Sub 20 cm-1 computational prediction of the CH bond energy - a case of systematic error in computational thermochemistry.

The bond dissociation energy of methylidyne, D0(CH), is studied using an improved version of the High-Accuracy Extrapolated ab initio Thermochemistry (HEAT) approach as well as the Feller-Peterson-Dixon (FPD) model chemistry. These calculations, which include basis sets up to nonuple (aug-cc-pCV9Z) quality, are expected to be capable of providing results substantially more accurate than the ca. 1 kJ mol-1 level that is characteristic of standard high-accuracy protocols for computational thermochemistry. The calculated 0 K CH bond energy (27 954 ± 15 cm-1 for HEAT and 27 956 ± 15 cm-1 for FPD), along with equivalent treatments of the CH ionization energy and the CH+ dissociation energy (85 829 ± 15 cm-1 and 32 946 ± 15 cm-1, respectively), were compared to the existing benchmarks from Active Thermochemical Tables (ATcT), uncovering an unexpected difference for D0(CH). This has prompted a detailed reexamination of the provenance of the corresponding ATcT benchmark, allowing the discovery and subsequent correction of a systematic error present in several published high-level calculations, ultimately yielding an amended ATcT benchmark for D0(CH). Finally, the current theoretical results were added to the ATcT Thermochemical Network, producing refined ATcT estimates of 27 957.3 ± 6.0 cm-1 for D0(CH), 32 946.7 ± 0.6 cm-1 for D0(CH+), and 85 831.0 ± 6.0 cm-1 for IE(CH).

Elaborated thermochemical treatment of HF, CO, N2, and H2O: Insight into HEAT and its extensions.

Empirical, highly accurate non-relativistic electronic total atomization energies (eTAEs) are established by combining experimental or computationally converged treatments of the nuclear motion and relativistic contributions with the total atomization energies of HF, CO, N2, and H2O obtained from the Active Thermochemical Tables. These eTAEs, which have estimated (2σ) uncertainties of less than 10 cm-1 (0.12 kJ mol-1), form the basis for an analysis of high-level ab initio quantum chemical calculations that aim at reproducing these eTAEs for the title molecules. The results are then employed to analyze the performance of the high-accuracy extrapolated ab initio thermochemistry, or High-Accuracy Extrapolated Ab Initio Thermochemistry (HEAT), family of theoretical methods. The method known as HEAT-345(Q), in particular, is found to benefit from fortuitous error cancellation between its treatment of the zero-point energy, extrapolation errors in the Hartree-Fock and coupled cluster contributions, neglect of post-(T) core-correlation, and the basis-set error involved in higher-level correlation corrections. In addition to shedding light on a longstanding curiosity of the HEAT protocol-where the cheapest HEAT-345(Q) performs comparably to the theoretically more complete HEAT-456QP procedure-this study lays the foundation for extended HEAT variants that offer substantial improvements in accuracy relative to the established approaches.

Using isotopologues to probe the potential energy surface of reactions of C2H2 ++C3H4.

Investigations into bimolecular reaction kinetics probe the details of the underlying potential energy surface (PES), which can help to validate high-level quantum chemical calculations. We utilize a combined linear Paul ion trap with a time-of-flight mass spectrometer to study isotopologue reactions between acetylene cations (C2H2 +) and two isomers of C3H4: propyne (HC3H3) and allene (H2C3H2). In a previous study [Schmid et al., Phys. Chem. Chem. Phys. 22, 20303 (2020)],1 we showed that the two isomers of C3H4 have fundamentally different reaction mechanisms. Here, we further explore the calculated PES by isotope substitution. While isotopic substitution of reactants is a standard experimental tool in the investigation of molecular reaction kinetics, the controlled environment of co-trapped, laser-cooled Ca+ ions allows the different isotopic reaction pathways to be followed in greater detail. We report branching ratios for all of the primary products of the different isotopic species. The results validate the previously proposed mechanism: propyne forms a bound reaction complex with C2H2 +, while allene and C2H2 + perform long-range charge exchange only.

Exhaustive Product Analysis of Three Benzene Discharges by Microwave Spectroscopy.

