Multipolar Atom Types from Theory and Statistical Clustering (MATTS) Data Bank: Restructurization and Extension of UBDB.

A fast and accurate operational model of electron density is crucial in many scientific disciplines including crystallography, molecular biology, pharmaceutical, and structural chemistry. In quantum crystallography, the aspherical refinement of crystal structures is becoming increasingly popular because of its accurate description in terms of physically meaningful properties. The transferable aspherical atom model (TAAM) is quick and precise, though it requires a robust algorithm for atom typing and coverage of the most popular atom types present in small organic molecules. Thus, the University at Buffalo Databank (UBDB) has been renamed to the Multipolar Atom Types from Theory and Statistical clustering (MATTS) data bank, broadened, restructured, and implemented into the software DiSCaMB with 651 atom types obtained from 2316 small-molecule crystal structures containing C, H, N, O, P, S, F, Cl, and Br atoms. MATTS2021 data bank now covers most of the small molecules, peptides, RNA, DNA, and some frequently occurring cations and anions in biological, pharmaceutical, and organic materials, including the majority of known crystal structures composed of the above elements. The multipole model parameters (Pval, κ, κ', Plm) obtained for different atom types were greatly influenced by neighboring atom types, hybridization, geometrical strain in the ring system, and charges on the molecule. Contrary to previous findings, the atoms showing variable oxidation states and ions deviate from the linear dependence of monopole-derived charges on the expansion-contraction κ parameter.

Activation of the Hg-C Bond of Methylmercury by [S2]-Donor Ligands.

Here we report that [S2]-donor ligands BmmOH, BmmMe, and BmeMe bind rapidly and reversibly to the mercury centers of organomercurials, RHgX, and facilitate the cleavage of Hg-C bonds of RHgX to produce stable tetracoordinated Hg(II) complexes and R2Hg. Significantly, the rate of cleavage of Hg-C bonds depends critically on the X group of RHgX (X = BF4-, Cl-, I-) and the [S2]-donor ligands used to induce the Hg-C bonds. For instance, the initial rate of cleavage of the Hg-C bond of MeHgI induced by BmeMe is almost 2-fold higher than the initial rate obtained by BmmOH or BmmMe, indicating that the spacer between the two imidazole rings of [S2]-donor ligands plays a significant role here in the cleavage of Hg-C bonds. Surprisingly, we noticed that the initial rate of cleavage of the Hg-C bond of MeHgI induced by BmeMe (or BmmMe) is almost 10-fold and 100-fold faster than the cleavage of Hg-C bonds of MeHgCl and [MeHg]BF4 respectively, under identical reaction conditions, suggesting that the Hg-C bond of [MeHg]BF4 is highly inert at room temperature (21 °C). We also show here that the nature of the final stable cleaved products, i.e. Hg(II) complexes, depends on the X group of RHgX and the [S2]-donor ligands. For instance, the reaction of BmmMe with MeHgCl (1:1 molar ratio) afforded the formation of the 16-membered metallacyclic dinuclear mercury compound (BmmMe)2Hg2Cl4, in which the two Cl atoms are located inside the ring, whereas due to the large size of the I atom, a similar reaction with MeHgI yielded polymeric [(BmmMe)2HgI2]m·(MeHgI)n. However, the treatment of BmmMe with ionic [RHg]BF4 led to the formation of the tetrathione-coordinated mononuclear mercury compound [(BmmMe)2Hg](BF4)2, where BF4- serves as a counteranion.

Synthesis of novel 5-arylidenethiazolidinones with apoptotic properties via a three component reaction using piperidine as a bifunctional reagent.

The synthesis of a new library of 5-arylidenethiazolidinone compounds using an efficient three component reaction with thiazolidine-2,4-dione, piperidine and appropriate aldehydes is reported. This reaction is excellently high yielding, tolerant towards a variety of aldehydes and provides access to these compounds in a single step (in comparison to low yielding multistep syntheses reported in the literature). Once the reaction is complete, the desired product precipitates out of the reaction mixture and is isolated by filtration and purified by washing and recrystallization. These compounds revealed anti-proliferative activities against human breast cancer cells (MCF7 and MDA). Phenotypic profiling established the most active compound 17i (EC50 = 4.52 µM) as an apoptotic agent. A novel chemical proteomics approach identified ß-actin-like protein 2, γ-enolase and macrophage migration inhibitory factor (MMIF) as putative cellular binding partners of 17i.

TAAM refinement on high-resolution experimental and simulated 3D ED/MicroED data for organic molecules.

