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Abstract Enhancing corrosion resistance is essential for developing efficient electrocatalysts for acidic oxygen evolution reaction (OER). Herein, we report the strategic manipulation of the local compressive strain to reinforce the anti-corrosion properties of the non-precious Co3O4 support. The incorporation of Ru single atoms, larger in atomic size than Co, into the Co3O4 lattice (Ru-Co3O4), triggers localized strain compression and lattice distortion on the Co-O lattice. A comprehensive exploration of the correlation between this specific local compressive strain and electrocatalytic performance is conducted through experimental and theoretical analyses. The presence of the localized strain in Ru-Co3O4 is confirmed by operando X-ray absorption studies and supported by quantum calculations. This local strain, presented in a shortened Co-O bond length, enhances the anti-corrosion properties of Co3O4 by suppressing metal dissolutions. Consequently, Ru-Co3O4 shows satisfactory stability, maintaining OER for over 400 hours at 30 mA cm−2 with minimal decay. This study demonstrates the potential of the local strain effect in fortifying catalyst stability for acidic OER and beyond.

Abstract Metal–organic frameworks have drawn attention as potential catalysts owing to their unique tunable surface chemistry and accessibility. However, their application in thermal catalysis has been limited because of their instability under harsh temperatures and pressures, such as the hydrogenation of CO2 to methanol. Herein, we use a controlled two-step method to synthesize finely dispersed Cu on a zeolitic imidazolate framework-8 (ZIF-8). This catalyst suffers a series of transformations during the CO2 hydrogenation to methanol, leading to ~14 nm Cu nanoparticles encapsulated on the Zn-based MOF that are highly active (2-fold higher methanol productivity than the commercial Cu–Zn–Al catalyst), very selective (>90%), and remarkably stable for over 150 h. In situ spectroscopy, density functional theory calculations, and kinetic results reveal the preferential adsorption sites, the preferential reaction pathways, and the reverse water gas shift reaction suppression over this catalyst. The developed material is robust, easy to synthesize, and active for CO2 utilization.

Abstract Photocatalytic selective C(sp3)–H activation/cross-coupling reactions are appealing in organic synthesis. In this manuscript, we describe the development of photoexcited-state Pd-catalyzed dehydrogenative β-sulfonylation reactions using amines and aryl sulfonyl chlorides via intermolecular hydrogen atom transfer and C−S cross-coupling processes at room temperature. The transformation can be achieved by the direct generation of two distinct Pd-radical hybrid species and their capability to promote two different reactivities from Pd(0) and aryl sulfonyl chlorides, allowing for the efficient conversion of readily available amines into stable sulfonyl-substituted enamines at room temperature. The in-depth experimental, computational, and transient optical spectroscopic study and catalytic applications of a dehydrogenative functionalization event provide evidence for both static and dynamic quenching, as well as inner-sphere and outer-sphere mechanisms.

Amino acid ionic liquids (AAILs) have gained significant attention as green solvents that are biocompatible, biodegradable, and useful in various applications, including catalysts, absorbents, and solvents. This study investigates the detailed interactions of three amino acid anions (glycine [Gly]-, histidine [His]-, and arginine [Arg]-) with the cation 1-methoxylbutyl-3-methylimidazolium [MOBMIM]+ and their role in CO2 absorption using quantum mechanical calculations and molecular dynamics (MD) simulations. The Density Functional Theory (DFT) calculations elucidate the reaction mechanisms underlying CO2 absorption and cycloaddition, and facilitate a comparative analysis of the impact of different amino acids on these reactions, and the synergies between them. Notably, arginine displays superior CO2 absorption capacity in comparison to glycine and histidine. Additionally, the cycloaddition reaction with CO2 exhibits a lower energy barrier when arginine is involved. Insights from the MD simulations highlight the higher level of electrostatic interaction between [MOBMIM]+[Arg]- and CO2, relative to the other studied molecules. Moreover, the Lennard Jones interaction emerges as the dominant type of interaction in these systems. The diffusion coefficient for CO2 was highest when interacting with [MOBMIM]+[Gly]-, followed by [MOBMIM]+[Arg]-. Consequently, both MD and DFT investigations converge to suggest that [MOBMIM]+[Arg]- followed by [MOBMIM]+[Gly]- may serve as advantageous choices for CO2 fixation and cycloaddition. The findings from this study underscore the considerable potential of the investigated AAILs as materials conducive to CO2 capture and utilization, thus paving the way for the integration of CO2 capture into valuable chemical products.

