Publications by authors named "Pavlo O Dral"

33 Publications

Machine Learning for Absorption Cross Sections.

J Phys Chem A 2020 Sep 25;124(35):7199-7210. Epub 2020 Aug 25.

State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.

We present a machine learning (ML) method to accelerate the nuclear ensemble approach (NEA) for computing absorption cross sections. ML-NEA is used to calculate cross sections on vast ensembles of nuclear geometries to reduce the error due to insufficient statistical sampling. The electronic properties-excitation energies and oscillator strengths-are calculated with a reference electronic structure method only for a relatively few points in the ensemble. The KREG model (kernel-ridge-regression-based ML combined with the RE descriptor) as implemented in MLatom is used to predict these properties for the remaining tens of thousands of points in the ensemble without incurring much of additional computational cost. We demonstrate for two examples, benzene and a 9-dicyanomethylene derivative of acridine, that ML-NEA can produce statistically converged cross sections even for very challenging cases and even with as few as several hundreds of training points.
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http://dx.doi.org/10.1021/acs.jpca.0c05310DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7511037PMC
September 2020

Hierarchical machine learning of potential energy surfaces.

J Chem Phys 2020 May;152(20):204110

Department of Engineering, University of Cambridge, Cambridge CB2 1PZ, United Kingdom.

We present hierarchical machine learning (hML) of highly accurate potential energy surfaces (PESs). Our scheme is based on adding predictions of multiple Δ-machine learning models trained on energies and energy corrections calculated with a hierarchy of quantum chemical methods. Our (semi-)automatic procedure determines the optimal training set size and composition of each constituent machine learning model, simultaneously minimizing the computational effort necessary to achieve the required accuracy of the hML PES. Machine learning models are built using kernel ridge regression, and training points are selected with structure-based sampling. As an illustrative example, hML is applied to a high-level ab initio CHCl PES and is shown to significantly reduce the computational cost of generating the PES by a factor of 100 while retaining similar levels of accuracy (errors of ∼1 cm).
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http://dx.doi.org/10.1063/5.0006498DOI Listing
May 2020

The Impact of Aggregation on the Photophysics of Spiro-Bridged Heterotriangulenes.

Angew Chem Int Ed Engl 2020 Sep 9;59(37):16233-16240. Epub 2020 Jul 9.

Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany.

We report on the impact of the central heteroatom on structural, electronic, and spectroscopic properties of a series of spirofluorene-bridged heterotriangulenes and provide a detailed study on their aggregates. The in-depth analysis of their molecular structure by NMR spectroscopy and X-ray crystallography was further complemented by density functional theory calculations. With the aid of extensive photophysical analysis the complex fluorescence spectra were deconvoluted showing contributions from the peripheral fluorenes and the heteroaromatic cores. Beyond the molecular scale, we examined the aggregation behavior of these heterotriangulenes in THF/H O mixtures and analyzed the aggregates by static and dynamic light scattering. The excited-state interactions within the aggregates were found to be similar to those found in the solid state. A plethora of morphologies and superstructures were observed by scanning electron microscopy of drop-casted dispersions.
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http://dx.doi.org/10.1002/anie.202003504DOI Listing
September 2020

Quantum Chemistry in the Age of Machine Learning.

Authors:
Pavlo O Dral

J Phys Chem Lett 2020 Mar 9;11(6):2336-2347. Epub 2020 Mar 9.

State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.

As the quantum chemistry (QC) community embraces machine learning (ML), the number of new methods and applications based on the combination of QC and ML is surging. In this Perspective, a view of the current state of affairs in this new and exciting research field is offered, challenges of using machine learning in quantum chemistry applications are described, and potential future developments are outlined. Specifically, examples of how machine learning is used to improve the accuracy and accelerate quantum chemical research are shown. Generalization and classification of existing techniques are provided to ease the navigation in the sea of literature and to guide researchers entering the field. The emphasis of this Perspective is on supervised machine learning.
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http://dx.doi.org/10.1021/acs.jpclett.9b03664DOI Listing
March 2020

A Spherically Shielded Triphenylamine and Its Persistent Radical Cation.

Chemistry 2020 Mar 21;26(15):3264-3269. Epub 2020 Feb 21.

Institute of Organic Chemistry, Ruprecht-Karls-University Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany.

