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Westarp S, Brandt F, Neumair L, Betz C, Dagane A, Kemper S, Jacob CR, Neubauer P, Kurreck A, Kaspar F. Nucleoside Phosphorylases make N7-xanthosine. Nat Commun 2024; 15:3625. [PMID: 38684649 PMCID: PMC11058261 DOI: 10.1038/s41467-024-47287-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 03/26/2024] [Indexed: 05/02/2024] Open
Abstract
Modern, highly evolved nucleoside-processing enzymes are known to exhibit perfect regioselectivity over the glycosylation of purine nucleobases at N9. We herein report an exception to this paradigm. Wild-type nucleoside phosphorylases also furnish N7-xanthosine, a "non-native" ribosylation regioisomer of xanthosine. This unusual nucleoside possesses several atypical physicochemical properties such as redshifted absorption spectra, a high equilibrium constant of phosphorolysis and low acidity. Ultimately, the biosynthesis of this previously unknown natural product illustrates how even highly evolved, essential enzymes from primary metabolism are imperfect catalysts.
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Affiliation(s)
- Sarah Westarp
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstrasse 76, 13355, Berlin, Germany
- BioNukleo GmbH, Ackerstraße 76, 13355, Berlin, Germany
| | - Felix Brandt
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106, Braunschweig, Germany
| | - Lena Neumair
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstrasse 76, 13355, Berlin, Germany
| | - Christina Betz
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstrasse 76, 13355, Berlin, Germany
| | - Amin Dagane
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstrasse 76, 13355, Berlin, Germany
| | - Sebastian Kemper
- Institute for Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106, Braunschweig, Germany
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstrasse 76, 13355, Berlin, Germany
| | - Anke Kurreck
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstrasse 76, 13355, Berlin, Germany.
- BioNukleo GmbH, Ackerstraße 76, 13355, Berlin, Germany.
| | - Felix Kaspar
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany.
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2
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Focke K, De Santis M, Wolter M, Martinez B JA, Vallet V, Pereira Gomes AS, Olejniczak M, Jacob CR. Interoperable workflows by exchanging grid-based data between quantum-chemical program packages. J Chem Phys 2024; 160:162503. [PMID: 38686818 DOI: 10.1063/5.0201701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/02/2024] [Indexed: 05/02/2024] Open
Abstract
Quantum-chemical subsystem and embedding methods require complex workflows that may involve multiple quantum-chemical program packages. Moreover, such workflows require the exchange of voluminous data that go beyond simple quantities, such as molecular structures and energies. Here, we describe our approach for addressing this interoperability challenge by exchanging electron densities and embedding potentials as grid-based data. We describe the approach that we have implemented to this end in a dedicated code, PyEmbed, currently part of a Python scripting framework. We discuss how it has facilitated the development of quantum-chemical subsystem and embedding methods and highlight several applications that have been enabled by PyEmbed, including wave-function theory (WFT) in density-functional theory (DFT) embedding schemes mixing non-relativistic and relativistic electronic structure methods, real-time time-dependent DFT-in-DFT approaches, the density-based many-body expansion, and workflows including real-space data analysis and visualization. Our approach demonstrates, in particular, the merits of exchanging (complex) grid-based data and, in general, the potential of modular software development in quantum chemistry, which hinges upon libraries that facilitate interoperability.
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Affiliation(s)
- Kevin Focke
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Matteo De Santis
- CNRS, UMR 8523-PhLAM-Physique des Lasers Atomes et Molécules, Univ. Lille, F-59000 Lille, France
| | - Mario Wolter
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Jessica A Martinez B
- CNRS, UMR 8523-PhLAM-Physique des Lasers Atomes et Molécules, Univ. Lille, F-59000 Lille, France
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, USA
| | - Valérie Vallet
- CNRS, UMR 8523-PhLAM-Physique des Lasers Atomes et Molécules, Univ. Lille, F-59000 Lille, France
| | | | - Małgorzata Olejniczak
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
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3
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Focke K, Jacob CR. Coupled-Cluster Density-Based Many-Body Expansion. J Phys Chem A 2023; 127:9139-9148. [PMID: 37871170 PMCID: PMC10626589 DOI: 10.1021/acs.jpca.3c04591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/25/2023]
Abstract
While CCSD(T) is often considered the "gold standard" of computational chemistry, the scaling of its computational cost as N7 limits its applicability for large and complex molecular systems. In this work, we apply the density-based many-body expansion [ Int. J. Quantum Chem. 2020, 120, e26228] in combination with CCSD(T). The accuracy of this approach is assessed for neutral, protonated, and deprotonated water hexamers, as well as (H2O)16 and (H2O)17 clusters. For the neutral water clusters, we find that already with a density-based two-body expansion, we are able to approximate the supermolecular CCSD(T) energies within chemical accuracy (4 kJ/mol). This surpasses the accuracy that is achieved with a conventional, energy-based three-body expansion. We show that this accuracy can be maintained even when approximating the electron densities using Hartree-Fock instead of using coupled-cluster densities. The density-based many-body expansion thus offers a simple, resource-efficient, and highly parallelizable approach that makes CCSD(T)-quality calculations feasible where they would otherwise be prohibitively expensive.
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Affiliation(s)
- Kevin Focke
- Institute of Physical and
Theoretical Chemistry, Technische Universität
Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Christoph R. Jacob
- Institute of Physical and
Theoretical Chemistry, Technische Universität
Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
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4
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Brüggemann J, Chekmeneva M, Wolter M, Jacob CR. Structural Dependence of Extended Amide III Vibrations in Two-Dimensional Infrared Spectra. J Phys Chem Lett 2023; 14:9257-9264. [PMID: 37812580 PMCID: PMC10591501 DOI: 10.1021/acs.jpclett.3c02662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 10/05/2023] [Indexed: 10/11/2023]
Abstract
Two-dimensional infrared (2D-IR) spectroscopy is a powerful experimental method for probing the structure and dynamics of proteins in aqueous solution. So far, most experimental studies have focused on the amide I vibrations, for which empirical vibrational exciton models provide a means of interpreting such experiments. However, such models are largely lacking for other regions of the vibrational spectrum. To close this gap, we employ an efficient quantum-chemical methodology for the calculation of 2D-IR spectra, which is based on anharmonic theoretical vibrational spectroscopy with localized modes. We apply this approach to explore the potential of 2D-IR spectroscopy in the extended amide III region. Using calculations for a dipeptide model as well as alanine polypeptides, we show that distinct 2D-IR cross-peaks in the extended amide III region can potentially be used to distinguish α-helix and β-strand structures. We propose that the extended amide III region could be a promising target for future 2D-IR experiments.
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Affiliation(s)
- Julia Brüggemann
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Maria Chekmeneva
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Mario Wolter
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Christoph R. Jacob
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany
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5
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Brandt F, Jacob CR. Protein network centralities as descriptor for QM region construction in QM/MM simulations of enzymes. Phys Chem Chem Phys 2023. [PMID: 37489261 DOI: 10.1039/d3cp02713a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
The construction of a suitable QM region is the most crucial step in setting up hybrid quantum mechanics/molecular mechanics (QM/MM) simulations for enzymatic reactions. The QM region should ideally include all important amino acids residues, while being as small as possible to save computational effort. Most available methods for systematic QM region construction are based either on the distance of single amino acids to the active site or on their electrostatic effect. Such approaches might miss non-electrostatic and long-range allosteric interactions. Here, we present a proof of concept study for the application of protein network analysis to tackle this problem. Specifically, we explore the use of the protein network centralities as descriptor for QM region construction. We find that protein network centralities, in particular the betweenness centrality, can be a useful descriptor for systematic QM region construction. We show that in combination with our previously developed point charge variation analysis, they can be used to identify important residues that are missed in purely electrostatic approaches.
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Affiliation(s)
- Felix Brandt
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany.
| | - Christoph R Jacob
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany.
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6
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Brandt F, Jacob CR. Efficient automatic construction of atom-economical QM regions with point-charge variation analysis. Phys Chem Chem Phys 2023; 25:14484-14495. [PMID: 37190855 DOI: 10.1039/d3cp01263h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The setup of QM/MM calculations is not trivial since many decisions have to be made by the simulation scientist to achieve reasonable and consistent results. The main challenge to be tackled is the construction of the QM region to make sure to take into account all important parts of the adjacent environment and exclude less important ones. In our previous work [F. Brandt and Ch. R. Jacob, Systematic QM Region Construction in QM/MM Calculations Based on Uncertainty Quantification, J. Chem. Theory Comput., 2022, 18, 2584-2596.], we introduced the point charge variation analysis (PCVA) as a simple and reliable tool to systematically construct QM regions based on the sensitivity of the reaction energy with respect to variations of the MM point charges. Here, we assess several simplified variants of this PCVA approach for the example of catechol O-methyltransferase and apply PCVA for another system, the triosephosphate isomerase. Furthermore, we extend its scope by applying it to a DNA system. Our results indicate that PCVA offers an efficient and versatile approach of the automatic construction of atom-economical QM regions, but also identify possible pitfalls and limitations.
