Bimolecular Collisions Research Articles

Viscosity of Near-Boiling NonAssociated Liquids: Dependence on Surface Tension, Molecular Mass and IntraMolecular Conformational Transitions

The equation proposed for near-boiling nonassociated liquids describes a new functional dependence of their viscosity on such physico-chemical characteristics as surface tension and molecular mass. It is shown that the viscosity of liquids with conformationally flexible molecules can be calculated adequately by taking into account the influence of intramolecular conformational transitions on the number of bimolecular collisions in the liquid phase.

Multistep binding of transition metals to the H-N-H endonuclease toxin colicin E9.

We report the first stopped-flow fluorescence analysis of transition metal binding (Co(2+), Ni(2+), Cu(2+), and Zn(2+)) to the H-N-H endonuclease motif within colicin E9 (the E9 DNase). The H-N-H consensus forms the active site core of a number of endonuclease groups but is also structurally homologous to the so-called treble-clef motif, a ubiquitous zinc-binding motif found in a wide variety of metalloproteins. We find that all the transition metal ions tested bind via multistep mechanisms. Binding was further dissected for Ni(2+) and Zn(2+) ions through the use of E9 DNase single tryptophan mutants, which demonstrated that most steps reflect conformational rearrangements that occur after the bimolecular collision, many common to the two metals, while one appears specific to zinc. The kinetically derived equilibrium dissociation constants (K(d)) for transition metal binding to the E9 DNase agree with previously determined equilibrium measurements and so confirm the validity of the derived kinetic mechanisms. Zn(2+) binds tightest to the enzyme (K(d) approximately 10(-)(9) M) but does not support endonuclease activity, whereas the other metals (K(d) approximately 10(-)(6) M) are active in endonuclease assays implying that the additional step seen for Zn(2+) traps the enzyme in an inactive but high affinity state. Metal-induced conformational changes are likely to be a conserved feature of H-N-H/treble clef motif proteins since similar Zn(2+)-induced, multistep binding was observed for other colicin DNases. Moreover, they appear to be independent both of the conformational heterogeneity that is naturally present within the E9 DNase at equilibrium, as well as the conformational changes that accompany the binding of its cognate inhibitor protein Im9.

Diagnosing ozone loss in the extratropical lower stratosphere

Chemical ozone loss in the Southern Hemisphere lower stratosphere during winter and spring 1996 is investigated using a three‐dimensional chemical transport model. Model diagnostic quantities are developed to determine the underlying chemical mechanisms controlling the distribution of ozone. These diagnostic tracers quantify the ozone change due to individual catalytic cycles or reaction mechanisms that form or destroy ozone. Results from these tracers confirm the importance of halogens not only in the development of the ozone hole but also in midlatitude ozone depletion of which almost 50% is due to cycles involving halogens. The dominant chemical ozone loss mechanism in the middle latitudes is due to the cycle whose rate determining step involves the bimolecular collision between HO2 and O3. Observational evidence from ozonesonde measurements shows substantial ozone depletion in the polar subvortex region (altitudes below ∼14 km). These measurements also indicate that this ozone depletion must be due, at least in part, to in situ chemical ozone loss. Model results show that over a quarter of the ozone depletion associated with the ozone hole resides at subvortex altitudes. Diagnostic tracers designed to quantify ozone loss occurring above and below the subvortex transition altitude show that the majority of this ozone depletion is in situ ozone loss. Furthermore, at altitudes below the subvortex transition, polar ozone loss is efficiently transported to middle latitudes, where it contributes to midlatitude ozone decline.

The reactivity of ground-state carbon atoms with unsaturated hydrocarbons in combustion flames and in the interstellar medium

This article reviews recent crossed-beams and ab-initio studies of reactions of ground-state carbon atoms C(3P j ) with unsaturated hydrocarbons and their radicals. All reactions have no entrance barrier and are initiated via an addition of the carbon atom to the ~ system. With the exception of the carbon atom reaction with acetylene, which also shows a significant fraction of molecular hydrogen loss, these bimolecular collisions are dominated by an atomic carbon versus hydrogen atom exchange mechanism. In some systems, homolytic cleavages of carbon-carbon bonds present additional decomposition routes of typically a few per cent at the most. The impact-parameter-dependent chemical dynamics are interpreted in terms of statistical and non-statistical decomposition of reaction intermediates involved. The polyatomic reaction products are highly hydrogend-eficient resonance-stabilized free radicals. The latter are strongly suggested as suitable precursors to form the first (substituted) aromatic ring molecule, polycyclic aromatic hydrocarbon-like species and carbonaceous nanoparticles in combustion processes, chemical vapour deposition and the outflows of carbon stars.