This work reports the design and synthesis of a sterically protected triphenylamine scaffold which undergoes one-electron oxidation to form an amine-centered radical cation of remarkable stability. Several structural adjustments were made to tame the inherent reactivity of the radical cation. First, the parent propeller-shaped triphenylamine was planarized with sterically demanding bridging units and, second, protecting groups were deployed to block the reactive positions. The efficiently shielded triphenylamine core can be reversibly oxidized at moderate potentials (+0.38 V, vs. Fc/Fc in CH Cl ). Spectroelectrochemistry and chemical oxidation studies were employed to monitor the evolution of characteristic photophysical features. To obtain a better understanding of the impact of one-electron oxidation on structural and electronic properties, joint experimental and computational studies were conducted, including X-ray structural analysis, electron paramagnetic resonance (EPR), and density functional theory (DFT) calculations. The sterically shielded radical cation combines various desirable attributes: A characteristic and unobstructed absorption in the visible region, high stability which enables storage for weeks without spectroscopically traceable degradation, and a reliable oxidation/re-reduction process due to effective screening of the planarized triphenylamine core from its environment.
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http://dx.doi.org/10.1002/chem.202000355DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7154785PMC
March 2020

MLatom: A program package for quantum chemical research assisted by machine learning.

Authors:
Pavlo O Dral

J Comput Chem 2019 10 20;40(26):2339-2347. Epub 2019 Jun 20.

Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany.

MLatom is a program package designed for computationally efficient simulations of atomistic systems with machine-learning (ML) algorithms. It can be used out-of-the-box as a stand-alone program with a user-friendly online manual. The use of MLatom does not require extensive knowledge of machine learning, programming, or scripting. The user need only prepare input files and choose appropriate options. The program implements kernel ridge regression and supports Gaussian, Laplacian, and Matérn kernels. It can use arbitrary, user-provided input vectors and can convert molecular geometries into input vectors corresponding to several types of built-in molecular descriptors. MLatom saves and re-uses trained ML models as needed, in addition to estimating the generalization error of ML setups. Various sampling procedures are supported and the gradients of output properties can be calculated. The core part of MLatom is written in Fortran, uses standard libraries for linear algebra, and is optimized for shared-memory parallel computations. © 2019 Wiley Periodicals, Inc.
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http://dx.doi.org/10.1002/jcc.26004DOI Listing
October 2019

What is semiempirical molecular orbital theory approximating?

J Mol Model 2019 Apr 16;25(5):119. Epub 2019 Apr 16.

Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany.

We elucidate the approaches used to incorporate electron correlation in existing semiempirical molecular orbital theory (SEMO) methods and compare them with the techniques used in other quantum chemical methods. After analyzing expressions for electron correlation in ab initio wavefunction theory, density functional theory, and density functional-based tight-binding (TB) methods, we suggest a framework for developing hybrid TB-SEMO methods. We provide a numerical proof-of-concept for such a method based on the OM2 method.
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http://dx.doi.org/10.1007/s00894-019-4005-8DOI Listing
April 2019

Semiempirical Quantum-Chemical Methods with Orthogonalization and Dispersion Corrections.

J Chem Theory Comput 2019 Mar 27;15(3):1743-1760. Epub 2019 Feb 27.

Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1 , 45470 Mülheim an der Ruhr , Germany.

We present two new semiempirical quantum-chemical methods with orthogonalization and dispersion corrections: ODM2 and ODM3 (ODM x). They employ the same electronic structure model as the OM2 and OM3 (OM x) methods, respectively. In addition, they include Grimme's dispersion correction D3 with Becke-Johnson damping and three-body corrections E for Axilrod-Teller-Muto dispersion interactions as integral parts. Heats of formation are determined by adding explicitly computed zero-point vibrational energy and thermal corrections, in contrast to standard MNDO-type and OM x methods. We report ODM x parameters for hydrogen, carbon, nitrogen, oxygen, and fluorine that are optimized with regard to a wide range of carefully chosen state-of-the-art reference data. Extensive benchmarks show that the ODM x methods generally perform better than the available MNDO-type and OM x methods for ground-state and excited-state properties, while they describe noncovalent interactions with similar accuracy as OM x methods with a posteriori dispersion corrections.
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http://dx.doi.org/10.1021/acs.jctc.8b01265DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6416713PMC
March 2019

Big data analysis of ab Initio molecular integrals in the neglect of diatomic differential overlap approximation.