Using chirped and cavity microwave spectroscopies, automated double resonance, new high-speed fitting and deep learning algorithms, and large databases of computed structures, the discharge products of benzene alone, or in combination with molecular oxygen or nitrogen, have been exhaustively characterized between 6.5 and 26 GHz. In total, more than 3300 spectral features were observed; 89% of these, accounting for 97% of the total intensity, have now been assigned to 152 distinct chemical species and 60 of their variants (i.e., isotopic species and vibrationally excited states). Roughly 50 of the products are entirely new or poorly characterized at high resolution, including many heavier by mass than the precursor benzene. These findings provide direct evidence for a rich architecture of two- and three-dimensional carbon and indicate that benzene growth, particularly the formation of ring-chain molecules, occurs facilely under our experimental conditions. The present analysis also illustrates the utility of microwave spectroscopy as a precision tool for complex mixture analysis, irrespective of whether the rotational spectrum of a product species is known a priori or not. From this large quantity of data, for example, it is possible to determine with confidence the relative abundances of different product masses, but more importantly the relative abundances of different isomers with the same mass. The complementary nature of this type of analysis to traditional mass spectrometry is discussed.

Structure guided drug design to develop kallikrein 5 inhibitors to treat Netherton syndrome.

The connection between Netherton syndrome and overactivation of epidermal/dermal proteases particularly KLK5 has been well established. To treat sufferers of this severe condition we wished to develop a topical KLK5 inhibitor in order to normalise epidermal shedding and reduce the associated inflammation and itching. In this paper we describe structure-based optimisation of a series of brightly coloured weak KLK5 inhibitors into colourless, non-irritant molecules with good KLK5 activity and selectivity over a range of serine proteases.

Kallikrein 5 inhibitors identified through structure based drug design in search for a treatment for Netherton Syndrome.

Netherton syndrome (NS) is a rare and debilitating severe autosomal recessive genetic skin disease with high mortality rates particularly in neonates. NS is caused by loss-of-function SPINK5 mutations leading to unregulated kallikrein 5 (KLK5) and kallikrein 7 (KLK7) activity. Furthermore, KLK5 inhibition has been proposed as a potential therapeutic treatment for NS. Identification of potent and selective KLK5 inhibitors would enable further exploration of the disease biology and could ultimately lead to a treatment for NS. This publication describes how fragmentation of known trypsin-like serine protease (TLSP) inhibitors resulted in the identification of a series of phenolic amidine-based KLK5 inhibitors 1. X-ray crystallography was used to find alternatives to the phenol interaction leading to identification of carbonyl analogues such as lactam 13 and benzimidazole 15. These reversible inhibitors, with selectivity over KLK1 (10-100 fold), provided novel starting points for the guided growth towards suitable tool molecules for the exploration of KLK5 biology.

Design and development of a series of borocycles as selective, covalent kallikrein 5 inhibitors.

The connection between Netherton syndrome and overactivation of epidermal/dermal proteases, particularly Kallikrein 5 (KLK5) has been well established and it is expected that a KLK5 inhibitor would improve the dermal barrier and also reduce the pain and itch that afflict Netherton syndrome patients. One of the challenges of covalent protease inhibitors has been achieving selectivity over closely related targets. In this paper we describe the use of structural insight to design and develop a selective and highly potent reversibly covalent KLK5 inhibitor from an initial weakly binding fragment.

High-accuracy extrapolated ab initio thermochemistry. IV. A modified recipe for computational efficiency.

A number of economical modifications to the high-accuracy extrapolated ab initio thermochemistry (HEAT) model chemistry are evaluated. The two resulting schemes, designated as mHEAT and mHEAT+, are designed for efficient and pragmatic evaluation of molecular energies in systems somewhat larger than can be practically studied by the unapproximated HEAT scheme. It is found that mHEAT+ produces heats of formation with nearly subchemical (±1 kJ/mol) accuracy at a substantially reduced cost relative to the full scheme. Total atomization energies calculated using the new thermochemical recipes are compared to the results of the HEAT-345(Q) model chemistry, and enthalpies of formation for the three protocols are also compared to Active Thermochemical Tables. Finally, a small selection of transition states is studied using mHEAT and mHEAT+, which illuminates some interesting features of reaction barriers and serves as an initial benchmark of the performance of these model chemistries for chemical kinetics applications.

Thermal Decomposition of Potential Ester Biofuels. Part I: Methyl Acetate and Methyl Butanoate.

