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We introduce unitary-gate randomized benchmarking (URB) for qudit gates by extending single- and multi-qubit URB to single- and multi-qudit gates. Specifically, we develop a qudit URB procedure that exploits unitary 2-designs. Furthermore, we show that our URB procedure is not simply extracted from the multi-qubit case by equating qudit URB to URB of the symmetric multi-qubit subspace. Our qudit URB is elucidated by using pseudocode, which facilitates incorporating into benchmarking applications.

BACKGROUND: Helicoverpa armigera and Helicoverpa zea are major caterpillar pests of Old and New World agriculture, respectively. Both, particularly H. armigera, are extremely polyphagous, and H. armigera has developed resistance to many insecticides. Here we use comparative genomics, transcriptomics and resequencing to elucidate the genetic basis for their properties as pests. RESULTS: We find that, prior to their divergence about 1.5 Mya, the H. armigera/H. zea lineage had accumulated up to more than 100 more members of specific detoxification and digestion gene families and more than 100 extra gustatory receptor genes, compared to other lepidopterans with narrower host ranges. The two genomes remain very similar in gene content and order, but H. armigera is more polymorphic overall, and H. zea has lost several detoxification genes, as well as about 50 gustatory receptor genes. It also lacks certain genes and alleles conferring insecticide resistance found in H. armigera. Non-synonymous sites in the expanded gene families above are rapidly diverging, both between paralogues and between orthologues in the two species. Whole genome transcriptomic analyses of H. armigera larvae show widely divergent responses to different host plants, including responses among many of the duplicated detoxification and digestion genes. CONCLUSIONS: The extreme polyphagy of the two heliothines is associated with extensive amplification and neofunctionalisation of genes involved in host finding and use, coupled with versatile transcriptional responses on different hosts. H. armigera's invasion of the Americas in recent years means that hybridisation could generate populations that are both locally adapted and insecticide resistant.

Protonated N'-benzyl-N'-L-prolyl-L-proline hydrazide has been developed as a highly enantioselective catalyst for the asymmetric direct aldol reaction of aromatic aldehydes with ketones.

The enantioselective hetero-Diels-Alder (HDA) reaction of Danishefsky's diene with benzaldehyde has been achieved catalytically by a series of alpha,alpha,alpha',alpha'-tetraaryl-1,3-dioxolane-4,5-dimethanol (TADDOL) derivatives through hydrogen-bonding activation, affording 2-phenyl-2,3-dihydro-4H-pyran-4-one after trifluoroacetic acid workup in moderate yield and good enantioselectivity. The alpha,alpha'-aryl substituents in the TADDOL molecules are found to exert a significant impact on both the activity and the enantioselectivity of the catalysis. In combination with the experimental investigations, the mechanism of the present reaction has also been studied theoretically using the ONIOM (133LYP/6-31G{*}:PM3) method with trans-1,3-dimethoxy-1,3-butadiene as the model for Danishefsky's diene. In agreement with the experimental findings, the calculation results indicate that this TADDOL-catalyzed HDA reaction proceeds via a concerted mechanism through an asynchronous and zwitterionic transition structure (TS). The carbonyl group of benzaldehyde is activated by forming an intermolecular hydrogen bond with one of the hydroxy groups of TADDOL. Meanwhile, the intramolecular hydrogen bond between the two hydroxy groups in TADDOL is found to facilitate the intermolecular hydrogen bonding with benzaldehyde. The sense of asymmetric induction is well-rationalized by the analysis of the relative energies of TADDOL-complexed TSs, while the different stereocontrol capabilities exhibited by TADDOLs in the reaction can be qualitatively established on the basis of the structural features of their corresponding TSs.

(Chemical Equation Presented) Electronic properties of the ligands switch the diastereoselectivity in the Cu-catalyzed 1,3-dipolar cycloaddition of azomethine ylides to nitroalkenes: exo- or endopyrrolidines were obtained with high diastereo- and enantioselectivities in the presence of different chiral (phosphanylferrocenyl)oxazoline ligands (e.g. 3a,b). © 2006 Wiley-VCH Verlag GmbH & Co. KGaA.

The reaction of 1-benzyl-1,4-dihydronicotinamide with a series of 1,1-di-p-substituted-phenyl-2,2-dinitroethylenes in oxygen-saturated acetonitrile produced various amounts of the corresponding ethanes and diaryl ketones according to the electronic structure of the substituent groups indicating a spectrum of intermediate mechanism between polar mechanism and SET mechanism. (c) 2005 Elsevier Ltd. All rights reserved.

The mechanisms of the cascade reactions of amino-substituted imidazoles, pyrroles, and pyrazoles with 1,3,5-triazines have been studied using first principle MP2/6-311++G{*}{*}//B3LYP/6-31G{*} calculations in both the gas phase and solution. Calculations indicate that these cascade reactions start with stepwise inverse-electron demand Diels-Alder (IDA) reactions, followed by elimination of ammonia from the IDA adducts, and retro Diels-Alder (RDA) reactions (referred as to the IER path). An alternative IRE path involving a reaction sequence of IDA, RDA, and elimination of ammonia is ruled out since the RDA transition states in this pathway are higher in energy than the reactants by as much as 50 kcal/mol. The preference of the IER over the IRE path is discussed.

