Initial Collision Complex Research Articles

Formation of the Elusive Silylenemethyl Radical (HCSiH2; X2B2) via the Unimolecular Decomposition of Triplet Silaethylene (H2CSiH2; a3A″).

We investigated the formation of small organosilicon molecules─potential precursors to silicon-carbide dust grains ejected by dying carbon-rich asymptotic giant branch stars─in the gas phase via the reaction of atomic carbon (C) in its 3P electronic ground state with silane (SiH4; X1A1) using the crossed molecular beams technique. The reactants collided under single collision conditions at a collision energy of 13.0 ± 0.2 kJ mol-1, leading to the formation of the silylenemethyl radical (HCSiH2; X2B2) via the unimolecular decomposition of triplet silaethylene (H2CSiH2; a3A″). The silaethylene radical was formed via hydrogen migration of the triplet silylmethylene (HCSiH3; X3A″) radical, which in turn was identified as the initial collision complex accessed via the barrierless insertion of atomic carbon into the silicon-hydrogen bond of silane. Our results mark the first observation of the silylenemethyl radical, where previously only its thermodynamically more stable methylsilylidyne (CH3Si; X2A″) and methylenesilyl (CH2SiH; X2A') isomers were observed in low-temperature matrices. Considering the abundance of silane and the availability of atomic carbon in carbon-rich circumstellar environments, our results suggest that future astrochemical models should be updated to include contributions from small saturated organosilicon molecules as potential precursors to pure gaseous silicon-carbides and ultimately to silicon-carbide dust.

Elucidating the Chemical Dynamics of the Elementary Reactions of the 1-Propynyl Radical (CH3CC; X2A1) with Methylacetylene (H3CCCH; X1A1) and Allene (H2CCCH2; X1A1).

The reactions of the 1-propynyl radical (CH3CC; X2A1) with two C3H4 isomers, methylacetylene (H3CCCH; X1A1) and allene (H2CCCH2; X1A1), along with their (partially) deuterated counterparts were explored at collision energies of 37 kJ mol-1, exploiting crossed molecular beams to unravel the chemical reaction dynamics to synthesize distinct C6H6 isomers under single collision conditions. The forward convolution fitting of the laboratory data along with ab initio and statistical calculations revealed that both reactions have no entrance barrier, proceed via indirect (complex-forming) reaction dynamics involving C6H7 intermediates with life times longer than their rotation period(s), and are initiated by the addition of the 1-propynyl radical with its radical center to the π-electron density of the unsaturated hydrocarbon at the terminal carbon atoms of methylacetylene (C1) and allene (C1/C3). In the methylacetylene system, the initial collision complexes undergo unimolecular decomposition via tight exit transition states by atomic hydrogen loss, forming dimethyldiacetylene (CH3CCCCCH3) and 1-propynylallene (H3CCCHCCCH2) in overall exoergic reactions (123 and 98 kJ mol-1) with a branching ratio of 9.4 ± 0.1; the methyl group of the 1-propynyl reactant acts solely as a spectator. On the other hand, in the allene system, our experimental data exhibit the formation of the fulvene (c-C5H4CH2) isomer via a six-step reaction sequence with two higher energy isomers-hexa-1,2-dien-4-yne (H2CCCHCCCH3) and hexa-1,4-diyne (HCCCH2CCCH3)-also predicted to be formed based on our statistical calculations. The pathway to fulvene advocates that, in the allene-1-propynyl system, the methyl group of the 1-propynyl reactant is actively engaged in the reaction mechanism to form fulvene. Because both reactions are barrierless and exoergic and all transition states are located below the energy of the separated reactants, the hydrogen-deficient C6H6 isomers identified in our investigation are predicted to be synthesized in low-temperature environments, such as in hydrocarbon-rich atmospheres of planets and their moons such as Titan along with cold molecular clouds such as Taurus Molecular Cloud-1.

Are Nonadiabatic Reaction Dynamics the Key to Novel Organosilicon Molecules? The Silicon (Si(3P))-Dimethylacetylene (C4H6(X1A1g)) System as a Case Study.

