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Background. The increasing amount of chemical reaction data makes traditional ways to navigate its corpus less effective, while the demand for novel approaches and instruments is rising. Recent data science and machine learning techniques support the development of new ways to extract value from the available reaction data. On the one side, Computer-Aided Synthesis Planning tools can predict synthetic routes in a model-driven approach; on the other side, experimental routes can be extracted from the Network of Organic Chemistry, in which reaction data are linked in a network. In this context, the need to combine, compare and analyze synthetic routes generated by different sources arises naturally. Results. Here we present LinChemIn, a python toolkit that allows chemoinformatics operations on synthetic routes and reaction networks. Wrapping some third-party packages for handling graph arithmetic and chemoinformatics and implementing new data models and functionalities, LinChemIn allows the interconversion between data formats and data models and enables route-level analysis and operations, including route comparison and descriptors calculation. Object-Oriented Design principles inspire the software architecture, and the modules are structured to maximize code reusability and support code testing and refactoring. The code structure should facilitate external contributions, thus encouraging open and collaborative software development. Conclusions. The current version of LinChemIn allows users to combine synthetic routes generated from various tools and analyze them, and constitutes an open and extensible framework capable of incorporating contributions from the community and fostering scientific discussion. Our roadmap envisages the development of sophisticated metrics for routes evaluation, a multi-parameter scoring system, and the implementation of an entire "ecosystem" of functionalities operating on synthetic routes. LinChemIn is freely available at https://github.com/syngenta/linchemin.

The use of stabilized cationic intermediates can be considered as a new frontier in the development of stereoselective reactions. An organocatalytic procedure mediated by the MacMillan imidazolidinone catalyst was coupled with an InBr3-mediated process for the development of a novel stereoselective allylation reaction of aldehydes. Up to 98 % ee and up to 5:1 d.r. were obtained in the process.

Neonicotinoid insecticides selectively target the invertebrate nicotinic acetylcholine receptor and disrupt excitatory cholinergic neurotransmission. First launched over 20 years ago, their broad pest spectrum, variety of application methods and relatively low risk to nontarget organisms have resulted in this class dominating the insecticide market with global annual sales in excess of $3.5 bn. This remarkable commercial success brings with it conditions in the field that favour selection of resistant phenotypes. A number of important pest species have been identified with mutations at the nicotinic acetylcholine receptor associated with insensitivity to neonicotinoids. The detailed characterization of these mutations has facilitated a greater understanding of the invertebrate nicotinic acetylcholine receptor.

The stereospecific oxidative decomposition of urate into allantoin is the core of purine catabolism in many organisms. The spontaneous decomposition of upstream intermediates and the nonenzymatic racemization of allantoin lead to an accumulation of (R)-allantoin, because the enzymes converting allantoin into allantoate are specific for the (S) isomer. The enzyme allantoin racemase catalyzes the reversible conversion between the two allantoin enantiomers, thus ensuring the overall efficiency of the catabolic pathway and preventing allantoin accumulation. On the basis of recent crystallographic and biochemical evidence, allantoin racemase has been assigned to the family of cofactor-independent racemases, together with other amino acid racemases. A detailed computational investigation of allantoin racemase has been carried out to complement the available experimental data and to provide atomistic insight into the enzymatic action. Allantoin, the natural substrate of the enzyme, has been investigated at the quantum mechanical level, in order to rationalize its conformational and tautomeric equilibria, playing a key role in protein-ligand recognition and in the following catalytic steps. The reaction mechanism of the enzyme has been elucidated through quantum mechanics/molecular mechanics (QM/MM) calculations. The potential energy surface investigation, carried out at the QM/MM level, revealed a stepwise reaction mechanism. A pair of cysteine residues promotes the stereoinversion of a carbon atom of the ligand without the assistance of cofactors. Electrostatic fingerprint calculations are used to discuss the role of the active site residues in lowering the pK(a) of the substrate. The planar unprotonated intermediate is compared with the enolic allantoin tautomer observed in the active site of the crystallized enzyme. Finally, the enzymatic catalysis featured by allantoin racemase (AllR) is compared with that of other enzymes belonging to the same family.

The unusual migration of a nitro group from the - to the -position of a -aryl--nitroethenyl moiety, following a nitrocyclopropane to isoxazoline N-oxide isomerization, has been studied from a mechanistic and synthetic points of view. As a result, two series of isomeric isoxazoline N-oxides could be obtained under controlled conditions. When reacted with diazomethane, a model transposed isoxazoline cleanly furnished a new, interesting pyrazolylisoxazole.

