Some practical aspects of free energy calculations from molecular dynamics simulation

In this work, we address two critical aspects of calculation of the free energy differences in molecular systems from molecular simulations. The first aspect involves checking whether the calculated free energy difference depends significantly on the extent of perturbation used for accomplishment of a given transformation. The second aspect of interest is to verify if the sampling errors in calculating the free energy differences between the wild-type molecule and a mutated one in its free state and in a complex are similar, or not, for a finite-length dynamic simulation. The reliability of the free energy estimates obtained from molecular simulations using thermodynamic cycles depends in part on this fact. For investigating these aspects, we use a self-transformation scheme in which a transformation of a part of a molecular system into itself is considered. We perform MD simulations of DNA fragments in which a part of a specific base is subjected to such a self-transformation. Results indicate that the estimated free energy differences do not depend significantly on the extent of perturbation used to achieve the transformation. Interestingly, the variation in the cumulative free energy difference, ΔA, with the coupling parameter, λ, depends significantly on the extent of perturbation. We examine the physical basis of the observed nature of the variation of the accumulated free energy difference, ΔA, against the λ value in the case of a self-transformation. In a thermodynamic cycle, the sampling errors due to the finite-length simulation for the molecular system are found to be similar to each other for the two perturbations (free and in a complex) justifying the use of such approach in calculating ΔΔA in molecular complexes. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 877–885, 1999     

Evaluation of PLE exhaustiveness for the extraction of PCBs from sediments and the influence of sediment characteristics

Pressurized liquid extractions were performed on eight sediments in order to investigate if a modified US EPA method (100 °C, 100 bar, n-heptane/acetone (1:1), 2 × 5 min) provided exhaustive extractions of polychlorinated biphenyls (PCBs) from sediment, and to study if the extractability of PCBs from the different sediments was affected by characteristics of the sediment. The recovery from the eight native sediments, contaminated in nature, was between 96.4% and 98.9%, as an average of the recoveries from 10 PCB congeners. Hundred percent recovery was defined as the sum of two consecutive extractions (2 × 5 min each) at the stated conditions. The recoveries of the individual congeners were above 94%, except for one congener in one sediment, which had a recovery of 92%. When the recoveries and different characteristics of the sediments were compared, no correlation appeared between recoveries and sediment PCB concentration, total organic carbon (TOC), soot carbon (SC) or amorphous carbon (AC). The fact that carbon did not influence the extractions was somewhat surprising, since previous experiments have indicated a connection. Instead, statistically significant (p < 0.05) correlations were observed for water content and carbon/nitrogen (C/N) ratio. The decrease in recoveries with decreased water content was attributed to less access of the solvent to the analytes due to less matrix swelling. The lowered recoveries with increased C/N ratio can indicate that a difference in structure of the organic matter exists, which influences the binding strength between the analytes and the matrix. The difference in structure can possibly be explained by different origin of the organic matter or by aging effects. Overall the method was found to be exhaustive and the excellent recoveries show that sediment characteristics do not influence the extractions markedly.     

Aggregation and the estimation of equation systems

Simulations based on two sets of data are used to assess the impact of combining equations on the accuracy of parameter estimates and their asymptotic standard errors.     

Polarized fluorescence and absorption spectroscopy of 1,32-dihydroxy-dotriacontane-bis-rhodamine 101 ester. A new and lipid bilayer-spanning probe

We report on the properties of 1,32-dihydroxy-dotriacontane-bis-rhodamine 101 ester (Rh101C₃₂Rh101) in lipid bilayers of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and in liquid solvents. The results are compared with those of rhodamine 101 octadecanyl ester (Rh101C₁₈). Both molecules are solubilized in the lipid bilayer and the Rh101 moieties are anchored in the lipid-water interface, so that the electronic transition dipole moments (S ₀ S ₁) are oriented preferentially in the plane of the bilayer. At low concentrations of the dyes in lipid bilayers of DOPC, the fluorescence relaxation is single exponential with a lifetime of =4.9±0.2 ns. The relative fluorescence quantum yield of _C32/_C18 0.95 in DOPC vesicles. These results strongly suggest that only a small fraction of the Rh101C₃₂Rh101 molecules are quenched, by, for example, intra- or intermolecular dimers in the ground state at mole fractions of less than 0.1% in the lipid bilayers. For Rh101C₃₂Rh101 in lipid vesicles, the steady-state and time-resolved fluorescence anisotropies are compatible with efficient intramolecular electronic energy transfer. It is concluded that nearly every Rh101C₃₂Rh101 molecule is spanning across the lipid bilayer of DOPC.     

