Showing papers in "Journal of Physical Chemistry A in 2017"

Extension of the ReaxFF Combustion Force Field toward Syngas Combustion and Initial Oxidation Kinetics

Abstract: 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 C3 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 ...

Resolving Transition Metal Chemical Space: Feature Selection for Machine Learning and Structure–Property Relationships

Abstract: 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 molecul...

Oxazine Ring-Related Vibrational Modes of Benzoxazine Monomers Using Fully Aromatically Substituted, Deuterated, 15N Isotope Exchanged, and Oxazine-Ring-Substituted Compounds and Theoretical Calculations

Abstract: 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–C2 stretching of the oxazine ring and the phenolic ring vibrational modes. Vibrational frequencies of 3-phenyl-3,4-dihydro-2H-benzo[e][1,3]oxazine (PH-a) and 3-(tert-butyl)-3,4-dihydro-2H-benzo[e][1,3]oxazine (PH-t) are compared with isotope-exchanged and all-substituted compounds. Deuterated benzoxazine monomers, 15N-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 CH2 in the O–CH2–N (2) and N–CH2–Ar (4) positions on the oxazine ring, or simultaneous deuteration of both positions. The chemical...

Importance of the Kinetic Energy Density for Band Gap Calculations in Solids with Density Functional Theory

Abstract: 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.

Natural Bond Orbitals and the Nature of the Hydrogen Bond

Abstract: 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.

Role of Capping Agent in Wet Synthesis of Nanoparticles.

Abstract: 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 ...

Ab Initio Computations and Active Thermochemical Tables Hand in Hand: Heats of Formation of Core Combustion Species

Abstract: 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 H2, CH4, H2O, and NH3 as references. Corrections for the complete-basis-set limit, higher-order excitations, anharmonic zero-point energy, core–valence, relativistic, and diago...

Formation Mechanisms of Naphthalene and Indene: From the Interstellar Medium to Combustion Flames

Abstract: 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 res...

Harmonic Vibrational Frequencies: Approximate Global Scaling Factors for TPSS, M06, and M11 Functional Families Using Several Common Basis Sets.

Abstract: 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.

Controlling Excited State Single versus Double Proton Transfer for 2,2'-Bipyridyl-3,3'-diol: Solvent Effect

Abstract: 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 (CHCl3)) to explore solvent effects on this system. Two intramolecular hydrogen bonds of BP(OH)2 are testified to be strengthened in the S1 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.

Efficient DLPNO–CCSD(T)-Based Estimation of Formation Enthalpies for C-, H-, O-, and N-Containing Closed-Shell Compounds Validated Against Critically Evaluated Experimental Data

Abstract: 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

Systematic Elucidation of Factors That Influence the Strength of Tetrel Bonds.

Abstract: Quantum calculations are used to examine the properties of heterodimers formed by a series of tetrel-containing molecules with NH3 as universal Lewis base. TH4 was taken as a starting point, with T = C, Si, Ge, and Sn. The H atoms were replaced by various numbers of F atoms—TH3F, TF3H, and TF4—so as to monitor the effects of adding electron-withdrawing substituents. Unsubstituted TH4 molecules form the weakest tetrel bonds, only up to about 2 kcal/mol. The bond is strengthened when the H opposite NH3 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 TH4 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 TF4 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. T...

The Many Facets of Chalcogen Bonding: Described by Vibrational Spectroscopy.

Abstract: 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 symm...

Excimer Formation and Symmetry-Breaking Charge Transfer in Cofacial Perylene Dimers

Abstract: 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 τCR = 72–85 ps to yield the excimer. The ...

Excited-State Decay Paths in Tetraphenylethene Derivatives.

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. Nonad...

Triplet Excited State of Bodipy Accessed by Charge Recombination and Its Application in Triplet-Triplet Annihilation Upconversion

Abstract: 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 (kCS = 2.2 × 1011 s–1 and 2 × 1012 s–1 for BDP-1 and BDP-2, respectively; kCR = 4.5 × 1010 and 1.5 × 1011 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 photoexci...

Mechanism of Photocatalytic Water Splitting with Graphitic Carbon Nitride: Photochemistry of the Heptazine-Water Complex.

Abstract: 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 H2, thereby regenerating two heptazine molecules. The proposed molecular photochemical reaction scheme within hy...

Direct Measurements of Unimolecular and Bimolecular Reaction Kinetics of the Criegee Intermediate (CH3)2COO

