Rearrangement Of Chemical Bonds Research Articles

Evaluation of coal-related model compounds using tandem mass spectrometry.

Gas chromatography/mass spectrometry (GC/MS) is a routine and basic instrumental method for the analysis of complex coal conversion products in the chemical industry. To further enhance the practical potential of GC/MS in chemical industry, a tandem MS method for the selection of ion pairs applied in monitoring coal conversions was established using GC/quadrupole time-of-flight MS (GC/Q-TOF MS). The corresponding fragmentation pathways were explored and suitable ion pairs were screened. Fourteen coal-related model compounds (CRMCs) were analyzed using GC/Q-TOF MS with different collision-induced dissociation (CID) energies (5-20eV). The fragmentation pathways can offer a better understanding of chemical bond breaking, hydrogen transfer, rearrangement reactions and elimination of neutral fragments for CRMCs during the CID process. The precursor ions of aromatic hydrocarbons without alkyl chains were difficult to fragment with a CID energy of 20eV. But aromatic hydrocarbons with branched chains were prone to fragment via the loss of alkyl chains and further fragmented through ring-opening reactions. Compared with the Calk Car bond, the Car Car bond was difficult to fragment due to its high bond dissociation energy. The existence of heteroatoms facilitated fragmentation that was conducive to the screening of ion pairs. The CID technique of GC/Q-TOF MS will contribute to studies on the organic composition of coals and to building monitoring methods for coal conversions via fragmentation and ion pair selection.

Development of reactive force fields using ab initio molecular dynamics simulation minimally biased to experimental data.

Incorporation of quantum mechanical electronic structure data is necessary to properly capture the physics of many chemical processes. Proton hopping in water, which involves rearrangement of chemical and hydrogen bonds, is one such example of an inherently quantum mechanical process. Standard ab initio molecular dynamics (AIMD) methods, however, do not yet accurately predict the structure of water and are therefore less than optimal for developing force fields. We have instead utilized a recently developed method which minimally biases AIMD simulations to match limited experimental data to develop novel multiscale reactive molecular dynamics (MS-RMD) force fields by using relative entropy minimization. In this paper, we present two new MS-RMD models using such a parameterization: one which employs water with harmonic internal vibrations and another which uses anharmonic water. We show that the newly developed MS-RMD models very closely reproduce the solvation structure of the hydrated excess proton in the target AIMD data. We also find that the use of anharmonic water increases proton hopping, thereby increasing the proton diffusion constant.

Curly arrows, electron flow, and reaction mechanisms from the perspective of the bonding evolution theory.

Despite the usefulness of curly arrows in chemistry, their relationship with real electron density flows is still imprecise, and even their direct connection to quantum chemistry is still controversial. The paradigmatic description - from first principles - of the mechanistic aspects of a given chemical process is based mainly on the relative energies and geometrical changes at the stationary points of the potential energy surface along the reaction pathway; however, it is not sufficient to describe chemical systems in terms of bonding aspects. Probing the electron density distribution during a chemical reaction can provide important insights, enabling us to understand and control chemical reactions. This aim has required an extension of the relationships between the concepts of traditional chemistry and those of quantum mechanics. Bonding evolution theory (BET), which combines the topological analysis of the electron localization function (ELF) and Thom's catastrophe theory (CT), provides a powerful method that offers insight into the molecular mechanism of chemical rearrangements. In agreement with the laws of physical and aspects of quantum theory, BET can be considered an appropriate tool to tackle chemical reactivity with a wide range of possible applications. In this work, BET is applied to address a long-standing problem: the ability to monitor the flow of electron density. BET analysis shows a connection between quantum mechanics and bond making/forming processes. Likewise, the present approach retrieves the classical curly arrows used to describe the rearrangements of chemical bonds and provides detailed physical grounds for this type of representation. We demonstrate this procedure using the test set of prototypical examples of thermal ring apertures, and the degenerated Cope rearrangement of semibullvalene.

