Head to Tail Distortion Wave Characterizes the Enantiomerization of Helicenes.

A fresh look on helicenes' enantiomerization process with a focus on ring conformation reveals that it can be described as a step-by-step mechanism in which maximal distortion is consecutively transferred along the helicene skeleton, head to tail. Density functional theory methods were used to compute the enantiomerization pathway, and continuous symmetry measures were applied to quantify the distortion of even-number helicenes with 8-14 rings. Our findings show that the distortion wave is additive-the process always starts from one edge of the helicene and progresses along the rings until the other edge is reached. As more rings are added to the helicene, extra steps are appended to the distortion wave. Implications of this fundamental process are discussed in light of similar natural phenomena from polymer dynamics to snake locomotion.

Affecting an Ultra-High Work Function of Silver.

An ultra-high increase in the WF of silver, from 4.26 to 7.42 eV, that is, an increase of up to circa 3.1 eV is reported. This is the highest WF increase on record for metals and is supported by recent computational studies which predict the potential ability to affect an increase of the WF of metals by more than 4 eV. We achieved the ultra-high increase by a new approach: Rather than using the common method of 2D adsorption of polar molecules layers on the metal surface, WF modifying components, l-cysteine and Zn(OH)2 , were incorporated within the metal, resulting in a 3D architecture. Detailed material characterization by a large array of analytical methods was carried out, the combination of which points to a WF enhancement mechanism which is based on directly affecting the charge transfer ability of the metal separately by cysteine and hydrolyzed zinc(II), and synergistically by the combination of the two through the known Zn-cysteine finger redox trap effect.

Chiral Ramachandran Plots II: General Trends and Protein Chirality Spectra.

The degree of chirality of protein backbone residues is used to enrich the Ramachandran plot (RP) and create three-dimensional chiral RPs with much more structural information. Detailed comparative analysis of the four classical RPs (general, glycine, proline, and pre-proline) is provided, including statistical analysis of quantitative chirality distributions in the maps and in the secondary structures. Our results show that points with outlier chirality levels represent special transitional points in the folded protein such as α-helix kinks, twists of ß-strands, and transition points between secondary structures. A protein chirality spectrum in which the degree of chirality of each residue is plotted against the sequence number explores these special points. More than 65000 residues extracted from 200 high-quality proteins are used for this study, which shows that quantitative chirality is a general and useful structural parameter for protein conformational studies.

Chiral Ramachandran Plots I: Glycine.

Ramachandran plots (RPs) map the wealth of conformations of the polypeptide backbone and are widely used to characterize protein structures. A limitation of the RPs is that they are based solely on two dihedral angles for each amino acid residue and provide therefore only a partial picture of the conformational richness of the protein. Here we extend the structural RP analysis of proteins from a two-dimensional (2D) map to a three-dimensional map by adding the quantitative degree of chirality-the continuous chirality measure (CCM)-of the amino acid residue at each point in the RP. This measure encompasses all bond angles and bond lengths of an amino acid residue. We focus in this report on glycine (Gly) because, due to its flexibility, it occupies a large portion of the 2D map, thus allowing a detailed study of the chirality measure, and in order to evaluate the justification of classically labeling Gly as the only achiral amino acid. We have analyzed in detail 4366 Gly residues extracted from high resolution crystallographic data of 160 proteins. This analysis reveals not only that Gly is practically always conformationally chiral, but that upon comparing with the backbone of all amino acids, the quantitative chirality values of Gly are of similar magnitudes to those of the (chiral) amino acids. Structural trends and energetic considerations are discussed in detail. Generally we show that adding chirality to Ramachandran plots creates far more informative plots that highlight the sensitivity of the protein structure to minor conformational changes.

Dispersion of Polymers in Metallic Gallium.

This work examines the concept of dispersing polymers in metals. Herein, this was mainly studied with molten gallium, in which 5-18 wt % of various short-chain polymers were incorporated and mixed. The nature of the solidified products was examined by using X-ray diffraction, electron microscopy, UV/Vis, differential scanning calorimetry, and thermal gravimetric analyses. It was found that some polymers can be dispersed as small domains within molten metals to form a heterogeneous solid. The ability to dope Ga with large polymers opens a new avenue to electronic materials.

The near-symmetry of proteins.