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Affiliation(s)
- Felix Brandt
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany.
| | - Christoph R Jacob
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany.
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7
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Vornweg JR, Wolter M, Jacob CR. A simple and consistent quantum-chemical fragmentation scheme for proteins that includes two-body contributions. J Comput Chem 2023; 44:1634-1644. [PMID: 37171574 DOI: 10.1002/jcc.27114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 05/13/2023]
Abstract
The Molecular Fractionation with Conjugate Caps (MFCC) method is a popular fragmentation method for the quantum-chemical treatment of proteins. However, it does not account for interactions between the amino acid fragments, such as intramolecular hydrogen bonding. Here, we present a combination of the MFCC fragmentation scheme with a second-order many-body expansion (MBE) that consistently accounts for all fragment-fragment, fragment-cap, and cap-cap interactions, while retaining the overall simplicity of the MFCC scheme with its chemically meaningful fragments. We show that with the resulting MFCC-MBE(2) scheme, the errors in the total energies of selected polypeptides and proteins can be reduced by up to one order of magnitude and relative energies of different protein conformers can be predicted accurately.
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Affiliation(s)
- Johannes R Vornweg
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Mario Wolter
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
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8
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Kaspar F, Brandt F, Westarp S, Eilert L, Kemper S, Kurreck A, Neubauer P, Jacob CR, Schallmey A. Biased Borate Esterification during Nucleoside Phosphorylase‐Catalyzed Reactions: Apparent Equilibrium Shifts and Kinetic Implications. Angew Chem Int Ed Engl 2023. [DOI: 10.1002/ange.202218492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Felix Kaspar
- Technische Universität Braunschweig: Technische Universitat Braunschweig Biotechnology Spielmannstraße 7 38106 Braunschweig GERMANY
| | - Felix Brandt
- Technische Universität Braunschweig: Technische Universitat Braunschweig Institute of Phytical and Theoretical Chemistry Gaußsstraße 17 38106 Braunschweig GERMANY
| | - Sarah Westarp
- Technische Universität Berlin: Technische Universitat Berlin Chair of Bioprocess Engineering Ackerstraße 76 13355 Berlin GERMANY
| | - Lea Eilert
- Technische Universität Braunschweig: Technische Universitat Braunschweig Institute for Biochemistry, Biotechnology and Bioinformatics Spielmannstraße 7 38106 Braunschweig GERMANY
| | - Sebastian Kemper
- Technische Universität Berlin: Technische Universitat Berlin Institute for Chemistry Straße des 17. Juni 135 10623 Berlin GERMANY
| | - Anke Kurreck
- Technische Universität Berlin: Technische Universitat Berlin Chair of Bioprocess Engineering Ackerstraße 76 13355 Berlin GERMANY
| | - Peter Neubauer
- Technische Universität Berlin: Technische Universitat Berlin Chair of Bioprocess Engineering Ackerstraße 76 13355 Berlin GERMANY
| | - Christoph R. Jacob
- Technische Universität Braunschweig: Technische Universitat Braunschweig Institute of Phytical and Theoretical Chemistry Gaußsstraße 17 38106 Braunschweig GERMANY
| | - Anett Schallmey
- Technische Universität Braunschweig: Technische Universitat Braunschweig Institute for Biochemistry, Biotechnology and Bioinformatics Spielmannstraße 7 38106 Braunschweig GERMANY
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9
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Kaspar F, Brandt F, Westarp S, Eilert L, Kemper S, Kurreck A, Neubauer P, Jacob CR, Schallmey A. Biased Borate Esterification during Nucleoside Phosphorylase-Catalyzed Reactions: Apparent Equilibrium Shifts and Kinetic Implications. Angew Chem Int Ed Engl 2023; 62:e202218492. [PMID: 36655928 DOI: 10.1002/anie.202218492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/20/2023]
Abstract
Biocatalytic nucleoside (trans-)glycosylations catalyzed by nucleoside phosphorylases have evolved into a practical and convenient approach to the preparation of modified nucleosides, which are important pharmaceuticals for the treatment of various cancers and viral infections. However, the obtained yields in these reactions are generally determined exclusively by the innate thermodynamic properties of the nucleosides involved, hampering the biocatalytic access to many sought-after target nucleosides. We herein report an additional means for reaction engineering of these systems. We show how apparent equilibrium shifts in phosphorolysis and glycosylation reactions can be effected through entropically driven, biased esterification of nucleosides and ribosyl phosphates with inorganic borate. Our multifaceted analysis further describes the kinetic implications of this in situ reactant esterification for a model phosphorylase.
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Affiliation(s)
- Felix Kaspar
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany.,Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstraße 76, 13355, Berlin, Germany
| | - Felix Brandt
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106, Braunschweig, Germany
| | - Sarah Westarp
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstraße 76, 13355, Berlin, Germany.,BioNukleo GmbH, Ackerstraße 76, 13355, Berlin, Germany
| | - Lea Eilert
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany.,Present address: Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Sebastian Kemper
- Institute for Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Anke Kurreck
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstraße 76, 13355, Berlin, Germany.,BioNukleo GmbH, Ackerstraße 76, 13355, Berlin, Germany
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstraße 76, 13355, Berlin, Germany
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106, Braunschweig, Germany
| | - Anett Schallmey
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany
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10
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Brüggemann J, Wolter M, Jacob CR. Quantum-chemical calculation of two-dimensional infrared spectra using localized-mode VSCF/VCI. J Chem Phys 2022; 157:244107. [PMID: 36586972 DOI: 10.1063/5.0135273] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Computational protocols for the simulation of two-dimensional infrared (2D IR) spectroscopy usually rely on vibrational exciton models which require an empirical parameterization. Here, we present an efficient quantum-chemical protocol for predicting static 2D IR spectra that does not require any empirical parameters. For the calculation of anharmonic vibrational energy levels and transition dipole moments, we employ the localized-mode vibrational self-consistent field (L-VSCF)/vibrational configuration interaction (L-VCI) approach previously established for (linear) anharmonic theoretical vibrational spectroscopy [P. T. Panek and C. R. Jacob, ChemPhysChem 15, 3365-3377 (2014)]. We demonstrate that with an efficient expansion of the potential energy surface using anharmonic one-mode potentials and harmonic two-mode potentials, 2D IR spectra of metal carbonyl complexes and dipeptides can be predicted reliably. We further show how the close connection between L-VCI and vibrational exciton models can be exploited to extract the parameters of such models from those calculations. This provides a novel route to the fully quantum-chemical parameterization of vibrational exciton models for predicting 2D IR spectra.
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Affiliation(s)
- Julia Brüggemann
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Mario Wolter
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
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11
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Abstract
While QM/MM studies of enzymatic reactions are widely used in computational chemistry, the results of such studies are subject to numerous sources of uncertainty, and the effect of different choices by the simulation scientist that are required when setting up QM/MM calculations is often unclear. In particular, the selection of the QM region is crucial for obtaining accurate and reliable results. Simply including amino acids by their distance to the active site is mostly not sufficient as necessary residues are missing or unimportant residues are included without evidence. Here, we take a first step toward quantifying uncertainties in QM/MM calculations by assessing the sensitivity of QM/MM reaction energies with respect to variations of the MM point charges. We show that such a point charge variation analysis (PCVA) can be employed to judge the accuracy of QM/MM reaction energies obtained with a selected QM region and devise a protocol to systematically construct QM regions that minimize this uncertainty. We apply such a PCVA to the example of catechol O-methyltransferase and demonstrate that it provides a simple and reliable approach for the construction of the QM region. Our PCVA-based scheme is computationally efficient and requires only calculations for a system with a minimal QM region. Our work highlights the promise of applying methods of uncertainty quantification in computational chemistry.
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Affiliation(s)
- Felix Brandt
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstr. 17, 38106 Braunschweig, Germany
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstr. 17, 38106 Braunschweig, Germany
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12
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Schürmann S, Vornweg JR, Wolter M, Jacob CR. Accurate quantum-chemical fragmentation calculations for ion--water clusters with the density-based many-body expansion. Phys Chem Chem Phys 2022; 25:736-748. [DOI: 10.1039/d2cp04539g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The many-body expansion (MBE) provides an attractive fragmentation method for the efficient quantum-chemical treatment of molecular clusters. However, its convergence with the many-body order is generally slow for molecular clusters...
