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See detailMolecular switches from benzene derivatives adsorbed on metal surfaces
Liu, W.; Filimonov, S. N.; Carrasco, J. et al

in Nature Communications (2013), 4

Transient precursor states are often experimentally observed for molecules adsorbing on surfaces. However, such precursor states are typically rather short-lived, quickly yielding to more stable ... [more ▼]

Transient precursor states are often experimentally observed for molecules adsorbing on surfaces. However, such precursor states are typically rather short-lived, quickly yielding to more stable adsorption configurations. Here we employ first-principles calculations to systematically explore the interaction mechanism for benzene derivatives on metal surfaces, enabling us to selectively tune the stability and the barrier between two metastable adsorption states. In particular, in the case of the tetrachloropyrazine molecule, two equally stable adsorption states are identified with a moderate and conceivably reversible barrier between them. We address the feasibility of experimentally detecting the predicted bistable behaviour and discuss its potential usefulness in a molecular switch. © 2013 Macmillan Publishers Limited. All rights reserved. [less ▲]

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See detailOn the accuracy of van der Waals inclusive density-functional theory exchange-correlation functionals for ice at ambient and high pressures
Santra, Biswajit; Klimes, Jiri; Tkatchenko, Alexandre UL et al

in JOURNAL OF CHEMICAL PHYSICS (2013), 139(15),

Density-functional theory (DFT) has been widely used to study water and ice for at least 20 years. However, the reliability of different DFT exchange-correlation (xc) functionals for water remains a ... [more ▼]

Density-functional theory (DFT) has been widely used to study water and ice for at least 20 years. However, the reliability of different DFT exchange-correlation (xc) functionals for water remains a matter of considerable debate. This is particularly true in light of the recent development of DFT based methods that account for van der Waals (vdW) dispersion forces. Here, we report a detailed study with several xc functionals (semi-local, hybrid, and vdW inclusive approaches) on ice Ih and six proton ordered phases of ice. Consistent with our previous study [B. Santra, J. Klimes, D. Alfe, A. Tkatchenko, B. Slater, A. Michaelides, R. Car, and M. Scheffler, Phys. Rev. Lett. 107, 185701 (2011)] which showed that vdW forces become increasingly important at high pressures, we find here that all vdW inclusive methods considered improve the relative energies and transition pressures of the high-pressure ice phases compared to those obtained with semi-local or hybrid xc functionals. However, we also find that significant discrepancies between experiment and the vdW inclusive approaches remain in the cohesive properties of the various phases, causing certain phases to be absent from the phase diagram. Therefore, room for improvement in the description of water at ambient and high pressures remains and we suggest that because of the stern test the high pressure ice phases pose they should be used in future benchmark studies of simulation methods for water. (C) 2013 AIP Publishing LLC. [less ▲]

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See detailNoncovalent Interactions of DNA Bases with Naphthalene and Graphene
Cho, Yeonchoo; Min, Seung Kyu; Yun, Jeonghun et al

in JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013), 9(4), 2090-2096

The complexes of a DNA base bound to graphitic systems are studied. Considering naphthalene as the simplest graphitic system, DNA base naphthalene complexes are scrutinized at high levels of ab initio ... [more ▼]

The complexes of a DNA base bound to graphitic systems are studied. Considering naphthalene as the simplest graphitic system, DNA base naphthalene complexes are scrutinized at high levels of ab initio theory including coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)] at the complete basis set (CBS) limit. The stacked configurations are the most stable, where the CCSD(T)/CBS binding energies of guanine, adenine, thymine, and cytosine are 9.31 8.48, 8.53, 7.30 kcal/mol, respectively. The energy components are investigated using symmetry-adapted perturbation theory based on density functional theory including the dispersion energy. We compared the CCSD(T)/CBS results with several density functional methods applicable to periodic systems. Considering accuracy and availability, the optB86b nonlocal functional and the Tkatchenko-Scheffler functional are used to study the binding energies of nucleobases on graphene. The predicted values are 18-24 kcal/mol, though many-body effects on screening and energy need to be further considered. [less ▲]

