Collision Complex Research Articles

Kinetic Characterization of the ATPase and Actin-activated ATPase Activities of Acanthamoeba castellanii Myosin-2

Phosphorylation of Ser-639 in loop-2 of the catalytic motor domain of the heavy chain of Acanthamoeba castellanii myosin-2 and the phosphomimetic mutation S639D have been shown previously to down-regulate the actin-activated ATPase activity of both the full-length myosin and single-headed subfragment-1 (Liu, X., Lee, D. Y., Cai, S., Yu, S., Shu, S., Levine, R. L., and Korn, E. D. (2013) Proc. Natl. Acad. Sci. U.S.A. 110, E23-E32). In the present study we determined the kinetic constants for each step in the myosin and actomyosin ATPase cycles of recombinant wild-type S1 and S1-S639D. The kinetic parameter predominantly affected by the S639D mutation is the actin-activated release of inorganic phosphate from the acto myosin·ADP·Pi complex, which is the rate-limiting step in the steady-state actomyosin ATPase cycle. As consequence of this change, the duty ratio of this conventional myosin decreases. We speculate on the effect of Ser-639 phosphorylation on the processive behavior of myosin-2 filaments.

Mechanism and Thermodynamics of Multichannel 1:1 Ammonia and Ozone Tropospheric Oxidation Reaction

The reaction of NH3 + O3 on the singlet potential energy surface has been investigated theoretically using CCSD(T) and G3B3 methods with the 6-311++G(3df,3pd) basis set based on the geometric parameters optimised at the B3LYP/6-311++G(3df,3pd) level of theory. The calculated results revealed that the reactants are firstly associated with the adduct NH3–O3, through a barrier-less process and two stable collision complexes, C1 and C2 have been considered. Six kinds of products P1 (HOO + H2NO), P2 (OH + H2NO2), P3 (O2 + H3NO), P4 (HNO + H2O2), P5 (HNO2 + H2O) and P6 (NO + HO2 + H2) are obtained through a variety of transformations of C1 and C2. Thermodynamic parameters of all possible products show five production channels which are spontaneous. After taking into account the reaction barrier and enthalpy, the most probable reaction pathways are P1(2) and P4. Also, P4 is the most stable product in comparison with the others and P1 yields the other important products from the kinetic viewpoint; this is relatively stable, with a negative Gibbs free energy. Branching ratio results show P1 is the major product at low temperature. Finally, the rates constant have been computed only for the P1(2) and P4 pathways by related theories in the temperature range of 200–2500 K.

Reprint of: Transition state theory for collision complexes: Product translational energy distributions

An approximate formula is derived for the distribution of relative translational energy of products from decay of collision complexes formed by bimolecular combination in molecular beams. The treatment applies to the case of large collisional angular momentum (often encountered in practice), for which centrifugal motion strongly affects the shape of the energy distribution.

Reaction Dynamics of CH3+ HBr → CH4+ Br at 150-1000 K

The kinetics of the radical-polar molecule reaction CH3 + HBr → CH4 + Br has been studied at temperatures between 150 and 1000 K using classical dynamics procedures. Potential energy surfaces constructed using analytical forms of inter- and intramolecular interaction energies show a shallow well and barrier in the entrance channel, which affect the collision dynamics at low temperatures. Different collision models are used to distinguish the reaction occurring at low- and high-temperature regions. The reaction proceeds rapidly via a complex-mode mechanism below room temperature showing strong negative temperature dependence, where the effects of molecular attraction, H-atom tunneling and recrossing of collision complexes are found to be important. The temperature dependence of the rate constant between 400 and 1000 K is positive, the values increasing in accordance with the increase of the mean speed of collision. The rate constant varies from 7.6 × 10 −12 at 150 K to 3.7 × 10 −12 at 1000 K via a minimum value of 2.5 × 10 −12 cm 3 molecule −1 s −1 at 400 K.

