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Unraveling the similarity of the photoabsorption of deprotonated p-coumaric acid in the gas phase and within the photoactive yellow protein

Using advanced QM/MM methods, the surprisingly negligible shift of the lowest-lying bright electronic excitation of the deprotonated p-coumaric acid (pCA(-)) within the photoactive yellow protein (PYP) is shown to stem from a subtle balance between hypsochromic and bathochromic effects. More specifically, it is found that the change in the excitation energy as a consequence of the disruption of the planarity of pCA(-) inside PYP is nearly canceled out by the shift induced by the intermolecular interactions of the chromophore and the protein as a whole. These results provide important insights about the primary absorption and the tuning of the chromophore by the protein environment in PYP

Good Computational Practice in the Assignment of Absolute Configurations by TDDFT Calculations of ECD Spectra

Quantum-mechanical calculations of chiroptical properties have rapidly become the most popular method for assigning absolute configurations (AC) of organic compounds, including natural products. Black-box time-dependent Density Functional Theory (TDDFT) calculations of electronic circular dichroism (ECD) spectra are nowadays readily accessible to nonexperts. However, an uncritical attitude may easily deliver a wrong answer. We present to the Chirality Forum a discussion on what can be called good computational practice in running TDDFT ECD calculations, highlighting the most crucial points with several examples from the recent literature

Electronic absorption spectra of pyridine and nicotine in aqueous solution with a combined molecular dynamics and polarizable QM/MM approach

The electronic absorption spectra of pyridine and nicotine in aqueous solution have been computed using a multistep approach. The computational protocol consists in studying the solute solvation with accurate molecular dynamics simulations, characterizing the hydrogen bond interactions, and calculating electronic transitions for a series of configurations extracted from the molecular dynamics trajectories with a polarizable QM/MM scheme based on the fluctuating charge model. Molecular dynamics simulations and electronic transition calculations have been performed on both pyridine and nicotine. Furthermore, the contributions of solute vibrational effect on electronic absorption spectra have been taken into account in the so called vertical gradient approximation. \ua9 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc

The Dalton quantum chemistry program system

Dalton is a powerful general\u2010purpose program system for the study of molecular electronic structure at the Hartree\u2013Fock, Kohn\u2013Sham, multiconfigurational self\u2010consistent\u2010field, M\uf8ller\u2013Plesset, configuration\u2010interaction, and coupled\u2010cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic\u2010structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge\u2010origin\u2010invariant manner. Frequency\u2010dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one\u2010, two\u2010, and three\u2010photon processes. Environmental effects may be included using various dielectric\u2010medium and quantum\u2010mechanics/molecular\u2010mechanics models. Large molecules may be studied using linear\u2010scaling and massively parallel algorithms. Dalton is distributed at no cost from http://www.daltonprogram.org for a number of UNIX platform

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Using advanced QM/MM methods, the surprisingly negligible shift of the lowest-lying bright electronic excitation of the deprotonated p-coumaric acid (pCA À ) within the photoactive yellow protein (PYP) is shown to stem from a subtle balance between hypsochromic and bathochromic effects. More specifically, it is found that the change in the excitation energy as a consequence of the disruption of the planarity of pCA À inside PYP is nearly canceled out by the shift induced by the intermolecular interactions of the chromophore and the protein as a whole. These results provide important insights about the primary absorption and the tuning of the chromophore by the protein environment in PYP