The 50 most-cited articles in The Journal of Physical Chemistry A, 2021

The recently developed physics-informed neural network (PINN) has achieved success in many science and engineering disciplines by encoding physics laws into the loss functions of the neural network such that the network not only conforms to the measurements and initial and boundary conditions but also satisfies the governing equations. This work first investigates the performance of the PINN in solving stiff chemical kinetic problems with governing equations of stiff ordinary differential equations (ODEs). The results elucidate the challenges of utilizing the PINN in stiff ODE systems. Consequently, we employ quasi-steady-state assumption (QSSA) to reduce the stiffness of the ODE systems, and the PINN then can be successfully applied to the converted non-/mild-stiff systems. Therefore, the results suggest that stiffness could be the major reason for the failure of the regular PINN in the studied stiff chemical kinetic systems. The developed stiff-PINN approach that utilizes QSSA to enable the PINN to solve stiff chemical kinetics shall open the possibility of applying the PINN to…

The application of quantum chemical, automatic multilevel modeling workflows for the determination of thermodynamic (e.g., conformation equilibria, partition coefficients, p K a values) and spectroscopic properties of relatively large, nonrigid molecules in solution is described. Key points are the computation of rather complete structure (conformer) ensembles with extremely fast but still reasonable GFN2-xTB or GFN-FF semiempirical methods in the CREST searching approach and subsequent refinement at a recently developed, accurate r 2 SCAN-3c DFT composite level. Solvation effects are included in all steps by accurate continuum solvation models (ALPB, (D)COSMO-RS). Consistent inclusion of thermostatistical contributions in the framework of the modified rigid-rotor-harmonic-oscillator approximation (mRRHO) based on xTB/FF computed PES is also recommended.

This article primarily discusses the utility of vibrational perturbation theory for the prediction of X-H stretching vibrations with particular focus on the specific variant, second-order vibrational perturbation theory with resonances (VPT2+K). It is written as a tutorial, reprinting most important formulas and providing numerous simple examples. It discusses the philosophy and practical considerations behind vibrational simulations with VPT2+K, including but not limited to computational method selection, cost-saving approximations, approaches to evaluating intensity, resonance identification, and effective Hamiltonian structure. Particular attention is given to resonance treatments, beginning with simple Fermi dyads and gradually progressing to arbitrarily large polyads that describe both Fermi and Darling-Dennison resonances. VPT2+K combined with large effective Hamiltonians is shown to be a reliable framework for modeling the complicated CH stretching spectra of alkenes. An error is also corrected in the published analytic formula for the VPT2 transition moment between the…

Chemical reactions occur in energy, environmental, biological, and many other natural systems, and the inference of the reaction networks is essential to understand and design the chemical processes in engineering and life sciences. Yet, revealing the reaction pathways for complex systems and processes is still challenging because of the lack of knowledge of the involved species and reactions. Here, we present a neural network approach that autonomously discovers reaction pathways from the time-resolved species concentration data. The proposed chemical reaction neural network (CRNN), by design, satisfies the fundamental physics laws, including the law of mass action and the Arrhenius law. Consequently, the CRNN is physically interpretable such that the reaction pathways can be interpreted, and the kinetic parameters can be quantified simultaneously from the weights of the neural network. The inference of the chemical pathways is accomplished by training the CRNN with species concentration data via stochastic gradient descent. We demonstrate the successful implementations and the…

The photophysical analysis of thermally activated delayed fluorescence (TADF) materials has become instrumental for providing insights into their stability and performance, which is not only relevant for organic light-emitting diodes but also for other applications such as sensing, imaging, and photocatalysis. Thus, a deeper understanding of the photophysics underpinning the TADF mechanism is required to push materials design further. Previously reported analyses in the literature of the kinetics of the various processes occurring in a TADF material rely on several a priori assumptions to estimate the rate constants for forward and reverse intersystem crossing. In this report, we demonstrate a method to determine these rate constants using a three-state model together with a steady-state approximation and, importantly, no additional assumptions. Further, we derive the exact rate equations, greatly facilitating a comparison of the TADF properties of structurally diverse emitters and providing a comprehensive understanding of the photophysics of these systems.

This Perspective presents recent advances in our knowledge of the fundamental elementary mechanisms involved in the low- and high-temperature molecular mass growth processes to polycyclic aromatic hydrocarbons in combustion systems and in extraterrestrial environments (hydrocarbon-rich atmospheres of planets and their moons, cold molecular clouds, circumstellar envelopes). Molecular beam studies combined with electronic structure calculations extracted five key elementary mechanisms: Hydrogen Abstraction-Acetylene Addition, Hydrogen Abstraction-Vinylacetylene Addition, Phenyl Addition-DehydroCyclization, Radical-Radical Reactions, and Methylidyne Addition-Cyclization-Aromatization. These studies, summarized here, provide compelling evidence that key classes of aromatic molecules can be synthesized in extreme environments covering low temperatures in molecular clouds (10 K) and hydrocarbon-rich atmospheres of planets and their moons (35-150 K) to high-temperature environments like circumstellar envelopes of carbon-rich Asymptotic Giant Branch Stars stars and combustion systems at…

