Fluorescence lifetime of Nile Red as a probe for the hydrogen bonding strength with its microenvironment

The fluorescence lifetime of Nile Red (NR) is not sensitive to dielectric solvent–solute interactions but markedly decreases with the increase of the hydrogen bond donating ability in alcohols because vibrations associated with hydrogen bonding are involved in the deactivation process. The negligible viscosity effect indicates that twisting of the diethylamino moiety of NR does not play significant role in the dissipation of the excitation energy.     

Diminished gradient dependence of density functionals: constraint satisfaction and self-interaction correction

The Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation for the exchange-correlation energy functional has two nonempirical constructions, based on satisfaction of universal exact constraints on the hole density or on the energy. We show here that, by identifying one possible free parameter in exchange and a second in correlation, we can continue to satisfy these constraints while diminishing the gradient dependence almost to zero (i.e., almost recovering the local spin density approximation or LSDA). This points out the important role played by the Perdew-Wang 1991 nonempirical hole construction in shaping PBE and later constructions. Only the undiminished PBE is good for atoms and molecules, for reasons we present, but a somewhat diminished PBE could be useful for solids; in particular, the surface energies of solids could be improved. Even for atoms and molecules, a strongly diminished PBE works well when combined with a scaled-down self-interaction correction (although perhaps not significantly better than LSDA). This shows that the undiminished gradient dependence of PBE and related functionals works somewhat like a scaled-down self-interaction correction to LSDA.     

Communication: Effect of the orbital-overlap dependence in the meta generalized gradient approximation

We study for the first time the effect of the dependence of meta generalized gradient approximation (MGGA) for the exchange-correlation energy on its input, the kinetic energy density, through the dimensionless inhomogeneity parameter, α, that characterizes the extent of orbital overlap. This leads to a simple MGGA exchange functional, which interpolates between the single-orbital regime, where α = 0, and the slowly varying density regime, where α ≈ 1, and then extrapolates to α → ∞. When combined with a variant of the Perdew-Burke-Ernzerhof GGA correlation, the resulting MGGA performs equally well for atoms, molecules, surfaces, and solids.     

Prescription for the design and selection of density functional approximations: more constraint satisfaction with fewer fits

We present the case for the nonempirical construction of density functional approximations for the exchange-correlation energy by the traditional method of "constraint satisfaction" without fitting to data sets, and present evidence that this approach has been successful on the first three rungs of "Jacob's ladder" of density functional approximations [local spin-density approximation (LSD), generalized gradient approximation (GGA), and meta-GGA]. We expect that this approach will also prove successful on the fourth and fifth rungs (hyper-GGA or hybrid and generalized random-phase approximation). In particular, we argue for the theoretical and practical importance of recovering the correct uniform density limit, which many semiempirical functionals fail to do. Among the beyond-LSD functionals now available to users, we recommend the nonempirical Perdew-Burke-Ernzerhof (PBE) GGA and the nonempirical Tao-Perdew-Staroverov-Scuseria (TPSS) meta-GGA, and their one-parameter hybrids with exact exchange. TPSS improvement over PBE is dramatic for atomization energies of molecules and surface energies of solids, and small or moderate for other properties. TPSS is now or soon will be available in standard codes such as GAUSSIAN, TURBOMOLE, NWCHEM, ADF, WIEN, VASP, etc. We also discuss old and new ideas to eliminate the self-interaction error that plagues the functionals on the first three rungs of the ladder, bring up other related issues, and close with a list of "do's and don't's" for software developers and users.     

Essential oil polymorphism of wild growing Hungarian thyme (Thymus pannonicus) populations in the Carpathian Basin