Atom transfer radical cyclization reactions of N-(4-pentenyl)iodoacetamides were investigated. The reactions were efficiently promoted by (BF3OEt2)-O-.. For N-alkenyl-substituted iodoamides, excellent regioselectivity in favor of 8-endo cyclization was observed, while both 7-exo and 8-endo cyclization products were formed with the 8-endo cyclization preferred in the cases of N-(2-allylphenyl)substituted iodoamides. Density functional theory calculations at the B3LYP/6-31G{*} level revealed that both the s-trans and the s-cis conformational transition structures were feasible for the 8-endo cyclization of N-alkenyl-substituted a-carbamoyl radicals while 7-exo transition structures were much less stable. For the cyclization of N-(2-allylphenyl)-substituted alpha-carbamoyl radicals, the transition structures for 8-endo and 7-exo cyclizations were of comparable energy. These results were in excellent agreement with the experimental observations.

A total of 6.2 mu s molecular dynamics simulations of amyloid-beta (10-35) (A beta) were performed in explicit water solvent. The results reveal that the collapsed-coil (cc) structure determined by experiments is stable at pH 5.6 for hundreds of nanoseconds, but it can exchange with a strand-loop-strand (SLS) structure on the microsecond time scale. The SLS structure has D23-K28 as a reverse loop and the central hydrophobic core and the C-terminal in hydrophobic contact. This SLS structure topologically resembles the proposed monomer conformation in fibrils. Since it has been suggested that a special conformation of A beta is needed when the monomer binds to fibril ends to elongate fibrils, we propose that the SLS structure may be an important intermediate binding structure for A beta fibril growth. Simulations at pH 2.0, which is used to mimic the mutation of E22Q and D23N, and at high temperature (400 K) indicate that the SLS structure is considerably populated under these conditions while the cc structure is disrupted. These results imply that the SLS structures may also be a binding intermediate in other conditions such as E22Q and/or D23N mutations and high temperature, which have been proved to promote fibril formation previously.

Complexes of fluorinated benzenes (o-C6H4-nF2+n) and Mg.+ are subjected to ultraviolet photodissociation (260-340 nm), producing efficiently benzyne radical cations (C(6)H(4-n)Fn(.+)) besides Mg.+ and MgF+. We show that the consecutive dissociation of C6H4-nFn.+ follows the [C4(+) + C2] pattern exclusively for n less than or equal to 2 after the parent complexes absorb one or two photons. However, the dissociation pattern is switched to [C5(+) + C1] and [C1(+) + C5] for n greater than or equal to 3. In particular, upon two-photon absorption at 340 nm by the complexes of Mg.+(C6HF5) (1) and Mg.+(C6F6) (2), photoproducts of CF+, C5H+, and C5HF.+ from C6HF3.+ and CF+, C5F+, C5F2.+, and C5F3+ from C6F4.+ are detected, respectively. Theoretical calculations are used to explain the switching of the dissociation patterns induced by the fluorine substitutions. It was found that the formation of C5(+) + C1 is energetically more favorable than that of C4(+) + C2 from C6HF3.+ and C6F4.+ and of C1(+) + C5. Except for C5H2F+ + CF, all the channels of [C5(+) + C1] and [C1(+) + C5] are energetically less favorable than those of [C4(+) + C2] from C6H3F.+ and C6H2F2.+. In most cases, the calculated results agree well with the experimental observations.

On the basis of the crystal structure of an aldehyde oxidoreductase, Huber et al. proposed a catalytic mechanism for the reductive half-reaction of xanthine oxidase which involves nucleophilic addition of Mo-bound hydroxide (Moco 1) to the substrate and hydride transfer from the substrate to sulfido group (Mo = S). Density functional theory calculations have been carried out for the oxidation of formaldehyde, acetaldehyde, formamide, and formamidine with Moco 2 to understand more detailed catalytic pathways. Our calculation results indicate that the anionic catalyst model acts as a nucleophile and is reactive for the oxidation of aldehyde substrates, which are reactive for nucleophilic addition. In these cases, a concerted mechanism is found to be more favorable than a stepwise mechanism. The concerted mechanism is further shown to be promoted by the presence of a nearby water molecule, in the active site, which serves as a Lewis acid for the nucleophilic addition of hydroxide. For less reactive formamide and formamidine (a model for xanthine) substrates, the calculated activation energies with the above mechanisms are high. These reactions also do not benefit from the presence of the water molecule. The results indicate that different catalyst forms might be responsible for the oxidation of different substrates, which could be regulated by the enzyme active site environment.

[graphics] Construction of the [5-7-6] tricyclic core of guanacastepenes was attempted by using the intramolecular Diels-Alder (IMDA) reaction and Me3Al-mediated ring opening of the oxabridge as key synthetic steps. The illustrated chemistry demonstrated a synthetic feasibility to build up the framework of guanacastepenes by the IMDA reaction.

In nonpolar solvents, the cyclic hexapeptide 2, which comprises alternating D-α-amino and D-α-aminoxy acids, adopts a C-3-symmetric conformation with alternating eight (N-O turns)- and seven (γ turns)-membered-ring hydrogen bonds. A series of anion-binding studies has suggested that 2 can function as an effective anion receptor that not only displays a high selectivity for chloride ions, but also the capability to extract chloride ions from aqueous solutions into organic phases.

