The 50 most-cited articles in The Journal of Physical Chemistry A, 2019

with the size of the system. Dependence of WTMAD2 for DSD functionals on the percentage of HF exchange is roughly quadratic; it is sufficiently weak that any reasonable value in the 64% to 72% range can be chosen semiarbitrarily. DSD-SCAN and DOD-SCAN double hybrids involving the SCAN nonempirical meta-GGA as the semilocal component have also been considered and offer a good alternative if one wishes to eliminate either the empirical dispersion correction or the same-spin correlation component. noDispSD-SCAN66 achieves WTMAD2 = 3.0 kcal/mol, compared to 2.7 kcal/mol for DOD-SCAN66-D4. However, the best performance without dispersion corrections (WTMAD2 = 2.8 kcal/mol) is reached by revωB97X-2, a slight reparametrization of the Chai-Head-Gordon range-separated double hybrid. Finally, in the context of double-hybrid functionals, the very recent D4 dispersion correction is clearly superior over D3(BJ).

In this study we examine the accuracy of domain-based local pair natural orbital coupled cluster theory with single, double, and perturbative triple excitations (DLPNO-CCSD(T)) on a large benchmark data set. To this end, we use the recently published GMTKN55 superset of molecules that contains 1505 relative energies and 2462 single-point calculations. To our knowledge this is the most comprehensive benchmark evaluation of any highly correlated wave function based ab initio method to date. In the first part of the study, canonical CCSD(T) reference calculations were carried out on the entire test set in order to guarantee that the reference data are of uniform quality. Second, DLPNO-CCSD(T) calculations were carried out under identical conditions. The main finding is that with the exception of two data sets, all data sets have a MAD of 0.4 kcal/mol or less and the majority of sets have a MAD of less than 0.2 kcal/mol. For open shells, the accuracy of the DLPNO calculations was significantly improved through an iterative version of the triples correction.

According to Hund’s rule, the lowest triplet state (T 1 ) is lower in energy than the lowest excited singlet state (S 1 ) in closed-shell molecules. The exchange integral lowers the energy of the triplet state and raises the energy of the singlet state of the same orbital character, leading to a positive singlet–triplet energy gap (Δ ST ). Exceptions are known for biradicals and charge-transfer excited states of large molecules in which the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) are spatially separated, resulting in a small exchange integral. In the present work, we discovered with ADC(2), CC2, EOM-CCSD, and CASPT2 calculations that heptazine (1,3,4,6,7,9,9b-heptaazaphenalene or tri- s -triazine) exhibits an inverted S 1 /T 1 energy gap (Δ ST ≈ −0.25 eV). This appears to be the first example of a stable closed-shell organic molecule exhibiting S 1 /T 1 inversion at its equilibrium geometry. The origins of this phenomenon are the nearly pure HOMO–LUMO excitation character of the S 1 and T 1 states and the lack of spatial overlap…

An alternative response function, based on the dual descriptor in terms of Koopmans’ approximation, is hereby proposed for the description of chemical reactivity in systems with (quasi-) degenerate frontier molecular orbitals. This descriptor is constructed from Fukui functions that include contributions from different orbitals, i.e., orbital-weighted Fukui functions. The methodology is applied to three case studies: the first case consists of a series of benchmark organic and inorganic molecules from which the dual descriptor, based only on frontier orbitals, is not appropriate to describe their reactivity. The second case deals with the proper description of chemical reactivity in Diels–Alder reactions between fullerene C 60 and cyclopentadiene (CP), revealing the importance of considering secondary orbital interactions for an adequate regioselectivity description. The third, and last case, consists of a series of polycyclic aromatic hydrocarbons (PAHs) possessing molecular orbital degeneracy. By means of analyzing of this descriptor, an alternative approach to the description of…

A new database of transition metal reaction barrier heights (MOBH35) is presented. Benchmark energies (forward and reverse barriers and reaction energy) are calculated using DLPNO-CCSD(T) extrapolated to the complete basis set limit using a Weizmann-1-like scheme. Using these benchmark energies, the performance of a wide selection of density functional theory (DFT) exchange-correlation functionals, including the latest from the Martin, Truhlar, and Head-Gordon groups, is evaluated. It was found, using the def2-TZVPP basis set, that the ωB97M-V (MAD 1.7 kcal/mol), ωB97M-D3BJ (MAD 1.9 kcal/mol), ωB97X-V (MAD 2.0 kcal/mol), and revTPSS0-D4 (MAD 2.2 kcal/mol) hybrid functionals are recommended. The double-hybrid functionals B2K-PLYP (MAD 1.7 kcal/mol) and revDOD-PBEP86-D4 (MAD 1.8 kcal/mol) also performed well, but this has to be balanced by their increased computational cost.

We have recently proposed a new unified theoretical scheme (the "middle" scheme) for thermostat algorithms for efficient and accurate configurational sampling of the canonical ensemble. In this paper, we extend the "middle" scheme to molecular dynamics algorithms for configurational sampling in systems subject to constraints. Holonomic constraints and isokinetic constraints are used for demonstration. Numerical examples indicate that the "middle" scheme presents a promising approach to calculate configuration-dependent thermodynamic properties and their thermal fluctuations.

