The 50 most-cited articles in The Journal of Physical Chemistry A, 2018

For the investigation of chemical reaction networks, the identification of all relevant intermediates and elementary reactions is mandatory. Many algorithmic approaches exist that perform explorations efficiently and in an automated fashion. These approaches differ in their application range, the level of completeness of the exploration, and the amount of heuristics and human intervention required. Here, we describe and compare the different approaches based on these criteria. Future directions leveraging the strengths of chemical heuristics, human interaction, and physical rigor are discussed.

High degrees of delithiation of layered transition metal oxide cathode active materials (NCMs and HE-NCM) for lithium-ion batteries (LIBs) was shown to lead to the release of singlet oxygen, which is accompanied by enhanced electrolyte decomposition. Here, we study the reactivity of chemically produced singlet oxygen with the commonly used cyclic and linear carbonate solvents for LIB electrolytes. On-line gassing analysis of the decomposition of ethylene carbonate (EC) and dimethyl carbonate (DMC) reveals different stability toward the chemical attack of singlet oxygen, which is produced in situ by photoexcitation of the Rose Bengal dye. Ab initio calculations and on-the-fly simulations reveal a possible reaction mechanism, confirming the experimental findings. In the case of EC, hydrogen peroxide and vinylene carbonate (VC) are found to be the products of the first reaction step of EC with singlet oxygen in the reaction cascade of the EC chemical decomposition. In contrast to EC, simulations suggested DMC to be stable in the presence of singlet oxygen, which was also confirmed…

As the most important component of deep red pigments, alkannin is investigated theoretically in detail based on time-dependent density functional theory (TDDFT) method. Exploring the dual intramolecular hydrogen bonds (O1–H2···O3 and O4–H5···O6) of alkannin, we confirm the O1–H2···O3 may play a more important role in the first excited state than the O4–H5···O6 one. Infrared (IR) vibrational analyses and subsequent charge redistribution also support this viewpoint. Via constructing the S 1 -state potential energy surface (PES) and searching transition state (TS) structures, we illuminate the excited state double proton transfer (ESDPT) mechanism of alkannin is the stepwise process that can be first launched by the O1–H2···O3 hydrogen bond wire in gas state, acetonitrile (CH 3 CN) and cyclohexane (CYH) solvents. We present a novel mechanism that polar aprotic solvents can contribute to the first-step proton transfer (PT) process in the S 1 state, and nonpolar solvents play important roles in lowering the potential energy barrier of the second-step PT reaction.

Various methods have been developed to perform atomistic-scale simulations for the cross-linking of polymers. Most of these methods involve connecting the reactive sites of the monomers, but these typically do not capture the entire reaction process from the reactants to final products through transition states. Experimental time scales for cross-linking reactions in polymers range from minutes to hours, which are time scales that are inaccessible to atomistic-scale simulations. Because simulating reactions on realistic time scales is computationally expensive, in this investigation, an accelerated simulation method was developed within the ReaxFF reactive force field framework. In this method, the reactants are tracked until they reach a nonreactive configuration that provides a good starting point for a reactive event. Subsequently, the reactants are provided with a sufficient amount of energy-equivalent or slightly larger than their lowest-energy reaction barrier-to overcome the barrier for the cross-linking process and form desired products. This allows simulation of…

Hexanitrohexaazaisowurtzitane (CL-20) has a high detonation velocity and pressure, but its sensitivity is also high, which somewhat limits its applications. Therefore, it is important to understand the mechanism and characteristics of thermal decomposition of CL-20. In this study, a ε-CL-20 supercell was constructed and ReaxFF-lg reactive molecular dynamics simulations were performed to investigate thermal decomposition of ε-CL-20 at various temperatures (2000, 2500, 2750, 3000, 3250, and 3500 K). The mechanism of thermal decomposition of CL-20 was analyzed from the aspects of potential energy evolution, the primary reactions, and the intermediate and final product species. The effect of temperature on thermal decomposition of CL-20 is also discussed. The initial reaction path of thermal decomposition of CL-20 is N–NO 2 cleavage to form NO 2, followed by C–N cleavage, leading to the destruction of the cage structure. A small number of clusters appear in the early reactions and disappear at the end of the reactions. The initial reaction path of CL-20 decomposition is the same at…

The result of the application of different approaches based on the ideal gas/rigid rotor/harmonic oscillator (IGRRHO) model, commonly used in popular software packages, for the calculation of free energies in solution is compared with that of ab initio molecular dynamics for a process involving ligand exchange in palladium complexes. The IGRRHO-based approaches considered differ in most cases in the extent to which the rotational and translational contributions are included in the correction. Our study supports the use the free energy values directly obtained from dispersion-corrected DFT functionals without any correction or with minor corrections at most.

pH is one of the most basic chemical properties of aqueous solution, but its measurement in nanoscale aerosol particles presents many challenges. The pH of aerosol particles is of growing interest in the atmospheric chemistry community because of its demonstrated effects on heterogeneous chemistry and human health, as well as potential effects on climate. The authors have shown that phase transitions of aerosol particles are sensitive to pH, focusing on systems that undergo liquid-liquid phase separation. Currently, aerosol pH is calculated indirectly from knowledge of species present in the gas and aerosol phases through the use of thermodynamic models. From these models, ambient aerosol is expected to be highly acidic (pH ∼ 0-3). Direct measurements have focused on model systems due to the difficulty of this measurement. This area is one in which physical chemists should be encouraged to contribute because of the potential consequences for aerosol processes in the environment.

