518 CHIMIA 2012, 66, No. 7/8 Computational Chemistry

doi:10.2533/chimia.2012.518 Chimia 66 (2012) 518–531 © Schweizerische Chemische Gesellschaft

ComputationalChemistry ComputationalChemistry Computational Chemistry,Talk 155 Computational Chemistry,Talk 156 ExploringPhotoinduced Intermolecular Electrontransferwith Local Control Theory in Trajectory-based Nonadiabatic Dynamics

Molecular Dynamics Simulations B. F. E. Curchod1,T.J.Penfold1,2,3,U.Rothlisberger1,and I. Tavernelli1

A. Gamiz-Hernandez1,E.Vauthey2,M.Meuwly1 1Laboratory of Computational Chemistry and Biochemistry, Ecole Poly- technique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland 1UniversityofBasel/DepartmentofChemistry, Klingelbergstr. 80, CH-4055 2Laboratoire de Spectroscopie Ultrarapide, Ecole Polytechnique Fédérale de Basel, Switzerland Lausanne, CH-1015 Lausanne, Switzerland 2UniversityofGeneva/DepartmentofPhysicalChemistry, 30 quaiErnest- 3SwissFEL, Paul Scherrer Inst., CH-5232 Villigen, Switzerland. Ansermet, CH-1211 Geneva 4, Switzerland In the last years, linear-response time-dependent density functional theory (LR-TDDFT) has become widely used for the calculation of vertical elec- Understandingthe dynamics of photoinduced chemical processes involving tronic excitation energies of medium to large size molecular systems in gas electron transfer(ET)isacrucialstep for the designofnew technologies and condensed phases. In addition, excited state LR-TDDFT forces and such as efficient solar energy conversion devices. Photoinduced ET pro- nonadiabatic couplings have also been implementedindifferent software cesses have been investigated for some time [1], nevertheless thereare still packages, which enables LR-TDDFT based ab initio molecular dynamics severalquestionsregarding intermolecular ET reactions such as theoccur- approaches for the study of photochemical reactions. renceoflongdistancereactions andthe ChargeSeparation(CS)products. Manyexperiments have corroborated Marcus theory[2] for ET, however, Here, we present adevelopment of aLR-TDDFTtrajectory surface hopping most of these models aresimplifications as theyconsiderthe reactants as scheme that couples nuclear and electronic degrees of freedom with an ex- spheres andquantities such as the reorganizationenergyare computed using ternal electromagnetic field [1,2]. This further allows the on-the-fly calcula- continuum models for the solvent. Molecular Dynamics (MD)simulations tion of an electric pulse, which controls the population transfer between of photoinduced reactions have the potential to provide abetterinsightto electronic states using local control theory. This method is applied to the explore for example, at whatdistance CS takesplace, what is the nature of molecule lithium fluoride and the results are compared with nuclear quan- the primaryion pair product, computationofmore accurate reorganization tum dynamics using the MCTDH method. In addition, we will present an energies basedonanexplicitsolvent models andhow intermolecularinter- example of how acontrolled pulse can trigger aphotochemical reaction like actions influencethe orientations of the reactants. proton transfer in 4-hydroxyacridine. This research will presentsome resultsfromMDSimulations of bimolecu- [1] I. Tavernelli, B. F. E. Curchod, and U. Rothlisberger, Phys. Rev. A lar photoinduced ET reactions [1], in particularthe Perylene- 2010, 81,052508. Dimethylaniline system.Weinvestigate how the solvent adoptsdifferent [2] B. F. E. Curchod, T. J. Penfold, U. Rothlisberger, and I. Tavernelli, configurations as well as possible pathwaysfor CS. These conformations Phys. Rev. A 2011, 84,042507. areusedfor quantum-chemical calculations to generateabsorption/emission spectra,helping to explain experimentalresults. [1] E. Vauthey, J. Photochem. Photobiol. A, 2006,179, 1. [2] R. A. Marcus andN.Sutin, Biochim. Biophys. Acta, 1985,811, 265.

