Energy Isomers Research Articles

When Gold Is Not Enough: Platinum Standard of Quantum Chemistry with N7 Cost.

In this paper, we extend the rank-reduced coupled-cluster formalism to the calculation of non-iterative energy corrections due to quadruple excitations. There are two major components of the proposed formalism. The first is an approximate compression of the quadruple excitation amplitudes using the Tucker format. The second is a modified functional used for the evaluation of the corrections which gives exactly the same results for the exact amplitudes, but is less susceptible to errors resulting from the aforementioned compression. We show, both theoretically and numerically, that the computational cost of the proposed method scales as the seventh power of the system size. Using reference results for a set of small molecules, the method is calibrated to deliver relative accuracy of a few percent in energy corrections. To illustrate the potential of the theory, we calculate the isomerization energy of ortho/meta benzyne (C6H4) and the barrier height for the Cope rearrangement in bullvalene (C10H10). The method retains a near-black-box nature of the conventional coupled-cluster formalism and depends on only one additional parameter that controls the accuracy.

Reducing the Quantum Many-Electron Problem to Two Electrons with Machine Learning.

An outstanding challenge in chemical computation is the many-electron problem where computational methodologies scale prohibitively with system size. The energy of any molecule can be expressed as a weighted sum of the energies of two-electron wave functions that are computable from only a two-electron calculation. Despite the physical elegance of this extended "aufbau" principle, the determination of the distribution of weights─geminal occupations─for general molecular systems has remained elusive. Here we introduce a new paradigm for electronic structure where approximate geminal-occupation distributions are "learned" via a convolutional neural network. We show that the neural network learns the N-representability conditions, constraints on the distribution for it to represent an N-electron system. By training on hydrocarbon isomers with only 2-7 carbon atoms, we are able to predict the energies for isomers of octane as well as hydrocarbons with 8-15 carbons. The present work demonstrates that machine learning can be used to reduce the many-electron problem to an effective two-electron problem, opening new opportunities for accurately predicting electronic structure.

Performance of local G4(MP2) composite ab initio procedures for fullerene isomerization energies

Composite ab initio methods based on local coupled-cluster approaches calculate the CCSD(T)/CBS energy at a significantly reduced computational cost than the corresponding canonical methods. While showing promising performance for general thermochemistry, local composite ab initio methods have not been tested for fullerenes. Here we examine the performance of several local G4(MP2)-based methods for calculating the relative stability of a diverse set of C40 fullerenes. We use canonical G4(MP2) isomerization energies as reference data. Fullerenes provide a challenging problem for DLPNO-G4(MP2)-based methods. The DLPNO-based methods result in overall root-mean-square deviations (RMSDs) of 28.6 (NormalPNO with CCSD(T0)), 23.0 (NormalPNO with CCSD(T1)), and 16.1 (TightPNO with CCSD(T0)) kJ mol−1. The local natural orbital LNO-G4(MP2) method provides the best overall performance with an RMSD of 4.9 kJ mol−1. The DLPNO-G4(MP2) and LNO-G4(MP2) methods systematically overestimate the canonical G4(MP2) isomerization energies. Therefore, they provide valuable upper limits of the fullerene isomerization energies.

Parametrization of the PM7 Semiempirical Quantum Mechanical Method for Silver Nanoclusters.

Semiempirical quantum mechanical methods (SEQMs) are widely used in computational chemistry because of their low computational cost, but their accuracy depends on the quality of the parameters. The neglect of diatomic differential overlap method PM7 is among the few SEQMs that contain parameters for Ag, but the experimental reference data was insufficient to obtain reliable parameters in the original parametrization. In this work, we reparametrize the PM7 parameters for Ag to accurately reproduce the ground-state potential energy surfaces of Ag clusters. Since little experimental data is available, we use reference data obtained from the ab initio method CCSD(T). The resulting parameters significantly reduce the errors in binding energies, energies required to displace clusters along their normal modes, and relative energies of isomers compared to the default PM7 Ag parameters.