Recent advances in the calculation and interpretation of the activation energy for a dynamical process are described. Specifically, new approaches that apply the fluctuation theory of statistical mechanics to dynamics enable the direct determination of the activation energy for an arbitrary dynamical time scale from simulations at a single temperature. This opens up significant new possibilities for understanding activated processes in cases where a traditional Arrhenius analysis is not possible. The methods also enable a rigorous decomposition of the activation energy into contributions associated with the different interactions and motions present in the system. These components can be understood in the context of Tolman's interpretation of the activation energy. Specifically, they provide insight into how energy can be most effectively deposited to accelerate the dynamics of interest, promising important new mechanistic information for a broad range of chemical processes. The general approach can be extended beyond activation energies to the examination of non-Arrhenius behavior…

Atmospheric oxidation of monoterpenes (emitted primarily by evergreen trees) is known to contribute to the formation and growth of aerosol particles. While recent research has tied the formation of organic aerosol to unimolecular chemistry of the organic peroxy radicals (RO 2 ) formed in the oxidation of monoterpenes, the fundamental physical chemistry of these RO 2 remains obscure. Here we use isomer-specific measurements and ab initio calculations to determine the unimolecular reaction rates and products of RO 2 derived from the hydroxyl radical (OH) oxidation of α-pinene and β-pinene. Among all of the structural isomers of the first-generation RO 2 from both monoterpenes, we find that the first-generation RO 2 produced following opening of the four-membered ring undergo fast unimolecular reactions (4 ± 2 and 16 ± 5 s –1 for α-pinene and β-pinene, respectively) at 296 K, in agreement with high-level ab initio calculations. The presence of the hydroxy group and carbon–carbon double bond in the ring-opened RO 2 enhances the rates of these unimolecular reactions, including…

With an annual emission of about 500 Tg, isoprene is an important molecule in the atmosphere. While much of its chemistry is well constrained by either experiment or theory, the rates of many of the unimolecular peroxy radical hydrogen-shift (H-shift) reactions remain speculative. Using a high-level multiconformer transition state theory (MC-TST) approach, we determine recommended temperature dependent reaction rate coefficients for a number of the H-shift reactions in the isoprene oxidation mechanism. We find that most of the (1,4, 1,5, and 1,6) aldehydic and (1,5 and 1,6) α-hydroxy H-shifts have rate constants at 298.15 K in the range 10 –2 to 1 s –1, which make them competitive with bimolecular reactions in the atmosphere under typical atmospheric conditions. In addition, we find that the rate coefficients of different diastereomers can differ by up to 3 orders of magnitude, illustrating the importance of chirality. Implementation of our calculated reaction rate coefficients into the most recent GEOS-Chem model for isoprene oxidation shows that at least 30% of all isoprene…

The ability of Kohn-Sham density functional theory (KS-DFT) to accurately predict various types of electronic excitation energies with (necessarily approximate) exchange-correlation functionals faces several challenges. Chief among these is that valence excitations are usually inherently multiconfigurational and therefore best treated by functionals with local exchange, whereas Rydberg and charge-transfer excitations are often better treated with nonlocal exchange. The question arises regarding whether one can optimize a functional such that all three kinds of excitations (valence, Rydberg, and charge transfer, including long-range charge transfer) are treated in a balanced and accurate way. The goal of the present work is to try to answer that question and then to optimize a functional with the best possible balanced behavior. Of the variety of functional types available, we choose to use a range-separated hybrid meta functional for the following reasons: (i) Range separation allows the percentage of Hartree-Fock (HF) exchange to change with interelectronic separation, and…

We present a methodology for graph based enumeration of surfaces and unique chemical adsorption structures bonded to those surfaces. Utilizing the graph produced from a bulk structure, we create a unique graph representation for any general slab cleave and further extend that representation to include a large variety of catalytically relevant adsorbed molecules. We also demonstrate simple geometric procedures to generate 3D initial guesses of these enumerated structures. While generally useful for generating a wide variety of structures used in computational surface science and heterogeneous catalysis, these techniques are also key to facilitating an informatics approach to the high-throughput search for more effective catalysts.

The modification of vibrational dynamics is essential for controlling chemical reactions and IR photonic applications. The hybridization between cavity modes and molecular vibrational modes provides a new way to control molecular dynamics. In this work, we study the dynamics of molecular vibrational polaritons in various solvent environments. We find the dynamics of the polariton system is strongly influenced by the nature of the solvents. While the relaxation from upper polariton (UP) to dark modes is always fast (<5 ps) regardless of the medium, lower polariton (LP) in low polarity solvents shows much slower transfer (10-30 ps) into dark modes, despite the fact that the LP lifetime remains within 5 ps. This result suggests that in the latter media, the energy pumped into the LP is first transferred into intermediate states which only subsequently decay into dark modes. In contrast, in solvent environments that strongly interact with the solute, the LP population relaxes into the dense dark state manifold within a much faster time scale. We propose the intermediate state to be the…

Machine learning provides promising new methods for accurate yet rapid prediction of molecular properties, including thermochemistry, which is an integral component of many computer simulations, particularly automated reaction mechanism generation. Often, very large data sets with tens of thousands of molecules are required for training the models, but most data sets of experimental or high-accuracy quantum mechanical quality are much smaller. To overcome these limitations, we calculate new high-level data sets and derive bond additivity corrections to significantly improve enthalpies of formation. We adopt a transfer learning technique to train neural network models that achieve good performance even with a relatively small set of high-accuracy data. The training data for the entropy model are carefully selected so that important conformational effects are captured. The resulting models are generally applicable thermochemistry predictors for organic compounds with oxygen and nitrogen heteroatoms that approach experimental and coupled cluster accuracy while only requiring molecular…

We studied the configurational sampling of noncovalently bonded molecular clusters relevant to the atmosphere. In this article, we discuss possible approaches to searching for optimal configurations and present one alternative based on systematic configurational sampling, which seems able to overcome the typical problems associated with searching for global minima on multidimensional potential energy surfaces. Since atmospheric molecular clusters are usually held together by intermolecular bonds, we also present a cost-effective strategy for treating hydrogen bonding and proton transferring by using rigid molecules and ions in different protonation states and illustrate its performance on clusters containing guanidine and sulfuric acid.