ComputationalChemistry ComputationalChemistry Computational Chemistry,Talk 157 Computational Chemistry,Talk 158 EffectofProtein EnvironmentonExcitation EnergyofRetinal Spectral Tuning in Rhodopsin Early Photointermediates

Xiuwen Zhou1,Tomasz A. Wesolowski2 Pablo Campomanes,Ursula Röthlisberger

1 University of Geneva,Department of Physical Chemistry, Quai Ernest- Ecole Polytechnique Fédérale Lausanne, CH-1015, Lausanne, Switzerland Ansermet 30, CH-1211 Geneva,Switzerland The visual pigment rhodopsin is ahighly specialized member of the GPCR Retinalisachromophoreofkey importanceinthe photochemical process family found in vertebrate rod cells. Rhodopsin is able to capture and con- responsiblefor animalvision,which begins with cis-trans vert light into achemical signal, in what constitutes the first step of the vi- photoisomerization(seeFigure1)ofretinal bound to opsin(aprotein)[1]. sion. The photoinduced isomerization of its natural ligand (11-cis retinal) The absorbtion spectrumofthe chromophoreisaffectedbythe proteinto inside the binding pocket initiates acascade of conformational changes that whichitisbound. The long range objectiveofthisproject is thedevelop- leads ultimately to receptor activation and subsequentdownstream signal- ment of an accurate modelingtechnique to predictthe effect of proteinmu- ing. Several spectroscopically distinguishable intermediates involved in the tations on theabsorption spectra of retinal.Suchtechnique couldbeusedto early steps of this photoactivation mechanism have been detected, and the help designing proteinmutations leadingtodesired spectralpropertiesofthe structures of some of them have been determined. However, the complete chromophore. Theappliedcomputationalmethod belongs to thecategoryof knowledge of the factors that selectively modulate retinal absorption during multi-levelsimulations andisbased on Frozen-Density EmbeddingTheory the initial events of the visual cascade is far from being achieved and, there- (FDET) [2-4]. Theresults of thefirst stage of this project will be reported fore, adirect relation between the structural changes caused by the relaxa- concerning: a) developmentofanefficient method to generatethe frozen tion of the photoexcited chromophoreupon isomerization and the corre- density forFDETcalculations developedbased on comparison between sponding optical shifts observed for the intermediates involved in the very benchmark supermolacularab-initio results [5]obtainedfor small models of early steps of the rhodopsin photocycle has not been established yet. the environment, andb)modelingthe effect of point mutations in proteins In this contribution, Iwill show how acombined strategy based on the com- on theabsorption spectra. putation of absorption energies, using the ZINDO/Ssemi-empiricalmethod, for astatistically relevant number of thermally sampled configurationsex- Figure 1.Photoisomerizationofretinal tracted from QM/MM trajectoriescan be used to establish aone-to-one cor- respondence between the structures of the different intermediates involved in the very early steps of the rhodopsin photocycle and their optical spectra. [1]R.Hubbard andG.Wald, J. Gen. Physiol., 1952-53,36, 269. The analysis of the results clarify the role played by some of the residues located in the protein-binding pocket as well as the importance of the struc- [2]T.A. Wesolowski andA.Warshel, J. Phys. Chem., 1993, 97,8050. tural features and conformation of the chromophore on the spectral shifts [3]T.A. Wesolowski, Computational Chemistry: ReviewsofCurrent observed between the intermediates. They also permit the identification of Trends,J.Leszczynski,Ed. WorldScientific, 2006, 10,1. the structural parameters that better describe the different transitions leading [4]T.A. Wesolowski, Phys. Rev. A, 2008, 77,012504. from dark- to lumi-rhodopsin, therefore allowing the characterization of the [5]V.R.I.Kaila,R.Send, D. Sundholm, J. Phys. Chem.B,2012, 116,2249. distinct states. Computational Chemistry CHIMIA 2012, 66, No. 7/8 519

Computational Chemistry Computational Chemistry Computational Chemistry,Talk 159 Computational Chemistry,Talk 160 Unravelling the electronic structureofmolecules with density-only Exploring the Limits of Modern Density Functional Approximations based detectors for Interaction Energies

