Study Of Reaction Dynamics Research Articles

Mechanism of Formation of the Nonstandard Product in the Prenyltransferase Reaction of the G115T Mutant of FtmPT1: A Case of Reaction Dynamics Calling the Shots?

FtmPT1 is a fungal indole prenyltransferase that affords Tryprostatin B from Brevianamide F and dimethylallyl pyrophosphate; however, when a single residue in the active site is mutated (Gly115Thr), a novel five-membered ring compound is obtained as the major product with Tryprostatin B as the minor product. Herein, we describe detailed studies of the catalysis of the Gly115Thr mutant of FtmPT1 with a focus on the observed regioselectivity of the reaction. We employ one- and two-dimensional potential of mean force simulations to explore the catalytic mechanism, along with molecular dynamics simulations exploring the reaction dynamics of the prenyl transfer reaction. Single-point electronic structure calculations were also used to explore the performance of the self-consistent charge density functional tight-binding method to model specific reaction steps. Importantly, we observe that the two reaction pathways have comparable activation parameters and propose that the origin of the novel product is predicated, at least in part, on the topology of the potential energy surface as revealed by reaction dynamics studies.

Effect of projectile on incomplete fusion reactions at low energies

Present work deals with the experimental studies of incomplete fusion reaction dynamics at energies as low as ≈ 4 - 7 MeV/A. Excitation functions populated via complete fusion and/or incomplete fusion processes in 12 C+175 Lu, and 13 C+169 Tm systems have been measured within the framework of PACE4 code. Data of excitation function measurements on comparison with different projectile-target combinations suggest the existence of ICF even at slightly above barrier energies where complete fusion (CF) is supposed to be the sole contributor, and further demonstrates strong projectile structure dependence of ICF. The incomplete fusion strength functions for 12 C+175 Lu, and 13 C+169 Tm systems are analyzed as a function of various physical parameters at a constant vrel ≈ 0.053c. It has been found that one neutron (1n) excess projectile 13 C (as compared to 12 C) results in less incomplete fusion contribution due to its relatively large negative α-Q-value, hence, α Q-value seems to be a reliable parameter to understand the ICF dynamics at low energies. In order to explore the reaction modes on the basis of their entry state spin population, the spin distribution of residues populated via CF and/or ICF in 16 O+159 Tb system has been done using particle-γ coincidence technique. CF-α and ICF-α channels have been identified from backward (B) and forward (F) α-gated γspectra, respectively. Reaction dependent decay patterns have been observed in different α emitting channels. The CF channels are found to be fed over a broad spin range, however, ICF-α channels was observed only for high-spin states. Further, the existence of incomplete fusion at low bombarding energies indicates the possibility to populate high spin states

Taking the plunge: chemical reaction dynamics in liquids.

The dynamics of chemical reactions in liquid solutions are now amenable to direct study using ultrafast laser spectroscopy techniques and advances in computer simulation methods. The surrounding solvent affects the chemical reaction dynamics in numerous ways, which include: (i) formation of complexes between reactants and solvent molecules; (ii) modifications to transition state energies and structures relative to the reactants and products; (iii) coupling between the motions of the reacting molecules and the solvent modes, and exchange of energy; (iv) solvent caging of reactants and products; and (v) structural changes to the solvation shells in response to the changing chemical identity of the solutes, on timescales which may be slower than the reactive events. This article reviews progress in the study of bimolecular chemical reaction dynamics in solution, concentrating on reactions which occur on ground electronic states. It illustrates this progress with reference to recent experimental and computational studies, and considers how the various ways in which a solvent affects the chemical reaction dynamics can be unravelled. Implications are considered for research in fields such as mechanistic synthetic chemistry.

