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Covalent peptidomimetic protease inhibitors have gained a lot of attention in drug development in recent years. They are designed to covalently bind the catalytically active amino acids through electrophilic groups called warheads. Covalent inhibition has an advantage in terms of pharmacodynamic properties but can also bear toxicity risks due to non-selective off-target protein binding. Therefore, the right combination of a reactive warhead with a well-suited peptidomimetic sequence is of great importance. Herein, the selectivities of well-known warheads combined with peptidomimetic sequences suited for five different proteases were investigated, highlighting the impact of both structure parts (warhead and peptidomimetic sequence) for affinity and selectivity. Molecular docking gave insights into the predicted binding modes of the inhibitors inside the binding pockets of the different enzymes. Moreover, the warheads were investigated by NMR and LC-MS reactivity assays against serine/threonine and cysteine nucleophile models, as well as by quantum mechanics simulations.
The development of ligands capable of effectively stabilizing highly reactive main‐group species has led to the experimental realization of a variety of systems with fascinating properties. In this work, we computationally investigate the electronic, structural, energetic, and bonding features of proximity‐enforced group 13–15 homodimers stabilized by a rigid expanded pincer ligand based on the 1,8‐naphthyridine (napy) core. We show that the redox‐active naphthyridine diimine (NDI) ligand enables a wide variety of structural motifs and element‐element interaction modes, the latter ranging from isolated, element‐centered lone pairs (e.g., E = Si, Ge) to cases where through‐space π bonds (E = Pb), element‐element multiple bonds (E = P, As) and biradical ground states (E = N) are observed. Our results hint at the feasibility of NDI‐E2 species as viable synthetic targets, highlighting the versatility and potential applications of napy‐based ligands in main‐group chemistry.
The facile synthesis and detailed investigation of a class of highly potent protease inhibitors based on 1,4-naphthoquinones with a dipeptidic recognition motif (HN-l-Phe-l-Leu-OR) in the 2-position and an electron-withdrawing group (EWG) in the 3-position is presented. One of the compound representatives, namely the acid with EWG = CN and with R = H proved to be a highly potent rhodesain inhibitor with nanomolar affinity. The respective benzyl ester (R = Bn) was found to be hydrolyzed by the target enzyme itself yielding the free acid. Detailed kinetic and mass spectrometry studies revealed a reversible covalent binding mode. Theoretical calculations with different density functionals (DFT) as well as wavefunction-based approaches were performed to elucidate the mode of action.
Electrophilic (het)arenes can undergo reactions with nucleophiles yielding π- or Meisenheimer (σ-) complexes or the products of the S\(_N\)Ar addition/elimination reactions. Such building blocks have only rarely been employed for the design of enzyme inhibitors. Herein, we demonstrate the combination of a peptidic recognition sequence with such electrophilic (het)arenes to generate highly active inhibitors of disease-relevant proteases. We further elucidate an unexpected mode of action for the trypanosomal protease rhodesain using NMR spectroscopy and mass spectrometry, enzyme kinetics and various types of simulations. After hydrolysis of an ester function in the recognition sequence of a weakly active prodrug inhibitor, the liberated carboxylic acid represents a highly potent inhibitor of rhodesain (K\(_i\) = 4.0 nM). The simulations indicate that, after the cleavage of the ester, the carboxylic acid leaves the active site and re-binds to the enzyme in an orientation that allows the formation of a very stable π-complex between the catalytic dyad (Cys-25/His-162) of rhodesain and the electrophilic aromatic moiety. The reversible inhibition mode results because the S\(_N\)Ar reaction, which is found in an alkaline solvent containing a low molecular weight thiol, is hindered within the enzyme due to the presence of the positively charged imidazolium ring of His-162. Comparisons between measured and calculated NMR shifts support this interpretation
Twisted boron-based biradicals featuring unsaturated C\(_2\)R\(_2\) (R=Et, Me) bridges and stabilization by cyclic (alkyl)(amino)carbenes (CAACs) were recently prepared. These species show remarkable geometrical and electronic differences with respect to their unbridged counterparts. Herein, a thorough computational investigation on the origin of their distinct electrostructural properties is performed. It is shown that steric effects are mostly responsible for the preference for twisted over planar structures. The ground-state multiplicity of the twisted structure is modulated by the σ framework of the bridge, and different R groups lead to distinct multiplicities. In line with the experimental data, a planar structure driven by delocalization effects is observed as global minimum for R=H. The synthetic elusiveness of C\(_2\)R\(_2\)-bridged systems featuring N-heterocyclic carbenes (NHCs) was also investigated. These results could contribute to the engineering of novel main group biradicals.