Piotr de Silva1,2,Jacek Korchowiec1,Tomasz A. Wesolowski2 StephanN.Steinmann and ClemenceCorminboeuf

1K. Guminski´ Department of Theoretical Chemistry,Faculty of Chemistry, Laboratory for Computational MolecularDesign, Institute of Chemical Jagiellonian University,R.Ingardena 3, 30-060 Krakow´ ,Poland Sciences and Engineering,Ecole Polytechnique Fédérale de Lausanne, 1015 2Universited´ eGenev` e, Departement´ de Chimie Physique 30, quai Lausanne, Switzerland Ernest-Ansermet, CH-1211 Genev` e4,Switzerland Charge transfer complexes and charged radical π-dimers span the field The Electron Localization Function (ELF) [1-3] has provedtobeanexcep- of organicelectronics,makingtheircharacterization of considerable interest. Theelectronic structure of charge transfer complexes is highly tionally useful concept in the elucidation of bonding patterns in molecules and challenging.1 We demonstrate that standard densityfunctionals fail to solids. The major drawbacks of ELF are its orbital dependence and the use of accurately describeinteraction energies of charge-transfer complexes not the homogeneous electron gasareference. In this contribution, we propose only because of the missing long-range exchange, as generally assumed, but an entirely newparadigm for the clarification of the electronic structure in predominantlybecauseofthe ubiquitously present, yet neglected dispersion terms of such intuitive concepts likebonds, core electrons and lone pairs. We interactions.2 These assertions are based on the evaluationofthe interaction introduce detectors which are calculated only from the electron density and energies using DFT coupled withour recent density-dependent dispersion its first and second derivatives. This feature makes them directly applicable at correction (dDsC)3 and high-level ab initio computations. While global anylevel of theory as well as to experimental densities. hybrid functionals describe well the electronic structure of neutral charge- transfer complexes, long-range corrected exchange is required for the correctqualitative potentialenergycurve of cationic π-dimers. Accounting fordispersion via dDsC is strongly recommendedinall cases. Our analysis reflects the delicate errorcancellation betweenthe delocalization error (overestimationofcharge-transfer)and the missing long-range interactions.

Figure 1: ELF (left) and one of the proposed detectors (right) for the fluo- renone molecule. [1] E. Ruiz, D.R. Salahub, A. Vela, J. Am. Chem.Soc. 1995, 117,1141. [1] Becke, A. D. and Edgecombe, K. E., J. Chem. Phys. 1990, 92,5397. [2] S.N.Steinmann, C. Piemontesi,A.Delachat,C.Corminboeuf, J. [2] Silvi, B. and Savin, A. , Nature 1994, 371,683. Chem. Theory Comput.,doi 10.1021/ct200930x. [3] Savin, A.; Nesper,R.; Wengert, S.; Fassler,T.F.,Angew. Chem. Int. Ed. [3] S.N. Steinmann, C. Corminboeuf, J. Chem. Theory Comput. 2011, 7, Engl. 1997, 36,1809. 3567.