In light of the intense recent interest in the methylammonium lead halides, CH 3 NH 3 PbX 3 (X = Cl, Br, and I) as sensitizers for photovoltaic cells, the dynamics of the methylammonium (MA) cation in these perovskite salts has been reinvestigated as a function of temperature via 2 H, 14 N, and 207 Pb NMR spectroscopy. In the cubic phase of all three salts, the MA cation undergoes pseudoisotropic tumbling (picosecond time scale). For example, the correlation time, τ 2, for the C–N axis of the iodide salt is 0.85 ± 0.30 ps at 330 K. The dynamics of the MA cation are essentially continuous across the cubic ↔ tetragonal phase transition; however, 2 H and 14 N NMR line shapes indicate that subtle ordering of the MA cation occurs in the tetragonal phase. The temperature dependence of the cation ordering is rationalized using a six-site model, with two equivalent sites along the c -axis and four equivalent sites either perpendicular or approximately perpendicular to this axis. As the cubic ↔ tetragonal phase transition temperature is approached, the six sites are nearly equally populated.…

The electronically excited states of methylene (CH 2 ), ethylene (C 2 H 4 ), butadiene (C 4 H 6 ), hexatriene (C 6 H 8 ), and ozone (O 3 ) have long proven challenging due to their complex mixtures of static and dynamic correlations. The semistochastic heat-bath configuration interaction (SHCI) algorithm, which efficiently and systematically approaches the full configuration interaction (FCI) limit, is used to provide close approximations to the FCI energies in these systems. This article presents the largest FCI-level calculation to date on hexatriene, using a polarized double-ζ basis (ANO-L-pVDZ), which gives rise to a Hilbert space containing more than 10 38 determinants. These calculations give vertical excitation energies of 5.58 and 5.59 eV, respectively, for the 2 1 A g and 1 1 B u states, showing that they are nearly degenerate. The same excitation energies in butadiene/ANO-L-pVDZ were found to be 6.58 and 6.45 eV. In addition to these benchmarks, our calculations strongly support the presence of a previously hypothesized ring-minimum species of ozone that lies 1.3 eV higher…

Spin fluctuations in Fe(II)-porphyrins are at the heart of heme-proteins functionality. Despite significant progress in porphyrin chemistry, the mechanisms that rule spin state stabilization remain elusive. Here, it is demonstrated by using multiconfigurational quantum chemical approaches, including the novel Stochastic-CASSCF method, that electron delocalization between the metal center and the π system of the macrocycle differentially stabilizes the triplet spin states over the quintet. This delocalization takes place via charge-transfer excitations, involving the π system of the macrocycle and the out-of-plane iron d orbitals, key linking orbitals between metal and macrocycle. Through a correlated breathing mechanism the 3d electrons can make transitions toward the π orbitals of the macrocycle. This guarantees a strong coupling between the on-site radial correlation on the metal and electron delocalization. Opposite-spin 3d electrons of the triplet can effectively reduce electron repulsion in this manner. Constraining the out-of-plane orbitals from breathing hinders…

Peroxy radical hydrogen shift (H-shift) reactions are key to the formation of highly oxidized organic molecules and particle growth in the atmosphere. In an H-shift reaction, a hydrogen atom is transferred to the peroxy radical from within the same molecule to form a hydroperoxy alkyl radical, which can undergo O 2 uptake and further H-shift reactions. Here we use an experimentally verified theoretical approach based on multi-conformer transition state theory to calculate rate constants for a systematic set of H-shifts. Our results show that substitution at the carbon, from which the hydrogen is abstracted, with OH, OOH, and OCH 3 substituents lead to increases in the rate constant by factors of 50 or more. Reactions with C═O and C═C substituents lead to resonance stabilized carbon radicals and have rate constants that increase by more than a factor of 400. In addition, our results show that reactions leading to secondary carbon radicals (alkyl substituent) are 100 times faster than those leading to primary carbon radicals, and those leading to tertiary carbon radicals a factor of…

Polypyrrole nanotubes rank among the most conducting forms of organic semiconductors. They are prepared by the oxidation of pyrrole in the presence of methyl orange. Other organic dyes, viz. ethyl orange, Acid Blue 25, and Acid Blue 129, have been used in the present study to prepare globules or nanofibers. The resulting polypyrroles were studied in detail by Raman spectroscopy. The apparent paradox when a dye contribution to spectra is absent with 785 nm excitation line and present with shorter wavelengths is explained by the resonance character of the Raman scattering, which allows the separation of the contributions from the polypyrrole surface and from the bulk. These differ depending on the laser excitation wavelength and the position of absorption maximum of the individual dyes in ultraviolet-visible spectra and affect both the laser-penetration depth and observation of the resonance effect. The spectra are discussed in terms of different ordering of polymer chains in individual morphologies. The correlation between conductivity, surface areas, and the proportions of ordered…

Five napthyridine-based fluorine–boron (BF 2 –napthyridine) conjugated compounds have been theoretically designed, and subsequently, their photophysical properties are investigated. The influence of electron-donating and electron-withdrawing groups attached with the N ∧ C ∧ O moiety of BF 2 –napthyridine molecule has been interpreted. The optoelectronic properties, including absorption spectra and emission spectra of the BF 2 –napthyridine derivatives are studied using density functional theory (DFT) and time-dependent density functional theory (TD-DFT) based methods. Different characteristics, such as HOMO–LUMO gap, molecular orbital density, ionization potential, electron affinity, and reorganization energy for hole and electron, are calculated. All these molecules show excellent π-electron delocalization. TD-DFT results illustrate that the amine-substituted BF 2 –napthyridine derivative has the highest absorption and emission maxima; it also shows a maximum Stoke shift. These results are well-correlated with the structural parameters and calculated HOMO–LUMO gap. Moreover, it is…