Glycosidase-substrate interactions analysis by STD-NMR spectroscopy: study of alpha-L-fucosidase

Saturation transfer difference-nuclear magnetic resonance (STD-NMR) is a recently developed method used to study the interaction between large proteins and small ligands. It has been successfully employed for various interactions including those between oligosaccharides or glycomimetics, and binding proteins such as lectins and antibodies. We have demonstrated that this method can be used to directly study the interaction between glycosidases and their substrates. We chose to study alpha-l-fucosidases, which, despite their wide distribution among living organisms and their biological significance, have not been studied with regard to their reaction mechanism. We were able for the first time to show direct evidences for the minimum structural requirements for a compound to interact with these enzymes. These findings will be useful for the design of new inhibitors and to optimize the synthetic properties (transglycosylation) of alpha-l-fucosidases.     

Ylide‐Functionalized Phosphines: Strong Donor Ligands for Homogeneous Catalysis

Phosphines are important ligands in homogenous catalysis and have been crucial for many advances, such as in cross‐coupling, hydrofunctionalization, or hydrogenation reactions. Herein we report the synthesis and application of a novel class of phosphines bearing ylide substituents. These phosphines are easily accessible via different synthetic routes from commercially available starting materials. Owing to the extra donation from the ylide group to the phosphorus center the ligands are unusually electron‐rich and can thus function as strong electron donors. The donor capacity surpasses that of commonly used phosphines and carbenes and can easily be tuned by changing the substitution pattern at the ylidic carbon atom. The huge potential of ylide‐functionalized phosphines in catalysis is demonstrated by their use in gold catalysis. Excellent performance at low catalyst loadings under mild reaction conditions is thus seen in different types of transformations.     

A high-frequency apparatus for chromatographic recording and for titration

Summary A high-frequency device, using the Q-meter principle, has been tested. It is compared with a simple crystal oscillator. It was found that the stability is increased about 100 times. The new device can find application in chromatographic recording and for monitoring purposes. A titration cell with a defined cell-constant is also described.

---

Zusammenfassung Ein Hochfrequenzgerät nach dem Q-Meter-Prinzip wurde getestet und mit einem einfachen Kristalloszillator verglichen. Die Stabilität des ersteren ist etwa 100fach größer. Das neue Gerät kann zur chromatographischen Registrierung und für Zwecke der Betriebsüberwachung verwendet werden. Eine Titrationszelle mit definierter Zellkonstante wurde gleichfalls beschrieben.

---

Résumé On a mis à l'essai un dispositif haute-fréquence mettant en application le principe du compteur-Q. On le compare avec un oscillateur simple à cristal. On a trouvé que la stabilité est augmentée d'environ cent fois. Le nouveau dispositif peut trouver une application dans l'enregistrement chromatographique et pour des usages de contrôle. On décrit également une cuve de titrage avec une constante de cellule définie.

     

[4+3] Cycloaddition of Donor–Acceptor Cyclopropanes with Amphiphilic Benzodithioloimine as Surrogate for ortho‐Bisthioquinone

Donor–acceptor cyclopropanes were reacted with amphiphilic benzodithioloimine to give seven‐membered heterocycles with two sulfur atoms. Formally, this transformation can be regarded as a [4+3] cycloaddition reaction of the three‐membered ring and ortho‐bisthioquinone. The benzodithioloimine serves as a surrogate for this highly reactive diene. The structure of the products was confirmed by X‐ray crystallography. Broad signals in ¹³C NMR studies suggest that several conformers, slowly interconverting on the NMR timescale, are present at room temperature.     

A New Green Thermoplastic Polymer with Improved Hydrophobic Character

Summary: A green thermoplastic polymer based on wheat flour was modified by the addition of a natural crosslinker genipin. Films of the polymer modified with different composition of genipin were prepared by extrusion. Free surface energy using contact angle method, moisture absorption test and hardness test were used to characterize the products. From moisture absorption and contact angle measurements, it was seen that for genipin amounts higher than 0.2% w/w, a hydrophobic character is achieved. Results obtained indicate enhancement in hydrophobic properties of the films.