Quantum-mechanical calculations of the stabilities of fluxional isomers of C4H(7)(+) in solution

Rearrangement, Elimination, and Ring-Opening Reactions of Cyclopropyl-Substituted Nitrenium Ions: A Computational and Experimental Investigation

N-(4-Biphenylyl)-N-cyclopropyl nitrenium ion 5 and N-benzyl-N-cyclopropyl nitrenium ion (6) were generated through photolysis of their corresponding N-aminopyridinium ion photoprecursors. In the case of 5, stable products result from a combination of cyclopropyl ring expansion (N-biphenylazetium ion) and ethylene elimination (biphenylisonitrilium ion). When present in high concentrations, methanol can add to the cyclopropyl ring-forming N-3-methoxypropyl-N-biphenyl iminium ion. In contrast, the only detectable product from the N-benzyl-N-cyclopropyl nitrenium ion (6) is benzylisonitrile, resulting from the elimination of ethylene. Density functional theory (DFT) calculations predict the product distributions from the more stable biphenyl system 5 with reasonable accuracy. However, product distributions from the less stable benzyl system 6 are forecast with less accuracy.

Cyclopropylmethyldiphosphates are substrates for sesquiterpene synthases: experimental and theoretical results

New homo-sesquiterpenes are accessible after conversion of presilphiperfolan-8β-ol synthase (BcBOT2) with cyclopropylmethyl analogs of farnesyl diphosphate, and this biotransformation is dependent on subtle structural refinements. Two of the three cyclisation products are homo variants of germacrene D and germacrene D-4-ol while the third product reported contains a new bicyclic backbone for which no analogue in nature has been described so far. The findings on diphosphate activation are discussed and rationalised by relaxed force constants and dissociation energies computed at the DFT level of theory.

Discrete Existence of Singlet Nitrenium Ions Revisited: Computational Studies of Non-Aryl Nitrenium Ions and Their Rearrangements

Nitrenium ion species are examined using computational methods (DFT, MP2, coupled-cluster, and a composite method, CBS-APNO) with a particular emphasis on nonaromatic species (i.e., those lacking an aromatic or heteroaromatic ring in direct conjugation with the formal nitrenium ion center.) The substitution of the N+ center with alkyl, alkoxy, vinyl, acyl, and sulfonyl, among others, was evaluated. For these species, three properties are considered. (1) The stability of the nitrenium ions to unimolecular isomerizations such as 1,2 alkyl or H shifts; to the extent that the singlet states could be characterized as discrete minima on the potential energy surface (PES), (2) the effect of the substituents on singlet-triplet energy splitting as well as (3) the relative stabilities of the nitrenium ions as defined by N-hydration enthalpies (RR'N+ + H2O → RR'NOH2 +). Nearly all simple alkyl and di-alkyl nitrenium ion singlet states are predicted to rearrange without detectable barriers, largely through 1,2 H or alkyl shifts. Methyl and N,N-dimethylnitrenium ion singlet states could be characterized as formal minima on the PES. However, these species show small or insignificant barriers to isomerization. Disubstituted nitrenium ions that include an alkyl group and a conjugating substituent such as alkoxyl, vinyl, or phenyl show meaningful barriers to isomerization and are thus predicted to possess nontrivial lifetimes in solution. Alkyl groups substantially stabilize the singlet state relative to the situation in the parent nitrenium ion NH2 + to the point where the two states are nearly degenerate. Other groups that interact with the nitrenium ion center decrease the ΔE st in the order formoyl < vinyl < phenyl < alkoxy ∼ sulfonyl < cyclopropyl ∼ cyclobutyl. The latter two substituents interact strongly with the (singlet) nitrenium ion center through the formation of a nonclassical bonding reminiscent of the bisected cyclopropylcarbinyl ion case for carbocations. When singlet-state stability is evaluated in the context of N-hydration enthalpies, it is found that the ordering is acyl < vinyl < alkoxyl < phenyl < cyclopropyl and cyclobutyl.

Nitrenium ion analogues of nonclassical carbocations: cyclopropylnitrenium, allylnitrenium, and azetidenium ions and mechanisms for their interconversion

Cyclopropylnitrenium 3S, allylnitreium 6S, and azetidenium (i.e., the nitrogen analogue of cyclobutylcarbenium) ions were examined using density functional theory and a complete basis set method. Similarly to the carbon analogues, the singlet states of these species have several local minima with nonclassical bonding. Structures characterized include 3S, an N analogue of the bisected cyclopropylcarbinyl cation, 11S, an N analogue of the bicyclobutonium ion, and 6S, an unsymmetric 2-azidinylcarbinyl cation.