Two methyl esters were examined as models for the pyrolysis of biofuels. Dilute samples (0.06-0.13%) of methyl acetate (CH3COOCH3) and methyl butanoate (CH3CH2CH2COOCH3) were entrained in (He, Ar) carrier gas and decomposed in a set of flash-pyrolysis microreactors. The pyrolysis products resulting from the methyl esters were detected and identified by vacuum ultraviolet photoionization mass spectrometry. Complementary product identification was provided by matrix infrared absorption spectroscopy. Pyrolysis pressures in the pulsed microreactor were about 20 Torr and residence times through the reactors were roughly 25-150 µs. Reactor temperatures of 300-1600 K were explored. Decomposition of CH3COOCH3 commences at 1000 K, and the initial products are (CH2═C═O and CH3OH). As the microreactor is heated to 1300 K, a mixture of CH2═C═O and CH3OH, CH3, CH2═O, H, CO, and CO2 appears. The thermal cracking of CH3CH2CH2COOCH3 begins at 800 K with the formation of CH3CH2CH═C═O and CH3OH. By 1300 K, the pyrolysis of methyl butanoate yields a complex mixture of CH3CH2CH═C═O, CH3OH, CH3, CH2═O, CO, CO2, CH3CH═CH2, CH2CHCH2, CH2═C═CH2, HCCCH2, CH2═C═C═O, CH2═CH2, HC≡CH, and CH2═C═O. On the basis of the results from the thermal cracking of methyl acetate and methyl butanoate, we predict several important decomposition channels for the pyrolysis of fatty acid methyl esters, R-CH2-COOCH3. The lowest-energy fragmentation will be a 4-center elimination of methanol to form the ketene RCH═C═O. At higher temperatures, concerted fragmentation to radicals will ensue to produce a mixture of species: (RCH2 + CO2 + CH3) and (RCH2 + CO + CH2═O + H). Thermal cracking of the ß C-C bond of the methyl ester will generate the radicals (R and H) as well as CH2═C═O + CH2═O. The thermochemistry of methyl acetate and its fragmentation products were obtained via the Active Thermochemical Tables (ATcT) approach, resulting in ΔfH298(CH3COOCH3) = -98.7 ± 0.2 kcal mol-1, ΔfH298(CH3CO2) = -45.7 ± 0.3 kcal mol-1, and ΔfH298(COOCH3) = -38.3 ± 0.4 kcal mol-1.

Electron Transfer Facilitated by Dendrimer-Encapsulated Pt Nanoparticles Across Ultrathin, Insulating Oxide Films.

Electrocatalytic oxygen reduction at carbon electrodes fully passivated by Al2O3 is reported. Specifically, pyrolyzed polymer film (PPF) electrodes were prepared and then coated with pinhole-free Al2O3 layers ranging in thickness from 2.5 to 5.7 nm. All of these ultrathin oxide film thicknesses completely passivated the PPF electrodes, resulting in no faradaic current for either inner-sphere or outer-sphere electrochemical reactions. The electrodes could, however, be reactivated by immobilizing Pt dendrimer-encapsulated nanoparticles (DENs), containing an average of 55 atoms each, on the oxide surface. These PPF/Al2O3/Pt DEN electrodes were completely stable under a variety of electrochemical and solution conditions, and they are active for simple electron-transfer reactions and for more complex electrocatalytic processes. This approach for preparing well-defined oxide electrodes opens the door to a better understanding of the effect of oxide supports on reactions electrocatalyzed by metal nanoparticles.

A Potent and Selective Kallikrein-5 Inhibitor Delivers High Pharmacological Activity in Skin from Patients with Netherton Syndrome.

Regulation of proteolytic activity in the skin plays a pivotal role in epidermal homeostasis. This is best exemplified in Netherton syndrome, a severe genetic skin condition caused by loss-of-function mutations in the gene serine protease inhibitor Kazal-type 5 encoding lympho-epithelial Kazal-type-related inhibitor, a serine protease inhibitor that regulates kallikrein (KLK)-related peptidase 5, 7, and 14 activities. KLK5 plays a central role in stratum corneum shedding and inflammatory cell signaling, activates KLK7 and KLK14, and is therefore an optimal therapeutic target. We aimed to identify a potent and selective small-molecule inhibitor of KLK5 amenable to epidermal delivery. GSK951 was identified using a structure-based design strategy and showed a half maximal inhibitory concentration of 250 pM for KLK5 and greater than 100-fold selectivity over KLK7 and KLK14. Cocrystal structure analysis identified the critical catalytic site interactions to a surrogate for KLK5. Topical application of GSK951-containing cream inhibited KLK5 activity in TgKLK5 mouse skin, reduced transepidermal water loss, and decreased proinflammatory cytokine expression. GSK951 achieved high concentrations in healthy human epidermis following topical application in a cream formulation. Finally, KLK5 protease activity was increased in stratum corneum of patients with Netherton syndrome and significantly inhibited by GSK951. These findings unveil a KLK5-specific small-molecule inhibitor with a high therapeutic potential for patients with Netherton syndrome.