The human pathogen Mycobacterium tuberculosis requires the ESX-1 secretion system for full virulence. EspR plays a key role in ESX-1 regulation via direct binding and transcriptional activation of the espACD operon. Here, we describe the crystal structures of EspR, a C-terminally truncated form, EspR Delta 10, as well as an EspR-DNA complex. EspR forms a dimer with each monomer containing an N-terminal helix-turn-helix DNA binding motif and an atypical C-terminal dimerization domain. Structural studies combined with footprinting experiments, atomic force microscopy and molecular dynamic simulations allow us to propose a model in which a dimer of EspR dimers is the minimal functional unit with two subunits binding two consecutive major grooves. The other two DNA binding domains are thus free to form higher-order oligomers and to bridge distant DNA sites in a cooperative way. These features are reminiscent of nucleoid-associated proteins and suggest a more general regulatory role for EspR than was previously suspected.

(1 E ,3 Z )-1-Aryl-4-methanesulfonyl-2-nitro-1,3-butadienes ( 8 ), derived from the initial ring-opening of 3-nitrothiophene ( 5 ), have been found to undergo a facile base-induced cyclization leading to thiopyran S , S -dioxides ( 9 ), thus furnishing a further example of effective ring-enlargement from 5- to 6-membered sulfur heterocycles. Compounds 9 are obtained as single racemic mixtures in satisfactory yields; they still contain a nitrovinylic moiety, which can be exploited for further modifications targeted to new derivatives endowed with either synthetic or pharmacological potentialities e.g., in the field of L-type Ca 2+ -channel blockers.

Reference EPFL-ARTICLE-150326doi:10.2174/157017807781024165 URL: http://www.bentham.org/loc/contabs/loc4-4.htm#13 Record created on 2010-08-06, modified on 2017-05-12

In the last decade combined quantum mechanic/ molecular mechanic (QM/MM) methods have been applied to a large variety of chemical problems. This paper describes a new QM/MM implementation that acts as a flexible computational environment. Specifically, geometry optimizations, frequency calculations and molecular dynamics can be performed on the investigated system that can be split up to three different layers corresponding to different levels of accuracy. Here we report, together with a detailed description of the method and its implementation, some test examples on very different chemical problems, which span the wide and diversified area of chemistry (from ground to excited states topics) and show the flexibility, general applicability and accuracy of the presented hybrid approach. Biochemical, photobiological and supra/super-molecular applications are presented for this purpose: (a) the optimized geometry of a rotaxane is compared with its X-ray structure; (b) the computed absorption spectra of the green fluorescent protein and rhodopsin chromophores in different environments (namely solvent and protein) are compared to the corresponding experimental values and the role of the counter ion and ion pairs in tuning the geometrical and optical properties of charged organic chromophores in polar solvents is explored and discussed; (c) problems and open questions related to the model set-up of a protein are investigated in the framework of the TcPRAC-protein racemase; (d) similarities and differences between the QM and QM/MM reaction path for the HIV1-protease enzymatic mechanism are shown and discussed; (e) the delicate anomeric equilibrium of α- and β − D-glucopyranose in water is investigated via QM/MM optimizations and molecular dynamics to show the reliability of the actual implementation in the simulation of solvation effects and delicate balances. Finally, it will be shown that the current implementation (called COBRAMM: Computations at Bologna Relating Ab-initio and Molecular Mechanics Methods) is more than a simple QM/MM method, but a more general hybrid approach with a modular structure that is able to integrate some specialized programs, which may increase the flexibility/efficiency of QM, MM and QM/MM calculations.

A new ferrocene-based catalyst is designed in which the ferrocenyl group in connection with the geminal dialkylmethyl-linker impose the preferred conformation of the pyrrolidine moiety for intermediary enamine formation.