Making the second generation of molecular motors operate unidirectionally in response to electricity

Electricity is an attractive energy input to operate molecular motors. We found that anionization using constant potential could make the 2nd generation molecular motors operate under ground state unidirectionally, persistently, and free from ultraviolet light. In this approach, the original energetically uphill step with large energy barrier driven by ultraviolet could be replaced by a combination of an anionization step followed by an energetically downhill anionic isomerization and a neutralization step. Anionization decreases the energy barrier of the first isomerization step significantly, while the barrier of the second isomerization step still keeps high level, which ensures nearly 100% perfect unidirectionality kinetically. The free energy of the anionic intermediate isomer is lower enough than that of the original isomer, which makes the isomerization could be driven thermodynamically and ensures the nearly 100% perfect unidirectionality. We hope that our investigations could provide a new strategy for constructing electronic stimuli-responsive nanosystems based on the 2nd generation molecular motors.

Evaluating the performance of ReaxFF potentials for sp2 carbon systems (graphene, carbon nanotubes, fullerenes) and a new ReaxFF potential.

We study the performance of eleven reactive force fields (ReaxFF), which can be used to study sp2 carbon systems. Among them a new hybrid ReaxFF is proposed combining two others and introducing two different types of C atoms. The advantages of that potential are discussed. We analyze the behavior of ReaxFFs with respect to 1) the structural and mechanical properties of graphene, its response to strain and phonon dispersion relation; 2) the energetics of (n, 0) and (n, n) carbon nanotubes (CNTs), their mechanical properties and response to strain up to fracture; 3) the energetics of the icosahedral C60 fullerene and the 40 C40 fullerene isomers. Seven of them provide not very realistic predictions for graphene, which made us focusing on the remaining, which provide reasonable results for 1) the structure, energy and phonon band structure of graphene, 2) the energetics of CNTs versus their diameter and 3) the energy of C60 and the trend of the energy of the C40 fullerene isomers versus their pentagon adjacencies, in accordance with density functional theory (DFT) calculations and/or experimental data. Moreover, the predicted fracture strain, ultimate tensile strength and strain values of CNTs are inside the range of experimental values, although overestimated with respect to DFT. However, they underestimate the Young’s modulus, overestimate the Poisson’s ratio of both graphene and CNTs and they display anomalous behavior of the stress - strain and Poisson’s ratio - strain curves, whose origin needs further investigation.

An examination of the reaction pathways of XO + O → X + O2 (X = Br and I)

Kinetics and mechanism of potentially important atmospheric ozone depletion reactions XO + O → X + O2 (X = Br and I) have been explored at the ab initio level. Several minimum energy geometries and transition states are identified at the MP2 level using correlation consistent triple zeta and effective core potential basis sets and energetics are obtained at the QCISD(T)//MP2 level of theory. Possible reaction pathways are discussed on the basis of IRC calculations and changes of geometries along the reaction paths. A direct reaction mechanism as well as reaction path via transition states and equilibrium geometries are identified. For both the reactions, early transition states have been detected just after the reactions start. In case of BrO + O reaction, we obtained a transition state of Br.OO type before the product formation, whereas in case of IO + O reaction, an equilibrium geometry of I.OO type has been detected leading to the product formation. Similar to I.OO, for ClO + O reaction an equilibrium geometry of Cl.OO type was reported in literature for product formation. This anomaly for TS-Br.OO may be due the artifact of MP2 optimization method. A multi-reference approach is expected to reveal the correct picture. A detailed dynamical study of this transition state may lead to clear bond-breaking and bond-forming information, which may be helpful to predict the true reaction pathway. Heats of reaction are found to be consistent with experimental data. Bond dissociation energies of the ground state intermediate isomers to various dissociation asymptotes are also reported. This is the first theoretical report for the possible reaction pathways and may be served as a reference for future investigation using higher methodology.

Subunit promotion energies for channel opening in heterotetrameric olfactory CNG channels.

Cyclic nucleotide-gated (CNG) ion channels of olfactory sensory neurons contain three types of homologue subunits, two CNGA2 subunits, one CNGA4 subunit and one CNGB1b subunit. Each subunit carries an intracellular cyclic nucleotide binding domain (CNBD) whose occupation by up to four cyclic nucleotides evokes channel activation. Thereby, the subunits interact in a cooperative fashion. Here we studied 16 concatamers with systematically disabled, but still functional, binding sites and quantified channel activation by systems of intimately coupled state models transferred to 4D hypercubes, thereby exploiting a weak voltage dependence of the channels. We provide the complete landscape of free energies for the complex activation process of heterotetrameric channels, including 32 binding steps, in both the closed and open channel, as well as 16 closed-open isomerizations. The binding steps are specific for the subunits and show pronounced positive cooperativity for the binding of the second and the third ligand. The energetics of the closed-open isomerizations were disassembled to elementary subunit promotion energies for channel opening, [Formula: see text], adding to the free energy of the closed-open isomerization of the empty channel, E0. The [Formula: see text] values are specific for the four subunits and presumably invariant for the specific patterns of liganding. In conclusion, subunit cooperativity is confined to the CNBD whereas the subunit promotion energies for channel opening are independent.

