Covalent Bond Dissociation Research Articles

Molecular Dynamics Simulation of Cumulative Microscopic Damage in a Thermosetting Polymer under Cyclic Loading.

To develop durable composite materials, it is crucial to elucidate the correlation between nanoscale damage in thermosetting resins and the degradation of their mechanical properties. This study aims to investigate this correlation by performing cyclic loading tests on the cross-linked structure of diglycidyl ether bisphenol A (DGEBA) and 4,4'-diaminodiphenyl sulfone (44-DDS) using all-atom molecular dynamics (MD) simulations. To accurately represent the nanoscale damage in MD simulations, a bond dissociation algorithm based on interatomic distance criteria is applied, and three characteristics are used to quantify the microscopic damage: stress-strain curves, entropy generation, and the formation of voids. As a result, the number of covalent bond dissociations increases with both the cyclic loading and its amplitude, resulting in higher entropy generation and void formation, causing the material to exhibit inelastic behavior. Furthermore, our findings indicate the occurrence of a microscopic degradation process in the cross-linked polymer: Initially, covalent bonds align with the direction of the applied load. Subsequently, tensioned covalent bonds sequentially break, resulting in significant void formation. Consequently, the stress-strain curves exhibit nonlinear and inelastic behavior. Although our MD simulations employ straightforward criteria for covalent bond dissociation, they unveil a distinct correlation between the number of bond dissociations and microscale damage. Enhancing the algorithm holds promise for yielding more precise predictions of material degradation processes.

Noncovalent Interactions in Mechanical Response of Thermoset Epoxy Resin.

Free volume in polymers is known to influence the mechanical response of the polymers. Noncovalent interactions such as hydrogen bonds, Coulombic electrostatic interactions, and van der Waals interactions are present within these free volume regions. The manuscript presents a comprehensive identification, characterization, and evolution of noncovalent interactions as a thermoset epoxy resin (typically used as an interfacial adhesive material) is subjected to uniaxial tension, shear, and shock loading. Even though noncovalent interactions dominate uniaxial tension and shear response (up to strain levels of 50% wherein covalent bond dissociation is not observed), both covalent and noncovalent interactions define response for shock loading. Van der Waals interactions dominate the response as the samples are subjected to strain levels of 50% in tension and shear. In contrast, hydrogen bonds influence shock response.

A Molecular Dynamics Simulation for Thermal Activation Process in Covalent Bond Dissociation of a Crosslinked Thermosetting Polymer

A novel algorithm for covalent bond dissociation is developed to accurately predict fracture behavior of thermosetting polymers via molecular dynamics simulation. This algorithm is based on the Monte Carlo method that considers the difference in local strain and bond-dissociation energies to reproduce a thermally activated process in a covalent bond dissociation. This study demonstrates the effectiveness of this algorithm in predicting the stress-strain relationship of fully crosslinked thermosetting polymers under uniaxial tensile conditions. Our results indicate that the bond-dissociation energy plays an important role in reproducing the brittle fracture behavior of a thermosetting polymer by affecting the number of covalent bonds that are dissociated simultaneously.

Extension of natural reaction orbital approach to multiconfigurational wavefunctions.

Recently, we proposed a new orbital analysis method, natural reaction orbital (NRO), which automatically extracts orbital pairs that characterize electron transfer in reaction processes by singular value decomposition of the first-order orbital response matrix to the nuclear coordinate displacements [Ebisawa et al., Phys. Chem. Chem. Phys. 24, 3532 (2022)]. NRO analysis along the intrinsic reaction coordinate (IRC) for several typical chemical reactions demonstrated that electron transfer occurs mainly in the vicinity of transition states and in regions where the energy profile along the IRC shows shoulder features, allowing the reaction mechanism to be explained in terms of electron motion. However, its application has been limited to single configuration theories such as Hartree-Fock theory and density functional theory. In this work, the concept of NRO is extended to multiconfigurational wavefunctions and formulated as the multiconfiguration NRO (MC-NRO). The MC-NRO method is applicable to various types of electronic structure theories, including multiconfigurational theory and linear response theory, and is expected to be a practical tool for extracting the essential qualitative features of a broad range of chemical reactions, including covalent bond dissociation and chemical reactions in electronically excited states. In this paper, we calculate the IRC for five basic chemical reaction processes at the level of the complete active space self-consistent field theory and discuss the phenomenon of electron transfer by performing MC-NRO analysis along each IRC. Finally, issues and future prospects of the MC-NRO method are discussed.