Quantum mechanical investigations on the role of C-terminal residue in influencing the structural features of dipeptides containing N-terminal proline

This study investigates the influence of the side chain moiety of C-terminal residue on the structural and molecular properties of seven dipeptides having proline at their N-terminal positions. The C-terminal component of the dipeptides is varied with seven different combinations viz. Ala, Leu, Asp, Thr, Asn, Arg and Sec. The calculations are carried out using B3LYP/6-311++G(d,p) level of theory in gas and implicit aqueous phase. Effects of explicit aqueous environment on the dipeptide structures are also investigated for two systems. The results furnished by this DFT study provide valuable information regarding the role of the side chain groups of C-terminal residues in determining the structural features of the amide planes, values of the ψ and ф dihedrals, geometry about the α-carbon atoms, theoretical IR spectra as well as the number and type of intramolecular H-bond interactions existing in the dipeptides, and extend a fine corroboration to the earlier theoretical and experimental observations. In aqueous phase the dipeptide geometries exhibit larger values of total dipole moments, greater HOMO-LUMO energy gaps and enhanced thermodynamic stability than those in gas phase. The explicit water molecules are found to modify the geometrical parameters related to the amide planes and vibrational spectra of the dipeptides.

Strained small rings in gold-catalyzed rapid chemical transformations

Gold-catalyzed reactions, which have been widely explored over the past several years, are powerful tools in organic synthesis to access complex molecular frameworks, and some corresponding excellent reviews have been reported. However, little attention has been paid to summarize the reactions of strained small-ring-containing molecules catalyzed by gold. This critical review mainly puts its emphasis on the recent progress in the field of gold-catalyzed transformations of cyclopropyl-, cyclopropenyl-, epoxy- and aziridinyl-containing molecules. The rapid construction of interesting building blocks in organic synthesis from strained small rings catalyzed by gold has been summarized in this review (106 references).

Ab initio/GIAO-CCSD(T) study of structures, energies, and 13C NMR chemical shifts of C4H7(+) and C5H9(+) ions: relative stability and dynamic aspects of the cyclopropylcarbinyl vs bicyclobutonium ions

The structures and energies of the carbocations C 4H 7 (+) and C 5H 9 (+) were calculated using the ab initio method. The (13)C NMR chemical shifts of the carbocations were calculated using the GIAO-CCSD(T) method. The pisigma-delocalized bisected cyclopropylcarbinyl cation, 1 and nonclassical bicyclobutonium ion, 2 were found to be the minima for C 4H 7 (+) at the MP2/cc-pVTZ level. At the MP4(SDTQ)/cc-pVTZ//MP2/cc-pVTZ + ZPE level the structure 2 is 0.4 kcal/mol more stable than the structure 1. The (13)C NMR chemical shifts of 1 and 2 were calculated by the GIAO-CCSD(T) method. Based on relative energies and (13)C NMR chemical shift calculations, an equilibrium involving the 1 and 2 in superacid solutions is most likely responsible for the experimentally observed (13)C NMR chemical shifts, with the latter as the predominant equilibrating species. The alpha-methylcyclopropylcarbinyl cation, 4, and nonclassical bicyclobutonium ion, 5, were found to be the minima for C 5H 9 (+) at the MP2/cc-pVTZ level. At the MP4(SDTQ)/cc-pVTZ//MP2/cc-pVTZ + ZPE level ion 5 is 5.9 kcal/mol more stable than the structure 4. The calculated (13)C NMR chemical shifts of 5 agree rather well with the experimental values of C 5H 9 (+).

Microfluidic pump powered by self-organizing bacteria

Results are presented that demonstrate the successful use of live bacteria as mechanical actuators in microfabricated fluid systems. The flow deposition of bacteria is used to create a motile bacterial carpet that can generate local fluid motion inside a microfabricated system. By tracking the motion of tracer particles, we demonstrate that the bacterial cells that comprise the carpet self-organize, generating a collective fluid motion that can pump fluid autonomously through a microfabricated channel at speeds as high as 25 microm s(-1). The pumping performance of the system can also be augmented by changing the chemical environment. The addition of glucose to the working buffer raises the metabolic activity of the bacterial carpet, resulting in increased pumping performance. The performance of the bacterial pump is also shown to be strongly influenced by the global geometry of the pump, with narrower channels achieving a higher pumping velocity with a faster rise time.

