The 50 most-cited articles in The Journal of Physical Chemistry A, 2017

A detailed insight of key reactive events related to oxidation and pyrolysis of hydrocarbon fuels further enhances our understanding of combustion chemistry. Though comprehensive kinetic models are available for smaller hydrocarbons (typically C 3 or lower), developing and validating reaction mechanisms for larger hydrocarbons is a daunting task, due to the complexity of their reaction networks. The ReaxFF method provides an attractive computational method to obtain reaction kinetics for complex fuel and fuel mixtures, providing an accuracy approaching ab-initio-based methods but with a significantly lower computational expense. The development of the first ReaxFF combustion force field by Chenoweth et al. (CHO-2008 parameter set) in 2008 has opened new avenues for researchers to investigate combustion chemistry from the atomistic level. In this article, we seek to address two issues with the CHO-2008 ReaxFF description. While the CHO-2008 description has achieved significant popularity for studying large hydrocarbon combustion, it fails to accurately describe the chemistry of small…

Machine learning (ML) of quantum mechanical properties shows promise for accelerating chemical discovery. For transition metal chemistry where accurate calculations are computationally costly and available training data sets are small, the molecular representation becomes a critical ingredient in ML model predictive accuracy. We introduce a series of revised autocorrelation functions (RACs) that encode relationships of the heuristic atomic properties (e.g., size, connectivity, and electronegativity) on a molecular graph. We alter the starting point, scope, and nature of the quantities evaluated in standard ACs to make these RACs amenable to inorganic chemistry. On an organic molecule set, we first demonstrate superior standard AC performance to other presently available topological descriptors for ML model training, with mean unsigned errors (MUEs) for atomization energies on set-aside test molecules as low as 6 kcal/mol. For inorganic chemistry, our RACs yield 1 kcal/mol ML MUEs on set-aside test molecules in spin-state splitting in comparison to 15-20× higher errors for feature…

We propose new approximate global multiplicative scaling factors for the DFT calculation of ground state harmonic vibrational frequencies using functionals from the TPSS, M06, and M11 functional families with standard correlation consistent cc-pVxZ and aug-cc-pVxZ (x = D, T, and Q), 6-311G split valence family, Sadlej and Sapporo polarized triple-ζ basis sets. Results for B3LYP, CAM-B3LYP, B3PW91, PBE, and PBE0 functionals with these basis sets are also reported. A total of 99 harmonic frequencies were calculated for 26 gas-phase organic and nonorganic molecules typically found in detonated solid propellant residue. Our proposed approximate multiplicative scaling factors are determined using a least-squares approach comparing the computed harmonic frequencies to experimental counterparts well established in the scientific literature. A comparison of our work to previously published global scaling factors is made to verify method reliability and the applicability of our molecular test set.

Polymerization of benzoxazine resins is indicated by the disappearance of a 960–900 cm –1 band in infrared spectroscopy (IR). Historically, this band was assigned to the C–H out-of-plane bending of the benzene to which the oxazine ring is attached. This study shows that this band is a mixture of the O–C 2 stretching of the oxazine ring and the phenolic ring vibrational modes. Vibrational frequencies of 3-phenyl-3,4-dihydro-2 H -benzo[ e ][1,3]oxazine ( PH-a ) and 3-( tert -butyl)-3,4-dihydro-2 H -benzo[ e ][1,3]oxazine ( PH-t ) are compared with isotope-exchanged and all-substituted compounds. Deuterated benzoxazine monomers, 15 N-isotope exchanged benzoxazine monomers, and all-substituted benzoxazine monomers without aromatic C–H groups are synthesized and studied meticulously. The various isotopic-exchanges involved deuteration around the benzene ring of phenol, selective deuteration of each CH 2 in the O– CH 2 –N (2) and N– CH 2 –Ar (4) positions on the oxazine ring, or simultaneous deuteration of both positions. The chemical structures were confirmed by 1 H nuclear magnetic…

The fidelity of combustion simulations is strongly dependent on the accuracy of the underlying thermochemical properties for the core combustion species that arise as intermediates and products in the chemical conversion of most fuels. High level theoretical evaluations are coupled with a wide-ranging implementation of the Active Thermochemical Tables (ATcT) approach to obtain well-validated high fidelity predictions for the 0 K heat of formation for a large set of core combustion species. In particular, high level ab initio electronic structure based predictions are obtained for a set of 348 C, N, O, and H containing species, which corresponds to essentially all core combustion species with 34 or fewer electrons. The theoretical analyses incorporate various high level corrections to base CCSD(T)/cc-pVnZ analyses (n = T or Q) using H 2, CH 4, H 2 O, and NH 3 as references. Corrections for the complete-basis-set limit, higher-order excitations, anharmonic zero-point energy, core–valence, relativistic, and diagonal Born–Oppenheimer effects are ordered in decreasing importance.…

Aqueous-based synthesis is one of the most popular methods to prepare nanoparticles. In these procedures, surfactants are needed to regulate the growth and final particle size. While there are numerous evidence on the decisive role of surfactants, a quantitative description remains elusive. This study develops a theoretical model to correlate the surfactant activities to particle growth. In the model, the "penetrability" of ions within surfactant layer is used to combine surface reaction and adsorption/desorption processes. The penetrability was then directly correlated to surfactant size. The theory was verified by synthesis of iron oxide nanoparticles with series of cationic surfactants. Eight surfactants, with same headgroup and increasing hydrocarbon tail, were employed. The experimental data showed a deterministic correlation between surfactant tails and particle size. The experimental correlation between surfactant length and particle size was predicted by the model. The modeling results verify the role of surfactant as capping agent during particle growth. More importantly,…