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13
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Kolb S, Petzold M, Brandt F, Jones PG, Jacob CR, Werz DB. Electrocatalytic Activation of Donor-Acceptor Cyclopropanes and Cyclobutanes: An Alternative C(sp 3 )-C(sp 3 ) Cleavage Mode. Angew Chem Int Ed Engl 2021; 60:15928-15934. [PMID: 33890714 PMCID: PMC8362004 DOI: 10.1002/anie.202101477] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 04/21/2021] [Indexed: 12/03/2022]
Abstract
We describe the first electrochemical activation of D-A cyclopropanes and D-A cyclobutanes leading after C(sp3 )-C(sp3 ) cleavage to the formation of highly reactive radical cations. This concept is utilized to formally insert molecular oxygen after direct or DDQ-assisted anodic oxidation of the strained carbocycles, delivering β- and γ-hydroxy ketones and 1,2-dioxanes electrocatalytically. Furthermore, insights into the mechanism of the oxidative process, obtained experimentally and by additional quantum-chemical calculations are presented. The synthetic potential of the reaction products is demonstrated by diverse derivatizations.
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Affiliation(s)
- Simon Kolb
- Technische Universität BraunschweigInstitute of Organic ChemistryHagenring 3038106BraunschweigGermany
| | - Martin Petzold
- Technische Universität BraunschweigInstitute of Organic ChemistryHagenring 3038106BraunschweigGermany
| | - Felix Brandt
- Technische Universität BraunschweigInstitute of Physical and Theoretical ChemistryGaußstraße 1738106BraunschweigGermany
| | - Peter G. Jones
- Technische Universität BraunschweigInstitute of Inorganic and Analytical ChemistryHagenring 3038106BraunschweigGermany
| | - Christoph R. Jacob
- Technische Universität BraunschweigInstitute of Physical and Theoretical ChemistryGaußstraße 1738106BraunschweigGermany
| | - Daniel B. Werz
- Technische Universität BraunschweigInstitute of Organic ChemistryHagenring 3038106BraunschweigGermany
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14
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Schmitt-Monreal D, Jacob CR. Density-Based Many-Body Expansion as an Efficient and Accurate Quantum-Chemical Fragmentation Method: Application to Water Clusters. J Chem Theory Comput 2021; 17:4144-4156. [PMID: 34196558 DOI: 10.1021/acs.jctc.1c00340] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Fragmentation methods based on the many-body expansion offer an attractive approach for the quantum-chemical treatment of large molecular systems, such as molecular clusters and crystals. Conventionally, the many-body expansion is performed for the total energy, but such an energy-based many-body expansion often suffers from a slow convergence with respect to the expansion order. For systems that show strong polarization effects such as water clusters, this can render the energy-based many-body expansion infeasible. Here, we establish a density-based many-body expansion as a promising alternative approach. By performing the many-body expansion for the electron density instead of the total energy and inserting the resulting total electron density into the total energy functional of density functional theory, one can derive a density-based energy correction, which in principle accounts for all higher-order polarization effects. Here, we systematically assess the accuracy of such a density-based many-body expansion for test sets of water clusters. We show that already a density-based two-body expansion is able to reproduce interaction energies per fragment within chemical accuracy and is able to accurately predict the energetic ordering as well as the relative interaction energies of different isomers of water clusters.
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Affiliation(s)
- Daniel Schmitt-Monreal
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstr. 17, 38106 Braunschweig, Germany
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstr. 17, 38106 Braunschweig, Germany
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15
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Kolb S, Petzold M, Brandt F, Jones PG, Jacob CR, Werz DB. Electrocatalytic Activation of Donor–Acceptor Cyclopropanes and Cyclobutanes: An Alternative C(sp
3
)−C(sp
3
) Cleavage Mode. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101477] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Simon Kolb
- Technische Universität Braunschweig Institute of Organic Chemistry Hagenring 30 38106 Braunschweig Germany
| | - Martin Petzold
- Technische Universität Braunschweig Institute of Organic Chemistry Hagenring 30 38106 Braunschweig Germany
| | - Felix Brandt
- Technische Universität Braunschweig Institute of Physical and Theoretical Chemistry Gaußstraße 17 38106 Braunschweig Germany
| | - Peter G. Jones
- Technische Universität Braunschweig Institute of Inorganic and Analytical Chemistry Hagenring 30 38106 Braunschweig Germany
| | - Christoph R. Jacob
- Technische Universität Braunschweig Institute of Physical and Theoretical Chemistry Gaußstraße 17 38106 Braunschweig Germany
| | - Daniel B. Werz
- Technische Universität Braunschweig Institute of Organic Chemistry Hagenring 30 38106 Braunschweig Germany
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16
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Wolter M, von Looz M, Meyerhenke H, Jacob CR. Systematic Partitioning of Proteins for Quantum-Chemical Fragmentation Methods Using Graph Algorithms. J Chem Theory Comput 2021; 17:1355-1367. [PMID: 33591754 DOI: 10.1021/acs.jctc.0c01054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quantum-chemical fragmentation methods offer an efficient approach for the treatment of large proteins, in particular if local target quantities such as protein-ligand interaction energies, enzymatic reaction energies, or spectroscopic properties of embedded chromophores are sought. However, the accuracy that is achievable for such local target quantities intricately depends on how the protein is partitioned into smaller fragments. While the commonly employed naı̈ve approach of using fragments with a fixed size is widely used, it can result in large and unpredictable errors when varying the fragment size. Here, we present a systematic partitioning scheme that aims at minimizing the fragmentation error of a local target quantity for a given maximum fragment size. To this end, we construct a weighted graph representation of the protein, in which the amino acids constitute the nodes. These nodes are connected by edges weighted with an estimate for the fragmentation error that is expected when cutting this edge. This allows us to employ graph partitioning algorithms provided by computer science to determine near-optimal partitions of the protein. We apply this scheme to a test set of six proteins representing various prototypical applications of quantum-chemical fragmentation methods using a simplified molecular fractionation with conjugate caps (MFCC) approach with hydrogen caps. We show that our graph-based scheme consistently improves upon the naı̈ve approach.
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Affiliation(s)
- Mario Wolter
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstrasse 17, 38106 Braunschweig, Germany
| | - Moritz von Looz
- Department of Computer Science, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Henning Meyerhenke
- Department of Computer Science, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstrasse 17, 38106 Braunschweig, Germany
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17
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Abstract
Applications of density-functional theory (DFT) in computational chemistry rely on an approximate exchange-correlation (xc) functional. However, existing approximations can fail dramatically for open-shell molecules, in particular for transition-metal complexes or radicals. Most importantly, predicting energy differences between different spin-states with approximate exchange-correlation functionals remains extremely challenging. Formally, it is known that the exact xc functional should be spin-state dependent, but none of the available approximations feature such an explicit spin-state dependence [C. R. Jacob and M. Reiher, Int. J. Quantum Chem., 2012, 112, 3661-3684]. Thus, to find novel approximations for the xc functional for open-shell systems, the development of spin-state dependent xc functionals appears to be a promising avenue. Here, we set out to shed light on the spin-state dependence of the xc functional by investigating the underlying xc holes, which we extract from configuration interaction calculations for model systems. We analyze the similarities and differences between the xc holes of the lowest-energy singlet and triplet states of the dihydrogen molecule, the helium atom, and the lithium dimer. To shed further light on the spin-state dependence of these xc holes we also discuss exact conditions that can be derived from the spin structure of the reduced two-electron density matrix. Altogether, our results suggest several possible routes towards the construction of explicitly spin-state dependent approximations for the xc functional.
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Affiliation(s)
- Julia Brüggemann
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany.
