Can ortho-para transitions for water be observed?

The spectrum of water can be considered as the juxtaposition of the spectra of two molecules, with different total nuclear spin: ortho-H2O, and para-H2O. No transitions have ever been observed between the two different nuclear-spin isotopomers. The interconversion time is unknown and it is widely assumed that interconversion is forbidden without some other intervention. However, weak nuclear spin-rotation interaction occurs and can drive ortho to para transitions. Ab initio calculations show that the hyperfine nuclear spin-rotational coupling constants are about 30 kHz. These constants are used to explore the whole vibration-rotation spectrum with special emphasis on the coupling between nearby levels. Predictions are made for different spectral regions where the strongest transitions between ortho and para levels of water could be experimentally observed.     

Can multivalency be expressed kinetically? The answer is yes

Inspired by the concept of multivalency and in pursuit of ever more intricate artificial molecular machines, we investigated the strict self-assembly of a triply threaded two-component superbundle, starting from a tritopic receptor in which three benzo[24]crown-8 macrorings are fused onto a triphenylene core and a trifurcated trication wherein three bipyridinium units are linked 1,3,5 to a central benzenoid core. The result of the investigation was quite unexpected and surprising. It transpired that the rapid formation of a doubly threaded two-component complex was followed by an extremely slow conversion (a week at 253 K in CD3COCD3 to reach equilibrium) of this kinetically controlled product into a thermodynamically controlled one, namely a triply threaded two-component superbundle. This intriguing observation begs the question: are there instances in nature where multivalency is expressed as a kinetically controlled process, prior to an equilibrium state being reached, and if so, what are the biological implications, if any?     

Can prenylcysteines be exploited as ligands for mammalian multidrug-resistance transporters?

The overexpression of specific transport proteins in the membrane of many cancer cells renders these cells resistant to many therapeutic drugs. Some lipid-modified cysteine compounds inhibit one drug-transporting protein, indicating the potential of developing such compounds as therapeutic agents.     

Can simple enones be useful partners for the catalytic stereoselective alkylation of indoles?

A new catalytic system for the first example of enantioselective Friedel-Crafts-type (FC) addition of indoles to simple enones is described. The use of an equimolar amount of chiral [Al(salen)Cl] and 2,6-lutidine (10 mol %) was found to be effective in promoting the conjugate addition of indoles to (E)-arylcrotyl ketones, furnishing the corresponding beta-indolyl ketones in excellent yield and high enantioselectivity (ee up to 89%). The role of the base was investigated through spectroscopic as well as computational analyses, which suggested that in situ formation of a new chiral (base.[Al(salen)]) complex was operating under our reaction conditions. In particular, a stable cationic [Al(salen)] hexacoordinate trans complex with the additive base and the enone is suggested as being responsible for the stereocontrolled reaction. Finally, detailed monitoring of the reaction course was carried out showing that a conventional FC pathway induced by [Al(salen)Cl] acting as a Lewis acid is operating.     

Can the speed of sound be used for detecting critical states of fluid mixtures?

The phenomenology of sound speeds in fluid mixtures is examined near and across critical lines. Using literature data for binary and ternary mixtures, it is shown that the ultrasound speed along an isotherm-isopleth passes through a minimum value in the form of an angular (or V-shaped) point at critical states. The relation between critical and pseudo-critical coordinates is discussed. For nonazeotropic fixed-composition fluid mixtures, pseudo-critical temperatures and pressures are found to be lower than the corresponding critical temperatures and pressures. The analysis shows that unstable pseudo-critical states cannot be detected using acoustic methods. The thermodynamic link between sound speeds and isochoric heat capacities is formulated and discussed in terms of p-Vm-T derivatives capable of being calculated using cubic equations of state. Based on the Griffiths-Wheeler theory of critical phenomena, a new specific link between critical sound speeds and critical isochoric heat capacities is deduced in terms of the rate of change of critical pressures and critical temperatures along the p-T projection of the critical locus of binary fluid mixtures. It is shown that the latter link can be used to obtain estimates of critical isochoric heat capacities from the experimental determination of critical speeds of sound. The applicability domain of the new link does not include binary systems at compositions along the critical line for which the rate of change in pressure with temperature changes sign. The new equation is combined with thermodynamic data to provide approximate numerical estimates for the speed of sound in two mixtures of carbon dioxide and ethane at different temperatures along their critical isochores. A clear decrease in the sound speed is found at critical points. A similar behavior is suggested by available critical heat capacity data for several binary fluid mixtures. Using an acoustic technique, the critical temperature and pressure were determined for three different mixtures of methane and propane, and compared with literature data obtained using conventional methods. It is concluded that acoustic-based techniques are reliable to determine, for the most part, critical surfaces of fluid mixtures. The remaining few cases where the present analysis cannot be applied could be tested by the thermodynamic calculation of critical sound speeds using crossover equations of state in conjunction with experimentally determined critical isochoric heat capacities.     

