Crotonaldehyde formation from decomposition of ICH2CH2OH on powdered TiO2

Adsorption and reactions of 2-iodoethanol on TiO(2) have been studied by Fourier transform infrared spectroscopy. ICH(2)CH(2)OH possesses two reactive centers of C-I and C-OH. It is found that its decomposition leads to the formation of crotonaldehyde on TiO(2). A reaction sequence of ICH(2)CH(2)OH --> ICH(2)CH(2)O- --> CH(3)CHO --> CH(3)CH=CH-CHO is proposed. Although the decomposition routes of C(2)H(5)OH and C(2)H(5)I, both forming C(2)H(5)O- on TiO(2), suggest that -OCH(2)CH(2)O- may play a role in the crotonaldehyde formation, reaction of HOCH(2)CH(2)OH on TiO(2) shows that this is not the case. Adsorbed H(2)O is formed in the ICH(2)CH(2)OH decomposition on TiO(2); however, it is found that ICH=CH(2), possibly generated by ICH(2)CH(2)OH dehydration, is not important in the crotonaldehyde formation.     

Solvation-induced σ-complex structure formation in the gas phase: a revisit to the infrared spectroscopy of [C6H6-(CH3OH)2]+

Structures of the [C(6)H(6)-(CH(3)OH)(2)](+) cluster cation are investigated with infrared (IR) spectroscopy. While the noncovalent type structure has been confirmed for the n = 1 cluster of [C(6)H(6)-(CH(3)OH)(n)](+), only contradictory interpretations have been given for the spectra of n = 2, in which significant changes have been observed with the Ar tagging. In the present study, we revisit IR spectroscopy of the n = 2 cluster from the viewpoint of the σ-complex structure, which includes a covalent bond formation between the benzene and methanol moieties. The observed spectral range is extended to the lower-frequency region, and the spectrum is measured with and without Ar and N(2) tagging. A strongly hydrogen-bonded OH stretch band, which is characteristic to the σ-complex structure, is newly found with the tagging. The remarkable spectral changes with the tagging are interpreted by the competition between the σ-complex and noncovalent complex structures in the [C(6)H(6)-(CH(3)OH)(2)](+) system. This result shows that the microsolvation only with one methanol molecule can induce the σ-complex structure formation.     

Adsorption and reactions of ClCH2CH2OH on clean and oxygen-precovered Cu(100): experimental and computational studies

Temperature-programmed reaction/desorption, reflection-absorption infrared spectroscopy, and density functional theory calculations have been employed to investigate the adsorption and thermal reactions of ClCH2CH2OH on clean and oxygen-precovered Cu(100) surfaces. On Cu(100), ClCH2CH2OH is mainly adsorbed reversibly. The ClCH2CH2OH molecules at a submonolayer coverage can change their orientation with increasing temperature. However, on oxygen-precovered Cu(100), all of the adsorbed ClCH2CH2OH molecules below 0.5 langmuir exposures completely dissociate to generate ethylene and acetaldehyde via the intermediate of ClCH2CH2O-. The computational studies predict that the ClCH2CH2O- is most likely to be adsorbed at the 4-fold hollow sites of Cu(100), with its C-O bond only slightly titled away from the surface normal and with a gauche conformation with respect to the C-C bond. The hollow-site ClCH2CH2O- has an adsorption energy that is 4.4 and 19.2 kcal x mol(-1) lower than that of the ClCH2CH2O- bonded at the bridging and atop sites, respectively. No significant effect of precovered oxygen on the ClCH2CH2O- bonding geometry and infrared band frequencies has been observed, as compared with the case without oxygen.     

