What Role Does the Incident Light Intensity Play in Photocatalytic Conversion of CO2: Attenuation or Intensification?

Artificial photoreduction of CO₂ is vital for the sustainable development of human beings via solar energy storage in stable chemicals. This process involves intricate light-matter interactions, but the role of incident light intensity in photocatalysis remains obscure. Herein, the influence of excitation intensity on charge kinetics and photocatalytic activity is investigated. Model photocatalysts include the pure graphitic carbon nitride (g-C₃N₄) and g-C₃N₄ loaded with noble/non-noble-metal cocatalysts (Ag, TiN, and CuO). It is found that the increase of light intensity does not always improve the electron utilization. Overly high excitation intensities cause charge carrier congestion and changes the recombination mechanism, which is called the light congestion effect. The electron transport channels can be established to mitigate the light-induced effect via the addition of cocatalyst, leading to a nonlinear growth in the reaction rate with increasing light intensity. From experiments and simulations, it is found that the light intensity and active site density should be collectively optimized for increasing the energy conversion efficiency. This work elucidates the effect of light intensity on photocatalytic CO₂ reduction and emphasizes the synergistic relationship of matching the light intensity and the photocatalyst category. The study provides guidance for the design of efficient photocatalysts and the operation of photocatalytic systems.     

Enthalpy recovery in polymeric glasses: Does a correlation exist between the empirical (T-N-M) relationship parameters and the glass structures?

To characterize the enthalpy recovery which appears during physical aging in glassy materials and especially in glassy polymers, the empirical Tool-Narayanaswamy-Moynihan (TNM) relationship for the relaxation time is widely used. This relationship depends essentially on three parameters, the apparent activation energy Δh*, the non linearity parameter x and the fictive temperature T_f. Even if a great amount of data (x, Δ*) can be found in the literature, no direct correlation between the values of these parameters and the engaged structures are available. On the one hand, using some polymers like Poly(ethylene terephthalate), Polymethyl(α-n-alkyl)acrylates and three dimensional epoxy networks for which structural changes are controlled and on the other hand, using some recently published results concerning other materials including inorganic polymers (Ge-Se and Ge-Te glasses), we show that it is possible to propose some interesting tendencies. In particular it is shown that the value of x depends on the intermolecular strength for organic polymers and on the connectivity for inorganic polymer.     

Understanding the Role of Trapezoids in Honeycomb Self-Assembly—Pathways between a Columnar Liquid Quasicrystal and its Liquid-Crystalline Approximants

Quasiperiodic patterns and crystals—having long range order without translational symmetry—have fascinated researchers since their discovery. In this study, we report on new p-terphenyl-based T-shaped facial polyphiles with two alkyl end chains and a glycerol-based hydrogen-bonded side group that self-assemble into an aperiodic columnar liquid quasicrystal with 12-fold symmetry and its periodic liquid-crystalline approximants with complex superstructures. All represent honeycombs formed by the self-assembly of the p-terphenyls, dividing space into prismatic cells with polygonal cross-sections. In the perspective of tiling patterns, the presence of unique trapezoidal tiles, consisting of three rigid sides formed by the p-terphenyls and one shorter, incommensurate, and adjustable side by the alkyl end chains, plays a crucial role for these phases. A delicate temperature-dependent balance between conformational, entropic and space-filling effects determines the role of the alkyl chains, either as network nodes or trapezoid walls, thus resulting in the order-disorder transitions associated with emergence of quasiperiodicity. In-depth analysis suggests a change from a quasiperiodic tiling involving trapezoids to a modified one with a contribution of trapezoid pair fusion. This work paves the way for understanding quasiperiodicity emergence and develops fundamental concepts for its generation by chemical design of non-spherical molecules, aggregates, and frameworks based on dynamic reticular chemistry.     

