The low-lying electronic states and ultrafast relaxation dynamics of the monomers and J-aggregates of meso-tetrakis (4-sulfonatophenyl)-porphyrins.

The electronic and vibrational spectra of the meso-tetrakis(4-sulfonatophenyl)-porphyrins (TSPP) have been studied computationally using the PFD-3B functional with time-dependent density functional theory for the excited states. The calculated UV-vis absorption and emission spectra in aqueous solution are in excellent agreement with the experimental measurements of both H2TSPP-4 (monomer) at high pH and H4TSPP-2 (forming J-aggregate) at low pH. Moreover, our calculations reveal an infrared absorption at 1900 cm-1 in the singlet and triplet excited states that is absent in the ground state, which is chosen as a probe for transient IR absorption spectroscopy to investigate the vibrational dynamics of the excited state. Specifically, the S2 to S1 excited state internal conversion process time, the S1 state vibrational relaxation time, and the lifetime of the S1 excited electronic state are all quantitatively deduced.

Improved Geometries and Frequencies with the PFD-3B DFT Method.

Bond lengths have been calculated for a test set of 120 diatomic species, including all homonuclear diatomics, hydrides, fluorides, and oxides for elements H through Kr for which experimental data is available for comparison. The performance of the PFD-3B functional is significantly better than competitive DFT methods. The rms error in bond lengths is reduced to 0.01 Å using a moderate size 3Za1Pa + f triple-ζ basis set, with the rms error in harmonic vibrational constants, ωe, equal to 38 cm-1. A very small 2ZP0H basis set is sufficient to calculate anharmonic constants, ωeXe, within ±4 cm-1. The rotational constants, Be, agree with experiment to within ±2%, and the vibration-rotation coupling constants, αe, agree within 10%. The calculated vibrational zero-point energy, ZPE, agrees with experiment to within ±0.06 kcal mol-1 for the diatomic test set, and the error increases to just ±0.11 kcal mol-1 for a set of 12 small polyatomic species. Comparison of a detailed anharmonic analysis of the twisted ethylene cation to the PFI-ZEKE experimental data illustrates the reliability of the PFD-3B for atypical structures.

Three-Body Dispersion Corrections to the Spherical Atom Model: The PFD-3B Density Functional.

The performance of the isotropic spherical atom model can be significantly enhanced through combination with anisotropic three-body dispersion interactions to give the new PFD-3B density functional, which reduces the mean absolute deviation (MAD) relative to CCSD(T)/CBS benchmark energies from 0.78 to 0.19 kcal/mol for the S22 test set. Comparison with the extended S22 × 5 test set in the figure indicates that this accuracy is maintained through large variations in geometry. The performance of the PFD-3B functional over the S22 × 5 test set is superior to any of the functionals previously applied to this set. Over the S22 set of examples, the MADs from the CCSD(T)/CBS values for Re, De, and ωe, are 0.032 Å, 0.21 kcal/mol, and 6 cm-1, respectively. Over a comparable set of 26 examples containing second and third row atoms, the MADs from the CCSD(T)/CBS values for Re, De, and ωe, are 0.033 Å, 0.19 kcal/mol, and 5 cm-1, respectively. If used to optimize the geometry of the 48 examples, on average the PFD-3B functional introduces an error of only 0.042 kcal/mol in CCSD(T) single-point energies. This small error combines with the reported analytical first and second derivatives to makes the PFD-3B functional an attractive model for geometry optimization and zero-point energy calculations.

UV Photolysis of Pyrazine and the Production of Hydrogen Isocyanide.

Photolysis of the diazine heterocycle, pyrazine, following irradiation at 308, 248, and 193 nm was examined using nanosecond time-resolved Fourier transform infrared emission spectroscopy. The resulting time-resolved IR emission spectra reveal that for 308 and 248 nm vibrationally highly excited pyrazine is produced, but no photolysis products were detected. However, at 193 nm excitation, the measured IR emission spectra consist solely of resonances originating from rovibrationally excited photofragments, including acetylene (HCCH), hydrogen cyanide (HCN), and hydrogen isocyanide (HNC), indicating that photofragmentation proceeds from vibrationally highly excited pyrazine on the ground electronic state. Spectral fit analysis of the time-resolved HCN and HNC IR emission band shapes and intensities allowed an estimate of the nascent product population distributions, from which a lower bound estimate of the HNC/HCN branching ratio was deduced as Φ ≥ 0.07. Additionally, ab initio calculations were performed in order to examine the propensity of photoinduced reactions on the ground- and lowest-energy excited-state surfaces. The calculations provide a basis for understanding the wavelength dependence of the UV photolysis of pyrazine, the photolytic production of HNC, and also explain previous experimental observations in the literature.