Theoretical study of formic acid-sulfur dioxide dimers

We report the first theoretical study of noncovalent and covalent interactions in formic acid (FA)-SO(2) complexes. Using ab initio and DFT model chemistries, five stable noncovalent complexes were identified, as well as a covalent adduct, formic sulfurous anhydride HOSO(2)CHO. syn-FA is predicted to form two nonplanar bidentate complexes with SO(2): the more stable one contains a normal hydrogen bond donated by OH, and the less stable one contains a blue-shifted hydrogen bond donated by CH. Both are stabilized by charge transfer from FA to SO(2). anti-FA forms three planar complexes of nearly equal energy containing OH-to-SO(2) hydrogen bonds. Formic sulfurous anhydride forms via an endothermic concerted cycloaddition. Natural bond orbital analysis showed that the bidentate SO(2)-FA complexes are stabilized by n → π* donation from FA to SO(2), and back-donation from SO(2) n and π* orbitals into FA σ(OH)* or σ(CH)* orbitals. The bidentate formic acid-SO(2) complex that contains an O-H···O hydrogen bond is more stable than the similar nitric acid-SO(2) complex. The latter contains a stronger hydrogen bond but shows no O→S charge transfer interaction.     

Facial selectivity of the (R)-1,3-dimethyl-1-cyclohexyl cation in the gas phase

The model reaction between the (R)-1,3-dimethyl-1-cyclohexyl cation (I) and methanol has been investigated under gas-phase radiolytic conditions (750 Torr; 25-120 degrees C) with the aim of evaluating the intrinsic factors that govern the facial selectivity of biased carbocations. The peculiarity of the experimental approach allows the formation of different CH(3) (18)OH.I ionic adducts. Subsequent conversion of these adducts to give the corresponding E/Z covalent products follows different reaction coordinates, which are characterized by their own activation parameters. On the grounds of density functional theory (DFT) results, several [CH(3)OH.I] structures have been located on the relevant potential-energy surface (PES). The experimental results point to a gas-phase facial selectivity, which is mainly governed by entropic factors that arise as a result of the occurrence of different noncovalent ion-molecule "facial adducts" (FA). The formation of FAs may also play an important role in both the reaction dynamics and the positional selectivity. The present results cannot be interpreted by any of the models based on solution-phase experiments.     

3-甲基环状乙撑磷酸二酯醇解的反应途径的理论研究

采用密度泛函理论和MP2方法研究了3-甲基环状乙撑磷酸二酯(MEP)与甲醇的反应途径:(Ⅰ)CH3O-+MEP;(Ⅱ)CH3OH+MEP;(Ⅲ)CH3O-+HMEP(MEP的质子化形式);(Ⅳ)CH3OH+HMEP.在B3LYP/6-31++G(d,p)水平上优化了四条反应途径的反应物、中间体、过渡态及产物的几何构型,并在同水平上进行了自然电荷分析,然后在MP2/6-311++G(3df,2p)水平上计算了各驻点的单点能.采用极化连续介质模型(PCM)研究了各途径在苯、甲醇和水溶液中的溶剂化效应.计算结果表明,溶剂效应使途径(Ⅰ)的自由能垒降低,而使途径(Ⅱ)和(Ⅳ)的决速步骤的自由能垒升高.在气相和苯溶剂中途径(Ⅳ)是反应的优势途径,在甲醇和水溶剂中途径(Ⅰ)则成为最优.研究结果进一步表明实验条件下途径(Ⅱ)与(Ⅳ)对总醇解反应的贡献相当.     

Covalent and noncovalent intermediates of an NAD utilizing enzyme, human CD38

Enzymatic utilization of nicotinamide adenine dinucleotide (NAD) has increasingly been shown to have fundamental roles in gene regulation, signal transduction, and protein modification. Many of the processes require the cleavage of the nicotinamide moiety from the substrate and the formation of a reactive intermediate. Using X-ray crystallography, we show that human CD38, an NAD-utilizing enzyme, is capable of catalyzing the cleavage reactions through both covalent and noncovalent intermediates, depending on the substrate used. The covalent intermediate is resistant to further attack by nucleophiles, resulting in mechanism-based enzyme inactivation. The noncovalent intermediate is stabilized mainly through H-bond interactions, but appears to remain reactive. Our structural results favor the proposal of a noncovalent intermediate during normal enzymatic utilization of NAD by human CD38 and provide structural insights into the design of covalent and noncovalent inhibitors targeting NAD-utilization pathways.     