J Comput Chem 2019 Feb 14;40(4):638-649. Epub 2018 Dec 14.

Max-Planck-Institut für Kohlenforschung, 45470, Mülheim an der Ruhr, Germany.

Most modern semiempirical quantum-chemical (SQC) methods are based on the neglect of diatomic differential overlap (NDDO) approximation to ab initio molecular integrals. Here, we check the validity of this approximation by computing all relevant integrals for 32 typical organic molecules using Gaussian-type orbitals and various basis sets (from valence-only minimal to all-electron triple-ζ basis sets) covering in total more than 15.6 million one-electron (1-e) and 10.3 billion two-electron (2-e) integrals. The integrals are calculated in the nonorthogonal atomic basis and then transformed by symmetric orthogonalization to the Löwdin basis. In the case of the 1-e integrals, we find strong orthogonalization effects that need to be included in SQC models, for example, by strategies such as those adopted in the available OMx methods. For the valence-only minimal basis, we confirm that the 2-e Coulomb integrals in the Löwdin basis are quantitatively close to their counterparts in the atomic basis and that the 2-e exchange integrals can be safely neglected in line with the NDDO approximation. For larger all-electron basis sets, there are strong multishell orthogonalization effects that lead to more irregular patterns in the transformed 2-e integrals and thus cast doubt on the validity of the NDDO approximation for extended basis sets. Focusing on the valence-only minimal basis, we find that some of the NDDO-neglected integrals are reduced but remain sizable after the transformation to the Löwdin basis; this is true for the two-center 2-e hybrid integrals, the three-center 1-e nuclear attraction integrals, and the corresponding three-center 2-e hybrid integrals. We consider a scheme with a valence-only minimal basis that includes such terms as a possible strategy to go beyond the NDDO integral approximation in attempts to improve SQC methods. © 2018 Wiley Periodicals, Inc.
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http://dx.doi.org/10.1002/jcc.25748DOI Listing
February 2019

Deep Learning for Nonadiabatic Excited-State Dynamics.

J Phys Chem Lett 2018 Dec 12;9(23):6702-6708. Epub 2018 Nov 12.

Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry , Beijing Normal University , Beijing 100875 , China.

In this work we show that deep learning (DL) can be used for exploring complex and highly nonlinear multistate potential energy surfaces of polyatomic molecules and related nonadiabatic dynamics. Our DL is based on deep neural networks (DNNs), which are used as accurate representations of the CASSCF ground- and excited-state potential energy surfaces (PESs) of CHNH. After geometries near conical intersection are included in the training set, the DNN models accurately reproduce excited-state topological structures; photoisomerization paths; and, importantly, conical intersections. We have also demonstrated that the results from nonadiabatic dynamics run with the DNN models are very close to those from the dynamics run with the pure ab initio method. The present work should encourage further studies of using machine learning methods to explore excited-state potential energy surfaces and nonadiabatic dynamics of polyatomic molecules.
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http://dx.doi.org/10.1021/acs.jpclett.8b03026DOI Listing
December 2018

Nonadiabatic Excited-State Dynamics with Machine Learning.

J Phys Chem Lett 2018 Oct 13;9(19):5660-5663. Epub 2018 Sep 13.

Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 Mülheim an der Ruhr , Germany.

We show that machine learning (ML) can be used to accurately reproduce nonadiabatic excited-state dynamics with decoherence-corrected fewest switches surface hopping in a 1-D model system. We propose to use ML to significantly reduce the simulation time of realistic, high-dimensional systems with good reproduction of observables obtained from reference simulations. Our approach is based on creating approximate ML potentials for each adiabatic state using a small number of training points. We investigate the feasibility of this approach by using adiabatic spin-boson Hamiltonian models of various dimensions as reference methods.
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http://dx.doi.org/10.1021/acs.jpclett.8b02469DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6174422PMC
October 2018

Structure-based sampling and self-correcting machine learning for accurate calculations of potential energy surfaces and vibrational levels.

J Chem Phys 2017 Jun;146(24):244108

Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.

