For the investigation of chemical reaction networks, the efficient and accurate determination of all relevant intermediates and elementary reactions is mandatory. The complexity of such a network may grow rapidly, in particular if... more
For the investigation of chemical reaction networks, the efficient and accurate determination of all relevant intermediates and elementary reactions is mandatory. The complexity of such a network may grow rapidly, in particular if reactive species are involved that might cause a myriad of side reactions. Without automation, a complete investigation of complex reaction mechanisms is tedious and possibly unfeasible. Therefore, only the expected dominant reaction paths of a chemical reaction network (e.g., a catalytic cycle or an enzymatic cascade) are usually explored in practice. Here, we present a computational protocol that constructs such networks in a parallelized and automated manner. Molecular structures of reactive complexes are generated based on heuristic rules derived from conceptual electronic-structure theory and subsequently optimized by quantum-chemical methods to produce stable intermediates of an emerging reaction network. Pairs of intermediates in this network that m...
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The inherently high computational cost of iterative self-consistent field (SCF) methods proves to be a critical issue delaying visual and haptic feedback in real-time quantum chemistry. In this work, we introduce two schemes for SCF... more
The inherently high computational cost of iterative self-consistent field (SCF) methods proves to be a critical issue delaying visual and haptic feedback in real-time quantum chemistry. In this work, we introduce two schemes for SCF acceleration. They provide a guess for the initial density matrix of the SCF procedure generated by extrapolation techniques. SCF optimizations then converge in fewer iterations, which decreases the execution time of the SCF optimization procedure. To benchmark the proposed propagation schemes, we developed a test bed for performing quantum chemical calculations on sequences of molecular structures mimicking real-time quantum chemical explorations. Explorations of a set of six model reactions employing the semi-empirical methods PM6 and DFTB3 in this testing environment showed that the proposed propagation schemes achieved speedups of up to 30% as a consequence of a reduced number of SCF iterations.
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Real-time feedback from iterative electronic structure calculations requires to mediate between the inherently unpredictable execution times of the iterative algorithm used and the necessity to provide data in fixed and short time... more
Real-time feedback from iterative electronic structure calculations requires to mediate between the inherently unpredictable execution times of the iterative algorithm used and the necessity to provide data in fixed and short time intervals for real-time rendering. We introduce the concept of a mediator as a component able to deal with infrequent and unpredictable reference data to generate reliable feedback. In the context of real-time quantum chemistry, the mediator takes the form of a surrogate potential that has the same local shape as the first-principles potential and can be evaluated efficiently to deliver atomic forces as real-time feedback. The surrogate potential is updated continuously by electronic structure calculations and guarantees to provide a reliable response to the operator for any molecular structure. To demonstrate the application of iterative electronic structure methods in real-time reactivity exploration, we implement self-consistent semiempirical methods as...
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We describe how to efficiently construct the quantum chemical Hamiltonian operator in matrix product form. We present its implementation as a density matrix renormalization group (DMRG) algorithm for quantum chemical applications.... more
We describe how to efficiently construct the quantum chemical Hamiltonian operator in matrix product form. We present its implementation as a density matrix renormalization group (DMRG) algorithm for quantum chemical applications. Existing implementations of DMRG for quantum chemistry are based on the traditional formulation of the method, which was developed from the point of view of Hilbert space decimation and attained higher performance compared to straightforward implementations of matrix product based DMRG. The latter variationally optimizes a class of ansatz states known as matrix product states, where operators are correspondingly represented as matrix product operators (MPOs). The MPO construction scheme presented here eliminates the previous performance disadvantages while retaining the additional flexibility provided by a matrix product approach, for example, the specification of expectation values becomes an input parameter. In this way, MPOs for different symmetries - abelian and non-abelian - and different relativistic and non-relativistic models may be solved by an otherwise unmodified program.