Stability, atomic charges, bond‐order analysis, and the directionality of lone‐electron pairs on nitriles and isocyanides

AbstractThe carbon atoms in :CN and the nitrogen atoms in CN: are always the global electrostatic minima in the whole molecules of nitriles and isocyanides. The global molecular electrostatic potential minima (Vmin) values and the electrostatic potential isosurfaces higher than Vmin by 10 kcal/mol were investigated and visualized based on the optimized geometrical structures at B3LYP‐D3(BJ)/def2‐QZVP level for a series of nitriles and isocyanides with the selected 21 functional groups. The relative stability between RCN: and :CNR was quantified with isomerization energies and bond dissociation enthalpies by single‐point energy (SPE) calculations at B2PLYP‐D3(BJ)/cc‐pVTZ level. The bond dissociation enthalpies of RCN: were evaluated, and the standard molar enthalpies of formation for RCN: and R· were also calculated to estimate the bond dissociation enthalpies. The theoretical results show that the directionality of the lone pairs influences electrostatic distribution. The population analyses in terms of Hirshfeld and ADCH atomic charges and bond‐order analyses via Laplacian and fuzzy bond orders were also discussed in detail.

Band Gap Calculations for Thorium‐Doped LiCAF

AbstractThe large band gap insulator LiCaAlF6 (LiCAF) has been proposed as a possible host crystal for future realizations of a solid‐state based thorium‐229 nuclear clock, due to its excellent optical transmission in the vacuum ultraviolet range. To enable direct optical manipulation of the thorium isomeric state, the band gap has to remain larger than the nuclear excitation energy upon crystal doping. Here, a systematic search for possible charge compensation mechanisms, defect locations, and the emergence of other compounds, using density functional theory, is presented. Out of 535 optimized structures, the energetically most favorable arrangement is with an estimated band gap of 11.4 eV. Evaluating relevant uncertainties of the used methods suggests that the doped material remains transparent at the 229Th isomer energy for all investigated configurations.

Comprehensive theoretical study of the correlation between the energetic and thermal stabilities for the entire set of 1812 C60 isomers

The thermal stability of fullerenes plays a fundamental role in their synthesis and in their thermodynamic and kinetic properties. Here, we perform extensive molecular dynamics (MD) simulations using an accurate machine-learning-based Gaussian Approximation Potential (GAP-20) force field to investigate the energetic and thermal properties of the entire set of 1812 C60 isomers. Our MD simulations predict a comprehensive and quantitative correlation between the relative isomerization energy distribution of the C60 isomers and their thermal fragmentation temperatures. We find that the 1812 C60 isomers span over an energetic range of over 400 kcal mol−1, where the majority of isomers (∼85%) lie in the range between 90 and 210 kcal mol−1 above the most stable C60-Ih buckminsterfullerene. Notably, the MD simulations show a clear statistical correlation between the relative energies of the C60 isomers and their fragmentation temperature. The maximum fragmentation temperature is 4800 K for the C60-Ih isomer and 3700 K for the energetically least stable isomer, where nearly 80% of isomers lie in a temperature window of 4000–4500 K. In addition, an Arrhenius-based approach is used to map the timescale gap between simulation and experiment and establish a connection between the MD simulations and fragmentation temperatures.

The Au12 Gold Cluster: Preference for a Non-Planar Structure

The transition point from a two-dimensional (2D) to a three-dimensional (3D) structure in a series of small gold clusters remains a topic of continuing debate. In the present study, coupled-cluster CCSD(T) and DFT calculations are performed to re-examine the relative energies of several low-lying isomers of Au12, aiming to shed new light on this issue. At odds with many previous reports on the preference of a planar di-capped elongated-hexagon structure, the Au12 size is found to energetically prefer a globular cup-like form with C2v symmetry. While DFT results are not able to assign the most stable form of Au12 as the relative energies between the lowest-lying isomers are strongly functional-dependent, coupled-cluster theory calculations point out the preference of a 3D structure for having a D3h symmetry. Such a prediction is further supported by a comparison of the vibrational spectra computed using the revTPSS density functional with the available experimental infrared ones that were previously recorded from the far-IR multiple photon dissociation (FIR-MPD) experiment.

