Exact conditions in finite-temperature density-functional theory

Density-functional theory (DFT) for electrons at finite temperature is increasingly important in condensed matter and chemistry. The exact conditions that have proven crucial in constraining and constructing accurate approximations for ground-state DFT are generalized to finite temperature, including the adiabatic connection formula. We discuss consequences for functional construction.     

Activation of hafnocene catalyzed polymerization of 1-hexene with MAO and borate

A study of 1-hexene polymerization with ethylene-bis(9-fluorenyl) hafnium dichloride has been carried out using two different cocatalyst systems, methyl-aluminoxane/trimethylaluminum (MAO/TMA) and tris-isobutyl-aluminum/N,N-dimethylanilinium tetrakis(pentafluorophenyl) borate (TIBA/borate). When MAO/TMA was used, 1-hexene polymerized into a low molar mass poly(1-hexene) with low catalytic activity. Activation with TIBA/borate increased polymerization activity drastically as well as the molar mass of the polymers. In order to analyze differences in the activity profiles, UV-Vis spectroscopy was employed to investigate ligand to metal charge transitions (LMCT) of the hafnocene dichloride during the activation process. The low catalytic activity and the fast chain transfer to the cocatalyst with MAO/TMA may originate from strong bonding between the metallocene cation and the MAO/TMA species thus obstructing monomer coordination and insertion.     

A new glucosidic phthalide from Helichrysum microphyllum subsp. tyrrhenicum from La Maddalena Island (Sardinia,Italy)

In this study, we reported the analysis of the medium polarity fraction obtained from an accession of Helichrysum microphyllum subsp. tyrrhenicum from La Maddalena Island. Besides several compounds already evidenced in this species and related genera, i.e. micropyrone (1), arzanol (2), helipyrone (3), acetyl-bitalin derivatives (4, 5), gnaphaliol (6), caffeic acid (7), ursolic acid (8), 7-O-β-(d-glucopyranosyl)-5-methoxy-1(3H)-isobenzofuranone (9), gnaphaliol-9-O-β-d-glucopyranoside (11) and gnaphaliol-3-O-β-d-glucopyranoside (12), the presence of a new glycosidic phthalide, 6-O-β-(d-glucopyranosyl)-4-methoxy-1(3H)-benzofuranone (10), was evidenced for the first time, which resulted in a structural isomer of compound (9). The occurrence of this new benzofuranone derivative is an additional evidence of the deep intraspecific variability expressed by this species, which was also stated for the non-volatile components, and may be a distinctive trait of the population growing on La Maddalena Island.     

Theoretical modeling of enzyme reactions: the thermodynamics of formation of compound 0 in horseradish peroxidase

In this paper, by using the perturbed matrix method (PMM) in combination with basic statistical mechanical relations both based on nanosecond time-scale molecular dynamics (MD) simulations, we quantitatively address the thermodynamics of compound 0 (Cpd 0) formation in horseradish peroxidase (HRP) enzyme. Our results, in the same trend of low-temperature experimental data, obtained in cryoenzymology studies indicate that such a reaction can be described essentially as a stepwise spontaneous process: a first step mechanically constrained, strongly exothermic proton transfer from the heme-H2O2 complex to the conserved His42, followed by a solvent-protein relaxation involving a large entropy increase. Critical evaluation of PMM/MD data also reveals the crucial role played by specific residues in the reaction pocket and, more in general, by the conformational fluctuations of the overall environment in physiological conditions.     

Complex formation processes of terminally protected peptides containing two or three histidyl residues. Characterization of the mixed metal complexes of peptides

Copper(ii), nickel(ii) and zinc(ii) complexes of the peptides Ac-HVVH-NH(2) and Ac-HAAHVVH-NH(2) have been studied by potentiometric, UV-vis, CD, EPR and NMR spectroscopic measurements. Both tetra and heptapeptides can form relatively stable macrochelates with copper(ii), nickel(ii) and zinc(ii) ions, in which the ligands are coordinated via the side-chain imidazole functions. Formation of the macrochelates slightly suppresses, but cannot prevent the copper(ii) and nickel(ii) ion promoted deprotonation and coordination of the amide functionalities. The overall stoichiometry of the major species is [MH(-3)L](-) with a 4N (= N(-),N(-),N(-),N(im)) coordination mode. In the case of Ac-HAAHVVH-NH(2), coordination isomers of this species can exist with a preference for copper(ii) or nickel(ii) binding at the internal histidyl residue. In the copper(ii)-Ac-HAAHVVH-NH(2) system, the presence of the two anchoring sites results in the formation of dinuclear complexes. The existence of these species requires the involvement of amide functions in metal binding. Both equilibrium and spectroscopic data support the fact that the copper(ii) ions of the dinuclear species are independent from each other providing a good chance for the formation of various mixed metal complexes. It was found that zinc(ii) is not able to significantly alter the copper(ii) binding of the heptapeptide, but it can occupy the uncoordinated histidyl sites. The formation of the copper(ii)-nickel(ii) mixed species was obtained in alkaline solutions and CD spectra suggest the statistical distribution of the two metal ions among the histidyl residues. The binding of HAAHVVH to palladium(ii) is exclusive below pH 8 and the mixed metal species of palladium(ii) and copper(ii) ions are formed only in slightly basic solutions.     