Feline infectious peritonitis (FIP) is a grave and frequently lethal ailment instigated by feline coronavirus (FCoV) in wild and domestic feline species. The spike (S) protein of FCoV assumes a critical function in viral ingress and infection, thereby presenting a promising avenue for the development of a vaccine. In this investigation, an immunoinformatics approach was employed to ascertain immunogenic epitopes within the S-protein of FIP and formulate an innovative vaccine candidate. By subjecting the amino acid sequence of the FIP S-protein to computational scrutiny, MHC-I binding T-cell epitopes were predicted, which were subsequently evaluated for their antigenicity, toxicity, and allergenicity through in silico tools. Our analyses yielded the identification of 11 potential epitopes capable of provoking a robust immune response against FIPV. Additionally, molecular docking analysis demonstrated the ability of these epitopes to bind with feline MHC class I molecules. Through the utilization of suitable linkers, these epitopes, along with adjuvants, were integrated to design a multi-epitope vaccine candidate. Furthermore, the stability of the interaction between the vaccine candidate and feline Toll-like receptor 4 (TLR4) was established via molecular docking and molecular dynamics simulation analyses. This suggests good prospects for future experimental validation to ascertain the efficacy of our vaccine candidate in inducing a protective immune response against FIP.

The selective construction of C-C double bonds in alkenes, which can be one of two isomers, is a fundamental focus of organic chemistry. Here, the authors systematically investigated the stereoselectivity in allylic C(sp3)-H bond arylations and demonstrated a ligand switch could allow a stereodivergent synthesis of silyl enol ethers.

Radioactive molecular iodine (I2) and methyl iodide (CH3I) coexist in the off-gas stream of nuclear power plants at low concentrations and only few adsorbents can effectively adsorb low-concentration I2 and CH3I simultaneously. Here, the authors demonstrate simultaneous capture of I2 and CH3I at low concentrations by exploiting different adsorptive sites in a covalent organic framework.

Although the combination of photo- and nickel catalysis has garnered intense interest in the preceding years, the mechanisms by which these transformations occur are to some degree unresolved. Here the authors provide computational and spectroscopic support for a Dexter energy-transfer mechanism in the context of a C(sp3)–H alkylation.

The reaction mechanism of carbon dioxide to high-value hydrocarbons over metal-zeolite bifunctional catalysts remains ambiguous. Here, the authors demonstrate that active zeolite catalysts’ topology and hybrid nature are descriptors; regulating the reaction mechanism and ultimate product selectivity.

Abstract Engineering the solid electrolyte interphase (SEI) that forms on the electrode is crucial for achieving high performance in metal‐ion batteries. However, the mechanism of SEI formation resulting from electrolyte decomposition is not fully understood at the molecular scale. Herein, a new strategy of switching electrolyte to tune SEI properties is presented, by which a unique and thinner SEI can be pre‐formed on the graphite electrode first in an ether‐based electrolyte, and then the as‐designed graphite electrode can demonstrate extremely high‐rate capabilities in a carbonate‐based electrolyte, enabling the design of fast‐charging and wide‐temperature lithium‐ion batteries (e.g., graphite | LiNi0.6Co0.2Mn0.2O2 (NCM622)). A molecular interfacial model involving the conformations and electrochemical stabilities of the Li+‐solvent‐anion complex is presented to elucidate the differences in SEI formation between ether‐based and carbonate‐based electrolytes, then interpreting the reason for the obtained higher rate performances. This innovative concept combines the advantages of different electrolytes into one battery system. It is believed that the switching strategy and understanding of the SEI formation mechanism opens a new avenue to design SEI, which is universal for pursuing more versatile battery systems with greater stability.