We present an efficient approach for generating highly accurate molecular potential energy surfaces (PESs) using self-correcting, kernel ridge regression (KRR) based machine learning (ML). We introduce structure-based sampling to automatically assign nuclear configurations from a pre-defined grid to the training and prediction sets, respectively. Accurate high-level ab initio energies are required only for the points in the training set, while the energies for the remaining points are provided by the ML model with negligible computational cost. The proposed sampling procedure is shown to be superior to random sampling and also eliminates the need for training several ML models. Self-correcting machine learning has been implemented such that each additional layer corrects errors from the previous layer. The performance of our approach is demonstrated in a case study on a published high-level ab initio PES of methyl chloride with 44 819 points. The ML model is trained on sets of different sizes and then used to predict the energies for tens of thousands of nuclear configurations within seconds. The resulting datasets are utilized in variational calculations of the vibrational energy levels of CHCl. By using both structure-based sampling and self-correction, the size of the training set can be kept small (e.g., 10% of the points) without any significant loss of accuracy. In ab initio rovibrational spectroscopy, it is thus possible to reduce the number of computationally costly electronic structure calculations through structure-based sampling and self-correcting KRR-based machine learning by up to 90%.
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http://dx.doi.org/10.1063/1.4989536DOI Listing
June 2017

On the feasibility of reactions through the fullerene wall: a theoretical study of NH@C.

Phys Chem Chem Phys 2017 Jul 22;19(26):17199-17209. Epub 2017 Jun 22.

Computer-Chemie-Centrum and Interdisciplinary Center for Molecular Materials, Department of Chemie und Pharmazie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstr. 25, 91052 Erlangen, Germany.

We propose a new approach to the synthesis of AH@fullerene structures via reactions through the fullerene wall. To investigate the feasibility of the approach, the step-by-step hydrogenation of the template endofullerene N@C up to NH@C has been studied using DFT and MP2 calculations. Protonation of the endohedral guest through the fullerene wall is competitive with escape of the guest, whereas reaction with a hydrogen atom is less favorable. Each protonation step is highly exothermic, so that less active acids can also protonate the guest with less accumulation of energy. The final product, NH@C is a novel concentric ion pair NH@C˙ in which the charge-centers of the two ions coincide.
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http://dx.doi.org/10.1039/c7cp02865bDOI Listing
July 2017

Dithiafulvenyl-Extended N-Heterotriangulenes and Their Interaction with C : Cooperative Fluorescence.

Chemistry 2017 Sep 1;23(50):12353-12362. Epub 2017 Aug 1.

Department of Chemistry and Pharmacy, University of Erlangen-Nürnberg, Henkestrasse 42, 91054, Erlangen, Germany.

We describe the synthesis as well as the electronic and photophysical characterization of novel N-heterotriangulene derivatives decorated with methoxycarbonyl- and methyl-sulfanyl-substituted dithiafulvenyl moieties. The association of these electron-rich compounds with fullerene C as electron acceptor was investigated by means of photophysical, voltammetric, and mass spectrometric methods and rationalized by DFT calculations. Importantly, light-induced interactions between the dithiafulvene-substituted N-heterotriangulene bearing methoxycarbonyl substituents with C leads to cooperative fluorescence. Quantitative Job plot analyses by means of fluorescence spectroscopy and voltammetry confirm a 1:1 association with binding constants in the order of 10  m . Supportive results for the supramolecular assembly of both N-heterotriangulenes with C were obtained by ESI mass spectrometric investigations in the gas phase.
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http://dx.doi.org/10.1002/chem.201701625DOI Listing
September 2017

Organic Electron Acceptors Comprising a Dicyanomethylene-Bridged Acridophosphine Scaffold: The Impact of the Heteroatom.

Chemistry 2017 May 26;23(29):6988-6992. Epub 2017 Apr 26.

Department of Chemistry and Pharmacy, Chair of Organic Chemistry I, University of Erlangen-Nürnberg, Henkestrasse 42, 91054, Erlangen, Germany.

Stable two-electron acceptors comprising a dicyanomethylene-bridged acridophosphine scaffold were synthesized and their reversible reduction potentials were efficiently tuned through derivatization of the phosphorus center. X-ray crystallographic analysis combined with NMR, UV/Vis, IR spectroscopic, and electrochemical studies, supported by theoretical calculations, revealed the crucial role of the phosphorus atom for the unique redox, structural, and photophysical properties of these compounds. The results identify the potential of these electron deficient scaffolds for the development of functional n-type materials and redox active chromophores upon further functionalization.
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http://dx.doi.org/10.1002/chem.201701412DOI Listing
May 2017

Stability of Odd- Versus Even-Electron Gas-Phase (Quasi)Molecular Ions Derived from Pyridine-Substituted N-Heterotriangulenes.