Bei der Einelektronenreduktion eines durch eine cyclisches (Alkyl)(amino)carben (CAAC) stabilisierten Arylborylen-Carbonylkomplexes erfolgt die Bildung eines dimeren Borylketyl-Radikalanions, bedingt durch eine intramolekulare Arylmigration zum CO Kohlenstoffatom. Computergestützte Analyse liefert Hinweise auf eine radikalanionische [(CAAC)B(CO)Ar]\(^{.-}\) Zwischenstufe. Weiterführende Reduktion des entstandenen Komplexes liefert ein hoch nukleophiles (Boranyliden)methanolat.
The concepts of aromaticity and antiaromaticity have a long history, and countless demonstrations of these phenomena have been made with molecules based on elements from the p, d, and f blocks of the periodic table. In contrast, the limited oxidation‐state flexibility of the s‐block metals has long stood in the way of their participation in sophisticated π‐bonding arrangements, and truly antiaromatic systems containing s‐block metals are altogether absent or remain poorly defined. Using spectroscopic, structural, and computational techniques, we present herein the synthesis and authentication of a heterocyclic compound containing the alkaline earth metal beryllium that exhibits significant antiaromaticity, and detail its chemical reduction and Lewis‐base‐coordination chemistry.
Geringe HOMO-LUMO-Abstände und eine hohe Ladungsträgermobilität prädestinieren die höheren Acene für Anwendungen im Bereich der Organoelektronik. Die Leistungsfähigkeit derartiger Verbindungen steigt hierbei dramatisch mit der Anzahl anellierter Benzolringe. Größere Acenmengen sind synthetisch bisher jedoch nur für Acene bis Heptacen verlässlich zugänglich. Theoretischen Studien zufolge besitzen (Oligo)acene offenschalige Singulettbiradikal- und (Poly)acene polyradikalische Grundzustände. Eindeutige experimentelle Belege für diese Vorhersagen sind hingegen äußerst selten. Durch den Einbau von zwei Boratomen in das Anthracengrundgerüst konnten wir den HOMO-LUMO-Abstand von Acenen dramatisch verringern und zwar ohne die Notwendigkeit einer Ausweitung des konjugierten π-Systems. Stabilisierung der Borzentren durch cyclische (Alkyl)(amino)carbene lieferte hierbei neutrale 9,10-Diboraanthracene mit disjunkten, offenschaligen Singulettbiradikal-Grundzuständen.
cAAC‐Stabilized 9,10‐diboraanthracenes—Acenes with Open‐Shell Singlet Biradical Ground States
(2020)
Narrow HOMO–LUMO gaps and high charge‐carrier mobilities make larger acenes potentially high‐efficient materials for organic electronic applications. The performance of such molecules was shown to significantly increase with increasing number of fused benzene rings. Bulk quantities, however, can only be obtained reliably for acenes up to heptacene. Theoretically, (oligo)acenes and (poly)acenes are predicted to have open‐shell singlet biradical and polyradical ground states, respectively, for which experimental evidence is still scarce. We have now been able to dramatically lower the HOMO–LUMO gap of acenes without the necessity of unfavorable elongation of their conjugated π system, by incorporating two boron atoms into the anthracene skeleton. Stabilizing the boron centers with cyclic (alkyl)(amino)carbenes gives neutral 9,10‐diboraanthracenes, which are shown to feature disjointed, open‐shell singlet biradical ground states.
Diplatinum A‐frame complexes with a bridging (di)boron unit in the apex position were synthesized in a single step by the double oxidative addition of dihalo(di)borane precursors at a bis(diphosphine)‐bridged Pt\(^{0}\)\(_{2}\) complex. While structurally analogous to well‐known μ‐borylene complexes, in which delocalized dative three‐center‐two‐electron M‐B‐M bonding prevails, theoretical investigations into the nature of Pt−B bonding in these A‐frame complexes show them to be rare dimetalla(di)boranes displaying two electron‐sharing Pt−B σ‐bonds. This is experimentally reflected in the low kinetic stability of these compounds, which are prone to loss of the (di)boron bridgehead unit.