Influence of Intra-Molecular Conformational Transitions and some Physico-Chemical Quantities of Liquids on their Thermal Conductivity

It is shown that the thermal conductivity of various liquids can be described adequately by taking into account the influence of intra-molecular conformational transitions on the number of bimolecular collisions in the liquid phase. The proposed equations allow the calculation of this transport property at different temperatures.

Direct measurement of the preferred sense of NO rotation after collision with argon.

The preferred sense of product molecule rotation (clockwise or counterclockwise) in a bimolecular collision system has been measured. Rotationally inelastic collisions of nitric oxide (NO) molecules with Ar atoms were studied by combining crossed molecular beams, circularly polarized resonant multiphoton ionization probing, and velocity-mapped ion imaging detection. The observed sense of NO product rotation varies with deflection angle and is a strong function of the NO final rotational state. The largest preferences for sense of rotation are observed at the highest kinematically allowed product rotational states; for lower rotational states, the variation with deflection angle becomes oscillatory. Quantum calculations on the most recently reported NO-Ar potential give good agreement with the observed oscillation patterns in the sense of rotation.

Dependence of Collision Lifetimes on Translational Energy

Clusters and collision complexes are stabilized by three-body collisions that are two-step bimolecular collisions A + B → AB* and AB* + M → AB + M, where M is a bath molecule that removes the excess energy from AB. The lifetime of AB* determines the probability of a third-body collision; therefore, we have calculated binary collision lifetimes as a function of translational energy and temperature by quasiclassical trajectory calculations and compared the results with the analytical expressions of Bunker (J. Chem. Phys. 1960, 32, 1001). We find that the analytical expressions, which were developed for centrosymmetric potentials, are in poor agreement with the trajectory results of benzene/Ar for low values and in good agreement for high values of translational energies and temperatures.

Pulse saturation recovery, pulse ELDOR, and free induction decay electron paramagnetic resonance detection using time-locked subsampling

Time locked subsampling (TLSS) in electron paramagnetic resonance (EPR) involves the steps of (i) translation of the signal from a microwave carrier to an intermediate frequency (IF) carrier where the (IF) offset between the signal oscillator and local oscillator frequencies is synthesized, (ii) sampling the IF carrier four times in an odd number of cycles, say 4 in 3, where the analog-to-digital (A/D) converter is driven by a frequency synthesizer that has the same clock input as the IF synthesizer, (iii) signal averaging as required for adequate signal to noise, (iv) separating the even and odd digitized words into two separate signal channels, which correspond to signals in phase and in quadrature with respect to the IF carrier, i.e., I and Q, and (v) detecting the envelope of I and also of Q by changing the signs of alternate words in each of the two channels. TLSS detection has been demonstrated in three forms of pulse EPR spectroscopy at X band: saturation recovery, pulse electron–electron double resonance, and free induction decay. The IF was 187.5 MHz, the A/D converter frequency was 250 MHz, the overall bandwidth was 125 MHz, and the bandwidths for the separate I and Q channels were each 62.5 MHz. Experiments were conducted on nitroxide radical spin labels. The work was directed towards development of methodology to monitor bimolecular collisions of oxygen with spin labels in a context of site-directed spin labeling.