The DLPNO-CCSD(T) method is designed to study large molecular systems at significantly reduced cost relative to its canonical counterpart. However, the error in this approach is also size-extensive and relies on cancellation of errors for the calculation of relative energies. This work provides a direct comparison of canonical CCSD(T) and TightPNO DLPNO-CCSD(T) calculations of reaction energies and barriers of a broad range of chemical reactions. The dataset includes acidities, anion binding affinities, enolization, Diels–Alder, nucleophilic substitution, and atom transfer reactions and complements existing theoretical datasets in terms of system size as well as new reaction types ( e.g., anion binding affinities and chlorine atom transfer reactions). The performance of DLPNO-CCSD(T) was further examined with respect to systematic variation of basis set and system size and amounts of nonbonded interaction present in the system. The errors in the DLPNO-CCSD(T) were found to be relatively insensitive to the choice of basis set for small systems but increase monotonically with system…

A recent study associates carbon with single photon emitters (SPEs) in hexagonal boron nitride (h-BN). This observation, together with the high mobility of carbon in h-BN, suggests the existence of SPEs based on carbon clusters. Here, by means of density functional theory calculations, we studied clusters of substitutional carbon atoms up to tetramers in h-BN. Two different conformations of neutral carbon trimers have zero-point line energies and shifts of the phonon sideband compatible with typical photoluminescence spectra. Moreover, some conformations of two small C clusters next to each other result in photoluminescence spectra similar to those found in the experiments. We also showed that vacancies are unable to reproduce the typical features of the phonon sideband observed in most measurements because of the large spectral weight of low-energy breathing modes, ubiquitous in such defects.

High Resolution Image Download MS PowerPoint Slide Organic dyes have shown high efficiencies in solar cells, which is mainly attributed to the push–pull strategy present in such dyes upon attaching to the semiconductor surfaces. We deeply studied the fundamental photophysical properties of cyanoacrylic dyes, mostly the L1 dye, and found unique emission properties that depend on many factors such as the solvent polarity and the concentration of the dye and could present a complete emission picture about this family of dyes. The L1 dye shows an intramolecular charge transfer (ICT) emission state at low concentrations (approximately nanomolar scale) and shows a twisted intramolecular charge transfer (TICT) emission state in specific solvents upon increasing the concentration to the micromolar scale. Moreover, the associated emission lifetimes of the ICT and TICT states of the L1 dye depend on solvent basicity, highlighting the role of hydrogen bond formation on controlling such states. Density functional theory calculations are performed to gain insight into the photophysical…

The asymmetric water-air interface provides a dynamic aqueous environment with properties that are often very different than bulk aqueous or gaseous phases and promotes reactions that are thermodynamically, kinetically, or otherwise unfavorable in bulk water. Prebiotic chemistry faces a key challenge: water is necessary for life yet reduces the efficiency of many biomolecular synthesis reactions. This perspective considers water-air interfaces as auspicious reaction environments for abiotic synthesis. We discuss recent evidence that (1) water-air interfaces promote condensation reactions including peptide synthesis, phosphorylation, and oligomerization; (2) photochemistry at water-air interfaces may have been a significant source of prebiotic molecular complexity, given the lack of oxygen and increased availability of near-ultraviolet radiation on early Earth; and (3) water-air interfaces can promote spontaneous reduction and oxidation reactions, potentially providing protometabolic pathways. Life likely began within a relatively short time frame, and water-air interfaces offer…

The full harvesting of both singlet and triplet excitons can pave the way toward more efficient molecular light-emission mechanisms (i.e., TADF or thermally activated delayed fluorescence) beyond the spin statistics limit. This TADF mechanism benefits from low (but typically positive) singlet–triplet energy gaps or Δ E ST . Recent research has suggested the possibility of inverting the order of the energy of lowest singlet and triplet excited states, thus opening new pathways to promote light emission without any energy barrier through triplet to singlet conversion, which is systematically investigated here by means of theoretical methods. To this end, we have selected a set of heteroatom-substituted triangle-shaped molecules (or triangulenes) for which Δ E ST < 0 is predicted. We successfully rationalize the origin of that energy inversion and the reasons for which theoretical methods might produce qualitatively inconsistent predictions depending on how they treat n -tuple excitations (e.g., the large contribution of double excitations for all of the ground and excited states…

Tessellations of kekulenes and cycloarenes are of considerable interest as nanomolecular belts in trapping and transportation of heavy metal ions and chloride ions, as they possess optimal electronic features and pore sizes. A class of cycloarenes called kekulenes have been the focus of several experimental and theoretical studies from the stand point of aromaticity, superaromaticity, chirality, and novel electrical and magnetic properties. In the present study, we investigate the entropies and topological characterization of different tessellations of kekulenes through topological computations of superaromatic structures with pores. We introduce the self-powered vertex degree-based topological indices and then derive the graph entropy measures for three different tessellations (zigzag, armchair, and rectangular) via various molecular descriptors that we derive here. Several applications to computing the molecular properties are pointed out. We demonstrate the existence of isentropic and yet nonisomorphic tessellations of kekulenes for the first time. The two tessellations are…

The thermally activated delayed fluorescence (TADF) phenomenon has attracted increasing attention because it can harvest 100% of the electro-pumped carriers to form singlet bound excited state for fluorescence. It is generally believed that the small energy gap between S 1 and T 1 (Δ E ST ) is essential for TADF to facilitate the reverse intersystem crossing (rISC). However, for a few donor–acceptor (D–A) organic compounds with small Δ E ST, the TADF phenomenon is absent, indicating that Δ E ST might not be a good molecular descriptor. Here, using our self-developed thermal vibration correlation function (TVCF) formalism in combination with quantum chemistry calculations, we revisit the key factors that dominate the TADF property for 11 D–A systems with small Δ E ST . Based on our theoretical results in comparison to experiments, we conclude that the activation energy Δ G is a good molecular descriptor to characterize the TADF performance because a significantly better linear relationship is observed between Δ G and the rISC rate constant ( k rISC ) compared to that between Δ E ST…