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DMSO-water mixtures exhibit a marked freezing point depression, reaching close to 60 K at n(DMSO) = 0.33. The phase diagram indicates that stable DMSO-water clusters may be responsible for this phenomenon. Using time-independent quantum... more
DMSO-water mixtures exhibit a marked freezing point depression, reaching close to 60 K at n(DMSO) = 0.33. The phase diagram indicates that stable DMSO-water clusters may be responsible for this phenomenon. Using time-independent quantum chemical methods, we investigate possible candidates for stable supermolecules at mole fractions n(DMSO) = 0.25 and 0.33. The model clusters are built by adding various numbers of water molecules to a single DMSO molecule. Structures and interaction energetics are discussed in the light of experimental and theoretical results from the literature. A comparison with results from molecular dynamics simulations is of particular interest. Our optimized structures are spatially very different from those previously identified through MD simulations. To identify the structural patterns characterizing the clusters, we classify them on the basis of hydrogen-acceptor interactions. These are well separated on an interaction energy scale. For the hydrophobic interactions of the methyl groups with water, attractive interactions of up to 8 kJ/mol are found. In forming clusters corresponding to a range of different mole fractions, up to four water molecules are added to each DMSO molecule. This corresponds to a rough local model of solvation. Examination of the trends in the interactions indicates that the methyl-water interaction becomes more important upon solvation. Finally, we investigate how the clusters interact and attempt to explain which role is played by the various structures and their intercluster interaction modes in the freezing behavior of DMSO-water.
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In this study, we investigate interference between several excited electronic states in resonance enhanced vibrational Raman optical activity (RROA) spectra. A gradient Franck-Condon model for the excited-state potential energy surface is... more
In this study, we investigate interference between several excited electronic states in resonance enhanced vibrational Raman optical activity (RROA) spectra. A gradient Franck-Condon model for the excited-state potential energy surface is applied in order to include vibronic effects in the description of the RROA intensities. Both sum-over-states and time-dependent expressions for the RROA intensities in case of close-lying excited states are given. As an example, we compare the calculated RROA and resonance Raman spectra of (S)-(+)-naproxen-OCD3 to the experimental ones. Subsequently, we examine the excitation profiles of (S)-(+)-naproxen and study the vibration at 1611 cm-1 in more detail in order to demonstrate how the consideration of a second excited electronic state can lead to significant changes in the RROA intensities.
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ABSTRACT
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We have studied transition metal clusters from a quantum information theory perspective using the density-matrix renormalization group (DMRG) method. We demonstrate the competition between entanglement and interaction localization. We... more
We have studied transition metal clusters from a quantum information theory perspective using the density-matrix renormalization group (DMRG) method. We demonstrate the competition between entanglement and interaction localization. We also discuss the application of the configuration interaction based dynamically extended active space procedure which significantly reduces the effective system size and accelerates the speed of convergence for complicated molecular electronic structures to a great extent. Our results indicate the importance of taking entanglement among molecular orbitals into account in order to devise an optimal orbital ordering and carry out efficient calculations on transition metal clusters. We propose a recipe to perform DMRG calculations in a black-box fashion and we point out the connections of our work to other tensor network state approaches.
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In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic... more
In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas-Kroll-Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm. Further, a module to run molecular dynamics simulations is added and two surface hopping algorithms are included to enable nonadiabatic calculations. Finally, we report on the subject of improvements with respects to alternative file options and parallelization. © 2015 Wiley Periodicals, Inc.
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The accurate description of spin-spin interactions in transition-metal cluster chemistry is a mandatory step to understanding and modelling the properties and reactivities of such systems. It cannot be achieved without a profound... more
The accurate description of spin-spin interactions in transition-metal cluster chemistry is a mandatory step to understanding and modelling the properties and reactivities of such systems. It cannot be achieved without a profound knowledge of the basic theory. Therefore, we provide in this review a survey from the most fundamental relativistic quantum chemical concepts and subsequent approximations towards conceptual problems such
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ABSTRACT In recent years, the calibration of parameters in approximate exchange-correlation density functionals was intensified by the proposition of diverse and increasingly unbiased reference datasets. It is, however, not obvious how... more
ABSTRACT In recent years, the calibration of parameters in approximate exchange-correlation density functionals was intensified by the proposition of diverse and increasingly unbiased reference datasets. It is, however, not obvious how sensitive the accuracy of a given functional is with respect to a small change of its parameters. Knowledge about this sensitivity would be desirable for the assessment of the general accuracy that can be expected for the calculation of a given observable—especially for notorious cases as found, for instance, in coordination chemistry. At the example of the well-known BP86 exchange-correlation functional, we investigate the dependence of the coordination energies in the WCCR10 reference set [Weymuth et al., J. Chem. Theory Comput. 2014, 10, 3092] on the empirical parameters of this density functional. The WCCR10 reactions were found to be a true challenge for contemporary density functionals. Here, we find that the parameter dependence is qualitatively the same for all reactions. This observation is important in view of the fact that the BP86 functional was never parametrized against transition-metal data. Still, within the parameter intervals investigated, the individual reaction energies vary significantly, which seems to suggest a reoptimization of the empirical parameters. However, it turns out that the overall description of all 10 reactions can be improved by only 9.5 kJ/mol, and therefore, such a reoptimization is not advisable. © 2014 Wiley Periodicals, Inc.