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18
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Brandenburg JG, Burke K, Cancio A, Erhard J, Fromager E, Ghosal A, Gidopoulos N, Gori-Giorgi P, Helgaker T, Hourahine B, Jacob CR, Kooi D, Maitra N, Mulay MR, Pernal K, Pribram-Jones A, Reining L, Romaniello P, Ryder MR, Savin A, Skylaris CK, Teale AM, Tozer D, Truhlar DG, Yang W. New density-functional approximations and beyond: general discussion. Faraday Discuss 2020; 224:166-200. [PMID: 33232402 DOI: 10.1039/d0fd90023k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Brandenburg JG, Burke K, Civalleri B, Cole DJ, Csányi G, David G, Gidopoulos NI, Gowland D, Helgaker T, Herbst MF, Hourahine B, Irons TJP, Jacob CR, Loos PF, Mehta N, Mulay MR, Neugebauer J, Pernal K, Pribram-Jones A, Romaniello P, Ryder MR, Savin A, Sirbu D, Skylaris CK, Truhlar DG, Wetherell J, Yang W. Challenges for large scale simulation: general discussion. Faraday Discuss 2020; 224:309-332. [PMID: 33227116 DOI: 10.1039/d0fd90024a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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De Santis M, Belpassi L, Jacob CR, Severo Pereira Gomes A, Tarantelli F, Visscher L, Storchi L. Environmental Effects with Frozen-Density Embedding in Real-Time Time-Dependent Density Functional Theory Using Localized Basis Functions. J Chem Theory Comput 2020; 16:5695-5711. [PMID: 32786918 PMCID: PMC8009524 DOI: 10.1021/acs.jctc.0c00603] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Indexed: 12/14/2022]
Abstract
Frozen-density embedding (FDE) represents a versatile embedding scheme to describe the environmental effect on electron dynamics in molecular systems. The extension of the general theory of FDE to the real-time time-dependent Kohn-Sham method has previously been presented and implemented in plane waves and periodic boundary conditions [Pavanello, M.; J. Chem. Phys. 2015, 142, 154116]. In the current paper, we extend our recent formulation of the real-time time-dependent Kohn-Sham method based on localized basis set functions and developed within the Psi4NumPy framework to the FDE scheme. The latter has been implemented in its "uncoupled" flavor (in which the time evolution is only carried out for the active subsystem, while the environment subsystems remain at their ground state), using and adapting the FDE implementation already available in the PyEmbed module of the scripting framework PyADF. The implementation was facilitated by the fact that both Psi4NumPy and PyADF, being native Python API, provided an ideal framework of development using the Python advantages in terms of code readability and reusability. We employed this new implementation to investigate the stability of the time-propagation procedure, which is based on an efficient predictor/corrector second-order midpoint Magnus propagator employing an exact diagonalization, in combination with the FDE scheme. We demonstrate that the inclusion of the FDE potential does not introduce any numerical instability in time propagation of the density matrix of the active subsystem, and in the limit of the weak external field, the numerical results for low-lying transition energies are consistent with those obtained using the reference FDE calculations based on the linear-response TDDFT. The method is found to give stable numerical results also in the presence of a strong external field inducing nonlinear effects. Preliminary results are reported for high harmonic generation (HHG) of a water molecule embedded in a small water cluster. The effect of the embedding potential is evident in the HHG spectrum reducing the number of the well-resolved high harmonics at high energy with respect to the free water. This is consistent with a shift toward lower ionization energy passing from an isolated water molecule to a small water cluster. The computational burden for the propagation step increases approximately linearly with the size of the surrounding frozen environment. Furthermore, we have also shown that the updating frequency of the embedding potential may be significantly reduced, much less than one per time step, without jeopardizing the accuracy of the transition energies.
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Affiliation(s)
- Matteo De Santis
- Dipartimento di
Chimica, Biologia e Biotecnologie, Università
degli Studi di Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
- Istituto di Scienze
e Tecnologie Chimiche (SCITEC), Consiglio Nazionale delle Ricerche
c/o Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Leonardo Belpassi
- Istituto di Scienze
e Tecnologie Chimiche (SCITEC), Consiglio Nazionale delle Ricerche
c/o Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Christoph R. Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstr. 17, 38106 Braunschweig, Germany
| | | | - Francesco Tarantelli
- Dipartimento di
Chimica, Biologia e Biotecnologie, Università
degli Studi di Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Lucas Visscher
- Theoretical Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Loriano Storchi
- Istituto di Scienze
e Tecnologie Chimiche (SCITEC), Consiglio Nazionale delle Ricerche
c/o Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
- Dipartimento di Farmacia, Università
degli Studi ‘G. D’Annunzio’, Via dei Vestini 31, 66100 Chieti, Italy
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21
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Saue T, Bast R, Gomes ASP, Jensen HJA, Visscher L, Aucar IA, Di Remigio R, Dyall KG, Eliav E, Fasshauer E, Fleig T, Halbert L, Hedegård ED, Helmich-Paris B, Iliaš M, Jacob CR, Knecht S, Laerdahl JK, Vidal ML, Nayak MK, Olejniczak M, Olsen JMH, Pernpointner M, Senjean B, Shee A, Sunaga A, van Stralen JNP. The DIRAC code for relativistic molecular calculations. J Chem Phys 2020; 152:204104. [PMID: 32486677 DOI: 10.1063/5.0004844] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
DIRAC is a freely distributed general-purpose program system for one-, two-, and four-component relativistic molecular calculations at the level of Hartree-Fock, Kohn-Sham (including range-separated theory), multiconfigurational self-consistent-field, multireference configuration interaction, electron propagator, and various flavors of coupled cluster theory. At the self-consistent-field level, a highly original scheme, based on quaternion algebra, is implemented for the treatment of both spatial and time reversal symmetry. DIRAC features a very general module for the calculation of molecular properties that to a large extent may be defined by the user and further analyzed through a powerful visualization module. It allows for the inclusion of environmental effects through three different classes of increasingly sophisticated embedding approaches: the implicit solvation polarizable continuum model, the explicit polarizable embedding model, and the frozen density embedding model.
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Affiliation(s)
- Trond Saue
- Laboratoire de Chimie et Physique Quantique, UMR 5626 CNRS-Université Toulouse III-Paul Sabatier, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Radovan Bast
- Department of Information Technology, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - André Severo Pereira Gomes
- Université de Lille, CNRS, UMR 8523-PhLAM-Physique des Lasers, Atomes et Molécules, F-59000 Lille, France
| | - Hans Jørgen Aa Jensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Lucas Visscher
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, NL-1081HV Amsterdam, The Netherlands
| | - Ignacio Agustín Aucar
- Instituto de Modelado e Innovación Tecnológica, CONICET, and Departamento de Física-Facultad de Ciencias Exactas y Naturales, UNNE, Avda. Libertad 5460, W3404AAS Corrientes, Argentina
| | - Roberto Di Remigio
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Kenneth G Dyall
- Dirac Solutions, 10527 NW Lost Park Drive, Portland, Oregon 97229, USA
| | - Ephraim Eliav
- School of Chemistry, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Elke Fasshauer
- Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000 Aarhus, Denmark
| | - Timo Fleig
- Laboratoire de Chimie et Physique Quantique, UMR 5626 CNRS-Université Toulouse III-Paul Sabatier, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Loïc Halbert
- Université de Lille, CNRS, UMR 8523-PhLAM-Physique des Lasers, Atomes et Molécules, F-59000 Lille, France
| | - Erik Donovan Hedegård
- Division of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Benjamin Helmich-Paris
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Miroslav Iliaš
- Department of Chemistry, Faculty of Natural Sciences, Matej Bel University, Tajovského 40, 974 01 Banská Bystrica, Slovakia
| | - Christoph R Jacob
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstr. 17, 38106 Braunschweig, Germany
| | - Stefan Knecht
- ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Jon K Laerdahl
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Marta L Vidal
- Department of Chemistry, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Malaya K Nayak
- Theoretical Chemistry Section, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Małgorzata Olejniczak
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
| | - Jógvan Magnus Haugaard Olsen
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | | | - Bruno Senjean
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, NL-1081HV Amsterdam, The Netherlands
| | - Avijit Shee
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Ayaki Sunaga
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji-city, Tokyo 192-0397, Japan
| | - Joost N P van Stralen
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, NL-1081HV Amsterdam, The Netherlands
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22
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Burkhardt L, Vukadinovic Y, Nowakowski M, Kalinko A, Rudolph J, Carlsson PA, Jacob CR, Bauer M. Electronic Structure of the Hieber Anion [Fe(CO) 3(NO)] - Revisited by X-ray Emission and Absorption Spectroscopy. Inorg Chem 2020; 59:3551-3561. [PMID: 32125149 DOI: 10.1021/acs.inorgchem.9b02092] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
While the Hieber anion [Fe(CO)3(NO)]- has been reincarnated in the last years as an active catalyst in organic synthesis, there is still a debate about the oxidation state of the central Fe atom and the resulting charge of the NO ligand. To shed new light on this question and to understand the Fe-NO interaction in the Hieber anion, it is investigated in comparison to the formal 3d8 reference Fe(CO)5 and the formal 3d10 reference [Fe(CO)4]2- by the combination of valence-to-core X-ray emission spectroscopy (VtC-XES), X-ray absorption near-edge structure spectroscopy (XANES), and high-energy-resolution fluorescence-detected XANES. In order to extract information about the electronic structure, time-dependent density functional theory and ground-state density functional theory calculations are applied. This combination of experimental and computational methods reveals that the electron density at the Fe center of the Hieber resembles that of the isoelectronic [Fe(CO)4]2-. These observations challenge recent descriptions of the Hieber anion and reopen the debate about the experimentally and computationally determined Fe oxidation state and charge on the NO ligand.
