Concerted Reaction Research Articles

Intasome architecture and chromatin density modulate retroviral integration into nucleosome.

BackgroundRetroviral integration depends on the interaction between intasomes, host chromatin and cellular targeting cofactors as LEDGF/p75 or BET proteins. Previous studies indicated that the retroviral integrase, by itself, may play a role in the local integration site selection within nucleosomal target DNA. We focused our study on this local association by analyzing the intrinsic properties of various retroviral intasomes to functionally accommodate different chromatin structures in the lack of other cofactors.ResultsUsing in vitro conditions allowing the efficient catalysis of full site integration without these cofactors, we show that distinct retroviral integrases are not equally affected by chromatin compactness. Indeed, while PFV and MLV integration reactions are favored into dense and stable nucleosomes, HIV-1 and ASV concerted integration reactions are preferred into poorly dense chromatin regions of our nucleosomal acceptor templates. Predicted nucleosome occupancy around integration sites identified in infected cells suggests the presence of a nucleosome at the MLV and HIV-1 integration sites surrounded by differently dense chromatin. Further analyses of the relationships between the in vitro integration site selectivity and the structure of the inserted DNA indicate that structural constraints within intasomes could account for their ability to accommodate nucleosomal DNA and could dictate their capability to bind nucleosomes functionally in these specific chromatin contexts.ConclusionsThus, both intasome architecture and compactness of the chromatin surrounding the targeted nucleosome appear important determinants of the retroviral integration site selectivity. This supports a mechanism involving a global targeting of the intasomes toward suitable chromatin regions followed by a local integration site selection modulated by the intrinsic structural constraints of the intasomes governing the target DNA bending and dictating their sensitivity toward suitable specific nucleosomal structures and density.Electronic supplementary materialThe online version of this article (doi:10.1186/s12977-015-0145-9) contains supplementary material, which is available to authorized users.

Oxime formation from hydroxylamine and ketone: a (computational) reality check on stage one of the mechanism.

Oxime formation from hydroxylamine and ketone: a (computational) reality check on stage one of the mechanism.

Ultrafast hydrolysis of a Lewis photoacid.

This study explores the concept that electronic excitation can dramatically enhance Lewis acidity. Specifically, it is shown that photoexcitation transforms an electron-deficient organic compound of negligible Lewis acidity in its electronic ground state into a potent excited-state Lewis acid that releases a proton from a nearby water molecule in 3.1 ps. It was shown previously (Peon et al. J. Phys. Chem. A 2001, 105, 5768) that the excited state of methyl viologen (MV(2+)) is quenched rapidly in aqueous solution with the formation of an unidentified photoproduct. In this study, the quenching mechanism and the identity of the photoproduct were investigated by the femtosecond transient absorption and fluorescence upconversion techniques. Transient absorption signals at UV probe wavelengths reveal a long-lived species with a pH-dependent lifetime due to reaction with hydronium ions at a bimolecular rate of 3.1 × 10(9) M(-1) s(-1). This species is revealed to be a charge-transfer complex consisting of a ground-state MV(2+) ion and a hydroxide ion formed when a water molecule transfers a proton to the bulk solvent. Formation of a contact ion pair between MV(2+) and hydroxide shifts the absorption spectrum of the former ion by a few nm to longer wavelengths, yielding a transient absorption spectrum with a distinctive triangle wave appearance. The slight shift of this spectrum, which is in excellent agreement with steady-state difference spectra recorded for MV(2+) at high pH, is consistent with an ion pair but not with a covalent adduct (pseudobase). The long lifetime of the ion pair at neutral pH indicates that dissociation occurs many orders of magnitude more slowly than predicted by the Smoluchowski-Debye equation. Remarkably, there is no evidence of geminate recombination, suggesting that the proton that is transferred to the solvent is conducted at least several water shells away. Although the hydrolysis mechanism has yet to be fully established, evidence suggests that the strongly oxidizing excited state of MV(2+) triggers the proton-coupled oxidation of a water molecule. The observed kinetic isotope effect of 1.7 seen in D2O vs H2O is of the magnitude expected for an ultrafast concerted proton-electron transfer reaction. The ultrafast hydrolysis seen here may be a general excited-state quenching mechanism for electronically excited Lewis acids and other powerful photooxidants in aqueous solution.