The majority of protein oligomers form clusters which are nearly symmetric. Understanding of that imperfection, its origins, and perhaps also its advantages requires the conversion of the currently used vague qualitative descriptive language of the near-symmetry into an accurate quantitative measure that will allow to answer questions such as: "What is the degree of symmetry deviation of the protein?," "how do these deviations compare within a family of proteins?," and so on. We developed quantitative methods to answer this type of questions, which are capable of analyzing the whole protein, its backbone or selected portions of it, down to comparison of symmetry-related specific amino-acids, and which are capable of visualizing the various levels of symmetry deviations in the form of symmetry maps. We have applied these methods on an extensive list of homomers and heteromers and found that apparently all proteins never reach perfect symmetry. Strikingly, even homomeric protein clusters are never ideally symmetric. We also found that the main burden of symmetry distortion is on the amino-acids near the symmetry axis; that it is mainly the more hydrophilic amino-acids that take place in symmetry-distortive interactions; and more. The remarkable ability of heteromers to preserve near-symmetry, despite the different sequences, was also shown and analyzed. The comprehensive literature on the suggested advantages symmetric oligomerizations raises a yet-unsolved key question: If symmetry is so advantageous, why do proteins stop shy of perfect symmetry? Some tentative answers to be tested in further studies are suggested in a concluding outlook.

Molecularly doped metals.

The many millions of organic, inorganic, and bioorganic molecules represent a very rich library of chemical, biological, and physical properties that do not show up among the approximately 100 metals. The ability to imbue metals with any of these molecular properties would open up tremendous potential for the development of new materials. In addition to their traditional features and their traditional applications, metals would have new traits, which would merge their classical virtues such as conductivity and catalytic activity with the diverse properties of these molecules. In this Account, we describe a new materials methodology, which enables, for the first time, the incorporation and entrapment of small organic molecules, polymers, and biomolecules within metals. These new materials are denoted dopant@metal. The creation of dopant@metal yields new properties that are more than or different from the sum of the individual properties of the two components. So far we have developed methods for the doping of silver, copper, gold, iron, palladium, platinum, and some of their alloys, as well as Hg-Ag amalgams. We have successfully altered classical metal properties (such as conductivity), induced unorthodox properties (such as rendering a metal acidic or basic), used metals as heterogeneous matrices for homogeneous catalysts, and formed new metallic catalysts such as metals doped with organometallic complexes. In addition, we have created materials that straddle the border between polymers and metals, we have entrapped enzymes to form bioactive metals, we have induced chirality within metals, we have made corrosion-resistant iron, we formed efficient biocidal materials, and we demonstrated a new concept for batteries. We have developed a variety of methods for synthesizing dopant@metals including aqueous homogeneous and heterogeneous reductions of the metal cations, reductions in DMF, electrochemical entrapments, thermal decompositions of zerovalent metal carbonyls, and dissolution during amalgam formation. The structures of these dopant@metal materials indicate that metals entrap the organic molecules within their agglomerated nanocrystals. As a result, these materials are porous, making the dopant accessible for chemical reactions, in particular for catalysis. We have prepared these materials in a variety of forms, including powder, granules, pressed discs, thin films, thick films, sub-micrometer particles, and nanometric particles decorating ceramic nanofibers. Entrapment and adsorption are very different processes. If entrapped, water-soluble molecules cannot be extracted, but the same molecules, if adsorbed, are easily washed away. Likewise, most of the special properties that we have observed, such as major improvements or changes in catalytic activity, completely different thermal gravimetric analysis behavior, and more, are observed only in the entrapped cases.

Continuous symmetry analyses: C(nv) and D(n) measures of molecules, complexes, and proteins.

The continuous symmetry methodology has been developed to provide a quantitative estimation for the degree of a selected symmetry point-group in a molecular structure. Previous developed measures included the C(S), C(n), S(n) (including C(i)) symmetries, several polyhedral symmetries, and the related chirality measure. Motivated by the abundance and importance of C(nv) symmetry in many key molecules and by the abundance of D(n) symmetry in many organometallic complexes and in many protein clusters, measures for these symmetries, based on the general definition of the continuous symmetry measure, were developed. Detailed description of the derivation of the measures, along with plenty of examples for their application, is provided.

Induction of amphiphilicity in polymer@silica particles: ceramic surfactants.