The article addresses the formation mechanisms of naphthalene and indene, which represent prototype polycyclic aromatic hydrocarbons (PAH) carrying two six-membered and one five- plus a six-membered ring. Theoretical studies of the relevant chemical reactions are overviewed in terms of their potential energy surfaces, rate constants, and product branching ratios; these data are compared with experimental measurements in crossed molecular beams and the pyrolytic chemical reactor emulating the extreme conditions in the interstellar medium (ISM) and the combustion-like environment, respectively. The outcome of the reactions potentially producing naphthalene and indene is shown to critically depend on temperature and pressure or collision energy and hence the reaction mechanisms and their contributions to the PAH growth can be rather different in the ISM, planetary atmospheres, and in combustion flames at different temperatures and pressures. Specifically, this paradigm is illustrated with new theoretical results for rate constants and product branching ratios for the reaction of phenyl…

Recently, exchange-correlation potentials in density functional theory were developed with the goal of providing improved band gaps in solids. Among them, the semilocal potentials are particularly interesting for large systems since they lead to calculations that are much faster than with hybrid functionals or methods like GW. We present an exhaustive comparison of semilocal exchange-correlation potentials for band gap calculations on a large test set of solids, and particular attention is paid to the potential HLE16 proposed by Verma and Truhlar. It is shown that the most accurate potential is the modified Becke-Johnson potential, which, most noticeably, is much more accurate than all other semilocal potentials for strongly correlated systems. This can be attributed to its additional dependence on the kinetic energy density. It is also shown that the modified Becke-Johnson potential is at least as accurate as the hybrid functionals and more reliable for solids with large band gaps.

The charge-transfer component of the energy of interaction between molecules has been a controversial issue for many years. In particular, the values reported from the use of the natural bond orbital analysis of Weinhold and his co-workers are several times larger than those obtained by other methods. I argue that these values are heavily contaminated with basis-set superposition error and are meaningless in the context of intermolecular interactions.

Many population analysis methods are based on the precept that molecules should be built from fragments (typically atoms) that maximally resemble the isolated fragment. The resulting molecular building blocks are intuitive (because they maximally resemble well-understood systems) and transferable (because if two molecular fragments both resemble an isolated fragment, they necessarily resemble each other). Information theory is one way to measure the deviation between molecular fragments and their isolated counterparts, and it is a way that lends itself to interpretation. For example, one can analyze the relative importance of electron transfer and polarization of the fragments. We present key features, advantages, and disadvantages of the information-theoretic approach. We also codify existing information-theoretic partitioning methods in a way that clarifies the enormous freedom one has within the information-theoretic ansatz.

The use of multiple chromophores as photosensitizers for catalysts involved in energy-demanding redox reactions is often complicated by electronic interactions between the chromophores. These interchromophore interactions can lead to processes, such as excimer formation and symmetry-breaking charge separation (SB-CS), that compete with efficient electron transfer to or from the catalyst. Here, two dimers of perylene bound either directly or through a xylyl spacer to a xanthene backbone were synthesized to probe the effects of interchromophore electronic coupling on excimer formation and SB-CS using ultrafast transient absorption spectroscopy. Two time constants for excimer formation in the 1–25 ps range were observed in each dimer due to the presence of rotational isomers having different degrees of interchromophore coupling. In highly polar acetonitrile, SB-CS competes with excimer formation in the more weakly coupled isomers followed by charge recombination with τ CR = 72–85 ps to yield the excimer. The results of this study of perylene molecular dimers can inform the design of…

An accurate and cost-efficient methodology for the estimation of the enthalpies of formation for closed-shell compounds composed of C, H, O, and N atoms is presented and validated against critically evaluated experimental data. The computational efficiency is achieved through the use of the resolution-of-identity (RI) and domain-based local pair-natural orbital coupled cluster (DLPNO–CCSD(T)) approximations, which results in a drastic reduction in both the computational cost and the number of necessary steps for a composite quantum chemical method. The expanded uncertainty for the proposed methodology evaluated using a data set of 45 thoroughly vetted experimental values for molecules containing up to 12 heavy atoms is about 3 kJ·mol –1, competitive with those of typical calorimetric measurements. For the compounds within the stated scope, the methodology is shown to be superior to a representative, more general, and widely used composite quantum chemical method, G4.

Quantum calculations are used to examine the properties of heterodimers formed by a series of tetrel-containing molecules with NH 3 as universal Lewis base. TH 4 was taken as a starting point, with T = C, Si, Ge, and Sn. The H atoms were replaced by various numbers of F atoms—TH 3 F, TF 3 H, and TF 4 —so as to monitor the effects of adding electron-withdrawing substituents. Unsubstituted TH 4 molecules form the weakest tetrel bonds, only up to about 2 kcal/mol. The bond is strengthened when the H opposite NH 3 is replaced by F, rising up to the 6–9 kcal/mol range. Another means of strengthening arises when the three peripheral H atoms of TH 4 are replaced by F. The effect of the latter is heavily dependent on the nature of the T atom and is particularly noticeable for larger tetrels. The two sorts of fluorination patterns are cooperative, in that their combination in TF 4 yields by far the most powerful tetrel bonding agent. The tetrel bond is strengthened as the T atom moves further down the periodic table column. The strongest bond amounts to 25.5 kcal/mol for SnF 4 ··NH 3 . A…

Abstract The photophysical properties of tetraphenylethene (TPE) compounds may differ widely depending on the substitution pattern, for example, with regard to the fluorescence quantum yield ϕf and the propensity to exhibit aggregation-induced emission (AIE). We report combined electronic structure calculations and nonadiabatic dynamics simulations to study the excited-state decay mechanisms of two TPE derivatives with four methyl substituents, either in the meta position (TPE-4mM, ϕf = 0.1%) or in the ortho position (TPE-4oM, ϕf = 64.3%). In both cases, two excited-state decay pathways may be relevant, namely, photoisomerization around the central ethylenic double bond and photocyclization involving two adjacent phenyl rings. In TPE-4mM, the barrierless S1 cyclization is favored; it is responsible for the ultralow fluorescence quantum yield observed experimentally. In TPE-4oM, both the S1 photocyclization and photoisomerization paths are blocked by non-negligible barriers, and fluorescence is thus feasible. Nonadiabatic dynamics simulations with more than 1000 surface hopping…