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ABSTRACT Within an inverse design approach applied to a nitrogen-fixation catalyst we discuss options for calculating “jacket” potentials that fulfill a purpose-oriented target requirement. As a target requirement we choose the vanishing... more
ABSTRACT Within an inverse design approach applied to a nitrogen-fixation catalyst we discuss options for calculating “jacket” potentials that fulfill a purpose-oriented target requirement. As a target requirement we choose the vanishing geometric gradients on all atoms of a subsystem consisting of a metal center binding the small molecule to be activated - in our case dinitrogen. The additional potential can be represented within a full quantum model or by a sequence of approximations of which a field of electrostatic point charges is the simplest. In order to analyze the feasibility of this approach, we dissect a known dinitrogen-fixating complex and analyze its ligand environment expressed by the “jacket” potential. It is discussed how this ligand-bypotential replacement can be generalized for future applications that eventually allow us to find a competitive synthetic nitrogen-fixation transition metal complex. It can be expected that such a ligand-by-potential replacement approach will be applicable to any type of host-guest chemical process.
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In this work, we present a transition-state optimization protocol based on the Mode-Tracking algorithm [Reiher and Neugebauer, J. Chem. Phys., 2003, 118, 1634]. By calculating only the eigenvector of interest instead of diagonalizing the... more
In this work, we present a transition-state optimization protocol based on the Mode-Tracking algorithm [Reiher and Neugebauer, J. Chem. Phys., 2003, 118, 1634]. By calculating only the eigenvector of interest instead of diagonalizing the full Hessian matrix and performing an eigenvector following search based on the selectively calculated vector, we can efficiently optimize transition-state structures. The initial guess structures and eigenvectors are either chosen from a linear interpolation between the reactant and product structures, from a nudged-elastic band search, from a constrained-optimization scan, or from the minimum-energy structures. Alternatively, initial guess vectors based on chemical intuition may be defined. We then iteratively refine the selected vectors by the Davidson subspace iteration technique. This procedure accelerates finding transition states for large molecules of a few hundred atoms. It is also beneficial in cases where the starting structure is very di...
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... Relativistic DouglasKrollHess theory. Markus Reiher. ... Email: Markus Reiher (markus.reiher@phys.chem.ethz.ch). *Correspondence: Markus Reiher, Laboratorium für Physikalische Chemie, ETH Zurich, Zurich, Switzerland. Publication... more
... Relativistic DouglasKrollHess theory. Markus Reiher. ... Email: Markus Reiher (markus.reiher@phys.chem.ethz.ch). *Correspondence: Markus Reiher, Laboratorium für Physikalische Chemie, ETH Zurich, Zurich, Switzerland. Publication History. ...
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We present calculations of Raman and Raman optical activity spectra of the carbohydrate molecule 1,6-anhydro-beta-D-glucopyranose. It is shown that a change from the chair to the boat conformation has a strong influence on the calculated... more
We present calculations of Raman and Raman optical activity spectra of the carbohydrate molecule 1,6-anhydro-beta-D-glucopyranose. It is shown that a change from the chair to the boat conformation has a strong influence on the calculated Raman optical activity intensities. Similar results are found for different rotamers of this molecule. In order to investigate solvent effects, we perform calculations with and without the continuum model COSMO. In addition, explicit solvation with water molecules is investigated, and is shown to significantly affect the calculated Raman optical activity spectrum. The final spectra are constructed by overlaps of spectra of single conformers leading to a good agreement with the experimental spectra.
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Oxygen activation at the active sites of [FeFe] hydrogenases has been proposed to be the initial step of irreversible oxygen-induced inhibition of these enzymes. On the basis of a first theoretical study into the thermodynamics of O2... more
Oxygen activation at the active sites of [FeFe] hydrogenases has been proposed to be the initial step of irreversible oxygen-induced inhibition of these enzymes. On the basis of a first theoretical study into the thermodynamics of O2 activation [Inorg. Chem. 2009, 48, 7127] we here investigate the kinetics of possible reaction paths at the distal iron atom of the active site by means of density functional theory. A sequence of steps is proposed to either form a reactive oxygen species (ROS) or fully reduce O2 to water. In this reaction cascade, two branching points are identified where water formation directly competes with harmful oxygen activation reactions. The latter are water formation by O-O bond cleavage of a hydrogen peroxide-bound intermediate competing with H2O2 dissociation and CO2 formation by a putative iron-oxo species competing with protonation of the iron-oxo species to form a hydroxyo ligand. Furthermore, we show that proton transfer to activated oxygen is fast and that proton supply to the active site is vital to prevent ROS dissociation. If sufficiently many reduction equivalents are available, oxygen activation reactions are accelerated, and oxygen reduction to water becomes possible.