Chempluschem 2017 Feb 22;82(2):204-211. Epub 2016 Nov 22.

Physical Chemistry I, Department of Chemistry and Pharmacy, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Egerlandstrasse 3, 91058, Erlangen, Germany.

Electrospray ionisation of N-heterotriangulenes (i.e., dimethylmethylene-bridged triphenylamines) with up to three pyridyl groups at their periphery, produces the true radical cation ([M] ) and the protonated molecule ([M+H] ) simultaneously. These ions are studied as model systems to illustrate the stability alternation of odd- versus even-electron ions in energy-dependent collision-induced dissociation (CID) experiments. All ions show the same fragmentation pattern, the consecutive loss of three methyl radicals ( CH ) from the dimethylmethylene bridges of the central triangulene core. [M] ions dissociate at much lower collision energies than their [M+H] counterparts. The radical cation forms a singlet fragment with an extended aromatic system that is energetically favoured. Ab initio and density functional theory calculations support this interpretation and allow the assignment of the electronic structure of the fragment ions. Consecutive collision-induced dissociations provide a better match with theory when studied with an ion trap, rather than a linear quadrupole. This is attributed to the resonant nature of the excitation of intermediate ions.
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http://dx.doi.org/10.1002/cplu.201600416DOI Listing
February 2017

Stability of Odd- Versus Even-Electron Gas-Phase (Quasi)Molecular Ions Derived from Pyridine-Substituted N-Heterotriangulenes.

Chempluschem 2017 Feb 20;82(2):163. Epub 2016 Dec 20.

Physical Chemistry I, Department of Chemistry and Pharmacy, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Egerlandstrasse 3, 91058, Erlangen, Germany.

Invited for this month's cover are the collaborating groups at the Friedrich-Alexander University Erlangen-Nürnberg (FAU), Germany and at the Max-Planck-Institut für Kohlenforschung, Germany. The cover picture shows the symbiosis of quantum chemical theory and gas-phase collision experiment investigating the influence of the electronic state on stability of the radical cation ([M] ) and protonated triangulene ([M+H] ). The dissociation of the radical cation requires less energy due to the formation of an energetically favored extended aromatic π-system. Read the full text of the article at 10.1002/cplu.201600416.
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http://dx.doi.org/10.1002/cplu.201600596DOI Listing
February 2017

Configurationally Stable Chiral Dithia-Bridged Hetero[4]helicene Radical Cation: Electronic Structure and Absolute Configuration.

Chem Asian J 2017 Jan 5;12(1):31-35. Epub 2016 Dec 5.

Chair of Organic Chemistry I, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestrasse 42, 91054 Erlangen, Germany.

A stable chiral hetero[4]helicene radical cation was synthesized and characterized by UV/Vis absorption and EPR spectroscopy, as well as X-ray crystallography. For the first time, a combination of chiroptical methods involving ECD, ORD, and VCD, supported by quantum mechanical predictions, enabled the elucidation of the absolute configuration of such open-shell helical species.
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http://dx.doi.org/10.1002/asia.201601452DOI Listing
January 2017

Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge.

J Comput Aided Mol Des 2016 11 30;30(11):989-1006. Epub 2016 Aug 30.

Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.

One of the central aspects of biomolecular recognition is the hydrophobic effect, which is experimentally evaluated by measuring the distribution coefficients of compounds between polar and apolar phases. We use our predictions of the distribution coefficients between water and cyclohexane from the SAMPL5 challenge to estimate the hydrophobicity of different explicit solvent simulation techniques. Based on molecular dynamics trajectories with the CHARMM General Force Field, we compare pure molecular mechanics (MM) with quantum-mechanical (QM) calculations based on QM/MM schemes that treat the solvent at the MM level. We perform QM/MM with both density functional theory (BLYP) and semi-empirical methods (OM1, OM2, OM3, PM3). The calculations also serve to test the sensitivity of partition coefficients to solute polarizability as well as the interplay of the quantum-mechanical region with the fixed-charge molecular mechanics environment. Our results indicate that QM/MM with both BLYP and OM2 outperforms pure MM. However, this observation is limited to a subset of cases where convergence of the free energy can be achieved.
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http://dx.doi.org/10.1007/s10822-016-9936-xDOI Listing
November 2016

Semiempirical Quantum-Chemical Orthogonalization-Corrected Methods: Benchmarks for Ground-State Properties.