掺Cu对MoO3-TiO2/SiO2上光促甲烷和水表面反应的影响

 在固定床环隙反应器中,借助紫外光的激发,气相甲烷和水在MoO3-TiO2/SiO2催化剂表面生成了甲醇和氢气,当在催化剂中掺杂Cu2+后,光催化剂的活性明显提高. XRD,IR,UVDRS和TPD的研究结果表明,在催化剂表面形成了具有Mo-O-Ti和Mo-O-Cu基元的高度分散物种,不但使得吸光带边明显蓝移,而且扩展了催化剂的光响应范围. 所形成的复合结构还可以优化单组分的吸光性能并促进对反应物分子的吸附活化,同时可以有效地转移光生电子和空穴. 掺杂Cu2+能够进一步延长光生电子-空穴对的寿命,进而提高反应的量子产率.     

Discovery of novel cathepsin S inhibitors by pharmacophore-based virtual high-throughput screening

The cysteine protease cathepsin S (CatS) is involved in the pathogenesis of autoimmune disorders, atherosclerosis, and obesity. Therefore, it represents a promising pharmacological target for drug development. We generated ligand-based and structure-based pharmacophore models for noncovalent and covalent CatS inhibitors to perform virtual high-throughput screening of chemical databases in order to discover novel scaffolds for CatS inhibitors. An in vitro evaluation of the resulting 15 structures revealed seven CatS inhibitors with kinetic constants in the low micromolar range. These compounds can be subjected to further chemical modifications to obtain drugs for the treatment of autoimmune disorders and atherosclerosis.     

Designing highly specific biosensing surfaces using aptamer monolayers on gold

To build highly specific surfaces using aptamer affinity reagents, the effects of linker and coadsorbents were investigated for maximizing target binding and specificity for aptamer-based self-assembled monolayers (SAMs) supported on gold. An aptamer that binds the protein thrombin was utilized as a model system to compare different mixed monolayer systems toward maximizing binding and selectivity to the immobilized aptamer. Important factors used to optimize binding characteristics of thrombin to the aptamer-based monolayer films include changes in design elements of the linker and different coadsorbent thiols. Binding events measured by surface plasmon resonance (SPR) and ellipsometry showed that the binding performance of the aptamer SAMs depends principally on the linker and to a lesser extent on the coadsorbent. SAMs formed with HS-(CH2)6-OP(O)2O-(CH2CH2O)6-TTTTT-aptamer exhibited a 4-fold increase in binding capacity versus SAMs made using HS-(CH2)6-TTTTT-aptamer. Furthermore, SAMs made using HS-(CH2)6-OP(O)2O-(CH2CH2O)6-TTTTT-aptamer showed nearly complete specificity for thrombin versus bovine serum albumin (BSA, less than 2% bound), while a SAM incorporating a random DNA fragment (HS-(CH2)6-OP(O)2O-(CH2CH2O)6-TTTTT-RANDOM) showed little binding of thrombin. Irrespective of the aptamer-linker system, use of HS-(CH2)11(OCH2CH2)3OH, referred to as EG(3), as a coadsorbent enhanced binding of thrombin by approximately 2.5-fold compared to that of HS-(CH2)6-OH (mercaptohexanol, MCH).     