The orbital: a pivotal concept in the relationship between chemistry and physics? A comment to the work by Fortin and coauthors

The present work is a comment of a recent paper by Fortin and coauthors (Fortin et al. in Found Chem 19:43–59, 2017) in which the authors propose the introduction of Bohmian mechanics (BM) in the philosophy of chemistry and the use of standard quantum mechanics (SQM) as a mere instrument of prediction. This way would allow overcoming the obstacles found in linking molecular chemistry and quantum mechanics. Starting from some remarks on the orbital concept, we highlight and discuss some general issues that need to be taken into account when two scientific theories coexist within the same investigation field, i.e. SQM and BM.     

Comparison between Roesy and 13C NMR Complexation Shifts in Deriving the Geometry of Inclusion Compounds: A Study on the Interaction between Hyodeoxycholic Acid and 2-Hydroxypropyl-β-Cyclodextrin

Abstract

The formation and geometry of the hyodeoxycholic acid (HDCA)/2-hydroxypropyl-β-cyclodextrin (HPβCD) complex in methanol-d₄ solution was determined through a rotating frame nuclear Overhauser (ROESY) experiment. The reported results confirmed those independently and previously obtained though the use of ¹³C complexation shifts in the same solvent. The ¹³C approach, which needs shorter experimental times and is currently used in the study of HPβCD/bile acid systems, was then substantiated.     

Polyphenols in cocoa and cocoa products: is there a link between antioxidant properties and health?

Cocoa and cocoa products have received much attention due to their significant polyphenol contents. Cocoa and cocoa products, namely cocoa liquor, cocoa powder and chocolates (milk and dark chocolates) may present varied polyphenol contents and possess different levels of antioxidant potentials. For the past ten years, at least 28 human studies have been conducted utilizing one of these cocoa products. However, questions arise on which of these products would deliver the best polyphenol contents and antioxidant effects. Moreover, the presence of methylxanthines, peptides, and minerals could synergistically enhance or reduce antioxidant properties of cocoa and cocoa products. To a greater extent, cocoa beans from different countries of origins and the methods of preparation (primary and secondary) could also partially influence the antioxidant polyphenols of cocoa products. Hence, comprehensive studies on the aforementioned factors could provide the understanding of health-promoting activities of cocoa or cocoa products components.     

Water-mediated interactions in the CRP–cAMP–DNA complex: Does water mediate sequence-specific binding at the DNA primary-kink site?

The cyclic AMP receptor protein (CRP) of Escherichia coli binds preferentially to DNA sequences possessing a T:A base pair at position 6 (at which the DNA becomes kinked), but with which it does not form any direct interactions. It has been proposed that indirect readout is involved in CRP-DNA binding, in which specificity for this base pair is primarily related to sequence effects on the energetic susceptibility of the DNA to kink formation. In the current study, the possibility of contributions to indirect readout by water-mediated hydrogen bonding of CRP with the T:A base pair was investigated. A 1.0 ns molecular dynamics simulation of the CRP-cAMP-DNA complex in explicit solvent was performed, and assessed for water-mediated CRP-DNA hydrogen bonds; results were compared to several X-ray crystal structures of comparable complexes. While several water-mediated CRP-DNA hydrogen bonds were identified, none of these involved the T:A base pair at position 6. Therefore, the sequence specificity for this base pair is not likely enhanced by water-mediated hydrogen bonding with the CRP.     

Does the decomposition of peroxydicarbonates and diacyl peroxides proceed in a stepwise or concerted pathway?

M?ller-Plesset perturbation theory and density functional theory calculations are used to study decomposition mechanisms of polymerization initiators, such as diethyl peroxydicarbonate, trifluoroacetyl peroxide, and acetyl peroxide, which possess a general structure of RC(O)OO(O)CR. It is found that the decomposition of initiators with electron-donating R groups follows two favorable stepwise pathways: a two-bond cleavage mechanism in which the O-O single bond and one of R-C bonds of [R-C(O)O-O(O)C-R] break simultaneously followed by decomposition of the R-C(O)O(*) radical and a one-bond cleavage mechanism in which the single O-O bond cleavage produces a carboxyl radical pair and a subsequent decomposition of the carboxyl radicals. It is also found that the initiators with electron-withdrawing R groups follow the two-bond cleavage pathway only. Geometrical and energetic analyses indicate that despite the similar structures of the peroxydicarbonates, quite different decomposition energy barriers are determined by the nature of the R groups.     