Spin crossover (SCO) plays a major role in biochemistry, catalysis, materials, and emerging technologies such as molecular electronics and sensors, and thus accurate prediction and design of SCO systems is of high priority. However, the main tool for this purpose, density functional theory (DFT), is very sensitive to applied methodology. The most abundant SCO systems are Fe(II) and Fe(III) systems. Even with average good agreement, a functional may be significantly more accurate for Fe(II) or Fe(III) systems, preventing balanced study of SCO candidates of both types. The present work investigates DFT's performance for well-known Fe(II) and Fe(III) SCO complexes, using various design types and customized versions of GGA, hybrid, meta-GGA, meta-hybrid, double-hybrid, and long-range-corrected hybrid functionals. We explore the limits of DFT performance and identify proficient Fe(II)-Fe(III)-balanced functionals. We identify and quantify remarkable differences in the DFT description of Fe(II) and Fe(III) systems. Most functionals become more accurate once Hartree-Fock exchange is…

Substantial amounts of gas- and particle-phase organic nitrates have been reported in field studies of atmospheric chemistry conducted around the world, and it has been proposed that a significant fraction of these may be formed from the nighttime reaction of monoterpenes with NO 3 radicals. In the study presented here, β-pinene (a major global monoterpene emission) was reacted with NO 3 radicals in an environmental chamber and the molecular and functional group composition of the resulting secondary organic aerosol (SOA) was determined using a variety of methods. Eight products, which comprised ∼95% of the SOA mass, were identified and quantified. More than 90% (by mass) of these consisted of acetal heterodimers and heterotrimers that were apparently formed through acid-catalyzed reactions in phase-separated particles. The molar yield of the major oligomer was 16.7%, and the yields of the other six and the single monomer ranged from 1.1% to 2.9%, for a total yield of 30.7%. From these analyses it was determined that the yields of the two major monomer building blocks were 25.9% and…

We explore by means of modeling how absorptive–dispersive mixing between the second- and third-order terms modifies the imaginary χ total (2) responses from air/water interfaces under conditions of varying charge densities and ionic strength. To do so, we use published Im(χ (2) ) and χ (3) spectra of the neat air/water interface that were obtained either from computations or experiments. We find that the χ total (2) spectral lineshapes corresponding to experimentally measured spectra contain significant contributions from both interfacial χ (2) and bulk χ (3) terms at interfacial charge densities equivalent to less than 0.005% of a monolayer of water molecules, especially in the 3100 to 3300 cm –1 frequency region. Additionally, the role of short-range static dipole potentials is examined under conditions mimicking brine. Our results indicate that surface potentials, if indeed present at the air/water interface, manifest themselves spectroscopically in the tightly bonded H-bond network observable in the 3200 cm –1 frequency range.

Stabilized Criegee intermediates react with organic acids in the gas phase and at the air–water interface to form a class of ester hydroperoxides, α-acyloxyalkyl hydroperoxides (αAAHPs). A number of recent studies have proposed the importance of αAAHPs to the formation and growth of secondary organic aerosol (SOA). The chemistry of αAAHPs has not been investigated due to a lack of commercially available chemical standards. In this work, the behavior of αAAHPs in condensed phases is investigated for the first time. Experiments were performed with two synthesized αAAHP species. αAAHPs decomposed rapidly in the aqueous phase, with the rate highly dependent on the solvent, temperature, solution pH, and other compounds present in the solution. The measured 1 st -order decomposition rate coefficient varied between 10 –3 and 10 –5 s –1 under the conditions examined in this work. Elucidation of the reaction mechanism is complicated by byproducts arising from the synthetic procedure, but observations are consistent with a base-catalyzed hydrolysis of αAAHPs. The rapid hydrolysis of αAAHPs…

Exciton delocalization in dye aggregate systems is a phenomenon that is revealed by spectral features, such as Davydov splitting, J- and H-aggregate behavior, and fluorescence suppression. Using DNA as an architectural template to assemble dye aggregates enables specific control of the aggregate size and dye type, proximal and precise positioning of the dyes within the aggregates, and a method for constructing large, modular two- and three-dimensional arrays. Here, we report on dye aggregates, organized via an immobile Holliday junction DNA template, that exhibit large Davydov splitting of the absorbance spectrum (125 nm, 397.5 meV), J- and H-aggregate behavior, and near-complete suppression of the fluorescence emission (∼97.6% suppression). Because of the unique optical properties of the aggregates, we have demonstrated that our dye aggregate system is a viable candidate as a sensitive absorbance and fluorescence optical reporter. DNA-templated aggregates exhibiting exciton delocalization may find application in optical detection and imaging, light-harvesting, photovoltaics,…

We present an interacting quantum atoms (IQA) study of the gauche effect by comparing 1,2-difluoroethane, 1,2-dichloroethane, and three conformers of 1,2,3,4,5,6-hexafluorocyclohexane. In the 1,2-difluoroethane, the gauche effect is observed in that the gauche conformation is more stable than the anti, whereas in 1,2-dichloroethane the opposite is true. The analysis performed here is exhaustive and unbiased thanks to using the recently introduced relative energy gradient (REG) method [ Thacker , J. C. R. ; Popelier , P. L. A. Theor. Chem. Acc . 2017 , 136 , 86 ], as implemented in the in-house program ANANKE. We challenge the common explanation that hyperconjugation is responsible for the gauche stability in 1,2-difluoroethane and instead present electrostatics as the cause of gauche stability. Our explanation of the gauche effect is also is seen in other molecules displaying local gauche conformations, such as the recently synthesized "all-cis" hexafluorocyclohexane and its conformers where all the fluorine atoms are in the equatorial positions. Using our extension of the…

