A new lead for nonpeptidic active-site-directed inhibitors of the severe acute respiratory syndrome coronavirus main protease discovered by a combination of screening and docking methods.

The coronavirus main protease, Mpro, is considered to be a major target for drugs suitable for combating coronavirus infections including severe acute respiratory syndrome (SARS). An HPLC-based screening of electrophilic compounds that was performed to identify potential Mpro inhibitors revealed etacrynic acid tert-butylamide (6a) as an effective nonpeptidic inhibitor. Docking studies suggested a binding mode in which the phenyl ring acts as a spacer bridging the inhibitor's activated double bond and its hydrophobic tert-butyl moiety. The latter is supposed to fit into the S4 pocket of the target protease. Furthermore, these studies revealed etacrynic acid amide (6b) as a promising lead for nonpeptidic active-site-directed Mpro inhibitors. In a fluorimetric enzyme assay using a novel fluorescence resonance energy transfer (FRET) pair labeled substrate, compound 6b showed a Ki value of 35.3 M. Since the novel lead compound does not target the S1', S1, and S2 subsites of the enzyme's substrate-binding pockets, there is room for improvement that underlines the lead character of compound 6b.

Proton Formation in 2+1 Resonance Enhanced Multiphoton Excitation of HCl and HBr via „=0… Rydberg and Ion-Pair States

Molecular beam cooled HCl was state selected by two-photon excitation of the V (1) summation operator(0(+)) [v=9,11-13,15], E (1) summation operator(0(+)) [v=0], and g (3) summation operator(-)(0(+)) [v=0] states through either the Q(0) or Q(1) lines of the respective (1,3) summation operator(0(+))<--<--X (1) summation operator(0(+)) transition. Similarly, HBr was excited to the V (1) summation operator(0(+)) [v=m+3, m+5-m+8], E (1) summation operator(0(+)) [v=0], and H (1) summation operator(0(+)) [v=0] states through the Q(0) or Q(1) lines. Following absorption of a third photon, protons were formed by three different mechanisms and detected using velocity map imaging. (1) H(*)(n=2) was formed in coincidence with (2)P(i) halogen atoms and subsequently ionized. For HCl, photodissociation into H(*)(n=2)+Cl((2)P(12)) was dominant over the formation of Cl((2)P(32)) and was attributed to parallel excitation of the repulsive [(2) (2)Pi4llambda] superexcited (Omega=0) states. For HBr, the Br((2)P(32))Br((2)P(12)) ratio decreases with increasing excitation energy. This indicates that both the [(3) (2)Pi(12)5llambda] and the [B (2) summation operator5llambda] superexcited (Omega=0) states contribute to the formation of H(*)(n=2). (2) For selected intermediate states HCl was found to dissociate into the H(+)+Cl(-) ion pair with over 20% relative yield. A mechanism is proposed by which a bound [A (2) summation operatornlsigma] (1) summation operator(0(+)) superexcited state acts as a gateway state to dissociation into the ion pair. (3) For all intermediate states, protons were formed by dissociation of HX(+)[v(+)] following a parallel, DeltaOmega=0, excitation. The quantum yield for the dissociation process was obtained using previously reported photoionization efficiency data and was found to peak at v(+)=6-7 for HCl and v(+)=12 for HBr. This is consistent with excitation of the repulsive A(2) summation operator(12) and (2) (2)Pi states of HCl(+), and the (3) (2)Pi state of HBr(+). Rotational alignment of the Omega=0(+) intermediate states is evident from the angular distribution of the excited H(*)(n=2) photofragments. This effect has been observed previously and was used here to verify the reliability of the measured spatial anisotropy parameters.

Finite amplitude envelope solitons in pair-ion plasmas

The nonlinear coupling between finite amplitude ion thermal waves (ITWs) and quasistationary density perturbations in a pair-ion plasma is considered. A generalized nonlinear Schrödinger equation is derived for the ITW electric field envelope, accounting for large amplitude quasistationary plasma slow motion describing the ITW ponderomotive force. The present theory accounts for the trapping of ITWs in a large amplitude ion density hole. The small amplitude limit is considered and exact analytical solutions are obtained. Finite amplitude solutions are obtained numerically and their characteristics are discussed.

Mechanistic studies of amide bond scission during acidolytic deprotection of Pip containing peptide.

Unusual TFA catalyzed cleavage reaction is reported for peptide containing pipecolic acid residues. Although the use of TFA under standard cleavage conditions is sufficiently mild to prevent degradation of the desired products. the amide bond between consecutive pipecolic acid residues is unexpectedly hydrolyzed by standard TFA treatment. The hydrolysis is proposed to proceed via an oxazolinium ion intermediate, This mechanism is supported by H/D exchange as observed by ESI-MS and NMR experiments.

Co-existence of a pair of pelagic planktivorous coregonid fishes

Hypothesis: Ecological specialization facilitates co-existence of Coregonus spp. in Lake Stechlin. A difference in trophic ecology is the dominant means by which the species are ecologically segregated.