Electronegativity is a fundamental concept in chemistry that allows one to infer important aspects about the interactions between chemical species. In the present work we make use of the framework provided by the density functional theory of chemical reactivity, to discuss in a unified way the approaches to the concept of electronegativity developed by Pauling and by Mulliken. Our analysis starts by making use of the identification of the electronegativity of Mulliken with the chemical potential of density functional theory, and continues to show that the ionic correction proposed by Pauling can be derived, with certain approximations, from the quadratic smooth interpolation of the energy as a function of the number of electrons in terms of the chemical potentials and the hardnesses of the interacting species, from which one can infer the close qualitative relationship between Pauling's electronegativity and the electrophilicity concept.

In the present study, we propose a new set of descriptors that, along with a few structural features of nanoporous materials, can be used by machine learning algorithms for accurate predictions of the gas uptake capacities of these materials. All new descriptors closely resemble the helium atom void fraction of the material framework. However, instead of a helium atom, a particle with an appropriately defined van der Waals radius is used. The set of void fractions of a small number of these particles is found to be sufficient to characterize uniquely the structure of each material and to account for the most important topological features. We assess the accuracy of our approach by examining the predictions of the random forest algorithm in the relative small dataset of the computation-ready, experimental (CoRE) MOFs (∼4700 structures) that have been experimentally synthesized and whose geometrical/structural features have been accurately calculated before. We first performed grand canonical Monte Carlo simulations to accurately determine their methane uptake capacities at two…

. The reactive force field parameters have been trained against quantum mechanical (QM) calculations related to water binding energies, hydration energies and energies of proton transfer. The new force field has been validated by applying it to molecular dynamics (MD) simulations of the ionization of different electrolytes in water and comparison of the results with experimental observations and thermodynamics. Radial distribution functions (RDF) determined for most of the atom pairs (cation or anion with oxygen and hydrogen of water) show a good agreement with the RDF values obtained from DFT calculations. On the basis of the applied force field, the ReaxFF simulations have described the diffusion constants for water and electrolyte ions in alkali metal hydroxide and chloride salt solutions as a function of composition and electrolyte concentration. The obtained results open opportunities to advance ReaxFF methodology to a wide range of applications involving electrolyte ions and solutions.

While the primary bottleneck to a number of computational workflows was not so long ago limited by processing power, the rise of machine learning technologies has resulted in an interesting paradigm shift, which places increasing value on issues related to data curation-that is, data size, quality, bias, format, and coverage. Increasingly, data-related issues are equally as important as the algorithmic methods used to process and learn from the data. Here we introduce an open-source graphics processing unit-accelerated neural network (NN) framework for learning reactive potential energy surfaces (PESs). To obtain training data for this NN framework, we investigate the use of real-time interactive ab initio molecular dynamics in virtual reality (iMD-VR) as a new data curation strategy that enables human users to rapidly sample geometries along reaction pathways. Focusing on hydrogen abstraction reactions of CN radical with isopentane, we compare the performance of NNs trained using iMD-VR data versus NNs trained using a more traditional method, namely, molecular dynamics (MD)…

Thermodynamic properites of molecules are used widely in the study of reactive processes. Such properties are typically measured via experiments or calculated by a variety of computational chemistry methods. In this work, machine learning (ML) models for estimation of standard enthalpy of formation at 298.15 K are developed for three classes of acyclic and closed-shell hydrocarbons, viz. alkanes, alkenes, and alkynes. Initially, an extensive literature survey is performed to collect standard enthalpy data for training ML models. A commercial software (Dragon) is used to obtain a wide set of molecular descriptors by providing SMILES strings. The molecular descriptors are used as input features for the ML models. Support vector regression (SVR) and artificial neural networks are used with a two-level K-fold cross-validation (K-fold CV) workflow. The first level is for estimation of accuracy of both the ML models, and the second level is for generation of the final models. The SVR model is selected as the best model based on error estimates over 10-fold CV. The final SVR model is…

The spin–orbit coupling constants (SOCC) in atoms and ions of the first- through third-row transition elements were calculated for the low-lying atomic states whose main electron configuration is [ n d] q ( q = 1–4 and 6–9, n = the principal quantum number), using four different approaches: (1) a nonrelativistic Hamiltonian used to construct multiconfiguration self-consistent field (MCSCF) wave functions utilizing effective core potentials and their associated basis sets within the framework of second-order configuration interaction (SOCI) to calculate spin–orbit couplings (SOC) using one-electron Breit–Pauli Hamiltonian (BPH), (2) a nonrelativistic Hamiltonian used to construct MCSCF wave functions utilizing model core potentials and their associated basis sets within the framework of SOCI to calculate SOC using the full BPH, (3) nonrelativistic and spin-independent relativistic Hamiltonians used to construct MCSCF wave functions utilizing all-electron (AE) basis sets within the framework of SOCI to calculate SOC using the full BPH, and (4) a relativistic Hamiltonian given by the…