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See detailElectrodynamic response and stability of molecular crystals
Schatschneider, Bohdan; Liang, Jian-Jie; Reilly, Anthony M. et al

in PHYSICAL REVIEW B (2013), 87(6),

We show that electrodynamic dipolar interactions, responsible for long-range fluctuations in matter, play a significant role in the stability of molecular crystals. Density functional theory calculations ... [more ▼]

We show that electrodynamic dipolar interactions, responsible for long-range fluctuations in matter, play a significant role in the stability of molecular crystals. Density functional theory calculations with van der Waals interactions determined from a semilocal ``atom-in-a-molecule'' model result in a large overestimation of the dielectric constants and sublimation enthalpies for polyacene crystals from naphthalene to pentacene, whereas an accurate treatment of nonlocal electrodynamic response leads to an agreement with the measured values for both quantities. Our findings suggest that collective response effects play a substantial role not only for optical excitations, but also for cohesive properties of noncovalently bound molecular crystals. DOI: 10.1103/PhysRevB.87.060104 [less ▲]

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See detailUnderstanding Structure and Bonding of Multilayered Metal-Organic Nanostructures
Egger, David A.; Ruiz, Victor G.; Said, Wissam A. et al

in JOURNAL OF PHYSICAL CHEMISTRY C (2013), 117(6), 3055-3061

For organic and hybrid electronic devices, the physicochemical properties of the contained interfaces play a dominant role. To disentangle the various interactions occurring at such heterointerfaces we ... [more ▼]

For organic and hybrid electronic devices, the physicochemical properties of the contained interfaces play a dominant role. To disentangle the various interactions occurring at such heterointerfaces we here model a complex, yet prototypical, three-component system consisting of a Cu-phthalocyanine (CuPc) film on a 3,4,9,10-perylene-tetracarboxylic-dianhydride (PTCDA) monolayer adsorbed on Ag(111). The two encountered interfaces are similar, as in both cases there would be no bonding without van der Waals interactions. Still they are also distinctly different, as only at the Ag-(111) PTCDA interface do massive charge-rearrangements occur. Using recently developed theoretical tools, we show that it has become possible to provide atomistic insight into the physical and chemical processes in this comparatively complex nanostructure distinguishing between interactions involving local rearrangements of the charge density and long-range van der Waals attraction. [less ▲]

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See detailStructure and energetics of benzene adsorbed on transition-metal surfaces: density-functional theory with van der Waals interactions including collective substrate response
Liu, Wei; Ruiz, Victor G.; Zhang, Guo-Xu et al

in NEW JOURNAL OF PHYSICS (2013), 15

The adsorption of benzene on metal surfaces is an important benchmark system for hybrid inorganic/organic interfaces. The reliable determination of the interface geometry and binding energy presents a ... [more ▼]

The adsorption of benzene on metal surfaces is an important benchmark system for hybrid inorganic/organic interfaces. The reliable determination of the interface geometry and binding energy presents a significant challenge for both theory and experiment. Using the Perdew-Burke-Ernzerhof (PBE), PBE+vdW (van der Waals) and the recently developed PBE+vdW(surf) (density-functional theory with vdW interactions that include the collective electronic response of the substrate) methods, we calculated the structures and energetics for benzene on transition-metal surfaces: Cu, Ag, Au, Pd, Pt, Rh and Ir. Our calculations demonstrate that vdW interactions increase the binding energy by more than 0.70 eV for physisorbed systems (Cu, Ag and Au) and by an even larger amount for strongly bound systems (Pd, Pt, Rh and Ir). The collective response of the substrate electrons captured via the vdW(surf) method plays a significant role for most substrates shortening the equilibrium distance by 0.25 angstrom for Cu and decreasing the binding energy by 0.27 eV for Rh. The reliability of our results is assessed by comparison with calculations using the random-phase approximation including renormalized single excitations and the experimental data from temperature-programmed desorption microcalorimetry measurements and low-energy electron diffraction. [less ▲]