A computational study on thermal decomposition mechanism of β-1 linkage lignin dimer

In order to gain a better understanding of the detailed mechanism of lignin pyrolysis and the formation mechanism of its main products, the thermal decomposition processes of a β-1 linkage lignin dimer model compound 1 (1,2-p-hydroxyphenyl-1,3-propanediol) were theoretically investigated by employing density functional theory methods at B3LYP/6-31G(d, p) level. Three possible pyrolytic pathways: the homolytic cleavage of Cα–Cβ bond, the homolytic cleavage of Cβ–Cγ bond and the concerted reactions, were proposed. The activation energies of each reaction step in the pyrolysis processes were calculated and the temperature effect on the pyrolysis processes was analyzed. The calculation results indicate that the homolytic cleavage reaction of Cα–Cβ bond and concerted reaction pathway (3) could be the major reaction channels, and the homolytic cleavage reaction of Cβ–Cγ bond and concerted reaction pathway (1) could be the competitive reaction channels in the pyrolysis processes of β-1 linkage lignin dimer. The concerted reactions would dominate over the free-radical homolytic reactions at lower temperatures, while at high temperatures the free-radical reaction would dominate over the concerted reactions in the β-1 linkage lignin dimer pyrolysis processes.

Theoretical Study of the Free Energy Surface and Kinetics of the Hepatitis C Virus NS3/NS4A Serine Protease Reaction with the NS5A/5B Substrate. Does the Generally Accepted Tetrahedral Intermediate Really Exist?

The self-consistent charge density functional tight binding/molecular mechanics (SCC-DFTB/MM) and ensemble averaged variational transition state theory/multidimensional tunneling (EA-VTST/MT) methods have been employed to investigate the reaction mechanism and to calculate the rate constant of the NS3/NS4A + NS5A/5B acylation reaction. This reaction belongs to the vital cycle of the hepatitis C virus once it infects the human cell. A concerted reaction mechanism, with a single transition state in which the tetrahedral geometry has already been adopted and the peptide bond is starting to break, has been determined. This reaction supposes an example where the proposed general two-step serine protease acylation reaction mechanism does not occur, being related to the fact that the enzyme is particularly efficient for the NS5A/5B substrate. The transition state characterized here for the acylation reaction can be a good initial structure in the reach of NS3/NS4A inhibitors based on TS analogues. On the other hand, the calculated and experimental phenomenological free energy barriers only differ by 2.3 kcal mol–1, although this leads to a significant discrepancy between calculated and experimental. The rest of the calculated kinetic parameters, such as the kinetic isotopic effect (H/D), tunneling, and the recrossing contributions to reactivity, agree with the expected behavior for the studied reaction.

Quantum chemical insights into regioselective hydrolysis of C60F36

The hydrolysis reaction of fluorinated C60 to prepare fullerenols has been exposed by density functional theory for the first time. C60F36 was proved to hydrolyze via an SN2′ mechanism rather than SN1 or SN2 mechanism, and it is revealed that the hydrolysis is a regioselective reaction which may stem from the charge population of C60F36. The two adjacent carbon atoms connected by an isolated double bond possess opposite reactivities, and these two atoms exhibit a strong competition with each other to be attacked by water molecules during the hydrolysis. Bond order analyses using Wiberg indexes indicate that such a hydrolysis should be a concerted yet asynchronous reaction. Hydrolysis of fluorinated C60 can be considered as a method for fullerenol production via which structure-defined fullerenol will be obtained, and this method is greatly superior to traditional methods.

High chemoselectivity of an advanced iron catalyst for the hydrogenation of aldehydes with isolated C═C bond: a computational study.

Knölker's iron complex is a "green" catalyst that exhibits low toxicity and is abundant in nature. Density functional theory (DFT) was used to explore the highly chemoselective nature of the catalytic hydrogenation of CH2═CHCH2CHO. An outer-sphere concerted hydrogen transfer was found to be the most reasonable kinetic route for the hydrogenation of the olefin. However, the C═C hydrogenation reaction has a high free energy barrier of 28.1 kcal/mol, requiring a high temperature to overcome. By comparison, the CH═O bond concerted hydrogen-transfer reaction catalyzed using Knölker's iron catalyst has an energy barrier of only 14.0 kcal/mol. Therefore, only the CH═O of CH2═CHCH2CHO can be hydrogenated in the presence of Knölker's catalyst at room temperature, due to kinetic domination. All computational results were in good agreement with experimental results.