Pre-compound emission in low-energy heavy-ion interactions

Recent experimental studies have shown the presence of pre-compound emission component in heavy ion reactions at low projectile energy ranging from 4 to 7 MeV/nucleons. In earlier measurements strength of the pre-compound component has been estimated from the difference in forward-backward distributions of emitted particles. Present measurement is a part of an ongoing program on the study of reaction dynamics of heavy ion interactions at low energies aimed at investigating the effect of momentum transfer in compound, precompound, complete and incomplete fusion processes in heavy ion reactions. In the present work on the basis of momentum transfer the measurement of the recoil range distributions of heavy residues has been used to decipher the components of compound and pre-compound emission processes in the fusion of 16 O projectile with 159 Tb and 169 Tm targets. The analysis of recoil range distribution measurements show two distinct linear momentum transfer components corresponding to pre-compound and compound nucleus processes are involved. In order to obtain the mean input angular momentum associated with compound and pre-compound emission processes, an online measurement of the spin distributions of the residues has been performed. The analysis of spin distribution indicate that the mean input angular momentum associated with pre-compound products is found to be relatively lower than that associated with compound nucleus process. The pre-compound components obtained from the present analysis are consistent with those obtained from the analysis of excitation functions.

Oxidation of Acebutolol by Copper(III) Periodate Complex in Aqueous Alkaline Medium: A Kinetic and Mechanistic Approach

Illuminating the complex reactions of molecules in aqueous solution is one of the most important tasks of experimental studies of reaction dynamics. The oxidant diperiodatocuprate(III) (DPC) was used for the oxidation of acebutolol (ACBT) in aqueous alkaline medium, at an ionic strength of 0.30 mol·dm−3. The stoichiometry was found to be 1:2 ([ACBT]:[DPC]). The order of the reaction with respect to [DPC] was unity when [DPC] << [ACBT], while the orders with respect to [ACBT] and [OH−] were less than unity, whereas it was negative less than unity in [\( {\text{IO}}_{ 4}^{ - } \)] over the concentration range studied. The final products of oxidation were identified by GC–MS analysis. Based on the experimental observations, a plausible mechanism is proposed. The reaction constants involved in the different steps of the reaction mechanism were calculated. The activation parameters and the thermodynamic quantities were determined and discussed. Active species of diperiodatocuprate(III) was found to be monoperiodatocuprate(III), i.e. [Cu(H2IO6)(H2O)2]. An understanding of the mechanism allows the chemistry to be interpreted, understood and predicted.

Molecular Dynamics Study of Combustion Reactions in a Supercritical Environment. Part 1: Carbon Dioxide and Water Force Field Parameters Refitting and Critical Isotherms of Binary Mixtures

The oxy-fuel–carbon dioxide combustion process is expected to drastically increase the energy efficiency and enable easy carbon sequestration. In this technology, the combustion products (carbon dioxide and water) are used to control the temperature and nitrogen is excluded from the combustion chamber, so that nitrogen oxide pollutants do not form. Therefore, in oxy-combustion, carbon dioxide and water are present in large concentrations in their transcritical state and may play an important role in kinetics. The computational chemistry methods may assist in understanding these effects, and molecular dynamics with a reactive force field (ReaxFF) seems to be a suitable tool for such a study. Here, we investigate applicability of the ReaxFF to describe the critical phenomena in carbon dioxide and water and find that several non-bonding parameters need adjustment. We report the new parameter set, capable of reproducing the critical temperatures and pressures. The critical isotherms of CO2/H2O binary mixtures...

Reactive Force Field Modeling of Zinc Oxide Nanoparticle Formation

A ReaxFF reactive force field is developed and used for molecular dynamics studies of reactions that occur when diethyl zinc is exposed to a graphene surface that has been functionalized with epoxide groups. From past experiments, it is known that these conditions lead to zinc oxide nanoparticle formation. Molecular dynamics simulations are used to provide atom-level detail into the nanoparticle formation process, including the mechanisms whereby oxygen is abstracted from the graphene surface, thus enabling condensation reactions in which multiple zinc-containing species form zinc oxide fragments and ultimately nanoparticles. Structural properties of the nanoparticles show nonstoichiometric zinc oxide structures with average coordination numbers of 3.6 around each zinc. Time-dependent density functional theory calculations show that the absorption spectra of these clusters are red-shifted by a few tenths of an electronvolt compared to that of a wurtzite crystal structure, representing transitions from oxy...

Stimulated X-ray Raman scattering - a critical assessment of the building block of nonlinear X-ray spectroscopy.