J Chem Theory Comput 2016 Mar 29;12(3):1097-120. Epub 2016 Jan 29.

Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.

The semiempirical orthogonalization-corrected OMx methods (OM1, OM2, and OM3) go beyond the standard MNDO model by including additional interactions in the electronic structure calculation. When augmented with empirical dispersion corrections, the resulting OMx-Dn approaches offer a fast and robust treatment of noncovalent interactions. Here we evaluate the performance of the OMx and OMx-Dn methods for a variety of ground-state properties using a large and diverse collection of benchmark sets from the literature, with a total of 13035 original and derived reference data. Extensive comparisons are made with the results from established semiempirical methods (MNDO, AM1, PM3, PM6, and PM7) that also use the NDDO (neglect of diatomic differential overlap) integral approximation. Statistical evaluations show that the OMx and OMx-Dn methods outperform the other methods for most of the benchmark sets.
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http://dx.doi.org/10.1021/acs.jctc.5b01047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4785506PMC
March 2016

Semiempirical Quantum-Chemical Orthogonalization-Corrected Methods: Theory, Implementation, and Parameters.

J Chem Theory Comput 2016 Mar 29;12(3):1082-96. Epub 2016 Jan 29.

Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.

Semiempirical orthogonalization-corrected methods (OM1, OM2, and OM3) go beyond the standard MNDO model by explicitly including additional interactions into the Fock matrix in an approximate manner (Pauli repulsion, penetration effects, and core-valence interactions), which yields systematic improvements both for ground-state and excited-state properties. In this Article, we describe the underlying theoretical formalism of the OMx methods and their implementation in full detail, and we report all relevant OMx parameters for hydrogen, carbon, nitrogen, oxygen, and fluorine. For a standard set of mostly organic molecules commonly used in semiempirical method development, the OMx results are found to be superior to those from standard MNDO-type methods. Parametrized Grimme-type dispersion corrections can be added to OM2 and OM3 energies to provide a realistic treatment of noncovalent interaction energies, as demonstrated for the complexes in the S22 and S66×8 test sets.
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http://dx.doi.org/10.1021/acs.jctc.5b01046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4785507PMC
March 2016

Big Data Meets Quantum Chemistry Approximations: The Δ-Machine Learning Approach.

J Chem Theory Comput 2015 May 23;11(5):2087-96. Epub 2015 Apr 23.

Institute of Physical Chemistry and National Center for Computational Design and Discovery of Novel Materials, Department of Chemistry, University of Basel , Klingelbergstraße 80, CH-4056 Basel, Switzerland.

Chemically accurate and comprehensive studies of the virtual space of all possible molecules are severely limited by the computational cost of quantum chemistry. We introduce a composite strategy that adds machine learning corrections to computationally inexpensive approximate legacy quantum methods. After training, highly accurate predictions of enthalpies, free energies, entropies, and electron correlation energies are possible, for significantly larger molecular sets than used for training. For thermochemical properties of up to 16k isomers of C7H10O2 we present numerical evidence that chemical accuracy can be reached. We also predict electron correlation energy in post Hartree-Fock methods, at the computational cost of Hartree-Fock, and we establish a qualitative relationship between molecular entropy and electron correlation. The transferability of our approach is demonstrated, using semiempirical quantum chemistry and machine learning models trained on 1 and 10% of 134k organic molecules, to reproduce enthalpies of all remaining molecules at density functional theory level of accuracy.
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http://dx.doi.org/10.1021/acs.jctc.5b00099DOI Listing
May 2015

Machine Learning of Parameters for Accurate Semiempirical Quantum Chemical Calculations.

J Chem Theory Comput 2015 May 2;11(5):2120-2125. Epub 2015 Apr 2.

Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.