In Operando Structural and Acoustic Analysis of Lithium-Ion Batteries

Previously, we presented proof-of-concept results that demonstrated the promise of electrochemical-acoustic analysis as a scaleable method for in operando battery diagnostics. This technique is based on the redistribution of mass (density) and rearrangement of chemical bonds (modulus) that are fundamental to the operation of all closed, fixed-volume batteries. Using standard ultrasonic non-destructive testing hardware, we showed that for all closed batteries, each cell type (i.e., each chemistry and construction combination) has a unique acoustic fingerprint during cycling. These fingerprints display strong correlations between the acoustic properties of batteries and their state of charge (SOC). Here, we report on results gathered at beam line 6-BM-A at the Advanced Photon Source at Argonne National Laboratory. Simultaneous energy-dispersive x-Ray diffraction (EDXRD) and acoustic analysis measurements were made on several common types of commercial lithium-ion batteries, including LCO, LFP, and NCA. By comparing the in operando structural and acoustic data, we examine and discuss the physical underpinnings of these robust electrochemical-acoustic correlations.

ChemInform Abstract: Curly Arrows Meet Electron Density Transfers in Chemical Reaction Mechanisms: From Electron Localization Function (ELF) Analysis to Valence‐Shell Electron‐Pair Repulsion (VSEPR) Inspired Interpretation

AbstractReview: 173 refs.

Analysis of Time-Varying, Stochastic Gas Transport through Graphene Membranes

Molecular transport measurements through isolated nanopores can greatly inform our understanding of how such systems can select for molecular size and shape. In this work, we present a detailed analysis of experimental gas permeation data through single layer graphene membranes under batch depletion conditions parametric in starting pressure for He, H2, Ne, and CO2 between 100 and 670 kPa. We show mathematically that the observed intersections of the membrane deflection curves parametric in starting pressure are indicative of a time dependent membrane permeance (pressure normalized molecular flow). Analyzing these time dependent permeance data for He, Ne, H2, and CO2 shows remarkably that the latter three gases exhibit discretized permeance values that are temporally repeated. Such quantized fluctuations (called "gating" for liquid phase nanopore and ion channel systems) are a hallmark of isolated nanopores, since small, but rapid changes in the transport pathway necessarily influence a single detectable flux. We analyze the fluctuations using a Hidden Markov model to fit to discrete states and estimate the activation barrier for switching at 1.0 eV. This barrier is and the relative fluxes are consistent with a chemical bond rearrangement of an 8-10 atom vacancy pore. Furthermore, we use the relations between the states given by the Markov network for few pores to determine that three pores, each exhibiting two state switching, are responsible for the observed fluctuations; and we compare simulated control data sets with and without the Markov network for comparison and to establish confidence in our evaluation of the limited experimental data set.

Observation of hydrogen migration in cyclohexane under an intense femtosecond laser field.

We experimentally demonstrate hydrogen migration in photoionization and photofragmentation processes of cyclohexane (C6H12) under a near-infrared (800 nm) intense femtosecond laser field by the dc-slice imaging technique, and the observation of fragment ions CH3(+), C2H5(+), and C3H7(+) can be regarded as direct evidence that chemical bond rearrangement processes associated with hydrogen migration occur in the dissociative ionization process of cyclohexane. We measure the sliced images of fragment ions CH3(+), C2H5(+), and C3H7(+) and calculate their corresponding kinetic energy release (KER) and angular distributions, and it is confirmed that high-KER components of these fragment ions result from two-body Coulomb explosion of the doubly charged parent ion C6H12(2+) whereas low-KER components result from dissociative ionization of the singly charged parent ion C6H12(+). Moreover, we measure the maximally attainable relative yields of fragment ions CH3(+), C2H5(+), and C3H7(+), which approach 4.5%, 4.0%, and 3.0%, respectively.

Dynamical, spectroscopic and computational imaging of bond breaking in photodissociation: roaming and role of conical intersections.

Recent experimental and theoretical advances in the study of the dissociation of excited molecules are revealing unexpected mechanisms, when their outcomes are tackled by combining (i) space-time ion imaging of translational features, with (ii) spectroscopic probing of rotational and vibrational distributions; crucial is the assistance of (iii) the quantum chemistry of structural investigations of rearrangements of chemical bonds, and of (iv) the simulations of molecular dynamics to follow the evolution of selective bond stretching and breaking. Here we present results of such an integrated approach to methyl formate, HCOOCH3, the simplest of esters; the main focus is on the rotovibrationally excited CO (v=1) product and in general on the energy distribution in the fragments. Previous laser studies of dissociation into CO and CH3OH at a sequence of various wavelengths discovered signatures of a roaming mechanism by the late arrival of CO (v=0) products in time-of-flight ion imaging. Subsequent detailed investigations as a function of excitation energy provided the assessment of the threshold, which opens for triple breakdown into CO and further fragments H and CH3O, as spectroscopically characterized by ion imaging and FTIR respectively. Accompanying quantum mechanical electronic structure calculations and classical molecular dynamics simulations clarify the origin of these fragments through "roaming" pathways involving incipient radical intermediates at energies below the triple fragmentation threshold: a specific role is played by nonadiabatic transitions at a conical intersection between ground and excited states; alternative pathways focalize our attention to regions of the potential energy surfaces other than those in the neighbourhoods of saddle points along minimum energy paths: eventually this leads us to look for avenues in reaction kinetics beyond those of venerable transition state theories.

