Showing papers in "Journal of Physical Chemistry A in 2018"

Theoretical Insights Into the Excited State Double Proton Transfer Mechanism of Deep Red Pigment Alkannin.

Abstract: 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 S1-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 (CH3CN) 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 S1 state, and nonpolar solvents play important roles in lowering the potenti...

Excited States of Methylene, Polyenes, and Ozone from Heat-Bath Configuration Interaction.

Abstract: The electronically excited states of methylene (CH2), ethylene (C2H4), butadiene (C4H6), hexatriene (C6H8), and ozone (O3) 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 1038 determinants. These calculations give vertical excitation energies of 5.58 and 5.59 eV, respectively, for the 21Ag and 11Bu 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 hypothesiz...

Methylammonium Cation Dynamics in Methylammonium Lead Halide Perovskites: A Solid-State NMR Perspective.

Abstract: In light of the intense recent interest in the methylammonium lead halides, CH3NH3PbX3 (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 2H, 14N, and 207Pb NMR spectroscopy. In the cubic phase of all three salts, the MA cation undergoes pseudoisotropic tumbling (picosecond time scale). For example, the correlation time, τ2, 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, 2H and 14N 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 tem...

Calculation of Reaction Free Energies in Solution: A Comparison of Current Approaches.

Abstract: 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.

Information-Theoretic Approaches to Atoms-in-Molecules: Hirshfeld Family of Partitioning Schemes.

Abstract: 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.

Singlet Oxygen Reactivity with Carbonate Solvents Used for Li-Ion Battery Electrolytes

Abstract: 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 experimentally. Hydrogen peroxide is detrimental for cycling of a battery. For all known cathode active materials, the potential where singlet oxygen is released is found to be already high enough to electrochemically oxidize hydrogen peroxide. The formed protons and/or water both react with the typically used LiPF6 salt to HF that then leads to transition metal dissolution from the cathode active materials. This study shows how important the chemical stability toward singlet oxygen is for today's battery systems and that a trade-off will have to be found between chemical and electrochemical stability of the solvent to be used.

Thermal Decomposition Mechanism of CL-20 at Different Temperatures by ReaxFF Reactive Molecular Dynamics Simulations.

Abstract: 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 e-CL-20 supercell was constructed and ReaxFF-lg reactive molecular dynamics simulations were performed to investigate thermal decomposition of e-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–NO2 cleavage to form NO2, 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 re...

Accelerated ReaxFF Simulations for Describing the Reactive Cross-Linking of Polymers.

Abstract: 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

Kinetics of the Reactions between the Criegee Intermediate CH2OO and Alcohols

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 hydroperoxide (EMHP), and isopropoxymethyl hydroperoxide (PMHP). The experimental and theoretical results are compared to reactions of CH2OO with other hydroxylic compounds, such as water and carboxylic acids, and trends in reactivity are discussed.

Iron(II) and Iron(III) Spin Crossover: Toward an Optimal Density Functional

Abstract: 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 adjusted to 10-17%, regardless of the type of functionals involved. However, this typically introduces a clear Fe(II)-Fe(III) bias. The most accurate functionals measured by mean absolute errors <10 kJ/mol are CAMB3LYP-17, B3LYP*, and B97-15 with 15-17% Hartree-Fock exchange, closely followed by CAMB3LYP and CAMB3LYP-15, OPBE, rPBE-10, and B3P86-15. While GGA functionals display a small Fe(II)-Fe(III) bias, they are generally inaccurate, except the O exchange functional. Hybrid functionals (including B2PLYP double hybrids and meta hybrids) tend to favor HS too much in Fe(II) vs Fe(III), which is important in many studies where the oxidation state of iron can vary, e.g. rational SCO design and studies of catalytic processes involving iron. The only functional with a combined bias <5 kJ/mol and a decent MAE (15 kJ/mol) is our customized PBE0-12 functional. Alternatively one has to sacrifice Fe(II)-Fe(III) balance to use the best functionals for each group separately. We also investigated the precision (measured as the standard deviation of errors) and show that the target accuracy for iron SCO is 10 kJ/mol for accuracy and 5 kJ/mol for precision, and DFT is probably not going to break this limit in the near future. Importantly, all four types of functional behavior (accurate/precise, accurate/imprecise, inaccurate/precise, inaccurate/imprecise) are observed. More generally, our work illustrates the importance not only of overall accuracy but also of balanced accuracy for systems likely to occur in context.