Reactions of d(0) amides M(NMe2)(4) (M = Zr, 1; Hf, 2) with O-2 have been found to yield unusual trinuclear oxo aminoxide complexes M-3(NMe2)(6)(mu-NMe2)(3)(mu(3)-O)(mu(3)-ONMe2) (M = Zr, 3; Hf, 4) in high yields. Tetramethylhydrazine Me2N-NMe2 was also observed in the reaction mixtures. Crystal structures of 3 and 4 have been determined. Density functional theory calculations have been performed to explore the mechanistic pathways in the reactions of model complexes Zr(NR2)(4) (R = H, 5; Me, 1) and [Zr(NR2)(4)](2) (R H, 5a; Me, 1a) with triplet O-2. Monomeric and dimeric reaction pathways in the formation of the Zr complex 3 are proposed.

Theoretical calculations have been carried out to investigate the effect of the 4(R)-substituents (OH, F, NH2, and NH3+) in proline on the stability of the collagen triple helix. A series of substituted proline models were studied first with density functional (B3LYP/6-31+G{*}) calculations. The solvent effect was studied using the SCIPCM method. While the F, OH and NH2 groups increase the stability of the trans-up conformation with respect to the trans-down conformation, NH3+ appears to favor the trans-down conformation in an aqueous solution. Second, the triple helices of the tripeptide models, Ac-Pro-Pro(X)-Gly-H with the two proline residues in the down/down and down/up puckering conformations, were optimized with a repeating unit approach using the HF/6-31G{*} method. For the Ac-Pro-Pro-Gly-H model peptide, the calculated binding energies of the two triple helices with the different puckering modes are similar. All four substituents, F, OH, NH2, and NH3+, considerably increased the binding energy of the down/up helix, but only NH3+ stabilizes the down/down triple helix. Our calculations indicate that the inter-chain electrostatic interactions involving the 4(R)-substituents play an important role in stabilizing triple helical collagen models and allow the rationalization of all available experimental observations. Further model studies indicate that the substituent effects by the F, OH and NH2 substituents are local while the effect of NH3+ is long-range in nature.

We have investigated, using NMR, IR, and CD spectroscopy and X-ray crystallography, the conformational properties of peptides 1-10 of beta(3)-aminoxy acids (NH2OCHRCH2COOH) having different side chains on the beta carbon atom (e.g., R = Me, Et, COOBn, CH2CH2CH=CH2, i-Bu, i-Pr). The beta N-O turns and beta N-O helices that involve a nine-membered-ring intramolecular hydrogen bond between NHi+2 and COj, which have been found previously in peptides of beta(2,2)-aminoxy acids (NH2OCH2CMe2COOH), are also present in those beta(3)-aminoxy peptides. X-ray crystal structures and NMR spectral analysis reveal that, in the beta N-O turns and beta N-O helices induced by beta(3)-aminoxy acids, the N-O bond could be either anti or gauche to the C-alpha-C-beta bond depending on the size of the side chain; in contrast, only the anti conformation was found in beta(2,2)-aminoxy peptides. Both diamide 1 and triamide 9 exist in different conformations in solution and in the solid state: parallel sheet structures in the solid state and predominantly beta N-O turn and beta N-O helix conformations in nonpolar solvents. Theoretical studies on a series of model diamides rationalize very well the experimentally observed conformational features of these beta(3)-aminoxy peptides.

Although there are tremendous studies about the conformational feature of calix[4]arenes and its analogies, no theoretical study has been done systematically about why some structural modifications could completely lead to a change of conformational preference. For example, calix[4]arene 1 adopts a cone conformation while its analogue calix[4]pyrrole 7 only adopts a 1,3-alternate conformation. So if this is only because of the effect of OH-OH hydrogen bonds, then why does O-methyl substituted calix[4]arene 2 still has cone conformation? In this paper, the conformational features of a series of seven calix[4]axomatics, calix[4]arene and calix[4]pyrrole related structures, have been investigated at BLYP/6-31G{*} level both in the gas phase and in CH2Cl2 solution. The calculations demonstrated that three main factors influence the conformational preference of these calix[4] aromatics, i.e. the intramolecular hydrogen bond, the adjacent ring-ring electrostatic interaction and the intrinsic flexibility of the [1(4)] metacyclophane framework. Calix[4]benzene 3 and calix[4]pyridine 4 have little conformational preferences due to their flexible [1(4)] metacyclophane framework, the lack of hydrogen-bonding interactions and weak ring-ring electrostatic interactions. In contrast, calix[4] aromatics 1 and 5-7 have either intramolecular hydrogen bonds (1) or ring-ring electrostatic interactions (5-7). Consequently, calix[4]arene 1 has the cone preference and calix[4]pyrrole, calix[4]furan, and calixthiophene (5-7) have the 1,3-alternate preference. Methoxy calix[4]arene prefers a cone or partial cone conformation, because the 1,3-alternate and 1,2-alternate conformations are destabilized by electrostatic repulsions involving the methoxy group and the adjacent phenyl ring.

The ring-opening reaction of metallacyclobutenes derived from the addition of alkyne (HCdropCR, R = H, Me) to molybdenum alkylidene Mo(NH)(OR')(2)(=CHR'') (R' = Me, CF3, R'' = H, Me) has been studied using quantum mechanics methods. Two ring-opening paths, NH outward and NH inward ring-openings, have been found for metallacyclobutene intermediates Mo(NH)(OR')(2)(CH2)(HCCH) (R' = Me, CF3) and alpha- and beta-addition metallacyclobutene intermediates Mo(NH)(OMe)(2)(CH2)(C2HMe). The NH outward ring-opening is found to be favored over the NH inward ring-opening. The electron-withdrawing group (OCF3) in molybdenum alkylidene and alpha-methyl group further enhance the preference for the NH outward ring-opening pattern. Four ring-opening paths have been found for Mo(NH)(OMe)(2)(CHMe)(C2H2), an intermediate in the addition of acetylene to Mo(NH)(OMe)(2)(CHMe). The conformation of the product is found to be dependent upon the conformation of the molybdenum alkylidene. That is, when trans-molybdenum alkylidene is used as the catalyst, an anti-polymer is generated, while using cis-molybdenum alkylidene may lead to the polymer in different conformations. The anti/syn-isomerization of the electron-withdrawing group substituted molybdalkylidene is calculated to be much slower than the polymerization steps; therefore, an all-trans-polymer can be obtained.