Dengue virus (DENV) is an arboviral disease affecting more than 400 million people annually. Only a single vaccine formulation is available commercially and many others are still under clinical trials. Despite all the efforts in vaccine designing, the improvement in vaccine formulation against DENV is very much needed. In this study, we used a roboust immunoinformatics approach, targeting all the four serotypes of DENV to design a multi-epitope vaccine. A total of 13501 MHC II binding CD4+ epitope peptides were predicted from polyprotein sequences of four dengue virus serotypes. Among them, ten conserved epitope peptides that were interferon-inducing were selected and found to be conserved among all the four dengue serotypes. The vaccine was formulated using antigenic, non-toxic and conserved multi epitopes discovered in the in-silico study. Further, the molecular docking and molecular dynamics predicted stable interactions between predicted vaccine and immune receptor, TLR-5. Finally, one of the mapped epitope peptides was synthesized for the validation of antigenicity and antibody production ability where the in-vivo tests on rabbit model was conducted. Our in-vivo analysis clearly indicate that the imunogen designed in this study could stimulate the production of antibodies which further suggest that the vaccine designed possesses good immunogenicity.

The non-natural ethynylmethylpyridone C-nucleoside (W), a thymidine (T) analogue that can be incorporated in oligonucleotides by automated synthesis, has recently been reported to form a high fidelity base pair with adenosine (A) and to be well accommodated in B-DNA duplexes. The enhanced binding affinity for A of W, as compared to T, makes it an ideal modification for biotechnological applications, such as efficient probe hybridization for the parallel detection of multiple DNA strands. In order to complement the experimental study and rationalize the impact of the non-natural W nucleoside on the structure, stability and dynamics of DNA structures, we performed quantum mechanics (QM) calculations along with molecular dynamics (MD) simulations. Consistently with the experimental study, our QM calculations show that the A:W base pair has an increased stability as compared to the natural A:T pair, due to an additional CH-π interaction. Furthermore, we show that mispairing between W and guanine (G) causes a distortion in the planarity of the base pair, thus explaining the destabilization of DNA duplexes featuring a G:W pair. MD simulations show that incorporation of single or multiple consecutive A:W pairs in DNA duplexes causes minor changes to the intra- and inter-base geometrical parameters, while a moderate widening/shrinking of the major/minor groove of the duplexes is observed. QM calculations applied to selected stacks from the MD simulations also show an increased stacking energy for W, over T, with the neighboring bases.

Abstract Background Properly scoring protein-protein docking models to single out the correct ones is an open challenge, also object of assessment in CAPRI (Critical Assessment of PRedicted Interactions), a community-wide blind docking experiment. We introduced in the field CONSRANK (CONSensus RANKing), the first pure consensus method. Also available as a web server, CONSRANK ranks docking models in an ensemble based on their ability to match the most frequent inter-residue contacts in it. We have been blindly testing CONSRANK in all the latest CAPRI rounds, where we showed it to perform competitively with the state-of-the-art energy and knowledge-based scoring functions. More recently, we developed Clust-CONSRANK, an algorithm introducing a contact-based clustering of the models as a preliminary step of the CONSRANK scoring process. In the latest CASP13-CAPRI joint experiment, we participated as scorers with a novel pipeline, combining both our scoring tools, CONSRANK and Clust-CONSRANK, with our interface analysis tool COCOMAPS. Selection of the 10 models for submission was guided by the strength of the emerging consensus, and their final ranking was assisted by results of the interface analysis. Results As a result of the above approach, we were by far the first scorer in the CASP13-CAPRI top-1 ranking, having high/medium quality models ranked at the top-1 position for the majority of targets (11 out of the total 19). We were also the first scorer in the top-10 ranking, on a par with another group, and the second scorer in the top-5 ranking. Further, we topped the ranking relative to the prediction of binding interfaces, among all the scorers and predictors. Using the CASP13-CAPRI targets as case studies, we illustrate here in detail the approach we adopted. Conclusions Introducing some flexibility in the final model selection and ranking, as well as differentiating the adopted scoring approach depending on the targets were the key assets for our highly successful performance, as compared to previous CAPRI rounds. The approach we propose is entirely based on methods made available to the community and could thus be reproduced by any user.