STRUCTURAL YIELDS AND ASPECTS OF ISOMER IN DEEP-INELASTIC COLLISIONS

Structural yields and features in the meta-stable states of nuclei from the projectile like fragments of 8.36 MeV 76Ge in 198Pt target are reported. The dynamic features of deep inelastic collisions (DICs) are studied by dissipation energy versus transfer of nucleons. We have studied the yields as a function of excitation levels. The structural appears do not depend on the excitation energy of isomers persuaded in the DICs. This is in dissimilarity to the protuberant physical landscapes establishing in population yield of isotopes which disappear with Gaussian distribution.

Fullerenes Pose a Strain on Hybrid Density Functional Theory.

The computational modeling of fullerenes plays a fundamental role in designing low-dimension carbon nanostructures. Nevertheless, the relative energies of fullerenes larger than C20 and C24 have not been comprehensively examined by means of highly accurate ab initio methods, for example, the CCSD(T) method. Here we report such an investigation for a diverse set of 29 C40 isomers. We calculate the energies of the C40 fullerenes using the G4(MP2) composite ab initio method, which approximates the CCSD(T) energy in conjunction with a triple-ζ-quality basis set (CCSD(T)/TZ). The CCSD(T)/TZ isomerization energies span 43.1-763.3 kJ mol-1. We find a linear correlation (R2 = 0.96) between the CCSD(T)/TZ isomerization energies and the fullerene pentagon signatures (P1 index), which reflect the strain associated with fused pentagon-pentagon rings. Using the reference CCSD(T)/TZ isomerization energies, we examine the relationship between the percentage of exact Hartree-Fock (HF) exchange in hybrid density functional theory (DFT) methods and the pentagon-pentagon strain energies. We find that the performance of hybrid DFT methods deteriorates with the pentagon-pentagon strain energy. This deterioration in performance becomes more pronounced with the inclusion of high amounts of HF exchange. For example, for B3LYP (20% HF exchange), the root-mean-square deviation (RMSD) relative to G4(MP2) increases from 8.9 kJ mol-1 for the low-strain isomers (P1 = 11) to 18.0 kJ mol-1 for the high-strain isomers (P1 > 13). However, for BH&HLYP (50% HF exchange) the RMSD increases from 23.0 (P1 = 11) to 113.2 (P1 > 13) kJ mol-1. A similar trend is observed for the M06/M06-2X pair of functionals. Namely, for M06 (27% HF exchange) the RMSD increases from 0.8 (P1 = 11) to 21.0 (P1 > 13) kJ mol-1, whereas for M06-2X (54% HF exchange) the RMSD increases from 16.7 (P1 = 11) to 77.7 (P1 > 13) kJ mol-1. Overall, we find that the strain associated with pentagon adjacency is an inherently challenging problem for hybrid DFT methods involving high amounts of HF exchange and that there is an inverse relationship between the optimal percentage of HF exchange and the pentagon-pentagon strain energy. For example, for BLYP the optimal percentages of HF exchange are 13% (P1 = 11), 10% (P1 = 12), 7.5% (P1 = 13), and 6% (P1 > 13).

Metallic‐Ion Controlled Dynamic Bonds to Co‐Harvest Isomerization Energy and Bond Enthalpy for High‐Energy Output of Flexible Self‐Heated Textile (Adv. Sci. 20/2022)

Photothermal Energy Storage A series of photo responsive azobenzene-based polymers interacts with different metal ions showing excellent photothermal energy storage and low-temperature output capabilities through co-harvesting of isomerization energy and bond enthalpy for a thermal management wearable device to realize temperature control. More details can be found in article number 2201657 by Yiyu Feng, Wei Feng, and co-workers.