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Affiliation(s)
- Lukas Burkhardt
- Department of Chemistry and Center for Sustainable Systems Design, Paderborn University, Warburger Straße 100, 33098 Paderborn, Germany
| | - Yannik Vukadinovic
- Department of Chemistry and Center for Sustainable Systems Design, Paderborn University, Warburger Straße 100, 33098 Paderborn, Germany
| | - Michał Nowakowski
- Department of Chemistry and Center for Sustainable Systems Design, Paderborn University, Warburger Straße 100, 33098 Paderborn, Germany
| | - Aleksandr Kalinko
- Department of Chemistry and Center for Sustainable Systems Design, Paderborn University, Warburger Straße 100, 33098 Paderborn, Germany
| | - Julian Rudolph
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Per-Anders Carlsson
- Department of Chemistry and Chemical Engineering and Competence Centre for Catalysis, Chalmers University of Technology, 41296 Gothenburg, Sweden
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Matthias Bauer
- Department of Chemistry and Center for Sustainable Systems Design, Paderborn University, Warburger Straße 100, 33098 Paderborn, Germany
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23
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Drescher W, Schmitt-Monreal D, Jacob CR, Kleeberg C. [(Me3P)3Co(Bcat)3]: Equilibrium Oxidative Addition of a B–B Bond and Interconversion between the fac-Tris-Boryl and the mer-Tris-Boryl Complex. Organometallics 2020. [DOI: 10.1021/acs.organomet.9b00748] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wiebke Drescher
- Institut für Anorganische und Analytische Chemie, Technische Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
| | - Daniel Schmitt-Monreal
- Institut für Physikalische und Theoretische Chemie, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Christoph R. Jacob
- Institut für Physikalische und Theoretische Chemie, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Christian Kleeberg
- Institut für Anorganische und Analytische Chemie, Technische Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
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24
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Bergmann TG, Welzel MO, Jacob CR. Towards theoretical spectroscopy with error bars: systematic quantification of the structural sensitivity of calculated spectra. Chem Sci 2019; 11:1862-1877. [PMID: 34123280 PMCID: PMC8148348 DOI: 10.1039/c9sc05103a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Molecular spectra calculated with quantum-chemical methods are subject to a number of uncertainties (e.g., errors introduced by the computational methodology) that hamper the direct comparison of experiment and computation. Judging these uncertainties is crucial for drawing reliable conclusions from the interplay of experimental and theoretical spectroscopy, but largely relies on subjective judgment. Here, we explore the application of methods from uncertainty quantification to theoretical spectroscopy, with the ultimate goal of providing systematic error bars for calculated spectra. As a first target, we consider distortions of the underlying molecular structure as one important source of uncertainty. We show that by performing a principal component analysis, the most influential collective distortions can be identified, which allows for the construction of surrogate models that are amenable to a statistical analysis of the propagation of uncertainties in the molecular structure to uncertainties in the calculated spectrum. This is applied to the calculation of X-ray emission spectra of iron carbonyl complexes, of the electronic excitation spectrum of a coumarin dye, and of the infrared spectrum of alanine. We show that with our approach it becomes possible to obtain error bars for calculated spectra that account for uncertainties in the molecular structure. This is an important first step towards systematically quantifying other relevant sources of uncertainty in theoretical spectroscopy. Uncertainty quantification is applied in theoretical spectroscopy to obtain error bars accounting for the structural sensitivity of calculated spectra.![]()
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Affiliation(s)
- Tobias G Bergmann
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry Gaußstraße 17 38106 Braunschweig Germany
| | - Michael O Welzel
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry Gaußstraße 17 38106 Braunschweig Germany
| | - Christoph R Jacob
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry Gaußstraße 17 38106 Braunschweig Germany
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25
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Abstract
Efficient quantum-chemical methods that are able to describe intermolecular charge transfer are crucial for modeling organic semiconductors. However, the correct description of intermolecular charge transfer with density-functional theory (DFT) is hampered by the fractional charge error of approximate exchange-correlation (xc) functionals. Here, we investigate the charge transfer induced by an external electric field in a tetrathiafulvalene-tetracyanoquinodimethane (TTF-TCNQ) complex as a test case. For this seemingly simple model system, a supermolecular DFT treatment fails with most conventional xc functionals. Here, we present an extension of subsystem DFT to subsystems with a fractional number of electrons. We show that within such a framework, it becomes possible to overcome the fractional charge error by enforcing the correct dependence of each subsystem's total energy on the subsystem's fractional charge. Such a subsystem DFT approach allows for a correct description of the intermolecular charge transfer in the TTF-TCNQ model complex. The approach presented here can be generalized to larger molecular aggregates and will thus allow for modeling organic semiconductor materials accurately and efficiently.
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Affiliation(s)
- Anika Schulz
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstr. 17, 38106 Braunschweig, Germany
| | - Christoph R Jacob
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstr. 17, 38106 Braunschweig, Germany
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26
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Abstract
![]()
We
present the QMflows Python package for quantum chemistry workflow
automatization. QMflows allows users to write complex workflows in
terms of simple Python scripts. It supports the development of interoperable
workflows involving multiple quantum chemistry codes and executes
them efficiently on large scale parallel computers. This open source
library provides standardized interfaces to a number of quantum chemistry
packages and can be easily extended to accommodate additional codes.
QMflows features are described and illustrated with a number of representative
applications.
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Affiliation(s)
- Felipe Zapata
- Division of Theoretical Chemistry, Faculty of Science , Vrije Universiteit Amsterdam , de Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands.,Netherlands eScience Center , Science Park 140 (Matrix I) , 1098 XG Amsterdam , The Netherlands
| | - Lars Ridder
- Netherlands eScience Center , Science Park 140 (Matrix I) , 1098 XG Amsterdam , The Netherlands
| | - Johan Hidding
- Netherlands eScience Center , Science Park 140 (Matrix I) , 1098 XG Amsterdam , The Netherlands
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry , TU Braunschweig , Gaußstraße 17 , 38106 Braunschweig , Germany
| | - Ivan Infante
- Division of Theoretical Chemistry, Faculty of Science , Vrije Universiteit Amsterdam , de Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands.,Department of Nanochemistry , Istituto Italiano di Tecnologia , Via Morego 30 , 16163 Genova , Italy
| | - Lucas Visscher
- Division of Theoretical Chemistry, Faculty of Science , Vrije Universiteit Amsterdam , de Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
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27
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Rudolph J, Jacob CR. Computational Insights into the Mechanism of the Selective Catalytic Reduction of NO x : Fe- versus Cu-Exchanged Zeolite Catalysts. ACS Omega 2019; 4:7987-7993. [PMID: 31172035 PMCID: PMC6545547 DOI: 10.1021/acsomega.9b00600] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 04/02/2019] [Indexed: 06/09/2023]
Abstract
We computationally investigate the mechanism of the reduction half-cycle of the selective catalytic reduction of nitrogen oxides with ammonia. We compare both Fe- and Cu-exchanged zeolite catalysts and aim at exploring all accessible reaction pathways. From our calculations, a comprehensive picture emerges that unifies several previous mechanistic proposals. We find that both for Fe and for Cu catalysts different reaction pathways are feasible but some of the possible reaction pathways differ in these two cases. Our computational results provide a basis for the interpretation of in situ spectroscopic investigations that can possibly distinguish the different mechanistic pathways.
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28
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Solarczek J, Klünemann T, Brandt F, Schrepfer P, Wolter M, Jacob CR, Blankenfeldt W, Schallmey A. Position 123 of halohydrin dehalogenase HheG plays an important role in stability, activity, and enantioselectivity. Sci Rep 2019; 9:5106. [PMID: 30911023 PMCID: PMC6434027 DOI: 10.1038/s41598-019-41498-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 03/11/2019] [Indexed: 12/28/2022] Open
Abstract
HheG from Ilumatobacter coccineus is a halohydrin dehalogenase with synthetically useful activity in the ring opening of cyclic epoxides with various small anionic nucleophiles. This enzyme provides access to chiral β-substituted alcohols that serve as building blocks in the pharmaceutical industry. Wild-type HheG suffers from low thermostability, which poses a significant drawback for potential applications. In an attempt to thermostabilize HheG by protein engineering, several single mutants at position 123 were identified which displayed up to 14 °C increased apparent melting temperatures and up to three-fold higher activity. Aromatic amino acids at position 123 resulted even in a slightly higher enantioselectivity. Crystal structures of variants T123W and T123G revealed a flexible loop opposite to amino acid 123. In variant T123G, this loop adopted two different positions resulting in an open or partially closed active site. Classical molecular dynamics simulations confirmed a high mobility of this loop. Moreover, in variant T123G this loop adopted a position much closer to residue 123 resulting in denser packing and increased buried surface area. Our results indicate an important role for position 123 in HheG and give first structural and mechanistic insight into the thermostabilizing effect of mutations T123W and T123G.