We investigate possible improvements in the accuracy of semiempirical quantum chemistry (SQC) methods through the use of machine learning (ML) models for the parameters. For a given class of compounds, ML techniques require sufficiently large training sets to develop ML models that can be used for adapting SQC parameters to reflect changes in molecular composition and geometry. The ML-SQC approach allows the automatic tuning of SQC parameters for individual molecules, thereby improving the accuracy without deteriorating transferability to molecules with molecular descriptors very different from those in the training set. The performance of this approach is demonstrated for the semiempirical OM2 method using a set of 6095 constitutional isomers CHO, for which accurate atomization enthalpies are available. The ML-OM2 results show improved average accuracy and a much reduced error range compared with those of standard OM2 results, with mean absolute errors in atomization enthalpies dropping from 6.3 to 1.7 kcal/mol. They are also found to be superior to the results from specific OM2 reparameterizations (rOM2) for the same set of isomers. The ML-SQC approach thus holds promise for fast and reasonably accurate high-throughput screening of materials and molecules.
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http://dx.doi.org/10.1021/acs.jctc.5b00141DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4479612PMC
May 2015

Multiply bonded metal(II) acetate (rhodium, ruthenium, and molybdenum) complexes with the trans-1,2-bis(N-methylimidazol-2-yl)ethylene ligand.

Inorg Chem 2014 Dec 13;53(23):12305-14. Epub 2014 Nov 13.

Inorganic Chemistry and Interdisciplinary Center for Molecular Materials, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg , Egerlandstraße 1, 91058 Erlangen, Germany.

The synthesis and structural characterization of new coordination polymers with the N,N-donor ligand trans-1,2-bis(N-methylimidazol-2-yl)ethylene (trans-bie) are reported. It was found that the acetate-bridged paddlewheel metal(II) complexes [M2(O2CCH3)4(trans-bie)]n with M = Rh, Ru, Mo, and Cr are linked by the trans-bie ligand to give a one-dimensional alternating chain. The metal-metal multiple bonds were analyzed with density functional theory and CASSCF/CASPT2 calculations (bond orders: Rh, 0.8; Ru, 1.7; Mo, 3.3).
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http://dx.doi.org/10.1021/ic501435aDOI Listing
December 2014

The unrestricted local properties: application in nanoelectronics and for predicting radicals reactivity.

Authors:
Pavlo O Dral

J Mol Model 2014 Mar 16;20(3):2134. Epub 2014 Feb 16.

Computer-Chemie-Centrum and Interdisciplinary Center for Molecular Materials, University of Erlangen-Nuremberg, Nägelsbachstr. 25, 91052, Erlangen, Germany,

The local electron affinity (EA(L)) and the local ionization energy (IE(L)) are successfully used for predicting properties of closed-shell species for drug design and for nanoelectronics. Here the respective unrestricted Hartree-Fock variants of EA(L) and IE(L), i.e., the unrestricted local electron affinity (UHF-EA(L)) and ionization energy (UHF-IE(L)), have been shown to be useful for predicting properties of open-shell species. UHF-EA(L) and UHF-IE(L) have been applied for explaining unique electronic properties of an exemplary nanomaterial carbon peapod. It is also demonstrated that UHF-EA(L) is useful for predicting and better understanding reactivity of radicals related to alkanes activation.
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http://dx.doi.org/10.1007/s00894-014-2134-7DOI Listing
March 2014

Quantum chemistry structures and properties of 134 kilo molecules.

Sci Data 2014 5;1:140022. Epub 2014 Aug 5.

Department of Chemistry, Institute of Physical Chemistry, University of Basel , Klingelbergstrasse 80, CH-4056 Basel, Switzerland ; Argonne Leadership Computing Facility, Argonne National Laboratory , 9700S. Cass Avenue, Lemont, Illinois, 60439, USA.

Computational de novo design of new drugs and materials requires rigorous and unbiased exploration of chemical compound space. However, large uncharted territories persist due to its size scaling combinatorially with molecular size. We report computed geometric, energetic, electronic, and thermodynamic properties for 134k stable small organic molecules made up of CHONF. These molecules correspond to the subset of all 133,885 species with up to nine heavy atoms (CONF) out of the GDB-17 chemical universe of 166 billion organic molecules. We report geometries minimal in energy, corresponding harmonic frequencies, dipole moments, polarizabilities, along with energies, enthalpies, and free energies of atomization. All properties were calculated at the B3LYP/6-31G(2df,p) level of quantum chemistry. Furthermore, for the predominant stoichiometry, C7H10O2, there are 6,095 constitutional isomers among the 134k molecules. We report energies, enthalpies, and free energies of atomization at the more accurate G4MP2 level of theory for all of them. As such, this data set provides quantum chemical properties for a relevant, consistent, and comprehensive chemical space of small organic molecules. This database may serve the benchmarking of existing methods, development of new methods, such as hybrid quantum mechanics/machine learning, and systematic identification of structure-property relationships.
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http://dx.doi.org/10.1038/sdata.2014.22DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4322582PMC
December 2015