In this contribution we introduce the concept of bond order density (BOD) on the basis of a previous work on natural adaptive orbitals. We show that BODs may be used to visualize both the global spatial distribution of the covalent bond order and its eigencomponents, which we call bond(ing) channels. BODs can be equally computed at correlated and noncorrelated levels of theory and in ground or excited states, thus offering an appealing description of bond-forming, bond-breaking, and bond-evolution processes. We show the power of the approach by examining a number of homo- and heterodiatomics, including the controversial existence of a fourth bonding component in dicarbon, by analyzing a few interesting bonding situations in polyatomics and chemical transformations, and by exemplifying exotic bonding behaviors in simple excited electronic states.

The effect of the anion size and electronegativity of halide-based anions (Cl –, Br –, I –, and BF 4 – ) on the interionic interaction in 1-ethyl-3-methylimidazolium-based ionic liquids (ILs) C 2 mim X (X = Cl, Br, I, and BF 4 ) is studied by a combined approach of experiments (Raman, IR, UV–vis spectroscopy) and quantum chemical calculations. The fingerprint region of the Raman spectra of these C 2 mim X ion-pairs provides evidence of the presence of the conformational isomerism in the alkyl chain of the C 2 mim + cation. The Raman and IR bands of the imidazolium C 2 –H stretch vibration for C 2 mim X (X = Cl, Br, I, and BF 4 ) were noticeably blue-shifted with the systematic change in size of anions and the electronegativity. The observed blue shift in the C 2 –H stretch vibration follows the order C 2 mim BF 4 > C 2 mim I > C 2 mim Br > C 2 mim Cl, which essentially indicates the strong hydrogen bonding in the C 2 mim Cl ion-pair. DFT calculations predict at least four configurations for the cation–anion interaction. On the basis of relative optimized energies and…

Dysprosium(III) ions are the third most luminescent lanthanide(III) ions. Dy(III) is used as dopant in optical fibers and as shift reagent in NMR imaging and is the element at the forefront of research in single-molecule magnets. Nonetheless, the excited state manifold of the dysprosium(III) ion is not fully mapped and the nature of the emitting state has not been unequivocally assigned. In the work reported here, the photophysical properties of dysprosium(III) triflate dissolved in H 2 O, MeOH, and DMSO have been studied in great detail. The solvates are symmetric, all oxygen donor atom complexes where the coordination number is 8 or 9. By comparing protonated and deuterated solvents, performing variable temperature spectroscopy, and determining the excited state lifetimes and luminescence quantum yields, the solution structure can be inferred. For the three complexes, the observed electronic energy levels were determined using absorption and emission spectroscopy. The Dy(III) excited state manifolds of the three solvates differ from that reported by Carnall, in particular for the…

The coupling of a molecular ensemble to the confined electromagnetic modes of a microcavity can strongly modify the photophysics and photochemistry of the molecules upon photoexcitation. We investigate here how collective coupling effects lead to modifications of the mechanisms and rates of photochemical processes, in particular, photodissociation and nonradiative decay in NaI and pyrazine, respectively. We show that, after direct excitation into the lower polaritonic states, the lower-energy light-matter hybrid states, the dynamics of the molecular ensemble coupled to light is very similar to the dynamics of the corresponding isolated molecules. Conversely, excitation into the upper polaritonic states results in more complex dynamics that involve as a first step the population transfer toward the manifold of intermediate dark states. These dynamics differ substantially from those of the isolated molecules and may result in measurable time delays for nonradiative decay or excited-state reaction mechanisms. Similarly, we describe how addition of a buffer of nonreactive molecules…

Carbon dioxide is a greenhouse gas and is available in abundance in the atmosphere. Because of this, many researchers have searched for opportunities to utilize CO 2 and convert it into valuable materials. In this work, we study the electrochemical reduction of CO 2 to CO on an iron-porphyrin center using computational modeling. We tested two types of iron-porphyrins, namely, the tetraphenylporphyrin (TPP) and meso-(ortho-2-amide-phenyl)(triphenyl)porphyrin ligands. Density functional theory calculations investigated a catalytic cycle that involves a reduction, CO 2 binding, two protonations, and another reduction step. We tested several density functional theory methods, basis sets, and model structures. There is a certain degree of variation between the results obtained with different density functional methods, but the same general trends are found. The calculations show that during the reduction processes, a ligand rather than metal reduction takes place, which enables stable binding of CO 2 as an [Fe III (CO 2 2– )(TPP –• )] 2– complex. The subsequent proton transfer from…

High molecular weight “ROOR′” dimers, likely formed in the gas phase through self- and cross-reactions of complex peroxy radicals (RO 2 ), have been suggested to play a key role in forming ultrafine aerosol particles in the atmosphere. However, the molecular-level reaction mechanism producing these dimers remains unknown. Using multireference quantum chemical methods, we explore one potentially competitive pathway for ROOR′ production, involving the initial formation of triplet alkoxy radical (RO) pairs, followed by extremely rapid intersystem crossings (ISC) to the singlet surface, permitting subsequent recombination to ROOR′. Using CH 3 OO + CH 3 OO as a model system, we show that the initial steps of this reaction mechanism are likely to be very fast, as the transition states for both the formation and the decomposition of the CH 3 O 4 CH 3 tetroxide intermediate are far below the reactants in energy. Next, we compute ISC rates for seven different atmospherically relevant 3 (RO···R′O) complexes. The ISC rates vary significantly depending on the conformation of the complex and…