Candida dubliniensis is an opportunistic pathogen associated with oral and invasive fungal infections in immune-compromised individuals. Furthermore, the emergence of C. dubliniensis antifungal drug resistance could exacerbate its treatment. Hence, in this study a multi-epitope vaccine candidate has been designed using an immunoinformatics approach by targeting C. dubliniensis secreted aspartyl proteinases (SAP) proteins. In silico tools have been utilized to predict epitopes and determine their allergic potential, antigenic potential, toxicity, and potential to elicit interleukin-2 (IL2), interleukin-4 (IL4), and IFN-γ. Using the computational tools, eight epitopes have been predicted that were then linked with adjuvants for final vaccine candidate development. Computational immune simulation has depicted that the immunogen designed emerges as a strong immunogenic candidate for a vaccine. Further, molecular docking and molecular dynamics simulation analyses revealed stable interactions between the vaccine candidate and the human toll-like receptor 5 (TLR5). Finally, immune simulations corroborated the promising candidature of the designed vaccine, thus calling for further in vivo investigation.

Monkeypox is a self-limiting zoonotic viral disease and causes smallpox-like symptoms. The disease has a case fatality ratio of 3–6% and, recently, a multi-country outbreak of the disease has occurred. The currently available vaccines that have provided immunization against monkeypox are classified as live attenuated vaccinia virus-based vaccines, which pose challenges of safety and efficacy in chronic infections. In this study, we have used an immunoinformatics-aided design of a multi-epitope vaccine (MEV) candidate by targeting monkeypox virus (MPXV) glycoproteins and membrane proteins. From these proteins, seven epitopes (two T-helper cell epitopes, four T-cytotoxic cell epitopes and one linear B cell epitopes) were finally selected and predicted as antigenic, non-allergic, interferon-γ activating and non-toxic. These epitopes were linked to adjuvants to design a non-allergic and antigenic candidate MPXV-MEV. Further, molecular docking and molecular dynamics simulations predicted stable interactions between predicted MEV and human receptor TLR5. Finally, the immune-simulation analysis showed that the candidate MPXV-MEV could elicit a human immune response. The results obtained from these in silico experiments are promising but require further validation through additional in vivo experiments.

Classical Suzuki-Miyaura couplings require wasteful electrophilic coupling partners and an exogenous base often engaging in side-reactions. Here, the authors report an alternative Suzuki-type synthesis of biaryls, involving the base-free nickel-catalyzed deformylative coupling of aldehydes with organoboron reagents.

Summary: The development of more reactive, general, easily accessible, and readily available Pd(II)–NHC precatalysts remains a key challenge in homogeneous catalysis. In this study, we establish air-stable NHC–Pd(II) chloro-dimers, [Pd(NHC)(μ-Cl)Cl]2, as the most reactive Pd(II)–NHC catalysts developed to date. Most crucially, compared with [Pd(NHC)(allyl)Cl] complexes, replacement of the allyl throw-away ligand with chloride allows for a more facile activation step, while effectively preventing the formation of off-cycle [Pd2(μ-allyl)(μ-Cl)(NHC)2] products. The utility is demonstrated via broad compatibility with amide cross-coupling, Suzuki cross-coupling, and the direct, late-stage functionalization of pharmaceuticals. Computational studies provide key insight into the NHC–Pd(II) chloro-dimer activation pathway. A facile synthesis of NHC–Pd(II) chloro-dimers in one-pot from NHC salts is reported. Considering the tremendous utility of Pd-catalyzed cross-coupling reactions and the overwhelming success of [Pd(NHC)(allyl)Cl] precatalysts, we believe that NHC–Pd(II) chloro-dimers, [Pd(NHC)(μ-Cl)Cl]2, should be considered as go-to precatalysts of choice in cross-coupling processes.