Variational quantum eigensolver simulations with the multireference unitary coupled cluster ansatz: a case study of the C2v quasi-reaction pathway of beryllium insertion into a H2 molecule.

Variational quantum eigensolver (VQE)-based quantum chemical calculations have been extensively studied as a computational model using noisy intermediate-scale quantum devices. The VQE uses a parametrized quantum circuit defined through an "ansatz" to generate approximated wave functions, and the appropriate choice of an ansatz is the most important step. Because most chemistry problems focus on the energy difference between two electronic states or structures, calculating the total energies in different molecular structures with the same accuracy is essential to correctly understand chemistry and chemical processes. In this context, the development of ansatzes that are capable of describing electronic structures of strongly correlated systems accurately is an important task. Here we applied a conventional unitary coupled cluster (UCC) and a newly developed multireference unitary coupled cluster with partially generalized singles and doubles (MR-UCCpGSD) ansatzes to the quasi-reaction pathway of Be insertion into H2, LiH molecule under covalent bond dissociation, and a rectangular tetra-hydrogen cluster known as a P4 cluster; these are representative systems in which the static electron correlation effect is prominent. Our numerical simulations revealed that the UCCSD ansatz exhibits extremely slow convergence behaviour around the point where an avoided crossing occurs in the Be + H2 → BeH2 reaction pathway, resulting in a large discrepancy of the simulated VQE energy from the full-configuration interaction (full-CI) value. By contrast, the MR-UCCpGSD ansatz can give more reliable results with respect to total energy and the overlap with the full-CI solution, insisting the importance of multiconfigurational treatments in the calculations of strongly correlated systems. The MR-UCCpGSD ansatz allows us to compute the energy with the same accuracy regardless of the strength of multiconfigurational character, which is an essential property to discuss energy differences of various molecular systems.

Stimuli-responsive destructible polymeric hydrogels based on irreversible covalent bond dissociation

Covalently crosslinked stimuli-destructible hydrogels with the ability of irreversible bond dissociation have attracted great attentions due to their biodegradability, stability against hydrolysis, and controlled solubility upon insertion of desired triggers.

Simulation Study of the Effects of Interfacial Bonds on Adhesion and Fracture Behavior of Epoxy Resin Layers.

The adhesion and fracture behavior of tetraglycidyl-4,4'-diaminodiphenylmethane (TGDDM)/4,4'-diaminodiphenyl sulfone (44DDS)-bisphenol A diglycidyl ether (DGEBA)/44DDS layer interfaces were investigated by molecular dynamics (MD) simulation, mainly focusing on the role of covalent and noncovalent interactions. To accurately investigate the bond dissociation processes, the force field parameters of several bond potentials of the epoxy resin polymers were optimized by density functional theory calculations. In the MD simulations under a tensile load, small voids gradually developed without covalent bond dissociation in the plateau region. In the final large strain region, the stress rapidly increased with bond breaking, leading to failure. When the chemical bonds across the interface between the two layers were removed, the stress-strain curve in the initial elastic region was almost the same as that with interfacial bonds. This showed that the nonbonded interactions governed adhesion strength in the initial elastic region. In contrast, the bonded interactions at interfaces played important roles in the hardening regions because the bonded interactions made the major contribution to the fracture energies. We also investigated the effect of the etherification reaction in cross-linking. It was found that the etherification reaction mainly contributed to the behavior in the late region with large strain. These simulation results revealed that the nonbonded interactions, especially, van der Waals interactions, are important factors for adhesion of the different polymer layers in the small strain region up to the yield point.

