Dissociation Path Research Articles

Potential Mean Force from Umbrella Sampling Simulations: What Can We Learn and What Is Missed?

Changes in free energy provide valuable information for molecular recognition, including both ligand-receptor binding thermodynamics and kinetics. Umbrella sampling (US), a widely used free energy calculation method, has long been used to explore the dissociation process of ligand-receptor systems and compute binding free energy. In existing publications, the binding free energy computed from the potential of mean force (PMF) with US simulation mostly yielded "ball park" values with experimental data. However, the computed PMF values are highly influenced by factors such as initial conformations and/or trajectories provided, the reaction coordinate, and sampling of conformational space in each US window. These critical factors have rarely been carefully studied. Here we used US to study the guest aspirin and 1-butanol dissociation processes of β-cyclodextrin (β-CD) and an inhibitor SB2 dissociation from a p38α mitogen-activated protein kinase (MAPK) complex. For β-CD, we used three different β-CD conformations to generate the dissociation path with US windows. For p38α, we generated the dissociation pathway by using accelerated molecular dynamics followed by conformational relaxing with short conventional MD, steered MD, and manual pulling. We found that, even for small β-CD complexes, different β-CD conformations altered the height of the PMF, but the pattern of PMF was not affected if the MD sampling in each US window was well-converged. Because changing the macrocyclic ring conformation needs to rotate dihedral angles in the ring, a bound ligand largely restrains the motion of cyclodextrin. Therefore, once a guest is in the binding site, cyclodextrin cannot freely change its initial conformation, resulting in different absolute heights of the PMF, which cannot be overcome by running excessively long MD simulations for each US window. Moreover, if the US simulations were not converged, the important barrier and minimum were missed. For ligand-protein systems, our studies also suggest that the dissociation trajectories modeled by an enhanced sampling method must maintain a natural molecular movement to avoid biased PMF plots when using US simulations.

A dissociative path to phosphorylation

X-ray structures of reactant and product states, as well as theoretical calculations, have helped uncover the mechanism of Escherichia coli phosphofructokinase 2.

A valence bond study of the activation of methyl halides bonds by electric fields

In the present work, the activation of methyl halides bonds under experience of an external electric field (EEF) is explained from the Valence Bond theory perspective. The dissociation mechanism of C–X bonds (X [Formula: see text] Cl, Br, I) influenced by a homogeneous and a heterogeneous field placed parallel to the bond axis is presented. For all examples, an increase in the electric field strength have similar consequences: (i) the decrease of the energy depth along the dissociation path, (ii) an increase of the equilibrium interatomic distance (at high EEFs), and (iii) the transition from a homolytic to a heterolytic dissociation after some field magnitude. These general behaviors are explained through the curve crossing between the ionic and the covalent structure at some field strength.

Dissociation path competition of radiolysis ionization-induced molecule damage under electron beam illumination.

Radiolysis ionization under electron beam illumination induces dissociation and damage of organic and biological molecules; thus, it is impossible to image the related materials by transmission electron microscopy (TEM). To understand the atomistic mechanism of radiolysis damage, we developed a systematical procedure based on real-time time-dependent density functional theory (rt-TDDFT) for simulating the radiolysis damage processes of molecules; this procedure can describe the ionization cross sections of the electronic states and the fast dissociation processes caused by hot carrier cooling and the Auger decay on deep levels. For the radiolysis damage of C2H6O2, our simulation unexpectedly showed that there is strong competition among three different dissociation paths, including fast dissociation caused by nonadiabatic cooling of the hot carrier; fast dissociation caused by Auger decay, which induces double ionization and Coulomb explosion; and slow dissociation caused by increased kinetic energy. As the energy of the incident electron beam changes, the time scales of these dissociation paths and their relative contributions to the molecule damage change significantly. These simulation results explain the measured mass spectra of the C2H6O2 dissociation fragments and also provide clear competition mechanisms for blocking these dissociation paths in the TEM imaging of organic and biological materials.

A dimer path for CO dissociation on PtSn

Density functional theory calculations are used to investigate CO adsorption, dissociation and SnOX formation on Pt3Sn.

Catalytic activity of palladium-doped silver dilute nanoalloys for formate oxidation from a theoretical perspective.