A diverse set of 100 chalcogen-bonded complexes comprising neutral, cationic, anionic, divalent, and double bonded chalcogens has been investigated using ωB97X-D/aug-cc-pVTZ to determine geometries, binding energies, electron and energy density distributions, difference density distributions, vibrational frequencies, local stretching force constants, and associated bond strength orders. The accuracy of ωB97X-D was accessed by CCSD(T)/aug-cc-pVTZ calculations of a subset of 12 complexes and by the CCSD(T)/aug-cc-pVTZ //ωB97X-D binding energies of 95 complexes. Most of the weak chalcogen bonds can be rationalized on the basis of electrostatic contributions, but as the bond becomes stronger, covalent contributions can assume a primary role in the strength and geometry of the complexes. Covalency in chalcogen bonds involves the charge transfer from a lone pair orbital of a Lewis base into the σ* orbital of a divalent chalcogen or a π* orbital of a double bonded chalcogen. We describe for the first time a symmetric chalcogen-bonded homodimer stabilized by a charge transfer from a lone…

The triplet excited state properties of two BODIPY phenothiazine dyads ( BDP-1 and BDP-2 ) with different lengths of linker and orientations of the components were studied. The triplet state formation of BODIPY chromophore was achieved via photoinduced electron transfer (PET) and charge recombination (CR). BDP-1 has a longer linker between the phenothiazine and the BODIPY chromophore than BDP-2 . Moreover, the two chromophores in BDP-2 assume a more orthogonal geometry both at the ground and in the first excited state (87°) than that of BDP-1 (34–40°). The fluorescence of the BODIPY moiety was significantly quenched in the dyads. The charge separation (CS) and CR dynamics of the dyads were studied with femtosecond transient absorption spectroscopy ( k CS = 2.2 × 10 11 s –1 and 2 × 10 12 s –1 for BDP-1 and BDP-2, respectively; k CR = 4.5 × 10 10 and 1.5 × 10 11 s –1 for BDP-1 and BDP-2, respectively; in acetonitrile). Formation of the triplet excited state of the BODIPY moiety was observed for both dyads upon photoexcitation, and the triplet state quantum yield depends on both the…

In this work, we theoretically investigate the sequential excited state double proton transfer (ESDPT) mechanism of a representative intramolecular hydroxyl (OH)-type hydrogen molecule 2,2′-bipyridyl-3,3′-diol (BP(OH) 2 ). We mainly adopt three kinds of different polar solvents (nonpolar cyclohexane (CYH), polar acetonitrile (ACN), and moderate chloroform (CHCl 3 )) to explore solvent effects on this system. Two intramolecular hydrogen bonds of BP(OH) 2 are testified to be strengthened in the S 1 state, which provides possibility for ESDPT process. Explorations of charge redistribution and potential energy surfaces (PESs) reveal ESDPT process. Searching transition state (TS) structures in different polar aprotic solvents, we successfully regulate and control the stepwise ESDPT behaviors of BP(OH) 2 through solvent polarity.

Atmospheric aerosol acidity impacts key multiphase processes, such as acid-catalyzed reactions leading to secondary organic aerosol formation, which impact climate and human health. However, traditional indirect methods of estimating aerosol pH often disagree with thermodynamic model predictions, resulting in aerosol acidity still being poorly understood in the atmosphere. Herein, a recently developed method coupling Raman microspectroscopy with extended Debye–Hückel activity calculations to directly determine the acidity of individual particles (1−15 μm projected area diameter, average 6 μm) was applied to a range of atmospherically relevant inorganic and organic acid–base equilibria systems (HNO 3 /NO 3 –, HC 2 O 4 – /C 2 O 4 2–, CH 3 COOH/CH 3 COO –, and HCO 3 – /CO 3 2– ) covering a broad pH range (−1 to 10), as well as an inorganic–organic mixture (sulfate-oxalate). Given the ionic strength of the inorganic solutions, the H + activity, γ(H + ), yielded lower values (0.68–0.75) than the organic and mixed systems (0.72–0.80). A consistent relationship between increasing peak…

The development of metal-free organic room temperature phosphorescence (RTP) materials has attracted increasing attention because of their applications in sensors, biolabeling (imaging) agents and anticounterfeiting technology, but remains extremely challenging owing to the restricted spin-flip intersystem crossing (ISC) followed by low-yield phosphorescence that cannot compete with nonradiative relaxation processes. Here, we report a facile strategy to realize highly efficient RTP by doping iodo difluoroboron dibenzoylmethane (I-BF 2 dbm-R) derivatives into a rigid crystalline 4-iodobenzonitrile (Iph-C≡N) matrix. We found that halogen bonding between cyano group of Iph-C≡N matrix and iodine atom of I-BF 2 dbm-R dopant is formed in doped crystals, i.e., Iph-C≡N···I-BF 2 dbm-R, which not only suppresses nonradiative relaxation of triplets but also promotes the spin–orbit coupling (SOC). As a result, the doped crystals show intense RTP with an efficiency up to 62.3%. By varying the substituent group R in I-BF 2 dbm-R from electron donating −OCH 3 to electron accepting −F, −CN groups,…