Historical perspective on: Transition state theory for collision complexes: Product translational energy distributions [Volume 12, Issue 4, 15 January 1972, Pages 564–568

Historical perspective on: Transition state theory for collision complexes: Product translational energy distributions [Volume 12, Issue 4, 15 January 1972, Pages 564–568

Cyclopropenyl cation – the simplest Huckel's aromatic molecule – and its cyclic methyl derivatives in Titan's upper atmosphere

The recent measurements by Cassini Ion Neutral Mass Spectrometer (INMS) showed the presence of numerous carbocations and shed light on their composition in Titan's upper atmosphere. The present research identifies an important class of ion-molecule reactions proceeding via carbocation collision complexes, and its implications in the chemistry of Titan's thermosphere and ionosphere. An analysis (based on the kinetics and dynamics of the elementary chemical processes identified) of the Cassini measurements reveals the mechanism of formation of the three-membered Huckel aromatic rings-Cyclopropenyl cation and its cyclic methyl derivatives. For carbocations, a nonclassical three-carbon-center two-electron-bond structure is no longer a controversial topic in chemistry literature. Emphasis has been placed on a future coordinated effort of state-of-the-art laboratory experiments, quantum-chemical calculations, and astronomical ALMA and JWST observations including planetary in situ measurements at millimeter and submillimeter wavelengths to elucidate the structure, energetics and dynamics of the compositions of carbocations detected by Cassini cationic mass spectrometry. The carbocation chemistry in Titan's upper atmosphere has a possible bearing on the organic chemistry and aromaticity in the atmosphere of primitive earth.

Ab initio study on the paths of oxygen abstraction of hydrogen trioxide (HO3) molecule in the HO3 + SO2 reaction

The reaction paths of hydrogen trioxide (HO3) with sulphur dioxide (SO2) have been investigated on the doublet potential energy surface, theoretically. All species of the title reaction have been optimized at the PMP2(FC)/cc-pVDZ computational level. Energetic data have been obtained at the CCSD(T)//PMP2 level employing the cc-pVDZ basis set. No stable collision complexes have been found between the SO2 and HO3 molecules. Therefore, the SO2 + HO3 reaction starts without initial associations. The four possible paths, P1 through P4, have been obtained for the formation of SO3 (D\(_{3\text{h}}\)) + HOO∙ product. Our results show that these four paths include relatively high energy barriers to produce the final product of the SO3 (D\(_{3\text{h}}\)) + HOO∙. Therefore, the SO2 + HO3 → SO3(D\(_{3\text{h}}\)) + HOO∙ reaction is difficult to perform under atmospheric conditions. This means that the importance of SO2 + HO3 → SO3 (D\(_{3\text{h}}\)) + HOO∙ reaction increases with increasing temperature and, this reaction plays an important role in the SO3(D\(_{3\text{h}}\)) production as the main molecule of the formation of acid rain at high temperatures. Details of the reaction paths of SO2 + HO3 → SO3(D3h) + HOO have been investigated theoretically. All paths of the reaction are difficult to perform under atmospheric conditions. This reaction plays an important role in the SO3 (D3h) production as a main factor of acid rain formation in high temperatures.

Reactions of O22+ with CO2, OCS and CS2

The reactivity of O22+ with CO2, OCS and CS2 has been investigated for the first time, at centre-of-mass collision energies of 7.0, 7.9 and 8.5eV, respectively. The position-sensitive coincidence technique we employ shows the reactivity in the three collision systems is dominated by double- and single-electron transfer. Analysis of the observed electron transfer reactivity indicates that the two-electron transfer is concerted and the translational energy does not couple efficiently to the electronic co-ordinates. In the O22++OCS collision system we observe a channel forming a new chemical bond, generating SO++CO++O. The angular scattering in this channel indicates that this reaction proceeds via complexation, then fragmentation of the complex to form SO2++CO+. The primary SO2+ product then dissociates to SO++O. Ab initio calculations support the presence of a collision complex in the pathway to SO++CO++O. The single-electron transfer reactions are direct and the energy releases we extract for the subsequent dissociation of the primary products (e.g. O2++CO2+) show that the internal vibrational energy of the O22+ reactant does not participate in the reaction.