A DFT simulation on induction reactions involved radicals during pyrolysis of heavy organics

With the free radical reaction during the pyrolysis process of heavy organics as the background, the research approach based on density functional theory was adopted to exploring the induction of free radicals on covalent bond and its effect on covalent bond dissociation energy. The energies of seven kinds of covalent bond reactions induced respectively by ·CH3, ·OH and ·H were calculated theoretically on the Gaussian 09 program at the level of ωB97XD/6-31G**. The results indicate that the steric hindrance effect plays a significant role in the energy barrier of free radical induced reaction, while the influence of the covalent bond type plays a minor role. When the isogroup induced exchange reaction of ·OH and ·H does not proceed, the induced energy barrier of ·OH is about 40 kJ/mol higher than that of ·H and the induced energy barrier of ·CH3 is about 50 and 90 kJ/mol higher than that of ·OH and ·H respectively. When the isogroup induced exchange reaction of ·OH and ·H works, it will result in the increasing of 70 kJ/mol of the energy barrier. During the process of calculation, the specific situation of induced reaction should be judged and revised. The above values can be used to estimate the energy barriers of different covalent bond induced reactions.

A quantum algorithm for spin chemistry: a Bayesian exchange coupling parameter calculator with broken-symmetry wave functions.

The Heisenberg exchange coupling parameter J (H = −2JSi · Sj) characterises the isotropic magnetic interaction between unpaired electrons, and it is one of the most important spin Hamiltonian parameters of multi-spin open shell systems. The J value is related to the energy difference between high-spin and low-spin states, and thus computing the energies of individual spin states are necessary to obtain the J values from quantum chemical calculations. Here, we propose a quantum algorithm, B̲ayesian ex̲change coupling parameter calculator with b̲roken-symmetry wave functions (BxB), which is capable of computing the J value directly, without calculating the energies of individual spin states. The BxB algorithm is composed of the quantum simulations of the time evolution of a broken-symmetry wave function under the Hamiltonian with an additional term jS2, the wave function overlap estimation with the SWAP test, and Bayesian optimisation of the parameter j. Numerical quantum circuit simulations for H2 under a covalent bond dissociation, C, O, Si, NH, OH+, CH2, NF, O2, and triple bond dissociated N2 molecule revealed that the BxB can compute the J value within 1 kcal mol−1 of errors with less computational costs than conventional quantum phase estimation-based approaches.

Evaporation and Fragmentation of Organic Molecules in Strong Electric Fields Simulated with DFT

Atom probe tomography allows us to measure the three-dimensional composition of materials with up to atomic resolution by evaporating the material using high electric fields. Initially developed for metals, it is increasingly used for covalently bound structures. To aid the interpretation of the obtained fragmentation pattern, we modeled the fragmentation and desorption of self-assembled monolayers of thiolate molecules on a gold surface in strong electrostatic fields using density functional theory. We used a cluster model and a periodic model of amino-undecanethiolate, NH2(CH2)11S, and fluoro-decanethiolate, CF3(CF2)7(CH2)2S. In the former molecule, the fragment CH2NH2+ was found to evaporate at fields of 5.4-7.7 V/nm. It was followed by different hydrocarbon fragments. Fluoro-decanethiolate evaporates CF3+ at fields of 5.7-6.7 V/nm in the cluster model and at 15.4-23.1 V/nm in the periodic model, followed by CF2+ and C2F42+. Detailed analysis of the electronic structure during the evaporation process revealed a stepwise accumulation of the charge in the head groups exposed to the strongest fields, followed by dissociation of covalent bonds. These observations will facilitate the analysis of atom probe experiments of covalently bound structures.

Mechanical Properties of Cellulose Nanocrystal (CNC) Bundles: Coarse-Grained Molecular Dynamic Simulation

Cellulose nanocrystals (CNCs) is a promising biodegradable nanomaterial with outstanding physical, chemical, and mechanical properties for many applications. Although aligned CNCs can self-assemble into bundles, their mechanical performance is reduced by interfacial strength between CNCs and a twisted structure. In this paper, we employ developed coarse-grained (CG) molecular dynamic (MD) simulations to investigate the influence of twist and interface energy on the tensile performance of CNC bundles. CNC bundles of different sizes (number of particles) are tested to also include the effect of size on mechanical performance. The effect of interfacial energy and twist on the mechanical performance shows that elastic modulus, strength, and toughness are more sensitive to twisted angle than interfacial energy. In addition, the effect of size on the bundle and twist on their mechanical performance revealed that both size and twist have a significant effect on the results and can reduce the strength and elastic modulus by 75% as a results of covalent bond dissociation. In addition, a comparison of the broken regions for different values of twist shows that by increasing the twist angle the crack propagates in multiple locations with a twisted shape.