激光溅射Ni等离子体与气相CH3OH团簇的反应

The gas phase reaction of Ni plasma and methanol clusters is studied by the laser ablation-molecular beam（LAMB） method. Five species of clustered complex ions Ni+（CH3OH）n,NiO+（CH3OH）n,H+（CH3OH）n,H3O+（CH3OH）n,CH3O-（CH3OH）n（n≤25）are observed. Interestingly,the species and sizes of the product clusters vary observably when the plasma acts on the different parts of the pulsed methanol molecular beam. When the laser ablated Ni plasma acts on the head and tail of the beam,the metal methanol complex clusters Ni+（CH3OH）n and the oxidation clusters NiO+（CH3OH）n（n=1-15）together with protonated methanol clusters H +（CH3OH）n are domain. While the plasma acts on the middle of the beam,however,Ni+（CH3OH）1-2 and H+（CH3OH）n along with the mixed methanol-water clusters H3O+（CH3OH）n（n=15-25）turn to be the main resulting clusters. By comparing the intensities and the cluster sizes of NiO+（CH3OH）n with Ni+（CH3OH）n,the formation of NiO+（CH3OH）n is contributed to the intracluster demethanation reaction of Ni+（CH3OH）n and evaporation of several methanol molecules. As the H3O+（CH3OH）n is observed only when the plasma acts on the high density part of the beam,and their intensities are only 0. 5% of the protonated methanol molecule,it is concluded that the species are partially due to the recombination of H+（CH3OH）n and water,which come from the plasma-molecule reaction.     

Sensitivity of methyl thiolate desulfurization selectivity to reaction temperature and hydroxyl coverage

The adsorption and reaction of methanethiol (CH3SH) and dimethyl disulfide (CH3SSCH3) on Mo(110)-(1 x 6)-O have been studied using temperature-programmed reaction spectroscopy and reflection-absorption infrared spectroscopy over the temperature range of 110-550 K. The S-H bond is broken upon adsorption to form adsorbed OH, water, and methyl thiolate (CH3S-) at low temperature. Water is evolved at 210 and 310 K via molecular desorption and disproportionation of OH, respectively. Some hydroxyl remains on the surface up to 350 K. Methyl thiolate is also formed from CH3SSCH3 on Mo(110)-(1 x 6)-O. Methyl thiolate undergoes C-S cleavage above 300 K, yielding methane and methyl radicals. There is also a minor amount of nonselective decomposition leading to the formation of carbon and hydrogen. Methane production is promoted by adsorbed hydroxyl. As the hydroxyl coverage increases, the yield of methyl radicals relative to methane diminishes. Accordingly, there is more methane produced from methanethiol reaction than from dimethyl disulfide, since S-H dissociation in CH3SH produces OH. The maximum coverage of the thiolate is approximately 0.5 monolayers, based on the amount of sulfur remaining after reaction measured by Auger electron spectroscopy. In contrast to cyclopropylmethanethiol (c-C3H5CH2SH), for which alkyl transfer from sulfur to oxygen is observed, there is no evidence for transfer of the methyl group of methyl thiolate to oxygen on the surface. Specifically, there is no evidence for methoxy (CH3O-) in infrared spectroscopy or temperature-programmed reaction experiments.     

Kinetics of the reaction of methyl radical with hydroxyl radical and methanol decomposition

The CH3 + OH bimolecular reaction and the dissociation of methanol are studied theoretically at conditions relevant to combustion chemistry. Kinetics for the CH3 + OH barrierless association reaction and for the H + CH2OH and H + CH3O product channels are determined in the high-pressure limit using variable reaction coordinate transition state theory and multireference electronic structure calculations to evaluate the fragment interaction energies. The CH3 + OH --> 3CH2 + H2O abstraction reaction and the H2 + HCOH and H2 + H2CO product channels feature localized dynamical bottlenecks and are treated using variational transition state theory and QCISD(T) energies extrapolated to the complete basis set limit. The 1CH2 + H2O product channel has two dynamical regimes, featuring both an inner saddle point and an outer barrierless region, and it is shown that a microcanonical two-state model is necessary to properly describe the association rate for this reaction over a broad temperature range. Experimental channel energies for the methanol system are reevaluated using the Active Thermochemical Tables (ATcT) approach. Pressure dependent, phenomenological rate coefficients for the CH3 + OH bimolecular reaction and for methanol decomposition are determined via master equation simulations. The predicted results agree well with experimental results, including those from a companion high-temperature shock tube determination for the decomposition of methanol.     