Understanding the Mechanism Stabilizing Intermediate Spin States in Fe(II)-Porphyrin

Abstract: 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 mann...

Isoprene-Derived Organosulfates: Vibrational Mode Analysis by Raman Spectroscopy, Acidity-Dependent Spectral Modes, and Observation in Individual Atmospheric Particles

Abstract: 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–SO3) (846 ± 4 cm–1) and νs(SO3) (1065 ± 2 cm–1), along with a lower intensity δ(SO3) mode (586 ± 2 cm–1). For ...

Second-Order Vibrational Lineshapes from the Air/Water Interface.

Abstract: We explore by means of modeling how absorptive–dispersive mixing between the second- and third-order terms modifies the imaginary χtotal(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 χtotal(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 f...

Theoretical Descriptors of Electrides.

Abstract: 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.

Detection of Aliphatically Bridged Multi-Core Polycyclic Aromatic Hydrocarbons in Sooting Flames with Atmospheric-Sampling High-Resolution Tandem Mass Spectrometry.

Abstract: 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 correspond to the loss of saturated and unsaturated units containing up to a total of 6 carbon atoms. Furthermore, the aromatic structures that form the foundational building blocks of the larger PAHs were identified to be smaller single-ring and pericondensed aromatic species with repetitive structural features. For demonstrative purposes, details are provided for the CID of molecular ions at masses 202 and 434. Insights into the role of the aliphatically substituted and bridged aromatics in the reaction network of PAH growth chemistry were obtained from spatially resolved measurements of the flame. The experimental results are consistent with a growth mechanism in which alkylated aromatics are oxidized to form pericondensed ring structures or react and recombine with other aromatics to form larger, potentially three-dimensional, aliphatically bridged multicore aromatic hydrocarbons.

Exploration versus Exploitation in Global Atomistic Structure Optimization.

Abstract: 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 ...

Rapid Aqueous-Phase Hydrolysis of Ester Hydroperoxides Arising from Criegee Intermediates and Organic Acids.

Abstract: 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 1st-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 wit...

Role of Electron-Donating and Electron-Withdrawing Groups in Tuning the Optoelectronic Properties of Difluoroboron-Napthyridine Analogues.

Abstract: Five napthyridine-based fluorine-boron (BF2-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 BF2-napthyridine molecule has been interpreted. The optoelectronic properties, including absorption spectra and emission spectra of the BF2-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 BF2-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 found that introduction of an electron-donating group into the BF2-napthyridine complex improves the hole transport properties and provides useful clues in designing new materials for organic light emitting diodes (OLED). As a whole, this work demonstrates that electron-donating and electron-withdrawing groups in BF2 derivatives can extend their effectiveness toward designing of OLED materials, vitro cellular studies, ex vivo assays, and in vivo imaging agents.

Low-Temperature Oxidation of Ethylene by Ozone in a Jet-Stirred Reactor.

Abstract: 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 C2H4 + O3 adduct C2H4O3 is identified as a keto-hydroperoxide (hydroperoxy-acetaldehyde, HOOCH2CHO) 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 eV results in 5 ppm at atmospheric conditions, which decreases monotonically with temperature until 550 K. Other hydroperoxide species that contribute in larger amounts to the low-temperature oxidation of C2H4, like H2O2, CH3OOH, and C2H5OOH, are identified and their temperature-dependent mole fractions are reported. The experimental evidence for additional oxygenated species such as methanol, ketene, acetaldehyde, and hydroxy-acetaldehyde suggest multiple active oxidation routes. This experimental investigation closes the gap between ozonolysis at atmospheric and elevated temperature conditions and provides a database for future modeling.