In LaMer burst nucleation, the individual nucleation events happen en masse, quasi-simultaneously, and at nearly identical homogeneous conditions. These properties make LaMer burst nucleation important for applications that require monodispersed particles and also for theoretical analyses. Sugimoto and co-workers predicted that the number of nuclei generated during a LaMer burst depends only on the solute supply rate and the growth rate, independent of the nucleation kinetics. Some experiments confirm that solute supply kinetics control the number of nuclei, but flaws in the original theoretical analysis raise questions about the predicted roles of growth and nucleation kinetics. We provide a rigorous analysis of the coupled equations that govern concentrations of nuclei and solutes. Our analysis confirms that the number of nuclei is largely determined by the solute supply and growth rates, but our predicted relationship differs from that of Sugimoto et al. Moreover, we find that additional nucleus size dependent corrections should emerge in systems with slow growth kinetics.…

Recent experimental evidence suggests that diamines can enhance atmospheric new particle formation more efficiently compared to monoamines such as dimethylamine. Here we investigate the molecular interactions between sulfuric acid (sa) and the diamine putrescine (put) using computational methods. The molecular structure of up to four sulfuric acid molecules and up to four putrescine molecules were obtained at the ωB97X-D/6-31++G(d,p) level of theory. We utilized a domain local pair natural orbital coupled cluster method (DLPNO-CCSD(T)/aug-cc-pVTZ) to obtain highly accurate binding energies of the clusters. We find that the (sa) 1–4 (put) 1–4 clusters show more ionic character than clusters consisting of sulfuric acid and dimethylamine (dma) by readily forming several sulfate ions in the cluster. To estimate the stability of the clusters, we calculate the evaporation rates and compare them to ESI-APi-TOF measurements. Using the atmospheric cluster dynamics code (ACDC), we simulate and compare the new particle formation rates between the (sa) 1–4 (put) 1–4 and (sa) 1–4 (dma) 1–4…

Acid dissociation constants (p K a ’s) are key physicochemical properties that are needed to understand the structure and reactivity of molecules in solution. Theoretical p K a ’s have been calculated for a set of 72 organic compounds with −OH and −OOH groups (48 with known experimental p K a ’s). This test set includes 17 aliphatic alcohols, 25 substituted phenols, and 30 hydroperoxides. Calculations in aqueous medium have been carried out with SMD implicit solvation and three hybrid DFT functionals (B3LYP, ωB97XD, and M06-2X) with two basis sets (6-31+G(d,p) and 6-311++G(d,p)). The effect of explicit water molecules on calculated p K a ’s was assessed by including up to three water molecules. p K a ’s calculated with only SMD implicit solvation are found to have average errors greater than 6 p K a units. Including one explicit water reduces the error by about 3 p K a units, but the error is still far from chemical accuracy. With B3LYP/6-311++G(d,p) and three explicit water molecules in SMD solvation, the mean signed error and standard deviation are only −0.02 ± 0.55; a linear fit…

Impressive progress has recently been achieved in photocatalytic hydrogen evolution with polymeric carbon nitride materials consisting of heptazine building blocks. However, the fundamental mechanistic principles of the catalytic cycle are as yet poorly understood. Here, we provide first-principles computational evidence that water splitting with heptazine-based materials can be understood as a molecular excited-state reaction taking place in hydrogen-bonded heptazine–water complexes. The oxidation of water occurs homolytically via an electron/proton transfer from water to heptazine, resulting in ground-state heptazinyl and OH radicals. It is shown that the excess hydrogen atom of the heptazinyl radical can be photodetached by a second photon, which regenerates the heptazine molecule. Alternatively to the photodetachment reaction, two heptazinyl radicals can recombine in a dark reaction to form H 2, thereby regenerating two heptazine molecules. The proposed molecular photochemical reaction scheme within hydrogen-bonded chromophore–water complexes is complementary to the traditional…

We report the measurement of the entangled two-photon absorption (ETPA) cross section, σ E, at 808 nm on organic chromophores in solution in a low photon flux regime. We performed measurements on zinc tetraphenylporphyrin (ZnTPP) in toluene and rhodamine B (RhB) in methanol. This is, to the best of our knowledge, the first time that σ E is measured for RhB. Additionally, we report a study of the dependence of σ E on the molecular concentration for both molecular systems. In contrast to previous experiments, our measurements are based on detecting the pairs of photons that are transmitted by the molecular system. By using a coincidence count circuit it was possible to improve the signal-to-noise ratio. This type of work is important for the development of spectroscopic and microscopic techniques using entangled photons.

Abstract Reactions of the simplest Criegee intermediate (CH2OO) with a series of alcohols have been studied in a flash photolysis flow reactor. Laser photolysis of diiodomethane at 355 nm in the presence of molecular oxygen was used to produce CH2OO, and the absolute number densities were determined as a function of delay time from analysis of broadband transient absorption spectra obtained using a pulsed LED. The kinetics for the reactions of CH2OO with methanol, ethanol, and 2-propanol were measured under pseudo-first-order conditions at 295 K, yielding rate constants of (1.4 ± 0.4) × 10–13 cm3 s–1, (2.3 ± 0.6) × 10–13 cm3 s–1, and (1.9 ± 0.5) × 10–13 cm3 s–1, respectively. Complementary ab initio calculations were performed at the CCSD(T)/aug-cc-pVTZ//CCSD/cc-pVDZ level of theory to characterize stationary points on the reaction enthalpy and free energy surfaces and to elucidate the thermochemistry and mechanisms. The reactions proceed over free energy barriers of ∼8 kcal mol–1 to form geminal alkoxymethyl hydroperoxides: methoxymethyl hydroperoxide (MMHP), ethoxymethyl…