1,3 Dichloro- and 1,3 dibromotetra- n-butyldistannoxane mixtures: ligand redistribution and fluxional dynamics in distannoxanes

The halogen redistribution reaction in the binary [ n Bu 2SnCl] 2O/[ n Bu 2SnBr] 2O system is examined by 119Sn- and 13C-NMR spectroscopy. Binary mixtures of [ n Bu 2SnCl] 2O and [ n Bu 2SnBr] 2O reach equilibrium rapidly at room temperature. The reactant dimers are found to be in equilibrium with all five possible mixed distannoxane dimers in the equimolar mixture. These mixed distannoxane dimers differ in the ratio of Cl and Br as well as the relative positioning of the halogens. The mechanism responsible for the rapid formation of the mixed Cl:Br distannoxane dimers is found to proceed via bimolecular collisions producing a four-centered transition state, which in turn undergoes a concerted exchange of the halogens. The equilibrium concentrations of the reactant and product dimers are well represented by a statistical distribution, indicating that Cl and Br exhibit equivalent donor abilities. At 298 K, the NMR spectral data are consistent with time-averaged structures arising from rapidly interconverting rigid ladder pairs. Lowering the temperature to 173 K failed to freeze out this fluxional process. A reversible configurational rearrangement is also observed in which rotation about the oxygenexocyclic tin bond results in the mutual exchange of halogens associated with the same exocyclic tin atom.

Spatial Energetics of Protonated LiH: Lower-Lying Potential Energy Surfaces from Valence Bond Calculations

The detailed features of the interaction forces within the LiH2+ triatomic system are calculated using the spin-coupled valence bond (SCVB) method in terms of the three Jacobi coordinates of the LiH(LiH+) and H+/H fragments within a broad range of relative orientations and of internuclear distances. The specific features of the systems and of their asymptotic molecular fragments are examined with the view of estimating from them the collisional probabilities for producing rovibrationally excited partners with detectable radiative behavior. The possibility of having a charge-transfer process within the two electronic states of the LiH2+ ion is also analyzed and discussed. The calculations suggest, albeit still qualitatively, that a direct charge-transfer reaction between LiH + H+ into LiH+ + H is unlikely to take place during bimolecular collisions in a low-density medium.

Optimized Imploding Waves in the Coherent Control of Bimolecular Processes: Atom−Rotor Scattering

Considerable work, over the past three decades, has gone into the study of atom-molecule inelastic collisions, including the development of extensive formalism and the calculation of cross sections for rotational, vibrational, and electronic excitations. All of these studies are designed to analyze the natural outcome of the inelastic scattering of atoms and molecules. By contrast, current interest lies in the ability to control the outcome of atomic and molecular processes. In particular, modern efforts in coherent control1-12 have aimed at using lasers to introduce controllable quantum interference terms into the cross sections of atomic and molecular processes. As a consequence, varying specific laser parameters induce changes in these quantum interference terms which, in turn, significantly alter the natural yields and cross sections. Both detailed1 and elementary2 reviews of this coherent control approach are available. Examining the coherent-control literature shows that the vast majority of controlled processes previously considered are unimolecular in nature, e.g., the photodissociation or photoionization of isolated molecules. Only recently have we shown3-6 that the essential principle of coherent control can be used effectively to alter cross sections for scattering processes. That is, we demonstrated that if one collides two molecules in a superposition of energetically degenerate scattering states, then the resultant scattering cross section contains controllable interference terms. For a general bimolecular collision of the type

The concept of coherent resonances in the nuclear motion of bimolecular collisions: femtosecond probing and the classical picture

In this Letter, we report studies of coherent resonances in the course of a single bimolecular collision on the femtosecond timescale. A classical picture is presented with molecular dynamics simulations. The observed persistence of coherence elucidates the origin of the very limited spreading of the wavepacket and the crucial role of selective probing of a limited range of impact parameters. The study of this three-body system (iodine and argon) at room temperature is important for the mechanism of resonances and caging with implications for the condensed phase.

The cleavage step of ribonuclease P catalysis is determined by ribozyme-substrate interactions both distal and proximal to the cleavage site.

