Markus Reiher

Swiss Federal Institute of Technology (ETH), Laboratory of Physical Chemistry, Faculty Member

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Papers by Markus Reiher

Heuristics-Guided Exploration of Reaction Mechanisms

Journal of chemical theory and computation, Jan 8, 2015

For the investigation of chemical reaction networks, the efficient and accurate determination of ... 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...

Accelerating Wave Function Convergence in Interactive Quantum Chemical Reactivity Studies

Journal of chemical theory and computation, Jan 3, 2016

The inherently high computational cost of iterative self-consistent field (SCF) methods proves to... 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.

Real-time feedback from iterative electronic structure calculations

Journal of computational chemistry, Jan 17, 2015

Real-time feedback from iterative electronic structure calculations requires to mediate between t... 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...

An efficient matrix product operator representation of the quantum chemical Hamiltonian

The Journal of Chemical Physics, 2015

We describe how to efficiently construct the quantum chemical Hamiltonian operator in matrix prod... 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.

A Wavefunction-Based Criterion for the Detection of Intermolecular Interactions in Molecular Dynamics Simulations

The Journal of Physical Chemistry a, Apr 24, 2003

The availability of quantum mechanical wave functions in molecular dynamics simulations s for exa... more The availability of quantum mechanical wave functions in molecular dynamics simulations s for example in those of the Car-Parrinello type s offers the ability to analyze intermolecular interactions of a system in terms of quantum chemical descriptors. We demonstrate how standard population analyses can be utilized for a semiquantitative analysis of intermolecular interactions. The approach is therefore of particular value for the study of those systems for which geometric criteria and predefined interaction potentials have not yet been obtained. This is demonstrated for a DMSO-water mixture, for which the population-analysis criterion provides a simple measure for different interaction types, e.g., between water-oxygen and methyl-hydrogen atoms. In the case of a polypeptide, it is shown that the wave-function-based criterion provides insight into hydrogen bonding of the CdO groups with a hydrogen atom attached to a carbon atom from the peptide's backbone.

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The secret of dimethyl sulfoxide-water mixtures. A quantum chemical study of 1DMSO-nwater clusters

Journal of the American Chemical Society, May 29, 2002

DMSO-water mixtures exhibit a marked freezing point depression, reaching close to 60 K at n(DMSO)... 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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Enhancement and de-enhancement effects in vibrational resonance Raman optical activity

The Journal of Chemical Physics, Jan 28, 2010

In this study, we investigate interference between several excited electronic states in resonance... 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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Metal thiolate complexes binding molecular nitrogen under mild conditions: [μ-N2{Ru(P1Pr3)(N2Me2S2)}2], the first dinuclear example

Inorganica Chimica Acta, 2003

Binding N 2 to the metal sulfur cofactors of nitrogenase is considered the first step of biologic... more Binding N 2 to the metal sulfur cofactors of nitrogenase is considered the first step of biological N 2 fixation. In quest of lowmolecular weight complexes modeling this step [m-N 2 {Ru(P i Pr 3 )(N 2 Me 2 S 2 )} 2 ] (3) was synthesized and completely characterized. 2 )] (2) and N 2 at standard conditions (20 8C, 1 bar) such that the formation of 3 corresponds with a binding of molecular nitrogen to metal thiolate complex fragments under mild conditions, not requiring abiologically strong reductants. Complex 3 forms as racemate of (R ,R )-3 and (S ,S )-3 enantiomers which spontaneously separate upon crystallization and could both be characterized by X-ray crystallography. Complex 3 exhibits short bonds trans to the N 2 ligand, a n (N 2 ) frequency (2042 cm (1 ) low in comparison with that of 1 (2113 cm (1 ) and a non-linear [Ru Ã/N Å/N Ã/Ru] entity. The thiolate donors of 3 represent Broensted-basic sites for reversible protonations so that 3 becomes a complex suited for investigations aiming at the reduction of N 2 by nitrogenase-like coupled [2H ' /2e ( ] transfer steps. #

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Theoretical Raman Optical Activity Study of the β Domain of Rat Metallothionein

The Journal of Physical Chemistry B, 2010

ABSTRACT

Quantum information analysis of electronic states at different molecular structures

We have studied transition metal clusters from a quantum information theory perspective using the... 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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D: Relations for Pauli and Dirac Matrices

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B: Kinetic Energy in Generalized Coordinates

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Kerr gated resonance Raman study of tetracyclines and their complexes with divalent metal ions

Von der Natur lernen: Theorie der Stickstoff-Fixierung unter milden Bedingungen

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Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table

Journal of Computational Chemistry, 2015

In this report, we summarize and describe the recent unique updates and additions to the Molcas q... 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.

The Dirac Hydrogen Atom

Relativistic Quantum Chemistry, 2009

Spin Interactions in Cluster Chemistry

Advances in Inorganic Chemistry, 2010

The accurate description of spin-spin interactions in transition-metal cluster chemistry is a man... 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

New Benchmark Set of Transition-Metal Coordination Reactions for the Assessment of Density Functionals

Journal of Chemical Theory and Computation, 2014

We present the WCCR10 data set of ten ligand dissociation energies of large cationic transition m... more We present the WCCR10 data set of ten ligand dissociation energies of large cationic transition metal complexes for the assessment of approximate exchangecorrelation functionals. We analyze nine popular functionals, namely BP86, BP86-D3, B3LYP, B3LYP-D3, B97-D-D2, PBE, TPSS, PBE0, and TPSSh by mutual comparison and by comparison to experimental gas-phase data measured with wellknown precision. The comparison of all calculated data reveals a large, systemdependent scattering of results with nonnegligible consequences for computational chemistry studies on transition metal compounds. Considering further the comparison with experiment, the non-empirical functionals PBE and TPSS turn out to be among the best functionals for our reference data set. The deviation can be lowered further by including Hartree-Fock exchange. Accordingly, PBE0 and TPSSh are the two most accurate functionals for our test set, but also these functionals exhibit deviations from experiment by up to 50 kJ mol −1 for individual reactions. As an important result we found no functional to be reliable for all reactions. Furthermore, for some of the ligand dissociation energies studied in this work, dispersion corrections yield results which increase the deviation from experiment. This deviation increases further if structure optimization including dispersion corrections is performed. Finally, we compare our results to other benchmark studies and highlight that the performance assessed for different density functionals depends significantly on the reference molecule set chosen.

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Systematic dependence of transition-metal coordination energies on density-functional parametrizations

International Journal of Quantum Chemistry, 2014

ABSTRACT In recent years, the calibration of parameters in approximate exchange-correlation densi... 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.

Toward an Inverse Approach for the Design of Small-Molecule Fixating Catalysts

MRS Proceedings, 2013

ABSTRACT Within an inverse design approach applied to a nitrogen-fixation catalyst we discuss opt... 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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