Core-core and core-valence correlation energy atomic and molecular benchmarks for Li through Ar.

We have established benchmark core-core, core-valence, and valence-valence absolute coupled-cluster single double (triple) correlation energies (±0.1%) for 210 species covering the first- and second-rows of the periodic table. These species provide 194 energy differences (±0.03 mEh) including ionization potentials, electron affinities, and total atomization energies. These results can be used for calibration of less expensive methodologies for practical routine determination of core-core and core-valence correlation energies.

A density functional for core-valence correlation energy.

A density functional, εCV-DFT(ρc, ρv), describing the core-valence correlation energy has been constructed as a linear combination of εLY P (corr)(ρc), εV WN5 (corr)(ρc, ρv), εPBE (corr)(ρc, ρv), εSlater (ex)(ρc, ρv), εHCTH (ex)(ρc, ρv), εHF (ex)(ρc, ρv), and FCV-DFTNi,Zi, a function of the nuclear charges. This functional, with 6 adjustable parameters, reproduces (±0.27 kcal/mol rms error) a benchmark set of 194 chemical energy changes including 9 electron affinities, 18 ionization potentials, and 167 total atomization energies covering the first- and second-rows of the periodic table. This is almost twice the rms error (±0.16 kcal/mol) obtained with CCSD(T)/MTsmall calculations, but less than half the rms error (±0.65 kcal/mol) obtained with MP2/GTlargeXP calculations, and somewhat smaller than the rms error (±0.39 kcal/mol) obtained with CCSD/MTsmall calculations. The largest positive and negative errors from εCV-DFT(ρc, ρv) were 0.88 and -0.75 kcal/mol with the set of 194 core-valence energy changes ranging from +3.76 kcal/mol for the total atomization energy of propyne to -9.05 kcal/mol for the double ionization of Mg. Evaluation of the εCV-DFT(ρc, ρv) functional requires less time than a single SCF iteration, and the accuracy is adequate for any model chemistry based on the CCSD(T) level of theory.

A computational study of RXHn X-H bond dissociation enthalpies.

Bond dissociation enthalpies can exhibit dramatic variations resulting from substituent effects. These variations result from changes in electronic structure that accompany bond dissociation. We have studied bond dissociation enthalpies (BDEs) at the W1BD level of theory for a series of RX-H compounds where X = CH2, NH, O, PH, and S. The substituents, R, included H, H3C, H2N, HO, F, H2P, HS, and Cl. The experimentally available BDEs were reproduced in a very satisfactory fashion. Most of the substituent effects could be related to a conjugative interaction in the two-center three-electron systems in the radicals formed by H abstraction. Comparisons of isoelectronic species demonstrate the important roles that variations in electronegativity and hybridization can play in determining BDEs. The OH and SH BDEs were linearly related, and the same was found with N-H and P-H BDEs. The relative effects of H2P and HS as substituents, in contrast to H2N and HO, could be related to the need to promote a 3s electron to 3p before H2P can participate in π-bonding. We must also include electronegativity differences to account for the observed transfer of a sulfur lone pair to an oxygen but the absence of the reverse process.

Substituent effects on O-H bond dissociation enthalpies: a computational study.

Bond dissociation enthalpies (BDEs) can exhibit dramatic variations resulting from substituent effects. The remarkable range of experimental OH bond dissociation enthalpies have been reproduced using CBS-APNO calculations with very good accuracy, so we have employed these calculations to extend the available BDE data. The effect on these BDEs of lone pairs on the atom adjacent to oxygen shows that conjugation in the product radicals is the most important interaction leading to the wide range of values. The BDE's were found to be linearly related to both the spin density at the radical center and to the change in X-O bond order in going from X-O-H to X-O·.

Evaluation of the heats of formation of corannulene and C60 by means of inexpensive theoretical procedures.

Inexpensive ab initio procedures that employ homologous sequences of isodesmic reactions for the calculation of enthalpies of formation of moderate-sized organic molecules were tested with benzene, naphthalene, phenanthrene, and triphenylene. Two size-consistent adjustable parameters were found to bring the calculated values within the uncertainty of the experimental values. These procedures were then applied to C20H10 (corannulene) and C60 (buckminsterfullerene). The results, specifically, Δ(f)H(298)(0)(C20H10) = 484 ± 4 kJ mol(-1) and Δ(f)H(298)(0)(C60) = 2531 ± 15 kJ mol(-1), are in excellent agreement with both the recent definitive W1h calculations of Karton et al. for corannulene [Δ(f)H(298)(0)(C20H10) = 485.2 ± 7.9 kJ mol(-1)] and their estimated value for buckminsterfullerene [Δ(f)H(298)(0)(C60) = 2521.6 ± 13.6 kJ mol(-1)] ( J. Phys. Chem. A 2013, 117, 1834-1842). We support their conclusion that the experimental values should be reexamined.