It is shown that, in general, when submicrometer hybrid particles of polymer@silica are subjected to thermal treatment, phase-separated hydrophobicity emerges at particles surface; and that the triggering of hydrophobicity results in particles which show amphiphilic behavior, arranging themselves at water interfaces and stabilizing W/O and O/W emulsions. Many polymer@silica particles show this behavior, and the entrapped polymers include polyethylene Engage, poly(dimethylsiloxane), poly-l-lactic acid, poly(ethylene-block-ethyleneglycol), poly(styrene-co-allyl-achohol), and poly(dimethylesiloxane-block-ethyleneoxide-co-propyleneoxide). The concept is attractive because, by doping the particles with functional molecules, one can get various surfactants from the same treated particle; this is demonstrated with fluorescent probes. It is proposed that the amphiphilic activity is due to Janus heterogeneous distribution of the hydrophobic moieties on the surface.

Symmetry-enthalpy correlations in Diels-Alder reactions.

Woodward-Hoffmann (WH) rules provide strict symmetry selection rules: when they are obeyed, a reaction proceeds; when they are not obeyed, there is no reaction. However, the voluminous experimental literature provides ample evidence that strict compliance to symmetry requirements is not an obstacle for a concerted reaction to proceed, and therefore the idea has developed that it is enough to have a certain degree of the required symmetry to have reactivity. Here we provide quantitative evidence of that link, and show that as one deviates from the desired symmetry, the enthalpy of activation increases, that is, we show that concerted reactions slow down the further they are from the ideal symmetry. Specifically, we study the deviation from mirror symmetry (evaluated with the continuous symmetry measure (CSM)) of the [4+2] carbon skeleton of the transition state of a series of twelve Diels-Alder reactions in seven different solvents (and in the gas phase), in which the dienes are butadiene, cyclopentadiene, cyclohexadiene, and cycloheptadiene; the dienophiles are the 1-, 1,1-, and 1,1,2-cyanoethylene derivatives; the solvents were chosen to sample a range of dielectric constants from heptane to ethanol. These components provide twenty-four symmetry-enthalpy DFT-calculated correlation lines (out of which only one case is a relatively mild exception) that show the general trend of increase in enthalpy as symmetry decreases. The various combinations between the dienophiles, cyanoethylenes, and solvents provide all kinds of sources for symmetry deviations; it is therefore remarkable that although the enthalpy of activation is dictated by various parameters, symmetry emerges as a primary parameter. In our analysis we also bisected this overall picture into solvent effects and geometry variation effects to evaluate under which conditions the electronic effects are more dominant than symmetry effects.

Glucose oxidase converted into a general sugar-oxidase.

Entrapment of glucose oxidase (GOx) within metallic gold converts this widely used enzyme into a general saccharide oxidase. The following sugar molecules were oxidized by the entrapped enzyme (in addition to D-glucose): fructose, xylose, L-glucose, glucose-6-phosphate, sucrose, lactose, methylglucoside, and the tri-saccharide raffinose. With the exception of raffinose, none of these sugars have a natural specific oxidase. The origin of this generalization of activity is attributed to the strong protein-gold 3D interactions and to the strong interactions of the co-entrapped CTAB with both the gold, and the protein. It is proposed that these interactions induce conformational changes in the channel leading to the active site, which is located at the interface between the two units of the dimeric GOx protein. The observations are compatible with affecting the specific conformation change of pulling apart and opening this gate-keeper, rendering the active site accessible to a variety of substrates. The entrapment methodology was also found to increase the thermal stability of GOx up to 100 °C and to allow its convenient reuse, two features of practical importance.

Quantitative symmetry and chirality--a fast computational algorithm for large structures: proteins, macromolecules, nanotubes, and unit cells.

Symmetry is one of the most fundamental properties of nature and is used to understand and investigate physical properties. Classically, symmetry is treated as a binary qualitative property, although other physical properties are quantitative. Using the continuous symmetry measure (CSM) methodology one can quantify symmetry and correlate it quantitatively to physical, chemical, and biological properties. The exact analytical procedures for calculating the CSM are computationally expensive and the calculation time grows rapidly as the structure contains more atoms. In this article, we present a new method for calculating the CSM and the related continuous chirality measure (CCM) for large systems. The new method is much faster than the full analytical procedures and it reduces the calculation time dependency from N! to N(2), where N is the number of atoms in the structure. We evaluate the cost of the applied approximations, estimate the error of the method, and show that deviations from the analytical solutions are within an error of 2%, and in many cases even less. The method is applicable at the moment for the cyclic symmetry point groups- C(i), C(s), C(n), and S(n), and therefore it can be used also for chirality measures, which are the minimal of the S(n) measures. We demonstrate the application of the method for large structures across chemistry: proteins, macromolecules, nanotubes, and large unit cells of crystals.

