Estimating relative free energies from a single ensemble: Hydration free energies

The ability to determine the free energy of solvation for a number of small organic molecules with varying sizes and properties from the coordinate trajectory of a single simulation of a given reference state was investigated. The relative free energies were estimated from a single step perturbation using the perturbation formula. The reference state consisted of a cavity surrounded by solvent. To enhance sampling a soft-core interaction was used for the cavity. The effect of the size of the cavity, the effective core height, and the length of simulation on the ability to reproduce results obtained from thermodynamic integration calculations was considered. The results using a single step perturbation from an appropriately chosen initial state were comparable to results from thermodynamic integration calculations for a wide range of compounds. Using a large number of compounds the computational efficiency was potentially increased by 2–3 orders of magnitude over traditional free energy approaches. Factors determining the efficiency of the approach are discussed. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1604–1617, 1999     

Fabrication of antibody arrays using thermally responsive elastin fusion proteins

A general method has been developed to immobilize antibodies onto an array surface by employing fusion proteins consisting of an elastin domain with tunable hydrophobic properties and an antibody-binding domain with high binding affinity and specificity for antibodies. Antibodies conjugated with the elastin fusion proteins can be directly printed on a self-assembled monolayer-modified glass slide in a functionally active orientation with a spatially defined pattern. An antibody array sensor for detection of tumor markers was fabricated to demonstrate the utility of the method. We expect that the method presented here could be a simple and universal platform to immobilize antibodies for the fabrication of a variety of antibody array sensors.     

Molecular dynamics simulations of liquid methanol and methanol-water mixtures with polarizable models

A polarizable model for simulation of liquid methanol, compatible with the COS/G2 water model, has been developed using the Charge-on-Spring (COS) technique. The model consists of three point charges, with one polarizable center on the oxygen atom. The Lennard-Jones parameters on the oxygen atom together with the molecular polarizability were varied to reproduce the experimental heat of vaporization and density of liquid methanol at ambient conditions. We examined the energies of various methanol dimers in the gas phase and compared them with values obtained from ab initio calculations. The model was then used to study the thermodynamic, dynamic, structural, and dielectric properties of liquid methanol as well as of a methanol-water mixture. A microscopic picture of the structure of pure liquid methanol and of the methanol-water mixture is provided. Good agreement was found between the results from our model simulations and available experimental and ab initio calculation data. In particular, the experimental dielectric permittivity of 32 could be reproduced, which had been shown to be difficult when using nonpolarizable models.     

Species-specific identification of ruminant components contaminating industrial crude porcine heparin using real-time fluorescent qualitative and quantitative PCR

Ever since the emergence of bovine spongiform encephalopathy, the source of pharmaceutical heparin has been restricted to porcine intestinal mucosa. In this project, two real-time fluorescent PCR methods were developed to assist with quality control analysis. The first is a qualitative method which relies on SYBR Green I chemistry to confirm the porcine origin of industrial crude porcine heparin (ICPH), identify any ruminant contaminants, and generally control purity. The second is based on TaqMan chemistry and is able to quantitatively identify porcine, bovine, caprine, and ovine components and contaminants in ICPH. By targeting mitochondrial DNA, both PCR systems showed a detection limit of 1 pg DNA and amplification efficiencies ranging between 96% and 102%. Moreover, quantitative PCR showed a detection limit of 0.02 ppm in samples comprising porcine, bovine, caprine, and ovine DNA. The results of qualitative PCR over 27 ICPH samples showed that all samples were porcine in origin and that 17 had ruminant contaminants. The results of quantitative PCR further showed that out of all 17 samples with ruminant contaminants, seven samples had bovine, ovine, and caprine contaminants, two samples had bovine and ovine contaminants, and eight samples had only ovine contaminants. In conclusion, the qualitative PCR system was found to be a relatively inexpensive, rapid, and flexible method of identifying the porcine origin of and ruminant contaminants in ICPH, while the quantitative PCR was found suitable to accurately analyze the components and contaminants in detail. Both methods are suitable for routine control assays for the evaluation of ICPH purity and origins of contaminants.     

On developing coarse-grained models for biomolecular simulation: a review

So-called coarse-grained models are a popular type of model for accessing long time scales in simulations of biomolecular processes. Such models are coarse-grained with respect to atomic models. But any modelling of processes or substances involves coarse-graining, i.e. the elimination of non-essential degrees of freedom and interactions from a more fine-grained level of modelling. The basic ingredients of developing coarse-grained models based on the properties of fine-grained models are reviewed, together with the conditions that must be satisfied in order to preserve the correct physical mechanisms in the coarse-graining process. This overview should help the reader to determine how realistic a coarse-grained model of a biomolecular system is, i.e. whether it reflects the underlying physical mechanisms or merely provides a set of pretty pictures of the process or substances of interest.     

Surface chemistry of isopropoxy tetramethyl dioxaborolane on Cu(111)

The surface chemistry of isopropoxy tetramethyl dioxaborolane (ITDB), tetramethyl dioxaborolane (TDB), and 2-propanol is studied on a clean Cu(111) single crystal using temperature-programmed desorption (TPD). 2-Propanol is found to have two competing reactions on the copper surface. Dehydration results in water and propene formation, and dehydrogenation results in the formation of acetone and hydrogen. ITDB directly adsorbed on the surface reacts completely and does not molecularly desorb. TDB and 2-propanol decompose desorbing mainly 2,3-dimethyl 2-butene and acetone, respectively. Both of those products desorb above room temperature and are present in TPDs of ITDB. An additional acetone desorption peak was observed for ITDB at higher temperatures than acetone desorption from 2-propanol. This higher temperature peak at ～391 K was attributed to two acetone molecules forming from the tetramethyl end group resulting from a stronger bound surface species in ITDB compared to TDB despite their identical end groups. The copper surface seems to be reactive enough toward ITDB at room temperature that a potential boron-containing tribofilm could be produced for copper-copper sliding contacts. Despite their similarities, ITDB and TDB have different surface species present at room temperature, so their tribological properties will be investigated in the future.     

Assessment of enveloping distribution sampling to calculate relative free enthalpies of binding for eight netropsin-DNA duplex complexes in aqueous solution

The performance of enveloping distribution sampling (EDS) simulations to estimate free enthalpy differences associated with seven alchemical transformations of A-T into G-C base pairs at the netropsin binding site in the minor groove of a 13-base pair DNA duplex in aqueous solution is evaluated. It is demonstrated that sufficient sampling can be achieved with a two-state EDS Hamiltonian even for large perturbations such as the simultaneous transformation of up to three A-T into three G-C base pairs. The two parameters required to define the EDS reference state Hamiltonian are obtained automatically using a modified version of a scheme presented in earlier work. The sensitivity of the configurational sampling to a variation of these parameters is investigated in detail. Although for relatively small perturbations, that is, one base pair, the free enthalpy estimate depends only weakly on the EDS parameters, the sensitivity is stronger for the largest perturbation. Yet, EDS offers various convenient measures to evaluate the degree of sampling and thus the reliability of the free enthalpy estimate and appears to be an efficient alternative to the conventional thermodynamic integration methodology to obtain free energy differences for molecular systems.     

Specific Role of Reactor Configurations on the Mass Transfer and Energy Yield: Case of “Batch” and "Circulating” Gliding arc Liquid–Gas Reactors—Part 1: Experimental Study

Plasma Chemistry and Plasma Processing - The mass transfer and energy efficiency in the “batch” and “Circulating” gliding arc configuration reactors for the direct...