Statistical evaluation of single nano-object fluorescence

Single nano-objects display strong fluctuations of their fluorescence signals. These random and irreproducible variations must be subject to statistical analysis to provide microscopic information. We review the main evaluation methods used so far by experimentalists in the field of single-molecule spectroscopy: time traces, correlation functions, distributions of "on" and "off" times, higher-order correlations. We compare their advantages and weaknesses from a theoretical point of view, illustrating our main conclusions with simple numerical simulations. We then review experiments on different types of single nano-objects, the phenomena which are observed and the statistical analyses applied to them.

Unsubstituted Bicyclo[1.1.0]but-2-ylcarbinyl Cations

A synthesis for the unsubstituted bicyclo[1.1.0]but-2-ylmethanols (endo- and exo-9) from 1,3-butadiene has been developed. Solvolyses of their sulfonates 10 and 11 took entirely different courses, as the endo compound 10 gave rise exclusively to rearranged products such as cyclopent-3-en-1-ol (14), while the exo compound 11 underwent only the substitution of the tosylate group with complete retention of the exo-bicyclo[1.1.0]but-2-ylmethyl skeleton. Under solvolytic conditions, 10 reacted at very similar rates to the corresponding monocyclic substrate, that is, cyclopropylcarbinyl mesylate (19); in contrast, 11 reacted only three times as fast as n-butyl tosylate and about 1000-fold slower than 10. The nature of the bicyclo[1.1.0]but-2-ylcarbinyl cations has been probed by quantum chemical calculations. Whereas, the exo isomer (exo-18) corresponds to a local energy minimum, the endo isomer is only a transition state [endo-18(TS)] for an automerization of the nonclassical cyclopent-3-en-1-yl cation (13) and converts into 13 by a Wagner-Meerwein rearrangement. The most favorable isomerization of exo-18 also leads to 13 but via a transition state resembling the 2-vinylcycloprop-1-yl cation [25(TS)]. On the introduction of methyl groups at positions 1 and 3 of exo-18, the cation is no longer an energy minimum and it becomes a transition state [27(TS)] for an automerization of the nonclassical 1,3-dimethylcyclopent-3-en-1-yl cation (28). The large effect of the methyl substitution rationalizes the puzzling results of the previous product and rate studies, which utilized various substituted derivatives of bicyclo[1.1.0]but-2-ylcarbinyl sulfonates as substrates.

Single Chromophore Spectroscopy of MEH-PPV: Homing-In on the Elementary Emissive Species in Conjugated Polymers

Low-temperature, single-molecule spectroscopy can provide unparalleled access to the primary emissive species of conjugated polymers. We demonstrate this with the example of one of the most commonly studied polymers, poly(2-methoxy-5-(2'-ethylhexoxy)-1,4-phenylenevinylene), MEH-PPV, which is shown to exhibit sharp fluorescence signatures over one hundred times narrower than the ensemble. These unprecedented narrow emission features can be assigned to single chromophores on the polymer chain, which are selectively addressed by the narrow band excitation. As with organic dye systems, the emission from single chromophores is not static with time, but shows a substantial spectral fluctuation. We find that, for single chromophores, this spectral fluctuation always follows a universal Gaussian statistical distribution. High-resolution spectroscopy provides unique insight into low-energy vibrational modes in the polymer emission, which are generally inaccessible with conventional spectroscopic methods such as site-selective fluorescence or Raman spectroscopy. Interchromophoric coupling can also occur owing to the flexible nature of the polymer backbone. This leads to substantial spectral broadening and a loss of resolution in the vibronic progression. We observe reversible switching within one single molecule between narrow and broad emission, which directly correlates with a discrete switching in emission intensity. We conclude that one and the same single molecule can support aggregated and nonaggregated emission, that is, emission from isolated and aggregated chromophores in one single molecule, rather than the tendency for aggregate emission being intrinsic to the molecule.

