No abstract

The solid-state, low-temperature linkage isomerism in a series of five square planar group 10 phosphino nitro complexes have been investigated by a combination of photocrystallographic experiments, Raman spectroscopy and computer modelling. The factors influencing the reversible solid-state interconversion between the nitro and nitrito structural isomers have also been investigated, providing insight into the dynamics of this process. The cis-[Ni(dcpe)(NO2)2] (1) and cis-[Ni(dppe)(NO2)2] (2) complexes show reversible 100 % interconversion between the η1-NO2 nitro isomer and the η1-ONO nitrito form when single-crystals are irradiated with 400 nm light at 100 K. Variable temperature photocrystallographic studies for these complexes established that the metastable nitrito isomer reverted to the ground-state nitro isomer at temperatures above 180 K. By comparison, the related trans complex [Ni(PCy3)2(NO2)2] (3) showed 82 % conversion under the same experimental conditions at 100 K. The level of conversion to the metastable nitrito isomers is further reduced when the nickel centre is replaced by palladium or platinum. Prolonged irradiation of the trans-[Pd(PCy3)2(NO2)2] (4) and trans-[Pt(PCy3)2(NO2)2] (5) with 400 nm light gives reversible conversions of 44 and 27 %, respectively, consistent with the slower kinetics associated with the heavier members of group 10. The mechanism of the interconversion has been investigated by theoretical calculations based on the model complex [Ni(dmpe)Cl(NO2)].

Low temperature, single crystal photocrystallographic studies have been carried out on four square planar Group 10 complexes [Ni(PEt(3))(2)(NO(2))(2)] 1, [Pd(PPh(3))(2)(NO(2))(2)] 2, [Pd(AsPh(3))(2)(NO(2))(2)] 3 and [Pt(PPh(3))(2)(NO(2))(2)] 4, in which the two nitro groups adopt the trans configuration. Irradiation with UV light, at 100 K, of single crystals of complexes 1-3 photoisomerise from the η(1)-NO(2) nitro form to the η(1)-ONO nitrito form occurred. Complex 1 underwent 25% conversion to the nitrito form before crystal decomposition occurred. 2 and 3 underwent 46% and 39% conversion, respectively, to the nitrito form when a photostationary state was reached. While under the same experimental conditions 4 showed no isomerisation. The photocrystallographic results can be correlated with the results of DFT calculations and with the observed trends in the solution UV/visible absorption spectroscopy obtained for these complexes. The results suggest that while steric factors in the isomerization processes are important there may also be a kinetic effect relating to the lability of the metal involved.

Nirmatrelvir (PF-07321332) is a nitrile-bearing small-molecule inhibitor that, in combination with ritonavir, is used to treat infections by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Nirmatrelvir interrupts the viral life cycle by inhibiting the SARS-CoV-2 main protease (M pro ), which is essential for processing viral polyproteins into functional nonstructural proteins. We report studies which reveal that derivatives of nirmatrelvir and other M pro inhibitors with a nonactivated terminal alkyne group positioned similarly to the electrophilic nitrile of nirmatrelvir can efficiently inhibit isolated M pro and SARS-CoV-2 replication in cells. Mass spectrometric and crystallographic evidence shows that the alkyne derivatives inhibit M pro by apparent irreversible covalent reactions with the active site cysteine (Cys145), while the analogous nitriles react reversibly. The results highlight the potential for irreversible covalent inhibition of M pro and other nucleophilic cysteine proteases by alkynes, which, in contrast to nitriles, can be functionalized at their terminal position to optimize inhibition and selectivity, as well as pharmacodynamic and pharmacokinetic properties.