Injectisomes are multi-protein transmembrane machines allowing pathogenic bacteria to inject effector proteins into eukaryotic host cells, a process called type III secretion. Here we present the first three-dimensional structure of Yersinia enterocolitica and Shigella flexneri injectisomes in situ and the first structural analysis of the Yersinia injectisome. Unexpectedly, basal bodies of injectisomes inside the bacterial cells showed length variations of 20%. The in situ structures of the Y. enterocolitica and S. flexneri injectisomes had similar dimensions and were significantly longer than the isolated structures of related injectisomes. The crystal structure of the inner membrane injectisome component YscD appeared elongated compared to a homologous protein, and molecular dynamics simulations documented its elongation elasticity. The ring-shaped secretin YscC at the outer membrane was stretched by 30–40% in situ, compared to its isolated liposome-embedded conformation. We suggest that elasticity is critical for some two-membrane spanning protein complexes to cope with variations in the intermembrane distance. DOI: http://dx.doi.org/10.7554/eLife.00792.001, eLife digest Humans and other animals can use the five senses—touch, taste, sight, smell, and hearing—to interpret the world around them. Single-celled organisms, however, must rely on molecular cues to understand their immediate surroundings. In particular, bacteria gather information about external conditions, including potential hosts nearby, by secreting protein sensors that can relay messages back to the cell. Bacteria export these sensors via secretion systems that enable the organism both to receive information about the environment and to invade a host cell. A total of seven separate secretion systems, known as types I–VII, have been identified. These different secretion systems handle distinct cargoes, allowing the bacterial cell to respond to a range of feedback from the external milieu. The type III secretion system, also known as the ‘injectisome’, is found in bacterial species that are enclosed by two membranes separated by a periplasmic space. The injectisome comprises different components that combine to form the basal body, which spans the inner and outer membranes, and a projection from the basal body, called the hollow needle, that mediates the export of cargo from a bacterium to its host or the local environment. The distance between the inner and outer membranes may vary across species or according to environmental conditions, so the basal body must be able to accommodate these changes. However, no mechanism has yet been established that might introduce such elasticity into the injectisome. Now, Kudryashev et al. have generated three-dimensional structures for the injectisomes of two species of bacteria, Shigella flexneri and Yersinia enterocolitica, and shown that the size of the basal body can fluctuate by up to 20%. Kudryashev et al. imaged whole injectisomes in these two species and found that the height of the basal body was proportional to the distance between the inner and outer membranes. To probe how this could occur, the properties of two proteins that are important components of the basal body were studied in greater detail. YscD, a protein that extends across the periplasmic space, was crystallized and its structure was then determined and used to develop a computer model to assess its compressibility: this model indicated that YscD could stretch or contract by up to 50% of its total length. The outer membrane component YscC also appeared elastic: when the protein was isolated and introduced into synthetic membranes, its length was reduced 30–40% relative to that observed in intact bacterial membranes. A further experiment confirmed the adaptability of the basal body: when the separation of the membranes was deliberately increased by placing bacteria in a high-salt medium, the basal body extended approximately 10% in length. Cumulatively, therefore, these experiments suggest that the in-built flexibility of the basal body of the injectisome allows bacteria to adjust to environmental changes while maintaining their sensory abilities and host-invasion potential. DOI: http://dx.doi.org/10.7554/eLife.00792.002

Ironing out the details: Proline and pyrrolidine derivatives (Hayashi- Jørgensen catalysts) are considered "work horses" in organocatalysis. This report describes a new effective ferrocenyl pyrrolidine catalyst that is able to perform well in benchmark organocatalytic reactions (see figure). The ferrocene moiety controls the conformational space and a simple alkyl group effectively covers a face of the derived enamine. This new framework can find applications in organocatalysis, and in general, in new ligand design.

Transcription Activator-Like (TAL) effectors are DNA-binding proteins secreted by phytopathogenic bacteria that interfere with native cellular functions by binding to plant DNA promoters. The key element of their architecture is a domain of tandem-repeats with almost identical sequences. Most of the polymorphism is located at two consecutive amino acids termed Repeat Variable Diresidue (RVD). The discovery of a direct link between the RVD composition and the targeted nucleotide allowed the design of TAL-derived DNA-binding tools with programmable specificities that revolutionized the field of genome engineering. Despite structural data, the molecular origins of this specificity as well as the recognition mechanism have remained unclear. Molecular simulations of the recent crystal structures suggest that most of the protein-DNA binding energy originates from non-specific interactions between the DNA backbone and non-variable residues, while RVDs contributions are negligible. Based on dynamical and energetic considerations we postulate that, while the first RVD residue promotes helix breaks - allowing folding of TAL as a DNA-wrapping super-helix - the second provides specificity through a negative discrimination of matches. Furthermore, we propose a simple pharmacophore-like model for the rationalization of RVD-DNA interactions and the interpretation of experimental findings concerning shared affinities and binding efficiencies. The explanatory paradigm presented herein provides a better comprehension of this elegant architecture and we hope will allow for improved designs of TAL-derived biotechnological tools.