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See detailAdsorption Geometry Determination of Single Molecules by Atomic Force Microscopy
Schuler, Bruno; Liu, Wei; Tkatchenko, Alexandre UL et al

in PHYSICAL REVIEW LETTERS (2013), 111(10),

We measured the adsorption geometry of single molecules with intramolecular resolution using noncontact atomic force microscopy with functionalized tips. The lateral adsorption position was determined ... [more ▼]

We measured the adsorption geometry of single molecules with intramolecular resolution using noncontact atomic force microscopy with functionalized tips. The lateral adsorption position was determined with atomic resolution, adsorption height differences with a precision of 3 pm, and tilts of the molecular plane within 0.2 degrees. The method was applied to five pi-conjugated molecules, including three molecules from the olympicene family, adsorbed on Cu(111). For the olympicenes, we found that the substitution of a single atom leads to strong variations of the adsorption height, as predicted by state-of-the-art density-functional theory, including van der Waals interactions with collective substrate response effects. [less ▲]

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See detailAssessment and Validation of Machine Learning Methods for Predicting Molecular Atomization Energies
Hansen, Katja; Montavon, Gregoire; Biegler, Franziska et al

in JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013), 9(8), 3404-3419

The accurate and reliable prediction of properties of molecules typically requires computationally intensive quantum-chemical calculations. Recently, machine learning techniques applied to ab initio ... [more ▼]

The accurate and reliable prediction of properties of molecules typically requires computationally intensive quantum-chemical calculations. Recently, machine learning techniques applied to ab initio calculations have been proposed as an efficient approach for describing the energies of molecules in their given ground-state structure throughout chemical compound space (Rupp et al. Phys. Rev. Lett. 2012 108, 058301). In this paper we outline a number of established machine learning techniques and investigate the influence of the molecular representation on the methods performance. The best methods achieve prediction errors of 3 kcal/mol for the atomization energies of a wide variety of molecules. Rationales for this performance improvement are given together with pitfalls and challenges when applying machine learning approaches to the prediction of quantum-mechanical observables. [less ▲]

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See detailExploring the bonding of large hydrocarbons on noble metals: Diindoperylene on Cu(111), Ag(111), and Au(111)
Buerker, C.; Ferri, N.; Tkatchenko, Alexandre UL et al

in PHYSICAL REVIEW B (2013), 87(16),

We present a benchmark study for the adsorption of a large pi-conjugated organic molecule on different noble metal surfaces, which is based on x-ray standing wave (XSW) measurements and density functional ... [more ▼]

We present a benchmark study for the adsorption of a large pi-conjugated organic molecule on different noble metal surfaces, which is based on x-ray standing wave (XSW) measurements and density functional theory calculations with van der Waals (vdW) interactions. The bonding distances of diindenoperylene on Cu(111), Ag(111), and Au(111) surfaces (2.51, 3.01, and 3.10 angstrom, respectively) determined with the normal-incidence XSW technique are compared with calculations. Excellent agreement with the experimental data, i.e., deviations less than 0.1 angstrom, is achieved using the Perdew-Burke-Ernzerhof (PBE) functional with vdW interactions that include the collective response of substrate electrons (the PBE + vdW(surf) method). It is noteworthy that the calculations show that the vdW contribution to the adsorption energy increases in the order Au(111) < Ag(111) < Cu(111). [less ▲]

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See detailMany-Body Dispersion Interactions in Molecular Crystal Polymorphism
Marom, Noa; DiStasio, Jr; Atalla, Viktor et al

in ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2013), 52(26), 6629-6632

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See detailMachine learning of molecular electronic properties in chemical compound space
Montavon, Gregoire; Rupp, Matthias; Gobre, Vivekanand et al

in NEW JOURNAL OF PHYSICS (2013), 15

The combination of modern scientific computing with electronic structure theory can lead to an unprecedented amount of data amenable to intelligent data analysis for the identification of meaningful ... [more ▼]