The iron(III) and aluminium(III) complexes of 1,3-di(4-pyridyl)propane-1,3-dionato (dppd) and 1,3-di(3-pyridyl)propane-1,3-dionato (dmppd), [Fe(dppd)(3)] 1, [Fe(dmppd)(3)] 2, [Al(dppd)(3)] 3 and [Al(dmppd)(3)] 4 have been prepared. These complexes adopt molecular structures in which the metal centres contain distorted octahedral geometries. In contrast, the copper(II) and zinc(II) complexes [Cu(dppd)(2)] 5 and [Zn(dmppd)(2)] 6 both form polymeric structures in which coordination of the pyridyl groups into the axial positions of neighbouring metal centres links discrete square-planar complexes into two-dimensional networks. The europium complex [Eu(dmppd)(2)(H(2)O)(4)]Cl·2EtOH·0.5H(2)O 7 forms a structure containing discrete cations that are linked into sheets through hydrogen bonds, whereas the lanthanum complex [La(dmppd)(3)(H(2)O)]·2H(2)O 8 adopts a one-dimensional network structure, connected into sheets by hydrogen bonds. The iron complexes 1 and 2 act as metalloligands in reactions with silver(I) salts, with the nature of the product depending on the counter-ions present. Thus, the reaction between 1 and AgBF(4) gave [AgFe(dppd)(3)]BF(4)·DMSO 9, in which the silver centres link the metalloligands into discrete nanotubes, whereas reactions with AgPF(6) and AgSbF(6) gave [AgFe(dppd)(3)]PF(6)·3.28DMSO 10 and [AgFe(dppd)(3)]SbF(6)·1.25DMSO 11, in which the metalloligands are linked into sheets. In all three cases, only four of the six pyridyl groups present on the metalloligands are coordinated. The reaction between 2 and AgNO(3) gave [Ag(2)Fe(dmppd)(3)(ONO(2))]NO(3)·MeCN·CH(2)Cl(2)12. Compound 12 adopts a layer structure in which all pyridyl groups are coordinated to silver centres and, in addition, a nitrate ion bridges between two silver centres. A similar structure is adopted by [Ag(2)Fe(dmppd)(3)(O(2)CCF(3))]CF(3)CO(2)·2MeCN·0.25CH(2)Cl(2)13, with a bridging trifluoroacetate ion playing the same role as the nitrate ion in 12.

A series of one-dimensional coordination polymers with parallel chains has been prepared by linking together M 2 (O 2 CR) 4 paddle wheel units, where M is Cu or Zn and R is biphenyl or iodobenzoate, with pyrazine (pyz), 2-aminopyrazine (apyz) or 1,4-diazabicyclo[2.2.2]octane (dabco) bridging ligands. The longer length of the substituent in biphenyl-4-carboxylate (bpc) allows for greater separation of the chains in [Cu 2 (bpc) 4 (pyz)]•3.8BzOH 1 than has been previously observed in related benzoate compounds, leading to the formation of larger channels within the structure. In [Cu 2 (bpc) 4 (dabco)]•BzOH 2 and [Zn 2 (bpc) 4 (dabco)]•2DMF 3, neighbouring chains are offset relative to each other, enabling them to pack more efficiently and reducing the channel width from that seen in 1. For the 4-iodobenzoate (ibz) compounds [Cu 2 (ibz) 4 (pyz)] 4, [Cu 2 (ibz) 4 (apyz)]•2BzOH 5 and [Zn 2 (ibz) 4 (dabco)]•3.25DMF 6, the chains are closer together than in the bpc compounds, and again when the neighbouring chains are offset with respect to each other, they are able to pack more efficiently. When similar reactions were carried out using 4,4'-bipyridyl (4,4'-bipy) as the bridging ligand, the products were very different. [Cu(bpc) 2 (4,4'-bipy)(BzOH) 2 ]•2BzOH 7, [Zn(bpc) 2 (4,4'-bipy)] 8 and [Zn(ibz) 2 (4,4'-bipy)] 9 all have structures in which single metal centres, as opposed to M 2 (O 2 CR) 4 dimers, are bridged into chains by the ditopic linker ligand, and the chains pack efficiently without forming channels.

The focus in macromolecular crystallography is moving towards even more challenging target proteins that often crystallize on much smaller scales and are frequently mounted in opaque or highly refractive materials. It is therefore essential that X-ray beamline technology develops in parallel to accommodate such difficult samples. In this paper, the use of X-ray microradiography and microtomography is reported as a tool for crystal visualization, location and characterization on the macromolecular crystallography beamlines at the Diamond Light Source. The technique is particularly useful for microcrystals and for crystals mounted in opaque materials such as lipid cubic phase. X-ray diffraction raster scanning can be used in combination with radiography to allow informed decision-making at the beamline prior to diffraction data collection. It is demonstrated that the X-ray dose required for a full tomography measurement is similar to that for a diffraction grid-scan, but for sample location and shape estimation alone just a few radiographic projections may be required.

Macromolecular crystallography (MX) is the most powerful technique available to structural biologists to visualize in atomic detail the macromolecular machinery of the cell. Since the emergence of structural genomics initiatives, significant advances have been made in all key steps of the structure determination process. In particular, third-generation synchrotron sources and the application of highly automated approaches to data acquisition and analysis at these facilities have been the major factors in the rate of increase of macromolecular structures determined annually. A plethora of tools are now available to users of synchrotron beamlines to enable rapid and efficient evaluation of samples, collection of the best data, and in favorable cases structure solution in near real time. Here, we provide a short overview of the emerging use of collecting X-ray diffraction data directly from the crystallization experiment. These in situ experiments are now routinely available to users at a number of synchrotron MX beamlines. A practical guide to the use of the method on the MX suite of beamlines at Diamond Light Source is given.