=Paper=
{{Paper
|id=None
|storemode=property
|title=Orbital analysis of Oxo and Peroxo Dicopper Complexes via Quantum Chemical Workflows in MoSGrid
|pdfUrl=https://ceur-ws.org/Vol-993/paper3.pdf
|volume=Vol-993
|dblpUrl=https://dblp.org/rec/conf/iwsg/Herres-PawlisHGP13
}}
==Orbital analysis of Oxo and Peroxo Dicopper Complexes via Quantum Chemical Workflows in MoSGrid==
https://ceur-ws.org/Vol-993/paper3.pdf
Orbital analysis of oxo and peroxo dicopper
complexes via quantum chemical workflows in
MoSGrid
Sonja Herres-Pawlis, Alexander Hoffmann* Richard Grunzke
Fakultät für Chemie und Pharmazie, Department Chemie Zentrum für Informationsdienste und Hochleistungsrechnen,
Ludwig-Maximilians-Universität München Technische Universität Dresden
Butenandtstr. 5-13, 81377 München, Germany Zellescher Weg 12-14, 01062 Dresden, Germany
alexander.hoffmann@cup.uni-muenchen.de
Lars Packschies
Regionales Rechenzentrum
Universität zu Köln
Weyertal 121, 50931 Germany
Abstract—The science gateway MoSGrid (Molecular Simulation two copper centers and the subsequent design of
Grid) is a valuable tool to submit and process molecular simulation environmentally benign oxidation catalysts.
studies on a large scale. An orbital analysis of oxo and peroxo
dicopper complexes, which are bioinspired models of tyrosinase, is II. BACKGROUND
presented as a real-world chemical example. The orbital analysis is
result of a quantum chemical workflow which has been employed on A. Workflow-enabled Science Gateways
several tyrosinase model complexes as well as on simple
{Cu2O2(NH3)x} cores (with x = 4,6). The structures were optimized
Science gateways in general aim to enable users to
using Gaussian09 and the orbitals visualized after production of intuitively access DCIs. This way, users can concentrate on
formatted checkpoint files. All meta- and post-processing steps have their particular field of research and are thus liberated from
been performed in this portlet. All workflow features are installing and maintaining any software with at the same time
implemented via WS-PGRADE and submitted to UNICORE. having the advantage of using well designed user interfaces.
These science gateways allow for the easy handling of tools
Keywords—Quantum chemistry, Workflows, Copper complexes, and workflows on DCIs. The MoSGrid science gateway in
Service Grids, DCIs particular uses the DCI visualization environment gUSE and
its graphical interface WS-PGRADE. Both have been
I. INTRODUCTION extended in the course of the MoSGrid project [2]. It supports
Molecular Simulation Grid (MoSGrid) [1] is a science the three main molecular simulation domains: quantum
gateway for researchers from chemistry and biology which chemistry, molecular dynamics and docking. The research
enables the access to high-performance computing (HPC) presented here takes advantage of the quantum chemistry area.
facilities. MoSGrid aims to enable more researchers to use Apart from specific domain support users can also create,
distributed computing infrastructures (DCIs) by reducing the manage and submit generic workflows by selecting and
initial hurdle of using computational chemistry software on concatenating applications and using output from applications
DCIs. It provides graphical user interfaces that allow even as input for subsequent ones. As closely related science
inexperienced scientists to run molecular simulations of high gateway Gridchem [3] has to be named: it offers chemists
complexity. similarly easy access to computing resources but not the
Here, we present a quantum chemical orbital analysis of option of workflow usage. For building up science gateways
oxo and peroxo dicopper complexes which is highly relevant further efforts are described in [4].
for the design of tyrosinase models. This has been achieved B. Application Domain
using the MoSGrid portal. Tyrosinase is a ubiquitous copper
enzyme which selectively hydroxylates phenols to quinones A primary goal of bio-inorganic chemistry is the ability to
for pigment and hormone production [1]. This bioinorganic leverage the insights taken from enzymatic systems to create
study helps a better understanding of the oxygen activation by catalytically functional analogs that can affect transformations
and operate in conditions not practicable by the enzyme [5]. III. ORBITAL ANALYSIS OF OXO AND PEROXO DICOPPER
Proposing catalytic chemistry based on enzymatic COMPLEXES
mechanisms, evolved by selection pressures for efficiency, Understanding of the formation of P and O cores as well as
exploits the important fact that a path through the energetic their distinct reactivity relies on comprehensive orbital
landscape has already been mapped. Reproducing enzymatic analyses (Figure 2). However, detailed understanding and
transformations and characterizing intermediates are crucial computational modeling of these species are still major
for insights into the reaction mechanism. In metal-based challenges. In spite of many efforts, the equilibrium between P
oxidative chemistry, achieving turnover is a substantial and O cores is still regarded as a ‘‘torture track’’ for
challenge, as evidenced by the limited number of good computation [24]. Very large variations in the predicted
examples in biomimetic chemistry. Catalytic systems must relative stabilities of P and O core motifs have been reported.
