First-principles simulation of the photoreaction of a capped azobenzene: the rotational pathway is feasible.

We present first-principles molecular dynamics simulations of azobenzene and a sterically hindered derivative in the first excited state. The restricted open-shell Kohn-Sham (ROKS) approach is employed to describe the motion in the lowest excited state. The rotational pathway is observed in the molecular dynamics simulations for both azobenzene and its azacrown ether capped derivative.     

Stress response decay with aging visualized using a dual-channel logic-based fluorescent probe

Diagnosing aging for preventative intervention generally relies on the tracking of aging biomarkers in the resting state. However, the static marker levels are insufficient to fully evaluate aging, particularly given that the stress response capacity (SRC) decay is currently viewed as a critical feature of aging. Therefore, we have developed a dual-channel fluorescent probe ROKS capable of the logic-based visualization of thiophenol (stressor) and HOCl (thiophenol-activated stress response product) in vivo, which provides a new strategy from the time dimension to precisely assess the SRC of individuals under stress using the dual-channel fluorescence ratio. Using ROKS we observed that the SRC of live cells decayed with senescence, and that a higher SRC was found for young vs. aged Caenorhabditis elegans. As such, our study offers a promising strategy for the fluorescence-guided diagnosis of aging and paves the way for accurate evaluation of the efficacy of anti-aging drugs.

Rather than tracking aging using the resting state, ROKS, an optical probe, was developed for evaluating the degree of aging dynamically by precisely monitoring the stress response of individuals under stress.     

Spin-spin contributions to the zero-field splitting tensor in organic triplets, carbenes and biradicals-a density functional and ab initio study

An evaluation study for the direct dipolar electron spin-spin (SS) contribution to the zero-field splitting (ZFS) tensor in electron paramagnetic resonance (EPR) spectroscopy is presented. Calculations were performed on a wide variety of organic systems where the SS contribution to the ZFS dominates over the second-order spin-orbit coupling (SOC) contribution. Calculations were performed using (hybrid) density functional theory (DFT), as well as complete active space self-consistent field (CASSCF) wave functions. In the former case, our implementation is an approximation, because we use the two-particle reduced spin-density matrix of the noninteracting reference system. In the latter case, the SS contribution is approximated by a mean-field method which, nevertheless, gives accurate results, compared to the approximation free computation of the SS part in a CASSCF framework. For the case of the triplet dioxygen molecule, it was shown that restricted open-shell density functional theory (RODFT), as well as CASSCF, can provide accurate spin-spin couplings while spin-unrestricted DFT leads to much larger errors. Furthermore, 15 organic radicals, including several 1,3 and 1,5 diradicals, dinitroxide biradicals, and even a chlorophyll a model system, were examined as test cases to demonstrate the accuracy and efficiency of our approach within a DFT framework. Accurate D values with root-mean-square deviations of 0.0035 cm(-1) were obtained. Furthermore, all trends, including those due to substituent effects, were correctly reproduced. In a different set of calculations, the polyacenes benzene, naphthalene, anthracene, and tetracene were studied. Applying DFT, the absolute D values were noticeably underestimated, but it was possible to correctly reproduce the trend to smaller D values with larger size of the systems. Finally, it was demonstrated that our approach is also well-suited for the study of carbenes. The smaller organic radicals of this work were also studied, through the use of CASSCF wave functions. This was a special advantage in the case of the triplet polyacenes, where the CASSCF approach gave better results than the DFT method. In comparing spin-restricted and spin-unrestricted results, it was shown through a natural orbital analysis and comparison to high-level ab initio calculations that even small amounts of spin polarization introduced by the unrestricted calculations lead to large deviations between the unrestricted Kohn-Sham (UKS) and restricted open-shell Kohn-Sham (ROKS) approaches. It is challenging to understand why the ROKS results show much better correlation with the experimental data.     

Semi-quantitative "spot-test" of cyanide.

A selective, sensitive, rapid and simple-handling analytical method for the determination of cyanide at low detection limits in surface and underground water, soil and industrial waste samples was developed. The method is based on a reaction, proposed by Guilbault and Kramer, where free cyanide reacts with p-nitrobenzaldehyde to form an intermediate cyanohydrin, which reacts with o-dinitrobenzene to give a highly colored purple compound. The original procedure was modified for application in a small device containing a gas-permeable membrane. The cyanide is converted in the volatile hydrogen cyanide, which permeates through a PTFE membrane, reaching colorimetric reagents. In order to obtain semi-quantitative results, printed color scales were built. The method allows rapid, accurate, selective, low-cost and simple-handling determinations of free cyanide, even in complex samples. About 150 real samples were analyzed. Less than 10 ng of free cyanide per ml (10 microg l(-1)) can be easily detected. For more concentrated solutions, the results had been compared to those obtained using differential pulse polarography. The standard addition method was used for more diluted solutions.     