The mixed-reference spin–flip time-dependent density functional theory (MRSF-TD-DFT) method eliminates the erroneous spin contamination of the SF-TD-DFT methodology, while retaining the conceptual and practical simplicity of the latter. The availability of the analytic gradient of the energy of the MRSF-TD-DFT response states enables automatic geometry optimization of the targeted states. Here, we apply the new method to optimize the geometry of several S 1 /S 0 conical intersections occurring in typical organic molecules. We demonstrate that MRSF-TD-DFT is capable of producing the correct double-cone topology of the intersections and describing the geometry of the lowest-energy conical intersections and their relative energies with accuracy matching that of the best multireference wavefunction ab initio methods. In this regard, MRSF-TD-DFT differs from many popular single-reference methods, such as, e.g., the linear response TD-DFT method, which fail to produce the correct topology of the intersections. As the new methodology completely eliminates the ambiguity with the…

Applying fine grids of nucleus independent chemical shift (NICS) probes (BQs) at different distances from the molecular plane of aromatic and antiaromatic molecules suggests that, at short distances, NICS π,zz is maximal (absolute values) off the geometrical center of the systems. In nonsymmetric systems, the center of the induced ring current may be a little off the geometrical center, but the difference is negligible at distances ≥2 Å. At these distances, the change of NICS π,zz with the distance from the ring follows a power relation. It is shown that the order of diatropicity and paratropicity within a group of molecules depends on the distance from the system (namely, the order of NICS( r ) π,zz depends on r ). It is thus suggested to use ∫NICS π,zz as a quantitative measure of aromaticity.

Finding globally optimal structures of nanoclusters is critically important to understand their physicochemical properties but remains prohibitively expensive even with comparatively efficient density functionals. Semiempirical methods such as density functional tight-binding (DFTB), on the other hand, offer a better accuracy-efficiency trade-off but require suitable parametrization. In the present work, we present a largely automatic scheme where, starting from initial guesses based on bulk properties, the atomic confinement, and repulsive potentials are further refined so as to accurately represent the potential energy landscapes of 13- and 55-atom nanoclusters of the late transition metals (Ni, Cu, Pd, Ag, Pt, and Au). With the exception of Ni 13, Ni 55, Cu 55, and Ag 55, low-symmetry (often disordered) structures are found to be preferred over the symmetric icosahedral arrangement. Similar to what has been previously reported for Au 55, the lowest-energy Pt 55 structures also appear to contain small cavities below the outer shell.

The abundance and basicity of a stabilizing base have shown to be key factors in sulfuric acid driven atmospheric new-particle formation. However, since experiments indicate that a low concentration of ammonia enhances particle formation from sulfuric acid and dimethylamine, which is a stronger base, there must be additional factors affecting the particle formation efficiency. Using quantum chemistry, we provide a molecular-level explanation for the synergistic effects in sulfuric acid-dimethylamine-ammonia cluster formation. Because of the capability of ammonia to form more intermolecular interactions than dimethylamine, it can act as a bridge-former in sulfuric acid-dimethylamine clusters. In many cluster compositions, ammonia is more likely to be protonated than dimethylamine, although it is a weaker base. By nanoparticle formation rate simulations, we show that due to the synergistic effects, ammonia can increase the particle formation rate by up to 5 orders of magnitude compared to the two-component sulfuric acid-amine system.

Electron transfer coupling is a critical factor in determining electron transfer rates. This coupling strength can be sensitive to details in molecular geometries, especially intermolecular configurations. Thus, studying charge transporting behavior with a full first-principle approach demands a large amount of computation resources in quantum chemistry (QC) calculation. To address this issue, we developed a machine learning (ML) approach to evaluate electronic coupling. A prototypical ML model for an ethylene system was built by kernel ridge regression with Coulomb matrix representation. Since the performance of the ML models highly dependent on their building strategies, we systematically investigated the generality of the ML models, the choice of features and target labels. The best ML model trained with 40 000 samples achieved a mean absolute error of 3.5 meV and greater than 98% accuracy in predicting phases. The distance and orientation dependence of electronic coupling was successfully captured. Bypassing QC calculation, the ML model saved 10–10 4 times the computation cost.…

Replica exchange molecular dynamics simulations and vibrational spectroscopy calculations are performed using halide-water many-body potential energy functions to provide a bottom-up analysis of the structures, energetics, and hydrogen-bonding arrangements in X−(H2O)n=3−6 clusters, with X = F, Cl, Br, and I. Independently of the cluster size, it is found that all four halides prefer surface-type structures in which they occupy one of the vertices in the underlying three-dimensional hydrogen-bond networks. For fluoride-water clusters, this is in contrast with previous reports suggesting that fluoride prefers interior-type arrangements, where the ion is fully hydrated. These differences can be ascribed to the variability in how various molecular models are capable to reproduce the subtle interplay between halide-water and water-water interactions. Our results thus emphasize the importance of a correct representation of individual many-body contributions to the molecular interactions for a quantitative description of halide ion hydration.