finely balance energetics, minimizing activation barriers and The situation appears confusing since (i) different levels of
avoiding energetic wells which halt the cycle at products or theory are used in the calculations and (ii) the chemical
intermediates. The stability achieved in an enzyme, where equilibrium and properties of the µ-2:2-peroxo dicopper(II)-
tethering site-isolated metals to a peptide matrix discourages and the bis-µ-oxo-dicopper(III) dimers depends sensitively on
destructive decay, opens up thermal regimes favorable to ligands, solvent, and counterions. Many calculations in this
efficient catalysis. In synthetic analogs, stability at kinetically context [15,24-27] use density-functional theory (DFT) with
advantageous temperatures often comes at the expense of either local (pure) functionals or hybrid functionals such as
inherent reactivity. Additionally, undesired side reactions can B3LYP [16,22,28,29] to describe the electron exchange and
lead to thermodynamically stable complexes which take correlation (XC) energy.
catalysts out of the cycle, limiting turnover numbers [6,7]. In Figure 2, HOMO is the abbreviation for highest
The most important metals in biological dioxygen
occupied molecular orbital and LUMO for lowest unoccupied
activation are iron and copper, and enzymes utilizing these
molecular orbital. The molecular orbitals are occupied
metals are valued sources of inspiration to chemists developing
oxidative or oxygen-insertion chemistry. Examples of catalytic maximal with two electrons. The general frontier orbitals
oxygen-insertion reactions, in which dioxygen is the sole combine contributions of the copper dxy orbitals and the
source of oxygen, are extremely limited, despite the antibonding oxygen orbitals as positive or negative linear
indisputable advantages of using the earth’s oxygen combinations, hence constructing delocalized molecular
reserves.[7-9] Tyrosinase (see Figure 1, upper left and upper orbitals for the whole Cu2O2 core.
right) is a ubiquitous binuclear copper enzyme that catalyzes Here, we report on orbital analyses of small model systems
the hydroxylation of phenols to catechols and the oxidation of (Figure 3, left) containing ammonia ligands which are not
catechols to quinones [10,11]. The quinones are then experimentally accessible and a “real life” system which has
transformed to biologically important molecules, such as the been synthesized by us (right).[31] The ammonia complexes
pigment melanin [12] or the neurotransmitter noradrenalin deliver a more principle understanding of the orbital
[13]. In the oxygenated form of tyrosinase, a µ-2:2- contributions of the copper ions, the peroxide/oxido and
peroxodicopper(II) species has been crystallographically ammonia ligands.
identified with an intact O–O bond [14].
The hydroxylation of phenols proceeds through a
mechanism consistent with an electrophilic aromatic
substitution [11,15,16]. During the last decade, numerous
model studies provided insights that the stoichiometric
hydroxylation of phenolates can be mediated via synthetic µ-
2:2-dicopper(II) cores [17-20] and bis(µ-oxo) dicopper(III)
cores [15,16,21-23] (see Figure 1, below).
Fig. 2. Molecular orbital diagram of the frontier orbitals of the P core
(left) and the O core (right) [30]
Fig. 1. Tyrosinase (upper left), active site of tyrosinase (upper right) [14] Fig. 3. Complex containing the ammonia ligands (left) and the “real life”
and equilibrium of a P core and an O core (below) system (right, H atoms are omitted for clarity)
IV. METHODS automatically used for to access several key aspects of the
MoSGrid science gateway; first it is used to access the grid
A. MoSGrid Science Gateway middleware UNICORE [33] for the submission and handling
The orbital analyses on N donor copper complexes were of jobs. Secondly the MoSGrid repository can be accessed
carried out using the MoSGrid science gateway [2], which which includes the distributed cloud file system XtreemFS
uses the open-source, commonly used, and very flexible portal [34] for raw file storage and UNICORE for enabling the use of
framework Liferay [32] as its basis. The science gateway metadata and search functionality. Thirdly advanced users can
enables scientists from the wide field of molecular simulations utilize WS-PGRADE to create and manage customized
to design and compose workflows for simple and complex workflows. The token is subsequently used by a so called
tasks to be computed in a distributed computing infrastructure submitter which enables the communication between gUSE
(DCI). MoSGrid was designed and implemented to relieve [35] and UNICORE. Jobs and workflows are managed and
scientists from the necessity to have detailed knowledge about applications installed on HPC systems can be selected and
(i) program specific input- and output files and (ii) detailed used. This allows for an efficient jobs submission, since
knowledge of how to access and utilize high performance applications don't have to be re-transferred with each job. This
computing infrastructures (remote access and security aspects, is especially important for software packages like Gaussian
use of remote command line interfaces). The science gateway which has to be installed on HPC resources due to its license
supports every step in an intuitive way from the generation of scheme.