Entangled Photonic-Nuclear Molecular Dynamics of LiF in Quantum Optical Cavities

Abstract: 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 1Σ potential energy curves (covalent-ionic diabatic crossing). Without field, after prompt excitation from the ground state 1 1Σ, the excited nuclear wave packet moves back and forth in the upper 2 1Σ state, but in the proximity of the avoided crossing, the nonadiabatic coupling transfers part of the nuclear wave packet to the lower 1 1Σ 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 Schrodinger equation by using the multiconfigurational time-dependent Hartree metho...

Ultrafast Transmission Modulation and Recovery via Vibrational Strong Coupling.

Abstract: 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 that the Rabi splitting recovers with the characteristic vibrational relaxation lifetime and anisotropy decay of uncoupled W(CO)6, implying that polaritons are not directly involved in the relaxation we observe after the first few ps. The results help corroborate the model that we proposed to describe the results at higher concentrations and show that the ground-state bleach of cavity-coupled molecules has a broad, multisigned spectral response.

Effect of Ammonia and Formic Acid on the OH• + HCl Reaction in the Troposphere: Competition between Single and Double Hydrogen Atom Transfer Pathways.

Abstract: Quantum chemical calculations at QCISD and CCSD(T) levels of theory have been performed to investigate the effect of NH3 and HCO2H on the reaction between OH• and HCl. Potential energy profiles indicate that both NH3 and HCO2H catalyzed reactions could proceed through two different channels, namely, single and double hydrogen atom transfer. Theoretically calculated rate constants for both the catalysts show that both NH3 and HCO2H catalyzed channels prefer a single hydrogen atom transfer path. Besides, both NH3 and HCO2H catalyzed paths have higher rate constant values as compared to that of the water catalyzed path.

Tailoring Photoisomerization Pathways in Donor-Acceptor Stenhouse Adducts: The Role of the Hydroxy Group.

Abstract: 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), 1H NMR in situ-irradiation studies at 213 K reveal that for nonhydroxy DASAs E–Z phot...

A 100 kHz Pulse Shaping 2D-IR Spectrometer Based on Dual Yb:KGW Amplifiers

Abstract: 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 robust...

Theoretical Investigation of the Reaction Mechanism of Photodeamination Induced by Excited-State Intramolecular Proton Transfer of Cresol Derivatives

Abstract: The novel photodeamination process of cresol derivatives 1 and 3 has been reported experimentally (J. Org. Chem. 2015, 80, 10817). However, a full theoretical interpretation of the mechanism is still lacking. In the present study, we aim to provide insight into the factors that promote the deamination reaction through density functional theory (DFT) and time-dependent DFT methods. Calculated absorption and emission spectra are in good agreement with the experimental results. Hydrogen-bond strengthening in the excited state has been verified by analyzing relevant bond parameters and vibrational frequencies as well as frontier molecular orbitals (FMOs), implying that hydrogen-bond interaction acts as the important parameter for the excited-state intramolecular proton-transfer (ESIPT) reaction. The proton-transfer and deamination reactions have been qualitatively analyzed through Gibbs free-energy reaction profiles in different electronic states. It can be concluded that the ESIPT and photodeamination reacti...

Effect of Mixing Ammonia and Alkylamines on Sulfate Aerosol Formation.

Abstract: 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 ar...

Quantum Chemical Calculation of pKas of Environmentally Relevant Functional Groups: Carboxylic Acids, Amines, and Thiols in Aqueous Solution

Abstract: Developing accurate quantum chemical approaches for calculating pKas 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 pK 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 pKas calculated with the original SMD model show errors of 6–10 pK units, and we traced these errors to inaccuracies in the solvation free energies of the anions. To improve the accuracy of pKas calculated with DFT and the SMD model, we developed a scaled solvent-accessible surf...

Hydration of Atmospheric Molecular Clusters: A New Method for Systematic Configurational Sampling

Abstract: 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 mo...

Resonance Raman Spectroscopy of Conducting Polypyrrole Nanotubes: Disordered Surface versus Ordered Body

Abstract: 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 co...

Large Davydov Splitting and Strong Fluorescence Suppression: An Investigation of Exciton Delocalization in DNA-Templated Holliday Junction Dye Aggregates

Abstract: 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 applic...