In low-temperature flash photolysis of NH 3 /O 2 /N 2 mixtures, the NH 2 consumption rate and the product distribution is controlled by the reactions NH 2 + HO 2 → products (R1), NH 2 + H (+M) → NH 3 (+M) (R2), and NH 2 + NH 2 (+M) → N 2 H 4 (+M) (R3). In the present work, published flash photolysis experiments by, among others, Cheskis and co-workers, are re-interpreted using recent direct measurements of NH 2 + H (+N 2 ) and NH 2 + NH 2 (+N 2 ) from Altinay and Macdonald. To facilitate analysis of the FP data, relative third-body collision efficiencies compared to N 2 for R2 and R3 were calculated for O 2 and NH 3 as well as for other selected molecules. Results were in good agreement with the limited experimental data. Based on reported NH 2 decay rates in flash photolysis of NH 3 /O 2 /N 2, a rate constant for NH 2 + HO 2 → NH 3 + O 2 (R1a) of k 1a = 1.5(±0.5) × 10 14 cm 3 mol –1 s –1 at 295 K was derived. This value is higher than earlier determinations based on the FP results but in good agreement with recent theoretical work. Kinetic modeling of reported N 2 O yields…

The development of high-brilliance third- and fourth-generation light sources such as synchrotrons and X-ray free-electron lasers (XFELs), the emergence of laboratory-based X-ray spectrometers, and instrumental and methodological advances in X-ray absorption (XAS) and (non)resonant emission (XES and RXES/RIXS) spectroscopies have had far-reaching effects across the natural sciences. However, new kinds of experiments, and their ever-higher resolution and data acquisition rates, have brought acutely into focus the challenge of accurately, quickly, and cost-effectively analyzing the data; a far-from-trivial task that demands detailed theoretical calculations that are capable of capturing satisfactorily the underlying physics. The past decade has seen significant advances in the theory of core-hole spectroscopies for this purpose, driven by all of the developments above and—crucially—a surge in demand. In this Perspective, we discuss the challenges of calculating core-excited states and spectra, and state-of-the-art developments in electronic structure theory, dynamics, and data-driven…

We present a benchmark investigation on the O-H bond dissociation enthalpies (BDEs) and ionization potential (IP) for gallic acid (GA), a widely known polyphenolic antioxidant. These properties were determined in the gas-phase and in water through the use of density functional theory (DFT), second-order Møller-Plesset perturbation theory (MP2), coupled-cluster with single and double excitations (CCSD), and coupled-cluster with single and double excitations as well as perturbative inclusion of triples (CCSD(T)). The 6-311++G(df,p), cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, and aug-cc-pVTZ basis sets were used. Regarding DFT functionals, the M06-2X provided the best agreement for the BDEs when compared to the corresponding CCSD(T)/aug-cc-pVTZ results; M06-2X was also found to be the most suitable for probing the IP for the protonated forms of GA while LC-ωPBE was the most reliable in the case of deprotonated GA. Given that these properties represent important descriptors for examining mechanisms related to the antioxidant potential of a given polyphenol, we hope that the present work can serve…

Astrochemistry lies at the nexus of astronomy, chemistry, and molecular physics. On the basis of precise laboratory data, a rich collection of more than 200 familiar and exotic molecules have been identified in the interstellar medium, the vast majority by their unique rotational fingerprint. Despite this large body of work, there is scant evidence in the radio band for the basic building blocks of chemistry on earth-five- and six-membered rings-despite long-standing and sustained efforts during the past 50 years. In contrast, a peculiar structural motif, highly unsaturated carbon in a chainlike arrangement, is instead quite common in space. The recent astronomical detection of cyanobenzene, the simplest aromatic nitrile, in the dark molecular cloud TMC-1, and soon afterward in additional prestellar and possibly protostellar sources, establishes that aromatic chemistry is likely widespread in the earliest stages of star formation. The subsequent discovery of cyanocyclopentadienes and even cyanonaphthalenes in TMC-1 provides further evidence that organic molecules of considerable…

Bond dissociation energy (BDE) has been calculated for a series of compounds that contain N–O bonds. These structures encompass model N, N, O -trisubstituted hydroxylamines that include O -methoxy, O -acyl, and O -phenyl hydroxylamines. The calculations used three accurate composite methods, CBS-QB3, CBS-APNO, and G4 methods and the computationally more affordable M06-2X/6-311+G(3df,2p) density functional theory (DFT) functional. The calculated N–O single-bond BDEs are 5–15 kcal/mol higher than a generic N–O BDE of 48 kcal/mol quoted in the literature and in textbooks. The M06-2X DFT functional provides BDEs that are in excellent agreement with the higher-level composite methods. We also provided a comparison of the N–O BDE for pyridine- N -oxide to simple trialkylamine oxides. Based on an experimental BDE of 63.3 ± 0.5 kcal/mol for pyridine- N -oxide, our best estimate gives 56.7 ± 0.9 kcal/mol N–O BDE for trimethylamine- N -oxide and 59.0 ± 0.8 kcal/mol for triethylamine- N -oxide.

