Relativistic Hirshfeld atom refinement of an organo-gold(I) compound.
Ontology highlight
ABSTRACT:
SUBMITTER: Pawledzio S
PROVIDER: S-EPMC8256711 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustrated via the example of crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly-l-Ala measured at 12, 50, 100, 150, 220 and 295?K, using Hartree-Fock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs) are freely refined without constraints or restraints - even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295?K. Although non-hydrogen-atom ADPs differ by up to three combined standard uncertainties (csu's), all other structural parameters agree within less than 2?csu's. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules), the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009?Å for temperatures of 150?K or below; for hydrogen-atom ADPs it is better than 0.006?Å(2) as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements - an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65?Å.
| S-EPMC4174878 | biostudies-literature
Project description:In this work, various models of atomic electron density were applied in a generalized version of the Hirshfeld atom refinement to three organic structures. Hirshfeld atom refinement is one of the most successful methods for the accurate determination of structural parameters for hydrogen atoms from X-ray diffraction data. This work introduces a generalization of the method [generalized atom refinement (GAR)], consisting of the application of various methods of partitioning electron density into atomic contributions. These were tested on three organic structures using the following partitions: Hirshfeld, iterative Hirshfeld, iterative stockholder, minimal basis iterative stockholder and Becke. The effects of partition choice were also compared with those caused by other factors such as quantum chemical methodology, basis set, representation of the crystal field and a combination of these factors. The differences between the partitions were small in terms of R factor (e.g. much smaller than for refinements with different quantum chemistry methods, i.e. Hartree–Fock and coupled cluster) and therefore no single partition was clearly the best in terms of experimental data reconstruction. In the case of structural parameters the differences between the partitions are comparable to those related to the choice of other factors. We have observed the systematic effects of the partition choice on bond lengths and ADP values of polar hydrogen atoms. The bond lengths were also systematically influenced by the choice of electron density calculation methodology. This suggests that GAR-derived structural parameters could be systematically improved by selecting an optimal combination of the partition and quantum chemistry method. The results of the refinements were compared with those of neutron diffraction experiments. This allowed a selection of the most promising partition methods for further optimization of GAR settings, namely the Hirshfeld, iterative stockholder and minimal basis iterative stockholder.
| S-EPMC7642787 | biostudies-literature
Project description: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 Å for 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 Å on 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.
| S-EPMC11364029 | biostudies-literature
Project description:Hirshfeld atom refinement (HAR) is a novel X-ray structure refinement technique that employs aspherical atomic scattering factors obtained from stockholder partitioning of a theoretically determined tailor-made static electron density. HAR overcomes many of the known limitations of independent atom modelling (IAM), such as too short element-hydrogen distances, r(X-H), or too large atomic displacement parameters (ADPs). This study probes the accuracy and precision of anisotropic hydrogen and non-hydrogen ADPs and of r(X-H) values obtained from HAR. These quantities are compared and found to agree with those obtained from (i) accurate neutron diffraction data measured at the same temperatures as the X-ray data and (ii) multipole modelling (MM), an established alternative method for interpreting X-ray diffraction data with the help of aspherical atomic scattering factors. Results are presented for three chemically different systems: the aromatic hydro-carbon rubrene (orthorhombic 5,6,11,12-tetra-phenyl-tetracene), a co-crystal of zwitterionic betaine, imidazolium cations and picrate anions (BIPa), and the salt potassium hydrogen oxalate (KHOx). The non-hydrogen HAR-ADPs are as accurate and precise as the MM-ADPs. Both show excellent agreement with the neutron-based values and are superior to IAM-ADPs. The anisotropic hydrogen HAR-ADPs show a somewhat larger deviation from neutron-based values than the hydrogen SHADE-ADPs used in MM. Element-hydrogen bond lengths from HAR are in excellent agreement with those obtained from neutron diffraction experiments, although they are somewhat less precise. The residual density contour maps after HAR show fewer features than those after MM. Calculating the static electron density with the def2-TZVP basis set instead of the simpler def2-SVP one does not improve the refinement results significantly. All HARs were performed within the recently introduced HARt option implemented in the Olex2 program. They are easily launched inside its graphical user interface following a conventional IAM.
| S-EPMC5755575 | biostudies-literature
Project description:The crystal structure of complex [Pb{HB(pz)3}Au(C6Cl5)2] 1 displays an unsupported Au(i)···Pb(ii) interaction. This complex emits at 480 nm in the solid state due to an aurate(i) to lead(ii) charge transfer, in which the existence of a metallophilic interaction is a pre-requisite. Ab initio calculations show a very strong Au(i)···Pb(ii) closed-shell interaction of -390 kJ mol-1, which has an ionic plus a dispersive (van der Waals) nature strengthened by large relativistic effects (>17%).