Tectonic processes, from rifting to collision via subduction, in SE Asia and the western Pacific: A key to understanding the architecture of the Central Asian Orogenic Belt

We review the processes of accretion of continental blocks during the Tertiary in SE Asia and the western Pacific with the aim of better understanding the evolution of the Central Asian Orogenic Belt, which is a Neoproterozoic to mid-Phanerozoic orogenic collage surrounded by the East European, Siberian, Tarim, and North China cratons. In the western Pacific, there is abundant evidence of sequential plate-tectonic processes from accretion to continent-arc/continent collision, via exhumation and suprasubduction. Early processes involve seafloor spreading, subduction, accretion, arc formation, and back-arc extension. Two important types of tectonic setting and evolution are recognized along the present Pacific convergent margin: sediment/crust accretion and tectonic erosion. Five major accretionary complexes are well illustrated in the Japanese Islands. Tectonic erosion removes material by underscraping the lower part of the upper plate. Subduction is also associated with back-arc extension, particularly in Indonesia and the SW Pacific region. Arc-arc collisional complexes are present in Taiwan, the Philippines, and Japan. The geological record of SE Asia and the western Pacific provides a robust modern analogue for the geological and tectonic history of the Central Asian Orogenic Belt, before it was affected by high-temperature metamorphism.

Collision between high and low viscosity droplets: Direct Numerical Simulations and experiments

Binary droplet collisions are of importance in a variety of practical applications comprising dispersed two-phase flows. In the present work we focus on the collision of miscible droplets, where one droplet is composed of a high viscous liquid and the other one is of lower viscosity. This kind of collisions take place in, for instance, spray drying processes when droplets with different solid content collide in recirculation zones. The aim of this paper is to investigate the details of the flow inside the colliding droplets. For this purpose, two prototype cases are considered, namely the collision of equal sized droplets and the collision between a small and highly viscous droplet and a bigger low viscous droplet. A new experimental method has been developed in order to visualize the penetration and mixing process of two colliding droplets, where a fluorescence marker is added to one liquid and the droplets are excited by a laser. The results show a delay in the coalescence which takes place during the initial stage of a collision of droplets with different viscosities. Direct Numerical Simulations based on the Volume-of-Fluid method are used to study these collisions and to allow for a more detailed inspection of the mixing process. The method is extended to consider a second liquid with a different viscosity. In order to reproduce the delay of coalescence, an algorithm for the temporal suppression of the coalescence is applied. A predictive simulation of the delay is not possible, because the extremely thin air gap separating the droplets cannot be resolved by the numerics. This approach is validated by comparison with experimental data. The results provide local field data of the flow inside the collision complex, showing in particular a pressure jump at the liquid–liquid interface although no surface tension is present. The detailed analysis of the terms in the momentum balance show that the pressure jump results from the viscosity jump at the liquid–liquid interface.

The effect of the Coriolis coupling on H+ND reaction: A time dependent wave packet study

We present a quantum scattering calculation of initial-state-resolved reaction probabilities, integral cross section, initial state selected reaction rate constants and thermal rate constant for exchange and depletion channels of the H+ND reaction. The calculations are carried out using Coriolis coupling (CC) method on the modified NH2Ã2A1 potential energy surface(PES). The initial state selected reaction probabilities are calculated for 0.0–0.5eV of collision energy range. The reaction probabilities for depletion channel shows some sharp and large resonances associated with long-lived collision complexes, as compared to exchange channel. Integral cross sections for both reactions depend strongly on initial rotational states. The calculated thermal reaction rate constant for the depletion channel is in a good agreement with the values previously obtained by the centrifugal sudden approximation, experimental and semiclassical results.

Spectral system for measuring gaseous atmospheric components with a fiber-optic tracking system, and certain analysis results of atmospheric spectra

A spectral system for measuring atmospheric gaseous components based on a Brucker IFS 125M Fourier Transform Spectrometer (FTS) with a fiber-optic tracker is described. Experimental results on the determination of CO2 and H2O contents in the atmosphere above Tomsk from the analysis of atmospheric transmission spectra of solar radiation, recorded with the FTS, are presented. The atmospheric transmission spectra are compared for solar zenith angles of 34° and 78°, which show a significant quantity of oxygen collision complexes in the surface air layer.