Ethylene oxidation initiated by ozone addition (ozonolysis) is carried out in a jet-stirred reactor from 300 to 1000 K to explore the kinetic pathways relevant to low-temperature oxidation. The temperature dependencies of species’ mole fractions are quantified using molecular-beam mass spectrometry with electron ionization and single-photon ionization employing tunable synchrotron-generated vacuum-ultraviolet radiation. Upon ozone addition, significant ethylene oxidation is found in the low-temperature regime from 300 to 600 K. Here, we provide new insights into the ethylene ozonolysis reaction network via identification and quantification of previously elusive intermediates by combining experimental photoionization energy scans and ab initio threshold energy calculations for isomer identification. Specifically, the C 2 H 4 + O 3 adduct C 2 H 4 O 3 is identified as a keto-hydroperoxide (hydroperoxy-acetaldehyde, HOOCH 2 CHO) based on the calculated and experimentally observed ionization energy of 9.80 (±0.05) eV. Quantification using a photoionization cross-section of 5 Mb at 10.5…

Electrides are ionic substances in which the anionic species is stoichiometrically replaced with localized electrons that reside within crystal voids. Originally discovered in 1983, the past decade has seen a sharp rise in the number of known electride materials, most notably the isolation of the first air- and water-stable electride. As the presence of localized interstitial electrons cannot be directly detected experimentally, researchers have turned to density-functional theory (DFT) to discover new electrides. In this work, we survey eight common theoretical descriptors of electrides for their efficacy in identifying these materials. Illustrative examples are presented for all classes of electrides: organic, inorganic, 2D, elemental, and molecular electrides. In general, density-based descriptors such as the electron localization function (ELF) and localized-orbital locator (LOL) are shown to be the most consistently reliable. Limitations of DFT treatments of electrides are also discussed.

OH, o-hydroxybenzaldehyde, methylcatechols, and light products, such as methane, carbon monoxide, ethylene, and hydrogen. A detailed kinetic model based on a combustion model for light aromatics and anisole has been extended to guaiacol. Thermochemical data of guaiacol and main products were calculated theoretically at the CBS-QB3 level of theory. The model predicts well the conversion of guaiacol and the formation of the main products. Guaiacol decomposes mainly through a unimolecular O-C bond breaking to hydroxy phenoxy and methyl radicals in both pyrolysis and oxidation, but H atom abstractions are also of importance in the low temperature range of the study. The unimolecular mechanism leads mainly to pyrocatechol and methylcatechols, whereas the chain radical mechanism is responsible for the formation of hydroxybenzaldehyde. As for anisole but in a much lower extent, an early formation of benzene and soot precursors is observed.

Blue-shifting H-bonded (C–D···O) complexes between CDCl 3 and CH 3 HCO, (CH 3 ) 2 CO, and C 2 H 5 (CH 3 )CO, and red-shifting H-bonded (C–D···S) complexes between CDCl 3 with (CH 3 ) 2 S and (C 2 H 5 ) 2 S have been identified by Fourier transform infrared spectroscopy in the gas phase at room temperature. With increasing partial pressure of the components, a new band appears in the C–D stretching region of the vibrational spectra. The intensity of this band decreases with an increase in temperature at constant pressure, which provides the basis for identification of the H-bonded bands in the spectrum. The C–D stretching frequency of CDCl 3 is blue-shifted by +7.1, +4, and +3.2 cm –1 upon complexation with CH 3 HCO, (CH 3 ) 2 CO, and C 2 H 5 (CH 3 )CO, respectively, and red-shifted by −14 and −19.2 cm –1 upon complexation with (CH 3 ) 2 S and (C 2 H 5 ) 2 S, respectively. By using quantum chemical calculations at the MP2/6-311++G** level, we predict the geometry, electronic structural parameters, binding energy, and spectral shift of H-bonded complexes between CDCl 3 and two series…

Developing accurate quantum chemical approaches for calculating p K a s is of broad interest. Useful accuracy can be obtained by using density functional theory (DFT) in combination with a polarizable continuum solvent model. However, some classes of molecules present problems for this approach, yielding errors greater than 5 p K units. Various methods have been developed to improve the accuracy of the combined strategy. These methods perform well but either do not generalize or introduce additional degrees of freedom, increasing the computational cost. The Solvation Model based on Density (SMD) has emerged as one of the most commonly used continuum solvent models. Nevertheless, for some classes of organic compounds, e.g., thiols, the p K a s calculated with the original SMD model show errors of 6–10 p K units, and we traced these errors to inaccuracies in the solvation free energies of the anions. To improve the accuracy of p K a s calculated with DFT and the SMD model, we developed a scaled solvent-accessible surface approach for constructing the solute–solvent boundary. By using…

Sulfate aerosols' cooling effect on the global climate has spurred research to understand their mechanisms of formation. Both theoretical and laboratory studies have shown that the formation of sulfate aerosols is enhanced by the presence of a base like ammonia. Stronger alkylamine bases such as monomethylamine (MMA), dimethylamine (DMA), and trimethylamine (TMA) further increase aerosol formation rates by many orders of magnitude relative to that of ammonia. However, recent lab measurements have found that the presence of ammonia and alkylamines together increases nucleation rates by another 1-2 orders of magnitude relative to the stronger alkylamines alone. This work explores that observation by studying the thermodynamic stability of clusters containing up to two sulfuric acids and two bases of the same or different type. Initial configurational sampling is performed using genetic algorithm (GA) interfaced to semiempirical methods to find a large number of low-energy configurations. These structures are then subject to quantum mechanical calculations using PW91, M06-2X, and…