Oxidation of CO into CO 2 is a prototypical reaction in heterogeneous catalysis and is one of the extensively studied reactions in the gas phase to explore the underlying mechanisms of related catalysis. In this Feature Article, we present and discuss our recent advances in the fundamental understanding of catalytic CO oxidation by O 2 mediated with heteronuclear metal oxide clusters (HMOCs) using state-of-the-art mass spectrometry and quantum chemistry calculations. The HMOCs can be considered as ideal models for active sites on mixed or oxide supported catalysts at a strictly molecular level. A concept of electronegativity-ladder effect was proposed to account for the enhanced reactivity of noble metal (NM) doped HMOCs, and then this effect was successfully extended in the design of NM-free HMOCs in catalytic CO oxidation by O 2 . The future directions and the challenges were also discussed.

In 2005, Calvert and Lindberg (Calvert, J. G.; Lindberg, S. E. Atmos. Environ. 2005, 39, 3355–3367) wrote that the use of laboratory-derived rate constants for OH + Hg(0) “...to determine the extent of Hg removal by OH in the troposphere will greatly overestimate the importance of Hg removal by this reaction.” The HOHg • intermediate formed from OH + Hg will mostly fall apart in the atmosphere before it can react. By contrast, in laboratory experiments, Calvert and Lindberg expected HOHg • to react with radicals (whose concentrations are much higher than in the atmosphere). Yet, almost all models of oxidation of Hg(0) ignore the argument of Calvert and Lindberg. We present a way for modelers to include the OH + Hg reaction while accounting quantitatively for the dissociation of HOHg • . We use high levels of quantum chemistry to establish the HO–Hg bond energy as 11.0 kcal/mol and calculate the equilibrium constant for OH + Hg = HOHg • . Using the measured rate constant for the association of OH with Hg, we determine the rate constant for HOHg • dissociation. Theory is also used to…

Calculation of the solvation free energy of ionic molecules is the principal source of errors in the quantum chemical evaluation of p K a values using implicit polarizable continuum solvent models. One of the important parameters affecting the performance of these models is the choice of atomic radii. Here, we assess the performance of the solvation model based on density (SMD) implicit solvation model employing SMD default radii (SMD) and Bondi radii (SMD-B), a set of empirical atomic radii developed based on the crystallographic data. For a set of 112 ions (60 anions and 52 cations), the SMD-B model showed lower mean unsigned error (MUE) for predicted aqueous solvation free energies (4.0 kcal/mol for anions and 2.4 kcal/mol for cations) compared to the standard SMD model (MUE of 5.0 kcal/mol for anions and 2.9 kcal/mol for cations). In particular, usage of Bondi radii improves the aqueous solvation energies of sulfur-containing ions by >5 kcal/mol compared to the SMD default radii. Indeed, for a set of 45 thiols, the SMD-B model was found to dramatically improve the predicted p K…

Transition-metal-centered monocyclic boron wheel clusters (M©B n q ) represent a family of interesting borometallic compounds with double aromaticity. A variety of early and late transition metal atoms have been found to form such structures with high symmetries and various B n ring sizes. Here we report a combined photoelectron spectroscopy and quantum-chemistry theoretical study of two M©B n – clusters from the middle of the transition metal series: Re©B 8 – and Re©B 9 – . Global minimum structure searches revealed that ReB 8 – adopts a pseudo- C 8 v structure while ReB 9 – is a perfectly planar D 9 h molecular wheel. Chemical bonding analyses showed that both clusters exhibit σ and π double aromaticity and obey the electronic design principle for metal-centered borometallic molecular wheels. The central Re atoms are found to possess unusually low oxidation states of +I in Re©B 8 – and +II in Re©B 9 –, i.e., the Re atom behaves similarly to late transition metal elements (Ru, Fe, Co, Rh, Ir) in the M©B n – molecular wheels. These two clusters become new members of the family of…

Confined systems often exhibit unusual behavior regarding their structure, stability, reactivity, bonding, interactions, and dynamics. Quantization is a direct consequence of confinement. Confinement modifies the electronic energy levels, orbitals, electronic shell filling, etc. of a system, thereby affecting its reactivity as well as various response properties as compared to the cases of corresponding unconfined systems. Confinement may force two rare gas atoms to form a partly covalent bond. Gas storage is facilitated through confinement and unprecedented optoelectronic properties are observed in certain cases. Some slow reactions get highly accelerated in an appropriate confined environment. In the current Feature Article we analyze these aspects with a special emphasis on the work done by our research group.