Diagnostic Laparoscopy with 5-Aminolevulinic-Acid-Mediated Photodynamic Diagnosis Enhances the Detection of Peritoneal Micrometastases in Advanced Gastric Cancer

Objects: Recently, we reported that diagnostic laparoscopy with photodynamic diagnosis using oral 5-aminolevulinic acid (ALA-PDD) is a promising tool for diagnosing early peritoneal metastases in gastric cancer. The present study evaluated the usefulness of adding ALA-PDD to conventional diagnostic laparoscopy and assessed the association of the ALA-PDD results with peritoneal fluid cytology and molecular diagnostic testing. Methods: Diagnostic laparoscopy using sequential white light (WL) and ALA-PDD observations was performed in 52 advanced gastric cancer patients, and the sensitivity of ALA-PDD for detecting peritoneal disease was compared to WL. Peritoneal fluid samples from the same patients were also subjected to cytological examination and molecular diagnosis using a transcription-reverse transcription concerted reaction (TRC). Results: Twenty-four of the 52 patients (46%) had no macroscopic evidence of peritoneal metastases on WL examination; however, ALA-PDD detected dissemination in 5 of these 24 patients (21%) (pd-P). Cytological examination was negative in 4 of the 5 pd-P patients, and molecular testing using TRC was negative in 3 of the 5 pd-P patients. Conclusions: This study demonstrated that diagnostic laparoscopy with ALA-PDD improved the sensitivity for the detection of peritoneal metastases. ALA-PDD may be a useful technique for the preoperative staging of advanced gastric cancer and can complement examinations of peritoneal lavage fluids.

An analysis of model proton-coupled electron transfer reactions via the mixed quantum-classical Liouville approach.

The nonadiabatic dynamics of model proton-coupled electron transfer (PCET) reactions is investigated for the first time using a surface-hopping algorithm based on the solution of the mixed quantum-classical Liouville equation (QCLE). This method provides a rigorous treatment of quantum coherence/decoherence effects in the dynamics of mixed quantum-classical systems, which is lacking in the molecular dynamics with quantum transitions surface-hopping approach commonly used for simulating PCET reactions. Within this approach, the protonic and electronic coordinates are treated quantum mechanically and the solvent coordinate evolves classically on both single adiabatic surfaces and on coherently coupled pairs of adiabatic surfaces. Both concerted and sequential PCET reactions are studied in detail under various subsystem-bath coupling conditions and insights into the dynamical principles underlying PCET reactions are gained. Notably, an examination of the trajectories reveals that the system spends the majority of its time on the average of two coherently coupled adiabatic surfaces, during which a phase enters into the calculation of an observable. In general, the results of this paper demonstrate the applicability of QCLE-based surface-hopping dynamics to the study of PCET and emphasize the importance of mean surface evolution and decoherence effects in the calculation of PCET rate constants.

Density functional theory studies on pyrolysis mechanism of β-O-4 type lignin dimer model compound

Lignin is the main component of biomass with a complex, heterogeneous, three-dimensional polymeric structure of three main monolignols (p-coumaryl, coniferyl, and sinapyl alcohol). In order to understand the pyrolysis mechanism of lignin and identify the chemical pathways for the formations of key products during pyrolysis, the pyrolysis processes of β-O-4 type lignin dimer model compound 1 (1-phenyl-2-phenoxy-1,3-propanediol) were theoretically investigated by employing density functional theory (DFT) methods at the B3LYP/6-31G(d,p) level. Based on related experimental and calculation results of bond dissociation energies of β-O-4 type lignin dimer, three possible pyrolytic pathways (the homolytic cleavage of CβO bond, the homolytic cleavage of CαCβ bond and the concerted reactions) were proposed, the activation energies of each reaction step were calculated, and the temperature effect on pyrolysis processes was analyzed. The calculation results indicate that the homolytic cleavage reaction of CβO bond and concerted reaction pathways (3) could be the major reaction channels, and the homolytic cleavage reaction of CαCβ bond and concerted reaction pathways (1) and (2) could be the competitive reaction channels in pyrolysis processes. The concerted reactions would dominate over free-radical homolytic reactions at lower temperatures, while at high temperatures the free-radical reaction (CO homolysis) would dominate over the concerted reactions.