We present a new systematic configurational sampling algorithm for investigating the potential energy surface of hydrated atmospheric molecular clusters. The algorithm is based on creating a Fibonacci sphere around each atom in the cluster and adding water molecules to each point in nine different orientations. For the sampling of water molecules to existing hydrogen bonds, the cluster is displaced along the hydrogen bond, and a water molecule is placed in between in three different orientations. Generated redundant structures are eliminated based on minimizing the root-mean-square distance of different conformers. Initially, the clusters are sampled using the semiempirical PM6 method and subsequently using density functional theory (M06-2X and ωB97X-D) with the 6-31++G(d,p) basis set. Applying the developed algorithm, we study the hydration of sulfuric acid with up to 15 water molecules. We find that the addition of the first four water molecules "saturate" the sulfuric acid molecule and that they are more thermodynamically favorable than the addition of water molecules 5-15. Using…

This paper provides experimental evidence for the chemical structures of aliphatically substituted and bridged polycyclic aromatic hydrocarbon (PAH) species in gas-physe combustion environments. The identification of these single- and multicore aromatic species, which have been hypothesized to be important in PAH growth and soot nucleation, was made possible through a combination of sampling gaseous constituents from an atmospheric pressure inverse coflow diffusion flame of ethylene and high-resolution tandem mass spectrometry (MS-MS). In these experiments, the flame-sampled components were ionized using a continuous VUV lamp at 10.0 eV and the ions were subsequently fragmented through collisions with Ar atoms in a collision-induced dissociation (CID) process. The resulting fragment ions, which were separated using a reflectron time-of-flight mass spectrometer, were used to extract structural information about the sampled aromatic compounds. The high-resolution mass spectra revealed the presence of alkylated single-core aromatic compounds and the fragment ions that were observed…

The ability to navigate vast energy landscapes of molecules, clusters, and solids is a necessity for discovering novel compounds in computational chemistry and materials science. For high-dimensional systems, it is only computationally feasible to search a small portion of the landscape, and hence, the search strategy is of critical importance. Introducing Bayesian optimization concepts in an evolutionary algorithm framework, we quantify the concepts of exploration and exploitation in global minimum searches. The method allows us to control the balance between probing unknown regions of the landscape (exploration) and investigating further regions of the landscape known to have low-energy structures (exploitation). The search for global minima structures proves significantly faster with the optimal balance for three test systems (molecular compounds) and to a lesser extent also for a crystalline surface reconstruction. In addition, global search behaviors are analyzed to provide reasonable grounds for an optimal balance for different problems.

Pentahelicene ( PH ) exhibits the largest absorption ( g abs ) and luminescence ( g lum ) dissymmetry factors among the helicene family but is configurationally and (photo)chemically labile, encumbering its application to chiroptical materials. To bypass the pitfalls, three PH units are merged in a single molecule to build D 3 -symmetric triple pentahelicene, hexabenzotriphenylene ( HBT ), which attains indeed the configurational and (photo)chemical robustness through equilibrium with a C 2 -symmetric conformer that interrupts the racemization and photocyclization. UV–vis, circular dichroism (CD), and circularly polarized luminescence (CPL) spectral examinations reveal the significantly larger g abs and g lum values for HBT than for any of configurationally robust single [ n ]helicene ( n ≥ 6) and C 2 -symmetric triple pentahelicene, trinaphthotriphenylene ( TNT ). Theoretical calculations precisely reproduce the main features of the experimental CD and CPL spectra of PH, HBT, and TNT, and the relevant electric and magnetic transition moments and their mutual angles well rationalize…

Strong coupling between vibrational modes and cavity optical modes leads to the formation of vibration–cavity polaritons, separated by the vacuum Rabi splitting. The splitting depends on the square root of the concentration of absorbers confined in the cavity, which has important implications on the response of the coupled system after ultrafast infrared excitation. In this work, we report on solutions of W(CO) 6 in hexane with a concentration chosen to access a regime that borders on weak coupling. Under these conditions, large fractions of the W(CO) 6 oscillators can be excited, and the anharmonicity of the molecules leads to a commensurate reduction in the Rabi splitting. We report excitation fractions > 0.4, depending on excitation pulse intensity, and show drastic increases in transmission that can be modulated on the picosecond time scale. In comparison to previous experiments, the transient spectra that we observe are much simpler because excited-state transitions lie outside of the transmission spectrum of the cavity, thereby contributing only weakly to the spectra. We find…

The tetravalent character of tetrel atoms leaves only limited room for an incoming nucleophile to approach and engage in a noncovalent bond with a tetrel atom. Any such approach can only occur at the expense of internal geometric distortions. The balance between attractive forces and repulsive steric crowding was studied for a series of Lewis acids of the type FTR 3 (T = Si, Ge, Sn, Pb) which were allowed to interact with various bases. The strength and other properties of the tetrel bond are examined as the R groups are made progressively larger, varying from H and CH 3 to isopropyl and tert -butyl, which induce steric crowding with the incoming base. The effects of crowding which impede the bond can be offset by enlarging the T atom, by adding electron-withdrawing substituents to the Lewis acid, or by considering stronger bases such as anions. The tetrel bond energies reach up to 10 kcal/mol for a pair of neutral molecules with no electron-withdrawing substituents on the Lewis acid. Adding −CF 3 substituents grows the interaction energy to as high as 35 kcal/mol, and a further…

Pair interaction energy decomposition analysis in the fragment molecular orbital (FMO) method is extended to treat density functional theory (DFT) and density-functional tight-binding (DFTB). Fluctuations of energy contributions are obtained from molecular dynamics simulations. Interactions at the DFT and DFTB levels are compared to the values obtained with Hartree-Fock, second-order Møller-Plesset (MP2), and coupled cluster methods. Hydrogen bonding in water clusters is analyzed. 200 ps NVT molecular dynamics simulations are performed with FMO for two ligands bound to the Trp-cage miniprotein (PDB 1L2Y ); the fluctuations of fragment energies and interactions are analyzed.

