An excited state coupled-cluster study on indigo dyes

In the present study, the domain-based pair natural orbital implementation of the similarity-transformed equation of motion method is employed to reproduce the vibrationally resolved absorption spectra of indigo dyes. After an initial investigation of multireference, basis set and implicit solvent effects, our calculated 0–0 transition energies are compared to a benchmark set of experimental absorption band maxima. It is established that the agreement between our method and experimental results is well below the desired 0.1 eV threshold in virtually all cases and that the shift in excitation energies upon chemical substitution is also well reproduced. Finally, the entire spectra of some of the main components of the Tyrian purple dye mixture are reproduced and it is found that our computed spectra match the experimental ones without an empirical shift

A perturbative approach to multireference equation-of-motion coupled cluster

We introduce a variant of the multireference equation-of-motion coupled-cluster (MR-EOMCC) method where the amplitudes used for the similarity transformations are estimated from perturbation theory. Consequently, the new variant retains the many-body formalism, a reliance on at most two-body densities, and the state-universal character. As a non-iterative variant, computational costs are reduced, and no convergence difficulties with near-singular amplitudes can arise. Its performance was evaluated on several test sets covering transition metal atoms, small diatomics, and organic molecules against (near-)full CI quality reference data. We further highlight its efficacy on the weakly avoided crossing of LiF and place MR-EOMCC and the new variant into context with linear response theory. The accuracy of the variant was found to be at least on par with expectations for multireference perturbation theories, judging by the NEVPT2 method. The variant can be especially useful in multistate situations where the high accuracy of the iterative MR-EOMCC method is not required

Fragment-Based Local Coupled Cluster Embedding Approach for the Quantification and Analysis of Noncovalent Interactions: Exploring the Many-Body Expansion of the Local Coupled Cluster Energy

Herein, we introduce a fragment-based local coupled cluster embedding approach for the accurate quantification and analysis of noncovalent interactions in molecular aggregates. Our scheme combines two different expansions of the domain-based local pair natural orbital coupled cluster (DLPNO-CCSD(T)) energy: the many-body expansion (MBE) and the local energy decomposition (LED). The low-order terms in the MBE are initially computed in the presence of an environment that is treated at a low level of theory. Then, LED is used to decompose the energy of each term in the embedded MBE into additive fragment and fragment-pairwise contributions. This information is used to quantify the total energy of the system while providing at the same time in-depth insights into the nature and cooperativity of noncovalent interactions. Two different approaches are introduced and tested, in which the environment is treated at different levels of theory: the local coupled cluster in the Hartree–Fock (LCC-in-HF) method, in which the environment is treated at the HF level; and the electrostatically embedded local coupled cluster method (LCC-in-EE), in which the environment is replaced by point charges. Both schemes are designed to preserve as much as possible the accuracy of the parent local coupled cluster method for total energies, while being embarrassingly parallel and less memory intensive. These schemes appear to be particularly promising for the study of large and complex molecular aggregates at the coupled cluster level, such as condensed phase systems and protein–ligand interactions

Carbon Monoxide Binding to the Iron–Molybdenum Cofactor of Nitrogenase: a Detailed Quantum Mechanics/Molecular Mechanics Investigation

Carbon monoxide (CO) is a well-known inhibitor of nitrogenase activity. Under turnover conditions, CO binds to FeMoco, the active site of Mo nitrogenase. Time-resolved IR measurements suggest an initial terminal CO at 1904 cm–1 that converts to a bridging CO at 1715 cm–1, and an X-ray structure shows that CO can displace one of the bridging belt sulfides of FeMoco. However, the CO-binding redox state(s) of FeMoco (En) and the role of the protein environment in stabilizing specific CO-bound intermediates remain elusive. In this work, we carry out an in-depth analysis of the CO–FeMoco interaction based on quantum chemical calculations addressing different aspects of the electronic structure. (1) The local electronic structure of the Fe–CO bond is studied through diamagnetically substituted FeMoco. (2) A cluster model of FeMoco within a polarizable continuum illustrates how CO binding may affect the spin-coupling between the metal centers. (3) A QM/MM model incorporates the explicit influence of the amino acid residues surrounding FeMoco in the MoFe protein. The QM/MM model predicts both a terminal and a bridging CO in the E1 redox state. The scaled calculated CO frequencies (1922 and 1716 cm–1, respectively) are in good agreement with the experimentally observed IR bands supporting CO binding to the E1 state. Alternatively, an E2 state QM/MM model, which has the same atomic structure as the CO-bound X-ray structure, features a semi-bridging CO with a scaled calculated frequency (1718 cm–1) similar to the bridging CO in the E1 model

Outer-Sphere Contributions to the Electronic Structure of Type Zero Copper Proteins

Bioinorganic canon states that active-site thiolate coordination promotes rapid electron transfer (ET) to and from type 1 copper proteins. In recent work, we have found that copper ET sites in proteins also can be constructed without thiolate ligation (called “type zero” sites). Here we report multifrequency electron paramagnetic resonance (EPR), magnetic circular dichroism (MCD), and nuclear magnetic resonance (NMR) spectroscopic data together with density functional theory (DFT) and spectroscopy-oriented configuration interaction (SORCI) calculations for type zero Pseudomonas aeruginosa azurin variants. Wild-type (type 1) and type zero copper centers experience virtually identical ligand fields. Moreover, O-donor covalency is enhanced in type zero centers relative that in the C112D (type 2) protein. At the same time, N-donor covalency is reduced in a similar fashion to type 1 centers. QM/MM and SORCI calculations show that the electronic structures of type zero and type 2 are intimately linked to the orientation and coordination mode of the carboxylate ligand, which in turn is influenced by outer-sphere hydrogen bonding