The volatile oil compositions of Thymus pannonicus All. from nineteen different localities of Hungary were analyzed by GC/MS. The essential oil content of the Hungarian thyme samples varied between very low (0.14 mL/100 g DW) and fairly high (1.9 mL/100 g DW) values. Significant essential oil polymorphism was found: altogether twelve chemovarieties may have been determined, representing a way of adaptation to different habitat conditions. The main volatile compound of chemotype 1 was thymol (24.6-67.5%), while in the case of chemotype 2, thymol (36.5-63.7%) and p-cymene (11.5-27.3%) predominated. Thymol (28.4-63.7%), p-cymene (11.5-31.8%) and gamma-terpinene (9.7-20.9%) were identified as the chief monoterpenes of chemotype 3, while chemotype 4 contained thymol (36.5%), p-cymene (27.3%) and neral (11.2%). Chemotype 5 accumulated thymol (38.5%), p-cymene (20.6%), gamma-terpinene (12.0%) and beta-bisabolene (10.3%) as its main volatiles. The oil of chemotype 6 can be characterized by thymol (41.9%), p-cymene (20.2%), isoborneol (10.3%) and gamma-terpinene (9.9%), while that of chemotype 7 consisted of thymol (27.7%), linalyl acetate (18.8%), gamma-terpinene (18.6%) and alpha-cubebene (13.9%). In the oil of chemotype 8, p-cymene (45.0%), geraniol (13.6%) and linalyl acetate (9.9%) were found in higher percentages, while chemotype 9 mainly produced linalyl acetate (36.2%) and geranyl acetate (20.2%). Chemotype 10 accumulated germacrene-D (43.4) and beta-caryophyllene (15.0%), while the oil of chemotype 11 contained caryophyllene oxide (45.2%), alpha-cubebene (15.7%) and linalool (13.8%) in high proportions. Germacrene-D (29.7%), beta-caryophyllene (22.0%) and farnesol (10.4%) were identified as main essential oil compounds of chemotype 12. The last nine chemotypes were new for the literature, while the first seven contained thymol as their chief compound. The role of certain sesquiterpenes was found to be considerable.     

Assignment of Vibrational Circular Dichroism Cross-Referenced Electronic Circular Dichroism Spectra of Flexible Foldamer Building Blocks: Towards Assigning Pure Chiroptical Properties of Foldamers

Assignment of the most established electronic circular dichroism (ECD) spectra of polypeptides and foldamers is either “evidence based” or relies on the 3D structures of longer oligomers of limited internal dynamics, which are derived from NMR spectroscopy (or X-ray) data. Critics warn that the use of NMR spectroscopy and ECD side by side has severe limitations for flexible molecules because explicit knowledge of conformational ensembles is a challenge. Herein, an old–new method of comparing ab initio computed and measured vibrational circular dichroism (VCD) data is presented to validate both the structures (conf(i)) and their relative weights (c(i)) that make up the conformational ensemble. Based on the array of {conf(i), c(i)}, the pure ECD spectra, g(i)^conf(i), can be ab initio calculated. The reconstructed spectrum Σc(i)g(i)^conf(i) can thus help to assign any experimental ECD counterparts. Herein, such a protocol is successfully applied to flexible foldamer building blocks of sugar β-amino acid diamides. The epimeric pair of the model system was selected because these molecules were conformationally tunable by simple chemical modification, and thus, the robustness of the current approach could be probed. The initial hydrogen bond (NH⋅⋅⋅O) eliminated by N-methylation reorients the amide plain, which influences the chiroptical properties of the foldamer building block; this structural change is successfully monitored by changes to the VCD and ECD transitions, which are now assigned to pure conformers. The current method seems to be general and effective without requiring extensive CPU and spectroscopic resources.     

Development and validation of a cyclodextrin‐modified capillary electrophoresis method for the enantiomeric separation of vildagliptin enantiomers

The enantiomers of vildagliptin, an orally available and selective dipeptidyl‐peptidase‐4 inhibitor used for the treatment of type II diabetes, have been separated by CD‐modified CZE, using uncoated fused‐silica capillary. After screening 13 negatively charged CD derivatives as potential chiral selectors, sulfobutyl‐ether‐α‐CD (SBE‐α‐CD) was selected for the enantioseparation. For the optimization, a factorial analysis study was performed by orthogonal experimental design. Six experimental factors were chosen as variable parameters: temperature, applied voltage, chiral selector and BGE concentrations, pH, and the parameters of the hydrodynamic injection. The optimized system still was not considered final as the second peak (S‐enantiomer) migrated too close to the EOF, resulting in a potential inaccuracy during the determination of the chiral impurity. To fine‐tune the method “one factor at a time” variation approach was applied. The final method (applying 15°C capillary temperature, 40 mbar × 4 s hydrodynamic injection, 25 kV voltage in 75 mM acetate‐Tris buffer [pH 4.75] containing 20 mM SBE‐α‐CD as chiral selector) was validated according to the ICH guideline. RSD percentage of the resolution value, migration times, and corrected peak areas were below 5% during testing repeatability and intermediate precision. LOD and LOQ values were found to be 2.5 and 7.5 μg/mL, respectively. The method is considered linear in the 7.5–180 μg/mL range for the R‐enantiomer. The robustness of the method was justified using Plackett–Burmann statistical experimental design.     