ComputationalChemistry Computational Chemistry Computational Chemistry,Talk 161 Computational Chemistry,Poster Talk 162 Newadvancesinadiabatic reactive moleculardynamicssimulations DFTstudiesofHNCO adsorption at the stabilizedironcomplexes in theZSM-5 pore Tibor Nagy,Juvenal Yosa,MarkusMeuwly* I. Czekaj,S.Brandenberger, O. Kröcher University of Basel, Klingelbergstrasse 80,4056Basel Paul Scherrer Institute,Villigen, Switzerland Adiabaticreactivemoleculardynamics (ARMD) simulation is asurface- [email protected] crossing algorithm[1–4] that allows onetofollowbond-breaking andbond- The stabilization of monomeric and dimeric ironcomplexes [1], such as Fe- formingprocessesinclassical moleculardynamicssimulations. OH andHO-Fe-O-Fe-OH and Fe-O-Fe, in the ZSM-5 pore has been inves- In ARMD thedynamics of thesystemispropagatedonthe tigated usingaDFT approach withacluster model.ASi20O53H28 cluster V0(x)=min[VR(x)+δ, VP(x)] surface,where VR and VP arethe potentialenergy waschosen to representpart of asingle channelinthe ZSM-5. In this basic surfaces of reactantsand products,respectively, and δ is used to adjust the cluster, two Si atomswere replaced by twoaluminumatomstosimulate the asymptoticsofthe twosurfaces.Duringdynamicswhenthe energy of the exchangesites in the ZSM-5 and to determine the energetically favorable twosurfaces become equal, thesystemisre-simulatedfromawhile earlier locationsfor Al-Al couples. Inside the clustersofthe ZSM-5structure, iron by graduallyswitching in time from VR + δ to VP thus surfacecrossing can oxohydroxide and oxidespecies formed stable monomer anddimmercon- take place. - figurations.Inboth cases, the iron sitesbound to the oxygen atomsofAlO4 ; - Althoughthe totalenergycan be approximatelyconserved over the this occurred because AlO4 tetrahedra carry greater negative charges and shortswitching times[1],the algorithmcan be improved.Furthermore de- attract iron cationsstronger than SiO4 tetrahedra. The stabilization energy pendingonthe speed of approach to thebarrier different barrier region is periron sitewas about 3.5eVfor themonomeric iron complex and 1.0 eV felt by theatoms andevenspurious transientmaximacan appear.These arti- to 2.5 eV for the different dimericiron sites. These similar energy levels, in factsmay alterthe dynamics duringcrossingsignificantly andlead to differ- combinationwith adetailed study of the geometric structureofthe iron and entfinal-state specific reaction probabilities.Analternative geometry-based oxygen centers in the zeolite,supportour hypotheses that thedistribution of switchingfunctionwas proposed,which curesall theseproblemsand elimi- iron sites follows the distribution of theAlatomsand thatnopreferred con- natesthe need forrepeatedsimulation. figurationsexist fortheseinteractions. Additionally molecular and dissocia- Thenew algorithmisapplied to theunimoleculardecomposition of tive adsorption of isocyanicacidatironparticleshas been investigated. The sulphuricacidafter overtone excitation of theOHvibration [3,5], andtothe resultsoftheoretical vibration frequencies have beencomparedwith ex- + perimental DRIFT data [2]. charge-transferreactionbetween N2 andN2 at lowtemperatures. Thedif- ferences compared to theoriginalapproachare discussed. [1] S. Brandenberger, O. Kröcher, A. Tissler, R. Althoff, Appl.Catal. [1]J.Danielsson, M. Meuwly, J. Chem.Theory. Comput. 2008, 4,1083. A 2010, 373,168. [2]S.Mishra, M. Meuwly. J. Am.Chem. Soc. 2010,132,2968. [2] G. Piazzesi, D.Nicosia,M.Devadas, O. Kröcher, M. Elsener, A. Wo- [3]J.Yosa, M. Meuwly. J. Phys.Chem. B 2011, 115, 14350. kaun, Catal. Lett. 2007, 115,33. [4]S.Lutz, M. Meuwly. ChemPhysChem 2012,13, 305. [5]V.Vaida,D.J.Donaldson,H.G.Kjaergaard, P.E. Hintze Science 2003,299,1566. 520 CHIMIA 2012, 66, No. 7/8 Computational Chemistry

