is studied both experimentally and by atomistic molecular dynamics simulation with explicit solvents. The composition range in which the conformation transition of the hydrogel occurs is determined experimentally at 268.15, 298.15, and 313.15 K. In these experiments, cononsolvency, i.e., collapse at intermediate methanol concentrations while the hydrogel is swollen in both pure solvents, is observed at 268.15 and 298.15 K. The composition range in which cononsolvency is present does not significantly depend on the amount of cross-linker. The conformation transition of the hydrogel is caused by the conformation transition of the polymer chains of its backbone. Therefore, conformation changes of single backbone polymer chains are studied by massively parallel molecular dynamics simulations. The hydrogel backbone polymer is described with the force field OPLS-AA, water with the SPC/E model, and methanol with the model of the GROMOS-96 force field. During simulation, the mean radius of gyration of the polymer chains is monitored. The conformation of the polymer chains is studied at 268, 298, and 330 K as a function of the methanol mole fraction. Cononsolvency is observed at 268 and 298 K, which is in agreement with the present experiments. The structure of the solvent around the hydrogel backbone polymer is analyzed using H-bond statistics and visualization. It is found that cononsolvency is caused by the fact that the methanol molecules strongly attach to the hydrogel's backbone polymer, mainly with their hydroxyl group. This leads to the effect that the hydrophobic methyl groups of methanol are oriented toward the bulk solvent. The hydrogel+solvent shell hence appears hydrophobic and collapses in water-rich solvents. As more methanol is present in the solvent, the effect disappears again.

Menisci of the truncated and shifted Lennard-Jones fluid between parallel planar walls are investigated by molecular dynamics simulation. Thereby, the characteristic energy of the unlike dispersive interaction between fluid molecules and wall atoms is systematically varied to determine its influence on the contact angle. The temperature is varied as well, covering most of the range between the triple-point temperature and the critical temperature of the bulk fluid. The transition between obtuse and acute angles is found to occur at a temperature-independent magnitude of the fluid-wall dispersive interaction energy. On the basis of the present simulation results, fluid-wall interaction potentials can be adjusted to contact angle measurements.

Negative ion mode nanoliquid chromatography/mass spectrometry (nano-LC/MS) on porous graphitic carbon columns at pH 11 was studied and compared to capillary LC/MS at pH 8 for the analysis of neutral and acidic glycan alditols. Oligosaccharides were chromatographed with an acetonitrile gradient containing 0.04% ammonium hydroxide and analyzed with a linear ion trap mass spectrometer (LTQ) equipped with a modified nanospray interface. Analysis of acidic N- and O-glycan standards revealed that good quality MS/MS spectra could be obtained when loading 1-3 fmol, a 10-fold increase in sensitivity compared to capillary-LC/MS at pH 8. Analysis of a complex mixture of O-glycans from porcine colonic mucins with nano-LC/MS and MS/MS at high pH revealed 170 oligosaccharides in one analysis, predominantly corresponding to sulfated glycans with up to 11 residues. Analysis of the same sample with capillary-LC/MS showed a lower sensitivity for multiply sulfated glycans. Nano-LC/MS of O-linked oligosaccharides on MUC2 from a human colon biopsy also illustrated that the ionization of oligosaccharides with multiple sialic acid groups was increased compared to those with only one sialic acid residue. Nano-LC/MS at high pH is, thus, a highly sensitive approach for the analysis of acidic oligosaccharides.

We have analyzed the structures of the glycans on immunoprecipitated proteins from small amounts of cell or tissue lysates, by liquid-chromatography electrospray mass spectrometry (LC-ESI-MS) and MS/MS. The sensitive and specific method was applied to the analysis of the O-glycosylation of MUC1 in breast, prostate and gastric cancer, including analysis of a patient tumor specimen. The method will be applicable for the glycosylation analysis of individual proteins.

Transport properties of liquid methanol and ethanol are predicted by molecular dynamics simulation. The molecular models for the alcohols are rigid, nonpolarizable, and of united-atom type. They were developed in preceding work using experimental vapor-liquid equilibrium data only. Self- and Maxwell-Stefan diffusion coefficients as well as the shear viscosity of methanol, ethanol, and their binary mixture are determined using equilibrium molecular dynamics and the Green-Kubo formalism. Nonequilibrium molecular dynamics is used for predicting the thermal conductivity of the two pure substances. The transport properties of the fluids are calculated over a wide temperature range at ambient pressure and compared with experimental and simulation data from the literature. Overall, a very good agreement with the experiment is found. For instance, the self-diffusion coefficient and the shear viscosity are predicted with average deviations of less than 8% for the pure alcohols and 12% for the mixture. The predicted thermal conductivity agrees on average within 5% with the experimental data. Additionally, some velocity and shear viscosity autocorrelation functions are presented and discussed. Radial distribution functions for ethanol are also presented. The predicted excess volume, excess enthalpy, and the vapor-liquid equilibrium of the binary mixture methanol + ethanol are assessed and agree well with experimental data.