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ABSTRACT In this theoretical study, the sensitivity of Fe4S4 cluster properties, such as potential energy, spin coupling, adiabatic detachment energy, inner-sphere reorganization energy, and reactivity, to structural distortions is... more
ABSTRACT In this theoretical study, the sensitivity of Fe4S4 cluster properties, such as potential energy, spin coupling, adiabatic detachment energy, inner-sphere reorganization energy, and reactivity, to structural distortions is investigated. [Fe4S4(SH)4]3−/2−/1− model clusters anchored by fixed hydrogen atoms are compared with Fe4S4 clusters coordinated by ethyl thiolates with fixations according to cysteine residues in crystal structures. For the model system, a dependence of the ground-state spin-coupling scheme on the hydrogen–hydrogen distances is observed. The minima of the potential energy surface of [Fe4S4(SH)4]2−/1− clusters are located at slightly smaller hydrogen–hydrogen distances than those of the [Fe4S4(SH)4]3− cluster. For inner-sphere reorganization energies the spin-coupling scheme adopted by the broken-symmetry wave function plays an important role, since it can change the reorganization energies by up to 13 kcal mol−1. For most structures, [Fe4S4(SR)4]2− and [Fe4S4(SR)4]1− (R=H or ethyl, derived from cysteine) favor the same coupling scheme. Therefore, the reorganization energies for this redox couple are relatively low (6–12 kcal mol−1) compared with the 2−/3− redox couple favoring different spin-coupling schemes before and after electron transfer (14–18 kcal mol−1). However, one may argue that more reliable reorganization energies are obtained if always the same spin-coupling pattern is enforced. All theoretical observations and insights are discussed in the light of experimental results distilled from the literature.
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ABSTRACT [FeFe] hydrogenases catalyse the reversible formation and oxidation of H2. They presumably feature a hydride species as a key intermediate. The H− ligand can either be bound between the iron atoms of the [2Fe]H subsite (μ-H) or... more
ABSTRACT [FeFe] hydrogenases catalyse the reversible formation and oxidation of H2. They presumably feature a hydride species as a key intermediate. The H− ligand can either be bound between the iron atoms of the [2Fe]H subsite (μ-H) or terminally to the distal iron atom of the active site (terminal-H). Although the μ-H species is thermodynamically most stable, experimental evidence points to the terminal-H species as the relevant intermediate. In order to understand these contradictory results, we investigate the catalytic cycle of [FeFe] hydrogenases (including transition states) with a special focus on the role of the two possible hydride intermediates. For this, density functional theory calculations were carried out for a large quantum mechanical active-site model. It is shown that formation of the μ-H intermediate is prohibited by high activation barriers which are caused by interactions of the H cluster with surrounding amino acids. We provide direct evidence for the anchoring of the H cluster in the protein to be decisive for the kinetic hindrance of μ-H formation.
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Vibrational spectroscopy of biomolecules like enzymes, nucleic acids, carbohydrates, lipids, and their components, is in most cases the vibrational spectroscopy of large molecules in aqueous solution or in vivo. Since large molecules in... more
Vibrational spectroscopy of biomolecules like enzymes, nucleic acids, carbohydrates, lipids, and their components, is in most cases the vibrational spectroscopy of large molecules in aqueous solution or in vivo. Since large molecules in solution are likely to yield conventional infrared (IR) and Raman spectra with many close-lying peaks, spectroscopic techniques which filter out information selectively are of special interest in
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... Syntheses of N-(Diphenylphosphanyl)-2-pyridylmethylamine and Its Use as a Ligand in Magnesium and Zinc Complexes Dirk Olberta, Alexander Kalischa, Nicole Herzera, Helmar Görlsa, Peter Mayerb, Lian Yuc, Markus Reiherc,*, and Matthias... more
... Syntheses of N-(Diphenylphosphanyl)-2-pyridylmethylamine and Its Use as a Ligand in Magnesium and Zinc Complexes Dirk Olberta, Alexander Kalischa, Nicole Herzera, Helmar Görlsa, Peter Mayerb, Lian Yuc, Markus Reiherc,*, and Matthias Westerhausena,* ...