3D electron diffraction (3D ED), or microcrystal electron diffraction (MicroED), has become an alternative technique for determining the high-resolution crystal structures of compounds from sub-micron-sized crystals. Here, we considered L-alanine, α-glycine and urea, which are known to form good-quality crystals, and collected high-resolution 3D ED data on our in-house TEM instrument. In this study, we present a comparison of independent atom model (IAM) and transferable aspherical atom model (TAAM) kinematical refinement against experimental and simulated data. TAAM refinement on both experimental and simulated data clearly improves the model fitting statistics (R factors and residual electrostatic potential) compared to IAM refinement. This shows that TAAM better represents the experimental electrostatic potential of organic crystals than IAM. Furthermore, we compared the geometrical parameters and atomic displacement parameters (ADPs) resulting from the experimental refinements with the simulated refinements, with the periodic density functional theory (DFT) calculations and with published X-ray and neutron crystal structures. The TAAM refinements on the 3D ED data did not improve the accuracy of the bond lengths between the non-H atoms. The experimental 3D ED data provided more accurate H-atom positions than the IAM refinements on the X-ray diffraction data. The IAM refinements against 3D ED data had a tendency to lead to slightly longer X-H bond lengths than TAAM, but the difference was statistically insignificant. Atomic displacement parameters were too large by tens of percent for L-alanine and α-glycine. Most probably, other unmodelled effects were causing this behaviour, such as radiation damage or dynamical scattering.

Hirshfeld atom refinement and dynamical refinement of hexagonal ice structure from electron diffraction data.

Reaching beyond the commonly used spherical atomic electron density model allows one to greatly improve the accuracy of hydrogen atom structural parameters derived from X-ray data. However, the effects of atomic asphericity are less explored for electron diffraction data. In this work, Hirshfeld atom refinement (HAR), a method that uses an accurate description of electron density by quantum mechanical calculation for a system of interest, was applied for the first time to the kinematical refinement of electron diffraction data. This approach was applied here to derive the structure of ordinary hexagonal ice (Ih). The effect of introducing HAR is much less noticeable than in the case of X-ray refinement and it is largely overshadowed by dynamical scattering effects. It led to only a slight change in the O-H bond lengths (shortening by 0.01 Å) compared with the independent atom model (IAM). The average absolute differences in O-H bond lengths between the kinematical refinements and the reference neutron structure were much larger: 0.044 for IAM and 0.046 Šfor HAR. The refinement results changed considerably when dynamical scattering effects were modelled - with extinction correction or with dynamical refinement. The latter led to an improvement of the O-H bond length accuracy to 0.021 Šon average (with IAM refinement). Though there is a potential for deriving more accurate structures using HAR for electron diffraction, modelling of dynamical scattering effects seems to be a necessary step to achieve this. However, at present there is no software to support both HAR and dynamical refinement.

Aspherical atom refinements on X-ray data of diverse structures including disordered and covalent organic framework systems: a time-accuracy trade-off.

Aspherical atom refinement is the key to achieving accurate structure models, displacement parameters, hydrogen-bond lengths and analysis of weak interactions, amongst other examples. There are various quantum crystallographic methods to perform aspherical atom refinement, including Hirshfeld atom refinement (HAR) and transferable aspherical atom model (TAAM) refinement. Both HAR and TAAM have their limitations and advantages, the former being more accurate and the latter being faster. With the advent of non-spherical atoms in Olex2 (NoSpherA2), it is now possible to overcome some limitations, like treating disorder, twinning and network structures, in aspherical refinements using HAR, TAAM or both together. TAAM refinement in NoSpherA2 showed significant improvement in refinement statistics compared with independent atom model (IAM) refinements on a diverse set of X-ray diffraction data. The sensitivity of TAAM towards poor data quality and disorder was observed in terms of higher refinement statistics for such structures. A comparison of IAM with TAAM and HAR in NoSpherA2 indicated that the time taken by TAAM refinements was of the same order of magnitude as that taken by IAM, while in HAR the time taken using a minimal basis set was 50 times higher than for IAM and rapidly increased with increasing size of the basis sets used. The displacement parameters for hydrogen and non-hydrogen atoms were very similar in both HAR and TAAM refinements. The hydrogen-bond lengths were slightly closer to neutron reference values in the case of HAR with higher basis sets than in TAAM. To benefit from the advantages of each method, a new hybrid refinement approach has been introduced, allowing a combination of IAM, HAR and TAAM in one structure refinement. Refinement of coordination complexes involving metal-organic compounds and network structures such as covalent organic frameworks and metal-organic frameworks is now possible in a hybrid mode such as IAM-TAAM or HAR-TAAM, where the metal atoms are treated via either the IAM or HAR method and the organic part via TAAM, thus reducing the computational costs without compromising the accuracy. Formal charges on the metal and ligand can also be introduced in hybrid-mode refinement.

TAAM: a reliable and user friendly tool for hydrogen-atom location using routine X-ray diffraction data.