Ring-breaking electron attachment to uracil: following bond dissociations via evolving resonances

Calculations are carried out at various distinct energies to obtain both elastic cross sections and S-matrix resonance indicators (poles) from a quantum treatment of the electron scattering from gas-phase uracil. The low-energy region confirms the presence of pi(*) resonances as revealed by earlier calculations and experiments which are compared with the present findings. They turn out to be little affected by bond deformation, while the transient negative ions (TNIs) associated with sigma(*) resonances in the higher energy region ( approximately 8 eV) indeed show that ring deformations which allow vibrational redistribution of the excess electron energy into the molecular target strongly affect these shape resonances: They therefore evolve along different dissociative pathways and stabilize different fragment anions. The calculations further show that the occurrence of conical intersections between sigma(*) and pi(*)-type potential energy surfaces (real parts) is a very likely mechanism responsible for energy transfers between different TNIs. The excess electron wavefunctions for such scattering states, once mapped over the molecular space, provide nanoscopic reasons for the selective breaking of different bonds in the ring region.     

N‐ and O‐linked glycosylation site profiling of the human basic salivary proline‐rich protein 3M

In the present study, we show that the heterogeneous mixture of glycoforms of the basic salivary proline‐rich protein 3M, encoded by PRB3‐M locus, is a major component of the acidic soluble fraction of human whole saliva in the first years of life. Reversed‐phase high‐performance liquid chromatography with high‐resolution electrospray ionization mass spectrometry analysis of the intact proteoforms before and after N‐deglycosylation with Peptide‐N‐Glycosidase F and tandem mass spectrometry sequencing of peptides obtained after Endoproteinase GluC digestion allowed the structural characterization of the peptide backbone and identification of N‐ and O‐glycosylation sites. The heterogeneous mixture of the proteoforms derives from the combination of 8 different neutral and sialylated glycans O‐linked to Threonine 50, and 33 different glycans N‐linked to Asparagine residues at positions 66, 87, 108, 129, 150, 171, 192, and 213.     

A Friendly Complexing Agent for Spectrophotometric Determination of Total Iron

Iron, one of the most common metals in the environment, plays a fundamental role in many biological as well as biogeochemical processes, which determine its availability in different oxidation states. Its relevance in environmental and industrial chemistry, human physiology, and many other fields has made it necessary to develop and optimize analysis techniques for accurate determination. Spectrophotometric methods are the most frequently applied in the analytical determination of iron in real samples. Taking advantage of the fact that desferrioxamine B, a trihydroxamic acid used since the 1970s in chelation therapy for iron overload treatment, forms a single stable 1:1 complex with iron in whichever oxidation state it can be found, a smart spectrophotometric method for the analytical determination of iron concentration was developed. In particular, the full compliance with the Lambert-Beer law, the range of iron concentration, the influence of pH, and the interference of other metal ions have been taken into account. The proposed method was validated in terms of LoD, LoQ, linearity, precision, and trueness, and has been applied for total iron determination in natural water certified material and in biological reference materials such as control human urine and control serum.     

Complexes of helium with neutral molecules: Progress toward a quantitative scale of bonding character

The complexes of helium with nearly 30 neutral molecules (M) were investigated by various techniques of bonding analysis and symmetry-adapted perturbation theory (SAPT). The main investigated function was the local electron energy density H( r ), analyzed, in particular, so to estimate the degree of polarization (DoP) of He in the various He(M). As we showed recently (Borocci et al., J. Comput. Chem., 2019, 40, 2318–2328), the DoP is a quantitative index that is generally informative about the role of polarization (induction plus charge transfer [CT]) and dispersion in noncovalent noble gas complexes. As further evidence in this regard, we presently ascertained quantitative correlations between the DoP(He) of the He(M) and indices based on the electron density ρ( r ), including the molecular electrostatic potential at the He M bond critical point, as well as the percentage contributions of induction and dispersion to the SAPT binding energies. Based also on the explicit evaluation of the CT, accomplished through the study of the charge-displacement function, we derived a quantitative scale that ranks the He(M) according to their dispersive, inductive, and CT bonding character. Our taken approach could be conceivably extended to other types of noncovalent complexes.     

Comparison of virtual high-throughput screening methods for the identification of phosphodiesterase-5 inhibitors

Reliable and effective virtual high-throughput screening (vHTS) methods are desperately needed to minimize the expenses involved in drug discovery projects. Here, we present an improvement to the negative image-based (NIB) screening: the shape, the electrostatics, and the solvation state of the target protein's ligand-binding site are included into the vHTS. Additionally, the initial vHTS results are postprocessed with molecular mechanics/generalized Born surface area (MMGBSA) calculations to estimate the favorability of ligand-protein interactions. The results show that docking produces very good early enrichment for phosphodiesterase-5 (PDE-5); however, in general, the NIB and the ligand-based screening performed better with or without the added electrostatics. Furthermore, the postprocessing of the NIB screening results using MMGBSA calculations improved the early enrichment for the PDE-5 considerably, thus, making hit discovery affordable.