The first turnover event of an olefin metathesis reaction using a new family of homogenous Ru-based catalysts bearing modified indenylidene ligands has been investigated, using methoxyethylene as a substrate. The study is carried out by means of density functional theory (DFT). The indenylidene ligands are decorated with ortho-methyl and isopropyl groups at both ortho positions of their phenyl ring. DFT results highlight the more sterically demanding indenylidenes have to undergo a more exothermic first phosphine dissociation step. Overall, the study emphasises advantages of increased steric hindrance in promoting the phosphine release, and the relative stability of the corresponding metallacycle over classical ylidene ligands. Mayer bond orders and steric maps provide structural reasons for these effects, whereas NICS aromaticity and conceptual DFT confirm that the electronic parameters do not play a significant role.

Mammalian cell surfaces are modified with complex arrays of glycans that play major roles in health and disease. Abnormal glycosylation is a hallmark of cancer; terminal sialic acid and fucose in particular have high levels in tumor cells, with positive implications for malignancy. Increased sialylation and fucosylation are due to the upregulation of a set of sialyltransferases (STs) and fucosyltransferases (FUTs), which are potential drug targets in cancer. In the past, several advances in glycostructural biology have been made with the determination of crystal structures of several important STs and FUTs in mammals. Additionally, how the independent evolution of STs and FUTs occurred with a limited set of global folds and the diverse modular ability of catalytic domains toward substrates has been elucidated. This review highlights advances in the understanding of the structural architecture, substrate binding interactions, and catalysis of STs and FUTs in mammals. While this general understanding is emerging, use of this information to design inhibitors of STs and FUTs will be helpful in providing further insights into their role in the manifestation of cancer and developing targeted therapeutics in cancer.

The crown of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is constituted by its spike (S) glycoprotein. S protein mediates the SARS-CoV-2 entry into the host cells. The “fusion core” of the heptad repeat 1 (HR1) on S plays a crucial role in the virus infectivity, as it is part of a key membrane fusion architecture. While SARS-CoV-2 was becoming a global threat, scientists have been accumulating data on the virus at an impressive pace, both in terms of genomic sequences and of three-dimensional structures. On 15 February 2021, from the SARS-CoV-2 genomic sequences in the GISAID resource, we collected 415,673 complete S protein sequences and identified all the mutations occurring in the HR1 fusion core. This is a 21-residue segment, which, in the post-fusion conformation of the protein, gives many strong interactions with the heptad repeat 2, bringing viral and cellular membranes in proximity for fusion. We investigated the frequency and structural effect of novel mutations accumulated over time in such a crucial region for the virus infectivity. Three mutations were quite frequent, occurring in over 0.1% of the total sequences. These were S929T, D936Y, and S949F, all in the N-terminal half of the HR1 fusion core segment and particularly spread in Europe and USA. The most frequent of them, D936Y, was present in 17% of sequences from Finland and 12% of sequences from Sweden. In the post-fusion conformation of the unmutated S protein, D936 is involved in an inter-monomer salt bridge with R1185. We investigated the effect of the D936Y mutation on the pre-fusion and post-fusion state of the protein by using molecular dynamics, showing how it especially affects the latter one.

A straightforward synthesis utilizing the ring-opening metathesis polymerization (ROMP) reaction is described for acid-triggered N,O-chelating ruthenium-based pre-catalysts bearing one or two 8-quinolinolate ligands. The innovative pre-catalysts were tested regarding their behavior in ROMP and especially for their use in the synthesis of poly(dicyclopentadiene) (pDCPD). Bearing either the common phosphine leaving ligand in the first and second Grubbs olefin metathesis catalysts, or the Ru–O bond cleavage for the next Hoveyda-type catalysts, this work is a step forward towards the control of polymer functionalization and living or switchable polymerizations.

The haloarchaeon Halorubrum lacusprofundi is among the few polyextremophilic organisms capable of surviving in one of the most extreme aquatic environments on Earth, the Deep Lake of Antarctica (−18 °C to +11.5 °C and 21–28%, w/v salt content). Hence, H. lacusprofundi has been proposed as a model for biotechnology and astrobiology to investigate potential life beyond Earth. To understand the mechanisms that allow proteins to adapt to both salinity and cold, we structurally (including X-ray crystallography and molecular dynamics simulations) and functionally characterized the β-galactosidase from H. lacusprofundi (hla_bga). Recombinant hla_bga (produced in Haloferax volcanii) revealed exceptional stability, tolerating up to 4 M NaCl and up to 20% (v/v) of organic solvents. Despite being cold-adapted, hla_bga was also stable up to 60 °C. Structural analysis showed that hla_bga combined increased surface acidity (associated with halophily) with increased structural flexibility, fine-tuned on a residue level, for sustaining activity at low temperatures. The resulting blend enhanced structural flexibility at low temperatures but also limited protein movements at higher temperatures relative to mesophilic homologs. Collectively, these observations help in understanding the molecular basis of a dual psychrophilic and halophilic adaptation and suggest that such enzymes may be intrinsically stable and functional over an exceptionally large temperature range.