The liquid structure of five different amide-based deep eutectic solvents (DESs) as a function of the chemical structure of the hydrogen bond acceptor (HBA) was investigated by linear Fourier transform infrared (FTIR) and two-dimensional infrared (2DIR) spectroscopies. Linear FTIR spectroscopy shows that the amide band of the DESs is not significantly affected by the chemical structure and symmetry of the HBA cation. However, its excitonic nature does not allow us to draw further conclusions. Analysis of the 13 C amide line shapes derived from the 2DIR spectra reveals that the different DESs do not show appreciable differences in the level of disorganization. The vibrational dynamics, derived from the photon echo experiments on the 13 C amide, shows that there is a fast component with a time scale of ∼1 ps irrespective of the HBA. The ultrafast dynamics is assigned to hydrogen bond making and breaking between amides. In addition, a slow dynamical component is observed in the time evolution of the photon echo signal. This contribution appears to be correlated with the asymmetry and…

Ammonia and amines are important common trace atmospheric species that can enhance new particle formation (NPF) in the Earth’s atmosphere. However, the synergistic effect of these two bases involving nucleation is still lacking. We studied the most stable geometric structures and thermodynamics of quaternary (NH 3 )(CH 3 NH 2 )(H 2 SO 4 ) m (H 2 O) n ( m = 1–3, n = 0–4) clusters at the PW91PW91/6-311++G(3df,3pd) level of theory for the first time. We find that the proton transfer from H 2 SO 4 molecule to CH 3 NH 2 molecule is easier than to NH 3 molecule in the free or hydrated H 2 SO 4 -base clusters, and thus leads to the stability. The energetically favorable formation of the (NH 3 )(CH 3 NH 2 )(H 2 SO 4 ) m (H 2 O) n ( n = 0–4) clusters, by hydration or attachment of base or substitution of ammonia by methylamine at 298.15 K, indicate that ammonia and methylamine together could enhance the stabilization of small binary clusters. At low RH and an ambient temperature of 298.15 K, the concentration of total hydrated (NH 3 )(CH 3 NH 2 )(H 2 SO 4 ) 2 clusters could reach that of…

The fast and reliable determination of wave functions and electron densities of macromolecules has been one of the goals of theoretical chemistry for a long time, and in this context, several linear scaling techniques have been successfully devised over the years. Different approaches have been adopted to tackle this problem, and one of them exploits the fact that, according to the traditional chemical perception, molecules can be seen as constituted of recurring units (e.g., functional groups) with well-defined chemical features. This has led to the development of methods in which the global wave functions or electron densities of macromolecules are obtained by simply transferring density matrices or fuzzy electron densities associated with molecular fragments. In this context, we propose an alternative strategy that aims at quickly reconstructing wave functions and electron densities of proteins through the transfer of extremely localized molecular orbitals (ELMOs), which are orbitals strictly localized on small molecular units and, for this reason, easily transferable from…

Abstract High-level ab initio calculations (DF-LCCSD(T)-F12a//B3LYP/aug-cc-pVTZ) are performed on a range of stabilized Criegee intermediate (sCI)–alcohol reactions, computing reaction coordinate energies, leading to the formation of α-alkoxyalkyl hydroperoxides (AAAHs). These potential energy surfaces are used to model bimolecular reaction kinetics over a range of temperatures. The calculations performed in this work reproduce the complicated temperature-dependent reaction rates of CH2OO and (CH3)2COO with methanol, which have previously been experimentally determined. This methodology is then extended to compute reaction rates of 22 different Criegee intermediates with methanol, including several intermediates derived from isoprene ozonolysis. In some cases, sCI–alcohol reaction rates approach those of sCI–(H2O)2. This suggests that in regions with elevated alcohol concentrations, such as urban Brazil, these reactions may generate significant quantities of AAAHs and may begin to compete with sCI reactions with other trace tropospheric pollutants such as SO2. This work also…

The oxidation of biogenically emitted volatile organic compounds (BVOC) plays an important role in the formation of secondary organic aerosols (SOA) in the atmosphere. Peroxy radicals (RO 2 ) are central intermediates in the BVOC oxidation process. Under clean (low-NO x ) conditions, the main bimolecular sink reactions for RO 2 are with the hydroperoxy radical (HO 2 ) and with other RO 2 radicals. Especially for small RO 2, the RO 2 + HO 2 reaction mainly leads to closed-shell hydroperoxide products. However, there exist other known RO 2 + HO 2 and RO 2 + RO 2 reaction channels that can recycle radicals and oxidants in the atmosphere, potentially leading to lower-volatility products and enhancing SOA formation. In this work, we present a thermodynamic overview of two such reactions: (a) RO 2 + HO 2 → RO + OH + O 2 and (b) R′O 2 + RO 2 → R′O + RO + O 2 for selected monoterpene + oxidant derived peroxy radicals. The monoterpenes considered are α-pinene, β-pinene, limonene, trans -β-ocimene, and Δ 3 -carene. The oxidants considered are the hydroxyl radical (OH), the nitrate radical (NO…

Using computational methods, we study the gas phase hydration of three different atmospherically relevant organic acids with up to 10 water molecules. We study a dicarboxylic acid (pinic acid) and a tricarboxylic acid (3-methyl-1,2,3-butanetricarboxylic acid (mbtca)) that are both identified as products from α-pinene oxidation reactions. We also study a 2-oxohexanediperoxy acid (ohdpa) that has been identified as a product from cyclohexene autoxidation. To sample the cluster structures, we employ our recently developed systematic hydrate sampling technique and identify a total of 551 hydrate clusters. The cluster structures and thermochemical parameters (at 298.15 K and 1 atm) are obtained at the ωB97X-D/6-31++G(d,p) level of theory, and the single point energy of the clusters have been refined using a high level DLPNO-CCSD(T)/aug-cc-pVTZ calculation. We find that all three tested organic acids interact significantly more weakly with water compared to the primary nucleation precursor sulfuric acid. Even at 100% relative humidity (298.15 K and 1 atm), we find that ohdpa remains…