Mechanical Unfolding of Macromolecules Coupled to Bond Dissociation.

Single-molecule force spectroscopy has become a powerful tool to investigate molecular mechanisms in biophysics and materials science. In particular, the new field of polymer mechanochemistry has emerged to study how tension may induce chemical reactions in a macromolecule. A rich example is the mechanical unfolding of the metalloprotein rubredoxin coupled to dissociation of iron-sulfur bonds that has recently been studied in detail by atomic force microscopy. Here, we present a simple molecular model composed of a classical all-atom force field description, implicit solvation, and steered molecular dynamics simulation to describe the mechanical properties and mechanism of forced unfolding coupled to covalent bond dissociation of macromolecules. We apply this model and test it extensively to simulate forced rubredoxin unfolding, and we dissect the sensitivity of the calculated mechanical properties with model parameters. The model provides a detailed molecular explanation of experimental observables such as force-extension profiles and contour length increments. Changing the points of force application along the macromolecule results in different unfolding mechanisms, characterized by disruption of hydrogen bonds and secondary protein structure, and determines the degree of solvent access to the reactive center. We expect that this molecular model will be broadly applicable to simulate (bio)polymer mechanochemistry.

Accurate Dissociation of Chemical Bonds Using DFT-in-DFT Embedding Theory with External Orbital Orthogonality.

Our recent density functional theory (DFT)-in-DFT embedding protocol, which enforces intersubsystem (or external orbital) orthogonality, is used for the first time to investigate covalent bond dissociation and is shown to do so accurately. Full potential energy curves for the dissociation of a H-O bond in H2O and the C-C bond in H3C-CH3 have been constructed using the new embedding method, as have the challenging ionic bonds in LiH and LiF, and were found to match the reference Kohn-Sham (KS)-DFT curves to at least one part in 106. The added constraint of external orbital orthogonality allows for the formulation of an embedding protocol that does not rely on approximate kinetic energy functionals for the evaluation of the so-called nonadditive kinetic potential, does not introduce compensatory potentials, and does not require a total system calculation at any stage. The present work extends the demonstrated applicability of the external orthogonality variant of embedding theory by more than a factor of 2 to the interaction strength range of strong single bonds. In particular, it is demonstrated that homolytic cleavage of both covalent and ionic bonds into radicals can be accomplished.

Atomistic modeling framework for a cyclobutane-based mechanophore-embedded nanocomposite for damage precursor detection

An atomistic modeling framework is developed to simulate mechanophore activation and evaluate the sensitivity of cyclobutane-based mechanophores. Mechanophores are force-responsive functional units, which when embedded in an epoxy-based thermoset polymer matrix provide self-sensing capability in polymeric composites. In the presence of damage or damage precursors, covalent bond dissociation of the mechanophore generates fluorescence, which is referred to as the mechanophore activation. A Tris-(Cinnamoyloxymethyl)-Ethane (TCE) monomer is used to synthesize the cyclobutane structure through ultra-violet (UV) dimerization; the synthesized cyclobutanes are incorporated into the thermoset polymer matrix. A hybrid molecular dynamics (MD) simulation framework is developed by integrating two force-fields: a classical force-field, Merck Molecular Force Field (MMFF) and a bond-order based force-field, Reactive Force Field (ReaxFF). The hybrid MD methodology enables construction of the molecular model of the cyclobutane-based mechanophore embedded nanocomposite and simulation of the mechanophore activation. The synthesis of epoxy network and cyclobutane structure is numerically simulated by a covalent bond generation method employing MMFF. Through this numerical synthesis, the physical entanglement between the epoxy network and cyclobutane chain is also captured, which determines the local force distribution within the novel nanocomposite. Covalent bond dissociation due to the applied local force on the mechanophore is simulated using ReaxFF and results from the virtual deformation tests show successful mechanophore activation. A local work analysis method is developed to evaluate the sensitivity of mechanophore. Results from the simulation framework show increment in the number of activated cyclobutanes during the deformation test. Good agreement is observed with experimental results: the intensity of fluorescence was found to be directly proportional to the deformation.