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Page 1. ARTICLE DOI: 10.1002/zaac.200801328 Syntheses, Crystal Structure and Reactivity of Tin(II) Bis[N-(diphenylphos-phanyl)(2-pyridylmethyl)amide] Dirk Olbert,[a] Alexander Kalisch,[a] Helmar Görls,[a] Irina Malkin Ondik,[b] Markus... more
Page 1. ARTICLE DOI: 10.1002/zaac.200801328 Syntheses, Crystal Structure and Reactivity of Tin(II) Bis[N-(diphenylphos-phanyl)(2-pyridylmethyl)amide] Dirk Olbert,[a] Alexander Kalisch,[a] Helmar Görls,[a] Irina Malkin Ondik,[b] Markus Reiher,*[b] Matthias Westerhausen*[ ...
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... Abstract A unitary transformation allows to separate (block-diagonalize) the Dirac Hamiltonian into two parts: one part solely describes electrons, while the other gives rise to negative-energy states, which are the so-called... more
... Abstract A unitary transformation allows to separate (block-diagonalize) the Dirac Hamiltonian into two parts: one part solely describes electrons, while the other gives rise to negative-energy states, which are the so-called positronic states. ...
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In this study, we compute and analyze theoretical Raman optical activity spectra of large model β-sheets in order to identify reliable signatures for this important secondary structure element. We first review signatures that have already... more
In this study, we compute and analyze theoretical Raman optical activity spectra of large model β-sheets in order to identify reliable signatures for this important secondary structure element. We first review signatures that have already been proposed to be indicative of β-sheets. From these signatures, we find that only the couplet in the amide I region can be regarded as a truly reliable signature. In addition, we propose a strong negative peak at ∼1350 cm(-1) to be another good signature for parallel as well as antiparallel β-sheets. We study the robustness of these signatures with respect to perturbations induced by the amino acid side chains, the overall conformation of the sheet structure, and microsolvation. It is found that the latter effects can be very well understood and separated employing the concept of localized modes. Finally, we investigate whether Raman optical activity is capable of discriminating between parallel and antiparallel β-sheets. The amide III region turns out to be most promising for this purpose.
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By means of density functional theory, we investigate the catalytic cycle of active-site model complexes of [Fe] hydrogenase and study how ligand substitutions in the first coordination sphere of the reactive Fe center affect the... more
By means of density functional theory, we investigate the catalytic cycle of active-site model complexes of [Fe] hydrogenase and study how ligand substitutions in the first coordination sphere of the reactive Fe center affect the free-energy surface of the whole reaction pathway. Interestingly, dispersion interactions between the active site and the hydride acceptor MPT render the hydride transfer step less endergonic and lower its barrier. Substitution of CO by CN(-), which resembles [FeFe] hydrogenase-like coordination, inverts the elementary steps H(-) transfer and H2 cleavage. A simplified kinetic model reveals the specifics of the interplay between active-site composition and catalysis. Apparently, the catalytic efficiency of [Fe] hydrogenase can be attributed to a flat energy profile throughout the catalytic cycle. Intermediates that are too stable, as they occur, e.g., when one CO ligand is substituted by CN(-), significantly slow down the turnover rate of the enzyme. The catalytic activity of the wild-type form of the active-site model could, however, be enhanced by a PH3 ligand substitution of the CO ligand.
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Electronic structure theory faces many computational challenges in transition metal chemistry. Usually, density functional theory is the method of choice for theoretical studies on transition metal complexes and clusters mostly because it... more
Electronic structure theory faces many computational challenges in transition metal chemistry. Usually, density functional theory is the method of choice for theoretical studies on transition metal complexes and clusters mostly because it is the only feasible one, although its results are not systematically improvable. By contrast, multireference ab initio methods could provide a correct description of the electronic structure, but are limited to small molecules because of the tremendous computational resources required. In recent years, conceptually new ab initio methods emerged that turned out to be promising for theoretical coordination chemistry. We review and discuss two efficient parametrization schemes for the electronic wave function, the matrix product states and the complete-graph tensor network states. Their advantages are demonstrated at example transition metal complexes. Especially, tensor network states might provide the key to accurately describe strongly correlated and magnetic molecular systems in transition metal chemistry.