Density functionals that are one- and two- are not always many-electron self-interaction-free, as shown for H2+, He2+, LiH+, and Ne2+

The common density functionals for the exchange-correlation energy make serious self-interaction errors in the molecular dissociation limit when real or spurious noninteger electron numbers N are found on the dissociation products. An "M-electron self-interaction-free" functional for positive integer M is one that produces a realistic linear variation of total energy with N in the range of M-12. Thus all these SIC's produce an exact binding energy curve for H2+, and an accurate one for He2+, but only the unscaled Perdew-Zunger SIC produces an accurate one for Ne2+, where there are more than two electrons on each fragment Ne+0.5. We also discuss LiH+, which is relatively free from self-interaction errors. We suggest that the ability of the original and unscaled Perdew-Zunger SIC to be nearly M-electron self-interaction-free for atoms of all M stems in part from its formal resemblance to the Hartree-Fock theory, with which it shares a sum rule on the exchange-correlation hole of an open system.     

Comparative study of the three different fluorophore antibody conjugation strategies

The progression in bioconjugational chemistry has significantly contributed to the evolution and success of protein biology. Mainly, antibody chemistry has been a subject of intensive study owing to the expansion of research areas warranted by using various derivatives of conjugated antibodies. Three reactive moieties (amine, sulfhydryl and carbohydrate) in the antibodies are chiefly favored for the conjugational purpose. This feature is known for decades, nevertheless, amine based conjugation is still the most preferred strategy despite the appreciation the other two methods receive in conserving the antigen binding affinity (ABA). No single report has been published, according to our knowledge, where these three conjugation strategies were applied to the same fluorophore antibody systems. In this study, we evaluated conjugation yield, time demand and cost efficiency of these conjugation procedures. Our results showed that amine based conjugations was by far the best technique due to its simplicity, rapidity, ease of operation, higher conjugate yield, cheaper cost and potential for larger fluorophore/protein labeling ratio without having much effect in ABA. Furthermore, sulfhydryl labeling clearly excelled in terms of reduced non-specific binding and mild effect in ABA but was usually complicated by an asymmetric antibody reduction due to mercaptoethylamine while carbohydrate oxidation based strategy performed the worst during our experiment.     

Binding energy curves from nonempirical density functionals. I. Covalent bonds in closed-shell and radical molecules

Binding or potential energy curves have been calculated for the ground-state diatomics H(2)(+), He(2)(+), LiH(+), H(2), N(2), and C(2), for the transition state H(3), and for the triplet first excited state of H(2) using the nonempirical density functionals from the first three rungs of a ladder of approximations: the local spin density (LSD) approximation, the Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA), and the Tao-Perdew-Staroverov-Scuseria (TPSS) meta GGA. Good binding energy curves in agreement with coupled cluster or configuration interaction calculations are found from the PBE GGA and especially from the TPSS meta GGA. Expected exceptions are the symmetric radicals H(2)(+) and He(2)(+), where the functionals suffer from self-interaction error, and the exotically bonded C(2). Although the energy barrier for the reaction H(2) + H --> H + H(2) is better in PBE than in TPSS, the transition state H(3) is a more properly positioned and curved saddle point of the energy surface in TPSS. The triplet first excited state of H(2) obeys the Aufbau principle and thus is one of the exceptional excited states that are computable in principle from the ground-state functional. The PBE GGA and TPSS meta GGA are useful not only for chemical applications but also for the construction of higher-rung nonempirical functionals that can further improve the binding energy curves.