L-Prolinamides 2, prepared from L-proline and simple aliphatic and aromatic amines, have been found to be active catalysts for the direct aldol reaction of 4-nitrobenzaldehyde with neat acetone at room temperature. They give moderate enantioselectivities of up to 46\% enantiomeric excess (ee). The enantioselectivity increases as the amide N-H becomes a better hydrogen bond donor. L-Prolinamides 3, derived from the reaction Of L-proline with alpha,beta-hydroxyamines such that there is a terminal hydroxyl group, show more efficient catalysis and higher enantioselectivities. In particular, catalyst 3h, prepared from L-proline and (1S,2S)-diphenyl-2-aminoethanol, exhibits high enantioselectivities of up to 93\% ee for aromatic aldehydes and up to >99\% ee for aliphatic aldehydes under -25degreesC. Model reactions of benzaldehyde with three enamines derived from the condensation of prolinamides with acetone have been studied by quantum mechanics calculations. The calculations reveal that the amide N-H and the terminal hydroxyl groups form hydrogen bonds with the benzaldehyde substrate. These hydrogen bonds reduce the activation energy and cause high enantioselectivity. Our results suggest a new strategy in the design of new organic catalysts for direct asymmetric aldol reactions and related transformations.

Photoinduced reactions have been systematically studied on mass-selected complexes of Mg.+ with tri- and tetrasubstituted benzene by F and/or CH3. The complexes fall into two groups. The Group I complexes involve bidentate coordination of the o-F atoms to Mg.+, whereas the Group II complexes feature the linkage of Mg.+ to only one of the F atoms. The o-benzyne radical cations were found to be the predominant photolysis products from the Group I complexes, but the yields of the benzyne radical cation products were low for Group II. For each group of complexes, different substituents. including CH3 (medium sigma-electron donor) and F (strong pi-electron acceptor and weak pi-electron donor), affect the branching ratios significantly. For example, they result in different decomposition thresholds of the o-benzyne radical cations. Through the studies of aromatic substitution, the pathways for the formation and decomposition of o-benzyne radical cations have been brought to light. With the help of quantum mechanics calculations, the observed substitutent effects on the photoformation and decomposition of the o-benzyne radical cations are explained mainly from the energy point of view. We found that although o-benzyne radical cations are formed by the direct abstraction of the F atoms, the formation of m-benzyne radical cations is stepwise, involving a pi-+MgF intermediate.

Experimental studies on the modification of (1R,2S)-1,2-diphenyl-2-aminoethanol, which is used to promote the alkylation of N-diphenylphosphinoyl benzalimine with diethylzinc, revealed that N-monosubstituted amino alcohols exhibited higher enantioselectivities than their N,N-disubstituted counterparts and imino alcohols. Application of the optimal chiral ligand 3c to activate the reaction of N-diphenylphosphinoyl arylimines with diethylzinc and dibutylzinc resulted in excellent enantiomeric selectivities of up to 98\% ee. The origin of the experimentally observed enantioselectivities was revealed by density functional calculations (B3LYP/6-31G{*}) on the transition structures of several model reactions.

The transient organoindium intermediates formed in the reaction of propargyl bromide with indium in aqueous media and tetrahydrofuran were investigated by NMR spectroscopy and found to be allenylindium(I) and allenylindium(III) dibromide. The influence of solvent and methyl substitution on the propargyl-allenylindium system was also studied. The experimental observations were supported by theoretical calculations using the B3LYP/6-311+G{*} method.

It is known that the seven-membered-ring intramolecular hydrogen bond (γ-turn) is seldom formed in naturally occurring peptides composed of α-amino acids. Here we report a new strategy to induce γ-turns in short linear peptides. We designed and synthesized several peptides (1-5) containing alternating α-L-aminoxy acids and α-D-amino acids. 1H NMR studies revealed that the γ-turn could be initiated by the following N-O turn, an eight-membered-ring intramolecular hydrogen bond induced by an α-aminoxy acid. Moreover, NOESY and CD studies suggested peptides 4 and 5 form a novel secondary structure, a mixed 7-8 helix. Theoretical calculations on several di-, tri-, and tetrapeptide models provided strong support to the above conclusions. Copyright © 2003 American Chemical Society.

Episulfidation of alkenes by dinitrogen sulfide, generated from thermolysis of 5-aryloxy-1,2,3,4-thiatriazoles, was found to be an S(N)2-like reaction involving simultaneous sulfur addition and dinitrogen extrusion. The preference for the one-step S(N)2 mechanism instead of the two-step (2+3) dipolar cycloaddition. and denitrogenation is attributed to the higher geometry distortion penalty in the (2+3) transition state than that in the S(N)2-like transition state.