During a Ru-catalyzed reaction of an olefin with an alkylidene moiety that leads to a metallacycle intermediate, the cis insertion of the olefin can occur from two different directions, namely side and bottom with respect to the phosphine or N-heterocyclic ligand (NHC), depending on the first or second generation Grubbs catalyst. Here, DFT calculations unravel to which extent the bottom coordination of olefins with respect is favored over the side coordination through screening a wide range of catalysts, including first and second generation Grubbs catalysts as well as the subsequent Hoveyda derivatives. The equilibrium between bottom and side coordination is influenced by sterics, electronics, and polarity of the solvent. The side attack is favored for sterically less demanding NHC and/or alkylidene ligands. Moreover the generation of a 14-electron species is also discussed, with either pyridine or phosphine ligands to dissociate.

Two ruthenium olefin metathesis initiators featuring electronically modified quinoline-based chelating carbene ligands are introduced. Their reactivity in RCM and ROMP reactions was tested and the results were compared to those obtained with the parent unsubstituted compound. The studied complexes are very stable at high temperatures up to 140 °C. The placement of an electron-withdrawing functionality translates into an enhanced activity in RCM. While electronically modified precatalysts, which exist predominantly in the trans-dichloro configuration, gave mostly the RCM and a minor amount of the cycloisomerization product, the unmodified congener, which preferentially exists as its cis-dichloro isomer, shows a switched reactivity. The position of the equilibrium between the cis- and the trans-dichloro species was found to be the crucial factor governing the reactivity of the complexes.

In view of the increasing interest both in inhibitors of protein-protein interactions and in protein drugs themselves, analysis of the three-dimensional structure of protein-protein complexes is assuming greater relevance in drug design. In the many cases where an experimental structure is not available, protein-protein docking becomes the method of choice for predicting the arrangement of the complex. However, reliably scoring protein-protein docking poses is still an unsolved problem. As a consequence, the screening of many docking models is usually required in the analysis step, to possibly single out the correct ones. Here, making use of exemplary cases, we review our recently introduced methods for the analysis of protein complex structures and for the scoring of protein docking poses, based on the use of inter-residue contacts and their visualization in inter-molecular contact maps. We also show that the ensemble of tools we developed can be used in the context of rational drug design targeting protein-protein interactions.

In this study we have tested the ability of a standard DFT computational protocol to reproduce the experimentally obtained stereoselectivity of 26 different C2-symmetric zirconocene catalysts active in propylene polymerization. The catalysts were chosen for their relevance in metallocene catalyzed polymerization of propylene. To this end, primary insertion of both si- and re-propylene enantiofaces into the Zr-CH2-CH(CH3)2 bond was considered to simulate the growing chains step. The energy difference between these two transition states, ΔEre-si, was taken as a measure of the stereoselectivity (pentad: mmmm%) of different catalysts. The results clearly indicated that there was a good agreement between ΔEre-si and the mmmm% values, so that greater ΔEre-si could correspond to higher mmmm%. A model was fitted to the experimentally obtained mmmm% against theoretical ΔEre-si. The coefficient of determination (R2) of the resultant plot was 0.9793, which indicated a good accuracy of the model. Finally, to quantify the steric role of the studied ligands in the observed stereoselectivity, the analysis of the buried volume (VBur) and of the steric maps was performed for two representative complexes. The images revealed that a greater asymmetric localization of the %VBur around the metal center led to a higher mmmm% in the resultant polymer.