A parametrization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic data. The geometry of the molecular models is specified according to the atom positions determined by QM energy minimization. The electrostatic interactions are modeled by reducing the electron density distribution to point dipoles and point quadrupoles located in the center of mass of the molecules. Dispersive and repulsive interactions are described by Lennard-Jones sites, for which the parameters are iteratively optimized to experimental vapor-liquid equilibrium (VLE) data, i.e., vapor pressure, saturated liquid density, and enthalpy of vaporization of the considered substance. The proposed modeling strategy was applied to a sample set of ten molecules from different substance classes. New molecular models are presented for iso-butane, cyclohexane, formaldehyde, dimethyl ether, sulfur dioxide, dimethyl sulfide, thiophene, hydrogen cyanide, acetonitrile, and nitromethane. Most of the models are able to describe the experimental VLE data with deviations of a few percent.

Molecular dynamics simulation results on hydrogen bonding in mixtures of methanol with CO2 at supercritical, liquid-like conditions are compared to 1H NMR spectroscopic data that have recently become available. The molecular models are parametrized using vapor-liquid equilibrium data only, which they reliably describe. A new molecular model for methanol of Lennard-Jones plus point charge type is presented. This molecular methanol model is investigated in terms of its capability to yield hydrogen-bonding statistics. Simple assumptions are made regarding the assignment of NMR chemical shifts to the different types of hydrogen-bonded species. Only two state-independent parameters are fitted to the large NMR data set on the basis of hydrogen-bonding statistics from molecular simulations. Excellent agreement between the molecular simulation results and the NMR data is found. This shows that the molecular models of the simple type studied here cannot only describe thermodynamic properties but also structural effects of hydrogen bonding in solutions.

Because of the important role of membrane proteins in adhesion, invasion, and intracellular survival of pathogens in the host, membrane proteins are of potential interest in the search for drug targets or biomarkers. We have established a mass spectrometry-based method that allows characterization of the outer membrane protein (OMP) profile of clinical isolates from of the human gastric pathogen Helicobacter pylori. Subcellular fractionation and one-dimensional gel electrophoresis (1D-GE) analysis was combined with nano-liquid chromatography Fourier transform-ion cyclotron resonance mass spectrometry (nano-LC FT-ICR MS) and tandem mass spectrometry (MS/MS) analysis of fifteen H. pylori strains associated either with duodenal ulcers, gastric cancer, or isolated from asymptomatic H. pylori infected carriers. Over 60 unique membrane or membrane-associated proteins, including 30 of the 33 theoretically predicted OMPs, were identified from the strains. Several membrane proteins, including Omp11 and BabA, were found to be expressed by all strains. In the search for clinical markers we found that Omp26 was expressed by all disease-related strains but was only present in one out of five strains from asymptomatic carriers, which makes Omp26 a potential target for further investigation in the search for proteins unique to disease-related H. pylori strains. In addition, presence of Omp30 and absence of Omp6 seemed to be associated with H. pylori strains causing duodenal ulcer.

This paper describes how the introduction of "cationic" aliphatic amino groups in the chalcone scaffold results in potent antibacterial compounds. It is shown that the most favorable position for the aliphatic amino group is the 2-position of the B-ring, in particular in combination with a lipophilic substituent in the 5-position of the B-ring. We demonstrate that the compounds act by unselective disruption of cell membranes. Introduction of an additional aliphatic amino group in the A-ring results in compounds that are selective for bacterial membranes combined with a high antibacterial activity against both Gram-positive and -negative pathogens. The most potent compound in this study (78) has an MIC value of 2 muM against methicillin resistant Staphylococus aureus.