Abstract A long-held view of the origin of covalent binding is based on the notion that electrostatic forces determine the stability of a system of charged particles and that, therefore, potential energy changes drive the stabilization of molecules. A key argument advanced for this conjecture is the rigorous validity of the virial theorem. Rigorous in-depth analyses have however shown that the energy lowering of covalent bonding is due to the wave mechanical drive of electrons to lower their kinetic energy through expansion. Since the virial theorem applies only to systems with Coulombic interaction potentials, its relevance as a foundation of the electrostatic view is tested here by calculations on analogues of the molecules H2+ and H2, where all 1/r interaction potentials are replaced by Gaussian-type potentials that yield one-electron “atoms” with realistic stability ranges. The virial theorem does not hold in these systems, but covalent bonds are found to form nonetheless, and the wave mechanical bonding analysis yields analogous results as in the case of the Coulombic…

The research on heteroaromatic azoswitches has been blossoming in recent years due to their astonishingly broad range of properties. Minimal chemical modifications can drastically change the demeanor of these switches, regarding photophysical and (photo)chemical properties, promoting them as ideal scaffolds for a vast variety of applications based on bistable light-addressable systems. However, most of the characteristics exhibited by heteroaryl azoswitches were found empirically, and only a few works focus on their rationalization. Herein we report on a mechanistic study employing phenylazoindoles as a model reference, combining spectroscopic experiments with comprehensive computational analysis. This approach will elucidate the intrinsic correlations between the molecular structure of the switch and its thermal behavior, allowing a more rational design transferable to various heteroaryl azoswitches.

The nature of resonance-assisted hydrogen bonds (RAHB) is still subject of an ongoing debate. We therefore analyzed the σ and π charge redistributions associated with the formation of intramolecular hydrogen bonds in malonaldehyde (MA) and its saturated analogue 3-hydroxypropanal (3-OH) and addressed the question whether there is a resonance assistance phenomenon in the sense of a synergistic interplay between the σ and π electron systems. Our quantum chemical calculations at the BP86/TZ2P level of theory show that the π charge flow is indeed in line with the Lewis structure as proposed by the RAHB model. This typical rearrangement of charge is only present in the unsaturated system, and not in its saturated analogue. Resonance in the π electron system assists the intramolecular hydrogen bond by reducing the hydrogen bond distance, and by providing an additional stabilizing component to the net bonding energy. The σ orbital interaction plays an important role in the enhanced hydrogen bond strength in MA as well. However, there is no resonance assistance in the sense of an interplay…

Fast pyrolysis is a promising technology for the production of renewable fuels and chemicals from lignocellulosic biomass. The product distribution (bio-oil, char) and the composition of bio-oil are significantly influenced by the presence of naturally occurring alkali and alkaline-earth metals (AAEMs). In this paper, we investigate, at the molecular level, the influence of Na(I), K(I), Ca(II), and Mg(II) ions on glycosidic bond breaking reactions using density functional theory. Glycosidic bond breaking reactions are categorized as direct C–O breaking mechanisms, namely, transglycosylation, glycosylation, and ring contraction and the two-step pathways, which include the mannose pathway, dehydration, and ring opening. Our calculations show that in the absence of metal, transglycosylation and dehydration pathways (activation barriers ∼55 kcal.mol –1 ) are kinetically most facile. The linkage type (α- or β-1,4) has an insignificant effect on kinetics of glycosidic bond cleavage. Mg(II) ions have a pronounced effect on lowering the activation barriers of glycosylation, ring…

As one of the most widely used chemical concepts whose origin can be traced back to Lewis theory of bonding a century ago, a covalent bond involves sharing one or more pairs of electrons between atoms. A strong covalent interaction (SCI) is such a covalent bond that two or more electron pairs are shared, yielding a double, triple, quadruple, or even higher bond order. Despite its ubiquity and usefulness, a robust and generally applicable approach to accurately identify strong covalent interactions and determine their bond orders is still lacking. In this work, an SCI index is proposed from density functional theory using the Pauli energy, which is the contribution of the Pauli exclusion principle to the kinetic energy. Illustrative examples from organic, inorganic, and organometallic systems were provided. Its close relationship with the electron localization function (ELF) was elucidated. Both ELF and SCI generate similar results. Two complexes with a quintuple metal-metal bond have been confirmed. A stronger than quintuple bond has been showcased. This work should provide a robust…

A heavy-atom-free triplet sensitizer suitable for triplet-triplet annihilation-based photon upconversion was developed from the thermally activated delayed fluorescence (TADF) molecule 4CzPN by covalently tethering a pyrene derivative (DBP) as a triplet acceptor. The triplet exciton produced by 4CzPN is captured by the intramolecular pyrenyl acceptor and subsequently transferred via intermolecular triplet-triplet energy transfer (TTET) to freely diffusing pyrenyl acceptors in toluene. Transient absorption and time-resolved photoluminescence spectroscopy were employed to examine the dynamics of both the intra- and intermolecular TTET processes, and the results indicate that the intramolecular energy transfer from 4CzPN to DBP is swift, quantitative, and nearly irreversible. The reverse intersystem crossing is suppressed while intersystem crossing remains efficient, achieving high triplet yield and long triplet lifetime simultaneously. The ultralong excited state lifetime characteristic of the DBP triplet was shown to be crucial for enhancing the intermolecular TTET efficiency and the…