The Immobiline family: from "vacuum" to "plenum" chemistry.

We list here a total of 17 acrylamido acids and bases as potential buffers and titrants for isoelectric focusing separations in immobilized pH gradients. The chemistry of these compounds is reviewed and general guidelines are given for their proper use. In particular, it is shown that the most delicate compounds are the basic species, since they can undergo several degradation pathways, including: (i) spontaneous hydrolysis to acrylic acid and a diamine; (ii) spontaneous autopolymerization to oligomers and n-mers; (iii) oxidation to N-oxides during the persulfate polymerization step. A hydrophobicity scale has been constructed, by partitioning the deprotonated species in water/1-octanol phases. A scale of resistance to alkaline hydrolysis for the basic acrylamido buffers is also given, followed by general consideration on the structure/stability relationship of these chemicals.     

Carbon networks based on dehydrobenzoannulenes. 4. Synthesis of "star" and "trefoil" graphdiyne substructures via sixfold cross-coupling of hexaiodobenzene

The synthesis and characterization of star- and trefoil-shaped polyethynyl aromatic structures, which represent model substructures of the all-carbon network graphdiyne, are described. Assembly of these macrocycles is accomplished via 6-fold Sonogashira cross-coupling of hexaiodobenzene using Pd[P(o-Tol)(3)](2) and CuI as the catalytic system. The development of these modified Sonogashira conditions is detailed. This work has led to the synthesis of a new family of hexakis(phenylbutadiynyl)benzene derivatives (4a-c), the largest of which is the D(3)(h)()-symmetric "trefoil" 2 and is composed of three [18]annulenes fused at a common benzene ring. Attempts at the synthesis of "wheel" 3 are also described. Compound 2 represents the largest fragment of the graphdiyne network to date. UV-vis spectroscopic studies indicate enhanced electron delocalization throughout the extended pi-system.     

"Proteomineering" serum biomarkers. A study in scarlet

The performance of sera pre-treatment for biomarker searching via combinatorial peptide ligand libraries (CPLL) has recently been challenged (Proteomics 2010, 10, 1416-1425) and stated to allow discovery of only medium to high-abundance proteins. We have thus investigated four elution protocols, as published in recent reports: (i) in 4?M urea+1% CHAPS; (ii) in 4?M urea+1% CHAPS+5% acetic acid; (iii) in 8?M urea+2% CHAPS+5% acetic acid; (iv) in boiling 4% SDS+25?mM DTT. One milliliter of serum, in all cases, was captured with 50?μL of CPLL beads, which were then eluted with the four eluants described above. In the first three cases, after the first elution, the beads were re-eluted with cocktail (iv), known to offer maximal release of proteins adsorbed by the CPLL ligands. Eluant (i) released only ca. 20% of the species adsorbed, eluant (ii) ca. 60%, eluant (iii) ca. 80%. Thus, the poor performance of the CPLL methodology, as reported in (i) is not due to any fault of the capture technique, but simply to the adoption of a very poor elution protocol. Even those using eluants (ii) and (iii) should know that a substantial fraction of the captured species still remains bound to the beads and is thus not available to biomarker discovery. Once more, eluant (iv) is recognized as the only one able to offer optimal recovery from the CPLL baits.     

"Demonstration" vs. "designation" of measurement competence: the need to link accreditation to metrology

Formal acceptance of the results of chemical laboratories is increasingly organized through a) accreditation of measuring laboratories nationally and b) mutual recognition of accreditation internationally (through formal Multilateral Recognition Agreements, MRAs). However, real comparability of results of measurements is realized by using common (internationally agreed) measurement scales which make these results traceable to this scale, i.e. "traceable" to the same (internationally agreed) value of the unit of that scale. In addition, the criterion against which the evaluation is done, should be "external" to the measurement laboratories which are being evaluated. This is realized in IRMM's International Measurement Evaluation Programme (IMEP) where evaluation is performed against values which are anchored using "metrology", the science of measurement with its own rules, which offers a sound foundation for measurement in all scientific disciplines. It is argued in this paper that the demonstration of measurement capability against values on such scales provides a result-oriented rather than a procedure-oriented evaluation. Thus, competence can be "demonstrated" rather than just "designated" and this can be shown to both customers and regulators. It inspires more confidence.     

Stille couplings catalytic in tin: the "Sn-O" approach.