A continuous symmetry analysis of chemical bonding.

The ability to quantify the symmetry content of a given molecular system is important both for the quantitative prediction of its physical and chemical properties, as well as for the establishment of powerful theoretical concepts that can be derived solely from symmetry considerations. The symmetry content of a complex object such as a molecule relies, however, on the level of structural description that is chosen. This may range form a simple geometrical picture in which only the position of the nuclei is indicated, to a more or less detailed description of the electronic structure given by the different quantum chemical methods. Recently, a paper was published describing a new general methodology for calculating the symmetry content of diverse mathematical objects, such as vectors, operators, matrices, functions and more. In the present work we apply that approach to explore the inversion symmetry for diatomic molecules. Although it is a very simple system, general physical conclusions on the phenomenon of chemical bonding can be easily obtained from the symmetry analysis at different levels of description.

Chirality measures for vectors, matrices, operators and functions.

We introduce the general form of the continuous chirality measure (CCM), which is a quantitative estimation of the degree of chirality for a given object. The generalization makes it possible to calculate the chirality content of any mathematical description of a system by vectors, matrices, operators and functions. Another advantage of the new methodology is the ability to provide analytical expressions for the chirality measures. We apply it for specific cases, including vectors and molecules (amino acids), rotation matrices (metamaterials design), rotational potential operators (representing, for example, parity violation), and functions (the electronic structure of annulenes).

Quantifying asymmetry in concerted reactions: solvents effect on a Diels-Alder cycloaddition.

We propose the notion that if asymmetry characterizes a concerted reaction, a quantitative treatment in terms of continuous symmetry can bridge the gap between the Woodward-Hoffmann (WH) rules, originally formulated for symmetry-idealized unsubstituted reactants, and the fact that these rules hold for a much wider scope of reactions. Instead of focusing on symmetry conservation along the minimum energy path, we suggest that the distortion with respect to the original expected symmetry must attain a certain minimal value, not necessarily zero. To demonstrate this approach we studied the effect of solvents on the symmetry and reactivity of the classical [4 + 2] Diels-Alder cycloaddition of (E,E)-1,4-dimethoxy-1,3-butadiene with tetracyanoethylene, revealing the predictive value of this approach. Calculations of the enthalpy of activation and the charge separation at the transition state (TS) predict increased reactivity with the polarity of the solvent. The symmetry measure is in excellent correlation with the enthalpy of activation and the charge separation at the TS, indicating the higher reactivity of the more symmetric case, thus quantifying the main teaching of the WH rules. The advantages of using a global structural parameter that takes into account all geometrical parameters, i.e., the symmetry measure, over specific ones (e.g., asynchronicity) are discussed.

A web site for calculating the degree of chirality.

The web site, http://www.csm.huji.ac.il/, uses the Continuous Chirality Measure to evaluate quantitatively the degree of chirality of a molecule, a structure, a fragment. The value of this measure ranges from zero, the molecule is achiral, to higher values (the upper limit is 100); the higher the chirality value, the more chiral the molecule is. The measure is based on the distance between the chiral molecule and the nearest structure that is achiral. Questions such as the following can be addressed: by how much is one molecule more chiral than the other? how does chirality change along conformational motions? is there a correlation between chirality and enantioselectivity in a series of molecules? Both elementary and advanced features are offered. Related calculation options are the symmetry measures and shape measures.

Entrapment of glucose oxidase within gold converts it to a general monosaccharide-oxidase.

We report that entrapping glucose oxidase (GOx) within metallic gold, expands its activity to become an oxidase for monosaccharides that do not have a natural enzyme with that activity-fructose and xylose-and that this entrapment also removes the enantioselectivity, rendering this enzyme capable of oxidizing the "wrong" L-enantiomer of glucose. These observations suggest that in this biomaterial adsorptive interactions of the outer regions of the protein with the gold cage, pull apart and widen the tunnel between the two monomeric units of GOx, to a degree that its stereoselectivity is compromised; then, the active sites which are more versatile than currently attributed to, are free and capable of acting on the foreign sugars. To test this proposition, we entrapped in gold L-asparaginase, which is also a dimeric enzyme (a dimer of tight dimers), and found, again, that this metallic biomaterial widens the activity of that enzyme, to include the D-amino acid counter enantiomer as well. Detailed kinetic analyses for all substrates are provided for the gold bio-composites, including determination of the difference between the activation energies towards two opposite enantiomers.