Role of protein structure and the role of individual fingers in zinc finger protein–DNA recognition: a molecular dynamics simulation study and free energy calculations

Molecular dynamics and MM_GBSA energy calculations on various zinc finger proteins containing three and four fingers bound to their target DNA gave insights into the role of each finger in the DNA binding process as part of the protein structure. The wild type Zif 268 (PDB code: 1AAY) gave a ΔG value of ??76.1 (14) kcal/mol. Zinc fingers ZF1, ZF2 and ZF3 were mutated in one experiment and in another experiment one finger was cut and the rest of the protein was studied for binding. The ΔΔG values for the Zinc Finger protein with both ZF1 and ZF2 mutated was +?80 kcal/mol, while mutating only ZF1 the ΔΔG value was +?52 kcal/mol (relative to the wild type). Cutting ZF3 and studying the protein consisting only of ZF1 linked to ZF2 gave a ΔΔG value of +?68 kcal/mol. Upon cutting ZF1, the resulting ZF2 linked to ZF3 protein gave a ΔΔG value of +?41 kcal/mol. The above results shed light on the importance of each finger in the binding process, especially the role of ZF1 as the anchoring finger followed in importance by ZF2 and ZF3. The energy difference between the binding of the wild type protein Zif268 (1AAY) and that for individual finger binding to DNA according to the formula: ΔΔG_{linkers, otherstructuralfactors}?=?ΔG_zif268???(ΔG_F1+F2+F3) gave a value?=???44.5 kcal/mol. This stabilization can be attributed to the contribution of linkers and other structural factors in the intact protein in the DNA binding process. DNA binding energies of variant proteins of the wild type Zif268 which differ in their ZF1 amino acid sequence gave evidence of a good relationship between binding energy and recognition and specificity, this finding confirms the reported vital role of ZF1 in the ZF protein scanning and anchoring to the target DNA sequence. The role of hydrogen bonds in both specific and nonspecific amino acid-DNA contacts is discussed in relation to mutations. The binding energies of variant Zinc Finger proteins confirmed the role of ZF1 in the recognition, specificity and anchoring of the zinc finger protein to DNA.     

Metalloid Al- and Ga-clusters: a novel dimension in organometallic chemistry linking the molecular and the solid-state areas?

Formation and fragmentation of metal-metal bonds on the way between stable metal compounds in which the metal atoms are oxidised (e.g. isolated species in solution or metal salts in bulk) and the bulk metal are the fundamental steps to understand this process in which formation and chemical behaviour of metalloid Al and Ga clusters as intermediates are essential. Many examples of metalloid Al and Ga clusters show that their formation reflects a high degree of complexity like that of the simple seeming formation of the bulk metal itself: starting from metastable Al(i) and Ga(i) solutions containing small molecular entities, metalloid clusters grow during many self-organization steps including aggregation as well as irreversible redox cascades. This novel class of clusters seems to open a new dimension in chemistry between the molecular and the solid-state area, because, for the first time, it is shown that under well selected conditions definite molecular species, i.e. metalloid clusters, grow via the formation of additional metal-metal bonds and that the solid metal represents the final step.     

p-Phenylenecarbenonitrene and its halogen derivatives: how does resonance interaction between a nitrene and a carbene center affect the overall electronic configuration?