a task within a predefined workflow, the submission, and The third area includes the domain specific user interfaces
monitoring of a running workflow to the point of accessing for the chemical applications. These were developed to just
output files as well as automatically generated visualizations. show necessary information to the user to make the use
To allow this the MoSGrid science gateway comprises of experience as intuitive as possible. The Quantum Chemistry
several sections. First, a public area with general project user interface, used for the research presented in this paper,
information, help texts and tutorials about how to conduct offers user-friendly access to the Gaussian application. To
simulations is offered. The user is pointed to writing a mail to make the workflow submission as easy and quick as possible
get activated and getting used to run workflows. Secondly, an default values are offered. On the other hand workflows can
area for activated users is presented. It includes a certificate be fine-tuned to ones specific simulation needs by adjusting a
portlet to easily and seamlessly enable the access to the multitude of parameters. These include job type (optimization,
underlying computing clusters. A security token is almost job type, energy, or a combination of these), method (DFT,
automatically generated from the users certificate to allow the TD-DFT, Hartree-Fock), basis set (3-21G, 6-31G(d), cc-
science gateway to act on behalf of the user. gUSE, the pVQZ), resource specifications (main memory, number of
underlying middleware to enable submission of jobs to a wide cores, job length), and other options. Another aspect of the
range of DCI systems, is transparently made available to the interface allows for the monitoring of the currently running
user. WS-PGRADE as the graphical user interface to gUSE is workflows and the related results. In addition, MoSGrid
completely hidden from users by the use of specific graphical administrators have an extra area which enables the easy
interface for the three chemical domains, quantum chemistry, management of the whole science gateway and user related
molecular dynamics, and docking. The security token is tasks.
Fig. 4. Workflow of the orbital analysis
B. Workflows with oxo/peroxo complexes combination of the dxy atom orbital of the copper and the *
The orbital analysis can be mapped to a multi-step atom orbital of the peroxide, whereas the HOMO-1 is the
workflow (Figure 4) which consists of the following tasks: linear combination of the dxy atom orbital of the copper and
The first step is the job definition (1). Here, the user uploads the v* atom orbital of the peroxide. The transition at 350 nm
predefined files containing all necessary information about the is an in-plane transition, so there is more overlap between the
copper complex simulation. In particular, the starting orbitals, resulting in a higher intensity than in the out-of-plane
structures of the oxo and peroxo complexes are given by the transition at 550 nm. In the O core, the first transition is the
user and a file which functional and basis sets shall be used. A interaction between the HOMO-2 and the LUMO. The
generator port builds the input files stack (20 jobs for each HOMO-2 is a linear combination of the dxy atom orbital of the
complex). As typical functionals, B3LYP, BLYP, BP86 and copper and the * atom orbital of the oxido bridges, whereas
TPSSh have been applied, 6-31g(d), cc-pvdz, def2-TZVP the LUMO is a linear combination of the d xy atom orbital of
were used as basis sets. Meta-processing (2) as second step the copper and the u* atom orbital of the oxido bridges. The
checks the user input for consistency and, if necessary, second UV band arises from a transition of the HOMO (a
completes the configuration. A complete set of job-meta- linear combination of the d xy copper orbital and the u*
information contains the molecule structure, application, oxygen orbital) into the LUMO+1 (a linear combination of the
method, temperature and basis set. If not all information is dxy copper orbital and the * oxygen orbital).
given, the user is guided through the configuration by Time dependent-DFT calculated spectra predict the
providing sensible default values that the user can accept or experimental optical spectrum with the four LMCT bands at
overwrite. The last step of the configuration is the definition of 340 nm, 366 nm, 381 nm and 547 nm. The description of these
the length of the simulation and the amount of needed bands with canonical orbitals shows heavily mixed and
resources (20000 MB). The definition of the simulation length complicated transitions. So we describe the transitions with
is a tricky task, because quantum calculations tend to be non- the natural transition orbitals [37]. These transition orbital
deterministic. Therefore, the length of the simulation should assigns the most prominent features near 350 nm (340 and 366
be guessed long enough. Afterwards, this molecular nm) to be an in-plane peroxide πσ* dxy transition and the
simulation meta-description is translated to the simulation lowest energy feature near 550 nm to an out-of-plane peroxide
specific format by a preprocessing step (3). For this process πv* dxy. The absorbance near 430 nm (calculated at 381
adapters are developed for several quantum codes. nm) is assigned to a pyrazole/pyridyl π* dxy charge transfer
Following, the job submission is initiated (4). The submitter transition, as is positioned for other peroxo complexes with
translates the job information into the UNICORE job format unsaturated, nitrogen-containing ligands [38]. Hence, the
and transfers the job through the UNICORE middleware to the difference to the small model systems show the large
target cluster environment, where it is executed in Gaussian09 difference between the frontier orbitals and the significant
[36] (5). The job information includes the user credentials, ligand influence which will be evaluated in further studies.
structure format, and input file staging information. Post-
processing is performed after the successful execution of the
workflow to extract the application independent information
from the result files (6) and to generate checkpoint files which
enable visualization of the orbitals. Optionally, afterwards an
NTO analysis can be accomplished (7, see Results section).