A Quantum Mechanics/Molecular Mechanics (QM/MM) computational investigation of the catalytic mechanism of the human glutathione transferase A3-3 (hGSTA3-3) has been carried out. The results demonstrate that the isomerization reaction is concerted, but highly asynchronous: in the first reaction phase the glutathione (GSH) negative sulfur (thiolate) acts as a base and deprotonates carbon C4 of the substrate Delta(5)-androstene-3,17-dione (Delta(5)-AD); in the second reaction phase the hydroxyl proton of the tyrosine fragment Y9 is AD). The initial state of the enzyme is subsequently restored by transferred to C6 affording the Delta(4)-androstene-3,17-dione product (Delta(4)-transferring a proton from the GSH sulfur to the tyrosine negative oxygen. There is no evidence for a "genuine" stepwise mechanism involving the formation of a real dienolate intermediate as suggested in previous papers. Furthermore, our computations have evidenced that, when we consider the whole process (including the restoring of the enzyme), GSH behaves as a base/acid catalyst (as hypothesized by some authors), but it requires the participation of the tyrosine Y9 acting as a proton shuttle. A "fingerprint analysis" has been used to rank the electrostatic effects on the catalysis of the various residues surrounding the active site. This analysis highlights the role played by the arginine residue R15 in stabilizing the initial complex in agreement with previous suggestions based on-crystal structures.

The human pathogen Mycobacterium tuberculosis requires the ESX-1 secretion system for full virulence. EspR plays a key role in ESX-1 regulation via direct binding and transcriptional activation of the espACD operon. Here, we describe the crystal structures of EspR, a C-terminally truncated form, EspRΔ10, as well as an EspR-DNA complex. EspR forms a dimer with each monomer containing an N-terminal helix-turn-helix DNA binding motif and an atypical C-terminal dimerization domain. Structural studies combined with footprinting experiments, atomic force microscopy and molecular dynamic simulations allow us to propose a model in which a dimer of EspR dimers is the minimal functional unit with two subunits binding two consecutive major grooves. The other two DNA binding domains are thus free to form higher-order oligomers and to bridge distant DNA sites in a cooperative way. These features are reminiscent of nucleoid-associated proteins and suggest a more general regulatory role for EspR than was previously suspected.

The photochemical cis-trans isomerization of retinal in rhodopsin is investigated by structure sampling and excited state QM/MM trajectories with surface hopping. The calculations uncover the motions responsible for photoproduct formation and elucidate the reasons behind the efficient photoisomerization in the primary event of visual transduction.

The needle length of the Yersinia spp. injectisome is determined by Yop secretion protein P (YscP), an early substrate of the injectisome itself. There is a linear correlation between the length of YscP and the length of the needle, suggesting that YscP acts as a molecular ruler. However, it is not known whether one single molecule of YscP suffices to control the length of one needle or whether several molecules of YscP are exported in alternation with the needle subunit YscF until the needle length matches the ruler length, which would stop needle growth. To address this question, three different strains expressing simultaneously a short and a long version of YscP were engineered. The experimentally obtained needle length distribution was compared with the distributions predicted by stochastic modeling of the various possible scenarios. The experimental data are compatible with the single ruler model and not with the scenarios involving more than one ruler per needle.

Asymmetric phase-transfer catalysis (PTC) has risen to prominence over the last decade as a straightforward synthetic methodology for the preparation of pharmacologically active compounds in enantiomerically pure form. However, the complex interplay of weak nonbonded interactions (between catalyst and substrate) that could account for the stereoselection in these processes is still unclear, with tentative pictorial mechanistic representations usually proposed. Here we present a full account dealing with the enantioselective phase-transfer-catalyzed intramolecular aza-Michael reaction (IMAMR) of indolyl esters, as a valuable synthetic tool to obtain added-value compounds, such as dihydro- pyrazinoindolinones. A combined computational and experimental investigation has been carried out to elucidate the key mechanistic aspects of this process.

We have employed hybrid CASPT2//CASSCF/AMBER calculations to map the (1)L(a)(1pipi*) deactivation path of a single quantum mechanical adenine in a d(A)(10).d(T)(10) double strand in water that is treated at the molecular mechanics level. We find that (a) the L(a) relaxation route is flatter in DNA than in vacuo and (b) the L(a) relaxation energy in DNA is much larger than the stabilization energy of the corresponding L(a) excimer. An intra-monomer relaxation process is found to be compatible with the multiexponential decay recorded in DNA, possibly including the longer (4100 ps) lifetime component.