Density Functional Theory Study of the Concerted Pyrolysis Mechanism for Lignin Models

Studies on the pyrolysis mechanisms of lignin model compounds have largely focused on initial homolytic cleavage reactions. It has been noted, however, that concerted mechanisms may also account for observed product formation. In the current work, the latter processes are examined and compared to the former, by the application of density functional theory calculations to fully substituted lignin models. Results show that activation energies for the concerted reactions are somewhat lower than the bond dissociation energies of the homolysis reactions. Kinetic analysis revealed that the concerted pathway is the retro-ene fragmentation mechanism.

A density functional theory study on formation mechanism of CO, CO2 and CH4 in pyrolysis of lignin

In order to understand formation mechanisms of CO, CO2 and CH4 in lignin pyrolysis, the decarbonylation, decarboxylation and demethylation reactions of various phenylic lignin model compounds were theoretically investigated by using density functional theory methods at B3LYP/6-31G++(d,p) level. Eight decarbonylation reaction pathways (1)–(8), eight decarboxylation reaction pathways (9)–(16) and a demethylation reaction pathways (17) were designed. The standard kinetic and thermodynamic parameters of every reaction pathway at different temperatures were calculated. The calculation results show that energy barriers of decarbonylation reaction pathways (1)–(4) are apparently higher than those of decarbonylation reaction pathways (5)–(8), and then CO is formed more easily through decarbonylation of phenyl (p-hydroxyphenyl, guaiacyl and syringyl) acetaldehyde; energy barriers of decarboxylation reaction pathways (9)–(12) are lower than those of decarboxylation reaction pathways (13)–(16), and then CO2 is formed more easily through decarboxylation of phenyl (p-hydroxyphenyl, guaiacyl and syringyl) formic acid. Compared with step-by-step radical reaction, the energy barrier of concerted reaction is lower, and CH4 is formed more easily through concerted reaction.

ChemInform Abstract: Base‐Catalyzed Tandem Michael/Dehydro‐Diels—Alder Reaction of α,α‐Dicyanoolefins with Electron‐Deficient 1,3‐Conjugated Enynes: A Facile Entry to Angularly Fused Polycycles.

Angularly fused carbocyclic frameworks and their heteroatom-substituted analogues exist in many natural products that display a broad and interesting range of biological activities. Preparation of polycyclic products by cycloaddition reactions have been the long-standing hot topic in the synthetic community. Dehydro-Diels-Alder (DDA) reactions are one class of dehydropericyclic reactions that are derived conceptually by systematic removal of hydrogen atom pairs. A base-promoted tandem Michael addition and DDA reaction of α,α-dicyanoolefins with electron-deficient 1,3-conjugated enynes was realized in which a DDA reaction takes place between the arylalkynes and electron-deficient tetrasubstituted olefin. The control experiments support the stepwise anionic reaction pathway rather than the concerted reaction pathway.

Detection and characterization of spacer integration intermediates in type I-E CRISPR-Cas system.

The adaptation against foreign nucleic acids by the CRISPR–Cas system (Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated proteins) depends on the insertion of foreign nucleic acid-derived sequences into the CRISPR array as novel spacers by still unknown mechanism. We identified and characterized in Escherichia coli intermediate states of spacer integration and mapped the integration site at the chromosomal CRISPR array in vivo. The results show that the insertion of new spacers occurs by site-specific nicking at both strands of the leader proximal repeat in a staggered way and is accompanied by joining of the resulting 5′-ends of the repeat strands with the 3′-ends of the incoming spacer. This concerted cleavage-ligation reaction depends on the metal-binding center of Cas1 protein and requires the presence of Cas2. By acquisition assays using plasmid-located CRISPR array with mutated repeat sequences, we demonstrate that the primary sequence of the first repeat is crucial for cleavage of the CRISPR array and the ligation of new spacer DNA.

Concerted ligand exchange and the roles of counter anions in the reversible structural switching of crystalline peptide metallo-macrocycles.