A series of para-conjugatively coupled phenylenecarbenonitrenes [(4-nitrenophenyl)methylene (3a), (4-nitrenophenyl)fluoromethylene (3b), (4-nitrenophenyl)chloromethylene (3c), and (4-nitrenophenyl)bromomethylene (3d)] were generated in argon matrix at low temperature (10 or 13 K) and characterized by IR and UV/vis spectroscopy. Density functional theory (B3LYP/6-31G(d)) and ab initio (MCSCF, CASPT2) methods were used to study the ground- and some low-lying excited states of 3a-d. The experimental and computational data suggest that 3a-d have singlet ground states (S0) and can be thought of as quinonoidal biradicals. In all cases, the lowest triplet (T1) and quintet (Q1) states lie about 2 kcal mol(-1) and 28-29 kcal mol(-1), respectively, higher in energy than S0. On the other hand the substituent is found to have a significant effect on the relative energy of the second excited triplet (T2) state. This state tends to become relatively more stable as the ability of the substituent to enforce a closed-shell configuration at the carbene subunit increases. Interestingly, the energy difference between the T2 and S0 states in 3a-d is found to depend linearly on the S-T gap of the corresponding phenylcarbenes 7a-d. This relationship is helpful in predicting when a substituted p-phenylenecarbenonitrene may have a triplet ground state instead of a singlet one.     

How Does Diet Influence Our Lives? Evaluating the Relationship between Isotopic Signatures and Mortality Patterns in Italian Roman Imperial and Medieval Periods

The present research investigates the relationship between dietary habits and mortality patterns in the Roman Imperial and Medieval periods. The reconstructions of population dynamics and subsistence strategies provide a fascinating source of information for understanding our history. This is particularly true given that the changes in social, economic, political, and religious aspects related to the transition from the Roman period to the Middle Ages have been widely discussed. We analyzed the isotopic and mortality patterns of 616 individuals from 18 archeological sites (the Medieval Latium sites of Colonna, Santa Severa, Allumiere, Cencelle, and 14 Medieval and Imperial funerary contexts from Rome) to compile a survivorship analysis. A semi-parametric approach was applied, suggesting variations in mortality patterns between sexes in the Roman period. Nitrogen isotopic signatures influenced mortality in both periods, showing a quadratic and a linear effect for Roman Imperial and Medieval populations, respectively. No influence of carbon isotopic signatures has been detected for Roman Imperial populations. Conversely, increased mortality risk for rising carbon isotopic values was observed in Medieval samples.     

Chymistry and taste in the seventeenth century: Franciscus dele Boë Sylvius as a chymical physician between Galenism and Cartesianism

Franciscus dele Bo? (1614-1672), known as Sylvius, was one of the foremost chymical physicians of the mid-seventeenth century. He developed a highly influential and equally controversial theory of chymistry and physiology based on the interaction of acids and alkalis, taught students from across Europe, and performed and guided experimental research on digestion, glands, respiration, and the motion of the heart. Throughout his work, Sylvius grounded his knowledge of the acid and alkali chymical principles in the practice of tasting. In this paper, I expand our knowledge of Sylvius's chymistry and recover the surprising extent and significance of his use of his senses to assay chymical substances. I compare the uses of taste in more traditional Galenic medicine and the emerging chymistry in order to argue that Sylvius's reliance on taste grew directly out of his favoured chymical traditions. Looking to the broader context of philosophical medicine also allows us to see Sylvius's explicit commitment to Cartesian matter theory as an ideal: a metaphysical dream that he accepted yet criticised for its poor fit with the hard work and bodily experience central to proper chymistry and medicine.     

Electrochemical signal modulation in homogeneous solutions using the formation of an inclusion complex between ferrocene and β-cyclodextrin on a DNA scaffold

Two DNA conjugates modified with ferrocene and β-cyclodextrin were prepared as a pair of probes that work cooperatively for DNA sensing, in which the electrochemical signal of ferrocene on one probe was significantly "quenched" by the formation of an inclusion complex with β-cyclodextrin of the other probe on the DNA templates.     