Computational Chemistry Computational Chemistry Computational Chemistry,Poster Talk 163 Computational Chemistry,Poster Talk 164 Atomic Multipole Moments for organic molecules:Reference axis The influence of heme doming on the rebinding of NO to Myoglobin systems andbenefits over point charges JaroslawJ.Szymczak and Markus Meuwly* ChristianKramer,1,2 PeterGedeck, 1 Markus Meuwly2 Chemistry Department, University of Basel, Klingelbergstrasse 80, 4056 1 Novartis Institutes forBioMedical Research, Campus St. Johann, Basel 4056 Basel, Switzerland 2 Department of Chemistry,University of Basel, Klingelbergstrasse80, Recent time-resolved resonance Raman experiments suggested that the pho- 4056 Basel,Switzerland todissociated NO can rebind to the domed, Fe-out-of-plane conformation of the heme unit[1]. This experiment found that the heme-iron motion and NO Atomic multipole moments represent aviable option forimproving the rebinding kinetics are not synchronized. Upon NO-photolysis, the transition standard termsused for intermolecularinteractions in current biomolecular from an in-plane to adomed-Fe conformation occurs on the subpicosecond force fields.Since atomicmultipoles are anisotropicbynature, local referenceaxissystems have to be introduced to align and rotate multipole time scale whereas the opposite process (domed to in-plane) takes ≈ 30 momentsinmolecular dynamics. We show how atomicmultipoles (MTPs) ps. On the other hand, in the infrared the rapid rebinding component occurs can be rigorouslyimplemented into common biomolecular force fields. For within 5pswhich suggests that the returning ligand can rebind to adomed- this, acomprehensive set of local reference axis systemsisintroduced iron conformation, which has already been suggested by Ionascu et al.[2]. To whichrepresents auniversal solutionfor treatingatom-centered multipoles shed additional light on the structural dynamics underlying this process, an for allsmall organic moleculesand proteins. extended model for the heme-NO interaction is currently being developed. Apart from the previously considered[3] relative orientation of the NO ligand We furthershow that atomicmultipolescan reduce the error in reproducing to the heme-iron, the iron-out-of-plane (doming) coordinate will be explicitly the electrostatic potential (ESP) by 50 – 90 %comparedtopoint charges. considered in the newly-designed molecular dynamics simulations. The result Also, thereproduction of the ESP can be dramatically improved by directly of performed simulations will help to understand howheme doming affects fitting themultipolestothe ESPcomparedtothe standardmethodsof rebinding of NO to Myoglobin. partitioning theelectrondensity and calculating multipole momentsfor atom-assigned electron densities. Additionally,for flexiblemolecules it is [1] S. G. Kruglik and B.-K. Yooand S. Franzen and M. H. Vosand J.-L. shown, that conformationally independent multipole momentscan be found Martin and M. Negrerie PNAS 2010, 107,1367-136838. thatacceptably reproduce theESP.However, thesemultipole moments can [2] D. Ionascu and F. Gruia and X. Ye and A. Yu and F. Rosca and C. Beck A. neither be obtainedfrom single conformations or as average of parameters Demidovand J. S. Olson and P. M. Champion, JACS 2005, 127,16921- fitted to individual molecules -they havetobefittedtothe conformational 16934. ensemble. [3] D. R. Nutt, D. R. and M. Karplus, and M. Meuwly, J. Phys. Chem. B 2005, 109,21118. [1] Kramer, C.; Gedeck, P.;Meuwly,M.AtomicMultipoles: Electrostatic Potential Fit,Local Reference Axis Systems and Conformational Dependence. J. Comp.Chem. accepted.

Computational Chemistry ComputationalChemistry Computational Chemistry,Talk 165 Computational Chemistry,Talk 166 CO transfer in the binuclear a site of cytochrome coxidase EndocyclicCleavage-Induced Anomerization Reactions of Glycosides: 3 QM/MMMolecular Dynamics Simulation Study Maksym Soloviov,Markus Meuwly� HirokoSatoh1,Teodoro Laino2,Jürg Hutter3 Department of Chemistry,University of Basel, Klingelbergstrasse 80, 1NationalInstituteofInformatics (NII), Tokyo,101-8430, Japan, 2IBMRe- CH-4056 Basel search Zürich,8803 Rüschlikon, 3UniversityofZürich, 8057 Zürich

Cytochrome coxidase (CcO) is aprotein involved in catalysis of the terminal Pyranosidescarrying2,3-trans-carbamate easilyundergoendocyclic step in cellular respiration in mitochondria or bacteria [1]. In fact, the cy- cleavage-induced anomerizationfromthe -form to the
-forminthe pres- tochrome heme a3 and CuB form abinuclear center that is the site of oxygen ence of aweakLewis acid, despiteofthe fact that theendocycliccleavage is reduction. In contrast to O2,COforms astable complexwith the enzyme. assumed to be aminor cleavage modeofglycosides. Manabe reportedex- Due to agreater affinity of CO for CuB than for Fe(II) of heme a3,CObinds perimental evidencethat confirms the existance of endocleavage in the class to CuB when Fe-CO bond is broken. As the Fe-C and CO vibrations are only of compounds [1]. With DFTcalculations as well as furtherexperiments, we weakly coupled, the Fe-C bond can only be broken by electronic excitation andcoworkers concludedthat, for glycosides with 2,3-trans cyclic protect-