The F12-TZ-cCR quartic force field (QFF) methodology, defined here as CCSD(T)-F12b/cc-pCVTZ-F12 with further corrections for relativity, is introduced as a cheaper and even more accurate alternative to more costly composite QFF methods like those containing complete basis set extrapolations within canonical coupled cluster theory. F12-TZ-cCR QFFs produce B 0 and C 0 vibrationally averaged principal rotational constants within 7.5 MHz of gas-phase experimental values for tetraatomic and larger molecules, offering higher accuracy in these constants than the previous composite methods. In addition, F12-TZ-cCR offers an order of magnitude decrease in the computational cost of highly accurate QFF methodologies accompanying this increase in accuracy. An additional order of magnitude in cost reduction is achieved in the F12-DZ-cCR method, while also matching the accuracy of the traditional composite method’s B 0 and C 0 constants. Finally, F12-DZ and F12-TZ are benchmarked on the same test set, revealing that both methods can provide anharmonic vibrational frequencies that are comparable…

The absence of d-orbital electrons or presence of full-filled d-orbital electrons in metal ions is a well-known Achilles’ heel problem for the detection of these metal ions by a simple UV-visible study. For this reason, detection of metal ions such as Al 3+ with no d-orbital electrons or Zn 2+ with filled d-orbital electrons is a challenging task. Herein, we report a 2-naphthol-based fluorescent probe [1-(( E )-(( E )-(5-bromo-2-hydroxybenzylidene)hydrazono)methyl)naphthalen-2-ol] ( H 2 L ) that has been used to sense and discriminate Al 3+ and Zn 2+ via solvent regulation. The probe exhibits excellent selectivity and swift sensitivity toward Al 3+ in MeOH–water (9:1, v/v) and toward Zn 2+ in dimethyl sulfoxide (DMSO)–water (9:1, v/v) among various metal ions. The respective detection limit is found to be 9.78 and 3.65 μM. The sensing mechanism is attributed to multiple processes, viz., the inhibition of photo-induced electron transfer (PET) along with the introduction of chelation-enhanced emission (CHEF) and excited-state intramolecular proton transfer (ESIPT) inhibition, which…

Accompanying the rapidly growing list of σ-hole bonds has come the acknowledgment of parallel sorts of noncovalent bonds which owe their stability in large part to a deficiency of electron density in the area above the molecular plane, known as a π-hole. The origins of these π-holes are probed for a wide series of molecules, comprising halogen, chalcogen, pnicogen, tetrel, aerogen, and spodium bonds. Much like in the case of their σ-hole counterparts, formation of the internal covalent π-bond in the Lewis acid molecule pulls density toward the bond midpoint and away from its extremities. This depletion of density above the central atom is amplified by an electron-withdrawing substituent. At the same time, the amplitude of the π*-orbital is enhanced in the region of the density-depleted π-hole, facilitating a better overlap with the nucleophile's lone pair orbital and a stabilizing n → π* charge transfer. The presence of lone pairs on the central atom acts to attenuate the π-hole and shift its position somewhat, resulting in an overall weakening of the π-hole bond. There is a…

-PBEP86-D4 marginally outperforms the previous "best in class" ωB97M(2) Berkeley double hybrid but without range separation and using fewer than half the number of empirical parameters. Range separation turns out to offer only marginal further improvements on GMTKN55 itself. While ωB97M(2) still yields better performance for small-molecule thermochemistry, this is compensated in WTMAD2 by the superior performance of the new functionals for conformer equilibria. Results for two external test sets with pronounced static correlation effects may indicate that range-separated double hybrids are more resilient to such effects.

Computational approaches for predicting drug-target interactions (DTIs) play an important role in drug discovery since conventional screening experiments are time-consuming and expensive. In this study, we proposed end-to-end representation learning of a graph neural network with an attention mechanism and an attentive bidirectional long short-term memory (BiLSTM) to predict DTIs. For efficient training, we introduced a bidirectional encoder representations from transformers (BERT) pretrained method to extract substructure features from protein sequences and a local breadth-first search (BFS) to learn subgraph information from molecular graphs. Integrating both models, we developed a DTI prediction system. As a result, the proposed method achieved high performances with increases of 2.4% and 9.4% for AUC and recall, respectively, on unbalanced datasets compared with other methods. Extensive experiments showed that our model can relatively screen potential drugs for specific protein. Furthermore, visualizing the attention weights provides biological insight.

Atmospheric particles can be viscous. The limitation in diffusion impedes the mass transfer of oxidants from the gas phase to the particle phase and hinders multiphase oxidation processes. On the other hand, nitrate photolysis has been found to be effective in producing oxidants such as OH radicals within the particles. Whether nitrate photolysis can effectively proceed in viscous particles and how it may affect the physicochemical properties of the particle have not been much explored. In this study, we investigated particulate nitrate photolysis in mixed sucrose–nitrate–sulfate particles as surrogates of atmospheric viscous particles containing organic and inorganic components as a function of relative humidity (RH) and the molar fraction of sucrose to the total solute ( F SU ) with an in situ micro-Raman system. Sucrose suppressed nitrate crystallization, and high photolysis rate constants (∼10 –5 s –1 ) were found, irrespective of the RH. For F SU = 0.5 and 0.33 particles under irradiation at 30% RH, we observed morphological changes from droplets to the formation of inclusions…