The synthetically useful nucleophilic attack on nitrobenzo-[b]thiophenes, a starting point for ring-opening/ring-closure pathways to different heterocyclic systems, has been investigated in detail. 3-Nitrobenzo[b]thiophene (9) and 2-nitrob-enzo[b]thiophene (10) react with sodium methoxide in either DMSO or methanol to give the relevant "Meisenheimer-type" adducts 9' and 10', identified by NMR spectroscopy. A UV study indicated that the equilibrium constants for the formation of 9' at 293 K are 10.1 and 40700 L mol -1 in methanol and in DMSO, respectively. Competition reactions showed that the stability constant of 10' is lower than that of 9': accordingly, DFT [B3LYP/6-31+G(d,p)] calculations indicate that the formation of 9' is thermodynamically more favoured than that of 10' both in the gas phase and in DMSO. The reason for the opposite sequence in the stability constants previously found for the corresponding gem-dimethoxy Meisenheimer adducts 7' and 8' was therefore investigated in depth and appears to be a consequence of different steric interactions in the starting compounds, 2-methoxy-3-nitro-(7) and 3-methoxy-2-nitrobenzo[b]thiophene (8), respectively. A study of 13 C NMR chemical shift changes accompanying the formation of adducts 9' and 10' confirms that the formation of the adduct exhibiting the larger stability constant is accompanied by a smaller π electron density redistribution, as we have previously found in other cases all governed by electronic effects. The opposite behaviour is observed in the formation of the gem-dimethoxy adducts 7' and 8', which is a consequence of the predominance of steric effects. Further outcomes of more general interest deal with the aromatic character of benzo[b]thiophenes. NMR spectroscopic data and calculated bond lengths show that in the studied reactions the benzene ring, unlike the thiophene one, is scarcely affected by methoxide addition, retaining its nearly "full" aromatic character. Benzocondensation increases the stability constants of σ-adducts mainly because of a marked reduction in the aromatic character of the thiophene ring in the substrates.

The reduction potentials of the title compounds 4 have been measured by cyclic voltammetry. The effect of the substituents has been evaluated by using a linear free energy relationship treatment, thus evidencing that the present ortho-substituents affect the Epc values basically by electronic effects. A comparison with data previously collected on ortho-substituted (aryl)(2-nitrobenzo[b]thiophen-3-yl)amines 3 has provided some interesting information. Different electrochemical behaviors are observed during the reduction (a reversible process and an irreversible process are operating in 3 and 4, respectively): to elucidate the reasons for this different behavior, the "reversible" reduction potentials of 5 and of 6 have been measured. Moreover, higher susceptibility constants have been calculated for compounds of series 4 with respect to those of series 3 (rho4 = 329 and rho3 = 182, respectively). A rationale for all of these findings has been offered.

High level ab initio correlated (CASPT2) computations have been used to elucidate the details of the photoinduced molecular motion and decay mechanisms of a realistic phytochrome chromophore model in vacuo and to explore the reasons underneath its photophysical/photochemical properties. Competitive deactivation routes emerge that unveil the primary photochemical event and the intrinsic photoisomerization ability of this system. The emerged in vacuo based static (i.e., nondynamical) reactivity model accounts for the formation of different excited state intermediates and suggests a qualitative rationale for the short (picosecond) excited state lifetime and ultrafast decay of the emission, its small quantum yield, and the multiexponential decay observed in both solvent and phytochromes. It is thus tentatively suggested that this is a more general deactivation scheme for photoexcited phytochrome chromophores that is independent of the surrounding environment. Spectroscopic properties have also been simulated in both isolated conditions and the protein that satisfactorily match experimental data. For this purpose, preliminary hybrid QM/MM computations at the correlated (CASPT2) level have been used in the protein and are reported here for the first time.