We proposed and implemented a combined molecular dynamics and coordinate driving (MD/CD) method for automatically searching multistep reaction pathways of chemical reactions. In this approach, the molecular dynamic (MD) method at the molecular mechanics (MM) or semiempirical quantum mechanical (QM) level is employed to explore the conformational space of the minimum structures, and the modified coordinate driving (CD) method is used to build reaction pathways for representative conformers. The MD/CD method is first applied to two model reactions (the Claisen rearrangement and the intermolecular aldol reaction). By comparing the obtained results with those of the existing methods, we found that the MD/CD method has a comparable performance in searching low-energy reaction pathways. Then, the MD/CD method is further applied to investigate two reactions: the electrocyclic reaction of benzocyclobutene-7-carboxaldehyde and the intramolecular Diels-Alder reaction of ketothioester with 11 effectively rotatable single bonds. For the first reaction, our results can correctly account for its…

Geometries and electronic properties of neutral Ag n, cationic Ag n +, and anionic Ag n – silver clusters with n = 2–22 were investigated by density functional theory (DFT) with M06 functional. For neutral clusters, transition from planar to “empty cage” structure occurs at n = 7, “empty cage” to “cage with one Ag atom” at n = 18, and to “cage with two Ag atoms” at n = 22. For lowest-energy Ag n clusters, Ag 8 and Ag 18 show lowest polarizability due to closed-shell valence electron configurations 1S 2 /1P 6 and 1S 2 /1P 6 /1D 10 . High stability of Ag 8 is manifested in small dissociation energies of Ag 9 to Ag 8 plus Ag 1 and Ag 10 cluster to Ag 8 plus Ag 2 . Cluster Ag 20 with configuration 1S 2 /1P 6 /1D 10 /2S 2 is stable due to low dissociation energy of Ag 21 to Ag 1 and Ag 22 to Ag 2 . Cationic clusters with even n namely Ag 10 + (9 valence electrons), Ag 16 + (15 valence electrons), and Ag 22 + (21 valence electrons) dissociate to Ag 1 and closed-shell Ag 9 + (1S 2 /1P 6 ), Ag 15 + (1S 2 /1D 10 /2S 2 ) and Ag 21 + (1S 2 /1P 6 /1D 10 /2S 2 ). For odd n, Ag 11 + and Ag 17 +…

Representation of multidimensional global potential energy surfaces suitable for spectral and dynamical calculations from high-level ab initio calculations remains a challenge. Here, we present a detailed study on constructing potential energy surfaces using a machine learning method, namely, Gaussian process regression. Tests for the 3 A″ state of SH 2, which facilitates the SH + H ↔ S( 3 P) + H 2 abstraction reaction and the SH + H′ ↔ SH′ + H exchange reaction, suggest that the Gaussian process is capable of providing a reasonable potential energy surface with a small number (∼1 × 10 2 ) of ab initio points, but it needs substantially more points (∼1 × 10 3 ) to converge reaction probabilities. The implications of these observations for construction of potential energy surfaces are discussed.

Isoprene, the most abundant biogenic volatile organic compound (BVOC) in the atmosphere, and its low-volatility oxidation products lead to secondary organic aerosol (SOA) formation. Isoprene-derived organosulfates formed from reactions of isoprene oxidation products with sulfate in the particle phase are a significant component of SOA and can hydrolyze forming polyols. Despite characterization by mass spectrometry, their basic structural and spectroscopic properties remain poorly understood. Herein, Raman microspectroscopy and density functional theory (DFT) calculations (CAM-B3LYP level of theory) were combined to analyze the vibrational modes of key organosulfates, 3-methyltetrol sulfate esters (racemic mixture of two isomers), and racemic 2-methylglyceric acid sulfate ester, and hydrolysis products, 2-methyltetrols, and 2-methylglyceric acid. Two intense vibrational modes were identified, ν(RO–SO 3 ) (846 ± 4 cm –1 ) and ν s (SO 3 ) (1065 ± 2 cm –1 ), along with a lower intensity δ(SO 3 ) mode (586 ± 2 cm –1 ). For 2-methylglyceric acid and its sulfate esters, deprotonation of…

In this article, ab initio calculations have been combined with a search in the Protein Data Bank (PDB) to demonstrate the importance of σ-hole tetrel bonding interactions in biological systems. In particular, we focus our attention on the ability of the −CF 3 group to participate in noncovalent interactions as Lewis acids, and we show the importance of this interaction in the inhibition mechanism of a NADP + -dependent isocitrate dehydrogenase (IDH) enzyme that converts isocitrate to α-ketoglutarate. IDH mutations are found in multiple hematologic and solid tumors, inducing premalignant disorders. A potent triazine-based inhibitor of the mutant IDH (enasidenib) presents two −CF 3 groups in the structure. One establishes a tetrel bonding interaction with an aspartate residue that contributes to the binding and selectivity of the inhibitor to the active site.

α-Keto acids are important, atmospherically relevant species, and their photochemistry has been considered in the formation and processing of aerosols. Despite their atmospheric relevance, the photochemistry of these species has primarily been studied under extremely low pH conditions. Using a variety of analytical techniques, we characterize the extent of hydration and deprotonation for solutions of two α-keto acids, pyruvic acid and 2-oxooctanoic acid, as a function of pH. We find that changes in the initial solution composition govern the accessibility of different photochemical pathways, resulting in slowed photolysis under high pH conditions and a shift in photoproducts that can be predicted mechanistically.

A scarcity of known chemical kinetic parameters leads to the use of many reaction rate estimates, which are not always sufficiently accurate, in the construction of detailed kinetic models. To reduce the reliance on these estimates and improve the accuracy of predictive kinetic models, we have developed a high-throughput, fully automated, reaction rate calculation method, AutoTST. The algorithm integrates automated saddle-point geometry search methods and a canonical transition state theory kinetics calculator. The automatically calculated reaction rates compare favorably to existing estimated rates. Comparison against high level theoretical calculations show the new automated method performs better than rate estimates when the estimate is made by a poor analogy. The method will improve by accounting for internal rotor contributions and by improving methods to determine molecular symmetry.