Theoretical calculations: Can Gibbs free energy for intermolecular complexes be predicted efficiently and accurately?

The theoretical study has been performed to refine the procedure for calculations of Gibbs free energy with a relative accuracy of less than 1 kcal/mol. Three benchmark intermolecular complexes are examined via several quantum-chemical methods, including the second-order Moller-Plesset perturbation (MP2), coupled cluster (CCSD(T)), and density functional (BLYP, B3LYP) theories augmented by Dunnings correlation-consistent basis sets. The effects of electron correlation, basis set size, and anharmonicity are systematically analyzed, and the results are compared with available experimental data. The results of the calculations suggest that experimental accuracy can be reached only by extrapolation of MP2 and CCSD(T) total energies to the complete basis set. The contribution of anharmonicity to the zero point energy and TDeltaSint values is fairly small. The new, economic way to reach chemical accuracy in the calculations of the thermodynamic parameters of intermolecular interactions is proposed. In addition, interaction energy (De) and free energy change (DeltaA) for considered species have been evaluated by Carr-Parrinello molecular dynamics (CPMD) simulations and static BLYP-plane wave calculations. The free energy change along the reaction paths were determined by the thermodynamic integration/"Blue Moon Ensemble" technique. Comparison between obtained values, and available experimental and conventional ab initio results has been made. We found that the accuracy of CPMD simulations is affected by several factors, including statistical uncertainty and convergence of constrained forces (TD integration), and the nature of DFT (density functional theory) functional. The results show that CPMD technique is capable of reproducing interaction and free energy with an accuracy of 1 kcal/mol and 2-3 kcal/mol respectively.     

Can TMS and DSS be used as NMR references for cyclodextrin species in aqueous solution?

Tetramethylsilane (TMS) can be included by -cyclodextrin (-CD), and sodium 2,2-dimethylsilapentane-5-sulphonate (DSS) can form inclusion complexes with - and -CD. The NMR chemical shifts are changed considerably as a result of the strong interaction between CD and the guest compound in the inclusion complexes. A downfield shift of as much as 0.63 ppm shift downfield has been observed for the protons of external TMS in CD aqueous solution. In view of this, the question arises of whether TMS and DSS can be used as internal references. DSS in D₂O is suggested as an external reference for aqueous cyclodextrin solution in NMR measurements.     

Can the nonadiabatic photodynamics of aminopyrimidine be a model for the ultrafast deactivation of adenine?

The reaction path for the ultrafast deactivation of 6-aminopyrimidine (6AP) has been investigated by means of ab initio surface-hopping dynamics. The electronic vertical excitation spectrum, excited-state S1 minima, and minima on the crossing seam of 6AP resemble well those found for adenine. The deactivation from the S1 to the S0 state takes place at the ultrafast time scale of 400 fs and involves the out-of-plane ring deformation of the C4 atom, a position that is sterically restricted in adenine by the imidazole ring. Mechanical restrictions have been used to simulate in a simple way the role of the imidazole group in adenine. As a result, deactivation via out-of-plane ring deformation of the C2 and N3 atoms are observed in good agreement with predictions for adenine. These dynamics results show that the previously suggested ring puckering deactivation paths really exist at a time scale, which is compatible with experimentally observed life times. The electronic structure of the crossing seam has been shown to have the same nature as those of simple biradicaloid systems, a feature which seems to be valid for any cyclic system.     

Can the usual validation standard series for quantitative methods,ISO 5725, be also applied for qualitative methods?

Repeatability standard deviation, laboratory standard deviation, and reproducibility standard deviation for quantitative methods according to ISO 5725 series were recently proposed to estimate the precision of qualitative measurements, giving a presence/absence response. In this paper, it is shown that for qualitative methods, the reproducibility standard deviation across laboratories does not reflect the performance of the method as suggested. It is demonstrated that the benefit of the respective laboratory standard deviation is very limited. Alternative performance measures are introduced which are based on another approach also directly linked to ISO 5725. Thereby, meaningful information about the precision of qualitative test methods can be achieved.     

Can glandular hair density be a breeding marker for Origanum vulgare subsp. hirtum with high essential oil content?