A one-pot tandem Pd-catalyzed hydrostannylation/Stille coupling protocol for the stereoselective generation of vinyltins and their subsequent union, employing only catalytic amounts of tin, is described. By recycling the organotin halide Stille byproduct back to organotin hydride, a hydrostannylation/cross-coupling sequence can be carried out with catalytic amounts of tin. Such a process is most effective with Me(3)SnCl serving as the tin source. This protocol allows a 94% reduction of the tin requirement, while maintaining good yields (up to 90%) for a variety of Stille products. Furthermore, since one cycle requires the tin to undergo at least four transformations, each moiety of trialkyltin is experiencing a minimum of 60 reactions over the course of the hydrostannylation/Stille sequence.     

Comment on "Using quaternions to calculate RMSD" [J. Comp. Chem. 25, 1849 (2004)

Coutsias et al. have recently published a method to find the optimal rotational superposition of two molecular structures, which is based on a representation of rotations by quaternions (J. Comp. Chem. 25(15), 1849 (2004)). The method, which has been suggested by other authors before, is compared to the one by Kabsch, where the elements of the rotation matrix are directly used as variables of the optimization problem. The statement that the two methods are equivalent is misleading in the sense that the Kabsch method may yield an improper optimal rotation, which must be explicitly checked for, whereas the quaternion method does not mix proper and improper rotations. Nevertheless, both types of solutions can be considered by solving the same eigenvector problem. The relation between the two types of solutions is briefly discussed and bounds for the eigenvalues are given.     

Probing the donor-acceptor proximity on the physicochemical properties of porphyrin-fullerene dyads: "tail-on" and "tail-off" binding approach.

A new approach of probing proximity effects in porphyrin-fullerene dyads by using an axial ligand coordination controlled "tail-on" and "tail-off" binding mechanism is reported. In the newly synthesized porphyrin-fullerene dyads for this purpose, the donor-acceptor proximity is controlled either by temperature variation or by an axial ligand replacement method. In o-dichlorobenzene, 0.1 M (TBA)ClO(4), the synthesized zincporphyrin-fullerene dyads exhibit seven one-electron reversible redox reactions within the accessible potential window of the solvent and the measured electrochemical redox potentials and UV-visible absorption spectra reveal little or no ground-state interactions between the C(60) spheroid and porphyrin pi-system. The proximity effects on the photoinduced charge separation and charge recombination are probed by both steady-state and time-resolved fluorescence techniques. It is observed that in the "tail-off" form the charge-separation efficiency changes to some extent in comparison with the results obtained for the "tail-on" form, suggesting the presence of some through-space interactions between the singlet excited zinc porphyrin and the C(60) moiety in the "tail-off" form. The charge separation rates and efficiencies are evaluated from the fluorescence lifetime studies. The charge separation via the singlet excited states of zinc porphyrin in the studied dyads is also confirmed by the quick rise-decay of the anion radical of the C(60) moiety within 20 ns. Furthermore, a long-lived ion pair with lifetime of about 1000 ns is also observed in the investigated zinc porphyrin-C(60) dyads.     

Supramolecular fullerene-porphyrin chemistry. Fullerene complexation by metalated "jaws porphyrin" hosts

Porphyrins and fullerenes are spontaneously attracted to each other. This new supramolecular recognition element is explored in discrete, soluble, coordinatively linked porphyrin and metalloporphyrin dimers. Jawlike clefts in these bis-porphyrins are effective hosts for fullerene guests. X-ray structures of the Cu complex with C60 and free-base complexes with C70 and a pyrrolidine-derivatized C60 have been obtained. The electron-rich 6:6 ring-juncture bonds of C60 show unusually close approach to the porphyrin or metalloporphyrin plane. Binding constants in toluene solution increase in the order Fe(II) < Pd(II) < Zn(II) < Mn(II) < Co(II) < Cu(II) < 2H and span the range 490-5200 M-1. Unexpectedly, the free-base porphyrin binds C60 more strongly than the metalated porphyrins. This is ascribed to electrostatic forces, enhancing the largely van der Waals forces of the pi-pi interaction. The ordering with metals is ascribed to a subtle interplay of solvation and weak interaction forces. Conflicting opinions on the relative importance of van der Waals forces, charge transfer, electrostatic attraction, and coordinate bonding are addressed. The supramolecular design principles arising from these studies have potential applications in the preparation of photophysical devices, molecular magnets, molecular conductors, and porous metal-organic frameworks.     