Mechanism of immunoglobulin G4 Fab-arm exchange

Immunoglobulin G (IgG) antibodies are symmetrical molecules that may be regarded as covalent dimers of 2 half-molecules, each consisting of a light chain and a heavy chain. Human IgG4 is an unusually dynamic antibody, with half-molecule exchange ("Fab-arm exchange") resulting in asymmetrical, bispecific antibodies with two different antigen binding sites, which contributes to its anti-inflammatory activity. The mechanism of this process is unknown. To elucidate the elementary steps of this intermolecular antibody rearrangement, we developed a quantitative real-time FRET assay to monitor the kinetics of this process. We found that an intrinsic barrier is the relatively slow dissociation of the CH3 domains that noncovalently connect the heavy chains, which becomes rate determining in case disulfide bonds between the heavy chains are reduced or absent. Under redox conditions that mimic the previously estimated in vivo reaction rate, i.e., 1 mM of reduced glutathione, the overall rate is ca. 20 times lower because only a fraction of noncovalent isomers is present (with intra- rather than interheavy chain disulfide bonds), formed in a relatively fast pre-equilibrium from covalent isomers. Interestingly, Fab arms stabilize the covalent isomer: the amount of noncovalent isomers is ca. 3 times higher for Fc fragments of IgG4 (lacking Fab domains) compared to intact IgG4, and the observed rate of exchange is 3 times higher accordingly. Thus, kinetic data obtained from a sensitive and quantitative real-time FRET assay as described here yield accurate data about interdomain interactions such as those between Fab and/or Fc domains. The results imply that in vivo, the reaction is under control of local redox conditions.     

Mechanistic and kinetic study of the O + CH2OH reaction

The mechanism for the O + CH2OH reaction was investigated by various ab initio quantum chemistry methods. For the chemical activation mechanism, that is, the addition/elimination path, the couple-cluster methods including CCSD and CCSD(T) were employed with the cc-pVXZ (X = D, T, Q, 5) basis sets. For the abstraction channels, multireference methods including CASSCF, CASPT2, and MRCISD were used with the cc-pVDZ and cc-pVTZ basis sets. It has been shown that the production of H + HCOOH is the major channel in the chemical activation mechanism. The minor channels include HCO + H2O and OH + CH2O. The hydrogen abstraction by an O atom from the CH2OH radical produces either OH + CH2O or OH + HCOH. Moreover, the two abstraction reactions are essentially barrierless processes. The rate constants for the association of O with CH2OH have been calculated using the flexible transition state theory. A weak negative temperature dependence of the rate constants is found in the range 250-1000 K. Furthermore, it is estimated that the abstraction processes also play an important role in the O + CH2OH reaction. Additionally, the falloff behavior for the OCH2OH --> H + HCOOH reaction has been investigated. The present theoretical results are compared to the experimental measurements to understand the mechanism and kinetic behavior of the O + CH2OH reaction and the unimolecular reaction of the OCH2OH radical.     

From Tethered to Freestanding Stabilizers of 14-3-3 Protein-Protein Interactions through Fragment Linking

Small-molecule stabilization of protein-protein interactions (PPIs) is a promising strategy in chemical biology and drug discovery. However, the systematic discovery of PPI stabilizers remains a largely unmet challenge. Herein we report a fragment-linking approach targeting the interface of 14-3-3 and a peptide derived from the estrogen receptor alpha (ERα) protein. Two classes of fragments—a covalent and a noncovalent fragment—were co-crystallized and subsequently linked, resulting in a noncovalent hybrid molecule in which the original fragment interactions were largely conserved. Supported by 20 crystal structures, this initial hybrid molecule was further optimized, resulting in selective, 25-fold stabilization of the 14-3-3/ERα interaction. The high-resolution structures of both the single fragments, their co-crystal structures and those of the linked fragments document a feasible strategy to develop orthosteric PPI stabilizers by linking to an initial tethered fragment.     