The combination of modern scientific computing with electronic structure theory can lead to an unprecedented amount of data amenable to intelligent data analysis for the identification of meaningful, novel and predictive structure-property relationships. Such relationships enable high-throughput screening for relevant properties in an exponentially growing pool of virtual compounds that are synthetically accessible. Here, we present a machine learning model, trained on a database of ab initio calculation results for thousands of organic molecules, that simultaneously predicts multiple electronic ground- and excited-state properties. The properties include atomization energy polarizability, frontier orbital eigenvalues, ionization potential electron affinity and excitation energies. The machine learning model is based on a deep multi-task artificial neural network, exploiting the underlying correlations between various molecular properties. The input is identical to ab initio methods, i.e. nuclear charges and Cartesian coordinates of all atoms. For small organic molecules, the accuracy of such a `quantum machine' is similar, and sometimes superior, to modern quantum-chemical methods-at negligible computational cost. [less ▲]

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See detailQuantification of finite-temperature effects on adsorption geometries of π-conjugated molecules: Azobenzene/Ag(111)
Mercurio, G.; Maurer, R. J.; Liu, W. et al

in Physical Review B - Condensed Matter and Materials Physics (2013), 88(3),

The adsorption structure of the molecular switch azobenzene on Ag(111) is investigated by a combination of normal incidence x-ray standing waves and dispersion-corrected density functional theory. The ... [more ▼]

The adsorption structure of the molecular switch azobenzene on Ag(111) is investigated by a combination of normal incidence x-ray standing waves and dispersion-corrected density functional theory. The inclusion of nonlocal collective substrate response (screening) in the dispersion correction improves the description of dense monolayers of azobenzene, which exhibit a substantial torsion of the molecule. Nevertheless, for a quantitative agreement with experiment explicit consideration of the effect of vibrational mode anharmonicity on the adsorption geometry is crucial. © 2013 American Physical Society. [less ▲]

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See detailFirst-Principles Modeling of Non-Covalent Interactions in Supramolecular Systems: The Role of Many-Body Effects
Tkatchenko, Alexandre UL; Alfe, Dario; Kim, Kwang S.

in JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012), 8(11), 4317-4322

Supramolecular host-guest Systems play an important role for a wide range of applications in chemistry and biology. The prediction of the stability of host-guest complexes represents a great challenge to ... [more ▼]

Supramolecular host-guest Systems play an important role for a wide range of applications in chemistry and biology. The prediction of the stability of host-guest complexes represents a great challenge to first-principles calculations Clue to, an interplay of a ride variety of covalent and noncovalent interactions in these systems. In particular van der Waals (vdW) dispersion interactions frequently play a prominent role in determining the structure, stability, and function of supramolecular systems. On the basis of the widely used benchmark case of the buckyball catcher complex (C-60@C60H28), we assess the feasibility of computing the binding energy of supramolecular host-guest complexes from first principles. Large-scale diffusion Monte Carlo (DMC) calculations are carried out to accurately determine the binding energy for the C-60@C60H28 complex (26 +/- 2 kcal/mol). On the basis of the DMC reference, we assess the accuracy of widely used and efficient density-functional theory (DFT) methods with dispersion interactions. The inclusion of vdW dispersion interactions in DFT leads to a large stabilization of the C-60@C60H28 complex. However, DFT methods including pairwise vdW interactions overestimate the stability of this complex by 9-17 kcal/mol compared to the DMC reference and the extrapolated experimental data. A significant part of this overestimation (9 kcal/mol) stems from the lack of dynamical dielectric screening effects in the description of the molecular polarizability in pairwise dispersion energy approaches. The remaining overstabilization. arises from the isotropic treatment of atomic polarizability tensors and the lack of Many-body dispersion interactions. A further; assessment of a different supramolecular system - glycine anhydride interacting with an amide macrocycle - demonstrates that both the dynamical screening and the many-body dispersion energy are complex contributions that are very sensitive to the underlying molecular geometry and type of bonding. We discuss the required improvements in theoretical methods for achieving ``chemical accuracy'' in the first-principles modeling of supramolecular systems. [less ▲]