Origanum vulgare subsp. hirtum (Link) Ietswaart is an essential oil rich plant traditionally used as oregano. Based on the interest of the essential oil producing sector, in 2000 we have started a breeding program of O. vulgare subsp. hirtum. Plant material for our breeding work consists of 6 progeny. Individual evaluation of the plant material was carried out in 2008-2009 with the primary aim of finding mother plants with appropriate morphological features, high essential oil content (> 7%) and with carvacrol as the main essential oil component. Among the survey of morphological characteristics special attention was given to glandular hair density in order to test the usability of it as a morphological marker for screening progeny for high essential oil content. The characteristics of the progeny can be described with high variability ensuring the possibility of a good selection base. Evaluating the morphology, essential oil content and constitution of the individuals, 20 plants were selected on the grounds of their high (7-8.6%) essential oil content, high ratio (70-93%) of carvacrol in the essential oil and typical morphological features of O. vulgare subsp. hirtum. From the results of glandular hair density it can be stated that the correlation between glandular hair density of the upper, middle and lower leaves either on vegetative or generative shoots and essential oil content was never strong enough (correlation coefficient < or = 0.5) to use it exclusively as a morphological marker for individual selection.     

Can a Procedure for the Growth of Single-layer Graphene on Copper be used in Different Chemical Vapor Deposition Reactors?

In the last decade, catalytic chemical vapor deposition (CVD) has been intensively explored for the growth of single-layer graphene (SLG). Despite the scattering of guidelines and procedures, variables such as the surface texture/chemistry of catalyst metal foils, carbon feedstock, and growth process parameters have been well-scrutinized. Still, questions remain on how best to standardize the growth procedure. The possible correlation of procedures between different CVD setups is an example. Here, two thermal CVD reactors were explored to grow graphene on Cu foil. The design of these setups was entirely distinct, one being a “showerhead” cold-wall type, whereas the other represented the popular “tubular” hot-wall type. Upon standardizing the Cu foil surface, it was possible to develop a procedure for cm²-scale SLG growth that differed only by the carrier gas flow rate used in the two reactors.     

Can a consecutive double turn conformation be considered as a peptide based molecular scaffold for supramolecular helix in the solid state?

Helices and sheets are ubiquitous in nature. However, there are also some examples of self-assembling molecules forming supramolecular helices and sheets in unnatural systems. Unlike supramolecular sheets there are a very few examples of peptide sub-units that can be used to construct supramolecular helical architectures using the backbone hydrogen bonding functionalities of peptides. In this report we describe the design and synthesis of two single turn/bend forming peptides (Boc-Phe-Aib-Ile-OMe 1 and Boc-Ala-Leu-Aib-OMe 2) (Aib: α-aminoisobutyric acid) and a series of double-turn forming peptides (Boc-Phe-Aib-Ile-Aib-OMe 3, Boc-Leu-Aib-Gly-Aib-OMe 4 and Boc-γ-Abu-Aib-Leu-Aib-OMe 5) (γ-Abu: γ-aminobutyric acid). It has been found that, in crystals, on self-assembly, single turn/bend forming peptides form either a supramolecular sheet (peptide 1) or a supramolecular helix (peptide 2), unlike self-associating double turn forming peptides, which have only the option of forming supramolecular helical assemblages.     

Can the absence of solvation of neutral reagents by ionic liquids be responsible for the high reactivity in base-assisted intramolecular nucleophilic substitutions in these solvents?

[reaction: see text] The kinetics of the rearrangement of the Z-phenylhydrazone of 3-benzoyl-5-phenyl-1,2,4-oxadiazole (1a) into the relevant 4-benzoylamino-2,5-diphenyl-1,2,3-triazole (2a) induced by amines have been studied in two room-temperature ionic liquids (IL-1, [BMIM][BF4] and IL-2, [BMIM][PF6]). The data collected show that the reaction occurs faster in ionic liquids than in other conventional solvents previously studied (both polar or apolar, protic or aprotic). Presumably, this could depend on their peculiar ability to minimize the strong substrate-solvent, amine-solvent and amine-amine interactions occurring in conventional solvents.     

Chemical characterization,computational analysis and biological views on Daphne gnidioides Jaub. & Spach extracts: Can a new raw material be provided for biopharmaceutical applications?