Cocktailed fragment screening by X-ray crystallography of the antibacterial target undecaprenyl pyrophosphate synthase from Acinetobacter baumannii.

Direct soaking of protein crystals with small-molecule fragments grouped into complementary clusters is a useful technique when assessing the potential of a new crystal system to support structure-guided drug discovery. It provides a robustness check prior to any extensive crystal screening, a double check for assay binding cutoffs and structural data for binding pockets that may or may not be picked out in assay measurements. The structural output from this technique for three novel fragment molecules identified to bind to the antibacterial target Acinetobacter baumannii undecaprenyl pyrophosphate synthase are reported, and the different physicochemical requirements of a successful antibiotic are compared with traditional medicines.

Evaluation of a crystallographic surrogate for kallikrein 5 in the discovery of novel inhibitors for Netherton syndrome.

The inhibition of kallikrein 5 (KLK5) has been identified as a potential strategy for treatment of the genetic skin disorder Netherton syndrome, in which loss-of-function mutations in the SPINK5 gene lead to down-regulation of the endogenous inhibitor LEKTI-1 and profound skin-barrier defects with severe allergic manifestations. To aid in the development of a medicine for this target, an X-ray crystallographic system was developed to facilitate fragment-guided chemistry and knowledge-based drug-discovery approaches. Here, the development of a surrogate crystallographic system in place of KLK5, which proved to be challenging to crystallize, is described. The biochemical robustness of the crystallographic surrogate and the suitability of the system for the study of small nonpeptidic fragments and lead-like molecules are demonstrated.

Identification of a RIP1 Kinase Inhibitor Clinical Candidate (GSK3145095) for the Treatment of Pancreatic Cancer.

RIP1 regulates cell death and inflammation and is believed to play an important role in contributing to a variety of human pathologies, including immune-mediated inflammatory diseases and cancer. While small-molecule inhibitors of RIP1 kinase have been advanced to the clinic for inflammatory diseases and CNS indications, RIP1 inhibitors for oncology indications have yet to be described. Herein we report on the discovery and profile of GSK3145095 (compound 6). Compound 6 potently binds to RIP1 with exquisite kinase specificity and has excellent activity in blocking RIP1 kinase-dependent cellular responses. Highlighting its potential as a novel cancer therapy, the inhibitor was also able to promote a tumor suppressive T cell phenotype in pancreatic adenocarcinoma organ cultures. Compound 6 is currently in phase 1 clinical studies for pancreatic adenocarcinoma and other selected solid tumors.

Discovery and Lead-Optimization of 4,5-Dihydropyrazoles as Mono-Kinase Selective, Orally Bioavailable and Efficacious Inhibitors of Receptor Interacting Protein 1 (RIP1) Kinase.

RIP1 kinase regulates necroptosis and inflammation and may play an important role in contributing to a variety of human pathologies, including inflammatory and neurological diseases. Currently, RIP1 kinase inhibitors have advanced into early clinical trials for evaluation in inflammatory diseases such as psoriasis, rheumatoid arthritis, and ulcerative colitis and neurological diseases such as amyotrophic lateral sclerosis and Alzheimer's disease. In this paper, we report on the design of potent and highly selective dihydropyrazole (DHP) RIP1 kinase inhibitors starting from a high-throughput screen and the lead-optimization of this series from a lead with minimal rat oral exposure to the identification of dihydropyrazole 77 with good pharmacokinetic profiles in multiple species. Additionally, we identified a potent murine RIP1 kinase inhibitor 76 as a valuable in vivo tool molecule suitable for evaluating the role of RIP1 kinase in chronic models of disease. DHP 76 showed efficacy in mouse models of both multiple sclerosis and human retinitis pigmentosa.

Unimolecular Reaction of Methyl Isocyanide to Acetonitrile: A High-Level Theoretical Study.