A theoretical study based on B3LYP/6-31G{*} calculations has been applied to the mechanisms and regiochemistry of reactions of 5-alkoxyoxazole with thioaldehydes, nitroso compounds, and aldehydes. All three reactions adopt similar mechanisms, which start with Diels-Alder (DA) reactions, followed by either a novel, concerted ring-opening-ring-closing (RORC) step to transfer the DA adduct to 2-alkoxycarbonyl-3-thiazoline and 2-alkoxycarbonyl-3-oxazoline for thioaldehydes and aldehydes, respectively, or stepwise ring-opening and ring-closing steps to generate 1,2,4-oxadiazoline for nitroso compounds. The reactions of 5-alkoxyoxazole with thioaldehydes and nitroso compounds can be conducted under thermal reaction conditions due to the 10 kcal/mol activation barriers for their rate-determining DA reactions. By contrast, the reaction of 5-alkoxyoxazole with aldehydes cannot take place under thermal conditions, since this bimolecular reaction has the rate-determining RORC transition state higher than the reactants by 30.5 kcal/mol.

The photochemistry of a gas-phase complex, Mg.+(2-fluoropyridine), has been studied in the spectral range of similar to230-440 nm with a molecular beam coupled with a time-of-flight mass spectrometer. Surprisingly rich chemistry has been observed. Aside from the evaporative photofragment, Mg.+, an abundant photoproduct, C4H4.+, is observed after the electronic excitation of Mg+. The formation of this photoproduct is associated with the loss of a stable species, CN-Mg-F. Also identified in this work are reactive pathways that occur with the elimination of HCN, HF, or MgF from the complex. The observed photoreactions have been examined in detail using quantum mechanics methods. A distinct structural feature of the complex is the direct attachment of Mg.+ to the N atom of fluoropyridine due to the strong electrostatic interaction. The key to the rich photochemistry is the formation of the FMg+(C5H4N) intermediate, through facile fluorine migration. Plausible photoreaction mechanisms have been proposed. These mechanisms account for the evolution of the energized complex with the pre-defined structure en route to the target photoproducts that we have detected.

Density functional calculations have been carried out to understand the anti-addition stereochemistry and Markovnikov regiochemistry of the hydrosilylation of terminal alkynes and the endo-dig product of intramolecular hydrosilylation of homopropargyl alcohols catalyzed by cationic cyclopentadienyl-ruthenium complexes. It has been found that hydride or silyl insertion is concerted with the oxidative addition of the H-Si bond. Hydride insertion is much more favorable than silyl insertion. Such a hydride insertion nicely reproduces the observed regioselectivity, while silyl insertion would predict the opposite result. The hydricle insertion leads to the formation of a eta(2)-vinylruthenium intermediate for the reaction of acetylene or a metallacyclopropene intermediate for the reaction of propyne. In the formation of both intermediates, there is a C-alpha-C-beta bond rotation so that the transferring hydricle becomes anti to the silyl group. This is followed by a facile reductive a-silyl migration transition state, which results in the overall anti-addition stereochemistry. The proposed mechanism also rationalizes the observed regio- and stereochemistry of the intramolecular reaction.

Our previous work revealed that two adjacent D-a-aminoxy acids could form two homochiral N-O turns, with the backbone folding into an extended helical structure (1.8(8)-helix). Here, we report the conformational studies of linear peptides 3-6, which contain a D,L-alpha-aminoxy acid dimer segment. The NMR and X-ray analysis of 3 showed that it folded into a loop conformation with two heterochiral N-O turns. This loop segment can be used to constrain tetrapeptides 4 and 6 to form a reverse turn structure. H-1 NMR dilution studies, DMSO-d(6) addition studies, and 2D-NOESY data indicated that tetrapeptides 4 and 6 folded into reverse turn conformations featured by a head-to-tail 16-membered-ring intramolecular hydrogen bond. In contrast, tetrapeptide 5 with L-Ala instead of Gly or D-Ala as the N-terminal amino acid could not form the desired reverse turn structure for steric reasons. Quantum mechanics calculations showed that model pentamide 7, with the same substitution pattern of 4, adopted a novel reverse turn conformation featuring two heterochiral N-O turns (each of an 8-membered ring hydrogen bond), a cross-strand 16-membered ring hydrogen bond, and a 7-membered ring gamma-turn.

The mechanism of ring-opening metathesis reaction of molybdenum alkylidene complexes with norbornadiene has been studied by quantum mechanics method. Both cycloaddition and ring-opening reactions have a twisted trigonal bipyramidal transition structure. The cycloaddition is the rate-determining step while the ring-opening step has very low activation energy. When the alkoxyl ligands are small (OCH3, OCF3), there is only a small preference for norbornadiene attacking syn to the imido group. When the size of the alkoxyl ligands increases, the syn preference for norbornadiene addition becomes more favorable. Our calculations strongly support Schrock's proposal for the stereoselectivity of ring-opening metathesis polymerization. That is, the stereochemistry is determined by the relative rates of alkylidene syn/anti interconversion and polymerization reaction. (C) 2002 Elsevier Science B.V. All rights reserved.