The large-scale practical application of formate oxidation reaction (FOR) catalysts is hindered by their low activity and high cost. Herein, for the first time, a series of Pd-doped Ag dilute nanoalloys is demonstrated to have high catalytic activity in FOR with reduced consumption of Pd metals through density functional theory calculations, where the effects of potential, solvent and spin on catalytic performance are discussed. The Pd1Ag(111) single-atom alloy (SAA) exhibits higher FOR catalytic activity as reflected by the low limiting potential of 0.026 eV for the direct association path and a value of 0.084 eV for the direct dissociation path, and the lowest activation energy of 0.774 eV for the rate-determining-step in the direct dissociation path compared with Pd2Ag(111) and Pd3Ag(111) dilute alloys. Pd1Ag(111) SAA exhibits an extremely narrow sharp peak in the partial density of states from -0.75 to -2.0 eV, which is due to the free-atom-like electronic structure of the single Pd atom. The isolated Pd single atom is more stable by -0.041 and -0.097 eV, respectively, than the aggregated Pd2 and Pd3 atom clusters on the Ag(111) surface, which verifies the potential application of Pd1Ag(111) SAA in experiments. Overall, this work further elucidates the theoretical profile of FOR and provides a new strategy for designing the catalytic reaction at the atomic level.

Characterization of the helicon plasma flux to the target of Proto-MPEX

The ITER divertor will have to handle the boundary plasma power exhaust in the form of high heat and particle flux. The Prototype Material Plasma Exposure eXperiment (Proto-MPEX) is a plasma source development device for the proposed Material Plasma Exposure eXperiment (MPEX), which is intended to create fusion reactor divertor-like plasma conditions for studying plasma material interactions. Here, ion fluxes to various targets within Proto-MPEX are found to be 5 ± 2.5 × 1023 m−2s-1 when using only a helicon plasma source. The fluxes along the flux tube are compared for both 30 cm in front of the target and a few cm in front of the target. The emission intensity fall-off distance in front of the target is studied via Balmer series from a visible camera looking at the target. This fall-off distance of ∼2–4 cm and the dissociation and ionization mean free path of D2 being over 0.5 m leads to a conclusion that Proto-MPEX is not in a high recycling regime with helicon only plasmas.

Interfacing Transition Metal Dichalcogenides with Carbon Nanodots for Managing Photoinduced Energy and Charge-Transfer Processes.

Exfoliated semiconducting MoS2 and WS2 were covalently functionalized with 1,2-dithiolane-modified carbon nanodots (CNDs). The newly synthesized CND-MoS2 and CND-WS2 hybrids were characterized by spectroscopic, thermal, and electron microscopy imaging methods. Based on electronic absorption and fluorescence emission spectroscopy, modulation of the optoelectronic properties of TMDs by interfacing with CNDs was accomplished. Electrochemical studies revealed facile oxidation of MoS2 over WS2 in the examined hybrids, suggesting it to be better electron donor. Excited state events, investigated by femtosecond transient absorption spectroscopic studies, revealed ultrafast energy transfer from photoexcited CNDs to both MoS2 and WS2. Interestingly, upon MoS2 photoexcitation, charge transfer from an exciton dissociation path of MoS2 to CNDs, within CND-MoS2, was observed. However, such a process in CND-WS2 was found to be absent due to energetic reasons. The present study highlights the importance of TMD-derived donor-acceptor hybrids in light energy harvesting and optoelectronic applications. Furthermore, the fundamental information obtained from the current results will benefit design strategies and impact the development of additional TMD-based hybrid materials to efficiently manage and perform in electron-transfer processes.

Exohedral complexation of [formula omitted] with ECp∗+ half-sandwich complexes (E[dbnd]Si, Ge, Sn, Pb): A DFT study