The bimolecular gas phase reaction of ground-state silicon (Si; 3P) with dimethylacetylene (C4H6; X1A1g) was investigated under single collision conditions in a crossed molecular beams machine. Merged with electronic structure calculations, the data propose nonadiabatic reaction dynamics leading to the formation of singlet SiC4H4 isomer(s) and molecular hydrogen (H2) via indirect scattering dynamics along with intersystem crossing (ISC) from the triplet to the singlet surface. The reaction may lead to distinct energetically accessible singlet SiC4H4 isomers (1p8-1p24) in overall exoergic reaction(s) (-107-20+12 kJ mol-1). All feasible reaction products are either cyclic, carry carbene analogous silylene moieties, or carry C-Si-H or C-Si-C bonds that would require extensive isomerization from the initial collision complex(es) to the fragmenting singlet intermediate(s). The present study demonstrates the first successful crossed beams study of an exoergic reaction channel arising from bimolecular collisions of silicon, Si(3P), with a hydrocarbon molecule.

Combined Experimental and Computational Investigation of the Elementary Reaction of Ground State Atomic Carbon (C; 3P j) with Pyridine (C5H5N; X1A1) via Ring Expansion and Ring Degradation Pathways.

We explored the elementary reaction of atomic carbon (C; 3P j) with pyridine (C5H5N; X1A1) at a collision energy of 34 ± 4 kJ mol-1 utilizing the crossed molecular beams technique. Forward-convolution fitting of the data was combined with high-level electronic structure calculations and statistical (RRKM) calculations on the triplet C6H5N potential energy surface (PES). These investigations reveal that the reaction dynamics are indirect and dominated by large range reactive impact parameters leading via barrier-less addition to the nitrogen atom and to two chemically nonequivalent "aromatic" carbon-carbon bonds forming three distinct collision complexes. At least two reaction pathways through atomic hydrogen loss were identified on the triplet surface. These channels involve multiple isomerization steps of the initial collision complexes via ring-opening and ring expansion forming an acyclic 1-ethynyl-3-isocyanoallyl radical (P1; 2A″) and a hitherto unreported seven-membered 1-aza-2-dehydrocyclohepta-2,4,6-trien-4-yl radical isomer (P3; 2A), respectively. For RRKM calculations at zero collision energy, representing conditions in cold molecular clouds, the ring expansion product P3 is formed nearly exclusively for the atomic hydrogen loss channel, but based on these computations, the molecular fragmentation channel forming acetylene (C2H2) plus 3-cyano-2-propen-1-ylidene (P6; 3A″) accounts for nearly all of the degradation products of the reaction of atomic carbon with pyridine, proposing a destruction pathway of interstellar pyridine, which may account for the absence in the detection of pyridine in the interstellar medium. These results are also discussed in light of the isoelectronic carbon-benzene (C6H6; X1A1) system with important implications to the rapid degradation of nitrogen-bearing polycyclic aromatic hydrocarbons (NPAHs) in the interstellar medium compared to mass growth processes of PAH counterparts through ring expansion.

Theoretical study on reaction mechanism of ground-state cyano radical with 1,3-butadiene: prospect of pyridine formation.

The reaction of ground-state cyano radicals, CN(X(2)Σ(+)), with the simplest polyene, 1,3-butadiene (C4H6(X(1)Ag)), is investigated to explore probable routes and feasibility to form pyridine at ultralow temperatures. The isomerization and dissociation channels for each of the seven initial collision complexes are characterized by utilizing the unrestricted B3LYP/cc-pVTZ and the CCSD(T)/cc-pVTZ calculations. With facilitation of RRKM rate constants, through ab initio paths composed of 7 collision complexes, 331 intermediates, 62 hydrogen atom, 71 hydrogen molecule, and 3 hydrogen cyanide dissociated products, the most probable paths at collision energies up to 10 kcal/mol, and thus the reaction mechanism, are determined. Subsequently, the corresponding rate equations are solved that the concentration evolutions of collision complexes, intermediates, and products versus time are obtained. As a result, the final products and yields are determined. The low-energy routes for the formation of most thermodynamically stable product, pyridine, are identified. This study, however, predicts that seven collision complexes would produce predominately 1-cyano-1,3-butadiene, CH2CHCHCHCN (p2) plus atomic hydrogen via the collision complex c1(CH2CHCHCH2CN) and intermediate i2(CH2CHCH2CHCN), with a very minor amount of pyridine. Our scheme also effectively excludes the presence of 2-cyano-1,3-butadiene, which has energy near-degenerate to 1-cyano-1,3-butadiene, as supported by experimental findings.