Density functional theory at the B3LYP/6-31G{*} level has been used to study the mechanisms and regio- and stereochemistry of the Lewis acid-catalyzed reactions of aldehydes with 5-alkoxyoxazoles. Similar to the uncatalyzed reaction between aldehyde and 5-methoxyoxazole, which has an activation energy of 30.5 kcal/mol and intrinsically favors production of 2-alkoxycarbonyl-3-oxazoline, the Lewis acid-catalyzed reaction also prefers to generate 2-alkoxycarbonyl-3-oxazoline in a more efficient way with an activation energy of about 3 kcal/mol (with respect to separated acetaldehyde-AlCl3 complex and 5-methoxyoxazole) in the gas phase. Only when an aryl group is introduced to the 2 position of 5-alkoxyoxazoles can the Lewis acid-catalyzed reactions furnish 4-alkoxycarbonyl-2-oxazolines. The reasons for this switch of regiochemistry and the factors affecting the stereochemistry are discussed.

Conformational features of oligomers of 3-(R)-butanoic acid have been studied using quantum mechanics methods. Conformational search of Ac-OCH(CH3)-CH2-COOCH3 indicates that the compound is quite flexible with several conformations similar in stability. Study of Ac-[OCH(CH3)-CH2-CO](n)OCH2CH3, n = 1-8, using a repeating unit approach for 2(1)-helix, 3(1)-helix, 4(1)-helix, 5(1)-helix, and pleated strand structure indicates that only the 31-helix has a cooperative effect and is also most stable. Crystal orbital calculations on the crystal packing energies of the 2(1)-, 3(1)-, and 4(1)-helices have been performed. The 2(1)-helix is found to have much stronger crystal packing stabilization than the 3(1)- and 4(1)-helices. This explains why the 2(1)-helix is found in crystal structures of poly((R)-3-hydroxybutanoic acid) (PHB) despite the fact that the 3(1)-helix is the most stable single helix. The stabilization of the 2(1)-helix in the crystal structure is mainly from the dipole interaction between adjacent parallel helices but not from adjacent antiparallel helices. The study also provides useful information for the study of ion channel structures of PHB.

Helium-3 NMR chemical shifts of various He-3-encapsulated fullerenes (He-3@C-n) and their derivatives have been calculated at the GIAO-B3LYP/3-21G and GIAO-HF/3-21G levels with AM1 and PM3 optimized structures. A good linear relationship between the computed He-3 NMR chemical shifts and the experimental data has been determined. Comparisons of the calculation methods of He-3 NMR chemical shifts show that GIAO-B3LYP/3-21G with AM1-optimized structures yields the best results. The corrected He-3 NMR chemical shifts were calculated from the correction equation that is obtained through linear regression fitting of the experimental and calculated He-3 NMR chemical shifts over a wide range of(3)He-encapsulated fullerene compounds. The corrected He-3 NMR chemical shifts match the experimental data very well. The current computational method can serve as a prediction tool and can be applied to the assignments and reassignments of the He-3 NMR chemical shifts of He-3@C-n and their derivatives.

The cooperativity in terms of enthalpy contribution for β-sheet formation of polyglycine models in a vacuum has been studied theoretically by using a repeating unit approach. No cooperativity is found in the parallel direction for both the parallel and antiparallel β-sheets. Cooperativity in the perpendicular direction is dependent upon the residue number (m) in each β-strand. While there is large cooperativity in the acetamide hydrogen-bond chain (m = 0), the cooperativity is not large in β-sheet networks (m > 0). SCIPCM solvent model calculations also significantly reduce the cooperativity in hydrogen-bond chains. It is concluded that cooperativity is mainly due to long-range electrostatic interactions and not due to the resonance effect. Copyright © 2002 American Chemical Society.

Structural and thermodynamic features of the sheets formed by beta-peptides have been studied by quantum mechanics calculations using peptide models. Calculations using dipeptide models indicate that the intrinsic hydrogen bond strength is great for both parallel and antiparallel sheets and that it is little affected by proper substituents. Heterochiral-beta(2,3)-peptides have much stronger sheet-forming propensity than other types of peptides because their favored backbone conformation is ideal for sheet formation. A planar or ideally pleated strand has a curved geometry, which is unfavorable for the formation of sheets. Thus, sheets have to adopt twisted geometries. There is a large cooperativity in the formation of the hydrogen bond network in the sheets of beta-peptides in the perpendicular direction due to long-range electrostatic attractions because all carbonyl groups are roughly in the same direction, in contrast to the situation in beta-sheets of alpha-peptides. (C) 2002 Wiley Periodicals, Inc.

Distonic o-, m-, and p-benzyne radical cations (1-3) have been generated by a novel photolysis reaction of mass-selected Mg+-difluorobenzene complexes. The energy required for the formation of these radical cations is within 2.2 eV. The formation of o-benzyne cation is most facile. The benzyne radical cations dissociate further to yield ethyne and 1,3-butadiyne radical cation as major products given a sufficient amount of energy. The whole process involves only a single photon, and is very efficient. The calculated threshold for the formation of 1,3-butadiyne radical cation from Mg+(o-C6H4F2) is about 4.6 eV, quite comparable with the experimental estimate.

9-Fluorenylidenemalononitrile reacts with 10-methyl-9,10-dihydroacridine in deaerated acetonitrile under irradiation with lambda > 320 nm to give a coupling product 9-dicyanomethyl-9-(10'-methyl-9'-acridinyl)fluorene, characterized by X-ray crystallographic, MS and NMR analyses.

