Small and efficient basis sets for the evaluation of accurate interaction-induced linear and non-linear electric properties in model hydrogen-bonded complexes

Interaction-induced electric dipole moment, polarisability and first hyperpolarisability are investigated in model hydrogen-bonded clusters built of hydrogen fluoride molecules organised in three linear chains parallel to each other. The properties are evaluated within the finite field approach, using the second order Møller–Plesset method, and the LPol-m (m = ds, dl) and the optical rotation prediction (ORP) basis sets. These bases and correlation method are selected after a systematic basis set and correlation method convergence study carried out on the smallest of the complexes and taking properties obtained with Dunning's bases and the coupled cluster singles and doubles (CCSD) and the CCSD including connected triple corrections (CCSD(T)) methods as reference. Results are analysed in terms of many-body and cooperative effects.     

Site‐Resolved Observation of Vibrational Energy Transfer Using a Genetically Encoded Ultrafast Heater

Allosteric information transfer in proteins has been linked to distinct vibrational energy transfer (VET) pathways in a number of theoretical studies. Experimental evidence for such pathways, however, is sparse because site‐selective injection of vibrational energy into a protein, that is, localized heating, is required for their investigation. Here, we solved this problem by the site‐specific incorporation of the non‐canonical amino acid β‐(1‐azulenyl)‐l ‐alanine (AzAla) through genetic code expansion. As an exception to Kasha's rule, AzAla undergoes ultrafast internal conversion and heating after S₁ excitation while upon S₂ excitation, it serves as a fluorescent label. We equipped PDZ3, a protein interaction domain of postsynaptic density protein 95, with this ultrafast heater at two distinct positions. We indeed observed VET from the incorporation sites in the protein to a bound peptide ligand on the picosecond timescale by ultrafast IR spectroscopy. This approach based on genetically encoded AzAla paves the way for detailed studies of VET and its role in a wide range of proteins.     

Modelling the active SARS-CoV-2 helicase complex as a basis for structure-based inhibitor design

The RNA helicase (non-structural protein 13, NSP13) of SARS-CoV-2 is essential for viral replication, and it is highly conserved among the coronaviridae family, thus a prominent drug target to treat COVID-19. We present here structural models and dynamics of the helicase in complex with its native substrates based on thorough analysis of homologous sequences and existing experimental structures. We performed and analysed microseconds of molecular dynamics (MD) simulations, and our model provides valuable insights to the binding of the ATP and ssRNA at the atomic level. We identify the principal motions characterising the enzyme and highlight the effect of the natural substrates on this dynamics. Furthermore, allosteric binding sites are suggested by our pocket analysis. Our obtained structural and dynamical insights are important for subsequent studies of the catalytic function and for the development of specific inhibitors at our characterised binding pockets for this promising COVID-19 drug target.

The RNA helicase (non-structural protein 13, NSP13) of SARS-CoV-2 is essential for viral replication, and it is highly conserved among the coronaviridae family, thus a prominent drug target to treat COVID-19.     

Polymer-assisted solution-phase (PASP) Suzuki couplings employing an anthracene-tagged palladium catalyst

A general method for polymer-assisted solution-phase (PASP) Suzuki reactions employing a combination of anthracene-tagged palladium catalyst and anthracene-tagged boronic acid with a polymer-supported carbonate base is reported. The anthracene-tagged catalyst allows for the easy removal of the Pd catalyst along with the dissociated phosphine ligand and phosphine oxide byproducts by sequestration through a chemoselective Diels-Alder reaction with a maleimide resin. The polymer-supported carbonate base facilitates the removal of excess boronic acid and the borane-containing byproducts present at the end of the coupling reaction. The Suzuki coupling reaction can be efficiently conducted by using combinations of the anthracene-tagged Pd catalyst, polymer-supported carbonate base, and anthracene-tagged boronic acid to yield the desired product in high purity and yield without the use of chromatography.     

An evolutionary analysis of the reaction mechanisms of photosystem I reduction by cytochrome c(6) and plastocyanin.