Crossed Beam Reactions of the Phenyl (C6H5; X2A1) and Phenyl-d5 Radical (C6D5; X2A1) with 1,2-Butadiene (H2CCCHCH3; X1A′)

We explored the reactions on the phenyl (C6H5; X(2)A1) and phenyl-d5 (C6D5; X(2)A1) radical with 1,2-butadiene (C4H6; X(1)A') at a collision energy of about 52 ± 3 kJ mol(-1) in a crossed molecular beam apparatus. The reaction of phenyl with 1,2-butadiene is initiated by adding the phenyl radical with its radical center to the π electron density at the C1/C3 carbon atom of 1,2-butadiene. Later, the initial collision complexes isomerize via phenyl group migration from the C1/C3 carbon atoms to the C2 carbon atom of the allene moiety of 1,2-butadiene. The resulting intermediate undergoes unimolecular decomposition through hydrogen atom emission from the methyl group of the 1,2-butadiene moiety via a rather loose exit transition state leading to 2-phenyl-1,3-butadiene in an overall exoergic reaction (ΔRG = -72 ± 10 kJ mol(-1)). This finding reveals the strong collision-energy dependence of this system when the data are compared with those of the phenyl radical with 1,2-butadiene previously recorded at collision energies up to 160 kJ mol(-1), with the previous study exhibiting the thermodynamically less stable 1-phenyl-3-methylallene (ΔRG = -33 ± 10 kJ mol(-1)) and 1-phenyl-2-butyne (ΔRG = -24 ± 10 kJ mol(-1)) to be the dominant products.

Directed gas-phase formation of the ethynylsulfidoboron molecule.

As a member of the organo sulfidoboron (RBS) family, the hitherto elusive ethynylsulfidoboron molecule (HCCBS) has been formed via the bimolecular reaction of the boron monosulfide radical (BS) with acetylene (C2H2) under single collision conditions in the gas phase, exploiting the crossed molecular beams technique. The reaction mechanism follows indirect dynamics via a barrierless addition of the boron monosulfide radical with its boron atom to the carbon atom of the acetylene molecule, leading to the trans-HCCHBS intermediate. As predicted by ab initio electronic structure calculations, the initial collision complex either isomerizes to its cis-form or undergoes a hydrogen atom migration to form H2CCBS. The cis-HCCHBS intermediate either isomerizes via hydrogen atom shift from the carbon to the boron atom, leading to the HCCBHS isomer, or decomposes to ethynylsulfidoboron (HCCBS). Both H2CCBS and HCCBHS intermediates were predicted to fragment to ethynylsulfidoboron via atomic hydrogen losses. Statistical (RRKM) calculations report yields to form the ethynylsulfidoboron molecule from cis-HCCHBS, H2CCBS, and HCCBHS to be 21%, 7%, and 72%, respectively, under current experimental conditions. Our findings open up an unconventional path to access the previously obscure class of organo sulfidoboron molecules, which are difficult to access through "classical" formation.

Computational study on mechanism of hydrogen abstraction and selenium insertion in the reaction of triplet and singlet selenium atom with hydrogen selenide

The reaction pathways of selenium vapor (Se) with hydrogen selenide (H 2Se) have been investigated theoretically on the triplet and singlet potential energy surfaces. All species for title reaction have been optimized at the UMP2(FC)/6-311++G(d, p) computational level. The energetic data have been obtained at the UCCSD(T)//UMP2 level employing the cc-pV5Z basis set. Three initial collision complexes, 3IN1 (Se–SeH 2), 3IN2 (Se–HSeH) and 1IN1 (Se–SeH 2) have been considered for the Se-atom with H 2Se reaction on the triplet and singlet potential energy surfaces. Four kinds products HSeSeH, HSe + HSe, H + HSe 2 and Se 2 + H 2 are obtained through variety of transformations of initial reactants and complexes. Calculations reveal that there exist two intersystem crossings between the triplet and singlet potential energy surfaces. Also, the investigation of Se + H 2Se reaction paths shows that reaction initiates on the triplet potential energy surface and continues on both triplet and singlet (through intersystem crossing) potential energy surfaces to form the main product of HSeSeH.