Synthesis and structural characterization of configurational isomers of tungsten-palladium complexes with bridging diphenyl(dithioalkoxycarbonyl)phosphine as a ligand and phosphine transfer from tungsten to palladium

Treatment of the complex [W(CO)5[PPh2(CS2Me)]] (2) with [Pd(PPh3)4] (1) affords binuclear complexes such as anti-[(Ph3P)2Pd[mu-eta 1,eta 2-(CS2Me)PPh2]W(CO)5] (3), syn-[(Ph3P)2Pd[mu-eta 1,eta 2-(CS2Me)PPh2]W(CO)5] (4), and trans-[W(CO)4(PPh3)2] (5). In 3 and 4, respectively, the W and Pd atoms are in anti and syn configurations with respect to the P-CS2 bond of the diphenyl(dithiomethoxycarbonyl)phosphine ligand, PPh2(CS2Me). Complex 3 undergoes extensive rearrangement in CHCl3 at room temperature by transfer of a PPh3 ligand from Pd to W, eliminating [W(CO)5(PPh3)] (7), while the PPh2CS2Me ligand transfers from W to Pd to give [[(Ph3P)Pd[mu-eta 1,eta 2-(CS2Me)PPh2]]2] (6). In complex 6, the [Pd(PPh3)] fragments are held together by two bridging PPh2(CS2Me) ligands. Each PPh2(CS2Me) ligand is pi-bonded to one Pd atom through the C=S linkage and sigma-bonded to the other Pd through the phosphorus atom, resulting in a six-membered ring. Treatment of Pd(PPh3)4 with [W(CO)5[PPh2[CS2(CH2)nCN]]] (n = 1, 8a; n = 2, 8b) in CH2Cl2 affords syn-[(Ph3P)2Pd[mu-eta 1,eta 2-[CS2(CH2)nCN]PPh2]W(CO)5] (n = 1, 9a; n = 2, 9b). Similar configurational products syn-[(Ph3P)2Pd[mu-eta 1,eta 2-(CS2R)PPh2]W(CO)5] (R = C2H5, C3H5, C2H4OH, C3H6CN, 11a-d) are synthesized by the reaction of Pd(PPh3)4 with [W(CO)5[PPh2(CS2R)]] (R = C2H5, C3H5, C2H4OH, C3H6CN, 10a-d). Although complexes 11a-d have the same configuration as 9a,b, the SR group is oriented away from Pd in the former and near Pd in the latter. In these complexes, the diphenyl(dithioalkoxycarbonyl)phosphine ligand is bound to the two metals through the C=S pi-bonding and to phosphorus through the sigma-bonding. All of the complexes are identified by spectroscopic methods, and the structures of complexes 3, 6, 9a, and 11d are determined by single-crystal X-ray diffraction. Complexes 3, 9, and 11d crystallize in the triclinic space group P1 with Z = 2, whereas 6 belongs to the monoclinic space group P2/c with Z = 4. The cell dimensions are as follows: for 3, a = 10.920(3) A, b = 14.707(5) A, c = 16.654(5) A, alpha = 99.98(3) degrees, beta = 93.75(3) degrees, gamma = 99.44(3) degrees; for 6, a = 15.106(3) A, b = 9.848(3) A, c = 20.528(4) A, beta = 104.85(2) degrees; for 9a, a = 11.125(3) A, b = 14.089(4) A, c = 17.947(7) A, alpha = 80.13(3) degrees, beta = 80.39(3) degrees, gamma = 89.76(2) degrees; for 11d, a = 11.692(3) A, b = 13.602(9) A, c = 18.471(10) A, alpha = 81.29(5) degrees, beta = 80.88(3) degrees, gamma = 88.82(1) degrees.