CCSD(T)/CBS atomic and molecular benchmarks for H through Ar.

We extrapolate to the coupled cluster single and double excitation and the perturbative triples (CCSD(T))/complete basis set (CBS) limit with a sequence of optimized n-tuple-ζ augmented polarization augmented (nZaPa) basis sets (n = 4, 5, 6, and 7) for 115 species representing the first two rows of the Periodic Table. The species include the entire set of atoms, positive and negative atomic ions, homonuclear diatomic molecules, and hydrides. The benchmark set also includes the rare gas dimers, polar molecules such as oxides and fluorides, and a few transition states for chemical reactions. The CCSD correlation energies agree with available CCSD-F12b/3C(FIX) values to within ±0.18 mEh root-mean-square (rms) deviation. The (T) components agree to within ±0.10 mEh and the total CCSD(T) correlation energies to within ±0.26 mEh or 0.1% rms deviation, which is probably the better measure, since the largest deviation is 0.43 mEh or 0.13%. These CBS limits can now be used as benchmarks to calibrate more approximate calculations using smaller basis sets. The sequence of basis sets provides data on convergence patterns for each component of the correlation energy.

A Bond-Energy/Bond-Order and Populations Relationship.

We report an analytical bond energy from bond orders and populations (BEBOP) model that provides intramolecular bond energy decompositions for chemical insight into the thermochemistry of molecules. The implementation reported here employs a minimum basis set Mulliken population analysis on well-conditioned Hartree-Fock orbitals to decompose total electronic energies into physically interpretable contributions. The model's parametrization scheme is based on atom-specific parameters for hybridization and atom pair-specific parameters for short-range repulsion and extended Hückel-type bond energy term fitted to reproduce CBS-QB3 thermochemistry data. The current implementation is suitable for molecules involving H, Li, Be, B, C, N, O, and F atoms, and it can be used to analyze intramolecular bond energies of molecular structures at optimized stationary points found from other computational methods. This first-generation model brings the computational cost of a Hartree-Fock calculation using a large triple-ζ basis set, and its atomization energies are comparable to those from widely used hybrid Kohn-Sham density functional theory (DFT, as benchmarked to 109 species from the G2/97 test set and an additional 83 reference species). This model should be useful for the community by interpreting overall ab initio molecular energies in terms of physically insightful bond energy contributions, e.g., bond dissociation energies, resonance energies, molecular strain energies, and qualitative energetic contributions to the activation barrier in chemical reaction mechanisms. This work reports a critical benchmarking of this method as well as discussions of its strengths and weaknesses compared to hybrid DFT (i.e., B3LYP, M062X, PBE0, and APF methods), and other cost-effective approximate Hamiltonian semiempirical quantum methods (i.e., AM1, PM6, PM7, and DFTB3).

Computational study of the properties and reactions of small molecules containing O, S, and Se.

The reactions and properties of a series of chalcogen-containing compounds (CH(3))(2)X and (CH(3))(2)C═X, where X = O, S, and Se, were studied computationally at the CBS-QB3 level to examine the differences among these molecules. The reactions and properties investigated include the double bond dissociation energy, the ionization potential, the interaction energies with a series of acids including a proton, CH(3)(+), Li(+), MeLi, and MeOH, and the enolization energies of the (CH(3))(2)C═X species. The effect of substituting the O of acetamide with S or Se also was studied. The changes that result from these reactions were examined via changes in structure and changes in charge distribution using the Hirshfeld charges.

Synthesis and characterization of fluorescent amino acid dimethylaminoacridonylalanine.

Fluorescent amino acids are powerful biophysical tools as they can be used in structural or imaging studies of a given protein without significantly perturbing its native fold or function. Here, we have synthesized and characterized 7-(dimethylamino)acridon-2-ylalanine (Dad), a red-shifted derivative of the genetically-incorporable amino acid, acridon-2-ylalanine. Alkylation increases the quantum yield and fluorescence lifetime of Dad relative to a previously published amino acid, 7-aminoacridon-2-ylalanine (Aad). These properties of Dad make it a potentially valuable protein label, and we have performed initial testing of its ability to be genetically incorporated using an evolved aminoacyl tRNA synthetase.

MP2/CBS atomic and molecular benchmarks for H through Ar.