Abstract: The Criegee intermediate acetone oxide, (CH3)2COO, is formed by laser photolysis of 2,2-diiodopropane in the presence of O2 and characterized by synchrotron photoionization mass spectrometry and by cavity ring-down ultraviolet absorption spectroscopy. The rate coefficient of the reaction of the Criegee intermediate with SO2 was measured using photoionization mass spectrometry and pseudo-first-order methods to be (7.3 ± 0.5) × 10-11 cm3 s-1 at 298 K and 4 Torr and (1.5 ± 0.5) × 10-10 cm3 s-1 at 298 K and 10 Torr (He buffer). These values are similar to directly measured rate coefficients of anti-CH3CHOO with SO2, and in good agreement with recent UV absorption measurements. The measurement of this reaction at 293 K and slightly higher pressures (between 10 and 100 Torr) in N2 from cavity ring-down decay of the ultraviolet absorption of (CH3)2COO yielded even larger rate coefficients, in the range (1.84 ± 0.12) × 10-10 to (2.29 ± 0.08) × 10-10 cm3 s-1. Photoionization mass spectrometry measurements with deuterated acetone oxide at 4 Torr show an inverse deuterium kinetic isotope effect, kH/kD = (0.53 ± 0.06), for reactions with SO2, which may be consistent with recent suggestions that the formation of an association complex affects the rate coefficient. The reaction of (CD3)2COO with NO2 has a rate coefficient at 298 K and 4 Torr of (2.1 ± 0.5) × 10-12 cm3 s-1 (measured with photoionization mass spectrometry), again similar to rate for the reaction of anti-CH3CHOO with NO2. Cavity ring-down measurements of the acetone oxide removal without added reagents display a combination of first- and second-order decay kinetics, which can be deconvolved to derive values for both the self-reaction of (CH3)2COO and its unimolecular thermal decay. The inferred unimolecular decay rate coefficient at 293 K, (305 ± 70) s-1, is similar to determinations from ozonolysis. The present measurements confirm the large rate coefficient for reaction of (CH3)2COO with SO2 and the small rate coefficient for its reaction with water. Product measurements of the reactions of (CH3)2COO with NO2 and with SO2 suggest that these reactions may facilitate isomerization to 2-hydroperoxypropene, possibly by subsequent reactions of association products.

Spectroscopic Determination of Aerosol pH from Acid–Base Equilibria in Inorganic, Organic, and Mixed Systems

Abstract: 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–Huckel 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 (HNO3/NO3–, HC2O4–/C2O42–, CH3COOH/CH3COO–, and HCO3–/CO32–) 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 ...

Theoretical Investigation of an Excited-State Intramolecular Proton-Transfer Mechanism for an Asymmetric Structure of 3,7-Dihydroxy-4-oxo-2-phenyl-4H-chromene-8-carbaldehyde: Single or Double?

Abstract: 3,7-Dihydroxy-4-oxo-2-phenyl-4H-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 S0 state, and upon excitation, the two intramolecular hydrogen bonds were strengthened in the S1 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 S1 and S0 states can explain the proton-transfer process. In the...

Improved pKa Prediction of Substituted Alcohols, Phenols, and Hydroperoxides in Aqueous Medium Using Density Functional Theory and a Cluster-Continuum Solvation Model.

Abstract: Acid dissociation constants (pKa’s) are key physicochemical properties that are needed to understand the structure and reactivity of molecules in solution. Theoretical pKa’s have been calculated for a set of 72 organic compounds with −OH and −OOH groups (48 with known experimental pKa’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 pKa’s was assessed by including up to three water molecules. pKa’s calculated with only SMD implicit solvation are found to have average errors greater than 6 pKa units. Including one explicit water reduces the error by about 3 pKa 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...

Entangled Two Photon Absorption Cross Section on the 808 nm Region for the Common Dyes Zinc Tetraphenylporphyrin and Rhodamine B

Abstract: We report the measurement of the entangled two-photon absorption (ETPA) cross section, σE, 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 σE is measured for RhB. Additionally, we report a study of the dependence of σE 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.

Representing Global Reactive Potential Energy Surfaces Using Gaussian Processes.

Abstract: 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 3A″ state of SH2, which facilitates the SH + H ↔ S(3P) + H2 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 × 102) of ab initio points, but it needs substantially more points (∼1 × 103) to converge reaction probabilities. The implications of these observations for construction of potential energy surfaces are discussed.

Systematic Coupled Cluster Study of Noncovalent Interactions Involving Halogens, Chalcogens, and Pnicogens.

Abstract: 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.

Diamines Can Initiate New Particle Formation in the Atmosphere.

Abstract: 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...

Correlations between Structure and Near-Infrared Spectra of Saturated and Unsaturated Carboxylic Acids. Insight from Anharmonic Density Functional Theory Calculations.

Abstract: 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 ...

Density Functional Study of Neutral and Charged Silver Clusters Agn with n = 2–22. Evolution of Properties and Structure

Abstract: Geometries and electronic properties of neutral Agn, cationic Agn+, and anionic Agn– 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 Agn clusters, Ag8 and Ag18 show lowest polarizability due to closed-shell valence electron configurations 1S2/1P6 and 1S2/1P6/1D10. High stability of Ag8 is manifested in small dissociation energies of Ag9 to Ag8 plus Ag1 and Ag10 cluster to Ag8 plus Ag2. Cluster Ag20 with configuration 1S2/1P6/1D10/2S2 is stable due to low dissociation energy of Ag21 to Ag1 and Ag22 to Ag2. Cationic clusters with even n namely Ag10+ (9 valence electrons), Ag16+ (15 valence electrons), and Ag22+ (21 valence electrons) dissociate to Ag1 and closed-shell Ag9+ (1S2/1P6), Ag15+ (1S2/1D10/2S2) and Ag21+ (1S2/1P6/1D10/2S2). For odd n, Ag11+ and A...

Importance of R-CF3···O Tetrel Bonding Interactions in Biological Systems.

Abstract: 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 −CF3 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 −CF3 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.

Ammonia Catalyzed Formation of Sulfuric Acid in Troposphere: The Curious Case of a Base Promoting Acid Rain

Abstract: Electronic structure calculations have been performed to investigate the role of ammonia in catalyzing the formation of sulfuric acid through hydrolysis of SO3 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 SO3 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 ∼105–107 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...

DFT/TDDFT Study on the Sensing Mechanism of a Fluorescent Probe for Hydrogen Sulfide: Excited State Intramolecular Proton Transfer Coupled Twisted Intramolecular Charge Transfer.

Abstract: 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 potenti...