Untangling the Chemical Dynamics of the Reaction of Boron Atoms, 11B(2Pj), with Diacetylene, C4H2(X1Σg+) — A Crossed Molecular Beams and Ab Initio Study

A crossed molecular beams experiment with ground state boron atoms, B((2)P(j)), and diacetylene, C(4)H(2)(X(1)Σ(g)(+)), was conducted at a collision energy of 21.1 ± 0.3 kJ mol(-1) under single collision conditions and combined with electronic structure calculations on the (11)BC(4)H(2) potential energy surface. Our combined experimental and computational studies indicate that the reaction proceeds without entrance barrier and involves indirect scattering dynamics. Three initial collision complexes, in which the boron atom adds to one or two carbon atoms, were characterized computationally. These intermediates rearranged via hydrogen shifts and/or successive ring-opening/ring closure processes on the doublet surface ultimately yielding a cyclic, C(s) symmetric (11)BC(4)H(2) intermediate. The latter was found to decompose via atomic hydrogen loss to yield a cyclic (11)BC(4)H(X(1)A') isomer; to a minor amount, the cyclic intermediate isomerized via ring-opening to the linear HCCBCCH(X(2)Σ(g)(+)) molecule, which in turn emitted a hydrogen atom to yield the linear HCCBCC(X(1)Σ(+)) molecule. The overall reactions to form these isomers were found to be exoergic by 55 and 61 J mol(-1), respectively, and involved rather loose exit transition states. On the basis of the energetics, upper limits of two energetically less stable species, the linear HBCCCC(X(1)Σ(+)) and BCCCCH(X(1)Σ(+)) species, were derived to be 12 and 2.2%, respectively. The dynamics of this reaction are also compared with the reaction of ground state boron atoms with acetylene studied earlier in our group.

ChemInform Abstract: Gas-Phase Association Reactions of Fullerene Cations: Modelling the Influence of Charge State and Other Molecular Parameters on Association Efficiency.

The efficiency of association reactions of fullerene cations observed in helium at pressures of 0.35–0.4 Torr sustained in a Selected-Ion Flow Tube (SIFT) at room temperature has been examined with a view to the influence of the charge state and the size of the fullerene ion and the size, structure, and degree of unsaturation of the neutral. The association efficiency is found to be strongly dependent on these molecular parameters. The calculated lifetime of the intermediate collision complex provides insight into the well depth associated with the formation of this complex and the effectiveness of vibrational and (or) rotational degrees of freedom of the reactants in the dispersal of the energy of complex formation. The results are considered in terms of single-well and double-well models for the potential energy surface leading to association and are best accommodated by the double-well model involving the formation of an initial electrostatic collision complex that must overcome a barrier to proceed to...

Crossed Molecular Beam Study on the Formation of Phenylacetylene and Its Relevance to Titan’s Atmosphere

The crossed molecular beam experiment of the deuterated ethynyl radical (C(2)D; X(2)Sigma(+)) with benzene [C(6)H(6)(X(1)A(1g))] and its fully deuterated analog [C(6)D(6)(X(1)A(1g))] was conducted at a collision energy of 58.1 kJ mol(-1). Our experimental data suggest the formation of the phenylacetylene-d(6) via indirect reactive scattering dynamics through a long-lived reaction intermediate; the reaction is initiated by a barrierless addition of the ethynyl-d(1) radical to benzene-d(6). This initial collision complex was found to decompose via a tight exit transition state located about 42 kJ mol(-1) above the separated products; here, the deuterium atom is ejected almost perpendicularly to the rotational plane of the decomposing intermediate and almost parallel to the total angular momentum vector. The overall experimental exoergicity of the reaction is shown to be 121 +/- 10 kJ mol(-1); this compares nicely with the computed reaction energy of -111 kJ mol(-1). Even though the experiment was conducted at a collisional energy higher than equivalent temperatures typically found in the atmosphere of Titan (94 K and higher), the reaction may proceed in Titan's atmosphere as it involves no entrance barrier, all transition states involved are below the energy of the separated reactants, and the reaction is exoergic. Further, the phenylacetylene was found to be the sole reaction product.