This study is devoted to a detailed theoretical study of an inverse-electron demand Diels-Alder reaction (IDA) with 1,3,5-triazine as the diene and 2-aminopyrrole 1A(alpha) as the dienophile, which is a key step in a cascade reaction for the one-pot synthesis of purine analogues. Geometries were optimized with the B3LYP/6-31G{*} method and energies were evaluated with the MP2/6-311++G{*}{*} method. This IDA reaction occurs through a stepwise mechanism, where the first step corresponds to the nucleophilic attack of 2-aminopyrrole to triazine to form a zwitterionic intermediate, which is in equilibrium with a neutral intermediate through a hydrogen transfer process, followed by a rate-determining ring-closure step. It is shown that the B3LYP method significantly overestimates the activation energy, whereas the MP2 method offers a reasonable activation barrier of 27.9 kcal/mol in the gas phase. The solvation effect has been studied by the PCM model. In DMSO, the calculated activation energy of the IDA reaction is decreased to 24.0 kcal/mol with a strong endothermicity of 17.4 kcal/mol due to the energy penalty of transforming two aromatic reactants into a nonaromatic IDA adduct. The possible stepwise [2+2] pathway is ruled out based on its higher activation and reaction energies than those of the [4+2] pathway. By comparing the IDA reactions of triazine to 2-aminopyrrole and pyrrole, we address two crucial roles of the alpha -amino substituent in lowering activation and reaction energies and controlling the reaction regiochemistry.

M(NMe2)(4) (M = Ti, Zr, Hf) were found to react with H2SiR ` Ph (R ` = H, Me, Ph) to yield H-2, arninosilanes, and black solids. Unusual amide hydride complexes [(Me2N)(3)M(mu -H)(mu -NMe2)(2)](2)M (M = Zr, 1; Hf, 2) were observed to be intermediates and characterized by single-crystal X-ray diffraction. [(Me2N)(3)M(mu -D)(mu -NMC2)(2)](2)M (1d(2), 2d(2)) were prepared through reactions of M(NMe2)(4) with D2SiPh2. Reactions of (Me2N)(3)ZrSi(SiMe3)(3) (5) with H2SiR ` Ph were found to give aminosilanes and (Me2N)(2)Zr(H)Si(SiMe3)(3) (6). These reactions are reversible through unusual equilibria such as (Me2N)(3)ZrSi(SiMe3)(3) (5) + H2SiPh2 reversible arrow (Me2N)(2)Zr(H)Si(SiMe3)(3) (6) + HSi(NMe2)Ph-2. The deuteride ligand in (Me2N)(2)Zr(D)Si(SiMe3)(3) (6-d(1)) undergoes H-D exchange with H2SiR ` Ph (R ` = Me, H) to give 6 and HDSiR ` Ph. The reaction of Ti(NMe2)(4) with SiH4 in chemical vapor deposition at 450 degreesC yielded thin Ti-Si-N ternary films containing TiN and Si3N4. Ti(NMe2)(4) reacts with SiH4 at 23 degreesC to give H-2, HSi(NMe2)(3), and a black solid. HNMe2 was not detected in this reaction. The reaction mixture, upon heating, gave TiN and Si3N4 powders. Analyses and reactivities of the black solid revealed that it contained -H and unreacted -NMe2 ligands but no silicon-containing ligand. Ab initio quantum chemical calculations of the reactions of Ti(NR2)(4) (R = Me, H) with SiH4 indicated that the formation of aminosilanes and HTi(NR2)(3) was favored. These calculations also showed that HTi(NH2)(3) (3b) reacted with SiH4 or H3Si-NH2 in the following step to give H2Ti(NH2)(2) (4b) and aminosilanes. The results in the current studies indicated that the role of SiH4 in its reaction with Ti(NMe2)4 was mainly to remove amide ligands as HSi(NMe2)3. The removal of amide ligands is incomplete, and the reaction thus yielded "=Ti(H)(NMe2)" as the black solid. Subsequent heating of the black solid and HSi-(NMe2)(3) may then yield TiN and Si3N4, respectively

The conformational preference of calix[4]pyrrole and its fluoride and chloride anion-binding properties have been investigated by density functional theory calculations. Geometries were optimized by the BLYP/3-21G and BLYP/6-31G{*} methods, and energies were evaluated with the BLYP/6-31+G{*}{*} method. To model the effect of medium, the SCIPCM solvent model was also employed. Four typical conformations of the parent substituent-free calix[4]pyrrole were studied. Both in the gas phase and in CH2Cl2 solution, the stability sequence is predicted to be 1,3-alternate > partial cone > 1,2-alternate > cone. The cone conformation is predicted to be about 16.0 and 11.4 kcal/mol less stable in the gas phase and CH2Cl2 solution, respectively. This is mainly due to electrostatic repulsions arising from the all-syn pyrrole/pyrrole/pyrrole/pyrrole arrangement present in this conformer. The existence of possible 1:1 and 1:2 anion-binding modes were explored in the case of fluoride anion, and the factors favoring the 1:1 binding mode are discussed. The calculated binding energy for fluoride anion is about 15 kcal/mol larger than that for chloride anion. The calculated binding energy for chloride anion agrees with the experimental value very well. The presence of meso-alkyl substituents destabilizes the cone conformer with respect to the 1,3-alternate conformer and, therefore, reduces the anion-binding affinity by 3-4 kcal/mol. The strength of N-H- - -anion hydrogen bonds in the various structures subject to study were estimated on the basis of the calculated anion-binding energies and the predicted structural deformation energies of substituent-free calix[4]pyrrole.