Photosystem I reduction by the soluble metalloproteins cytochrome c(6) and plastocyanin, which are alternatively synthesized by some photosynthetic organisms depending on the relative availability of copper and iron, has been investigated in cyanobacteria, green algae and plants. The reaction mechanism is classified in three different types on the basis of the affinity of the membrane complex towards its electron donor protein. The role of electrostatic interactions in forming an intermediate transient complex, as well as the structural and functional similarities of cytochrome c(6) and plastocyanin are analysed from an evolutionary point of view. The proposal made is that the heme protein was first "discovered" by nature, when iron was much more abundant on the Earth's surface, and replaced by plastocyanin when copper became available because of the oxidizing conditions of the new atmosphere.     

Anion-/cation-directed reaction routes to polymorphic forms of a pyrazole-type ligand and its coordination compounds with zinc. Key structural differences between polymorphs’

Synthetic paths toward the two polymorphs of a monohydrate, one anhydrous polymorph of 1-carboxamidino-5-hydroxy-3-methylpyrazole (hcmp) and two polymorphs of zinc complexes containing hcmp ligand are presented. By choosing ions which are not part of the final product, it is possible to direct the synthesis toward the particular polymorph. In all three modifications of hcmp, the same hydrogen bonding motif appears, leading to formation of similar molecular chains. Differences arise due to different modes of chain aggregation and the presence of solvent water. Analysis of the crystal packing and the energetic features of hcmp polymorphs is made using the PIXEL model. The thermal decomposition processes are examined using differential scanning calorimetry and thermogravimetry. Analysis of crystal packing in the two polymorphs of zinc complex suggests the key role of the hydrogen bonding capacity of the aqua ligand for the appearance of the two polymorphic forms. In both polymorphs of zinc complex, stacking interactions have an important role. However, the enhanced hydrogen bonding capacity of the aqua ligand influences the formation of multistacking arrangement.     

A new bis(1-naphthylimino)acenaphthene compound and its Pd(II) and Zn(II) complexes: synthesis, characterization, solid-state structures and density functional theory studies on the syn and anti isomers

A new rigid bidentate ligand, bis(1-naphthylimino)acenaphthene, L1, and its Zn(II) and Pd(II) complexes [ZnCl 2( L1)], 1, and [PdCl 2( L1)], 2, were synthesized. L1 was prepared by the "template method", reacting 1-naphthyl amine and acenaphthenequinone in the presence of ZnCl 2, giving 1, which was further demetallated. Reaction of 1-naphthyl amine with acenaphthenequinone and PdCl 2 afforded dichloride bis(1-naphthyl)acenaphthenequinonediimine palladium, 2. L1, 1, and 2 were obtained as a mixture of syn and anti isomers. Compound 2 was also obtained by the reaction of PdCl 2 activated by refluxing it in acetonitrile followed by the addition of L1; by this route also a mixture of syn and anti isomers was obtained, but at a different rate. The solid-state structures of L1 and the anti isomer of compound 2 have been determined by single-crystal X-ray diffraction. All compounds have been characterized by elemental analyses; matrix-assisted laser desorption ionization-time-of-flight-mass spectrometry; IR; UV-vis; (1)H, (13)C, and (1)H- (1)H correlation spectroscopy; (1)H- (13)C heteronuclear single quantum coherence; (1)H- (13)C heteronuclear single quantum coherence-total correlation spectroscopy; and (1)H- (1)H nuclear Overhauser effect spectrometry NMR spectroscopies when applied. Density functional theory studies showed that both conformers for [PdCl 2(BIAN)] are isoenergetic, and they can both be obtained experimentally. However, we can predict that the isomerization process is not available in a square-planar complex, but it is possible for the free ligand. The molecular geometry is very similar in both isomers, and only different orientations for naphthyl groups can be expected.     

A theoretical study of 1-amino-3-butene and 3-butene-1-thiol

Conformational analysis of 1-amino-3-butene and 3-butene-1-thiol was carried out using the 4-21G basis set. The conformers obtained were subjected to 6-31G^* single-point analysis for the calculation of energies, charge distributions, and dipole moments. The geometries and stabilities obtained are in good agreement with available experimental data. The results are interpreted in terms of intramolecular hydrogen bonding and anomeric interactions: Some of the most stable conformers of both molecules have intramolecular hydrogen bonds between the hydrogens of the amino or thiol groups and the electrons of the double bond. The 4-21G geometries were refined to obtain rotational constants closer to the experimental values.