Molecular dynamics in the isothermal-isobaric ensemble: the requirement of a "shell" molecule. III. Discontinuous potentials

Based on the approach of Gruhn and Monson [Phys. Rev. E 63, 061106 (2001)], we present a new method for deriving the collisions dynamics for particles that interact via discontinuous potentials. By invoking the conservation of the extended Hamiltonian, we generate molecular dynamics (MD) algorithms for simulating the hard-sphere and square-well fluids within the isothermal-isobaric (NpT) ensemble. Consistent with the recent rigorous reformulation of the NpT ensemble partition function, the equations of motion impose a constant external pressure via the introduction of a shell particle of known mass [M. J. Uline and D. S. Corti, J. Chem. Phys. 123, 164101 (2005); 123, 164102 (2005)], which serves to define uniquely the volume of the system. The particles are also connected to a temperature reservoir through the use of a chain of Nose-Hoover thermostats, the properties of which are not affected by a hard-sphere or square-well collision. By using the Liouville operator formalism and the Trotter expansion theorem to integrate the equations of motion, the update of the thermostat variables can be decoupled from the update of the positions of the particles and the momentum changes upon a collision. Hence, once the appropriate collision dynamics for the isobaric-isenthalpic (NpH) equations of motion is known, the adaptation of the algorithm to the NpT ensemble is straightforward. Results of MD simulations for the pure component square-well fluid are presented and serve to validate our algorithm. Finally, since the mass of the shell particle is known, the system itself, and not a piston of arbitrary mass, controls the time scales for internal pressure and volume fluctuations. We therefore consider the influence of the shell particle algorithm on the dynamics of the square-well fluid.     

Molecular dynamics in the isothermal-isobaric ensemble: the requirement of a "shell" molecule. II. Simulation results

The results of a series of constant pressure and temperature molecular-dynamics (MD) simulation studies based on the rigorous shell particle formulation of the isothermal-isobaric (NpT) ensemble are presented. These MD simulations validate the newly proposed constant pressure equations of motion in which a "shell" particle is used to define uniquely the volume of the system [M. J. Uline and D. S. Corti, J. Chem. Phys. (to be published), preceding paper]. Ensemble averages obtained with the new MD NpT algorithm match the ensemble averages obtained using the previously derived shell particle Monte Carlo NpT method [D. S. Corti, Mol. Phys. 100, 1887 (2002)]. In addition, we also verify that the Hoover NpT MD algorithm [W. G. Hoover, Phys. Rev. A 31, 1695 (1985); 34, 2499 (1986)] generates the correct ensemble averages, though only when periodic boundary conditions are employed. The extension of the shell particle MD algorithm to multicomponent systems is also discussed, in which we show for equilibrium properties that the identity of the shell particle is completely arbitrary when periodic boundary conditions are applied. Self-diffusion coefficients determined with the shell particle equations of motion are also identical to those obtained in other ensembles. Finally, since the mass of the shell particle is known, the system itself, and not a piston of arbitrary mass, controls the time scales for internal pressure and volume fluctuations. We therefore consider the effects of the shell particle on the dynamics of the system. Overall, the shell particle MD algorithm is an effective simulation method for studying systems exposed to a constant external pressure and may provide an advantage over other existing constant pressure approaches when developing nonequilibrium MD methods.     

Method to assess packing quality of transmembrane alpha-helices in proteins. 2. Validation by "correct vs misleading" test

We describe a set of tests designed to check the ability of the new "membrane score" method (see the first paper of this series) to assess the packing quality of transmembrane (TM) alpha-helical domains in proteins. The following issues were addressed: (1) Whether there is a relation between the score (S(mem)) of a model and its closeness to the "nativelike" conformation? (2) Is it possible to recognize a correct model among misfolded and erroneous ones? (3) To what extent the score of a homology-built model is sensitive to errors in sequence alignment? To answer the first question, two test cases were considered: (i) Several models of bovine aquaporin-1 (target protein) were built on the structural templates provided by its homologs with known X-ray structure. (ii) Side chains in the spatial models of visual rhodopsin and cytochrome c oxidase were rebuilt based on the backbone scaffolds taken from their crystal structures, and the resulting models were iteratively fitted into the full-atom X-ray conformations. It was shown that the higher the S(mem) value of a model is, the lower its root-mean-square deviation is from the "correct" (crystal) structure of a target. Furthermore, the "membrane score" method successfully identifies the rhodopsin crystal structure in an ensemble of "rotamer-type" decoys, thus providing the way to optimize mutual orientations of alpha-helices in models of TM domains. Finally, being applied to a set of homology models of rhodopsin built on its crystal structure with systematically shifted alignment, the approach demonstrates a prominent ability to detect alignment errors. We therefore assume that the "membrane score" method will be helpful in optimization of in silico models of TM domains in proteins, especially those in GPCRs.     

Correlation between Na* emission and "chemically active" acoustic cavitation bubbles.

The emission from electronically excited sodium atoms (Na*) from aqueous solutions containing NaCl or sodium dodecylsulfate under ultrasonic irradiation is studied. Evidence is presented that strongly suggests Na* emission arises from a population of bubbles that are sonochemically active but not producing sonoluminescence (SL). Results indicate that the Na* emission intensity is mainly dependent on the concentration of Na(+) ions near the bubble/solution interface. The results provide further insight into the origin of alkali metal spectral line emission from sonicated aqueous solutions containing sodium ions.