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Affiliation(s)
- Jennifer Solarczek
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Thomas Klünemann
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Felix Brandt
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstr. 17, 38106, Braunschweig, Germany
| | - Patrick Schrepfer
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Mario Wolter
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstr. 17, 38106, Braunschweig, Germany
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstr. 17, 38106, Braunschweig, Germany
| | - Wulf Blankenfeldt
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Anett Schallmey
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany.
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29
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Panek PT, Hoeske AA, Jacob CR. On the choice of coordinates in anharmonic theoretical vibrational spectroscopy: Harmonic vs. anharmonic coupling in vibrational configuration interaction. J Chem Phys 2019; 150:054107. [PMID: 30736699 DOI: 10.1063/1.5083186] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
By a suitable choice of coordinates, the computational effort required for calculations of anharmonic vibrational spectra can be reduced significantly. By using suitable localized-mode coordinates obtained from an orthogonal transformation of the conventionally used normal-mode coordinates, anharmonic couplings between modes can be significantly reduced. However, such a transformation introduces harmonic couplings between the localized modes. To elucidate the role of these harmonic couplings, we consider the vibrational self-consistent field (VSCF)/vibrational configuration interaction (VCI) calculations for both few-mode model systems and for ethene as a molecular test case. We show that large harmonic couplings can result in significant errors in localized-mode L-VSCF/L-VCI calculations and study the convergence with respect to the size of the VCI excitation space. To further elucidate the errors introduced by harmonic couplings, we discuss the connection between L-VSCF/L-VCI and vibrational exciton models. With the help of our results, we propose an algorithm for the localization of normal modes in suitable subsets that are chosen to strictly limit the errors introduced by the harmonic couplings while still leading to maximally localized modes.
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Affiliation(s)
- Paweł T Panek
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Adrian A Hoeske
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Christoph R Jacob
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany
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Abstract
X-ray absorption spectroscopy (XAS) at the Cu K-edge is an important tool for probing the properties of copper centers in transition-metal chemistry and catalysis. However, the interpretation of experimental XAS spectra requires a detailed understanding of the dependence of spectroscopic features on the local geometric and electronic structure, which can be established by theoretical X-ray spectroscopy. Here, we present a systematic computational study of the Cu K-edge XAS spectra of selected Cu complexes based on time-dependent density-functional theory in combination with a molecular orbital analysis of the relevant transitions. For a series of Cu ammine model complexes as well as a comprehensive test set of 12 Cu(I) and 5 Cu(II) complexes, we revisit the dependence of the pre-edge region in Cu K-edge XAS spectra on oxidation state and coordination geometry. While our calculations confirm earlier experimental assignments, we can also reveal additional signatures of the ligand orbitals and identify the underlying orbital interactions. The comprehensive picture revealed by this study will provide a reliable basis for the interpretation of in situ Cu K-edge XAS spectra of catalytic intermediates.
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Affiliation(s)
- Julian Rudolph
- Institute of Physical and Theoretical Chemistry , TU Braunschweig , Gaußstraße 17 , 38106 Braunschweig , Germany
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry , TU Braunschweig , Gaußstraße 17 , 38106 Braunschweig , Germany
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31
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Reinartz I, Sinner C, Nettels D, Stucki-Buchli B, Stockmar F, Panek PT, Jacob CR, Nienhaus GU, Schuler B, Schug A. Simulation of FRET dyes allows quantitative comparison against experimental data. J Chem Phys 2018; 148:123321. [DOI: 10.1063/1.5010434] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Ines Reinartz
- Department of Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
- Steinbuch Centre for Computing, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Claude Sinner
- Department of Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
- Steinbuch Centre for Computing, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Brigitte Stucki-Buchli
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Florian Stockmar
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
| | - Pawel T. Panek
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Christoph R. Jacob
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Gerd Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
- HEiKA–Heidelberg Karlsruhe Research Partnership, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Nanotechnology and Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Department of Physics, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Alexander Schug
- Steinbuch Centre for Computing, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- John von Neumann Institute for Computing, Jülich Supercomputing Centre, Forschungszentrum Jülich, 52425 Jülich, Germany
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32
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Abstract
Anharmonic vibrational calculations can already be computationally demanding for relatively small molecules. The main bottlenecks lie in the construction of the potential energy surface and in the size of the excitation space in the vibrational configuration interaction (VCI) calculations. To address these challenges, we use localized-mode coordinates to construct potential energy surfaces and perform vibrational self-consistent field and L-VCI calculations [P. T. Panek and C. R. Jacob, ChemPhysChem 15, 3365 (2014)] for all vibrational modes of two prototypical test cases, the ethene and furan molecules. We find that the mutual coupling between modes is reduced when switching from normal-mode coordinates to localized-mode coordinates. When using such localized-mode coordinates, we observe a faster convergence of the n-mode expansion of the potential energy surface. This makes it possible to neglect higher-order contributions in the n-mode expansion of the potential energy surface or to approximate higher-order contributions in hybrid potential energy surfaces, which reduced the computational effort for the construction of the anharmonic potential energy surface significantly. Moreover, we find that when using localized-mode coordinates, the convergence with respect to the VCI excitation space proceeds more smoothly and that the error at low orders is reduced significantly. This makes it possible to devise low-cost models for obtaining a first approximation of anharmonic corrections. This demonstrates that the use of localized-mode coordinates can be beneficial already in anharmonic vibrational calculations of small molecules and provides a possible avenue for enabling such accurate calculations also for larger molecules.
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Affiliation(s)
- Paweł T Panek
- TU Braunschweig, Institute of Physical and Theoretical Chemistry, Hans-Sommer-Str. 10, 38106 Braunschweig, Germany
| | - Christoph R Jacob
- TU Braunschweig, Institute of Physical and Theoretical Chemistry, Hans-Sommer-Str. 10, 38106 Braunschweig, Germany
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33
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Schlüns D, Franchini M, Götz AW, Neugebauer J, Jacob CR, Visscher L. Analytical gradients for subsystem density functional theory within the slater-function-based amsterdam density functional program. J Comput Chem 2016; 38:238-249. [DOI: 10.1002/jcc.24670] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/14/2016] [Accepted: 10/19/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Danny Schlüns
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster; Corrensstraße 40 Münster 48149 Germany
| | - Mirko Franchini
- Amsterdam Center for Multiscale Modeling; Vrije Universiteit Amsterdam; De Boelelaan 1083 HV Amsterdam 1081 The Netherlands
- Scientific Computing & Modelling NV; Vrije Universiteit; Theoretical Chemistry, De Boelelaan 1083 HV Amsterdam 1081 The Netherlands
| | - Andreas W. Götz
- San Diego Supercomputer Center; University of California San Diego; 9500 Gilman Drive La Jolla, California 92093-0505 USA
| | - Johannes Neugebauer
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster; Corrensstraße 40 Münster 48149 Germany
| | - Christoph R. Jacob
- Institute of Physical and Theoretical Chemistry; TU Braunschweig, Hans-Sommer-Straße 10 Braunschweig 38106 Germany
| | - Lucas Visscher
- Amsterdam Center for Multiscale Modeling; Vrije Universiteit Amsterdam; De Boelelaan 1083 HV Amsterdam 1081 The Netherlands
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34
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Abstract
Because of the size of polypeptides and proteins, the quantum-chemical prediction of their vibrational spectra presents an exceptionally challenging task. Here, we address one of these challenges, namely, the inclusion of anharmonicities. By performing the expansion of the potential energy surface in localized-mode coordinates instead of the normal-mode coordinates, it becomes possible to calculate anharmonic vibrational spectra of polypeptides efficiently and reliably. We apply this approach to calculate the infrared, Raman, and Raman optical activity spectra of helical alanine polypeptides consisting of up to 20 amino acids. We find that while anharmonicities do not alter the band shapes, simple scaling procedures cannot account for the different shifts found for the individual bands. This closes an important gap in theoretical vibrational spectroscopy by making it possible to quantify the anharmonic contributions and opens the door to a first-principles calculation of multidimensional vibrational spectra.