The hexagonal and heptagonal holes of B39- allow its complexation with a half sandwich complex ECp∗+ (ESi, Ge, Sn, Pb). Structure and the nature of bonding of (η6/7-B39)E(η5-Cp∗) are explored through the density functional theory based computation. (η6-B39)E(η5-Cp∗) isomers are more stable than (η7-B39)E(η5-Cp∗) and the energy difference between these two isomers decreases down the group from Si to Pb. The dissociation path, (η6/7-B39)E(η5-Cp∗) → B39-+ ECp∗+ is studied. For all E, (η6/7-B39)E(η5-Cp∗) is formed exergonically at 298 K temperature as given by the ΔG values of dissociation path [60.1(Si) to 68.3(Pb) kcal/mol for (η6-B39)E(η5-Cp∗) and 58.3(Si) to 67.8(Pb) kcal/mol for (η7-B39)E(η5-Cp∗)]. The adduct becomes bent around the central E atom when B39- gets attached to ECp∗+ and the amount of bending increases gradually down the group from Si to Pb. Bonding analysis of the stable isomer, (η6-B39)E(η5-Cp∗) has been done by natural bonding orbital (NBO) and energy decomposition analyses (EDA). The electron density from B39- is transferred to the ECp∗+ moiety as revealed by the NBO analysis. All the complexes are mainly stabilized by the electrostatic and orbital interactions between B39- and ECp∗+ fragments as highlighted by the EDA results.

Periodic and non-periodic DFT modeling of CO reduction on the surface of Ni-doped graphene nanosheet

Carbon monoxide, as a major pollutant of the environment, could be reduced to hydrocarbons by using transition metal catalysts. Different catalysts produce different hydrocarbons, ranging from methane to heavier hydrocarbons. Some catalysts prefer methanation, while some others do Fischer-Tropsch process. Both kinds of catalysts suffer from coke formation on their surfaces. Coke is produced from direct dissociation of CO on the surface of a catalyst. In this paper, direct and indirect dissociation paths of CO on the Ni-doped graphene are studied by periodic and non-periodic DFT calculations. It is shown that direct CO dissociation has very high barrier energy of 5.32 eV which prevents coke formation on the catalyst. Indirect path investigation shows that HCO intermediate is more feasible than COH one. With the addition of one H to CO, barrier energy is reduced from 5.3 eV to 3.09 eV, and introducing one more H to form CH2O intermediate, the barrier energy is reduced to 1.5 eV. In addition, NBO and QTAIM theories are used to study the donor-acceptor charge transfers and nature of interactions. Data shows that there is a large charge donation and back-donation for CO adsorption on the surface of Ni-doped graphene. Electron density difference graphs and NBO/QTAIM charges show that, in all studied complexes, charge transfer is occurred from Ni to the adsorbed species.

A generalized unimolecular impulsive model for curved reaction path.

This work aims to introduce a generalized impulsive model for unimolecular dissociation processes. This model allows us to take into account the curvature of the reaction path explicitly. It is a generalization of the previously developed multi-center impulsive model [P.-Y. Tsai and K.-C. Lin, J. Phys. Chem. A 119, 29 (2015)]. Several limitations of conventional impulsive models are eliminated by this study: (1) Unlike conventional impulsive models, in which a single molecular geometry is responsible for the impulse determination, the gradients on the whole dissociation path are taken into account. The model can treat dissociation pathways with large curvatures and loose saddle points. (2) The method can describe the vibrational excitation of polyatomic fragments due to the bond formation by multi-center impulse. (3) The available energy in conventional impulsive models is separated into uncoupled statistical and impulsive energy reservoirs, while the interplay between these reservoirs is allowed in the new model. (4) The quantum state correlation between fragments can be preserved in analysis. Dissociations of several molecular systems including the roaming pathways of formaldehyde, nitrate radical, acetaldehyde, and glyoxal are chosen as benchmarks. The predicted photofragment energy and vector distributions are consistent with the experimental results reported previously. In these examples, the capability of the new model to treat the curved dissociation path, loose saddle points, polyatomic fragments, and multiple-body dissociation is verified. As a cheaper computational tool with respect to ab initio on-the-fly direct dynamic simulations, this model can provide detailed information on the energy disposal, quantum state correlation, and stereodynamics in unimolecular dissociation processes.

Development of a Multicenter Density Functional Tight Binding Model for Plutonium Surface Hydriding.