The cleavage step of bacterial RNase P catalysis involves concentration-independent processes after the formation of the ribozyme-substrate complex that result in the breaking of a phosphodiester bond. The 2'OH group at the cleavage site of a pre-tRNA substrate is an important determinant in the cleavage step. We determined here that in contrast to a tRNA substrate, the 2'OH at the cleavage site of two in vitro selected substrates has no effect, whereas a 2'OH located adjacent to the cleavage site has a similarly large effect on the cleavage step. This result indicates that a unique 2'OH in the vicinity of the cleavage site interacts with the ribozyme to achieve the maximal efficiency of the cleavage step. Individual modifications in a pre-tRNA substrate that disrupt ES interactions proximal to the cleavage site generally have little effect on the usage of this unique 2'OH. Ribozyme modifications that delete the interactions involving the T stem-loop of the tRNA have a large effect on the usage of this unique 2'OH and also alter the location of this 2'OH. We propose a new ES complex prior to the bond-breaking step in the reaction scheme to explain these results. This second ES complex is in fast equilibrium with the initial ES complex formed by bimolecular collision. The ribozyme interaction with this unique 2'OH shifts the equilibrium in favor of the second ES complex. The formation of the second ES complex may require optimal geometry of the two independently folding domains of this ribozyme to precisely position crucial functional groups and Mg2+ ions in the active site. Such a domain geometry is significantly favored by the RNase P protein. In the absence of the protein, spatial rearrangement of these domains in the ES complex may be necessary.

Dynamics of ionization processes of methanol dimer: a direct ab initio dynamics study

Direct ab initio dynamics calculations have been applied to the ionization process of methanol dimer (CH 3OH) 2. Full dimensional ab initio potential energy surface including all degrees of freedom was used in the dynamics calculation. Total energies and gradients were calculated at each time step. The initial geometrical configurations at time zero were randomly selected from the geometries calculated for the neutral dimer at 10 K. It was found that the ionization of neutral methanol dimer leads directly to a long-lived complex formation (methanol dimer cation) which is composed of CH 3O and CH 3OH 2 +. The proton transfer was completed within 10-100 fs after several vibrations of the proton between the heavy molecules as expressed by CH 3O…H +…O(H)CH 3. For comparison, the bimolecular collision reaction, CH 3OH ++CH 3OH, was studied by the same dynamics calculations. Two reaction channels are concerned with the reaction. In addition to the long-lived complex formation channel, the proton transfer–dissociation channel (CH 3OH 2 ++CH 3O) was open as a product channel.

Binding and Electron Transfer between Cytochrome b5 and the Hemoglobin α- and β-Subunits through the Use of [Zn, Fe] Hybrids

We have measured the binding affinity (KA) and electron transfer (ET) rate constants (k) for the complex of hemoglobin (Hb) and cytochrome b5 (b5), using triplet quenching titrations of mixed-metal [ZnM, Fe3+(N3-)] Hb hybrids and of fully substituted Zn−mesoporphyrin (ZnM)Hb by b5 (trypsin-solubilized, bovine) (pH values 6.0 and 7.0). The use of the mixed-metal Hb hybrids with Zn in one chain type allows us to selectively monitor the 3ZnP → Fe3+P ET reaction of Fe3+b5 with either the α-chains or the β-chains. The self-consistent analysis of the results for the mixed-metal hybrids and those for the (ZnM)Hb allows us to determine the reactivity and affinity constants for the interactions of b5 with the individual subunits of T-state Hb. The results confirm that ET occurs within a complex between b5 and Hb, not through a simple bimolecular collision process. At pH 6.0, the binding affinity constant of the α-chains (Kα ≈ 2.0 × 104 M-1) is ∼4-fold larger than that of the β-chains (Kβ = 4.9 × 103 M-1); the intracomplex ET rate constant of the α-chains (kα ≈ 1500 s-1) is ∼2-fold larger than that of the β-chains (kβ ≈ 850 s-1). The binding affinity and ET rate constant of the α-chains both decrease as the pH is increased from 6.0 to 7.0; the binding affinity of the β-chains is essentially the same at pH 6.0 and 7.0, while the ET reactivity decreases. The kinetic results are consistent with a docking model in which each subunit binds a molecule of b5. However, they permit an alternative in which b5 reacts with the α-chains by binding at a site which spans the α1β2 dimer interface.