Though density functional theory is widely accepted as one of the most successful developments in theoretical chemistry in the past few decades, the knowledge of how to apply this new electronic structure theory, to help us better understand chemical processes and transformations, is still an unaccomplished task. The information-theoretic approach is emerging as a viable option for that purpose in the recent literature, providing new insights about steric effect, cooperativity, electrophilicity, nucleophilicity, stereoselectivity, homochirality, etc. In this work, based on the result from a recent paper by one of us [ J. Chem. Phys, 2019, 151, 141103], we present two quantifications of the relative Fisher information and discuss their physiochemical properties and possible applications. To that end, their analytical properties have been elucidated. They have also been applied to six categories of systems to illustrate their applicability. A better descriptor to quantify the single bond rotation barrier has been obtained. The relative Fisher information can also simultaneously…

Quantum chemistry studies of biradical systems are challenging due to the required multiconfigurational nature of the wavefunction. In this work, Variational Quantum Eigensolver (VQE) is used to compute the energy profile for the lithium superoxide dimer rearrangement, involving biradical species, on quantum simulators and devices. Considering that current quantum devices can only handle limited number of qubits, we present guidelines for selecting an appropriate active space to perform computations on chemical systems that require many qubits. We show that with VQE performed with a quantum simulator reproduces results obtained with full-configuration interaction (Full CI) for the chosen active space. However, results deviate from exact values by about 39 mHa for calculations on a quantum device. This deviation can be improved to about 4 mHa using the readout mitigation approach and can be further improved to 2 mHa, approaching chemical accuracy, using the state tomography technique to purify the calculated quantum state.

Pollution of water resources by various pollutants is a global environmental issue, particularly, dye pollution has a major contribution to it. From various studies, it is confirmed that adsorption is an excellent remediation technique compared to others. Mg–Al-layered double hydroxides (LDHs) intercalated with NO 3 – ions act as an effective adsorbent-removing ionic species like heavy metal and dyes. Another popular nanomaterial is graphene oxide (GO), which is successfully used as an adsorbent for different pollutants like dye and heavy metal ions. It is prepared based on the modified Hummers method. In this study, GO was introduced on the surface of LDH to improve its adsorption capacity. The adsorption process is well described by the Freundlich model. The maximum adsorption capacity was obtained at around 0.5 and 0.85 mmol of methylene blue (MB) per gram of Mg–Al LDH and modified Mg–Al LDH with GO, respectively. The reaction kinetics of MB with both adsorbents is determined to be the pseudo-second-order. To get more insights of the mechanism, molecular dynamics (MD) simulation…

Halogen bonding has received intensive attention recently for its applications in the construction of supramolecular assemblies and crystal engineering and its implications and potentials in chemical and biological processes and rational drug design. Peculiarly, in intermolecular interactions, halogen atoms are known as electron-donating groups carrying partial negative charges in molecules due to its high electronegativity, but they can counterintuitively act as Lewis acids and bind with Lewis bases in the form of a halogen bond. The unsettling issue regarding the nature of the halogen bonding is whether the electrostatics or charge transfer interaction dominates. The recently proposed σ-hole concept nicely reinforces the role of electrostatic attraction. Also, good correlations between the halogen bonding strength and the interaction energy from the simple point-charge model have been found. This leads to the claim that there is no need to invoke the charge transfer concept in the halogen bond. But there is alternative evidence supporting the importance of charge transfer…

Abstract Interfacial regions are unique chemical reaction environments that can promote chemistry not found elsewhere. The air–water interface is ubiquitous in the natural environment in the form of ocean surfaces and aqueous atmospheric aerosols. Here we investigate the chemistry and photochemistry of pyruvic acid (PA), a common environmental species, at the air–water interface and compare it to its aqueous bulk chemistry using two different experimental setups: (1) a Langmuir–Blodgett trough, which models natural water surfaces and provides a direct comparison between the two reaction environments, and (2) an atmospheric simulation chamber (CESAM) to monitor the chemical processing of nebulized aqueous PA droplets. The results show that surface chemistry leads to substantial oligomer formation. The sequence begins with the condensation of lactic acid (LA), formed at the surface, with itself and with pyruvic acid, and LA + LA – H2O and LA + PA – H2O are prominent among the products in addition to a series of higher-molecular-weight oligomers of mixed units of PA and LA. In…

The viomycin biosynthesis enzyme VioC is a nonheme iron and α-ketoglutarate-dependent dioxygenase involved in the selective hydroxylation of l -arginine at the C 3 -position for antibiotics biosynthesis. Interestingly, experimental studies showed that using the substrate analogue, namely, l -homo-arginine, a mixture of products was obtained originating from C 3 -hydroxylation, C 4 -hydroxylation, and C 3 –C 4 -desaturation. To understand how the addition of one CH 2 group to a substrate can lead to such a dramatic change in selectivity and activity, we decided to perform a computational study using quantum mechanical (QM) cluster models. We set up a large active-site cluster model of 245 atoms that includes the oxidant with its first- and second-coordination sphere influences as well as the substrate binding pocket. The model was validated against experimental work from the literature on related enzymes and previous computational studies. Thereafter, possible pathways leading to products and byproducts were investigated for a model containing l -Arg and one for l -homo-Arg as…

and require different mechanistic steps for initiating and propagating the autoxidation sequence. This Perspective reflects on these recent findings in the context of the direct aerosol precursor formation in urban atmospheres.