Hydrogen abstraction reactions in formic and thioformic acid isomers by hydrogen and deuterium atoms

Context.The isomerism of molecules in the interstellar medium and the mechanisms behind it are essential questions in the chemistry of organic molecules in space. In the particular case of simple formic and thioformic acids, the low temperatures found in molecular clouds indicate that cis-trans isomerization in the gas-phase must be impeded. Reactions taking place on top of interstellar dust grains may explain the isomer interconversion at low temperatures.Aims.We studied the isomerization processes of formic and thioformic acid that are likely to take place on the surface of interstellar dust grains after being initiated by H abstraction reactions. Similarly, deuterium enrichment of the acids can occur by the same mechanism. Our objective is to shed light on both topics to expand our understanding of the key precursors of organic molecules in space.Methods.We determined the rate constants for the H abstraction reactions as well as the binding energies for the acids on water ice using ab initio calculations and the instanton method for calculating the rate constants, including quantum tunneling. In addition, we tested the viability of the deuteration of formic acid with tailored experiments and looked for it on the L1544 source.Results.For formic acid, there is a clear dependence of the H abstraction reactions on the isomer of the reactant, with rate constants at ~50 K that differ by five orders of magnitude. Correspondingly, we did not observe the trans-cis reaction in our experiments. In the case of thioformic acid, a very similar cis-trans reactivity is found for abstraction reactions at the thiol (-SH) group in contrast to a preferential reactivity that is found when abstractions take place at the -CH moiety. We found comparable binding energies for both isomers with average binding energies of around −6200 and −3100 K for formic and thioformic acid, respectively. Our binding energy calculations show that the reactions are precluded for specific orientations, affecting the overall isomerization rate. For H abstractions initiated by deuterium atoms, we found very similar trends, with kinetic isotope effects varying in most cases between 13 and 20.Conclusions.Our results support the cis-trans interconversion of cis-formic acid on dust grains, suggesting that such an acid should not withstand the conditions found on these objects. On the other hand, the trans isomer is very resilient. Both isomers of thioformic acid are much more reactive. A non-trivial chemistry is behind the apparent excess of its trans isomer that is found in cold molecular clouds and star-forming regions due to a subtle combination of preferential reactivity and binding with the surface. In light of our results, all the deuterated counterparts of thioformic acid are viable molecules to be present on the ISM. In contrast, only the trans isomer of deuterated formic acid is expected, for which we provide upper bounds of detection. Given the mechanisms presented in this paper, other mechanisms must be at play to explain the tiny fraction of cis-formic acid observed in interstellar cold environments, as well as the current trans-DCOOH and trans-HCOOD abundances in hot-corinos.

Q-AQUA: A Many-Body CCSD(T) Water Potential, Including Four-Body Interactions, Demonstrates the Quantum Nature of Water from Clusters to the Liquid Phase.

Many model potential energy surfaces (PESs) have been reported for water; however, none are strictly from "first-principles". Here we report such a potential, based on a many-body representation at the CCSD(T) level of theory up to the four-body interaction. The new PES is benchmarked for the isomers of the water hexamer for dissociation energies, harmonic frequencies, and unrestricted diffusion Monte Carlo (DMC) calculations of the zero-point energies of the Prism, Book, and Cage isomers. Dissociation energies of several isomers of the 20-mer agree well with recent benchmark energies. Exploratory DMC calculations on this cluster verify the robustness of the new PES for quantum simulations. The accuracy and speed of the new PES are demonstrated for standard condensed phase properties, i.e., the radial distribution function and the self-diffusion constant. Quantum effects are shown to be substantial for these observables and also needed to bring theory into excellent agreement with experiment.

Metallic-Ion Controlled Dynamic Bonds to Co-Harvest Isomerization Energy and Bond Enthalpy for High-Energy Output of Flexible Self-Heated Textile.