Molecular dynamics study of brittle fracture in epoxy-based thermoset polymer

A novel molecular dynamics (MD) simulation methodology to capture brittle fracture in epoxy-based thermoset polymer under mechanical loading is presented. The ductile behavior of amorphous polymers has been captured through traditional MD simulation methods by estimating the stress-strain response beyond the yield point; however, brittle fracture in highly crosslinked polymer materials such as epoxy thermoset has not been addressed appropriately and is the primary objective of this work. In this study, a numerically cured epoxy system comprising molecules of epoxy resin and hardener is generated. During the virtual deformation test, it is observed that the inherent molecular vibration due to temperature re-equilibrates the elongated covalent bonds and this molecular vibration impedes further stretching the covalent bond leading to scission. In order to overcome the influence of thermal vibration, an approach that employs deformation tests at absolute zero temperature condition – a concept borrowed from the quasi-continuum method, is developed. Bond dissociation energy is measured to quantify the extent of failure in the system by calculating the bond potentials during the deformation tests. Applying zero temperature condition to the deformation test, however, requires a large amount of computational time due to intermediate energy minimization processes. To improve the computational efficiency, an ultra-high strain rate (UHSR ≈ 1013 s−1) approach is developed by which the thermal vibration is decoupled from the deformation test using a strain rate higher than molecular vibration frequency. Note that the deformation test performed by traditional MD simulation methods used strain rates ranging 108–1010 s−1. Simulation results show that the UHSR approach successfully captures brittle fracture in epoxy polymer due to covalent bond dissociation with high computational efficiency.

Dispersion Corrections Improve the Accuracy of Both Noncovalent and Covalent Interactions Energies Predicted by a Density-Functional Theory Approximation.

The use of pairwise dispersion corrections together with dispersion-correcting potentials (DCPs) offers a computationally low-cost approach to improving the performance of a density-functional theory based method with respect to the prediction of important chemical properties. In this work, we develop DCPs for the C, H, N, and O atoms for use with the BLYP generalized gradient approximation functional coupled with "D3" pairwise dispersion corrections and 6-31+G(2d,2p) basis sets. The combined approach, referred to as BLYP-D3-DCP, offers generally improved performance over both unadorned BLYP and BLYP with D3 corrections with respect to the prediction of noncovalent binding energies (BEs) and covalent bond dissociation enthalpies (BDEs). Predicted barrier heights for a set of pericyclic and Diels-Alder reactions are improved in some instances, as are organic bond separation reaction energies and radical stabilization energies. It is also shown that the BLYP-D3-DCP approach outperforms B3LYP-D3 in the prediction of many chemical properties, in particular noncovalent BEs and BDEs, suggesting that the addition of D3 and DCP corrections, which have negligible computational cost, to simple density functionals like BLYP may elevate their performance to that of more complex functionals such as B3LYP.

Modeling of kraft lignin pyrolysis based on bond dissociation and fragments coupling

It is generally recognized that pyrolysis of biomass involves two steps: dissociation of covalent bonds to generate free radical fragments and coupling of the free radical fragments to form products. Experiments and simulations on biomass pyrolysis in the literature, however, ignored the role of each step and provided only the overall results of the two steps. Based on the two-step mechanism, this work simulates pyrolysis of a structural unit of kraft lignin. The first step is assumed to be governed by Boltzmann distribution of each bond in the unit at a given temperature and time, while the second step is assumed to follow Monte-Carlo algorithm. The Boltzmann–Monte Carlo pyrolysis model built is analyzed with the aid of basic and secondary assumptions. The mode is further validated by simulating pyrolysis of kraft lignin and comparing the results with experimental data in the literature. It is found that the model simulates the pyrolysis behavior reasonably well, in terms of changes in bonds’ population and amounts of radicals formed versus temperature and time.