With the invention of femtosecond X-ray free-electron lasers (XFELs), studies of light-induced chemical reaction dynamics and structural dynamics reach a new era, allowing for time-resolved X-ray diffraction and spectroscopy. To ultimately probe coherent electron and nuclear dynamics on their natural time and length scales, coherent nonlinear X-ray spectroscopy schemes have been proposed. In this contribution, we want to critically assess the experimental realisation of nonlinear X-ray spectroscopy at current-day XFEL sources, by presenting first experimental attempts to demonstrate stimulated resonant X-ray Raman scattering in molecular gas targets.

A novel theoretical study of thermally-induced reaction and vibration dynamics of methanol dissociative adsorption onto a Si(001) surface

The thermally-induced reaction and vibration dynamics of methanol dissociative adsorption onto a Si(001) surface is studied by combining temperature-dependent DFT-based MD simulations with molecular adsorption sampling and wavelet transform.

Accurate ab initio-based double many-body expansion potential energy surface for the adiabatic ground-state of the C3 radical including combined Jahn-Teller plus pseudo-Jahn-Teller interactions.

A fully ab initio-based potential energy surface is first reported for the ground electronic state of the C3 radical using the double many-body expansion (DMBE) method. The DMBE form so obtained mimics the full set of energies calculated at the multireference configuration interaction level of theory with chemical accuracy. To account for the incompleteness of the one- and N-electron bases, the calculated external correlation energies have been scaled prior to the fitting procedure via DMBE-scaled external correlation method. Furthermore, the novel potential energy surface reproduces accurately dissociation energies, diatomic potentials, long-range interactions at all asymptotic channels, and the correct topological behavior at the region of 4 conical intersections with the partner state of the same symmetry near equilateral triangular geometries due to combined Jahn-Teller (E' ⊗ e') plus pseudo-Jahn-Teller [(E'+A1')⊗e'] interactions. Rovibrational calculations have also been performed, unveiling a good match of the vibrational spectrum of C3 for 53 calculated levels. The present DMBE form is, therefore, commended for both spectroscopic and reaction dynamics studies, some also performed in the present work.

Kinetic isotope effect of the (16)O + (36)O2 and (18)O + (32)O2 isotope exchange reactions: Dominant role of reactive resonances revealed by an accurate time-dependent quantum wavepacket study.

The O + O2 isotope exchange reactions play an important role in determining the oxygen isotopic composition of a number of trace gases in the atmosphere, and their temperature dependence and kinetic isotope effects (KIEs) provide important constraints on our understanding of the origin and mechanism of these and other unusual oxygen KIEs important in the atmosphere. This work reports a quantum dynamics study of the title reactions on the newly constructed Dawes-Lolur-Li-Jiang-Guo (DLLJG) potential energy surface (PES). The thermal reaction rate coefficients of both the (18)O + (32)O2 and (16)O + (36)O2 reactions obtained using the DLLJG PES exhibit a clear negative temperature dependence, in sharp contrast with the positive temperature dependence obtained using the earlier modified Siebert-Schinke-Bittererova (mSSB) PES. In addition, the calculated KIE shows an improved agreement with the experiment. These results strongly support the absence of the "reef" structure in the entrance/exit channels of the DLLJG PES, which is present in the mSSB PES. The quantum dynamics results on both PESs attribute the marked KIE to strong near-threshold reactive resonances, presumably stemming from the mass differences and/or zero point energy difference between the diatomic reactant and product. The accurate characterization of the reactivity for these near-thermoneutral reactions immediately above the reaction threshold is important for correct characterization of the thermal reaction rate coefficients.

Perspective: Stimulated Raman adiabatic passage: The status after 25 years.

The first presentation of the STIRAP (stimulated Raman adiabatic passage) technique with proper theoretical foundation and convincing experimental data appeared 25 years ago, in the May 1st, 1990 issue of The Journal of Chemical Physics. By now, the STIRAP concept has been successfully applied in many different fields of physics, chemistry, and beyond. In this article, we comment briefly on the initial motivation of the work, namely, the study of reaction dynamics of vibrationally excited small molecules, and how this initial idea led to the documented success. We proceed by providing a brief discussion of the physics of STIRAP and how the method was developed over the years, before discussing a few examples from the amazingly wide range of applications which STIRAP now enjoys, with the aim to stimulate further use of the concept. Finally, we mention some promising future directions.