Molecular light‐harvesting capabilities and the production of low‐temperature heat output are essential for flexible self‐heated textiles. An effective strategy to achieve these characteristics is to introduce photoresponsive molecular interactions (photodynamic bonds) to increase the energy storage capacity and optimize the low‐temperature photochromic kinetics. In this study, a series of sulfonic‐grafted azobenzene‐based polymers interacted with different metal ions (PAzo‐M, M = Mg, Ca, Ni, Zn, Cu, and Fe) to optimize the energy level and isomerization kinetics of these polymers is designed and prepared. Photoinduced formation and dissociation of M—O dynamic bonds enlarge the energy gap (∆E) between trans and cis isomers for high‐energy storage and favor a high rate of isomerization for low‐temperature heat release. The suitable binding energy and high ∆E enable PAzo‐M to store and release isomerization energy and bond enthalpy even in a low‐temperature (−5 °C) environment. PAzo‐Mg possesses the highest energy storage density of 408.6 J g−1 (113.5 Wh kg−1). A flexible textile coated with PAzo‐Mg can provide a high rise in temperature of 7.7–12.5 °C in a low‐temperature (−5.0 to 5.0 °C) environment by selectively self‐releasing heat indoors and outdoors. The flexible textile provides a new pathway for wearable thermal management devices.

Noncanonical Isomers of Nucleoside Cation Radicals: An Ab Initio Study of the Dark Matter of DNA Ionization.

Cation radicals of DNA nucleosides, 2'-deoxyadenosine, 2'-deoxyguanosine, 2'-deoxycytidine, and 2'-deoxythymidine, can exist in standard canonical forms or as noncanonical isomers in which the charge is introduced by protonation of the nucleobase, whereas the radical predominantly resides in the deoxyribose moiety. Density functional theory as well as correlated ab initio calculations with coupled clusters (CCSD(T)) that were extrapolated to the complete basis set limit showed that noncanonical nucleoside ion isomers were thermodynamically more stable than their canonical forms in both the gas phase and as water-solvated ions. This indicated the possibility of exothermic conversion of canonical to noncanonical forms. The noncanonical isomers were calculated to have very low adiabatic ion-electron recombination energies (REad) for the lowest-energy isomers 2'-deoxy-(N-3H)adenos-1'-yl (4.74 eV), 2'-deoxy-(N-7H)guanos-1'-yl (4.66 eV), 2'-deoxy-(N-3H)cytid-1'-yl (5.12 eV), and 2'-deoxy-5-methylene-(O-2H)uridine (5.24 eV). These were substantially lower than the REad value calculated for the canonical 2'-deoxyadenosine, 2'-deoxy guanosine, 2'-deoxy cytidine, and 2'-deoxy thymidine cation radicals, which were 7.82, 7.46, 8.14, and 8.20 eV, respectively, for the lowest-energy ion conformers of each type. Charge and spin distributions in noncovalent cation-radical dA⊂dT and dG⊂dC nucleoside pairs and dAT, dCT, dTC, and dGC dinucleotides were analyzed to elucidate the electronic structure of the cation radicals. Born-Oppenheimer molecular dynamics trajectory calculations of the dinucleotides and nucleoside pairs indicated rapid exothermic proton transfer from noncanonical T+· to A in both dAT+· and dA⊂dT+·, leading to charge and radical separation. Noncanonical T+· in dCT+· and dTC+· initiated rapid proton transfer to cytosine, whereas the canonical dCT+· dinucleotide ion retained the cation radical structure without isomerization. No spontaneous proton transfer was found in dGC+· and dG⊂dC+· containing canonical neutral and noncanonical ionized deoxycytidine.

Correlation between the energetic and thermal properties of C40 fullerene isomers: An accurate machine-learning force field study

The isomerisation energies and thermal stabilities of the entire set of C 40 fullerene isomers are investigated using molecular dynamics simulations with the recently developed machine-learning-based Gaussian Approximation Potential (GAP-20) force field. Our simulations predict high statistical correlation between the relative isomerisation energy distribution of all C 40 isomers and their thermal fragmentation temperatures. The most energetically and thermally stable isomer is the symmetric C 40 - D 2 isomer and its fragmentation temperature is 3875 ± 25 K. In contrast, the least stable isomer is the D 5d nanorod-shaped isomer which is 146.8 kcal mol −1 higher in energy and decomposes at 2975 ± 25 K, i.e., around 900 K below the most stable isomer. In addition, we show that most isomers lie in the range between 20 and 60 kcal mol −1 above the most stable isomer, and nearly 60% of isomers decompose in the temperature range of 3425–3675 K. These computational results provide valuable insights into the synthesis of C 40 fullerenes at high-temperatures. • Using the accurate machine-learning (GAP-20) carbon potential • Systematic study of the energetic and thermal properties of C40 fullerenes • We consider the entire set of C40 fullerene isomers. • We find a distinct correlation between the energetic and thermal stabilities.