Molecular functionalization of porphyrins opens countless new opportunities in tailoring their physicochemical properties for light-harvesting applications. However, the immense materials space spanned by a vast number of substituent ligands and chelating metal ions prohibits high-throughput screening of combinatorial libraries. In this work, machine-learning algorithms equipped with the domain knowledge of chemical graph theory were employed for predicting the energy gaps of >12 000 porphyrins from the Computational Materials Repository. Among a variety of graph-based molecular descriptors, the electrotopological-state index, which encodes electronic and topological structure information, captures the energy gaps of porphyrins with a prediction RMSE < 0.06 eV. Importantly, feature sensitivity analysis suggests that the carbon structural motif in methine bridges connected to the anchor group predominantly influences the energy gaps of porphyrins, consistent with the spatial distribution of their frontier molecular orbitals from quantum-chemical calculations.

The quantum photodynamics of a simple diatomic molecule with a permanent dipole immersed within an optical cavity containing a quantized radiation field is studied in detail. The chosen molecule under study, lithium fluoride (LiF), is characterized by the presence of an avoided crossing between the two lowest 1 Σ potential energy curves (covalent-ionic diabatic crossing). Without field, after prompt excitation from the ground state 1 1 Σ, the excited nuclear wave packet moves back and forth in the upper 2 1 Σ state, but in the proximity of the avoided crossing, the nonadiabatic coupling transfers part of the nuclear wave packet to the lower 1 1 Σ state, which eventually leads to dissociation. The quantized field of a cavity also induces an additional light crossing in the modified dressed potential energy curves with similar transfer properties. To understand the entangled photonic-nuclear dynamics, we solve the time-dependent Schrödinger equation by using the multiconfigurational time-dependent Hartree method (MCTDH). The single mode quantized field of the cavity is represented in…

Gas-phase autoxidation – the sequential regeneration of peroxy radicals (RO 2 ) via intramolecular hydrogen shifts (H-shifts) followed by oxygen addition – leads to the formation of organic hydroperoxides. The atmospheric fate of these peroxides remains unclear, including the potential for further H-shift chemistry. Here, we report H-shift rate coefficients for a system of RO 2 with hydroperoxide functionality produced in the OH-initiated oxidation of 2-hydroperoxy-2-methylpentane. The initial RO 2 formed in this chemistry are unable to undergo α-OOH H-shift (HOOC– H ) reactions. However, these RO 2 rapidly isomerize (>100 s –1 at 296 K) by H-shift of the hydroperoxy hydrogen (ROO– H ) to produce a hydroperoxy-substituted RO 2 with an accessible α-OOH hydrogen. First order rate coefficients for the 1,5 H-shift of the α-OOH hydrogen are measured to be ∼0.04 s –1 (296 K) and ∼0.1 s –1 (318 K), within 50% of the rate coefficients calculated using multiconformer transition state theory. Reaction of the RO 2 with NO produces alkoxy radicals which also undergo rapid isomerization via 1,6…

The new era with prosperous artificial intelligence (AI) and robotics technology is reshaping the materials discovery process in a more radical fashion. Here we present authentic intelligent robotics for chemistry (AIR-Chem), integrated with technological innovations in the AI and robotics fields, functionalized with modules including gradient descent-based optimization frameworks, multiple external field modulations, a real-time computer vision (CV) system, and automated guided vehicle (AGV) parts. AIR-Chem is portable and remotely controllable by cloud computing. AIR-Chem can learn the parametric procedures for given targets and carry on laboratory operations in standalone mode, with high reproducibility, precision, and availability for knowledge regeneration. Moreover, an improved nucleation theory of size focusing on inorganic perovskite quantum dots (IPQDs) is theoretically proposed and experimentally testified to by AIR-Chem. This work aims to boost the process of an unmanned chemistry laboratory from the synthesis of chemical materials to the analysis of physical chemical…

The role of a strong organobase, guanidine, in sulfuric acid-driven new-particle formation is studied using state-of-the-art quantum chemical methods and molecular cluster formation simulations. Cluster formation mechanisms at the molecular level are resolved, and theoretical results on cluster stability are confirmed with mass spectrometer measurements. New-particle formation from guanidine and sulfuric acid molecules occurs without thermodynamic barriers under studied conditions, and clusters are growing close to a 1:1 composition of acid and base. Evaporation rates of the most stable clusters are extremely low, which can be explained by the proton transfers and symmetrical cluster structures. We compare the ability of guanidine and dimethylamine to enhance sulfuric acid-driven particle formation and show that more than 2000-fold concentration of dimethylamine is needed to yield as efficient particle formation as in the case of guanidine. At similar conditions, guanidine yields 8 orders of magnitude higher particle formation rates compared to dimethylamine. Highly basic compounds…

Abstract The role of transition metals in chemical reactions is often derived from probing the metal 3d states. However, the relation between metal site geometry and 3d electronic states, arising from multielectronic effects, makes the spectral data interpretation and modeling of these optical excited states a challenge. Here we show, using the well-known case of red ruby, that unique insights into the density of transition metal 3d excited states can be gained with 2p3d resonant inelastic X-ray scattering (RIXS). We compare the experimental determination of the 3d excited states of Cr3+ impurities in Al2O3 with 190 meV resolution 2p3d RIXS to optical absorption spectroscopy and to simulations. Using the crystal field multiplet theory, we calculate jointly for the first time the Cr3+ multielectronic states, RIXS, and optical spectra based on a unique set of parameters. We demonstrate that (i) anisotropic 3d multielectronic interactions causes different scaling of Slater integrals, and (ii) a previously not observed doublet excited state exists around 3.35 eV. These results allow to…