Probing charge transfer in benzodifuran-C60 dumbbell-type electron donor-acceptor conjugates: ground- and excited-state assays.

Chemphyschem 2013 Sep 5;14(13):2910-9. Epub 2013 Aug 5.

Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern (Switzerland), Fax: (+41) 31 631 4399.

Rigid electron donor-acceptor conjugates (1-3) that combine π-extended benzodifurans as electron donors and C60 molecules as electron acceptors with different linkers have been synthesized and investigated with respect to intramolecular charge-transfer events. Electrochemistry, fluorescence, and transient absorption measurements revealed tunable and structure-dependent charge-transfer processes in the ground and excited states. Our experimental findings are underpinned by density-functional theory calculations.
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http://dx.doi.org/10.1002/cphc.201300378DOI Listing
September 2013

Doped polycyclic aromatic hydrocarbons as building blocks for nanoelectronics: a theoretical study.

J Org Chem 2013 Mar 31;78(5):1894-902. Epub 2012 Oct 31.

Computer-Chemie-Centrum and Interdisciplinary Center for Molecular Materials, Department Chemie und Pharmazie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052 Erlangen, Germany.

Density functional theory (DFT) and semiempirical UHF natural orbital configuration interaction (UNO-CI) calculations are used to investigate the effect of heteroatom substitution at the central position of a model polycyclic aromatic hydrocarbon. The effects of the substitution on structure, strain, electronic and spectral properties, and aromaticity of the compounds are discussed.
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http://dx.doi.org/10.1021/jo3018395DOI Listing
March 2013

A π-stacked porphyrin-fullerene electron donor-acceptor conjugate that features a surprising frozen geometry.

Chemistry 2012 Oct 27;18(44):14008-16. Epub 2012 Sep 27.

Dipartimento di Scienze e Tecnologie Chimiche, University of Rome-Tor Vergata, Italy.

A "frozen" electron donor-acceptor array that bears porphyrin and fullerene units covalently linked through the ortho position of a phenyl ring and the nitrogen of a pyrrolidine ring, respectively, is reported. Electrochemical and photophysical features suggest that the chosen linkage supports both through-space and through-bond interactions. In particular, it has been found that the porphyrin singlet excited state decays within a few picoseconds by means of a photoinduced electron transfer to give the rapid formation of a long-lived charge-separated state. Density functional theory (DFT) calculations show HOMO and LUMO to be localized on the electron-donating porphyrin and the electron-accepting fullerene moiety, respectively, at this level of theory. More specifically, semiempirical molecular orbital (MO) configuration interaction (CI) and unrestricted natural orbital (UNO)-CI methods shed light on the nature of the charge-transfer states and emphasize the importance of the close proximity of donor and acceptor for effective electron transfer.
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http://dx.doi.org/10.1002/chem.201202245DOI Listing
October 2012

The relationship between threshold voltage and dipolar character of self-assembled monolayers in organic thin-film transistors.

J Am Chem Soc 2012 Aug 17;134(30):12648-52. Epub 2012 Jul 17.

Organic Materials & Devices, Institute of Polymer Materials, University Erlangen-Nürnberg, Erlangen, Germany.

We report a quantitative study that describes and correlates the threshold voltage of low-voltage organic field-effect transistors with the molecular structure of self-assembled monolayer dielectrics. We have observed that the component of the dipole moment of such self-assembled molecules perpendicular to the surface correlates linearly with the threshold voltage shift in devices. The model was validated using three different organic semiconductors (pentacene, α,α'-dihexylsexithiophene, and fullerene-C(60)) on six different self-assembled monolayers. The correlation found can help optimize future devices, by tuning the dipole moments of the molecules that constitute the self-assembled monolayer.
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http://dx.doi.org/10.1021/ja303807uDOI Listing
August 2012