| S-EPMC5654245 | biostudies-literature
Project description:The organometallic "half-sandwich" compound [Os(?(6)-p-cymene)(4-(2-pyridylazo)-N,N-dimethylaniline)I]PF6 is 49× more potent than the clinical drug cisplatin in the 809 cancer cell lines that we screened and is a candidate drug for cancer therapy. We investigate the mechanism of action of compound 1 in A2780 epithelial ovarian cancer cells. Whole-transcriptome sequencing identified three missense mutations in the mitochondrial genome of this cell line, coding for ND5, a subunit of complex I (NADH dehydrogenase) in the electron transport chain. ND5 is a proton pump, helping to maintain the coupling gradient in mitochondria. The identified mutations correspond to known protein variants (p.I257V, p.N447S, and p.L517P), not reported previously in epithelial ovarian cancer. Time-series RNA sequencing suggested that osmium-exposed A2780 cells undergo a metabolic shunt from glycolysis to oxidative phosphorylation, where defective machinery, associated with mutations in complex I, could enhance activity. Downstream events, measured by time-series reverse-phase protein microarrays, high-content imaging, and flow cytometry, showed a dramatic increase in mitochondrially produced reactive oxygen species (ROS) and subsequent DNA damage with up-regulation of ATM, p53, and p21 proteins. In contrast to platinum drugs, exposure to this organo-osmium compound does not cause significant apoptosis within a 72-h period, highlighting a different mechanism of action. Superoxide production in ovarian, lung, colon, breast, and prostate cancer cells exposed to three other structurally related organo-Os(II) compounds correlated with their antiproliferative activity. DNA damage caused indirectly, through selective ROS generation, may provide a more targeted approach to cancer therapy and a concept for next-generation metal-based anticancer drugs that combat platinum resistance.
| S-EPMC4517206 | biostudies-literature
Project description:BACKGROUND: The reliable prediction of protein tertiary structure from the amino acid sequence remains challenging even for small proteins. We have developed an all-atom free-energy protein forcefield (PFF01) that we could use to fold several small proteins from completely extended conformations. Because the computational cost of de-novo folding studies rises steeply with system size, this approach is unsuitable for structure prediction purposes. We therefore investigate here a low-cost free-energy relaxation protocol for protein structure prediction that combines heuristic methods for model generation with all-atom free-energy relaxation in PFF01. RESULTS: We use PFF01 to rank and cluster the conformations for 32 proteins generated by ROSETTA. For 22/10 high-quality/low quality decoy sets we select near-native conformations with an average Calpha root mean square deviation of 3.03 A/6.04 A. The protocol incorporates an inherent reliability indicator that succeeds for 78% of the decoy sets. In over 90% of these cases near-native conformations are selected from the decoy set. This success rate is rationalized by the quality of the decoys and the selectivity of the PFF01 forcefield, which ranks near-native conformations an average 3.06 standard deviations below that of the relaxed decoys (Z-score). CONCLUSION: All-atom free-energy relaxation with PFF01 emerges as a powerful low-cost approach toward generic de-novo protein structure prediction. The approach can be applied to large all-atom decoy sets of any origin and requires no preexisting structural information to identify the native conformation. The study provides evidence that a large class of proteins may be foldable by PFF01.
| S-EPMC1832197 | biostudies-literature
Project description:We describe predictions made using the Rosetta structure prediction methodology for the Eighth Critical Assessment of Techniques for Protein Structure Prediction. Aggressive sampling and all-atom refinement were carried out for nearly all targets. A combination of alignment methodologies was used to generate starting models from a range of templates, and the models were then subjected to Rosetta all atom refinement. For the 64 domains with readily identified templates, the best submitted model was better than the best alignment to the best template in the Protein Data Bank for 24 cases, and improved over the best starting model for 43 cases. For 13 targets where only very distant sequence relationships to proteins of known structure were detected, models were generated using the Rosetta de novo structure prediction methodology followed by all-atom refinement; in several cases the submitted models were better than those based on the available templates. Of the 12 refinement challenges, the best submitted model improved on the starting model in seven cases. These improvements over the starting template-based models and refinement tests demonstrate the power of Rosetta structure refinement in improving model accuracy.
| S-EPMC3688471 | biostudies-literature
Project description:Gold compounds containing planar N-heterocyclic (NHC) carbene ligands are potent aryl hydrocarbon receptor (AHR) ligands. Further studies with the lead compound (called MC3), show that MC3 activates TGFβ signaling while repressing CD4+ T-cell activation in vitro, in human and mouse T-cells, and in scurfy mouse, while repression of AHR activity or TGFβ-SMAD cascades compensated its immune suppressive function. The in-vivo induction of Tgfb1 expression was associated with reduced severity of the autoimmune markers.
2019-01-16 | GSE125146 | GEO
Project description:Compared to molecular chemistry, nanochemistry is still far from being capable of tailoring particle structure and functionality at an atomic level. Numerous effective methodologies that can precisely tailor specific groups in organic molecules without altering the major carbon bones have been developed, but for nanoparticles, it is still extremely difficult to realize the atomic-level tailoring of specific sites in a particle without changing the structure of other parts (for example, replacing specific surface motifs and deleting one or two metal atoms). This issue severely limits nanochemists from knowing how different motifs in a nanoparticle contribute to its overall properties. We demonstrate a site-specific "surgery" on the surface motif of an atomically precise 23-gold-atom [Au23(SR)16]- nanoparticle by a two-step metal-exchange method, which leads to the "resection" of two surface gold atoms and the formation of a new 21-gold-atom nanoparticle, [Au21(SR)12(Ph2PCH2PPh2)2]+, without changing the other parts of the starting nanoparticle structure. This precise surgery of the nanocluster reveals the different reactivity of the surface motifs and the inner core: the least effect of surface motifs on optical absorption but a distinct effect on photoluminescence (that is, a 10-fold enhancement of luminescence after the tailoring). First-principles calculations further reveal the thermodynamically preferred reaction pathway for the formation of [Au21(SR)12(Ph2PCH2PPh2)2]+. This work constitutes a major step toward the development of atomically precise, versatile nanochemistry for the precise tailoring of the nanocluster structure to control its properties.
| S-EPMC5438218 | biostudies-literature