The importance of ensemble averaging in enzyme kinetics.

ConspectusThe active site of an enzyme is surrounded by a fluctuating environment of protein and solvent conformational states, and a realistic calculation of chemical reaction rates and kinetic isotope effects of enzyme-catalyzed reactions must take account of this environmental diversity. Ensemble-averaged variational transition state theory with multidimensional tunneling (EA-VTST/MT) was developed as a way to carry out such calculations. This theory incorporates ensemble averaging, quantized vibrational energies, energy, tunneling, and recrossing of transition state dividing surfaces in a systematic way. It has been applied successfully to a number of hydrogen-, proton-, and hydride-transfer reactions. The theory also exposes the set of effects that should be considered in reliable rate constants calculations.We first review the basic theory and the steps in the calculation. A key role is played by the generalized free energy of activation profile, which is obtained by quantizing the classical potential of mean force as a function of a reaction coordinate because the one-way flux through the transition state dividing surface can be written in terms of the generalized free energy of activation. A recrossing transmission coefficient accounts for the difference between the one-way flux through the chosen transition state dividing surface and the net flux, and a tunneling transmission coefficient converts classical motion along the reaction coordinate to quantum mechanical motion. The tunneling calculation is multidimensional, accounting for the change in vibrational frequencies along the tunneling path and shortening of the tunneling path with respect to the minimum energy path (MEP), as promoted by reaction-path curvature. The generalized free energy of activation and the transmission coefficients both involve averaging over an ensemble of reaction paths and conformations, and this includes the coupling of protein motions to the rearrangement of chemical bonds in a statistical mechanically correct way. The standard deviations of the transmissions coefficients provide information on the diversity of the distribution of reaction paths, barriers, and protein conformations along the members of an ensemble of reaction paths passing through the transition state.We first illustrate the theory by discussing the application to both wild-type and mutant Escherichia coli dihydrofolate reductase and hyperthermophilic Thermotoga maritima dihydrofolate reductase (DHFR); DHFR is of special interest because the protein conformational changes have been widely studied. Then we present shorter discussions of several other applications of EA-VTST/MT to transfer of protons, hydrogen atoms, and hydride ions and their deuterated analogs. Systems discussed include hydride transfer in alcohol dehydrogenase, xylose isomerase, and thymidylate synthase, proton transfer in methylamine dehydrogenase, hydrogen atom transfer in methylmalonyl-CoA mutase, and nucleophilic substitution in haloalkane dehalogenase and two-dimensional potentials of mean force for potentially coupled proton and hydride transfer in the β-oxidation of butyryl-coenzyme A catalyzed by short-chain acyl-CoA dehydrogenase and in the pyruvate to lactate transformation catalyzed by lactate dehydrogenase.

Atom mapping with constraint programming

Chemical reactions are rearrangements of chemical bonds. Each atom in an educt molecule thus appears again in a specific position of one of the reaction products. This bijection between educt and product atoms is not reported by chemical reaction databases, however, so that the “Atom Mapping Problem” of finding this bijection is left as an important computational task for many practical applications in computational chemistry and systems biology. Elementary chemical reactions feature a cyclic imaginary transition state (ITS) that imposes additional restrictions on the bijection between educt and product atoms that are not taken into account by previous approaches. We demonstrate that Constraint Programming is well-suited to solving the Atom Mapping Problem in this setting. The performance of our approach is evaluated for a manually curated subset of chemical reactions from the KEGG database featuring various ITS cycle layouts and reaction mechanisms.Electronic supplementary materialThe online version of this article (doi:10.1186/s13015-014-0023-3) contains supplementary material, which is available to authorized users.