Coherent exciton delocalization in dye aggregate systems gives rise to a variety of intriguing optical phenomena, including J- and H-aggregate behavior and Davydov splitting. Systems that exhibit coherent exciton delocalization at room temperature are of interest for the development of artificial light-harvesting devices, colorimetric detection schemes, and quantum computers. Here, we report on a simple dye system templated by DNA that exhibits tunable optical properties. At low salt and DNA concentrations, a DNA duplex with two internally functionalized Cy5 dyes (i.e., dimer) persists and displays predominantly J-aggregate behavior. Increasing the salt and/or DNA concentrations was found to promote coupling between two of the DNA duplexes via branch migration, thus forming a four-armed junction (i.e., tetramer) with H-aggregate behavior. This H-tetramer aggregate exhibits a surprisingly large Davydov splitting in its absorbance spectrum that produces a visible color change of the solution from cyan to violet and gives clear evidence of coherent exciton delocalization.

We have studied the specific requirements of a given neutral organic molecule to act as a stabilizer in sulfuric acid induced new particle formation. Based on an analysis of the reaction Gibbs free energies between simple functional groups and sulfuric acid, carboxylic acid groups are identified to show the strongest hydrogen bonding interaction with sulfuric acid. The free energy associated with the hydrogen bonding between sulfuric acid and 14 different carboxylic acids of atmospheric relevance reveal that the binding strength is very dependent on the ability of sulfuric acid to form an additional hydrogen bond via its vacant S-OH group to a γ-carbonyl group in the organic molecule. Extending the analysis to monoterpene oxidation products and further to large dimer esters, we identify the following necessary criteria for a given organic oxidation product to efficiently stabilize sulfuric acid clustering: (1) weak or no intramolecular hydrogen bonds in the isolated monomer; (2) more than two carboxylic acid groups. As a proof of concept we show that these requirements correspond to…

High pressure anion chemical ionization is commonly used for the detection of neutral molecules in the gas phase. The detection efficiency in these measurements depends on how strongly the reagent ion binds to the neutral target molecule. We have calculated the binding strength of nitrate (NO 3 – ), acetate (CH 3 C(O)O – ), lactate (CH 3 CH(OH)C(O)O – ), trifluoroacetate (CF 3 C(O)O – ), trifluoromethanolate (CF 3 O – ), bromide (Br – ), and iodide (I – ) reagent ions to ten different products derived from the OH radical-initiated oxidation of butadiene. We found that the binding of these oxidation products to the reagent ions depends almost linearly on the number of oxygen atoms in the target molecule, with the precise chemical identity of the compound (e.g., the number and relative position of hydroxyl or hydroperoxy groups) playing a more minor role. For acetate, the formation free energy decreases on average by around 4 kcal/mol when the number of oxygen atoms in the sample molecule increases by one. For the other reagent ions the corresponding decrease is around 3 kcal/mol. For…

Here we present a modified version of the on-the-fly string method for the localization of the minimum free energy path in a space of arbitrary collective variables. In the proposed approach the shape of the biasing potential is controlled by only two force constants, defining the width of the potential along the string and orthogonal to it. The force constants and the distribution of the string nodes are optimized during the simulation, improving the convergence. The optimized parameters can be used for umbrella sampling with a path CV along the converged string as the reaction coordinate. We test the new method with three fundamentally different processes: chloride attack to chloromethane in bulk water, alanine dipeptide isomerization, and the enzymatic conversion of isochorismate to piruvate. In each case the same set of parameters resulted in a rapidly converging simulation and a precise estimation of the potential of mean force. Therefore, the default settings can be used for a wide range of processes, making the method essentially parameter free and more user-friendly.

Electronic structure calculations have been performed to investigate the role of ammonia in catalyzing the formation of sulfuric acid through hydrolysis of SO 3 in Earth’s atmosphere. The uncatalyzed process involves a high activation barrier and, until date, is mainly known to occur in Earth’s atmosphere only when catalyzed by water and acids. Here we show that hydrolysis of SO 3 can be very efficiently catalyzed by ammonia, the most abundant basic component in Earth’s atmosphere. It was found, based on magnitude of relative potential energies as well as rate coefficients, that ammonia is the best among all the catalysts studied until now (water and acids) and could be a considerable factor in formation of sulfuric acid in troposphere. The calculated rate coefficient (at 298 K) of ammonia catalyzed reaction has been found to be ∼10 5 –10 7 times greater than that for water catalyzed ones. It was found, based on relative rates of ammonia and water catalyzed processes, that in troposphere ammonia, together with water, could be the key factor in determining the rate of formation of…

The molecular interactions between sulfuric acid (sa) and methylamine (ma) are investigated using computational methods. The molecular structures and vibrational frequencies of (sa) a (ma) b clusters, with a, b ≤ 4, were obtained with the ωB97X-D functional using a 6-31++G(d,p) basis set. The single-point energies were corrected using the domain-based local pair natural orbital coupled cluster method—DLPNO–CCSD(T)—with an aug-cc-pVTZ basis set. The calculated Gibbs free energies (Δ G ) of the clusters are used to calculate the evaporation rates of the (sa) a (ma) b cluster system and compare them to the corresponding ammonia clusters. With the atmospheric cluster dynamics code (ACDC), the new particle formation rates of the (sa) a (ma) b clusters were simulated and compared to the (sa) a (dma) b cluster system. It is found that methylamine is not capable of explaining observed new particle formation event in the ambient atmosphere. Looking into the calculated Gibbs free energy profiles it is found that the limiting steps in forming stable (sa) 3–4 (base) 3–4 clusters depend strongly…

