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.

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.

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.

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).

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.

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 calculations of the absorption and emission spectra of Acd derivatives, which agree well with experimental measurements.

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.

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.

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

This corrects the article DOI: 10.1038/ja.2015.

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.

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.

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.

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.

Aogacillins A and B produced by Simplicillium sp. FKI-5985: new circumventors of arbekacin resistance in MRSA.

Aogacillins A and B, capable of overcoming arbekacin resistance in methicillin-resistant Staphylococcus aureus (MRSA), were isolated from a culture broth of Simplicillium sp. FKI-5985. Their structures were elucidated by NMR spectroscopic studies and ECD analyses.

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).

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.

A Density Functional with Spherical Atom Dispersion Terms.

A new hybrid density functional, APF, is introduced, which avoids the spurious long-range attractive or repulsive interactions that are found in most density functional theory (DFT) models. It therefore provides a sound baseline for the addition of an empirical dispersion correction term, which is developed from a spherical atom model (SAM). The APF-D empirical dispersion model contains nine adjustable parameters that were selected based on a very small training set (15 noble gas dimers and 4 small hydrocarbon dimers), along with two computed atomic properties (ionization potential and effective atomic polarizability) for each element.

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.

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.

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.

Unrestricted Coupled Cluster and Brueckner Doubles Variations of W1 Theory.

Unrestricted coupled cluster spin contamination corrected [UCCSD(T)] and unrestricted Brueckner doubles [UBD(T)] variations of the Weizmann-1 theory (W1), denoted as W1U, W1Usc, and W1BD, respectively, are compared with the restricted open-shell W1 theory [W1(RO)]. The performances of the four W1 variants are assessed with 220 total atomization energies, electron affinities, ionization potentials, and proton affinities in the G2/97 test set, for consistency with the error analysis of the original W1(RO) study. The root-mean-square deviations from the experiment of W1U (0.

Intramolecular Nonbonded Attractive Interactions: 1-Substituted Propenes.

Whereas cis-substituted alkenes are normally significantly less stable than the trans-isomers, there is a group of 1-substituted propenes (X = F, OMe, Cl, Br, SMe) where the cis-isomers are the more stable. The calculated structures show that there is steric repulsion with the cis-isomers. However, this is overcome by attractive Coulombic interactions when X = F or OMe and by attractive dispersive interactions when X = Cl or Br.

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.

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.