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Affiliation(s)
- Paweł T Panek
- Institute of Physical and Theoretical Chemistry, TU Braunschweig , Hans-Sommer-Str. 10, 38106 Braunschweig, Germany
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, TU Braunschweig , Hans-Sommer-Str. 10, 38106 Braunschweig, Germany
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35
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Affiliation(s)
- Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, TU Braunschweig , Hans-Sommer-Straße 10, 38106 Braunschweig, Germany
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36
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Abstract
Contrary to previous claims, there is no formal need for enforcing external orthogonality in subsystem density-functional theory.
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Affiliation(s)
- Jan P. Unsleber
- Theoretische Organische Chemie
- Organisch-Chemisches Institut and Center for Multiscale Theory and Computation
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
| | - Johannes Neugebauer
- Theoretische Organische Chemie
- Organisch-Chemisches Institut and Center for Multiscale Theory and Computation
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
| | - Christoph R. Jacob
- Institute of Physical and Theoretical Chemistry
- TU Braunschweig
- 38106 Braunschweig
- Germany
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37
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von Looz M, Wolter M, Jacob CR, Meyerhenke H. Better Partitions of Protein Graphs for Subsystem Quantum Chemistry. Experimental Algorithms 2016. [DOI: 10.1007/978-3-319-38851-9_24] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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38
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Artiukhin DG, Jacob CR, Neugebauer J. Excitation energies from frozen-density embedding with accurate embedding potentials. J Chem Phys 2015; 142:234101. [DOI: 10.1063/1.4922429] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Denis G. Artiukhin
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
| | - Christoph R. Jacob
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Hans-Sommer-Straße 10, 38106 Braunschweig, Germany
| | - Johannes Neugebauer
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
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39
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Hofmann CH, Grobelny S, Panek PT, Heinen LKM, Wiegand AK, Plamper FA, Jacob CR, Winter R, Richtering W. Methanol-induced change of the mechanism of the temperature- and pressure-induced collapse of N
-Substituted acrylamide copolymers. ACTA ACUST UNITED AC 2015. [DOI: 10.1002/polb.23676] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Christian H. Hofmann
- Institute of Physical Chemistry, RWTH Aachen University; Landoltweg 2 52056 Aachen Germany
| | - Sebastian Grobelny
- Department of Chemistry and Chemical Biology; Physical Chemistry I, TU Dortmund University; Otto-Hahn-Straße 6 44227 Dortmund Germany
| | - Paweł T. Panek
- TU Braunschweig, Institute of Physical and Theoretical Chemistry; Hans-Sommer-Str. 10 38106 Braunschweig Germany
- Karlsruhe Institute of Technology (KIT), Institute of Physical Chemistry; Fritz-Haber-Weg 2 76131 Karlsruhe Germany
| | - Laura K. M. Heinen
- Institute of Physical Chemistry, RWTH Aachen University; Landoltweg 2 52056 Aachen Germany
| | - Ann-Kristin Wiegand
- Institute of Physical Chemistry, RWTH Aachen University; Landoltweg 2 52056 Aachen Germany
| | - Felix A. Plamper
- Institute of Physical Chemistry, RWTH Aachen University; Landoltweg 2 52056 Aachen Germany
| | - Christoph R. Jacob
- TU Braunschweig, Institute of Physical and Theoretical Chemistry; Hans-Sommer-Str. 10 38106 Braunschweig Germany
| | - Roland Winter
- Department of Chemistry and Chemical Biology; Physical Chemistry I, TU Dortmund University; Otto-Hahn-Straße 6 44227 Dortmund Germany
| | - Walter Richtering
- Institute of Physical Chemistry, RWTH Aachen University; Landoltweg 2 52056 Aachen Germany
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40
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Abstract
We apply high-energy-resolution fluorescence-detected (HERFD) X-ray absorption near-edge structure (XANES) spectroscopy to study iron carbonyl complexes.
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Affiliation(s)
- Andrew J. Atkins
- Karlsruhe Institute of Technology (KIT)
- Center for Functional Nanostructures and Institute of Physical Chemistry
- 76131 Karlsruhe
- Germany
| | - Matthias Bauer
- Universität Paderborn
- Naturwissenschaftliche Fakultät
- Department Chemie
- 33098 Paderborn
- Germany
| | - Christoph R. Jacob
- Karlsruhe Institute of Technology (KIT)
- Center for Functional Nanostructures and Institute of Physical Chemistry
- 76131 Karlsruhe
- Germany
- TU Braunschweig
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41
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Günter T, Carvalho HWP, Doronkin DE, Sheppard T, Glatzel P, Atkins AJ, Rudolph J, Jacob CR, Casapu M, Grunwaldt JD. Structural snapshots of the SCR reaction mechanism on Cu-SSZ-13. Chem Commun (Camb) 2015; 51:9227-30. [DOI: 10.1039/c5cc01758k] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structure of copper sites in Cu-SSZ-13 during NH3-SCR was unravelled by a combination of novel operando X-ray spectroscopic techniques.
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Affiliation(s)
- Tobias Günter
- Institute for Chemical Technology and Polymer Chemistry (ITCP)
- Karlsruhe Institute of Technology
- D-76131 Karlsruhe
- Germany
| | - Hudson W. P. Carvalho
- Institute for Chemical Technology and Polymer Chemistry (ITCP)
- Karlsruhe Institute of Technology
- D-76131 Karlsruhe
- Germany
| | - Dmitry E. Doronkin
- Institute for Chemical Technology and Polymer Chemistry (ITCP)
- Karlsruhe Institute of Technology
- D-76131 Karlsruhe
- Germany
- Institute of Catalysis Research and Technology (IKFT)
| | - Thomas Sheppard
- Institute for Chemical Technology and Polymer Chemistry (ITCP)
- Karlsruhe Institute of Technology
- D-76131 Karlsruhe
- Germany
| | - Pieter Glatzel
- European Synchrotron Radiation Facility
- F-38043 Grenoble Cedex
- France
| | - Andrew J. Atkins
- Center for Functional Nanostructures and Institute of Physical Chemistry
- Karlsruhe Institute of Technology
- D-76131 Karlsruhe
- Germany
| | - Julian Rudolph
- Institute of Physical and Theoretical Chemistry
- D-38106 Braunschweig
- Germany
| | - Christoph R. Jacob
- Center for Functional Nanostructures and Institute of Physical Chemistry
- Karlsruhe Institute of Technology
- D-76131 Karlsruhe
- Germany
- Institute of Physical and Theoretical Chemistry
| | - Maria Casapu
- Institute for Chemical Technology and Polymer Chemistry (ITCP)
- Karlsruhe Institute of Technology
- D-76131 Karlsruhe
- Germany
| | - Jan-Dierk Grunwaldt
- Institute for Chemical Technology and Polymer Chemistry (ITCP)
- Karlsruhe Institute of Technology
- D-76131 Karlsruhe
- Germany
- Institute of Catalysis Research and Technology (IKFT)
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42
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Krauter CM, Schirmer J, Jacob CR, Pernpointner M, Dreuw A. Plasmons in molecules: Microscopic characterization based on orbital transitions and momentum conservation. J Chem Phys 2014; 141:104101. [DOI: 10.1063/1.4894266] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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43
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Boubnov A, Carvalho HWP, Doronkin DE, Günter T, Gallo E, Atkins AJ, Jacob CR, Grunwaldt JD. Selective Catalytic Reduction of NO Over Fe-ZSM-5: Mechanistic Insights by Operando HERFD-XANES and Valence-to-Core X-ray Emission Spectroscopy. J Am Chem Soc 2014; 136:13006-15. [DOI: 10.1021/ja5062505] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Alexey Boubnov
- Institute
for Chemical Technology and Polymer Chemistry, Karlsruhe Institute of Technology, Engesserstr. 20, D-76131 Karlsruhe, Germany
- Institute
of Catalysis Research and Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Hudson W. P. Carvalho
- Institute
for Chemical Technology and Polymer Chemistry, Karlsruhe Institute of Technology, Engesserstr. 20, D-76131 Karlsruhe, Germany
| | - Dmitry E. Doronkin
- Institute
for Chemical Technology and Polymer Chemistry, Karlsruhe Institute of Technology, Engesserstr. 20, D-76131 Karlsruhe, Germany
- Institute
of Catalysis Research and Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Tobias Günter
- Institute
for Chemical Technology and Polymer Chemistry, Karlsruhe Institute of Technology, Engesserstr. 20, D-76131 Karlsruhe, Germany
| | - Erik Gallo
- European Synchrotron Radiation Facility, 6 rue Jules Horowitz, BP 220, F-38043 Grenoble Cedex, France
| | - Andrew J. Atkins
- Center
for Functional Nanostructures and Institute of Physical Chemistry, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1a, D-76131 Karlsruhe, Germany
| | - Christoph R. Jacob
- Center
for Functional Nanostructures and Institute of Physical Chemistry, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1a, D-76131 Karlsruhe, Germany
| | - Jan-Dierk Grunwaldt
- Institute
for Chemical Technology and Polymer Chemistry, Karlsruhe Institute of Technology, Engesserstr. 20, D-76131 Karlsruhe, Germany
- Institute
of Catalysis Research and Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
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44
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Affiliation(s)
- Christoph R. Jacob
- Center for Functional Nanostructures and Institute of Physical Chemistry; Karlsruhe Institute of Technology (KIT); Karlsruhe Germany
| | - Johannes Neugebauer
- Theoretische Organische Chemie, Organisch-Chemisches Institut; Westfälische Wilhelms-Universität Münster; Münster Germany
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45
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Panek PT, Jacob CR. Efficient calculation of anharmonic vibrational spectra of large molecules with localized modes. Chemphyschem 2014; 15:3365-77. [PMID: 25080397 DOI: 10.1002/cphc.201402251] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Indexed: 11/11/2022]
Abstract
The analysis and interpretation of the vibrational spectra of complex (bio)molecular systems, such as polypeptides and proteins, requires support from quantum-chemical calculations. Such calculations are currently restricted to the harmonic approximation. Here, we show how one of the main bottlenecks in such calculations, the evaluation of the potential energy surface, can be overcome by using localized modes instead of the commonly employed normal modes. We apply such local vibrational self-consistent field (L-VSCF) and vibrational configuration interaction (L-VCI) calculations to a cyclic water tetramer and a helical hexa-alanine peptide. The results show that the use of localized modes is equivalent to the commonly used normal modes, but offers several advantages. First, a faster convergence with respect to the excitation level is observed in L-VCI calculations. Second, the localized modes provide a reduced representation of the couplings between modes that show a regular coupling pattern. This can be used to disregard a significant number of small two-mode potentials a priori. Several such reduced coupling approximations are explored, and we show that the number of single-point calculations required to evaluate the potential energy surface can be significantly reduced without introducing noticeable errors in the resulting vibrational spectra.