Secondary organic aerosol formation in the atmospheric aqueous/particulate phase by photosensitized reactions is currently subject to uncertainties. To understand the impact of photosensitized reactions, photophysical and -chemical properties of photosensitizers, kinetic data, and reaction mechanisms of these processes are required. The photophysical properties of acetophenones, benzaldehydes, benzophenones, and naphthalenes were investigated in aqueous solution using laser flash excitation. Quantum yields of excited photosensitizers were determined giving values between 0.06–0.80 at 298 K and pH = 5. Molar absorption coefficients (ε max ( 3 PS*) = (0.8–13) × 10 4 L mol –1 cm –1 ), decay rate constants in water ( k 1st = (9.4 ± 0.5) × 10 2 to (2.2 ± 0.1) × 10 5 s –1 ), and quenching rate constants with oxygen ( k q (O 2 ) = (1.7 ± 0.1–4.4 ± 0.4) × 10 9 L mol –1 s –1 ) of the excited triplet states were determined at 298 K and pH = 5. Photosensitized reactions of carboxylic acids and alkenes show second-order rate constants in the range of (37 ± 7.0–0.55 ± 0.1) × 10 4 and (27 ±…

Photophysical properties of europium (Eu(III)) complexes are affected by ligand-to-metal charge transfer (LMCT) states. Two luminescent Eu(III) complexes with three tetramethylheptadionates (tmh) and pyridine (py), [Eu(tmh) 3 (py) 1 ] (seven-coordinated monocapped-octahedral structure) and [Eu(tmh) 3 (py) 2 ] (eight-coordinated square antiprismatic structure), were synthesized for geometrical-induced LMCT level control. Distances between Eu(III) and oxygen atoms of tmh ligands were estimated using single-crystal X-ray analyses. The contribution percentages of π–4 f mixing in HOMO and LUMO at the optimized structure in the ground state were calculated using DFT (LC-BLYP). The Eu–O distances and their π–4 f mixed orbitals affect the energy level of LMCT states in Eu(III) complexes. The LMCT energy level of an eight-coordinated Eu(III) complex was higher than that of a seven-coordinated Eu(III) complex. The energy transfer processes between LMCT and Eu(III) ion were investigated using temperature-dependent and time-resolved emission lifetime measurements of 5 D 0 → 7 F J transitions of…

Heptazine derivatives are promising dopants for electroluminescent devices. Recent studies raised the question whether heptazines exhibit a small regular or an inverted singlet–triplet (IST) gap. It was argued that the S 1 ← T 1 reverse intersystem crossing (RISC) is a downhill process in IST emitters and therefore does not require thermal activation, thus enabling efficient harvesting of triplet excitons. Rate constants were not determined in these studies. Modeling the excited-state properties of heptazine proves challenging because fluorescence and intersystem crossing (ISC) are symmetry-forbidden in first order. In this work, we present a comprehensive theoretical study of the photophysics of heptazine and its derivative HAP-3MF. The calculations of electronic excitation energies and vibronic coupling matrix elements have been conducted at the density functional theory/multireference configuration interaction (DFT/MRCI) level of theory. We have employed a finite difference approach to determine nonadiabatic couplings and derivatives of spin–orbit coupling and electric dipole…

A promising approach for simulating rare events with rigorous kinetics is the weighted ensemble path sampling strategy. One challenge of this strategy is the division of configurational space into bins for sampling. Here we present a minimal adaptive binning (MAB) scheme for the automated, adaptive placement of bins along a progress coordinate within the framework of the weighted ensemble strategy. Results reveal that the MAB binning scheme, despite its simplicity, is more efficient than a manual, fixed binning scheme in generating transitions over large free energy barriers, generating a diversity of pathways, estimating rate constants, and sampling conformations. The scheme is general and extensible to any rare-events sampling strategy that employs progress coordinates.

Spin-Coupled Generalized Valence Bond (SCGVB) theory provides the foundation for a comprehensive theory of the electronic structure of molecules. SCGVB theory offers a compelling orbital description of the electronic structure of molecules as well as an efficient and effective zero-order wave function for calculations striving for quantitative predictions of molecular structures, energetics, and other properties. The orbitals in the SCGVB wave function are usually semilocalized, and for most molecules, they can be interpreted using concepts familiar to all chemists (hybrid orbitals, localized bond pairs, lone pairs, etc.). SCGVB theory also provides new perspectives on the nature of the bonds in molecules such as C 2, Be 2 and SF 4 /SF 6 . SCGVB theory contributes unparalleled insights into the underlying cause of the first-row anomaly in inorganic chemistry as well as the electronic structure of organic molecules and the electronic mechanisms of organic reactions. The SCGVB wave function accounts for nondynamical correlation effects and, thus, corrects the most serious deficiency…

Polynuclear transition-metal (PNTM) clusters, ubiquitous in biological systems, owe their catalytic activity to the presence of a large manifold of low-lying spin states, and a number of stable oxidation states. The ab initio description of such systems - starting from the electronic Schrodinger equation - represents one of the greatest challenges of modern quantum chemistry, requiring highly multiconfigurational treatments. We propose a theoretical framework of simple and physically motivated molecular-orbital transformations that enable the resolution and characterization of targeted electronic wave functions with ease. This paradigm allows us to unravel the complicated electronic correlations in PNTM clusters. We apply it to two super-oxidized iron-sulfur cubane [Fe4S4] structures, and accurately characterize their singlet ground and low-lying excited states. Through direct access to their wave functions, we identify the important correlation mechanisms and their interplay with the geometrical distortions observed in these clusters. Our results unambiguously reveal a hidden…