Semiclassical Wigner theory of photodissociation in three dimensions: Shedding light on its basis

The semiclassical Wigner theory (SCWT) of photodissociation dynamics, initially proposed by Brown and Heller [J. Chem. Phys. 75, 186 (1981)] in order to describe state distributions in the products of direct collinear photodissociations, was recently extended to realistic three-dimensional triatomic processes of the same type [Arbelo-González et al., Phys. Chem. Chem. Phys. 15, 9994 (2013)]. The resulting approach, which takes into account rotational motions in addition to vibrational and translational ones, was applied to a triatomic-like model of methyl iodide photodissociation and its predictions were found to be in nearly quantitative agreement with rigorous quantum results, but at a much lower computational cost, making thereby SCWT a potential tool for the study of polyatomic reaction dynamics. Here, we analyse the main reasons for this agreement by means of an elementary model of fragmentation explicitly dealing with the rotational motion only. We show that our formulation of SCWT makes it a semiclassical approximation to an approximate planar quantum treatment of the dynamics, both of sufficient quality for the whole treatment to be satisfying.

Front-end electronics for CsI based charged particle array for the study of reaction dynamics

The characteristics and performance of a new detector system based on CsI(TI) scintillators, and its front-end electronics are presented. The detector system has been developed for the detection of light charged particles to investigate fusion–fission dynamics, and will also serve as ancillary detector for an array of neutron detectors. CsI scintillators are read by photo-diodes. The main feature of the array is its compact and simple high density front-end electronics which includes custom developed low noise charge sensitive preamplifiers (with very low power consumption for operation inside vacuum), NIM differential drivers, and commercially available Mesytec amplifiers with two different time constants for particle identification using a ballistic deficit technique.

Reaction dynamics studies for the system 7Be+58Ni

The study of reactions induced by exotic weakly bound nuclei at energies around the Coulomb barrier had attracted a large interest in the last decade, since the features of these nuclei can deeply affect the reaction dynamics. The discrimination between different reaction mechanisms is, in general, a rather difficult task. It can be achieved by using detector arrays covering high solid angle and with high granularity that allow to measure the reaction products and, possibly, coincidences between them, as, for example, recently done for stable weakly bound nuclei [1, 2]. We investigated the collision of the weakly bound nucleus 7Be on a 58Ni target at the beam energy of 1.1 times the Coulomb barrier, measuring the elastic scattering angular distribution and the energy and angular distributions of 3He and 4He. The 7Be radioactive ion beam was produced by the facility EXOTIC at INFN-LNL with an energy of 22 MeV and an intensity of ~3×105 pps. Results showed that the 4He yeld is about 4 times larger than 3He yield, suggesting that reaction mechanisms other than the break-up mostly produce the He isotopes. Theoretical calculations for transfer channels and compound nucleus reactions suggest that complete fusion accounts for (41±5%) of the total reaction cross section extracted from optical model analysis of the elastic scattering data, and that 3He and 4He stripping are the most populated reaction channels among direct processes. Eventually estimation of incomplete fusion contributions to the 3,4He production cross sections was performed through semi-classical calculations with the code PLATYPUS [3].

Movie-mode dynamic electron microscopy

Abstract

A molecular dynamics study of bond exchange reactions in covalent adaptable networks.