We detail the creation of a multicenter density functional tight binding (DFTB) model for hydrogen on δ-plutonium, using a framework of new Slater-Koster interaction parameters and a repulsive energy based on the Chebyshev Interaction Model for Efficient Simulation (ChIMES), where two- and three-center atomic interactions are represented by linear combinations of Chebyshev polynomials. We find that our DFTB/ChIMES model yields a total electron density of states for bulk δ-Pu that compares well to that from Density Functional Theory, as well as to a grid of energy calculations representing approximate H2 dissociation paths on the δ-Pu (100) surface. We then perform molecular dynamics simulations and minimum energy pathway calculations to determine the energetics of surface dissociation and subsurface diffusion on the (100) and (111) surfaces. Our approach allows for the efficient creation of multicenter repulsive energies with a relatively small investment in initial DFT calculations. Our efforts are particularly pertinent to studies that rely on quantum calculations for interpretation and validation, such as experimental determination of chemical reactivity both on surfaces and in condensed phases.

Reaction paths of alane dissociation on the Si(0 0 1) surface

Building on our earlier study, we examine the kinetic barriers to decomposition of alane, AlH3, on the Si(0 0 1) surface, using the nudged elastic band approach within density functional theory. We find that the initial decomposition to AlH with two H atoms on the surface proceeds without a significant barrier. There are several pathways available to lose the final hydrogen, though these present barriers of up to 1 eV. Incorporation is more challenging, with the initial structures less stable in several cases than the starting structures, just as was found for phosphorus. We identify a stable route for Al incorporation following selective surface hydrogen desorption (e.g. by scanning tunneling microscope tip). The overall process parallels PH3, and indicates that atomically precise acceptor doping should be possible.

Signatures of a Conical Intersection in Adiabatic Dissociation on the Ground Electronic State.

Conical intersections are known to cause nonadiabatic transitions, but their effects on adiabatic dynamics are often ignored. Using the overtone-induced dissociation of the hydroxymethyl radical as an example, we demonstrate that ground-state O-H bond rupture is significantly affected by a conical intersection with an electronically excited state along the dissociation path, despite the much lower energy of the dissociating state than that of the conical intersection. In addition to lifetime differences, the geometric phase leads to a different H2CO rotational state distribution compared with that obtained using the standard single-state adiabatic model, which constitutes a signature of the conical intersection.

DFT study of the adsorption and dissociation of 5-hydroxy-3-butanedithiol-1,4-naphthaquinone (Jug-C4-thiol) on Au(111) surface

Density functional theory has been used to investigate the adsorption and dissociation of 5-hydroxy-3-hexanediol-1,4-naphthaquinone (Jug-C4-thiol) at a coverage of p(4 × 4) on a Au(111) surface. Both physisorption and chemisorption processes are investigated. For each process, the surface energy potential is explored by an exhaustive test of the adsorption site. The most favorable site is found to be face-centered cubic. The adsorption energies are less than − 0.20 eV in the case of physisorption, while they range from − 1.70 to − 1.92 eV for chemisorption. The effect of the naphthoquinone function is negligible in the adsorption process. The alkyl chain inhibits electron delocalization between the surface and the conjugated head of the molecule. Analysis of the bonding shows the formation of two ionocovalent bonds between the sulfur and the gold atoms. The thermodynamics and kinetics of S–H bond dissociation are studied. The results reveal that adsorption involves a dissociation path in which a hydrogen atom moves to the most neighboring site and a hydrogen atom migrates to its most stable site. The maximum barrier energy of the first step is less than 2.7 eV while the migration barrier does not exceed 0.5 eV.

Investigation of the interactions between aptamer and misfolded proteins: From monomer and oligomer to fibril by single-molecule force spectroscopy.

Increasing knowledge on the understanding interactions of aptamer with misfolded proteins (including monomer, oligomer, and amyloid fibril) is crucial for development of aggregation inhibitors and diagnosis of amyloid diseases. Herein, the interactions of lysozyme monomer-, oligomer-, and amyloid fibril-aptamer were investigated using single-molecule force spectroscopy. The results revealed that the aptamer screened against lysozyme monomer could also bind to oligomer and amyloid fibril, in spite of the recognition at a lower binding probability. It may be attributed to the inherent structural differences of misfolded proteins and the flexible conformation of aptamer. In addition, dynamic force spectra showed that there were similar dissociation paths in the dissociation process of lysozyme monomer-, oligomer-, and amyloid fibril-aptamer complexes. It showed that the dissociation only passed 1 energy barrier from the binding state to the detachment. However, the dynamic parameters suggested that the oligomer- and amyloid fibril-aptamer were more stable than lysozyme monomer-aptamer. The phenomena may result from the exposure of aptamer-recognized sequences on the surface and the electrostatic interactions. This work demonstrated that single-molecule force spectroscopy could be a powerful tool to study the binding behavior of the aptamer with misfolded proteins at single-molecule level, providing abundant information for researches and comprehensive applications of aptamer probes in diagnosis of amyloid diseases.