To understand reversible structural switching in crystalline materials, we studied the mechanism of reversible crystal-to-crystal transformation of a tetranuclear Ni(II) macrocycle consisting of artificial β-dipeptides. On the basis of detailed structural analyses and thermodynamic measurements made in a comparison of pseudo-isostructural crystals (NO3 and BF4 salts), we herein discuss how ligand-exchange reactions take place in the crystal due to changes in water content and temperature. Observations of the structural transformation of NO3 salt indicated that a pseudo crystalline phase transformation takes place through concerted ligand-exchange reactions at the four Ni(II) centers of the macrocycle with hydrogen bond switching. A mechanism for this ligand exchange was supported by IR spectroscopy. Thermodynamic measurements suggested that the favorable compensation relationship of the enthalpy changes due to water uptake and structural changes are keys to the reversible structural transformation. On the basis of a comparison with the pseudo-isostructural crystals, it is apparent that the crystal packing structure and the types of counter anions are important factors for facilitating reversible ligand exchange with single crystallinity.

Scandal and military mediatization

Mediated responses to reports of abuse during the Global War on Terror are puzzling. Few of the many revelations of abuse prompted concerted reactions (e.g. scandals), and those that did were often very similar to reports that were ignored. This article draws from empirical research into responses to prisoner abuse at Abu Ghraib to develop new concepts that help untangle the mediatization of American wars. Feedback helps to model the variety of polemical interventions that are adopted in public discussions as a result of a scandal. The concept of feedforward, introduced here, enables us to model polemical interventions that develop within an organization in response to such feedback. Together, these concepts encourage greater sensitivity to the cultural horizon of mediated events. Further, they point to a new theoretical focus for mediatization research, namely the cycles of feedback and feedforward that help shape new forms of understanding and behaving within organizations.

Intermolecular Proton-Coupled Electron Transfer through H-Bond Complexes in a p-Phenylenediamine-Based Urea Use of the Wedge Scheme to Describe Reactions of this Type

There is a growing appreciation of the important role that H-bond complexes can play in the mechanism of proton-coupled electron transfer (PCET) reactions. Until relatively recently it had been thought that PCET reactions always proceeded step-wise with sequential electron and proton transfer. Much of the recent fundamental interest in PCET stems from the realization that a third option is available, concerted electron and proton transfer or CPET in which the electron and proton both move in a single kinetic step. This interest in the concerted process has increased awareness of H-bonding states in PCET, since the concerted reaction occurs within a H-bonded intermediate. However, even if the proton and electron transfer is not concerted, the H-bonded complex formed in the process of proton transfer can play an important role in the PCET mechanism if it is sufficiently long-lived.Recently we have introduced a generally useful mechanistic framework with which to include H-bonding steps within an overall PCET pathway. This scheme, which for obvious reasons we call a “wedge”, is shown in Scheme 1 for the generic 1e−, 1H+ oxidation, AH + B = A + HB+ + e−. The front face in the wedge (in bold) is the standard electron transfer/proton transfer square scheme, with the two possible electron transfer reactions on the top and bottom edges, and the two possible proton transfers on the left and right edges. However, proton transfer reactions actually go through a H-bond intermediate, so a more accurate description of the proton transfer follows the dashed lines on the triangular sides of the wedge to and from the H-bond intermediates, A-H-B or A-H-B+, which are meant to represent the thermodynamically most stable H-bond complex in each oxidation state. If the H-bonded intermediate has sufficient lifetime, then electron transfer to/from the H-bond complex is also possible, represented by the rear edge of the wedge (thin solid line). If the proton moves from being more attached to A in A-H-B to being more attached to B in A-H-B+, then E° of this reaction is that of the CPET step, if the proton doesn’t move then the E° is simply that of oxidation of the H-bond complex. Either way, it is straightforward to show that E°(A-H-B0/+) has to have a value in between E°(AH0/+) and E°(A−/0). Thus the possibility of electron transfer through the H-bond complex opens up a pathway of intermediate potential for the overall reaction AH + B = A + HB+ + e−.The usefulness of the wedge scheme is demonstrated by its ability to explain the unusual electrochemistry of the phenylenediamine-based urea, U(H)H, which we have shown undergoes a self proton transfer upon oxidation to give half equivalent of the doubly oxidized quinoidal cation and half-equivalent of the electroinactive, protonated reduced urea, Scheme 2. The reaction gives chemically irreversible voltammetry in acetonitrile as would be expected given that the quinoidal cation is harder to reduce than the initially formed radical cation. However, it gives reversible voltammetry in methylene chloride, which can be explained by the greater stability of the H-bonded intermediate in this solvent. In addition, in methylene chloride, we are able to clearly observe a concentration and scan rate dependent conversion between two different reduction pathways on the return scan. This behavior cannot be explained by a simple square scheme, but is readily explained by the wedge scheme.In this presentation, we will report recent results on the voltammetry of U(H)H in the presence of guest molecules that H-bond to the starting, reduced state. We will show that their effect on the voltammetry can be explained in terms of two interlinked wedge schemes, one representing the electron transfer / H-bonding / proton transfer reactions of U(H)H with itself and the other representing the reactions with the added guest.