Di- and Trinuclear Mixed-Valence Copper Amidinate Complexes from Reduction of Iodine

Molecular examples of mixed-valence copper complexes through chemical oxidation are rare but invoked in the mechanism of substrate activation, especially oxygen, in copper-containing enzymes. To examine the cooperative chemistry between two metals in close proximity to each other we began studying the reactivity of a dinuclear Cu(I) amidinate complex. The reaction of [(2,6-Me2C6H3N)2C(H)]2Cu2, 1, with I2 in tetrahydrofuran (THF), CH3CN, and toluene affords three new mixed-valence copper complexes [(2,6-Me2C6H3N)2C(H)]2Cu2(μ2-I3)(THF)2, 2, [(2,6-Me2C6H3N)2C(H)]2Cu2(μ2-I) (NCMe)2, 3, and [(2,6-Me2C6H3N)2C(H)]3Cu3(μ3-I)2, 4, respectively. The first two compounds were characterized by UV-vis and electron paramagnetic resonance spectroscopies, and their molecular structure was determined by X-ray crystallography. Both di- and trinuclear mixed-valence intermediates were characterized for the reaction of compound 1 to compound 4, and the molecular structure of 4 was determined by X-ray crystallography. The electronic structure of each of these complexes was also investigated using density functional theory

Structure–Spectroscopy Correlations for Intermediate Q of Soluble Methane Monooxygenase: Insights from QM/MM Calculations

The determination of the diiron core intermediate structures involved in the catalytic cycle of soluble methane monooxygenase (sMMO), the enzyme that selectively catalyzes the conversion of methane to methanol, has been a subject of intense interest within the bioinorganic scientific community. Particularly, the specific geometry and electronic structure of the intermediate that precedes methane binding, known as intermediate Q (or MMOHQ), has been debated for over 30 years. Some reported studies support a bis-μ-oxo-bridged Fe(IV)2O2 closed-core conformation Fe(IV)2O2 core, whereas others favor an open-core geometry, with a longer Fe–Fe distance. The lack of consensus calls for a thorough re-examination and reinterpretation of the spectroscopic data available on the MMOHQ intermediate. Herein, we report extensive simulations based on a hybrid quantum mechanics/molecular mechanics approach (QM/MM) approach that takes into account the complete enzyme to explore possible conformations for intermediates MMOHox and MMOHQ of the sMMOH catalytic cycle. High-level quantum chemical approaches are used to correlate specific structural motifs with geometric parameters for comparison with crystallographic and EXAFS data, as well as with spectroscopic data from Mössbauer spectroscopy, Fe K-edge high-energy resolution X-ray absorption spectroscopy (HERFD XAS), and resonance Raman 16O–18O difference spectroscopy. The results provide strong support for an open-core-type configuration in MMOHQ, with the most likely topology involving mono-oxo-bridged Fe ions and alternate terminal Fe-oxo and Fe-hydroxo groups that interact via intramolecular hydrogen bonding. The implications of an open-core intermediate Q on the reaction mechanism of sMMO are discussed

A little respect: four case studies of HCI’s disregard for other disciplines

HCI research often demonstrates lack of respect for other disciplines, evidenced by the way work from those disciplines are cited in CHI papers. We present 4 case studies that demonstrate; 1) that HCI researchers sometimes misunderstand and misrepresent work from other disciplines, and 2) how initial misrepresentations can become ‘accepted wisdom ’within HCI. This disregard for other disciplines leads to errors such as authors citing work to support ‘facts’ precisely opposite to those demonstrated by the cited literature. We conclude with recommendations for authors, editors, publishers and readers on how to reduce the risk of such failures

Electronic and Optical Properties of Eu²⁺-Activated Narrow-Band Phosphors for Phosphor-Converted Light-Emitting Diode Applications: Insights from a Theoretical Spectroscopy Perspective

In this work, we present a computational protocol that is able to predict the experimental absorption and emission spectral shapes of Eu2+-doped phosphors. The protocol is based on time-dependent density functional theory and operates in conjunction with an excited-state dynamics approach. It is demonstrated that across the study set consisting of representative examples of nitride, oxo-nitride, and oxide Eu2+-doped phosphors, the energy distribution and the band shape of the emission spectrum are related to the nature of the 4f–5d transitions that are probed in the absorption process. Since the 4f orbitals are very nearly nonbonding, the decisive quantity is the covalency of the 5d acceptor orbitals that become populated in the electronically excited state that leads to emission. The stronger the (anti) bonding interaction between the lanthanide and the ligands is in the excited state, the larger will be the excited state distortion. Consequently, the corresponding emission will get broader due to the vibronic progression that is induced by the structural distortion. In addition, the energy separation of the absorption bands that are dominated by states with valence 4f–5d and a metal to ligand charge transfer character defines a measure for the thermal quenching of the studied Eu2+-doped phosphors. Based on this analysis, simple descriptors are identified that show a strong correlation with the energy position and bandwidth of the experimental emission bands without the need for elaborate calculations. Overall, we believe that this study serves as an important reference for designing new Eu2+-doped phosphors with desired photoluminescence properties