α-Pinene, C 10 H 16, represents one of the most important biogenic emissions into the atmosphere. The formation of RO 2 radicals HO–C 10 H 16 O x, x = 2–6, and their closed-shell products from the OH + α-pinene reaction has been measured for close to atmospheric reaction conditions in the presence of NO with concentrations of (1.7–490) × 10 9 molecules cm –3 . Main closed-shell products are substances with the composition C 10 H 16 O 2 and C 10 H 16 O 4, most likely carbonyls, obtained with molar yields in the range 0.42–0.45 and 0.17–0.19, respectively, for NO concentrations >5 × 10 10 molecules cm –3 . The corresponding total product yields amount to 0.75–0.81, indicating efficient product detection by the mass spectrometric method applied. All stated molar yields represent lower limit values affected with an uncertainty of . Kinetic and product analysis consistently revealed the suppression of the formation of highly oxygenated organic molecules (HOMs) by a factor of 2–2.2 for the highest NO concentration used. The findings of this study provide insights into the RO 2 radical…

Perylenediimides (PDIs) are important molecular building blocks that are being investigated for their applicability in optoelectronic technologies. Covalently linking multiple PDI acceptors at the 2,5,8,11 (headland) positions adjacent to the PDI carbonyl groups is reported to yield higher power conversion efficiencies in photovoltaic cells relative to PDI acceptors linked at the 1,6,7,12 (bay) positions. While the photophysical properties of PDIs linked via the bay positions have been investigated extensively, those linked at the headland positions have received far less attention. We showed previously that symmetry-breaking charge separation (SB-CS) in PDIs hold promise as a strategy for increasing photovoltaic efficiency. Here we use transient absorption and emission spectroscopies to investigate the competition between SB-CS, fluorescence, and internal conversion in three related PDI dimers linked at the headland positions with o-, m-, and p -phenylene moieties: o - PDI 2, m - PDI 2, and p - PDI 2, respectively. It is found that o - PDI 2 supports SB-CS yielding PDI •+ –PDI •–,…

We investigate the effects of range separation of the exchange energy on electronic ground-state properties for recently published double-hybrid density functionals (DHDFs) with the extensive GMTKN55 database for general main-group thermochemistry, kinetics, and noncovalent interactions. We include the semiempirical range-separated DHDFs ωB2PLYP and ωB2GP-PLYP developed by our group for excitation energies, together with their ground-state-parametrized variants, which we denote herein as ωB2PLYP18 and ωB2GP-PLYP18. We also include the nonempirical range-separated DHDFs RSX-0DH and RSX-QIDH. For all six DHDFs, damping parameters for the DFT-D3 dispersion correction (and for its DFT-D4 variant) are presented. We comment on when the range-separated functionals can be more beneficial than their global counterparts and conclude that range separation alone is no guarantee for overall improved results. We observe that the BLYP-based functionals generally outperform the PBE-based functionals. We finally note that the best-performing DHDFs for GMTKN55 are still the semiempirical…

A cost-effective method of theoretically predicting electronic transition rate constants from the excited-states of molecules is reported. This method is based on density functional theory calculations of electronic states and quantitative rate constant determination with the Fermi golden rule.

The kinetics of a dynamical system comprising two metastable states is formulated in terms of a finite-time propagator in phase space (position and velocity) adapted to the underdamped Langevin equation. Dimensionality reduction to a subspace of collective variables yields familiar expressions for the propagator, committor, and steady-state flux. A quadratic expression for the steady-state flux between the two metastable states can serve as a robust variational principle to determine an optimal approximate committor expressed in terms of a set of collective variables. The theoretical formulation is exploited to clarify the foundation of the string method with swarms-of-trajectories, which relies on the mean drift of short trajectories to determine the optimal transition pathway. It is argued that the conditions for Markovity within a subspace of collective variables may not be satisfied with an arbitrary short time-step and that proper kinetic behaviors appear only when considering the effective propagator for longer lag times. The effective propagator with finite lag time is…

The chemical reactivity of a molecule as a whole or of an atom in a molecule varies during a chemical reaction. A variation of global and local reactivity descriptors in the course of a physicochemical process was studied within a quantum fluid density functional theory framework. Effects of a physical confinement and the electronic excitation therein were studied. In this Perspective, we also highlight the direction of a spontaneous chemical reaction in the light of the dynamical variants of the conceptual density functional theory-based electronic structure principles. An exhaustive state-of-the-art dynamical study is warranted in order to understand a chemical reaction from a reactivity perspective augmenting the associated molecular reaction dynamics analysis.

Scanning tunneling spectroscopy (STS), a technique that records the change in the tunneling current as a function of the bias (d I /d V ) across the gap between a tip and the sample, is a powerful tool to characterize the electronic structure of single molecules and nanomaterials. While performing STS, the structure and condition of the scanning probe microscopy (SPM) tips are critical for reliably obtaining high quality point spectra. Here, we present an automated program based on machine learning models that can identify the Au(111) Shockley surface state in d I /d V point spectra and perform tip conditioning on clean or sparsely covered gold surfaces with minimal user intervention. We employed a straightforward height-based segmentation algorithm to analyze STM topographic images to identify tip conditioning positions and used 1789 archived d I /d V spectra to train machine learning models that can ascertain the condition of the tip by evaluating the quality of the spectroscopic data. Decision tree based ensemble and boosting models and deep neural networks (DNNs) have been shown…