The chiral source and its mechanism in the molecular system are of great significance in many fields. In this work, we proposed visualized methods to investigate the physical mechanism of a chiral molecule, where the electric and magnetic interactions are visualized with the transitional electric dipole moment, the transitional magnetic dipole moment, and the transitional electric quadrupole moment, and their tensor product. This will also serve as an effective means of visualizing the interaction of light with matter. The relationship between the molecular Raman optical activity (ROA) response and molecular structure was analyzed in an intuitive way. The relationship between chromophore chirality and molecular vibration mode are revealed via interaction between the transition electric dipole moment and the transition magnetic dipole moment. The molecular chirality is derived from the anisotropy of the molecular transition electric dipole moment and the transition magnetic dipole moment. The anisotropic dipole moment localized molecular chromophore is the source of the vibration…

Many approaches have been used to improve the accuracy of implicit solvent models including solute cavity scaling, introducing explicit solvent molecules, and changing the level of theory for the solvation calculations. Here, we compare these strategies using a large test set of aqueous p K a values for amines, nucleobases, carboxylic acids, thiols, peptide carbon acids, alcohols, and anilines for the specific case of solvation model density (SMD) within the framework of a thermodynamic cycle in which the gas-phase component is consistently calculated via the accurate CBS-QB3 method. We show that the choice of theoretical level for solvation energies should be based on the original parameterization of the solvent model, with separate levels of theory for the solvation energies of neutrals, anions, or cations, outperforming the best compromise level of theory. However, when explicit solvent molecules are introduced, a higher level of theory is needed to describe the solute–solvent interactions. For the systems studied here, explicit solvation improved the results for acids (and hence…

For the consistent development of the field of photon upconversion via triplet–triplet annihilation (TTA-UC), it is pivotal to know the true quantum yield of TTA-UC emission. Although TTA-UC quantum yields have been determined by common relative measurements using quantum yield standards, there is still a discrepancy between the reported values even for the benchmark sensitizer–emitter pair of platinum(II) octaethylporphyrin (PtOEP) and 9,10-diphenylanthracene (DPA). Here, to resolve this situation, we show a method to obtain the absolute quantum yield of TTA-UC photoluminescence. The difficulty in obtaining absolute TTA-UC quantum yield by the integrating sphere measurement is to accurately calibrate the contribution of reabsorbed upconverted emission by triplet sensitizers. The reabsorption correction is successfully carried out by comparing sensitizer phosphorescence with and without the integrating sphere. An absolute TTA-UC quantum yield of the PtOEP–DPA pair is obtained as 36%, which shows a good agreement with the relative TTA-UC quantum yield. An absolute TTA-UC quantum…

Reaction of ammonia with SO 3 as a potential source of sulfamic acid in the troposphere has been investigated by means of electronic structure and chemical kinetic calculations. Besides, the hydrolysis reaction, which is known to be a major atmospheric decay channel of SO 3, has also been investigated. The catalytic effects of ammonia and water on both the reactions have been studied. Rate coefficients for all the studied reaction channels were calculated using the transition state theory employing pre-equilibrium approximation. Calculated rate coefficients for a number of catalyzed hydrolysis and ammonolysis processes were found to be much higher (by ∼10 5 to ∼10 9 times) than the gas kinetic limit at ambient temperature. With decrease in temperature because of negative temperature dependence of rate coefficients, that difference became even larger (up to ∼10 16 times). Therefore, in order to remove the discrepancies, rate coefficients for all the studied reaction channels were calculated by means of the master equation. The results showed marked improvements, with only one channel…

Porphyrins are present in many metalloproteins, and they are also important components of a variety of nonbiological functional materials. Furthermore, they are representative of the kind of large, strongly correlated system that is especially difficult for accurate calculations. For example, predicting the order of their spin states has been challenging. Here we study the energetic order of four states (one singlet, two triplets, and one quintet) of iron porphyrin, FeP, by the multiconfiguration pair-density functional theory (MC-PDFT). Five active space prescriptions, namely, CAS(8, 6), CAS(8, 11), CAS(16, 15), RAS(34,2,2;13,6,16), and DMRG(34, 35), are used to obtain the kinetic energy, density, and on-top density. Although the prediction of which spin state of FeP is the ground state depends on the selection of the active space when one uses multireference second-order perturbation theory and such calculations lead incorrectly to a quintet ground state with the largest studied active space, all five active spaces correctly lead to a triplet ground state when one uses MC-PDFT. We…

Because collecting precise and accurate chemistry data is often challenging, chemistry data sets usually only span a small region of chemical space, which limits the performance and the scope of applicability of data-driven models. To address this issue, we integrated an active learning machine with automatic ab initio calculations to form a self-evolving model that can continuously adapt to new species appointed by the users. In the present work, we demonstrate the self-evolving concept by modeling the formation enthalpies of stable closed-shell polycyclic species calculated at the B3LYP/6-31G(2df,p) level of theory. By combining a molecular graph convolutional neural network with a dropout training strategy, the model we developed can predict density functional theory (DFT) enthalpies for a broad range of polycyclic species and assess the quality of each predicted value. For the species which the current model is uncertain about, the automatic ab initio calculations provide additional training data to improve the performance of the model. For a test set composed of 2858 cyclic and…

The mixed-reference spin-flip (MRSF) time-dependent density functional theory (TDDFT) method eliminates the notorious spin contamination of SF-TDDFT, thus enabling identification of states of proper spin-symmetry for automatic geometry optimization and molecular dynamics simulations. Here, we analyze and optimize the MRSF-TDDFT in the calculations of the vertical excitation energies (VEEs) and the singlet-triplet (ST) gaps. The dependence of the obtained VEEs and ST gaps on the intrinsic parameters of the MRSF-TDDFT method is investigated, and prescriptions for the proper use of the method are formulated. For VEEs, MRSF-TDDFT displays similar or better accuracy than SF-TDDFT (ca. 0.5 eV), while considerably outperforming the LR-TDDFT for the ST gaps. As a result, a new functional of STG1X (dubbed here), especially for ST gaps is suggested on the basis of splitting between the components of the atomic multiplets.