Hybrid QM(CASPT2//CASSCF/6-31G*)/MM(Amber) computations have been used to map the photoisomerization path of the retinal chromophore in Rhodopsin and explore the reasons behind the photoactivity efficiency and spectral control in the visual pigments. It is shown that while the electrostatic environment plays a central role in properly tuning the optical properties of the chromophore, it is also critical in biasing the ultrafast photochemical event: it controls the slope of the photoisomerization channel as well as the accessibility of the S(1)/S(0) crossing space triggering the ultrafast decay. The roles of the E113 counterion, the E181 residue, and the other amino acids of the protein pocket are explicitly analyzed: it appears that counterion quenching by the protein environment plays a key role in setting up the chromophore's optical properties and its photochemical efficiency. A unified scenario is presented that discloses the relationship between spectroscopic and mechanistic properties in rhodopsins and allows us to draw a solid mechanism for spectral tuning in color vision pigments: a tunable counterion shielding appears as the elective mechanism for L--M spectral modulation, while a retinal conformational control must dictate S absorption. Finally, it is suggested that this model may contribute to shed new light into mutations-related vision deficiencies that opens innovative perspectives for experimental biomolecular investigations in this field.

The unusual behaviour of α-bromo vinylketenes in the cycloaddition reactions with imines is described. This class of vinylketenes behaves as dienophiles in [2+2] reactions, but also displays an unusual diene reactivity in [4+2] reactions. Interestingly, the reactivity of α-bromo vinylketenes can be modulated via a fine tuning of the substituents. For instance, a methyl group in the β-position completely inhibits the [2+2] reaction and the [4+2] pathway is almost exclusively followed. A more hindered ketimine (instead of a simple imine) is enough to activate again the [2+2] mechanism. We have carried out a DFT theoretical investigation to rationalise these experimental observations. We have considered two pathways for the [2+2] reaction involving imine, that is, the endo and exo pathways. The former is favoured in the case of α-bromo vinylketenes, while the latter is preferred for non-substituted vinylketenes. Since the [4+2] cycloaddition becomes possible only when the s-Z-conformation of vinylketene is significantly populated, the presence of bromine substituents in this substrate is crucial in determining the [2+2] or [4+2] mechanisms. For unsubstituted vinylketenes, the barrier connecting the s-E- to the s-Z-conformation is too high to be easily overcome. Thus, the s-Z-structure has a low population and the [2+2] mechanism is favoured. In the case of α-bromo vinylketenes (especially the β-methyl-substituted ones), this barrier can be surmounted and the [4+2] mechanism becomes available.

The enzyme proline racemase from the eukaryotic parasite Trypanosoma cruzi (responsible for endemic Chagas disease) catalyzes the reversible stereoinversion of chiral Calpha in proline. We employed a new combined quantum mechanical and molecular mechanical (QM/MM) potential to study the reaction mechanism of the enzyme. Three critical points were found: two almost isoenergetic minima (M1a and M2a), in which the enzyme is bound to L- and D-Pro, respectively, and a transition state (TSCa), unveiling a highly asynchronous concerted process. A systematic analysis was performed on the optimized geometries to point out the key role played by some residues in stabilizing the transition state.

Excited state QM(CASPT2//CASSCF)/MM(GAFF) calculations, by our recently developed code COBRAMM (Computations at Bologna Relating Ab‐initio and Molecular Mechanic Methods), were carried out in rhodopsin to investigate on the steric and electrostatic effects in retinal photoisomerization catalysis due to the β‐ionone ring and glutammate 181 (GLU 181), respectively. The excited state photoisomerization channel has been mapped and a new christallographyc structure (2.2 A resolution) has been used for this purpose. Two different set‐ups have been used to evaluate the electrostatic effects of GLU 181 (which is very close to the central double bond of the chromophore): the first with a neutral GLU 181 (as commonly accepted), the second with a negatively charged (i.e. deprotonated) GLU 181 (as very recent experimental findings seem to suggest). On the other hand, β‐ionone ring steric effects were evaluated by calculating the photoisomerization path of a modified chromophore, where the ring double bond has been saturated. Spectroscopic properties were calculated and compared with the available experimental data.

This work presents a QM/MM investigation of the spectral properties of the 11‐cis‐retinal and the GFP chromophore in polar solvents and protein. The results of the computations are in surprising agreement with the experimental values indicating the accuracy of our computational approach. In addition it has been demonstrated the key role of the solvent to create a “virtual conter‐ion”. This effect is due to the reorientation (i.e. polarization) of the polar solvent close to the chromophore: the polarized permanent dipoles of the solvent act similarly to the counter ion, stabilizing the ground state respect to the charge transfer excited state.