Further, the MoSGrid portal allows annotating the simulation
results with MSML and storing them in the MoSGrid data
repository for reuse.
Fig. 5. Molecular orbitals of the frontier orbitals of the small model
V. RESULTS systems (P core left; O core right)
The workflows give a large number of output files and
orbitals. Here, the most important results are summarised.
Optical benchmarking of calculated orbitals can be performed
via comparison to experimental electronic spectra. Typically, a
P core exhibits two absorption bands at 350 and 550 nm
whereas an O core possesses two bands at 300 and 400 nm
[30]. These features must be predicted correctly. The frontier
orbitals for the small model systems are shown in Figure 5 and
those of the real system in Figure 6. In the P core, we obtained
a UV/Vis spectrum with the two characteristic bands at 350
nm (HOMOLUMO) and the band at 550 nm (HOMO-
1LUMO) with minor intensity. The HOMO is the linear
combination of the dxy atom orbital of the copper with the *
atom orbital of the peroxide and the LUMO is the linear Fig. 8. Natural transitions orbitals (NTOs) of the “real life” system
VI. OUTLOOK [13] G. Eisenhofer, H. Tian, C. Holmes, J. Matsunaga, S. Roffler-Tarlov, V.
J. Hearing. Tyrosinase: a developmentally specific major determinant
With the results of this computational analysis, a better of peripheral dopamine, FASEB J. 17, 1248 (2003).
understanding of oxo and peroxo complexes is possible. In the [14] Y. Matoba, T. Kumagai, A. Yamamoto, H. Yoshitsu, M. Sugiyama,
next steps, we plan to extend the parameter-sweep workflow- Crystallographic Evidence That the Dinuclear Copper Center of
Tyrosinase Is Flexible during Catalysis, J. Biol. Chem. 281, 8981
driven features of MoSGrid in order to facilitate serial studies (2006).
even more. Then, benchmarking number can be provided. The [15] L. M. Mirica, M. Vance, D. J. Rudd, B. Hedman, K. O. Hodgson, E. I.
functional and basis set dependency of the copper-copper Solomon, T. D. P. Stack, Tyrosinase Reactivity in a Model Complex:
distances has to be studied in detail since it is crucial for the An Alternative Hydroxylation Mechanism, Science 308, 1890 (2005).
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ACKNOWLEDGMENT Chem. Soc. 131, 6421 (2009).
[17] S. Itoh, H. Kumei, M. Taki, S. Nagatomo, T. Kitagawa, S. Fukuzumi,
The authors would like to thank the BMBF (German
Oxygenation of Phenols to Catechols by A (µ-2:2-
Federal Ministry of Education and Research) for the Peroxo)dicopper(II) Complex: Mechanistic Insight into the Phenolase
opportunity to do research in the MoSGrid project (reference Activity of Tyrosinase, J. Am. Chem. Soc. 123, 6708 (2001).
01IG09006). Furthermore, financial support by the Deutsche [18] L. Santagostini, M. Gullotti, E. Monzani, L. Casella, R. Dillinger, F.
Forschungsgemeinschaft (DFG-FOR1405) is gratefully Tuczek, Reversible Dioxygen Binding and Phenol Oxygenation in a
Tyrosinase Model System, Chem. Eur. J. 6, 519 (2000).
acknowledged. The research leading to these results has also [19] L. M. Mirica, M. Vance, D. Jackson Rudd, B. Hedman, K. O. Hodgson,
partially been supported by the European Commission’s E. I. Solomon, T. D. P. Stack, A Stabilized µ-2:2 Peroxodicopper(II)
Seventh Framework Programme (FP7/2007-2013) under grant Complex with a Secondary Diamine Ligand and Its Tyrosinase-like
agreement no 312579 (ER-flow) and by the LSDMA project Reactivity, J. Am. Chem. Soc. 124, 9332 (2002).
[20] S. Palavicini, A. Granata, E. Monzani, L. Casella, Hydroxylation of
of the Helmholtz Association of German Research Centres. Phenolic Compounds by a Peroxodicopper(II) Complex: Further
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