Gas Phase Hydrolysis of Formaldehyde To Form Methanediol: Impact of Formic Acid Catalysis

We find that formic acid (FA) is very effective at facilitating diol formation through its ability to reduce the barrier for the formaldehyde (HCHO) hydrolysis reaction. The rate limiting step in the mechanism involves the isomerization of a prereactive collision complex formed through either the HCHO···H2O + FA and/or HCHO + FA···H2O pathways. The present study finds that the effective barrier height, defined as the difference between the zero-point vibrational energy (ZPE) corrected energy of the transition state (TS) and the HCHO···H2O + FA and HCHO + FA···H2O starting reagents, are respectively only ∼1 and ∼4 kcal/mol. These barriers are substantially lower than the ∼17 kcal/mol barrier associated with the corresponding step in the hydrolysis of HCHO catalyzed by a single water molecule (HCHO + H2O + H2O). The significantly lower barrier heights for the formic acid catalyzed pathway reveal a new important role that organic acids play in the gas phase hydrolysis of atmospheric carbonyl compounds.

State Specific Stabilization of H+ + H2(j) Collision Complexes

Stabilization of H3(+) collision complexes has been studied at nominal temperatures between 11 and 33 K using a 22-pole radio frequency (rf) ion trap. Apparent binary rate coefficients, k(*) = kr + k3[H2], have been measured for para- and normal-hydrogen at number densities between some 10(11) and 10(14) cm(-3). The state specific rate coefficients extracted for radiative stabilization, kr(T;j), are all below 2 × 10(-16) cm(3) s(-1). There is a slight tendency to decrease with increasing temperature. In contrast to simple expectations, kr(11 K;j) is for j = 0 a factor of 2 smaller than for j = 1. The ternary rate coefficients for p-H2 show a rather steep T-dependence; however, they are increasing with temperature. The state specific ternary rate coefficients, k3(T;j), measured for j = 0 and derived for j = 1 from measurements with n-H2, differ by an order of magnitude. Most of these surprising observations are in disagreement with predictions from standard association models, which are based on statistical assumptions and the separation of complex formation and competition between stabilization and decay. Most probably, the unexpected collision dynamics are due to the fact that, at the low translational energies of the present experiment, only a small number of partial waves participate. This should make exact quantum mechanical calculations of kr feasible. More complex is three-body stabilization, because it occurs on the H5(+) potential energy surface.

Probing the Interaction of Brain Fatty Acid Binding Protein (B-FABP) with Model Membranes

Brain fatty acid-binding protein (B-FABP) interacts with biological membranes and delivers polyunsaturated fatty acids (FAs) via a collisional mechanism. The binding of FAs in the protein and the interaction with membranes involve a motif called “portal region”, formed by two small α-helices, A1 and A2, connected by a loop. We used a combination of site-directed mutagenesis and electron spin resonance to probe the changes in the protein and in the membrane model induced by their interaction. Spin labeled B-FABP mutants and lipidic spin probes incorporated into a membrane model confirmed that B-FABP interacts with micelles through the portal region and led to structural changes in the protein as well in the micelles. These changes were greater in the presence of LPG when compared to the LPC models. ESR spectra of B-FABP labeled mutants showed the presence of two groups of residues that responded to the presence of micelles in opposite ways. In the presence of lysophospholipids, group I of residues, whose side chains point outwards from the contact region between the helices, had their mobility decreased in an environment of lower polarity when compared to the same residues in solution. The second group, composed by residues with side chains situated at the interface between the α-helices, experienced an increase in mobility in the presence of the model membranes. These modifications in the ESR spectra of B-FABP mutants are compatible with a less ordered structure of the portal region inner residues (group II) that is likely to facilitate the delivery of FAs to target membranes. On the other hand, residues in group I and micelle components have their mobilities decreased probably as a result of the formation of a collisional complex. Our results bring new insights for the understanding of the gating and delivery mechanisms of FABPs.

Theoretical investigation of 2+2 resonance enhanced multi-photon ionization probability

The analytic formula of the ionization probability in the process of 2+2 resonance enhanced multi-photon ionization (REMPI) is derived from the dynamic rate equation about the interaction of photon and material. Based on the formula, the influence of laser intensity, laser pulse duration and collision relaxation rate on the ionization probability is investigated theoretically. It is shown that the ionization probability increases with the laser intensity and laser pulse duration. The ionization probability will get to one until two steps saturation with the increase of laser intensity. After that, the ionization probability will oscillates narrowly around the saturation value if the laser intensity increases further. The results also show that the ionization probability will decrease in linear manner nearly with the increase of collision relaxation rate. But the variation is small. So the influence of the collision relaxation rate (or even sample pressure) on the ionization probability can be ignored. In the practical use of REMPI, higher sample pressure will reduce the intensity of the detection signal is due to the collision complex of the positive and negative ions. This will reduce the collection efficiency of the ions, and influence the magnitude of the ion signal further.