Asymmetric Amino Acid Activation by Class II Histidyl-tRNA Synthetase from Escherichia coli

Aminoacyl-tRNA synthetases (ARSs) join amino acids to their cognate tRNAs to initiate protein synthesis. Class II ARS possess a unique catalytic domain fold, possess active site signature sequences, and are dimers or tetramers. The dimeric class I enzymes, notably TyrRS, exhibit half-of-sites reactivity, but its mechanistic basis is unclear. In class II histidyl-tRNA synthetase (HisRS), amino acid activation occurs at different rates in the two active sites when tRNA is absent, but half-of-sites reactivity has not been observed. To investigate the mechanistic basis of the asymmetry, and explore the relationship between adenylate formation and conformational events in HisRS, a fluorescently labeled version of the enzyme was developed by conjugating 7-diethylamino-3-((((2-maleimidyl)ethyl)amino)carbonyl)coumarin (MDCC) to a cysteine introduced at residue 212, located in the insertion domain. The binding of the substrates histidine, ATP, and 5'-O-[N-(l-histidyl)sulfamoyl]adenosine to MDCC-HisRS produced fluorescence quenches on the order of 6-15%, allowing equilibrium dissociation constants to be measured. The rates of adenylate formation measured by rapid quench and domain closure as measured by stopped-flow fluorescence were similar and asymmetric with respect to the two active sites of the dimer, indicating that conformational change may be rate-limiting for product formation. Fluorescence resonance energy transfer experiments employing differential labeling of the two monomers in the dimer suggested that rigid body rotation of the insertion domain accompanies adenylate formation. The results support an alternating site model for catalysis in HisRS that may prove to be common to other class II aminoacyl-tRNA synthetases.

Inhibition and Binding Kinetics of the Hepatitis C Virus NS3 Protease Inhibitor ITMN-191 Reveals Tight Binding and Slow Dissociative Behavior

The protease activity of hepatitis C virus nonstructural protein 3 (NS3) is essential for viral replication. ITMN-191, a macrocyclic inhibitor of the NS3 protease active site, promotes rapid, multilog viral load reductions in chronic HCV patients. Here, ITMN-191 is shown to be a potent inhibitor of NS3 with a two-step binding mechanism. Progress curves are consistent with the formation of an initial collision complex (EI) that isomerizes to a highly stable complex (EI*) from which ITMN-191 dissociates very slowly. K(i), the dissociation constant of EI, is 100 nM, and the rate constant for conversion of EI to EI* is 6.2 x 10(-2) s(-1). Binding experiments using protein fluorescence confirm this isomerization rate. From progress curve analysis, the rate constant for dissociation of ITMN-191 from the EI* complex is 3.8 x 10(-5) s(-1) with a calculated complex half-life of approximately 5 h and a true biochemical potency (K(i)*) of approximately 62 pM. Surface plasmon resonance studies and assessment of enzyme reactivation following dilution of the EI* complex confirm slow dissociation and suggest that the half-life may be considerably longer. Abrogation of the tight binding and slow dissociative properties of ITMN-191 is observed with proteases that carry the R155K or D168A substitution, each of which is likely in drug resistant mutants. Slow dissociation is not observed with closely related macrocyclic inhibitors of NS3, suggesting that members of this class may display distinct binding kinetics.

Formation of the 1,3,5-Hexatriynyl Radical (C6H(X2Π)) via the Crossed Beams Reaction of Dicarbon (C2(X1Σg+/a3Πu)), with Diacetylene (C4H2(X1Σg+))

Crossed molecular beams experiments were conducted to investigate the chemical dynamics of the reaction of dicarbon molecules, C(2)(X(1)Sigma(g)(+)/a(3)Pi(u)), with diacetylene, C(4)H(2)(X(1)Sigma(g)(+)) at two collision energies of 12.1 and 32.8 kJ mol(-1). The dynamics were found to be indirect, involved C(6)H(2) intermediates, and were dictated by an initial addition of the dicarbon molecule to the carbon-carbon triple bond of diacetylene. The initial collision complexes could isomerize. On the singlet surface, the resulting linear triacetylene molecule (C(6)H(2)(X(1)Sigma(g)(+))) decomposed without an exit barrier to form the linear 1,3,5-hexatriynyl radical (C(6)H(X(2)Pi)). On the triplet surface, the dynamics suggested at least a tight exit transition state involved in the fragmentation of a triplet C(6)H(2) intermediate to yield the 1,3,5-hexatriynyl radical (C(6)H(X(2)Pi)) plus atomic hydrogen. On the basis of the experimental data, we recommend an experimentally determined enthalpy of formation of the 1,3,5-hexatriynyl radical of 1014 +/- 27 kJ mol(-1) at 0 K. Our experimental results and the derived reaction mechanisms gain full support from electronic structure calculations on the singlet and triplet C(6)H(2) potential-energy surfaces. The identification of the 1,3,5-hexatriynyl radical under single collision conditions implies that the neutral-neutral reaction of dicarbon with diacetylene can lead to the formation of 1,3,5-hexatriynyl radicals in the interstellar medium and possibly in the hydrocarbon-rich atmospheres of planets and their moons such as Saturn's satellite Titan.