Covalent adaptable networks are polymers that can alter the arrangement of network connections by bond exchange reactions where an active unit attaches to an existing bond then kicks off its pre-existing peer to form a new bond. When the polymer is stretched, bond exchange reactions lead to stress relaxation and plastic deformation, or the so-called reforming. In addition, two pieces of polymers can be rejoined together without introducing additional monomers or chemicals on the interface, enabling welding and reprocessing. Although covalent adaptable networks have been researched extensively in the past, knowledge about the macromolecular level network alternations is limited. In this study, molecular dynamics simulations are used to investigate the macromolecular details of bond exchange reactions in a recently reported epoxy system. An algorithm for bond exchange reactions is first developed and applied to study a crosslinking network formed by epoxy resin DGEBA with the crosslinking agent tricarballylic acid. The trace of the active units is tracked to show the migration of these units within the network. Network properties, such as the distance between two neighboring crosslink sites, the chain angle, and the initial modulus, are examined after each iteration of the bond exchange reactions to provide detailed information about how material behaviors and macromolecular structure evolve. Stress relaxation simulations are also conducted. It is found that even though bond exchange reactions change the macroscopic shape of the network, microscopic network characteristic features, such as the distance between two neighboring crosslink sites and the chain angle, relax back to the unstretched isotropic state. Comparison with a recent scaling theory also shows good agreement.

Observation of incomplete fusion at low angular momenta

Present work deals with experimental studies of incomplete fusion reaction dynamics using off-line γ -ray spectrometry at energies as low as ≈3-6 MeV/nucleon. Excitation functions for five reaction products populated via complete and/or incomplete fusion processes in 16 O+130 Te system have been measured and compared with the predictions of the statistical model code PACE4. A significant enhancement in the measured excitation functions compared to theoretical predictions for α -emitting channels has been observed and is attributed to incomplete fusion processes. The relative strength of incomplete fusion has been found to increase with projectile energy. Results show that incomplete fusion is associated even for angular momenta lesser than the critical angular momentum for complete fusion and also reveals importance of incomplete fusion even at energies as low as ≈3-6 MeV/nucleon.

Inverse-kinematics study of78Kr +40Ca at 10 AMeV

The CHIMERA multi-detector array at LNS Catania has been used to study the inverse-kinematics reaction of 78 Kr + 40 Ca at a bombarding energy of 10 AMeV. Analysis of the experimental data focused on a class of selected events consistent with the complete fusion and subsequent binary split of the of the reacting system. This class of events features a broad A, Z distribution of fission fragments centered about symmetric fission while exhibiting relative velocities significantly higher than given by Viola systematics. The center-ofmass angular distribution (dσ/dΘ) of the fission fragments exhibit an unexpected anisotropy inconsistent with a compound-nucleus reaction and indicates a dynamic fusion-fission like process. The observed angular distribution features an asymmetric forward-backward peaking most prevalent for mass-asymmetric events. Furthermore, the more massive fragment of mass-asymmetric events appears to emerge preferentially in the forward direction, along the beam axis, in analogy to dynamic fragmentation of projectile-like fragments. Analysis of the angular distribution of alpha particles emitted from these fission fragments suggests the events are associated mostly with central collisions. The study of low-energy heavy-ion reaction dynamics in the energy domain moderately in excess of the Coulomb barrier offers a unique insight into the large-scale collective motion of the nucleons in the nucleus. Fusion-fission constitutes an important reaction channel for many such nuclear reactions and is an important probe into the nuclear structure of matter. As the bombarding energy increases, the role of dynamically-induced decay modes

Effects of reactant rotational excitations on H2 + NH2 → H + NH3 reactivity.

Rotational mode specificity of the title reaction is examined using an initial state selected time-dependent wave packet method on an accurate ab initio based global potential energy surface. This penta-atomic reaction presents an ideal system to test several dynamical approximations, which might be useful for future quantum dynamics studies of polyatomic reactions, particularly with rotationally excited reactants. The first approximation involves a seven-dimensional (7D) model in which the two non-reactive N-H bonds are fixed at their equilibrium geometry. The second is the centrifugal sudden (CS) approximation within the 7D model. Finally, the J-shifting (JS) model is tested, again with the fixed N-H bonds. The spectator-bond approximation works very well in the energy range studied, while the centrifugal sudden and J-shifting integral cross sections (ICSs) agree satisfactorily with the coupled-channel counterparts in the low collision energy range, but deviate at the high energies. The calculated integral cross sections indicate that the rotational excitation of H2 somewhat inhibits the reaction while the rotational excitations of NH2 have little effect. These findings are compared with the predictions of the sudden vector projection model. Finally, a simple model is proposed to predict rotational mode specificity using K-averaged reaction probabilities.