Fragmentation mechanisms for methane induced by 55 eV, 75 eV, and 100 eV electron impact

The fragmentation of CH4 (2+) dications following 55 eV, 75 eV, and 100 eV electron impact double ionization of methane was studied using a cold target recoil-ion momentum spectroscopy. From the measured momentum of each recoil ion, the momentum of the neutral particles has been deduced and the kinetic energy release distribution for the different fragmentation channels has been obtained. The doubly charged molecular ions break up into three or more fragments in one or two-step processes, resulting in different signatures in the data. We observed the fragmentation of CH4 (2+) dications through different mechanisms according to the momentum of the neutral particles. For example, our result shows that there are three reaction channels to form CH2 (+), H(+), and H, one synchronous concerted reaction channel and two two-step reaction channels. For even more complicated fragmentation processes of CH4 (2+) dications, the fragmentation mechanism can still be identified in the present measurements. The slopes of the peak in the ion-ion coincidence spectra were also estimated here, as they are also related to the fragmentation mechanism.

Molecular electrochemistry and electrocatalysis: a dynamic view

The frequent simple gross redox reaction notation, where A is a solution species and Bads is its adsorbed reduction product, is misleading in its simplicity. It may represent a concerted reaction, i.e., a true elementary step in which the electron transfer (ET) to the solution species A is concerted with the creation of the electrode-species bond(s) in Bads. Conversely, the reaction may be a composite one involving two sequential steps. One such two-step mechanism may be termed as a CadsEads sequence where Cads stands for a pre-adsorption elementary step and Eads for the follow-up ET. Alternatively, the two steps may proceed in the reverse order, leading to an EsolnCads mechanism in which A is reduced into B, both being solution species, followed by adsorption of B onto the electrode.The present theoretical investigations show that a different panel of voltammetric behaviours may be produced by each mechanism. Hence, rationalising voltammetric peak positions and shapes in terms of surface or potential effects is challenging and may be completely erroneous if the wrong mechanistic sequence is considered.

Concerted Cyclization of Lanosterol C-Ring and D-Ring Under Human Oxidosqualene Cyclase Catalysis: An ab Initio QM/MM MD Study.

Human oxidosqualene cyclase (OSC) is one key enzyme in the biosynthesis of cholesterol. It can catalyze the linear-chain 2,3-oxidosqualene to form lanosterol, the tetracyclic (6-6-6-5 members for A-B-C-D rings) cholesterol precursor. It also has been treated as a novel antihyperlipidemia target. In addition, the structural diversity of cyclic terpenes in plants originates from the cyclization of 2,3-oxidosqualene. The enzyme catalytic mechanism is considered to be one of the most complicated ones in nature, and there are a lot of controversies about the mechanism in the past half a century. Herein, state-of-the-art ab initio QM/MM MD simulations are employed to investigate the detailed cyclization mechanism of C-ring and D-ring formation. Our study reveals that the C and D rings are formed near-synchronously from a stable "6-6-5" ring intermediate. Interestingly, the transition state of this concerted reaction presents a "6-6-6" structure motif, while this unstable "6-6-6" structure in our simulations is thought to be a stable intermediate state in most previous hypothetical mechanisms. Furthermore, as the tailed side chain of 2,3-oxidosqualene shows a β conformation while it is α conformation in lanosterol, finally, it is observed that the rotatable "tail" chain prefers to transfer β conformation to α conformation at the "6-6-5" intermediate state.