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See detailAccurate and Efficient Method for Many-Body van der Waals Interactions
Tkatchenko, Alexandre UL; DiStasio, Jr; Car, Roberto et al

in PHYSICAL REVIEW LETTERS (2012), 108(23),

An efficient method is developed for the microscopic description of the frequency-dependent polarizability of finite-gap molecules and solids. This is achieved by combining the Tkatchenko-Scheffler van ... [more ▼]

An efficient method is developed for the microscopic description of the frequency-dependent polarizability of finite-gap molecules and solids. This is achieved by combining the Tkatchenko-Scheffler van der Waals (vdW) method [Phys. Rev. Lett. 102, 073005 (2009)] with the self-consistent screening equation of classical electrodynamics. This leads to a seamless description of polarization and depolarization for the polarizability tensor of molecules and solids. The screened long-range many-body vdW energy is obtained from the solution of the Schrodinger equation for a system of coupled oscillators. We show that the screening and the many-body vdW energy play a significant role even for rather small molecules, becoming crucial for an accurate treatment of conformational energies for biomolecules and binding of molecular crystals. The computational cost of the developed theory is negligible compared to the underlying electronic structure calculation. [less ▲]

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See detailCollective many-body van der Waals interactions in molecular systems
DiStasio Jr., R. A.; Von Lilienfeld, O. A.; Tkatchenko, Alexandre UL

in Proceedings of the National Academy of Sciences of the United States of America (2012), 109(37), 14791-14795

Van der Waals (vdW) interactions are ubiquitous in molecules and condensed matter, and play a crucial role in determining the structure, stability, and function for a wide variety of systems. The accurate ... [more ▼]

Van der Waals (vdW) interactions are ubiquitous in molecules and condensed matter, and play a crucial role in determining the structure, stability, and function for a wide variety of systems. The accurate prediction of these interactions from first principles is a substantial challenge because they are inherently quantum mechanical phenomena that arise from correlations between many electrons within a given molecular system. We introduce an efficient method that accurately describes the nonadditive many-body vdW energy contributions arising from interactions that cannot be modeled by an effective pairwise approach, and demonstrate that such contributions can significantly exceed the energy of thermal fluctuations - a critical accuracy threshold highly coveted during molecular simulations - in the prediction of several relevant properties. Cases studied include the binding affinity of ellipticine, a DNA-intercalating anticancer agent, the relative energetics between the A- and B-conformations of DNA, and the thermodynamic stability among competing paracetamol molecular crystal polymorphs. Our findings suggest that inclusion of the many-body vdW energy is essential for achieving chemical accuracy and therefore must be accounted for in molecular simulations. [less ▲]

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See detailPhase transition between cubic and monoclinic polymorphs of the tetracyanoethylene crystal: the role of temperature and kinetics
Schatschneider, Bohdan; Liang, Jian-Jie; Jezowski, Sebastian et al

in CRYSTENGCOMM (2012), 14(14), 4656-4663

Prediction of the relative stabilities and phase transition behavior of molecular crystalline polymorphs is highly coveted as distinct phases can possess different physical and chemical properties while ... [more ▼]

Prediction of the relative stabilities and phase transition behavior of molecular crystalline polymorphs is highly coveted as distinct phases can possess different physical and chemical properties while having similar energies. Crystalline tetracyanoethylene (TCNE, C6N4) is known to exhibit rich solid state phase behavior under different thermodynamic conditions, as demonstrated by a wealth of experimental studies on this system. Despite this fact, the role of temperature and kinetics on the phase diagram of TCNE remains poorly understood. Here, first-principles calculations and high-resolution Fourier-transformed infrared (HR-FTIR) spectroscopy experiments are used to study the relative stabilities of the cubic and monoclinic phases of TCNE as a function of temperature. Specifically, density-functional theory with the van der Waals interactions method of Tkatchenko and Scheffler (DFT+vdW) is employed. The accuracy of this approach is demonstrated by the excellent agreement between the calculated and experimental structures. We find that the cubic phase is the most stable polymorph at 0 K, but becomes less favorable than the monoclinic phase at 160 K. This temperature-induced phase transition is explained on the basis of varying close contacts and vibrational entropies as a function of temperature. These findings are N vibrons. [less ▲]