Polynitrogen compounds have attracted great interest due to their potential applications as high energy density materials. Most recently, a rich variety of alkali polynitrogens (R x N y; R = Li, Na, and Cs) have been predicted to be stable at high pressures and one of them, CsN 5 has been recently synthesized. In this work, various potassium polynitrides are investigated using first-principles crystal structure search methods. Several novel molecular crystals consisting of N 4 chains, N 5 rings, and N 6 rings stable at high pressures are discovered. In addition, an unusual nitrogen-rich metallic crystal with stoichiometry K 2 N 16 consisting of a planar two-dimensional extended network of nitrogen atoms arranged in fused 18 atom rings is found to be stable above 70 GPa. An appreciable electron transfer from K to N atoms is responsible for the appearance of unexpected chemical bonding in these crystals. The thermodynamic stability and high pressure phase diagram is constructed. The electronic and vibrational properties of the layered polynitrogen K 2 N 16 compound are investigated,…

Formation of secondary organic aerosols (SOA) from biogenic volatile organic compounds (BVOC) occurs via O 3 - and OH-initiated reactions during the day and reactions with NO 3 during the night. We explored the effect of these three oxidation conditions on the molecular composition and aqueous photochemistry of model SOA prepared from two common BVOC. A common monoterpene, α-pinene, and sesquiterpene, α-humulene, were used to form SOA in a smog chamber via BVOC + O 3, BVOC + NO 3, and BVOC + OH + NO x oxidation. Samples of SOA were collected on filters, water-soluble compounds from SOA were extracted in water, and the resulting aqueous solutions were photolyzed to simulate the photochemical aqueous processing of SOA. The extent of change in the molecular level composition of SOA over 4 h of photolysis (approximately equivalent to 64 h of photolysis under ambient conditions) was assessed with high-resolution electrospray ionization mass spectrometry. The analysis revealed significant differences in the molecular composition between SOA formed by the different oxidation pathways. The…

The noncovalent interactions of 32 complexes involving pnicogens, chalcogens, and halogens atoms were investigated at the CCSD(T)/aug-cc-pVTZ level of theory. Two different types of complexes could be distinguished on the basis of geometric parameters, electron difference densities, and the charge transfer mechanisms associated with each type. In the type I conformation, the monomers adopt a skewed orientation allowing charge to be transfer between both monomers, whereas in the type II conformation the monomers adopt a linear arrangement, maximizing charge transfer in only one direction. Type I complexes involving the interaction between pnicogens and chalcogens cannot be unambiguously defined as chalcogen or pnicogen bonds, they are an admixture of both. The charge transfer dependence on the conformation adopted by the complexes described in this work can serve as a novel conformationally driven design concept for materials.

Substitution can be used to efficiently tune the photophysical properties of chromophores. In this study, we examine the effect of substituents on the absorption and fluorescence properties of anthracene. The effects of mono-, di-, and tetrasubstitution of electron-donating and -withdrawing functional groups were explored. In addition, the influence of a donor–acceptor substituent pair and the position of substitution were investigated. Eleven functional groups were varied on positions 1, 2, and 9 of anthracene, and on position 6 of 2-methoxyanthracene and 2-carboxyanthracene. Moreover, the donor–acceptor pair NH 2 /CO 2 H was added on different positions of anthracene for additional studies of doubly substituted anthracenes. Finally, we looked into quadruple substitutions on positions 1,4,5,8 and 2,3,6,7. Vertical excitation energies and oscillator strengths were computed using density functional theory with the hybrid CAM-B3LYP functional and 6-311G(d) basis set. Correlations between the excitation energies or oscillator strengths of the low-lying bright L a state and the Hammett…

By near-infrared (NIR) spectroscopy and anharmonic density functional theory (DFT) calculations, we investigate five kinds of saturated and unsaturated carboxylic acids belonging to the group of short-chain fatty acids: propionic acid, butyric acid, acrylic acid, crotonic acid, and vinylacetic acid. The experimental NIR spectra of these five kinds of carboxylic acids are reproduced by quantum chemical calculations in a broad spectral region of 7500–4000 cm –1 and for a wide range of concentrations. By employing anharmonic GVPT2 calculations on DFT level, a detailed interpretation of experimental spectra is achieved, elucidating structure–spectra correlations of these molecules in the NIR region. We emphasize the spectral features due to saturated and unsaturated alkyl chains, the location of a C═C bond within the alkyl chain, and the dimerization of carboxylic acids. In particular, the existence of a terminal C═C bond leads to the appearance of highly specific NIR bands. These pronounced bands are located at wavenumbers where no overlapping with other structure-specific bands…

3,7-Dihydroxy-4-oxo-2-phenyl-4 H - chromene-8-carbaldehyde in methylcyclohexane solvent was chosen to investigate excited-state intramolecular proton-transfer mechanisms by using a time-dependent density functional theory method. The results show that the single- and double-proton-transfer mechanisms are related and exist simultaneously in the excited states, which differs from those reported in previous experiments ( Serdiuk, I. E. et al. RSC Adv. 2015, 5, 102191−102203). The analyses of bond distance, bond angle, the molecular electrostatic potential surface, and infrared vibrational spectra show that two intramolecular hydrogen bonds were formed in the S 0 state, and upon excitation, the two intramolecular hydrogen bonds were strengthened in the S 1 state, which can facilitate the proton-transfer process. The calculated absorption and fluorescence spectra agree well with the experimental results. The constructed potential energy surfaces on the S 1 and S 0 states can explain the proton-transfer process. In the S 1 state, three types of proton-transfer processes exist as type 1…