Collision-induced activation of the β-hydride elimination reaction of isobutyl iodide dissociatively chemisorbed on Al(111)

The collision-induced activation of the endothermic surface reaction of isobutyl iodide chemisorbed on an Al(111) surface is demonstrated using inert-gas, hyperthermal atomic beams. The collision-induced reaction (CIR) is highly selective towards promoting the β-hydride elimination pathway of the chemisorbed isobutyl fragments. The cross section for the collision-induced reaction was measured over a wide range of energies (14–92 kcal/mol) at normal incidence for Ar, Kr, and Xe atom beams. The CIR cross section exhibits scaling as a function of the normal kinetic energy of the incident atoms. The threshold energy for the β-hydride elimination reaction calculated from the experimental results using a classical energy transfer model is ∼1.1 eV (∼25 kcal/mol). This value is in excellent agreement with that obtained from an analysis of the thermally activated kinetics of the reaction. The measured cross section shows a complex dependence on both the incident energy of the colliding atom and the thermal energy provided by the surface where the two energy modes are interchangeable. The dynamics are explained on the basis of an impulsive, bimolecular collision event where the β-hydride elimination proceeds via a possible tunneling mechanism. The threshold energy calculated in this manner is an upper limit given that it is derived from an analysis which ignores excitations of the internal modes of the chemisorbed alkyl groups.

Scattering state spectroscopy of the reaction Mg*(3s3p 1P1)+CH4→MgH(v=0,1;N)+CH3

We report scattering state spectroscopic studies of the chemical quenching dynamics of Mg*(3p(1P)) by CH4. We have measured the final-state resolved action spectra for the MgH(v=1,N) reactive product channels, following excitation of the Mg*(3p)–CH4 transient bimolecular collision complex. As in earlier work on the ground vibrational state of the product, we have found a strong electronic orbital alignment effect: Reaction to the vibrationally excited product follows only on the attractive excited potential-energy surfaces in “Π-like” symmetry. For both MgH(v=0 and 1) product channels we have found that the rotational quantum state distribution is independent of laser excitation wavelength, indicating that the rotational energy partitioning is determined by exit channel dynamics. However, our results show that the product vibrational energy disposal is a function of excitation laser wavelength, suggesting that the vibrational energy partitioning is correlated with the collisional impact parameter. We have also carried out a careful search for the MgCH3 reactive product in this system, finding no evidence for any observable branching to this product. We discuss the implications of these results for the chemical dynamics of this metal-alkane reaction system.

Laser control of chemical reactions

Experiments show how product pathways can be controlled by irradiation with one or more laser beams during individual bimolecular collisions or during unimolecular decompositions. For bimolecular collisions, control has been achieved by selective excitation of reagent vibrational modes, by control of reagent approach geometry, and by control of orbital alignment. For unimolecular reactions, control has been achieved by quantum interference between different reaction pathways connecting the same initial and final states and by adjusting the temporal shape and spectral content of ultrashort, chirped pulses of radiation. These collision-control experiments deeply enrich the understanding of how chemical reactions occur.

Femtosecond Dynamics of Solvation: Microscopic Friction and Coherent Motion in Dense Fluids

In this paper, we present detailed experimental and theoretical studies of the femtosecond dynamics of microscopic friction. The real-time rotational motion of a well-defined system of diatomic solute in monatomic solvent has been studied for two solvents ranging from gas to liquid densities. Both coherent inertial and diffusive limits of the motion and all stages in the transition between these two regimes are observed in detail. The transient anisotropies over the entire range of experimental densities and solvents are well-represented by the J-coherence bimolecular collision model presented here. This stochastic hard-sphere collision model explicitly relates the physical properties of the solvent to the anisotropy and the coefficient of rotational friction, permitting calculation of the transient anisotropy from the Enskog hard-sphere collision frequency. Friction coefficients obtained from J-coherence analysis of experimental anisotropies were compared with those from Gordon J-diffusion, and Langevin−...

Phase-Shifting Acceleration of Ions in an Ion Cyclotron Resonance Spectrometer: Kinetic Energy Distribution and Reaction Dynamics

The kinetic energy distribution of trapped ions in an ion cyclotron resonance spectrometer (ICR) under a periodically phase-reversed rf potential is determined. At the operating pressures typical for the ICR (10-7−10-5 Torr), the ions eventually achieve a kinetic energy distribution that varies across short time intervals (0.1 ms) but is constant on the time scale of bimolecular collisions. This provides the opportunity to study quantitatively the translational energy dependence of bimolecular reactions and sequential collisional activation processes. The kinetic energy distribution, although not Maxwell−Boltzmann, is readily calculable. Results obtained for the kinetic energy dependence of the reaction of Cl- + CH3Br are qualitatively and quantitatively consistent with reported nonstatistical behavior in that system. Experimental considerations are discussed.