The absence of fluorine from most biomolecules renders it an excellent probe for NMR spectroscopy to monitor inhibitor–protein interactions. However, predicting the binding mode of a fluorinated ligand from a chemical shift (or vice versa) has been challenging due to the high electron density of the fluorine atom. Nonetheless, reliable \(^{19}\)F chemical‐shift predictions to deduce ligand‐binding modes hold great potential for in silico drug design. Herein, we present a systematic QM/MM study to predict the \(^{19}\)F NMR chemical shifts of a covalently bound fluorinated inhibitor to the essential oxidoreductase tryparedoxin (Tpx) from African trypanosomes, the causative agent of African sleeping sickness. We include many protein–inhibitor conformations as well as monomeric and dimeric inhibitor–protein complexes, thus rendering it the largest computational study on chemical shifts of \(^{19}\)F nuclei in a biological context to date. Our predicted shifts agree well with those obtained experimentally and pave the way for future work in this area.
Density functional theory is applied to the calculation ofthe isotropic byperfine coupJing constants in some small molecules. Various functionals are tested. The agreement of the calculated values to experimental data and values obtained from sophisticated ab initio methods depends on the functionals used and the system under consideration. With respect to spin density calculations the functional of Lee, Yang and Parr with Becke's excbange functional (BLYP) is found to give good results for tbe heavier center of the CH and the NH molecule, while the spin densities of other molecules such as OH, H\(_2\)CN, H\(_2\)CO\(^+\), NO and O\(_2\) deviate considerably from experimental and/or other theoretical results (30%-60%). In cases where the singly occupied orbital can contribute to the isotropic hyperfine coupling constants, accurate results are obtained. The reason fortbis is analyzed.
The hyperfine structures of the isoelectronic molecules CCO. CNN, and NCN in their triplet ground states (X\(^3 \sum ^-\)) are investigated by means of ab initio methods. The infrared frequencies and geometries are detennined and compared with experiment. Configuration selected multireference configuration interaction calculations in combination with perturbation theory to correct the wave function (MRD-CI/B\(_K\)) employing extended atomic orbital (AO) basis sets yielded very accurate hyperfine properties. The theoretical values for CCO are in excellent agreement with the experimental values determined by Smith and Weltner [J. Chem. Phys. 62,4592 (1975)]. For CNN, the first assignment of Smith and Weltner for the two nitrogen atoms has to be changed. A qualitative discussion of the electronic structure discloses no simple relation between the structure of the singly occupied orbitals and the measured hyperfine coupling constants. Vibrational effects were found to be of little importance.
A comparative ab initio study of the Si\(_2\)C\(_4\), Si\(_3\)C\(_3\), Si\(_4\)C\(_2\) clusters
(1994)
Various structural possibilities for the Si\(_2\)C\(_4\) and Si\(_4\)C\(_2\) clusters are investigated by employing a basis set of triple-zeta plus polarization quality; electron correlation is generally accounted for by second-order M0ller-Plesset and, in certain instances, by higher-order perturbation (CASPT2) approaches. The building-up principle recently suggested from an analysis of Si\(_3\)C\(_3\) clusters is found to be fully operative for Si\(_2\)C\(_4\) and Si\(_4\)C\(_2\) clusters. A comparison of the structure and stability of various geometrical arrangements in the series C\(_6\) , Si\(_2\)C\(_4\) , Si\(_3\)C\(_3\) , Si\(_4\)C\(_2\), and Si\(_6\) shows that linear and planar structures become rapidly less stable if carbons are replaced by silicons and that the three-dimensional bipyramidal forms become less favorable as soon as silicons are exchanged by carbons in the parent Si\(_6\) structure. The effects can be rationalized in qualitative terms based on differences in silicon and carbon bonding.
Results ofan ab initio study ofthe hyperfine structure of the X\(^2\)A', A\(^2\) A" ( 1\(^2 \Pi\)) system ofthe formyl radical are presented. Special attention is paid to the analysis of the interplay between the vibronic and magnetic hyperfine etfects. The results of computations are in very good agreement with the available experimental findings. The values for the hyperfine coupling constants in lower bending Ievels of both electronic species are predicted.