Disulfide Cross-Linked Antiparallel Actin Dimer

Oxidation of actin monomer (G-actin) with copper o-phenanthroline resulted in a rapid, high yield of disulfide cross-linked dimer. The cross-link is due to an intermolecular disulfide bond between actin Cys374 of each molecule, resulting in a tail-to-tail, i.e., antiparallel, actin dimer. Analytical ultracentrifugation profiles of G-actin can be ascribed to the existence of actin monomers with very little, if any, dimer. Thus, actin dimers are not energetically favorable, indicating that cross-linked dimers are formed during random diffusional collisions. On the other hand, a similar oxidation of actin polymer (F-actin) resulted in a much lower yield of the cross-linked actin dimer that showed no sign of leveling off. Therefore, it is proposed that the cross-linked dimer from actin polymer is due to collisional complexes of actin monomers that are in equilibrium with the polymer during actin treadmilling. These results account for the reported observation that during the early stages of actin polymerization (where the actin monomer concentration is high) cross-linked antiparallel actin dimers are formed in relatively high yield whereas none are formed at later stages of polymerization. These findings raise questions concerning the validity of the antiparallel actin dimer model of in vitro actin polymerization that is based on the assumption that the ability to form cross-linked actin dimers implies the existence of stable dimers.

Dioxygen spectra and bioactivation

Intensities of spin‐forbidden transitions in electronic absorption and emission spectra of molecular oxygen are analyzed in order to understand the key mechanisms of spin‐states mixing induced by spin‐orbit coupling (SOC) and the ways to overcome spin prohibition for various photophysical and biochemical processes. Multireference configuration interaction calculations with SOC account are used to generalize spin‐selection rules for the oxygen atmospheric and Herzberg bands in free O2 molecule and in collision complexes. Intensity enhancement of the atmospheric a1Δg → X3Σg−, b1Σg+ → X3Σg−, and Noxon b1Σg+ → a1Δg transitions upon bimolecular collisions are compared with those for Herzberg III transitions A′3Δu ← X3Σg−. Electric quadrupole, dipole, and magnetic approximations are used for transition probability calculations. Intensity distribution in rotational lines is also considered. With this background, we propose some simple spin‐selection rules for dioxygen activation in enzymatic reactions. © 2013 Wiley Periodicals, Inc.

Scattering of ultracold molecules in the highly resonant regime

Compared to purely atomic collisions, ultracold molecular collisions potentially support a much larger number of Fano-Feshbach resonances due to the enormous number of rovibrational states available. In fact, for alkali-metal dimers we find that the resulting density of resonances cannot be resolved at all, even on the sub-$\ensuremath{\mu}$K temperature scale of ultracold experiments. As a result, all observables become averaged over many resonances and can effectively be described by simpler, nonresonant scattering calculations. Two particular examples are discussed: nonchemically reactive RbCs and chemically reactive KRb. In the former case, the formation of a long-lived collision complex may lead to the ejection of molecules from a trap. In the latter case, chemical reactions broaden the resonances so much that they become unobservable.

A study of resonance progressions in the F + HCl → Cl + HF reaction: A lifetime matrix analysis of pre-reactive and post-reactive collision complexes

Quantum scattering calculations were performed for the F + HCl → Cl + HF reaction for total angular momentum J = 0-6 using an ab initio potential energy surface. Employing a time-independent algorithm on a very fine energy grid allowed the resolution of hundreds of narrow resonances with lifetimes in the picosecond range. The resonances were assigned to rotationally excited van der Waals complexes lying in the entrance and exit channels. Resonance peaks observed in the J = 0 calculation broke into multiplets for J > 0 corresponding to the range of allowed helicity states. The Smith lifetime matrix, Q(E), was used to efficiently extract the resonance properties. The largest eigenvalue of Q(E) was used for the position and total width, while the corresponding eigenvector was used to obtain the partial widths. A simple model based on the conventional treatment of rotationally excited van der Waals triatomics was used to predict the resonance spectrum to an accuracy of ~0.02 kcal∕mol. The model predicts the density of resonance states in good agreement with the exact scattering results.