Researchers have suggested that the reason behind infertility is pernicious effect of broad spectrum pesticides on non target, beneficial microorganism of soil. Here, studying the chelating effect of selective organophosphate and carbamate pesticides with essential metal ions, at all possible combinations of three different pH (4 ± 0.05, 7 ± 0.05 and 9 ± 0.05) and three different temperatures (15 ± 0.5°C, 30 ± 0.5°C and 45 ± 0.5°C), shows very fast rate of reaction which further increases with increase of pH and temperature. Carbonyl oxygen of carbamate and phosphate oxygen of organophosphate were found to be common ligating sites among all the complexes. Formed metal complexes were found to be highly stable and water insoluble on interaction with essential metal ions in solvent medium as well as over silica. Density functional theory (DFT) calculations not only reinforced the experimental observations, but, after a wide computational conformational analysis, unraveled the nature of the high stable undesired species that consist of pesticides complexed by metal ions from the soil. All in all, apart from the direct toxicity of pesticides, the indirect effect by means of complexation of free metal ions impoverishes the soil.

Correctly scoring protein-protein docking models to single out native-like ones is an open challenge. It is also an object of assessment in CAPRI (Critical Assessment of PRedicted Interactions), the community-wide blind docking experiment. We introduced in the field the first pure consensus method, CONSRANK, which ranks models based on their ability to match the most conserved contacts in the ensemble they belong to. In CAPRI, scorers are asked to evaluate a set of available models and select the top ten ones, based on their own scoring approach. Scorers' performance is ranked based on the number of targets/interfaces for which they could provide at least one correct solution. In such terms, blind testing in CAPRI Round 30 (a joint prediction round with CASP11) has shown that critical cases for CONSRANK are represented by targets showing multiple interfaces or for which only a very small number of correct solutions are available. To address these challenging cases, CONSRANK has now been modified to include a contact-based clustering of the models as a preliminary step of the scoring process. We used an agglomerative hierarchical clustering based on the number of common inter-residue contacts within the models. Two criteria, with different thresholds, were explored in the cluster generation, setting either the number of common contacts or of total clusters. For each clustering approach, after selecting the top (most populated) ten clusters, CONSRANK was run on these clusters and the top-ranked model for each cluster was selected, in the limit of 10 models per target. We have applied our modified scoring approach, Clust-CONSRANK, to SCORE_SET, a set of CAPRI scoring models made recently available by CAPRI assessors, and to the subset of homodimeric targets in CAPRI Round 30 for which CONSRANK failed to include a correct solution within the ten selected models. Results show that, for the challenging cases, the clustering step typically enriches the ten top ranked models in native-like solutions. The best performing clustering approaches we tested indeed lead to more than double the number of cases for which at least one correct solution can be included within the top ten ranked models.

In this study we have investigated computationally the origin of the cis–trans selectivity in the Ru-catalyzed cross metathesis (CM) of a prototype monosubstituted olefin, i.e., propene. Our calculations suggest that the origin of the preferential formation of trans-olefins is in the product release step, which prevents the initially formed cis-olefin from escaping the metal, and returns it to the reaction pool until the trans-olefin is formed.

Anti-idiotype antibodies have potential therapeutic applications in many fields, including autoimmune diseases. Herein we report the isolation and characterization of AIM2, an anti-idiotype antibody elicited in a mouse model upon expression of the celiac disease-specific autoantibody MB2.8 (directed against the main disease autoantigen type 2 transglutaminase, TG2). To characterize the interaction between the two antibodies, a 3D model of the MB2.8-AIM2 complex has been obtained by molecular docking. Analysis and selection of the different obtained docking solutions was based on the conservation within them of the inter-residue contacts. The selected model is very well representative of the different solutions found and its stability is confirmed by molecular dynamics simulations. Furthermore, the binding mode it adopts is very similar to that observed in most of the experimental structures available for idiotype-anti-idiotype antibody complexes. In the obtained model, AIM2 is directed against the MB2.8 CDR region, especially on its variable light chain. This makes the concurrent formation of the MB2.8-AIM2 complex and of the MB2.8-TG2 complex incompatible, thus explaining the experimentally observed inhibitory effect on the MB2.8 binding to TG2.