Gradual hydrophobization of silica aerogel for controlled drug release.

We report on the successful fine-tuning of silica aerogel hydrophobicity, through a gas-phase surface modification process. Aerogel hydrophobicity is a widely discussed matter, as it contributes to the aerogel's preservation and determines its functionality. Still, a general procedure for tuning the hydrophobicity, without affecting other aerogel properties was missing. In the developed procedure, silica aerogel was modified with trimethylchlorosilane vapor for varying durations, resulting in gradual hydrophobicity, determined by solid-state NMR and contact angle measurements. The generality of this post-synthesis treatment allows its application on a variety of aerogel materials, while having minimum effect on their porosity and transparency. We demonstrate the applicability of the gradual hydrophobization by tuning drug release rates from the silica aerogel. Two chlorhexidine salts - widely employed as antiseptic agents - were used as model drugs, one representing a soluble drug, and the other an insoluble drug; they were entrapped in silica aerogel, following hydrophobization to varying degrees. The drug release patterns showed that depending on the degree, hydrophobization can increase or decrease release kinetics, compared to the unmodified aerogel. This arises from the effect of the hydrophobic degree on pore structure, diffusional rates and wetting of the aerogel carrier. We suggest the use of the gradual hydrophobization process for other drug-aerogel systems, as well as for other aerogel applications, such as transparent insulation panels, contaminate sorbents or catalysis supports.

Metal nanoparticles entrapped in metal matrices.

We developed synthetic methods for the doping of metals (M) with metallic nanoparticles (NPs). To the best of our knowledge - unlike oxides, polymers and carbon-based supports - metals were not used so far as supporting matrices for metallic NPs. The composites (denoted M1-NPs@M2) comprise two separate phases: the metallic NPs (the dopant) and the entrapping 3D porous metallic matrix, within which the NPs are intimately held and well dispersed. Two different general synthetic strategies were developed, each resulting in a group of materials with characteristic structure and properties. The first strategy uses pre-prepared NPs and these are entrapped during reductive formation of the metallic matrix from its cation. The second strategy is in situ growth of the doped metallic NPs within the pre-prepared entrapping metallic matrix. These two methods were developed for two types of entrapping metallic matrices with different morphologies: porous aggregated metallic matrices and metallic foams. The leading case in this study was the use of Pt as the NP dopant and Ag as the entrapping matrix, using all of the four combinations - entrapment or growth within aggregated Ag or Ag foam matrices. Full physical and chemical properties analysis of these novel types of materials was carried out, using a wide variety of analytical methods. The generality of the methods developed for these bi-metallic composites was investigated and demonstrated on additional metallic pairs: Au NPs within Ag matrices, Pd NPs within Ni matrices and Ir-NPs within a Rh matrix. As the main application of metallic NPs is in catalysis, the catalytic activity of M1-NPs@M2 is demonstrated successfully for entrapped Pt within Ag for reductive catalytic reactions, and for Pd within Ni for the electrocatalytic hydrogen oxidation reaction.

Dynamic Spin-Controlled Enantioselective Catalytic Chiral Reactions.

Enantioselective catalytic chiral reactions are important to all aspects of life sciences. Here we present the first utilization of the chiral induced spin selectivity (CISS) effect to form, enantioselectively, sp3 chiral centers in catalytic reactions, starting from achiral reagents. The enantiomeric symmetry is broken by affecting spin-controlled different reaction dynamics toward each of the enantiomers, using magnetic substrates. Two catalytic reactions are used for this purpose: a sulfide to sulfoxide oxidation and a Diels-Alder cycloaddition reaction, both catalyzed by hematite (Fe2O3). The proof of concept was evaluated by circular dichroism measurements and by chiral high-performance liquid chromatography techniques. These results provide direct evidence that the directionality of the electron spin can break enantiomeric symmetry, enabling asymmetric catalysis without using chiral reagents, solvents, or catalysts.