Role of hydration in determining the structure and vibrational spectra of L-alanine and N-acetyl L-alanine N′-methylamide in aqueous solution: a combined theoretical and experimental approach

In this work we have utilized recent density functional theory Born-Oppenheimer molecular dynamics simulations to determine the first principles locations of the water molecules in the first solvation shell which are responsible for stabilizing the zwitterionic structure of L-alanine. Previous works have used chemical intuition or classical molecular dynamics simulations to position the water molecules. In addition, a complete shell of water molecules was not previously used, only the water molecules which were thought to be strongly interacting (H-bonded) with the zwitterionic species. In a previous work by Tajkhorshid et al. (J Phys Chem B 102:5899) the L-alanine zwitterion was stabilized by 4 water molecules, and a subsequent work by Frimand et al. (Chem Phys 255:165) the number was increased to 9 water molecules. Here we found that 20 water molecules are necessary to fully encapsulate the zwitterionic species when the molecule is embedded within a droplet of water, while 11 water molecules are necessary to encapsulate the polar region with the methyl group exposed to the surface, where it migrates during the MD simulation. Here we present our vibrational absorption, vibrational circular dichroism and Raman and Raman optical activity simulations, which we compare to the previous simulations and experimental results. In addition, we report new VA, VCD, Raman and ROA measurements for L-alanine in aqueous solution with the latest commercially available FTIR VA/VCD instrument (Biotools, Jupiter, FL, USA) and Raman/ROA instrument (Biotools). The signal to noise of the spectra of L-alanine measured with these new instruments is significantly better than the previously reported spectra. Finally we reinvestigate the causes for the stability of the P_π structure of the alanine dipeptide, also called N-acetyl-L-alanine N′-methylamide, in aqueous solution. Previously we utilized the B3LYP/6-31G* + Onsager continuum level of theory to investigate the stability of the NALANMA4WC Han et al. (J Phys Chem B 102:2587) Here we use the B3PW91 and B3LYP hybrid exchange correlation functionals, the aug-cc-pVDZ basis set and the PCM and CPCM (COSMO) continuum solvent models, in addition to the Onsager and no continuum solvent model. Here by the comparison of the VA, VCD, Raman and ROA spectra we can confirm the stability of the NALANMA4WC due to the strong hydrogen bonding between the four water molecules and the peptide polar groups. Hence we advocate the use of explicit water molecules and continuum solvent treatment for all future spectral simulations of amino acids, peptides and proteins in aqueous solution, as even the structure (conformer) present cannot always be found without this level of theory. Festschift in Honor of Philip J. Stephens’ 65th Birthday. During the proof stage of this article a very relevant article has been published by M. Losada and Y. Xu titled “Chirality transfer through hydrogen-bonding: Experimental and ab initio analyses of vibrational circular dichroism spectra of methyl lactate in water” in Phys Chem Chem Phys 2007, 9: 3127–3135. In that work they confirm that the effects of water are seen in the VCD spectra and hence it is fundamental to include explicit water molecules in modeling studies of the vibrational spectra of biomolecules in aqueous solution.     

Revisiting proteus: do minor changes in lectin structure matter in biological activity? Lessons from and potential biotechnological uses of the Diocleinae subtribe lectins

Significant differences in function have been observed among lectins structurally similar to concanavalin A, but their high homology with this widely used lectin has kept them in obscurity. The observation of large differences in the potency of many of these Diocleinae lectins as stimulators of Interferon-g production by human peripheral blood mononuclear cells has lead to a major effort to unravel their chemical structure and biological activity. Modeling studies of some of these lectins reveal conformational changes in side chains of some residues involved in the carbohydrate-binding site, with possible effects on the ability of these proteins to recognize specific carbohydrate structures. Additionally, all them constitute in fact a mixture of isolectins, which in different proportions could lead to diverse effects. The present review of the biological actions of Diocleinae lectins includes several in vitro and in vivo immunological findings, as well as their effects on insect growth and reproduction. In these systems Diocleinae lectins proved to be quite diverse in their potency. Such diversity in the biological activity of highly related proteins recalls the origin of the name protein: like Proteus, the capability of assuming various forms is the essential feature of this class of molecules.