High Resolution Image Download MS PowerPoint Slide The accurate determination of equilibrium structures for isolated molecules plays a central role in the evaluation and interpretation of stereoelectronic, thermodynamic, and spectroscopic properties. For small semi-rigid systems, state-of-the-art quantum-chemical computations can rival the most sophisticated experimental results. For larger molecules, cheaper yet accurate approaches need to be defined. The double-hybrid rev-DSD-PBEP86 functional already delivers remarkable results that can be further improved by means of a “Lego brick” model. This is based on the idea that a molecular system can be seen as formed by different fragments (the “Lego bricks”), whose accurate semi-experimental (SE) equilibrium geometries are available. The template molecule (TM) approach can be used to account for the modifications occurring when going from the isolated fragment to the molecular system under investigation, with the linear regression (LR) model employed to correct the linkage between the different fragments. The resulting TM-SE_LR…

Multipole moments such as charge, dipole, and quadrupole are often invoked to rationalize intermolecular phenomena, but a low-order multipole expansion is rarely a valid description of electrostatics at the length scales that characterize nonbonded interactions. This is illustrated by examining several common misunderstandings rooted in erroneous electrostatic arguments. First, the notion that steric repulsion originates in Coulomb interactions is easily disproved by dissecting the interaction potential for Ar 2 . Second, the Hunter-Sanders model of π–π interactions, which is based on quadrupolar electrostatics, is shown to have no basis in accurate calculations. Third, curved “buckybowls” exhibit unusually large dipole moments, but these are ancillary to the forces that control their intermolecular interactions, as illustrated by two examples involving corannulene. Finally, the assumption that interactions between water and small anions are dictated by the dipole moment of H 2 O is shown to be false in the case of binary halide–water complexes. These examples present a compelling…

The structural properties and nonbonding interactions of a menthol-based deep eutectic solvent (DES) were investigated in detail employing experimental and computational methods. A mass spectrometry analysis confirmed the formation of 1:1 l-menthol/acetic acid. A molecular dynamics simulation was used to figure out energetically most favorable cluster conformers of the 1:1 l-menthol/acetic acid system. Density functional theory at the ωB97XD/6-311G (d,p) level of theory was employed to optimize the isolated structures and to calculate their thermochemical properties. Both experimental and computed IR spectra were analyzed for the samples. Additionally, vibrational circular dichroism (VCD) spectra of the samples were measured to prove the chirality transfer. Principal component analysis (PCA) was used to make the data interpretation more vivid. All the spectral data analyses and nanostructure elucidation proved the spontaneous formation of the DES through the formation of strong hydrogen bonding. Experimental solvatochromism and computed highest occupied molecular orbital-lowest…

Adsorption and activation of CO 2 is a key step in any chemical reaction, which aims to convert it to other useful chemicals. Therefore, it is important to understand the factors that drive the activation process and also search for materials that promote the process. We employ the density functional theory to explore the possibility of using small-sized bimetallic Cu–Zr clusters, Cu 4– n Zr n, with n = 1–3 for the above-mentioned key step. Our results suggest that after adsorption, a CO 2 molecule preferably resides on Zr atoms or at the bridge and triangular faces formed by Zr atoms in bimetallic Cu–Zr clusters accompanied with its high degree of activation. Importantly, maximum activation occurs when CO 2 is adsorbed on the CuZr 3 cluster. Interestingly, we find that the adsorption energy of CO 2 can be tuned by varying the extent of the Zr atom in Cu–Zr clusters. We rationalize the high adsorption of CO 2 with the increase in the number of Zr atoms using the d-band center model and the concept of chemical hardness. The strong chemisorption and high activation of CO 2 are…

Limonene is one of the monoterpenes with the largest biogenic emissions and is also widely used as an additive in cleaning products, leading to significant indoor emissions. Studies have found that the formation of secondary organic aerosols (SOAs) from limonene oxidation has important implications for indoor air quality. Although ozonolysis is considered the major limonene oxidation pathway under most indoor conditions, little is known about the mechanisms for SOA formation from limonene ozonolysis. Here, we calculate the rate coefficients of the possible unimolecular reactions of the first-generation peroxy radicals formed by limonene ozonolysis using a high-level multiconformer transition state theory approach. We find that all of the peroxy radicals formed initially in the ozonolysis of limonene react unimolecularly with rates that are competitive both indoors and outdoors, except under highly polluted conditions. Differences in reactivity between the peroxy radicals from ozonolysis and those formed by OH, NO 3, and Cl oxidation are discussed. Finally, we sketch possible…

Computational quantum chemistry provides fundamental chemical and physical insights into solvated reaction mechanisms across many areas of chemistry, especially in homogeneous and heterogeneous renewable energy catalysis. Such reactions may depend on explicit interactions with ions and solvent molecules that are nontrivial to characterize. Rigorously modeling explicit solvent effects with molecular dynamics usually brings steep computational costs while the performance of continuum solvent models such as polarizable continuum model (PCM), charge-asymmetric nonlocally determined local-electric (CANDLE), conductor-like screening model for real solvents (COSMO-RS), and effective screening medium method with the reference interaction site model (ESM-RISM) are less well understood for reaction mechanisms. Here, we revisit a fundamental aqueous hydride transfer reaction—carbon dioxide (CO 2 ) reduction by sodium borohydride (NaBH 4 )—as a test case to evaluate how different solvent models perform in aqueous phase charge migrations that would be relevant to renewable energy catalysis…