The scientific world tends to turn to natural products such as medicinal and aromatic plants because of the inadequacy of commercially available synthetic drugs as antibiotics or anticancer, and their adverse effects on healthy tissues. One of these plants is Daphne gnidioides Jaub. & Spach, which belongs to the Thymelaeaceae family, and there is no data in the literature on its biological activity. This study is aimed to elucidate the chemical profiles and in vitro anticancer, antibacterial and DNA protection and enzyme inhibitory properties of methanol extracts of root, stem, and leaf of D. gnidioides Jaub. & Spach. Polyphenolic components of the extracts were characterized by HPLC-MS/MS. The highest phenolic content was detected in the leaf extract (TIPC = 43.5 ± 0.5 mg/g DE), followed by stem (TIPC = 27.3 ± 0.7 mg/g DE) and root (TIPC = 18.3 ± 0.2 mg/g DE) extracts. Vicenin-2 and 3-O-p-coumaroyl-5-O-caffeoylquinic acid were the main identified compounds in leaf and both root and stem extracts, respectively. The extracts did not show any protective effect on DNA against experimental Fenton’s reagent. The minimum inhibitory concentration and the minimum bactericidal concentration values for the root and leaf extracts against tested bacterial strains ranged from 31.25 to 500 μg/mL. After 48 h interaction of the cancer cell lines with the extracts, only the stem extract had significant cytotoxicity on HeLa cells (IC₅₀ = 86.16 μg/mL). No remarkable activity of the extracts, which was tested against MDA-MB-231, was detected (IC₅₀ > 1000 μg/mL). These data showed that D. gnidioides Jaub. & Spach stem extract inhibited the survival of HeLa cells in a time-dependent manner. After the treatment of IC₅₀ concentration of stem extract with HeLa cells, an increase in LC3-II autophagic gene expression was detected. Also, the extracts exhibited significant tyrosinase inhibitory effects which were confirmed by molecular docking. To sum up, the tested extracts could be used as a starting point for the development of new multifunctional drugs.     

A reliable and efficient first principles-based method for predicting pKa values. III. Adding explicit water molecules: Can the theoretical slope be reproduced and pKa values predicted more accurately?

A popular method for predicting pK(a) values for organic molecules in aqueous solution is to establish empirical linear least-squares fits between calculated deprotonation energies and known experimental pK(a) values. In virtually all such calculations, the empirically observed slope of the pK(a) vs. ΔE fit is significantly less than the theoretical value, 1/(2.303RT) (which is 0.73 mol/kcal at room temperature). In our own continuum solvation calculations (Zhang et al., J Phys Chem A 2010, 114, 432), the empirical slope for carboxylic acids was only 0.23 mol/kcal, despite the excellent fit to the experimental pK(a) values. There has been much speculation about the reason for this phenomenon. Although the ΔE - pK(a) relation neglects entropic effects, these are expected to largely cancel. The most likely cause for the strange behavior of the fitted slope is explicit solute-solvent (water) interactions, especially involving the ions, which cannot be described accurately by continuum solvation models. We used our previously developed pK(a) protocol (OLYP/6-311+G(d,p)//3-21G(d) with the COSMO solvation model) to investigate the effect of adding one or two explicit water molecules to the system. The slopes for organic acids (especially carboxylic acids) are much closer to the theoretical value when explicit water molecules are added to both the neutral molecule and the anion. However, explicit water molecules have almost no effect on the slopes for organic bases. Adding explicit water molecules to the ions only produces intermediate results. Unfortunately, linear fits involving explicit water molecules have much larger errors than with continuum solvation models alone and are also much more expensive. Consequently, they are not suitable for large-scale pK(a) calculations. The results compared with literature values showed that our predicted pK(a) s are more accurate.     

Calculations of the effect of tunneling on the Swain-Schaad exponents (SSEs) for the 1,5-hydrogen shift in 5-methyl-1,3-cyclopentadiene. Can SSEs be used to diagnose the occurrence of tunneling?

MPW1K density functional calculations, carried out with the 6-31+G(d,p) basis set, have been combined with canonical variational transition state theory (CVT) and small-curvature tunneling (SCT) corrections in order to compute the primary kinetic isotope effects for rearrangement of 5-methyl-1,3-cyclopentadiene (1) to 1-methyl-1,3-cyclopentadiene (2). The Swain-Schaad exponents, SSE = ln(kH/kT)/ln(kD/kT), for this reaction have been computed over the temperature range 100-600 K. Tunneling results in both large positive and large negative deviations from the value of SSE = 3.26, expected from consideration of only the effect of the isotopic mass on passage over the reaction barrier. In the rearrangement of 1 to 2, SSE approximately 3.26, not only at temperatures >400 K, where tunneling is relatively unimportant, but also around 170 K, where tunneling by both H and D is the dominant mode of reaction. Thus, from an experimental finding that SSE approximately 3.26 at a single temperature, it cannot be rigorously concluded that tunneling is unimportant. Measurement of SSEs over a broad temperature range is advisable; but measurement of the temperature dependence of just kH/kD can be used to establish more unequivocally whether tunneling is important, without the necessity of measuring kT.