An outlook review: Mechanochromic materials and their potential for biological and healthcare applications

Macroscopic mechanical perturbations have been observed to result in optical changes for certain compounds and composite materials. This phenomenon could originate from chemical and physical changes across various length scales, from the rearrangement of chemical bonds to alteration of molecular domains on the order of several hundred nanometers. This review classifies the mechanisms and surveys of how each class of mechanochromic materials has been, and can potentially be applied in biological and healthcare innovations. The study of cellular and molecular responses to mechanical forces in biological systems is an emerging field; there is potential in applying mechanochromic principles and material systems for probing biological systems. On the other hand, application of mechanochromic materials for medical and healthcare consumer products has been described in a wide variety of concepts and inventions. It is hopeful that further understanding of mechanochromism and material innovations would initiate concrete, impactful studies in biological systems soon.

ChemInform Abstract: Coordination‐Induced Skeletal Rearrangements of Zirconacyclobutene‐Silacyclobutene Fused Complexes

AbstractReview: 198 refs.

Studies on the Pyrolysis Kinetic Behaviours of Polycarbosilan

The pyrolysis kinetic behaviors and reaction mechanism of polycarbosilane (PCS) were characterized by means of XRD, SEM and on-line TG-DSC-FTIR-MS coupling technique, which showed that the pyrolysis process accorded with the F2 integral model (300-600°C), and the values of apparent activation energy (Ea) and pre-exponential factor (A) were 56.10KJ/mol and 10.84, respectively. During the pyrolysis process, PCS was converted into amorphous inorganic solid from organic polymer with breakage and rearrangement of chemical bonds, then to well-defined crystal structure of good thermal stability. Furthermore, the weight loss occurred mainly among 300°C and 800°C with CH4, (CH3)4Si,(CH3)3SiH,(CH3)2SiH2and other silane gases releasing from pyrolysis product leading to the conversion from organic polymers to inorganic ceramic. The pyrolysis product was converted into β-SiC crystal completely at 1400°C, and the crystallization of α-SiC phase occurred after 1550°C which might influence the stability of SiC matrix. Key words:polycarbosilane, organic precursor, pyrolysis kinetic behavior

Fragmentation of Hydrocarbon Molecules in Intense Laser Fields Studied by Coincidence Momentum Imaging: A Review

Fragmentation of polyatomic molecules is a fundamental chemical reaction in intense laser fields when the electric field strength of the laser pulse is comparable to or exceeds the intra-molecular Coulomb binding fields. For hydrocarbon molecules, because of the migration of light hydrogen atom (or proton) that can lead to chemical bond rearrangement of molecules, fragmentation of hydrocarbon molecules may result in new fragment species that could not be realized from the initial geometry of molecules by direct bond breaking, making the full characterization of their dynamical fragmentation processes difficult. In this article, we will review recent progress in the study of fragmentation of hydrocarbon molecules induced by intense laser fields using the coincidence momentum imaging method that can provide definite information on the fragmentation channels of molecules. The effect of hydrogen migration on fragmentation of hydrocarbon molecules is reviewed, based on which new possible schemes for controlling chemical bond breaking/formation by controlling the motion of protons within a hydrocarbon molecule is discussed.

Molecular Mechanism of Polyacrylate Helix Sense Switching across Its Free Energy Landscape

Helical polymers with switchable screw sense are versatile frameworks for chiral functional materials. In this work, we reconstructed the free energy landscape of helical poly(2,7-bis(4-tert-butylphenyl)fluoren-9-yl acrylate) [poly(BBPFA)], as its racemization is selectively driven by light without any rearrangement of chemical bonds. The chirality inversion was enforced by atomistic free energy simulations using chirality indices as reaction coordinates. The free energy landscape reproduced the experimental electronic circular dichroism spectra. We propose that the chirality inversion of poly(BBPFA) proceeds from a left-handed 31 helix via multistate free energy pathways to reach the right-handed 31 helix. The inversion is triggered by the rotation of biphenyl units with an activation barrier of 38 kcal/mol. To the best of our knowledge, this is the first report on the chiral inversion mechanism of a helical polymer determined in a quantitative way in the framework of atomistic free energy simulations.