The minimum energy path for the reaction O(\(^3\)P\(_g\)) + C\(_2\)H\(_4\)(\(^1\)A\(_g\)) has been calculated by optimizing all relevant geometrical parameters along the approach of oxygen to ethene. A barrier of 4.7 kcal/mol in the \(^3\)A"( ... 9a'\(^2\)- 10a'3a") potential energy surface and an energy difference of 14.4 kcal/mol between the product and the fragments is found at the multireference-configuration interaction level. The corresponding values at the lower-level treatment CASSCF are 9 kcal/mol for the barrier and 9 kcal/mol for the depth of the potential; this shows the importance of inclusion of electron correlation. The barrier for CH\(_2\) rotation for the lowestenergy structure (asymmetric OC\(_2\)H\(_4\)) is around 5 kcal/mol. The energy gap to the first excited state \(^3\)A'( ... 9a'l0a'3a'12) is found tobe 3.6 kcal/mol in MRD-CI calculations at the ground-state minimum. Comparison with \(^3\)CH\(_2\) + C\(_2\)H\(_4\) shows that in this system the lowest-energy surface is \(^3\)A', i.e., the state which is the excited state in 0 + C\(_2\)H\(_4\). This difference in energy ordering of \(^3\)A' and \(^3\)A" states results from the fact that the p\(_x\), p\(_y\), p\(_z\) degeneracy of oxygen orbitals is lifted in \(^3\)CH\(_2\)leading to b\(_1\), b\(_2\). and a\(_1\) MOs whereby the lowest b\(_2\) (a") remains doubly occupied; as a consequence, the reaction pattem between the oxygen and \(^3\)CH\(_2\) approach is different, which is also quite apparent in the calculated charge transfer.
Various structural possibilities for Si\(_3\)C\(_3\) clusters are investigated by ab initio calculations employing basis sets of double- and triple-zeta quality augmented by d polarization functions. Correlation effects are included by a second-order Moeller Piesset perturbation treatment. For the two lowest-lying structures higher-order correlation corrections and multi-reference effects are also included. Bonding features are investigated by two different types of population analyses to obtain insight into the nature of chemical bonding. A total of 17 stationary points were investigated, 14 of which correspond to local minima and three being transition states. The energetically lowest-lying structures are: A "pyramidlike" structure with various multicenter bonds, followed by a es symmetric isomer closely related to the ground state Si6 structure. Planar structures, favoured in small carbon clusters, lie higher in energy and are transition states. The lowest-lying triplet system is found to be the linear nonsymmetric Si - C-C-C-Si -Si structure, which is calculated to lie about 38 kcalfmole above the singlet ground state. A building-up principle based on bonding criteria is suggested for the occurence of the various structural possibilities.
The energy difference between the three lowest-lying isomers of C\(_6\) the linear \(^3 \sum ^-\) state and the two ring forms,the benzene structure (\(^1\)A\(_{18}\)) possessing D\(_{6h}\) symmetry and a distorted cyclic form ( \(^1\)A'\(_1\), D\(_{3h}\) symmetry) have been calculated using various ab initio methods. Variational methods such as multireference configuration interaction (MR-CI) and complete active space second order perturbatiOn treatment (CASPT2) have been applied, as weil as perturbational treatments and coupled cluster calculations (CCD). The correlation of all valence shell electrons is found to be important for a balanced description of the isomers of C\(_6\) . Methods which do not account for higher-order effects appropriately proved to be unsuitable for calculating the energy difference correctly. The results from multireference configuration interaction methods show that the isomers are close in energy with the cyclic forms somewhat lower than the linear form. The ring form possessing D\(_{3h}\) symmetry (\(^1\)A'\(_1\)} is found tobe the lowest-lying structure.
In the present work the dimethylamino radical ( ( CH\(_3\)) \(_2\)N) and its protonated cation ( ( CH\(_3\))\(_2\)NH\(^+\)) are investigated by means of ab initio methods. The geometries of various conformations of both compounds are obtained with UMP2/6·31 G** calculations, while the hyperfine structure and its dependence on the geometry is studied using the MRD-Cl/B\(_K\) method. The two molecules are compared to study the inftuence of the protonation on geometry and hyperfine structure. The effects of the rotational barriers on the hyperfine structures of (CH\(_3\))\(_2\)N, (CH\(_3\)CH\(_2\))\(_2\)N and ( (CH\(_3\))\(_2\)CH)\(_2\)N will be discussed.