The addition of alkynes HC=CR to Mo(NH)(CH2)(OR')(2) (R = H, Me, Ph; R' = CH3, CF3) has been studied with both ab initio molecular orbital and density functional calculations. Geometry optimizations were carried out with the HF/3-21G, HF/HW3, and B3LYP/HW3 methods. The transition structures for these addition reactions are in distorted trigonal bipyramidal geometries, similar to those of alkene additions. The calculated activation enthalpy for HC=CH addition to Mo(NH)(CH2)(OR')(2) is about 10.3 kcal/mol for R' = CH3 and about 2.3 kcal/mol for R' = CF3, indicating a significant preference for acetylene addition to Mo-(NH)(CH2)(OCF3)(2) over Mo(NH)(CH2)(OCH3)(2). These barriers are higher than those of the corresponding ethylene addition by about 2-4 kcal/mol, even though the reaction of acetylene is much more exothermic. The a-addition of HC=CR (R = Me, Ph) is found to be considerably more favorable than the beta -addition to Mo(NH)(CH2)(OR')(2). Interestingly, the a-addition has a lower activation energy, while the beta -addition has a higher activation energy, compared to that of the parent acetylene addition. Thus, a-addition is intrinsically favored over beta -addition by over 4 kcal/mol. This preference is reduced by solvent effect. All these can be explained by a destabilizing interaction between the nonreacting pi -orbital of alkyne and one of the lone pairs on the imido nitrogen. The steric effect of the bulky ligands in the real catalysts is also investigated qualitatively by the PM3 method. These studies give results in good accord with the experimentally observed regioselectivity.

By using a simple repeating unit method, we have conducted a theoretical study which delineates the preferences for beta -strand, 2(7)-ribbon, 3(10)-helix, and alpha -helix formation for a series of polyglycine models up to 14 amino acid residues (Ac-(Gly)(n), n = 0, 1, 2,..., 14):`Interactions among residues, which result in cooperativity, are clearly indicated by variations in calculated energies of the residues. Whereas no cooperativity; is found in the formation of beta -strands and 2(7)-ribbons, there is a significant cooperativity: in the formation of 3(10)- and alpha -helices; especially for the latter. In the case of alpha -helices, the 14th residue is more stable than the 3rd by about 3 kcal/mol. A good correlation between calculated:residue energy and residue dipole-moment was uncovered, indicating the importance of long-range electrostatic interaction's to the cooperativity. The results of our calculations are compared with those of the AMBER and PM3 methods, and indicate that both methods, AMBER and PM3, need fur;ther development in the Cooperative view of electrostatic interactions. The result should be of importance-in providing insight into protein folding and-formation of helical structures in a variety of polymeric compounds. This also suggests a strategy for the development of more consistent molecular mechanics force fields.

A detailed mechanism for the Kulinkovich hydroxycyclopropanation reaction has been explored with density functional theory calculations on the reactions between (RCOOMe)-C-1 and Ti(OMe)(2)(CH2CHR2) (R-1 and R-2 are hydrogen and alkyl groups). Addition of ester to titanacyclopropane is found to be fast, exothermic, and irreversible. It has a preference for the alpha -addition manifold over the beta -addition manifold in which its cycloinsertion transition states suffer from the steric repulsion between the R-2 and ester. The following intramolecular methoxy migration step is also exothermic with reasonable activation energy. The cyclopropane forming step is the rate-determining step, which affords the experimentally observed cis-R-1/R-2 diastereoselectivity in the alpha -addition manifold by generating cis-R-1/R-2 1,2-disubstituted cyclopropanol when R-1 is primary alkyl groups. On the contrary, the unfavored beta -addition manifold offers the diastereoselectivity contradicting the experimental observations. The effects of R-1 and R-2 on the regio- and stereoselectivity are also discussed.

Methyltrioxorhenium (MTO),a high-oxidation-state transition metal complex, has been found to be a highly efficient catalyst in the last decade. The physical and chemical properties, the wide application to catalysis of a range of organic reactions, and theoretic as well is experimental researches on the catalytic mechanism of MTO are reviewed. Close attention has also been paid to the prospects of the work on MTO's catalyied reaction.

Reactions of silanes with d(o) Ta alkylidene and Group 4 amide complexes were found to involve the initial attack on silicon atoms in the silanes by nucleophilic alkylidene carbon or amide nitrogen atoms. The reaction of (Me3SiCH2)(3)Ta(PMe3)[=CHSiMe3] (1) with H2SiR'Ph (R' = Me, Ph) gave (Me3SiCH2)(3)Ta[=C(SiMe3)SiHR'Ph] (2a-b). Similar reactions of these two silanes and (H2PhSi)(2)CH2 with (Me3SiCH2)Ta(PMe3)(2)[=CHR](2) (R = SiMe3, 3; CMe3, 4) yielded novel metallasilacyclobutadienes and a metalladisilacyclohexadiene, respectively. In comparison, the reactions between M(NMe2)(4) (M = Ti, Zr, Hf) and silanes were found to give aminosilanes and metal amide hydride species which were perhaps involved in the formation of titanium-silicon-nitride (Ti-Si-N) ternary materials.

Chiral alpha -aminoxy acids of various side chains were synthesized with high optical purity starting from chiral alpha -amino acids. The conformations of diamides 13a-e, 15, and 16 were probed by using NMR, FT-IR, and CD spectroscopic methods as well as X-ray crystallography. The right-handed turns with eight-membered-ring intramolecular hydrogen bonds between adjacent residues (called the N-O turns) were found to be preferred for D-aminoxy acid residues, and they were independent of the side chains. The rigid chiral N-O turns should have great potential in molecular design.