The Mukaiyama-Michael-type addition of various silyl ketene acetals or silyl enol ethers on some 1,2-diaza-1,3-butadienes proceeds at room tem- perature in the presence of catalytic amounts of Lewis acid affording by heterocyclization 1-amino- pyrrol-2-ones and 1-aminopyrroles, respectively. 1- Aminoindoles have been also obtained by the same addition of 2-(trimethylsilyloxy)-1,3-cyclohexadiene on some 1,2-diaza-1,3-butadienes and subsequent ar- omatization. Mechanistic investigations indicate the coordination by Lewis acid of the enolsilyl derivative and its 1,4-addition on the azo-ene system of 1,2- diaza-1,3-butadienes. The migration of the silyl group from a hydrazonic to an amidic nitrogen, its acidic cleavage and the final internal heterocycliza- tion give the final products. Based on NMR studies and ab initio calculations, a plausible explanation for the migration of the silyl protecting group is presented.

Human Glutathione S‐Transferase A3‐3(hGSTA3‐3) is the most efficient human steroid double‐bond isomerase enzyme. It catalyzes the double bond isomerization of Δ5 ‐androstene–3,17–dione ( Δ5 ‐AD) and Δ5 ‐pregnene–3,20–dione ( Δ5 ‐PD). The isomerization products are the precursors of the steroid hormones testosterone and progesterone. We have carried out a QM/MM study to elucidate some interesting aspects of the enzyme catalytic mechanism. In particular, we have analyzed either a concerted or a stepwise reaction path. Moreover, we have attempted to rationalize the electrostatic effects on the catalytic activity of the residues surrounding the active site. Specifically, we have performed a “finger print” analysis to determine the electrostatic contribution of each aminoacid residue to the global electrostatic term, thus ranking the effect of the various aminoacids in the course of the reaction. In this way, we have highlighted the most important terms affecting the stabilization‐destabilization of the enzyme.

The catalytic activity of an interesting enzyme (involved in the life cycle of the Trypanosoma Cruzi eucariotic parasite) has been elucidated by mean of a QM/MM study. The reaction mechanism of the stereo‐inversion of the substrate has been studied by characterizing the associated PES. The nature of the found critical point has been checked by means of numerical frequencies calculations. The role of the various residues in the catalysis has been pointed out.

This contribution illustrates some features of a new of a newly implemented general hybrid approach. This method, included in the COBRAMM (Computations at Bologna Relating Ab‐initio and Molecular Mechanic Methods) suite of programs, has a modular structure that integrates some specialized programs and represents a flexible computational environment that increases the flexibility/efficiency of QM, and MM, and QM/MM calculations. Here we describe some aspects of the geometry optimization procedure and explain some approximations used in the frequency computation. Moreover we present two analysis procedures that allow to rank the contribution of the various aminoacid residues of an enzyme in determining the catalytic mechanism and the shape of a Potential Energy Surface (PES).

The reduction potential values of the title compounds (1Ar,o) have been evaluated by cyclic voltammetry at a platinum electrode in the presence of 0.1 M N(Et)4BF4 in DMSO. Compounds 1Ar,o give reversible reduction peaks. The ortho-substituent affects their values basically by electronic effects (good LFER have been observed). The peculiar behaviour of (2′-hydroxyphenyl)(2-nitrobenzo[b]thiophen-3-yl)amine 1Ar,o(i) (showing two quasi reversible systems of peaks) has been explained on the basis of the special effect of the 2′-hydroxy substituent, which is able to assist a proton transfer through a network of hydrogen bonds involving the amine nitrogen atom (proton shuttle). This behaviour is unexpected in anhydrous DMSO and has similarities with the reaction features observed in water. The above hypothesis has been confirmed by quantum-mechanical DFT calculations carried out on 1Ar,o(i). In this theoretical investigation all the possible species, that can form as a consequence of two mono-electron reduction ...