Role of Induced Fit in Enzyme Specificity: A Molecular Forward/Reverse Switch

Enzyme structures solved with and without bound substrate often show that substrate-induced conformational changes bring catalytic residues into alignment, alter the local environment, and position the substrate for catalysis. Although the structural data are compelling, the role of conformational changes in enzyme specificity has been controversial in that specificity is a kinetic property that is not easy to predict based upon structure alone. Recent studies on DNA polymerization have illuminated the role of substrate-induced conformational changes in enzyme specificity by showing that the rate at which the enzyme opens to release the bound substrate is a key kinetic parameter. The slow release of a correct substrate commits it to the forward reaction so that specificity is determined solely by the rate of substrate binding, including the isomerization step, and not by the slower rate of the chemical reaction. In contrast, fast dissociation of an incorrect substrate favors release rather than reaction. Thus, the conformational change acts as a molecular switch to select the right substrate and to recognize and disfavor the reaction of an incorrect substrate. A conformational switch may also favor release rather than reverse reaction of the product.

Reaction Dynamics of Phenyl Radicals (C6H5) with Propylene (CH3CHCH2) and Its Deuterated Isotopologues

The reactions between phenyl radicals (C6H5) and propylene (CH3CHCH2) together with its D6- and two D3-isotopologues were studied under single collision conditions using the crossed molecular beams technique. The chemical dynamics inferred from the center-of-mass translational and angular distributions suggests that the reactions are indirect and initiated by an addition of the phenyl radical to the alpha-carbon atom (C1 carbon atom) of the propylene molecule at the =CH2 unit to form a radical intermediate (CH3CHCH2C6H5) on the doublet surface. Investigations with D6-propylene specified that only a deuterium atom was emitted; the phenyl group was found to stay intact. Studies with 1,1,2-D3- and 3,3,3-D3-propylene indicated that the initial collision complexes CH3CDCD2C6H5 (from 1,1,2-D3-propylene) and CD3CHCH2C6H5 (from 3,3,3-D3-propylene) eject both a hydrogen atom via rather loose exit transition states to form the D3-isotopomers of cis/trans-1-phenylpropene (CH3CHCHC6H5) (80-90%) and 3-phenylpropene (H2CCHCH2C6H5) (10-20%), respectively. Implications of these findings for the formation of polycyclic aromatic hydrocarbons (PAHs) and their precursors in combustion flames are discussed.

Variegin, a Novel Fast and Tight Binding Thrombin Inhibitor from the Tropical Bont Tick

Tick saliva contains potent antihemostatic molecules that help ticks obtain their enormous blood meal during prolonged feeding. We isolated thrombin inhibitors present in the salivary gland extract from partially fed female Amblyomma variegatum, the tropical bont tick, and characterized the most potent, variegin, one of the smallest (32 residues) thrombin inhibitors found in nature. Full-length variegin and two truncated variants were chemically synthesized. Despite its small size and flexible structure, variegin binds thrombin with strong affinity (K(i) approximately 10.4 pM) and high specificity. Results using the truncated variants indicated that the seven residues at the N terminus affected the binding kinetics; when removed, the binding characteristics changed from fast to slow. Further, the thrombin active site binding moiety of variegin is in the region of residues 8-14, and the exosite-I binding moiety is within residues 15-32. Our results show that variegin is structurally and functionally similar to the rationally designed thrombin inhibitor, hirulog. However, compared with hirulog, variegin is a more potent inhibitor, and its inhibitory activity is largely retained after cleavage by thrombin.