Hydrogen is present in almost all of the molecules in living things. It is very reactive and forms bonds with most of the elements, terminating their valences and enhancing their chemistry. X-ray diffraction is the most common method for structure determination. It depends on scattering of X-rays from electron density, which means the single electron of hydrogen is difficult to detect. Generally, neutron diffraction data are used to determine the accurate position of hydrogen atoms. However, the requirement for good quality single crystals, costly maintenance and the limited number of neutron diffraction facilities means that these kind of results are rarely available. Here it is shown that the use of Transferable Aspherical Atom Model (TAAM) instead of Independent Atom Model (IAM) in routine structure refinement with X-ray data is another possible solution which largely improves the precision and accuracy of X-H bond lengths and makes them comparable to averaged neutron bond lengths. TAAM, built from a pseudoatom databank, was used to determine the X-H bond lengths on 75 data sets for organic molecule crystals. TAAM parametrizations available in the modified University of Buffalo Databank (UBDB) of pseudoatoms applied through the DiSCaMB software library were used. The averaged bond lengths determined by TAAM refinements with X-ray diffraction data of atomic resolution (dmin ≤ 0.83 Å) showed very good agreement with neutron data, mostly within one single sample standard deviation, much like Hirshfeld atom refinement (HAR). Atomic displacements for both hydrogen and non-hydrogen atoms obtained from the refinements systematically differed from IAM results. Overall TAAM gave better fits to experimental data of standard resolution compared to IAM. The research was accompanied with development of software aimed at providing user-friendly tools to use aspherical atom models in refinement of organic molecules at speeds comparable to routine refinements based on spherical atom model.

Copper-Driven Deselenization: A Strategy for Selective Conversion of Copper Ion to Nanozyme and Its Implication for Copper-Related Disorders.

Synthetic organic molecules, which can selectively convert excess intracellular copper (Cu) ions to nanozymes with an ability to protect cells from oxidative stress, are highly significant in developing therapeutic agents against Cu-related disorder like Wilson's disease. Here, we report 1,3-bis(2-hydroxyethyl)-1 H-benzoimidazole-2-selenone (1), which shows a remarkable ability to remove Cu ion from glutathione, a major cytosolic Cu-binding ligand, and thereafter converts it into copper selenide (CuSe) nanozyme that exhibits remarkable glutathione peroxidase-like activity, at cellular level of H2O2 concentration, with excellent cytoprotective effect against oxidative stress in hepatocyte. Cu-driven deselenization of 1, under physiologically relevant conditions, occurred in two steps. The activation of C═Se bond by metal ion is the crucial first step, followed by cleavage of the metal-activated C═Se bond, initiated by the OH group of N-(CH2)2OH substituent through neighboring group participation (deselenization step), resulted in the controlled synthesis of various types of Cu2-xSe nanocrystals (NCs) (nanodisks, nanocubes, and nanosheets) and tetragonal Cu3Se2 NCs, depending upon the oxidation state of the Cu ion used to activate the C═Se bond. Deselenization of 1 is highly metal-selective. Except Cu, other essential metal ions, including Mn2+, Fe2+, Co2+, Ni2+, or Zn2+, failed to produce metal selenide under identical reaction conditions. Moreover, no significant change in the expression level of Cu-metabolism-related genes, including metallothioneines MT1A, is observed in liver cells co-treated with Cu and 1, as opposed to the large increase in the concentrations of these genes observed in cells treated with Cu alone, suggesting the participation of 1 in Cu homeostasis in hepatocyte.

Reciprocal carbonyl-carbonyl interactions in small molecules and proteins.

Carbonyl-carbonyl n→π* interactions where a lone pair (n) of the oxygen atom of a carbonyl group is delocalized over the π* orbital of a nearby carbonyl group have attracted a lot of attention in recent years due to their ability to affect the 3D structure of small molecules, polyesters, peptides, and proteins. In this paper, we report the discovery of a "reciprocal" carbonyl-carbonyl interaction with substantial back and forth n→π* and π→π* electron delocalization between neighboring carbonyl groups. We have carried out experimental studies, analyses of crystallographic databases and theoretical calculations to show the presence of this interaction in both small molecules and proteins. In proteins, these interactions are primarily found in polyproline II (PPII) helices. As PPII are the most abundant secondary structures in unfolded proteins, we propose that these local interactions may have implications in protein folding.Carbonyl-carbonyl π* non covalent interactions affect the structure and stability of small molecules and proteins. Here, the authors carry out experimental studies, analyses of crystallographic databases and theoretical calculations to describe an additional type of carbonyl-carbonyl interaction.

Identification of Leishmania donovani Topoisomerase 1 inhibitors via intuitive scaffold hopping and bioisosteric modification of known Top 1 inhibitors.

A library of arylidenefuropyridinediones was discovered as potent inhibitors of Leishmania donovani Topoisomerase 1 (LdTop1) where the active molecules displayed considerable inhibition with single digit micromolar EC50 values. This molecular library was designed via intuitive scaffold hopping and bioisosteric modification of known topoisomerase 1 inhibitors such as camptothecin, edotecarin and etc. The design was rationalized by molecular docking analysis of the compound prototype with human topoisomerase 1 (HTop1) and Leishmania donovani topoisomerase 1(LdTop1). The most active compound 4 displayed no cytotoxicity against normal mammalian COS7 cell line (~100 fold less inhibition at the EC50). Similar to camptothecin, 4 interacted with free LdTop1 as observed in the preincubation DNA relaxation inhibition experiment. It also displayed anti-protozoal activity against Leishmania donovani promastigote. Crystal structure investigation of 4 and its molecular modelling with LdTop1 revealed putative binding sites in the enzyme that could be harnessed to generate molecules with better potency.