Capnocytophaga canimorsus is a usual member of dog's mouths flora that causes rare but dramatic human infections after dog bites. We determined the structure of C. canimorsus lipid A. The main features are that it is penta-acylated and composed of a “hybrid backbone” lacking the 4′ phosphate and having a 1 phosphoethanolamine (P-Etn) at 2-amino-2-deoxy-d-glucose (GlcN). C. canimorsus LPS was 100 fold less endotoxic than Escherichia coli LPS. Surprisingly, C. canimorsus lipid A was 20,000 fold less endotoxic than the C. canimorsus lipid A-core. This represents the first example in which the core-oligosaccharide dramatically increases endotoxicity of a low endotoxic lipid A. The binding to human myeloid differentiation factor 2 (MD-2) was dramatically increased upon presence of the LPS core on the lipid A, explaining the difference in endotoxicity. Interaction of MD-2, cluster of differentiation antigen 14 (CD14) or LPS-binding protein (LBP) with the negative charge in the 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo) of the core might be needed to form the MD-2 – lipid A complex in case the 4′ phosphate is not present., Author Summary Capnocytophaga canimorsus, a commensal bacterium in dog's mouths, causes rare but dramatic infections in humans that have been bitten by dogs. The disease often begins with mild symptoms but progresses to severe septicemia. The lipopolysaccharide (LPS), composed of lipid A, core and O-antigen, is one of the most pro-inflammatory bacterial compounds. The activity of the LPS has so far been attributed to the lipid A moiety. We present here the structure of C. canimorsus lipid A, which shows several features typical for low-inflammatory lipid A. Surprisingly, this lipid A, when attached to the core-oligosaccharide was far more pro-inflammatory than lipid A alone, indicating that in this case the core-oligosaccharide is able to contribute significantly to endotoxicity. Our further work suggests that a negative charge in the LPS-core can compensate the lack of such a charge in the lipid A and that this charge is needed not for stabilization of the final complex with its receptor but in the process of forming it. Overall the properties of the lipid A-core may explain how this bacterium first escapes the innate immune system, but nevertheless can cause a shock at the septic stage.

Type II topoisomerase (topoII) is a metalloenzyme targeted by clinical antibiotics and anticancer agents. Here, we integrate existing structural data with molecular simulation and propose a model for the yet uncharacterized structure of the reactant state of topoII. This model describes a canonical two-metal-ion mechanism and suggests how the metals could rearrange at the catalytic pocket during enzymatic turnover, explaining also experimental evidence for topoII inhibition. These results call for further experimental validation.

The nucleoid-associated protein EspR, a chromosome organizer, has pleiotropic effects on expression of genes associated with cell wall function and pathogenesis in Mycobacterium tuberculosis . In particular, EspR binds to several sites upstream of the espACD locus to promote its expression, thereby ensuring full function of the ESX-1 secretion system, a major virulence determinant. The N terminus of EspR contains the helix-turn-helix DNA-binding domain, whereas the C-terminal dimerization domain harbors residues involved in intersubunit interactions. While direct binding to DNA appears to be mediated by an EspR dimer-of-dimers, where two helix-turn-helix motifs remain free for long-range interactions, the mechanism of EspR higher-order organization and its impact on chromosome structure and gene expression are not understood. To investigate these processes, we identified seven amino acid residues using molecular dynamics and replaced them with Ala in order to probe interactions at either the dimer or the dimer-of-dimers interfaces. Arg70, Lys72, and Arg101 were important for protein stability and optimal DNA-binding activity. Moreover, the Arg70 mutant showed decreased dimerization in a mycobacterial two-hybrid system. To correlate these defects with higher-order organization and transcriptional activity, we used atomic force microscopy to observe different EspR mutant proteins in complex with the espACD promoter region. In addition, complementation of an M. tuberculosis espR knockout mutant was performed to measure their impact on EspA expression. Our results pinpoint key residues required for EspR function at the dimer (Arg70) and the dimer-of-dimers (Lys72) interface and demonstrate that EspR dimerization and higher-order oligomerization modulate espACD transcriptional activity and hence pathogenesis.

A QM/MM study has been carried out to clarify the catalytic mechanism of the enzyme diaminopimelate (DAP) epimerase. In particular the potential energy surface (PES) for the stereo‐inversion of the distal Cα of the substrate has been has been investigated. The nature of the critical points located on the PES has been checked by numerical frequencies calculations. The role of the various aminoacid residues in the catalysis has been elucidated using a recently developed analysis method.

When Ar is a low-aromaticity homo- or heterosystem, the sulfonyl-stabilized anion of nitrobutadienes 4 (which derive from the initial ring opening of 3-nitrothiophene) undergoes a rather surprising addition onto the aromatic ring itself, thereby leading to the construction of an unusual eight-membered sulfur heterocycle condensed with the original Ar ring. The competitiveness of such a pathway with respect to the formation of the thiopyran ring (i.e., addition onto the nitrovinyl moiety) is favored at low temperatures, thus revealing its nature as a kinetically controlled process.