A combination of high-level coupled-cluster calculations and two-dimensional master equation approaches based on semiclassical transition state theory is used to reinvestigate the classic prototype unimolecular isomerization of methyl isocyanide (CH3NC) to acetonitrile (CH3CN). The activation energy, reaction enthalpy, and fundamental vibrational frequencies calculated from first-principles agree well with experimental results. In addition, the calculated thermal rate constants adequately reproduce those of experiment over a large range of temperature and pressure in the falloff region, where experimental results are available, and are generally consistent with statistical chemical kinetics theory (such as Rice-Ramsperger-Kassel-Marcus (RRKM) and transition state theory (TST)).

RIP1 Kinase Drives Macrophage-Mediated Adaptive Immune Tolerance in Pancreatic Cancer.

Pancreatic ductal adenocarcinoma (PDA) is characterized by immune tolerance and immunotherapeutic resistance. We discovered upregulation of receptor-interacting serine/threonine protein kinase 1 (RIP1) in tumor-associated macrophages (TAMs) in PDA. To study its role in oncogenic progression, we developed a selective small-molecule RIP1 inhibitor with high in vivo exposure. Targeting RIP1 reprogrammed TAMs toward an MHCIIhiTNFα+IFNγ+ immunogenic phenotype in a STAT1-dependent manner. RIP1 inhibition in TAMs resulted in cytotoxic T cell activation and T helper cell differentiation toward a mixed Th1/Th17 phenotype, leading to tumor immunity in mice and in organotypic models of human PDA. Targeting RIP1 synergized with PD1-and inducible co-stimulator-based immunotherapies. Tumor-promoting effects of RIP1 were independent of its co-association with RIP3. Collectively, our work describes RIP1 as a checkpoint kinase governing tumor immunity.

Crystal structure of the complementary quadruplex formed by d(GCATGCT) at atomic resolution.

Here we report the crystal structure of the DNA heptanucleotide sequence d(GCATGCT) determined to a resolution of 1.1 A. The sequence folds into a complementary loop structure generating several unusual base pairings and is stabilised through cobalt hexammine and highly defined water sites. The single stranded loop is bound together through the G(N2)-C(O2) intra-strand H-bonds for the available G/C residues, which form further Watson-Crick pairings to a complementary sequence, through 2-fold symmetry, generating a pair of non-planar quadruplexes at the heart of the structure. Further, four adenine residues stack in pairs at one end, H-bonding through their N7-N6 positions, and are additionally stabilised through two highly conserved water positions at the structural terminus. This conformation is achieved through the rotation of the central thymine base at the pinnacle of the loop structure, where it stacks with an adjacent thymine residue within the lattice. The crystal packing yields two halved biological units, each related across a 2-fold symmetry axis spanning a cobalt hexammine residue between them, which stabilises the quadruplex structure through H-bonds to the phosphate oxygens and localised hydration.

Conformational and hydration effects of site-selective sodium, calcium and strontium ion binding to the DNA Holliday junction structure d(TCGGTACCGA)(4).

The role of metal ions in determining the solution conformation of the Holliday junction is well established, but to date the picture of metal ion binding from structural studies of the four-way DNA junction is very incomplete. Here we present two refined structures of the Holliday junction formed by the sequence d(TCGGTACCGA) in the presence of Na(+) and Ca(2+), and separately with Sr(2+) to resolutions of 1.85A and 1.65A, respectively. This sequence includes the ACC core found to promote spontaneous junction formation, but its structure has not previously been reported. Almost complete hydration spheres can be defined for each metal cation. The Na(+) sites, the most convincing observation of such sites in junctions to date, are one on either face of the junction crossover region, and stabilise the ordered hydration inside the junction arms. The four Ca(2+) sites in the same structure are at the CG/CG steps in the minor groove. The Sr(2+) ions occupy the TC/AG, GG/CC, and TA/TA sites in the minor groove, giving ten positions forming two spines of ions, spiralling through the minor grooves within each arm of the stacked-X structure. The two structures were solved in the two different C2 lattices previously observed, with the Sr(2+) derivative crystallising in the more highly symmetrical form with two-fold symmetry at its centre. Both structures show an opening of the minor groove face of the junction of 8.4 degrees in the Ca(2+) and Na(+) containing structure, and 13.4 degrees in the Sr(2+) containing structure. The crossover angles at the junction are 39.3 degrees and 43.3 degrees, respectively. In addition to this, a relative shift in the base pair stack alignment of the arms of 2.3A is observed for the Sr(2+) containing structure only. Overall these results provide an insight into the so-far elusive stabilising ion structure for the DNA Holliday junction.