By using density functional theory (DFT) and time-dependent density functional theory (TDDFT) methods, the sensing mechanism of a fluorescent probe 2-(2-hydroxyphenyl) benzothiazole (HBT) derivative HBTPP-S for hydrogen sulfide has been thoroughly studied. The thiolysis reaction has a moderate reaction barrier of 18.40 kcal mol –1, which indicates that the hydrogen sulfide sensing process has a favorable response speed. Because of the nonradiative donor-excited photoinduced electron transfer (d-PET, fluorophore as the electron donor) from the excited HBTPP group to the electron-withdrawing 2,4-dinitrophenyl group, as well as the inhibition of the proton transfer (PT) and the excited state intramolecular proton transfer (ESIPT) process by 2,4-dinitrophenyl group, the probe HBTPP-S is essentially nonfluorescent. On the other hand, the added hydrogen sulfide induces the thiolysis of the 2,4-dinitrophenyl ether bond, and then the thiolysis product HBTPP comes into existence. The theoretically simulated potential energy surface demonstrates that without the electron-withdrawing…

A high-speed, high-sensitivity and compact two-dimensional infrared (2D-IR) spectrometer based on 100 kHz Yb:KGW regenerative amplifier technology is described and demonstrated. The setup is three color, using an independent pump OPA and two separately tunable probe OPAs. The spectrometer uses 100 kHz acousto-optic pulse shaping on the pump beam for rapid 2D-IR acquisitions. The shot-to-shot stability of the laser system yields excellent signal-to-noise figures (∼10 μOD noise on 5000 laser shots). We show that the reduced bandwidth of the Yb:KGW amplifiers in comparison with conventional Ti:sapphire systems does not compromise the ability of the setup to generate high-quality 2D-IR data. Instrument responses of <300 fs are demonstrated and 2D-IR data presented for several systems of interest to physical chemists, showing spectral diffusion in NaSCN, amide I and II bands of a β sheet protein and DNA base-pair-backbone couplings. Overall, the increased data acquisition speed, intrinsic stability, and robustness of the Yb:KGW lasers are a significant step forward for 2D-IR spectroscopy.

Aerosol and molecular processing in the atmosphere occurs in a complex and variable environment consisting of multiple phases and interfacial regions. To explore the effects of such conditions on the reactivity of chemical systems, we employ an environmental simulation chamber to investigate the multiphase photolysis of pyruvic acid, which photoreacts in the troposphere in aqueous particles and in the gas phase. Upon irradiation of nebulized pyruvic acid, acetic acid and carbon dioxide are rapidly generated, which is consistent with previous literature on the bulk phase photolysis reactions. Additionally, we identify a new C 6 product, zymonic acid, a species that has not previously been reported from pyruvic acid photolysis under any conditions. Its observation here, and corresponding spectroscopic signatures, indicates it could be formed by heterogeneous reactions at the droplet surface. Prior studies of the aqueous photolysis of pyruvic acid have shown that high-molecular-weight compounds are formed via radical reactions; however, they are inhibited by the presence of oxygen,…

Donor–acceptor Stenhouse adducts (DASAs) are a rapidly emerging class of visible light-activatable negative photochromes. They are closely related to (mero)cyanine dyes with the sole difference being a hydroxy group in the polyene chain. The presence or absence of the hydroxy group has far-reaching consequences for the photochemistry of the compound: cyanine dyes are widely used as fluorescent probes, whereas DASAs hold great promise for visible light-triggered photoswitching. Here we analyze the photophysical properties of a DASA lacking the hydroxy group. Ultrafast time-resolved pump–probe spectroscopy in both the visible and IR region show the occurrence of E–Z photoisomerization on a 20 ps time scale, similar to the photochemical behavior of DASAs, but on a slower time scale. In contrast to the parent DASA compounds, where the initial photoisomerization is constrained to a single position (next to the hydroxy group), 1 H NMR in situ -irradiation studies at 213 K reveal that for nonhydroxy DASAs E–Z photoisomerization can take place at two different bonds, yielding two distinct…

The oxidation chemistry of the simplest conjugated hydrocarbon, 1,3-butadiene, can provide a first step in understanding the role of polyunsaturated hydrocarbons in combustion and, in particular, an understanding of their contribution toward soot formation. On the basis of our previous work on propene and the butene isomers (1-, 2-, and isobutene), it was found that the reaction kinetics of Ḣ-atom addition to the C═C double bond plays a significant role in fuel consumption kinetics and influences the predictions of high-temperature ignition delay times, product species concentrations, and flame speed measurements. In this study, the rate constants and thermodynamic properties for Ḣ-atom addition to 1,3-butadiene and related reactions on the Ċ 4 H 7 potential energy surface have been calculated using two different series of quantum chemical methods and two different kinetic codes. Excellent agreement is obtained between the two different kinetics codes. The calculated results including zero-point energies, single-point energies, rate constants, barrier heights, and thermochemistry…

We describe a novel theoretical approach to the bimolecular nucleophilic substitution (S N 2) reactions that is based on analytical potential energy surfaces (PESs) obtained by fitting a few tens of thousands high-level ab initio energy points. These PESs allow computing millions of quasi-classical trajectories thereby providing unprecedented statistical accuracy for S N 2 reactions, as well as performing high-dimensional quantum dynamics computations. We developed full-dimensional ab initio PESs for the F – + CH 3 Y [Y = F, Cl, I] systems, which describe the direct and indirect, complex-forming Walden-inversion, the frontside attack, and the new double-inversion pathways as well as the proton-transfer channels. Reaction dynamics simulations on the new PESs revealed (a) a novel double-inversion S N 2 mechanism, (b) frontside complex formation, (c) the dynamics of proton transfer, (d) vibrational and rotational mode specificity, (e) mode-specific product vibrational distributions, (f) agreement between classical and quantum dynamics, (g) good agreement with measured scattering angle…