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See detailFast and Accurate Modeling of Molecular Atomization Energies with Machine Learning
Rupp, Matthias; Tkatchenko, Alexandre UL; Mueller, Klaus-Robert et al

in PHYSICAL REVIEW LETTERS (2012), 108(5),

We introduce a machine learning model to predict atomization energies of a diverse set of organic molecules, based on nuclear charges and atomic positions only. The problem of solving the molecular ... [more ▼]

We introduce a machine learning model to predict atomization energies of a diverse set of organic molecules, based on nuclear charges and atomic positions only. The problem of solving the molecular Schrodinger equation is mapped onto a nonlinear statistical regression problem of reduced complexity. Regression models are trained on and compared to atomization energies computed with hybrid density-functional theory. Cross validation over more than seven thousand organic molecules yields a mean absolute error of similar to 10 kcal/mol. Applicability is demonstrated for the prediction of molecular atomization potential energy curves. [less ▲]

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See detailDensity-Functional Theory with Screened van der Waals Interactions for the Modeling of Hybrid Inorganic-Organic Systems
Ruiz, Victor G.; Liu, Wei; Zojer, Egbert et al

in PHYSICAL REVIEW LETTERS (2012), 108(14),

The electronic properties and the function of hybrid inorganic-organic systems (HIOS) are intimately linked to their interface geometry. Here we show that the inclusion of the many-body collective ... [more ▼]

The electronic properties and the function of hybrid inorganic-organic systems (HIOS) are intimately linked to their interface geometry. Here we show that the inclusion of the many-body collective response of the substrate electrons inside the inorganic bulk enables us to reliably predict the HIOS geometries and energies. This is achieved by the combination of dispersion-corrected density-functional theory (the DFT+ van der Waals approach) [Phys. Rev. Lett. 102, 073005 (2009)], with the Lifshitz-Zaremba-Kohn theory for the nonlocal Coulomb screening within the bulk. Our method yields geometries in remarkable agreement (approximate to 0.1 angstrom) with normal incidence x-ray standing wave measurements for the 3, 4, 9, 10-perylene-tetracarboxylic acid dianhydride (C24O6H8, PTCDA) molecule on Cu(111), Ag(111), and Au(111) surfaces. Similarly accurate results are obtained for xenon and benzene adsorbed on metal surfaces. [less ▲]

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See detailBenzene adsorbed on Si(001): The role of electron correlation and finite temperature
Kim, Hyun-Jung; Tkatchenko, Alexandre UL; Cho, Jun-Hyung et al

in PHYSICAL REVIEW B (2012), 85(4),

van der Waals energy-corrected density functional theory (DFT + vdW) as well as the exact exchange with electron correlation in the random-phase approximation are used to study the adsorption of benzene ... [more ▼]

van der Waals energy-corrected density functional theory (DFT + vdW) as well as the exact exchange with electron correlation in the random-phase approximation are used to study the adsorption of benzene on the Si(001) surface with respect to two controversial adsorption structures (termed ``butterfly'' and ``tight bridge''). Our finding that the tight-bridge structure is energetically favored over the butterfly structure agrees with standard DFT but conflicts with previous vdW-inclusive calculations. However, the inclusion of zero-point energy and thermal vibrations reverses the stability of the two structures with increasing temperature. Our results provide an explanation for the recent experimental observation that both structures coexist at room temperature. [less ▲]

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See detailReply to Comment on Fast and Accurate Modeling of Molecular Atomization Energies with Machine Learning
Rupp, M.; Tkatchenko, Alexandre UL; Müller, K.-R. et al

in Physical Review Letters (2012), 109(5),

[No abstract available]

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