CHASE, a charge-assisted sequencing algorithm for automated homology-based protein identifications with matrix-assisted laser desorption/ionization time-of-flight post-source decay fragmentation data

We describe CHASE, a novel algorithm for automated de novo sequencing based on the mass spectrometric (MS) fragmentation analysis of tryptic peptides. This algorithm is used for protein identification from sequence similarity criteria and consists of four steps: (1) derivatization of tryptic peptides at the N-terminus with a negatively charged reagent; (2) post-source decay (PSD) fragmentation analysis of peptides; (3) interpretation of the mass peaks with the CHASE algorithm and reconstruction of the amino acid sequence; (4) transfer of these data to software for protein identifications based on sequence homology (Basic Local Alignment Search Tool, BLAST). This procedure deduced the correct amino acid sequence of tryptic peptide samples and also was able to deduce the correct sequence from difficult mass patterns and identify the amino acid sequence. This allows complete automation of the process starting from MS fragmentation of complex peptide mixtures at low concentration (e.g. from silver-stained gel bands) to identification of the protein. We also show that if PSD data are collected in a single spectrum (instead of the segmented mode offered by conventional matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) instrumentation), the complete workflow from MS-PSD data acquisition to similarity-based identification can be completely automated. This strategy may be applied to proteomic studies for protein identification based on automated de novo sequencing instead of MS or tandem MS patterns. We describe the Charge Assisted Sequencing Engine (CHASE) algorithm, the working protocol, the performance of the algorithm on spectra from MALDI-TOFMS and the data comparison between a TOF and a TOF-TOF instrument.

Deformation of a helical filament by flow and electric or magnetic fields

Motivated by recent advances in the real-time imaging of fluorescent flagellar filaments in living bacteria [Turner, Ryu, and Berg, J. Bacteriol. 82, 2793 (2000)], we compute the deformation of a helical elastic filament due to flow and external magnetic or high-frequency electric fields. Two cases of deformation due to hydrodynamic drag are considered: the compression of a filament rotated by a stationary motor and the extension of a stationary filament due to flow along the helical axis. We use Kirchhoff rod theory for the filament, and work to linear order in the deflection. Hydrodynamic forces are described first by resistive-force theory, and then for comparison by the more accurate slender-body theory. For helices with a short pitch, the deflection in axial flow predicted by slender-body theory is significantly smaller than that computed with resistive-force theory. Therefore, our estimate of the bending stiffness of a flagellar filament is smaller than that of previous workers. In our calculation of the deformation of a polarizable helix in an external field, we show that the problem is equivalent to the classical case of a helix deformed by forces applied only at the ends.

Human breast epithelial stem cells and their regulation

This review summarizes the current evidence for the existence of human breast stem cells and the pathways involved in their regulation, and discusses how the disruption of these pathways may result in the generation of a population of cells with the capacity for unlimited self-renewal. Relevant data from mouse model systems are also discussed where appropriate. By understanding the molecular pathways that regulate self-renewal of normal mammary stem cells, it may be possible to target the activation of these pathways in breast tumours.

Rearrangements Concerted with Fragmentation of Cyclopropylmethoxychlorocarbene and Cyclobutoxychlorocarbene in Hydrocarbon Solvents and Ar Matrices

Fragmentations of cyclopropylmethoxychlorocarbene (6) and cyclobutoxychlorocarbene (10) lead to rearrangments that afford mixtures of cyclopropylmethyl chloride (7), cyclobutyl chloride (8), and 3-butenyl chloride (9). Isotopic substitution studies show that these rearrangments are accompanied by partial exchange of the methylene groups within 6 and 10. Surprisingly, these processes that are typical of carbocations persist in hydrocarbon solvents such as pentane and cyclohexane-d(12). Quantum chemical calculations reveal that the cis-conformers of the incipient oxychlorocarbenes C(4)H(7)OC(..)Cl decay to C(4)H(7)Cl + CO via transient hydrogen bonded C(4)H(7)(delta)(+)...Cl(delta-) complexes which possess significant ion pair character, even in the gas phase or in nonpolar solvents. In contrast to benzyloxychlorocarbene, no free radicals are formed upon generation or photolysis of 6 or 10 in Ar matrixes, although acid chlorides (the recombination products of these radical pairs) are observed. The IR spectra obtained in these experiments show the presence of several conformers of the two C(4)H(7)OC(..)Cl.

Hydrodynamic interactions between rotating helices

Escherichia coli bacteria use rotating helical flagella to swim. At this scale, viscous effects dominate inertia, and there are significant hydrodynamic interactions between nearby helices. These interactions cause the flagella to bundle during the "runs" of bacterial chemotaxis. Here we use slender-body theory to solve for the flow fields generated by rigid helices rotated by stationary motors. We determine how the hydrodynamic forces and torques depend on phase and phase difference, show that rigid helices driven at constant torque do not synchronize, and solve for the flows. We also use symmetry arguments based on kinematic reversibility to show that for two rigid helices rotating with zero phase difference, there is no time-averaged attractive or repulsive force between the helices.