How myosin VI coordinates its heads during processive movement

A processive molecular motor must coordinate the enzymatic state of its two catalytic domains in order to prevent premature detachment from its track. For myosin V, internal strain produced when both heads of are attached to an actin track prevents completion of the lever arm swing of the lead head and blocks ADP release. However, this mechanism cannot work for myosin VI, since its lever arm positions are reversed. Here, we demonstrate that myosin VI gating is achieved instead by blocking ATP binding to the lead head once it has released its ADP. The structural basis for this unique gating mechanism involves an insert near the nucleotide binding pocket that is found only in class VI myosin. Reverse strain greatly favors binding of ADP to the lead head, which makes it possible for myosin VI to function as a processive transporter as well as an actin-based anchor. While this mechanism is unlike that of any other myosin superfamily member, it bears remarkable similarities to that of another processive motor from a different superfamily--kinesin I.

Unimolecular Decomposition of Chemically Activated Pentatetraene (H2CCCCCH2) Intermediates: A Crossed Beams Study of Dicarbon Molecule Reactions with Allene

The reactions dynamics of the dicarbon molecule C2 in the 1Sigma (g)+ singlet ground state and 3Pi(u) first excited triplet state with allene, H2CCCH2(X1A1), was investigated under single collision conditions using the crossed molecular beam approach at four collision energies between 13.6 and 49.4 kJ mol(-1). The experiments were combined with ab initio electronic structure calculations of the relevant stationary points on the singlet and triplet potential energy surfaces. Our investigations imply that the reactions are barrier-less and indirect on both the singlet and the triplet surfaces and proceed through bound C5H4 intermediates via addition of the dicarbon molecule to the carbon-carbon double bond (singlet surface) and to the terminal as well as central carbon atoms of the allene molecule (triplet surface). The initial collision complexes isomerize to form triplet and singlet pentatetraene intermediates (H2CCCCCH2) that decompose via atomic hydrogen loss to yield the 2,4-pentadiynyl-1 radical, HCCCCCH2(X2B1). These channels result in symmetric center-of-mass angular distributions. On the triplet surface, a second channel involves the existence of a nonsymmetric reaction intermediate (HCCCH2CCH) that fragments through atomic hydrogen emission to the 1,4-pentadiynyl-3 radical [C5H3(X2B1)HCCCHCCH]; this pathway was found to account for the backward scattered center-of-mass angular distributions at higher collision energies. The identification of two resonance-stabilized free C5H3 radicals (i.e., 2,4-pentadiynyl-1 and 1,4-pentadiynyl-3) suggests that these molecules can be important transient species in combustion flames and in the chemical evolution of the interstellar medium.

A combined crossed-beam, ab initio, and Rice–Ramsperger–Kassel– Marcus investigation of the reaction of carbon atoms C(3Pj) with benzene, C6H6(X 1A1g) and d6-benzene, C6D6(X 1A1g)

The reactions of atomic carbon, C(3Pj), with benzene, C6H6(X 1A1g), and with d6-benzene, C6D6(X 1A1g) were investigated at twelve collision energies between 8.8 and 52.5 kJ mol−1 using the crossed molecular beams technique. Forward-convolution fitting of the data, high-level electronic structure calculations, and Rice–Ramsperger–Kassel–Marcus (RRKM) investigations on the singlet and triplet C7H6/C7D6 potential energy hyperface suggest that at low collision energies the chemical reaction dynamics are indirect and dominated by large impact parameters. As the collision energy increases, smaller impact parameters become more important, and the chemical dynamics is increasingly direct. At all collision energies, the reaction proceeds on the triplet surface via a barrierless addition of the carbon atom to form a bicyclic intermediate followed by ring opening of the initial collision complex to a seven-membered ring intermediate (cycloheptatrienylidene). The latter decomposes without exit barrier to the thermodynamically less stable 1,2-didehydrocycloheptatrienyl radical, C7H5(X 2B1)+H, and its deuterated C7D5(X 2B1)+D counterpart. The formation of a C7D6 adduct is observed as a second channel. The barrierless route for the destruction of benzene can help to model important pathways for the synthesis of higher polycyclic aromatic hydrocarbon derivatives in the interstellar medium, in outflows of dying carbon stars, in hydrocarbon-rich planetary atmospheres, as well as in oxygen-poor combustion flames.