The wasp toxin philanthotoxin-433 (PhTX-433) is a nonselective and noncompetitive antagonist of ionotropic receptors, such as ionotropic glutamate receptors and nicotinic acetylcholine receptors. Polyamine toxins are extensively used for the characterization of subtypes of ionotropic glutamate receptors, in particular Ca(2+)-permeable AMPA and kainate receptors. We have previously shown that an analogue of PhTX-433 with one of the amino groups replaced by a methylene group, philanthotoxin-83 (PhTX-83) is a selective and potent antagonist of AMPA receptors. We now describe the solid-phase synthesis of analogues of PhTX-83 and the electrophysiological characterization of these analogues on cloned AMPA and kainate receptors. The polyamine portion of PhTX-83 was modified systematically by changing the position of the secondary amino group along the polyamine chain. In another series of analogues, the acyl moiety of PhTX-83 was replaced by acids of different size and lipophilicity. Using electrophysiological techniques, PhTX-56 was shown to be a highly potent (K(i) = 3.3 +/- 0.78 nM) and voltage-dependent antagonist of homomeric GluR1 receptors and was more than 1000-fold less potent when tested on heteromeric GluR1+GluR2, as well as homomeric GluR5(Q) receptors, thus being selective for Ca(2+)-permeable AMPA receptors. Variation of the acyl group of PhTX-83 had only minor effect on antagonist potency at homomeric GluR1 receptors but led to a significant decrease in the voltage-dependence. In conclusion, PhTX-56 is a novel, very potent, and selective antagonist of Ca(2+)-permeable AMPA receptors and is a promising tool for structure/function studies of the ion channel of the AMPA receptor.

Homologation of (S)-glutamic acid (Glu, 1) and Glu analogues has previously provided ligands with activity at metabotropic Glu receptors (mGluRs). The homologue of ibotenic acid (7), 2-amino-3-(3-hydroxy-5-isoxazolyl)propionic acid (HIBO, 8), and the 4-phenyl derivative of 8, compound 9a, are both antagonists at group I mGluRs. Here we report the synthesis and molecular pharmacology of HIBO analogues 9b-h containing different 4-aryl substituents. All of these compounds possess antagonist activity at group I mGluRs but are inactive at group II and III mGluRs.

A number of 1-hydroxyazole derivatives were synthesized as bioisosteres of (S)-glutamic acid (Glu) and as analogues of the AMPA receptor agonist (R,S)-2-amino-3-(3-hydroxy-5-methyl-4-isoxazolyl)propionic acid (AMPA, 3b). All compounds were subjected to in vitro pharmacological studies, including a series of Glu receptor binding assays, uptake studies on native as well as cloned Glu uptake systems, and the electrophysiological rat cortical slice model. Compounds 7a,b, analogues of AMPA bearing a 1-hydroxy-5-pyrazolyl moiety as the distal carboxylic functionality, showed only moderate affinity for [3H]AMPA receptor binding sites (IC(50) = 2.7 +/- 0.4 microM and IC(50) = 2.6 +/- 0.6 microM, respectively), correlating with electrophysiological data from the rat cortical wedge model (EC(50) = 280 +/- 48 microM and EC(50) = 586 +/- 41 microM, respectively). 1-Hydroxy-1,2,3-triazol-5-yl analogues of AMPA, compounds 8a,b, showed high affinity for [3H]AMPA receptor binding sites (IC(50) = 0.15 +/- 0.03 microM and IC(50) = 0.13 +/- 0.02 microM, respectively). Electrophysiological data showed that compound 8a was devoid of activity in the rat cortical wedge model (EC(50) > 1000 microM), whereas the corresponding 4-methyl analogue 8b was a potent AMPA receptor agonist (EC(50) = 15 +/- 2 microM). In accordance with this disparity, compound 8a was found to inhibit synaptosomal [3H]D-aspartic acid uptake (IC(50) = 93 +/- 25 microM), as well as excitatory amino acid transporters (EAATs) EAAT1 (IC(50) = 100 +/- 30 microM) and EAAT2 (IC(50) = 300 +/- 80 microM). By contrast, compound 8b showed no appreciable affinity for Glu uptake sites, neither synaptosomal nor cloned. Compounds 9a-c and 10a,b, possessing 1-hydroxyimidazole as the terminal acidic function, were devoid of activity in all of the systems tested. Protolytic properties of compounds 7a,b, 8b, and 9b were determined by titration, and a correlation between the pK(a) values and the activity at AMPA receptors was apparent. Optimized structures of all the synthesized ligands were fitted to the known crystal structure of an AMPA-GluR2 construct. Where substantial reduction or abolition of affinity at AMPA receptors was observed, this could be rationalized on the basis of the ability of the ligand to fit the construct. The results presented in this article point to the utility of 1-hydroxypyrazole and 1,2,3-hydroxytriazole as bioisosteres of carboxylic acids at Glu receptors and transporters. None of the compounds showed significant activity at metabotropic Glu receptors.