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Affiliation(s)
- Paweł T Panek
- Karlsruhe Institute of Technology (KIT), Center for Functional Nanostructures and Institute of Physical Chemistry, Wolfgang-Gaede-Str. 1a, 76131 Karlsruhe (Germany) http://www.christophjacob.eu
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46
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Goez A, Jacob CR, Neugebauer J. Modeling environment effects on pigment site energies: Frozen density embedding with fully quantum-chemical protein densities. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.02.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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47
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Schinle F, Jacob CR, Wolk AB, Greisch JF, Vonderach M, Weis P, Hampe O, Johnson MA, Kappes MM. Ion mobility spectrometry, infrared dissociation spectroscopy, and ab initio computations toward structural characterization of the deprotonated leucine-enkephalin peptide anion in the gas phase. J Phys Chem A 2014; 118:8453-63. [PMID: 24884600 DOI: 10.1021/jp501772d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Although the sequencing of protonated proteins and peptides with tandem mass spectrometry has blossomed into a powerful means of characterizing the proteome, much less effort has been directed at their deprotonated analogues, which can offer complementary sequence information. We present a unified approach to characterize the structure and intermolecular interactions present in the gas-phase pentapeptide leucine-enkephalin anion by several vibrational spectroscopy schemes as well as by ion-mobility spectrometry, all of which are analyzed with the help of quantum-chemical computations. The picture emerging from this study is that deprotonation takes place at the C terminus. In this configuration, the excess charge is stabilized by strong intramolecular hydrogen bonds to two backbone amide groups and thus provides a detailed picture of a potentially common charge accommodation motif in peptide anions.
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Affiliation(s)
- Florian Schinle
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT) , 76021 Karlsruhe, Germany
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48
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Neff JL, Milde P, León CP, Kundrat MD, Eng LM, Jacob CR, Hoffmann-Vogel R. Epitaxial growth of pentacene on alkali halide surfaces studied by Kelvin probe force microscopy. ACS Nano 2014; 8:3294-3301. [PMID: 24601525 DOI: 10.1021/nn404257v] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In the field of molecular electronics, thin films of molecules adsorbed on insulating surfaces are used as the functional building blocks of electronic devices. Control of the structural and electronic properties of the thin films is required for reliably operating devices. Here, noncontact atomic force and Kelvin probe force microscopies have been used to investigate the growth and electrostatic landscape of pentacene on KBr(001) and KCl(001) surfaces. We have found that, together with molecular islands of upright standing pentacene, a new phase of tilted molecules appears near step edges on KBr. Local contact potential differences (LCPD) have been studied with both Kelvin experiments and density functional theory calculations. Our images reveal that differently oriented molecules display different LCPD and that their value is independent of the number of molecular layers. These results point to the formation of an interface dipole, which may be explained by a partial charge transfer from the pentacene to the surface. Moreover, the monitoring of the evolution of the pentacene islands shows that they are strongly affected by dewetting: Multilayers build up at the expense of monolayers, and in the Kelvin images, previously unknown line defects appear, which reveal the epitaxial growth of pentacene crystals.
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Affiliation(s)
- Julia L Neff
- Physikalisches Institut and DFG-Center for Functional Nanostructures, Karlsruhe Institute of Technology , Wolfgang-Gaede-Straße 1, 76131 Karlsruhe, Germany
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Abstract
For electronic excitations in the ultraviolet and visible range of the electromagnetic spectrum, the intensities are usually calculated within the dipole approximation, which assumes that the oscillating electric field is constant over the length scale of the transition. For the short wavelengths used in hard X-ray spectroscopy, the dipole approximation may not be adequate. In particular, for metal K-edge X-ray absorption spectroscopy (XAS), it becomes necessary to include higher-order contributions. In quantum-chemical approaches to X-ray spectroscopy, these so-called quadrupole intensities have so far been calculated by including contributions depending on the square of the electric-quadrupole and magnetic-dipole transition moments. However, the resulting quadrupole intensities depend on the choice of the origin of the coordinate system. Here, we show that for obtaining an origin-independent theory, one has to include all contributions that are of the same order in the wave vector consistently. This leads to two additional contributions depending on products of the electric-dipole and electric-octupole and of the electric-dipole and magnetic-quadrupole transition moments, respectively. We have implemented such an origin-independent calculation of quadrupole intensities in XAS within time-dependent density-functional theory, and demonstrate its usefulness for the calculation of metal and ligand K-edge XAS spectra of transition metal complexes.
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Affiliation(s)
- Stephan Bernadotte
- Karlsruhe Institute of Technology (KIT), Center for Functional Nanostructures, Wolfgang-Gaede-Str. 1a, 76131 Karlsruhe, Germany
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Atkins AJ, Bauer M, Jacob CR. The chemical sensitivity of X-ray spectroscopy: high energy resolution XANES versus X-ray emission spectroscopy of substituted ferrocenes. Phys Chem Chem Phys 2013; 15:8095-105. [PMID: 23579736 DOI: 10.1039/c3cp50999k] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
X-ray spectroscopy at the metal K-edge is an important tool for understanding catalytic processes and provides insight into the geometric and electronic structures of transition metal complexes. In particular, X-ray emission-based methods such as high-energy resolution fluorescence detection (HERFD), X-ray absorption near-edge spectroscopy (XANES) and valence-to-core X-ray emission spectroscopy (V2C-XES) hold the promise of providing increased chemical sensitivity compared to conventional X-ray absorption spectroscopy. Here, we explore the ability of HERFD-XANES and V2C-XES spectroscopy to distinguish substitutions beyond the directly coordinated atoms for the example of ferrocene and selected ferrocene derivatives. The experimental spectra are assigned and interpreted through the use of density functional theory (DFT) calculations. We find that while the pre-edge peaks in the HERFD-XANES spectra are affected by substituents at the cyclopentadienyl ring containing π-bonds [A. J. Atkins, Ch. R. Jacob and M. Bauer, Chem.-Eur. J., 2012, 18, 7021], the V2C-XES spectra are virtually unchanged. The pre-edge in HERFD-XANES probes the weak transition to unoccupied metal d-orbitals, while the V2C-XES spectra are determined by dipole-allowed transitions from occupied ligand orbitals to the 1s core hole. The latter turn out to be less sensitive to changes beyond the first coordination shell.
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Affiliation(s)
- Andrew J Atkins
- Karlsruhe Institute of Technology (KIT), Center for Functional Nanostructures and Institute of Physical Chemistry, Wolfgang-Gaede-Str. 1a, 76131 Karlsruhe, Germany
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