A General Quantum Mechanically Derived Force Field (QMDFF) for Molecules and Condensed Phase Simulations.

A black-box type procedure is presented for the generation of molecule-specific, classical potential energy functions (force-field, FF) solely from quantum mechanically (QM) computed input data. The approach can treat covalently bound molecules and noncovalent complexes with almost arbitrary structure. The necessary QM information consists of the equilibrium structure and the corresponding Hessian matrix, atomic partial charges, and covalent bond orders. The FF fit is performed automatically without any further input and yields a specific (nontransferable) potential which very closely resembles the QM reference potential near the equilibrium. The resulting atomistic, fully flexible FF is anharmonic and allows smooth dissociation of covalent bonds into atoms. A newly proposed force-constant-bond-energy relation with little empiricism provides reasonably accurate (about 5-10% error) atomization energies for almost arbitrary diatomic and polyatomic molecules. Intra- and intermolecular noncovalent interactions are treated by using well established and accurate D3 dispersion coefficients, CM5 charges from small basis set QM calculations, and a new interatomic repulsion potential. Particular attention has been paid to the construction of the torsion potentials which are partially obtained from automatic QM-tight-binding calculations for model systems. Detailed benchmarks are presented for conformational energies, atomization energies, vibrational frequencies, gas phase structures of organic molecules, and transition metal complexes. Comparisons to results from standard FF or semiempirical methods reveal very good accuracy of the new potential. While further studies are necessary to validate the approach, the initial results suggest QMDFF as a routine tool for the computation of a wide range of properties and systems (e.g., for molecular dynamics of isolated molecules, explicit solvation, self-solvation (melting) or even for molecular crystals) in particular when standard parametrizations are unavailable.

Local spin from strongly orthogonal geminal wavefunctions

Covalent bond dissociation is examined by three geminal-based theories. One approach (antisymmetrised product of strongly orthogonal geminals) assumes purely singlet geminals, while two others operate with mixtures of singlets and triplets (cf. restricted–unrestricted strongly orthogonal singlet-type geminals, hereafter RUSSG). The RUSSG is the wavefunction in the second method. It is spin contaminated. The spin contamination of RUSSG is projected out in a spin-purification step in the third method. Description of local (i.e. atomic) spin by geminal-based theories is examined. Prototype systems showing the deficiency of singlet coupling are taken as test cases. We find that the local spin of equilibrium structures is correctly described by purely singlet geminals. Triplet geminals are shown to be essential for the description of local spin when dissociating multiple bonds, or switching between two Lewis structures of the same molecule.

Dispersion-correcting potentials can significantly improve the bond dissociation enthalpies and noncovalent binding energies predicted by density-functional theory.

Dispersion-correcting potentials (DCPs) are atom-centered Gaussian functions that are applied in a manner that is similar to effective core potentials. Previous work on DCPs has focussed on their use as a simple means of improving the ability of conventional density-functional theory methods to predict the binding energies of noncovalently bonded molecular dimers. We show in this work that DCPs developed for use with the LC-ωPBE functional along with 6-31+G(2d,2p) basis sets are capable of simultaneously improving predicted noncovalent binding energies of van der Waals dimer complexes and covalent bond dissociation enthalpies in molecules. Specifically, the DCPs developed herein for the C, H, N, and O atoms provide binding energies for a set of 66 noncovalently bonded molecular dimers (the "S66" set) with a mean absolute error (MAE) of 0.21 kcal/mol, which represents an improvement of more than a factor of 10 over unadorned LC-ωPBE/6-31+G(2d,2p) and almost a factor of two improvement over LC-ωPBE/6-31+G(2d,2p) used in conjunction with the "D3" pairwise dispersion energy corrections. In addition, the DCPs reduce the MAE of calculated X-H and X-Y (X,Y = C, H, N, O) bond dissociation enthalpies for a set of 40 species from 3.2 kcal/mol obtained with unadorned LC-ωPBE/6-31+G(2d,2p) to 1.6 kcal/mol. Our findings demonstrate that broad improvements to the performance of DFT methods may be achievable through the use of DCPs.