Growth of thin vanadia nanobelts with improved lithium storage capacity in hydrothermally aged vanadia gels

A process of hydrothermal ageing of vanadia gels yields 10–20 nm thick and 90–100 nm wide nanobelts exceeding 10 microns in length. The diminished thickness and networking of anisotropic nanobelts lead to lithium intercalation capacities exceeding 450–500 mA h g−1 at a C/25 rate. The observed morphology features depend essentially on preparation conditions and allow to assume that this particular route results in a suitable morphology of nanobelts via chemical bond rearrangement in the course of olation and oxolation in the aged bulk gel. “Unzipping” of the layered structure of the precursor gel into single-crystalline nanobelts, and optimization of post-hydrothermal processing resulted in nanomaterials with enhanced electrochemical characteristics, making vanadia gels a precursor of choice for simple preparation of new battery nanomaterials.

Mechanism of the detonation of TNT-RDX mixtures as studied by the isotope tracer method

Data obtained using the isotope tracer method are explained by the occurrence of a sequence of rearrangements of chemical bonds with the formation of methane and free carbon in the early stages of chemical transformations and by the interdependent decomposition of TNT and RDX during detonation.

Hydrogen migration and C–C bond breaking in 1,3-butadiene in intense laser fields studied by coincidence momentum imaging

Two-body dissociation processes of H 2C CH–CH CH 2 2 + induced by an intense laser field were investigated by the coincidence momentum imaging method. Four dissociation pathways, C 4 H 6 2 + → CH 2 + + C 3 H 4 + , C 4 H 6 2 + → CH 3 + + C 3 H 3 + , C 4 H 6 2 + → C 2 H 3 + + C 2 H 3 + and C 4 H 6 2 + → C 2 H 2 + + C 2 H 4 + , were identified. The existence of the second and fourth pathways can be regarded as evidences of the chemical bond rearrangement processes associated with hydrogen migration in the intense laser field. It was found that the hydrogen atom bonded originally to one of the two central carbon atoms migrates preferentially to its neighboring terminal carbon atom site.

Ultrafast hydrogen migration in allene in intense laser fields: Evidence of two-body Coulomb explosion

Two-body Coulomb explosion of allene induced by an ultrashort (∼40 fs) intense laser field is investigated by the coincidence momentum imaging (CMI) method. From the CMI maps, two types of two-body Coulomb explosion pathways, C 3 H 4 2 + → CH m + + C 2 H 4 - m + ( m = 1–3) and C 3 H 4 2 + → C 3 H 4 - n + + H n + ( n = 1–3), are securely identified. The formation of CH 3 + , C 2 H 3 + , and H 3 + shows that the chemical bond rearrangement associated with the ultrafast hydrogen migration occurs prior to the ionization into C 3 H 4 2 + and that the extent of the hydrogen migration determines either one of the two initially identical C C chemical bonds is broken.

Analysis of carbon nitride growth in pedestal reactors by chemical vapor deposition

The chemical vapor deposition of polycrystalline carbon nitride in stagnation flow reactors is simulated. A model is used to predict the gas phase chemistry, temperature and velocity profiles, potential gaseous film growth precursors, and to evaluate the likelihood of bond rearrangement occurring in the bulk phase or on the deposition surface once the gaseous precursors are adsorbed. Numerical studies are carried out to predict the effects of inlet and substrate temperatures, reactor pressure, and inlet gas composition on the gas phase chemistry. Potential gaseous film growth precursors of carbon nitride are determined by quantitatively comparing the calculated results against existing experimental data. Results of the model indicate that the gas phase chemistry, including the gas composition at the deposition surface, is strongly affected by reactor pressure and inlet gas composition. However, the gas composition at the deposition surface does not depend strongly on the inlet temperature, while it is found to be strongly dependent on the substrate temperature. Since no correlation is found between the predicted near-surface concentrations of potential film growth precursors and experimentally measured bond types in the carbon nitride films, the experimentally measured bond types in the films must therefore result from chemical bond rearrangement occurring on the deposition surface or in the bulk phase once the gaseous precursors are adsorbed. Comparison between the calculated film growth rate using potential growth precursors and experimental data indicates that the CHx (x=0,2,3), C2H2, NHx (x=0,1,2), and HxCN (x=1,2) species are the most probable crystalline carbon nitride growth species. Among these, C and CH3 dominate the carbon contribution to the film growth, and N is the primary nitrogen bearing species responsible for the film growth. The sum of predicted film growth rates for carbon bearing species is comparable to the experimentally determined film growth rate.