We have developed a transferable ab initio intramolecular force field for zeolitic imidazolate frameworks (ZIFs), "ZIF-FF", that is capable of quantitatively describing the structural properties and relative stabilities of ZIFs. In contrast to nearly all prior force fields, ZIF-FF properly describes the relative stability of ZIF polymorphs, a crucial element in ZIF nucleation and crystal growth. Beginning with a general Amber force field (GAFF), Zn-related force field parameters were optimized against dispersion-corrected DFT-calculated properties using a genetic algorithm. We validated the resulting force field by examining bond and angle distributions, phonon density of states, mechanical properties, diffusion properties and via modeling a ZIF amorphization process. Furthermore, we find that ZIF-FF is transferable, successfully describing relative stability of various ZIF surface structures, as well as the densities of ZIFs with diverse functionalized linkers.

Photophysical properties of a synthesized asymmetric two-way proton transfer molecule 3-(benzo[ d ]thiazol-2-yl)-2-hydroxy-5-methoxybenzaldehyde ( BTHMB ) were studied in detail. BTHMB could undergo excited-state intramolecular proton transfer (ESIPT) involving a 6-membered H-bonded network toward either the N or the O atom present in the molecule as proton acceptors. From tedious spectroscopic dissection, however, it was established that ESIPT was driven exclusively toward the N center over the O center in the solid state as well as in the solution phase. The aforementioned deduction was based on spectral comparison with judicially designed molecules 2-hydroxy-5-methoxybenzaldehyde ( HMB ) and 2-(benzo[ d ]thiazol-2-yl)-4-methoxyphenol ( BTMP ). In solution, the coexistence of the anionic and neutral forms of BTHMB in basic solvents dimethylsulfoxide (DMSO) and dimethylformamide (DMF) enables BTHMB to behave as a white light emitter. Thus, apart from establishment of directionality of ESIPT in double ESIPT probes, the current work deserves special merit as BTHMB can be considered…

The Hamaker constants, which are coefficients providing quantitative information on intermolecular forces, were calculated for a number of different materials according to the Lifshitz theory via simple DFT calculations without any experimental measurements being performed. The physical properties (polarizability, dipole moment, molecular volume, and vibrational frequency) of organic molecules were calculated using the B3LYP density functional and the aug-cc-pVDZ basis set. Values for the Hamaker constants were obtained using the approximation of the Lorentz-Lorenz equation and Onsager's equation with these properties. It was found that, in the case of "nonassociative" materials, such as hydrocarbons, ethers, ketones, aldehydes, carboxylic acids, esters, nitriles, and hydrosilanes, and halides, the calculated Hamaker constants were similar in value to their experimentally determined counterparts. Moreover, with this calculation method, it is easy to create the molecular model and the CPU time can be shortened.

Facile charge transport is desired for many applications of organic semiconductors (OSCs). To take advantage of high-throughput screening methodologies for the discovery of novel OSCs, parameters relevant to charge transport are of high interest. The intramolecular reorganization energy (RE) is one of the important charge transport parameters suitable for molecular-level screening. Because the calculation of the RE with quantum-chemical methods is expensive for large-scale screening, we investigated the possibility of predicting the RE from the molecular structure by means of machine learning methods. We combinatorially generated a molecular library of 5631 molecules with extended conjugated backbones using benzene, thiophene, furan, pyrrole, pyridine, pyridazine, and cyclopentadiene as building blocks and obtained the target electronic data at the B3LYP level of theory with the 6-31G* basis set. We compared ridge, kernel ridge, and deep neural net (DNN) regression models based on graph- and geometry-based descriptors. We found that DNNs outperform the other methods and can predict…

Modular chromophoric systems with minimal electronic coupling between donor and acceptor moieties are well suited for establishing predictive relationships between molecular structure and excited-state properties. Here, we investigate the impact of naphthyl-based connectivity on the photophysics of phenoxazine-derived orthogonal donor–acceptor complexes. While compounds in this class are themselves interesting as potent organic photocatalysts useful for visible-light-driven organocatalyzed atom-transfer radical polymerization and small-molecule synthesis, many other systems (e.g., phenazine, phenothiazine, and acridinium) exploit charge-transfer excited states involving a naphthyl substituent. Therefore, aided by the facile tunability of the phenoxazine architecture, we aim to provide mechanistic insight into the effects of naphthyl connectivity that can help inform the understanding of other systems. We do so by employing time-resolved and steady-state spectroscopies, cyclic voltammetry, and temperature-dependent studies on two chemical series of phenoxazine compounds. In the first…

A novel degradation pathway of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) was identified using computational and experimental methods. Density functional theory (DFT) calculations were employed to obtain its unimolecular degradation pathway, and ultrahigh-performance liquid chromatography–high-resolution mass spectrometry, thermogravimetry–Fourier transform infrared spectrometry, thermogravimetry, and differential scanning calorimetric experimental data were used to validate the computationally deduced degradation pathways. Based on the indications from computational and experimental results, the cleavage of the strained fragment from CL-20 was identified instead of NO 2 or HONO elimination as in conventional high energy materials. This fragmentation results in the formation of two energetic species, dinitrodihydropyrazine and dinitroformimidamide, which makes CL-20 one of the most powerful energetic materials. This novel degradation pathway of CL-20 will be useful in understanding the decomposition of cage molecules, design of new practical energetic…