We extrapolate to the MP2/CBS limit with a sequence of optimized n-tuple-zeta augmented polarized basis sets (n=4, 5, 6, and 7) for the entire set of 72 atoms, positive and negative atomic ions, homonuclear diatomic molecules, and hydrides representing the first two rows of the Periodic Table. The second-order correlation energies agree with accurate (+/-0.01 mE(h)) numerical values (He, Be, Ne, Mg, Ar, Zn(+2), and Kr) to within +/-0.1%. These MP2/CBS limits of the 72 species can now be used as benchmarks to calibrate more approximate calculations using smaller basis sets.

Uniformly convergent n-tuple-zeta augmented polarized (nZaP) basis sets for complete basis set extrapolations. I. Self-consistent field energies.

We present a sequence of n-tuple-zeta augmented polarized (nZaP) basis sets designed for extrapolations of both self-consistent field (SCF) and correlation energies to the complete basis set (CBS) limit. These nZaP basis sets (n=2-6) are formulated to give consistent errors throughout the Periodic Table (e.g., a consistent of approximately 1 mhartree/electron error for the 2ZaP SCF energy and a consistent of approximately 1.4 muhartree/electron error for the 6ZaP SCF energy). The SCF energy exhibits systematic convergence to the CBS limit: E(SCF)(nZaP) approximately E(SCF)(CBS)+Ae(-an). A single parameter, a=6.30, describes the 2ZaP through 6ZaP errors of H through Xe within 10%. The SCF rms basis set truncation errors of H through Xe are 33.5mE(h), 4.58mE(h), 0.82mE(h), 0.18mE(h), and 0.047mE(h) for 2ZaP, 3ZaP, 4ZaP, 5ZaP, and 6ZaP, respectively. Linear extrapolations of the (2,3)ZaP, (3,4)ZaP, (4,5)ZaP, and (5,6)ZaP calculations (all with a=6.30) reduce these errors by an order of magnitude to 0.24mE(h), 0.056mE(h), 0.020mE(h), and 0.005mE(h), respectively. A test set of 34 atoms, ions, and molecules gives similar results, and the associated test set of 25 chemical energy differences also gives comparable absolute accuracy. However, the cancellation of errors between reactant and product is lost by extrapolation. As a result, these chemical energy differences show a more modest two-to-fourfold improvement with extrapolation.

The CCSD(T) complete basis set limit for Ne revisited.

Recent estimates of the CCSD(T)(FC) limit for the neon atom (-128.8690+/-0.001 and -128.8687+/-0.0005 hartree) are refined. Re-examination of the basis set convergence of the separate self-consistent field, MP2-alphabeta, MP2-alphaalpha, CCSD-MP2, and (T) components of the valence CCSD(T) energy gives a complete basis set limit of -128.869 236+/-0.000 02 hartree. This can now be used as an improved benchmark to calibrate more approximate calculations.

Improving the Fluorescent Probe Acridonylalanine Through a Combination of Theory and Experiment.

Acridonylalanine (Acd) is a useful fluorophore for studying proteins by fluorescence spectroscopy, but it can potentially be improved by being made longer wavelength or brighter. Here, we report the synthesis of Acd core derivatives and their photophysical characterization. We also performed ab initio calculations of the absorption and emission spectra of Acd derivatives, which agree well with experimental measurements. The amino acid aminoacridonylalanine (Aad) was synthesized in forms appropriate for genetic incorporation and peptide synthesis. We show that Aad is a superior FRET acceptor to Acd in a peptide cleavage assay, and that Aad can be activated by an aminoacyl tRNA synthetase for genetic incorporation. Together, these results show that we can use computation to design enhanced Acd derivatives which can be used in peptides and proteins.

Corrigendum: Iminimycin A, the new iminium metabolite produced by Streptomyces griseus OS-3601.

This corrects the article DOI: 10.1038/ja.2015.142.

Corrigendum: γ-Ionylidene-type sesquiterpenoids possessing antimicrobial activity against Porphyromonas gingivalis from Phellinus linteus and their absolute structure determination.

This corrects the article DOI: 10.1038/ja.2017.35.

Iminimycin A, the new iminium metabolite produced by Streptomyces griseus OS-3601.

A new natural product, designated iminimycin A, was isolated from the cultured broth of a streptomycin-producing microbial strain, Streptomyces griseus OS-3601, via a physicochemical screening method using HP-20, silica gel and ODS column chromatographies and subsequent preparative HPLC. Iminimycin A is an indolizidine alkaloid, containing of an unusual iminium group and a cyclopropane ring with a triene side chain. The absolute configuration of iminimycin A was elucidated by NMR studies and electronic circular dichroism analysis. Iminimycin A shows anti-bacterial activity against Bacillus subtilis, Kocuria rhizophila and Xanthomonas campestris pv. orizae, and cytotoxic activity against HeLa S3 and Jurkat cells with IC50 values of 43 and 36 µM, respectively.