New ways to break an old bond: the bacterial carbon-phosphorus hydrolases and their role in biogeochemical phosphorus cycling

Phosphonates are organophosphorus molecules that contain the highly stable C-P bond, rather than the more common, and more labile, C-O-P phosphate ester bond. They have ancient origins but their biosynthesis is widespread among more primitive organisms and their importance in the contemporary biosphere is increasingly recognized; for example phosphonate-P is believed to play a particularly significant role in the productivity of the oceans. The microbial degradation of phosphonates was originally thought to occur only under conditions of phosphate limitation, mediated exclusively by the poorly characterized C-P lyase multienzyme system, under Pho regulon control. However, more recent studies have demonstrated the Pho-independent mineralization by environmental bacteria of three of the most widely distributed biogenic phosphonates: 2-aminoethylphosphonic acid (ciliatine), phosphonoacetic acid, and 2-amino-3-phosphonopropionic acid (phosphonoalanine). The three phosphonohydrolases responsible have unique specificities and are members of separate enzyme superfamilies; their expression is regulated by distinct members of the LysR family of bacterial transcriptional regulators, for each of which the phosphonate substrate of the respective degradative operon serves as coinducer. Previously no organophosphorus compound was known to induce the enzymes required for its own degradation. Whole-genome and metagenome sequence analysis indicates that the genes encoding these newly described C-P hydrolases are distributed widely among prokaryotes. As they are able to function under conditions in which C-P lyases are inactive, the three enzymes may play a hitherto-unrecognized role in phosphonate breakdown in the environment and hence make a significant contribution to global biogeochemical P-cycling.

C-H bond activation over metal oxides: A new insight into the dissociation kinetics from density functional theory

The C-H activation on metal oxides is a fundamental process in chemistry. In this paper, we report a density functional theory study on the process of the C-H activation of CH4 on Pd(111), Pt(111), Ru(0001), Tc(0001), Cu(111), PdO(001), PdO(110), and PdO(100). A linear relationship between the C-H activation barrier and the chemisorption in the dissociation final state on the metal surfaces is obtained, which is consistent with the work in the literature. However, the relationship is poor on the metal oxide surfaces. Instead, a strong linear correlation between the barrier and the lattice O-H bond strength is found on the oxides. The new linear relationship is analyzed and the physical origin is identified. (c) 2008 American Institute of Physics.

Trends in C-O and C-N bond formations over transition metal surfaces: An insight into kinetic sensitivity in catalytic reactions

Transition metal catalyzed bond formation is a fundamental process in catalysis and is of general interest throughout chemistry. To date, however, the knowledge of association reactions is rather limited, relative to what is known about dissociative processes. For example, surprisingly little is known about how the bond-forming ability of a metal, in general, varies across the Periodic Table. In particular, the effect of reactant valency on such trends is poorly understood. Herein, the authors examine these key issues by using density functional theory calculations to study CO and CN formations over the 4d metals. The calculations reveal that the chemistries differ in a fundamental way. In the case of CO formation, the reaction enthalpies span a much greater range than those of CN formation. Moreover, CO formation is found to be kinetically sensitive to the metal; here the reaction barriers (E-a) are found to be influenced by the reaction enthalpy. CN formation, conversely, is found to be relatively kinetically insensitive to the metal, and there is no correlation found between the reaction barriers and the reaction enthalpy. Analysis has shown that at the final adsorbed state, the interaction between N and the surface is relatively greater than that of O. Furthermore, in comparison with O, relatively less bonding between the surface and N is observed to be lost during transition state formation. These greater interactions between N and the surface, which can be related to the larger valency of N, are found to be responsible for the relatively smaller enthalpy range and limited variation in E-a for CN formation. (C) 2007 American Institute of Physics.

The importance of hydrogen's potential-energy surface and the strength of the forming R-H bond in surface hydrogenation reactions

An understanding of surface hydrogenation reactivity is a prevailing issue in chemistry and vital to the rational design of future catalysts. In this density-functional theory study, we address hydrogenation reactivity by examining the reaction pathways for N+H -> NH and NH+H -> NH2 over the close-packed surfaces of the 4d transition metals from Zr-Pd. It is found that the minimum-energy reaction pathway is dictated by the ease with which H can relocate between hollow-site and top-site adsorption geometries. A transition state where H is close to a top site reduces the instability associated with bond sharing of metal atoms by H and N (NH) (bonding competition). However, if the energy difference between hollow-site and top-site adsorption energies (Delta E-H) is large this type of transition state is unfavorable. Thus we have determined that hydrogenation reactivity is primarily controlled by the potential-energy surface of H on the metal, which is approximated by Delta E-H, and that the strength of N (NH) chemisorption energy is of less importance. Delta E-H has also enabled us to make predictions regarding the structure sensitivity of these reactions. Furthermore, we have found that the degree of bonding competition at the transition state is responsible for the trend in reaction barriers (E-a) across the transition series. When this effect is quantified a very good linear correlation is found with E-a. In addition, we find that when considering a particular type of reaction pathway, a good linear correlation is found between the destabilizing effects of bonding competition at the transition state and the strength of the forming N-H (HN-H) bond. (c) 2006 American Institute of Physics.