Investigating the importance of edge-structure in the loss of H/H2 of PAH cations: The case of dibenzopyrene isomers

We present a detailed study of the main dehydrogenation processes of two dibenzopyrene cation (C24H14+) isomers, namely dibenzo(a,e)pyrene (AE+) and dibenzo(a,l)pyrene (AL+). First, action spectroscopy under VUV photons was performed using synchrotron radiation in the 8–20eV range. We observed lower dissociation thresholds for the non-planar molecule (AL+) than for the planar one (AE+) for the main dissociation pathways: H and 2H/H2 loss. In order to rationalize the experimental results, dissociation paths were investigated by means of density functional theory calculations. In the case of H loss, which is the dominant channel at the lowest energies, the observed difference between the two isomers can be explained by the presence in AL+ of two CH bonds with considerably lower adiabatic dissociation energies. In both isomers the 2H/H2 loss channels are observed only at about 1eV higher than H loss. We suggest that this is due to the propensity of bay H atoms to easily form H2. In addition, in the case of AL+, we cannot exclude a competition between 2H and H2 channels. In particular, the formation of a stable dissociation product with a five-membered ring could account for the low energy sequential loss of 2 hydrogens. This work shows the potential role of non-compact PAHs containing bay regions in the production of H2 in space.

Accurate potential surfaces for the ground state of H+C2 reaction

Three-dimensional potential energy surfaces (PESs) have been computed, and numerically fitted, for the ground states of C2H system, which are of importance for the smallest carbon cluster, dicarbon (C2) and dynamical study of the H–CC dissociation reaction. An accurate and over larger region of configuration space PES are produced. The potential shown that the linear dissociation path is the favorite for H–CC.

Adsorption and dissociation of H2S on Rh(100) surface by First-principle study

The adsorption and dissociation of H2S on Rh(100) surface have been investigated using self-consistent periodic density functional theory. The adsorption mechanisms on Rh(100) surface of H2S, HS, H and S were examined. It is found that H2S is weakly adsorbed on bridge, top and hollow sites with their adsorption energies of −0.98, −0.86 and −0.82eV, respectively. In contrast to H2S, HS is strongly chemisorbed on Rh(100) surface at hollow, top and bridge site with the adsorption energies of −4.33, −4.31 and −3.85eV, whereas S and H preferred to be absorbed at hollow site. By using climbing nudged elastic band method (CI-NEB), we found the four most feasible paths for H2S dissociation on Rh(100), with energy barriers of 0.19eV, 0.25eV, 44meV and 98 meV, respectively. The energy barrier to break the S-H bond of HS with H co-adsorption or without H co-adsorption was almost the same low. This study reveals that H2S decomposition on Rh(100) surface is a facile process both kinetically and thermodynamically.

A Jeziorski-Monkhorst fully uncontracted multi-reference perturbative treatment. I. Principles, second-order versions, and tests on ground state potential energy curves.

The present paper introduces a new multi-reference perturbation approach developed at second order, based on a Jeziorski-Mokhorst expansion using individual Slater determinants as perturbers. Thanks to this choice of perturbers, an effective Hamiltonian may be built, allowing for the dressing of the Hamiltonian matrix within the reference space, assumed here to be a CAS-CI. Such a formulation accounts then for the coupling between the static and dynamic correlation effects. With our new definition of zeroth-order energies, these two approaches are strictly size-extensive provided that local orbitals are used, as numerically illustrated here and formally demonstrated in the Appendix. Also, the present formalism allows for the factorization of all double excitation operators, just as in internally contracted approaches, strongly reducing the computational cost of these two approaches with respect to other determinant-based perturbation theories. The accuracy of these methods has been investigated on ground-state potential curves up to full dissociation limits for a set of six molecules involving single, double, and triple bond breaking together with an excited state calculation. The spectroscopic constants obtained with the present methods are found to be in very good agreement with the full configuration interaction results. As the present formalism does not use any parameter or numerically unstable operation, the curves obtained with the two methods are smooth all along the dissociation path.