[2,3]. Experimentally,arrivalofCOtoCuBsite is observed within 2psafter ing group, inner straincaused by the fusedringsisthe primaryfactor en- UV excitation [2]. hancingthe endocleavage reaction[2].Weperformed ab initioQM/MM Such time scales are ideal for atomistic simulations which are capable of fol- molecular dynamics simulations of the anomerizationreactiontogainabet- lowing in detail the trajectories of all the atoms involved. There are several ter understandingofthe reactionmechanism in solution as well as confor- mationaldetails along the reactionpathway. Thesimulations demonstrate possible mechanisms for the transfer of CO from Fe(II) to CuB:elongation of unequivocallythat the reactionpathischaracterized by peculiar conforma- Fe-CO followed by rotation, by forming an intermediate CuB-OC state or by forming free CO. To obtain an atomistically detailed mechanism and the dy- tionalchanges promotingthe endocyclicway.Wewill report here the first namics of the process, potential energy surfaces (PES) have been build based resultsofthe simulation study. on DFT calculations, the B3LYP functional and LANL2DZ (for Cu and Fe) and 6-31G++ basis sets have been used. The effective potential has been im- plemented in CHARMM and MD simulations of CO were carried out to study possible scenarios. The dynamics of CO bound and unbound to Fe of heme is analyzed in detail.

[1] J. Koepke, E. Olkhova, Biochimica et Bioph. Acta 2009, 1787,635-645. [2] J. Treuffet, K.J. Kubarych et al Proc. Natl. Acad. Sci. 2007, 104,15705- [1]Manabe,S.; Ishii,K.; Hashizume, D.; Koshino, H.; Ito, Y. Chem. 15710. Eur. J. 2009, 15,6894. [3] P.A.Anfinrud, C.Han, R.M.Hochstrasser, Proc. Natl. Acad. Sci. 1989, [2]Satoh, H.; Manabe,S.; Ito, Y.; Lüthi,H.P.; Laino,T.; Hutter,J.J. 86,8387-8391. Am. Chem. Soc. 2011, 133,5610. Computational Chemistry CHIMIA 2012, 66, No. 7/8 521

Computational Chemistry Computational Chemistry Computational Chemistry,Talk 167 Computational Chemistry,Talk 168 Intramolecular Symmetry-Adapted Perturbation Theory ForceMatching and Iterative Boltzmann Inversion to Improve DFTB Parameters forLiquid Water Jer´ omeˆ F. Gonthier,Clemence´ Corminbœuf M. Doemer1,J.Knaup2,I.Tavernelli1,U.Rothlisberger1 Laboratory of Computational Molecular Design, Institut des Sciences et Ingenierie´ Chimiques, Ecole Polytechnique Fed´ erale´ de Lausanne 1Ecole Polytechnique Fed´ erale,´ Lausanne, Switzerland Lausanne, CH-1015, Switzerland 2Universitat¨ Bremen -BCCMS, Bremen, Germany

Intermolecular interactions play an ubiquitous role in chemistry and biology, with representative examples including protein-ligand interactions, supramo- lecular assembly,pre-reactive complexes, etc. The theoretical decomposition of intermolecular interactions into physically meaningful terms enhances our understanding of such processes. Among the various existing decomposition schemes, Symmetry-Adapted Perturbation Theory (SAPT)[1] may be consid- ered as the most successful, as it naturally decomposes the interaction energy into physical and intuitive terms such as electrostatics, exchange, dispersion and induction. On the other hand, the analyses of intramolecular noncovalent interactions, which are responsible for phenomenon such as intramolecular charge transfer (e.g. transannular interactions), conformational and isomer energy differences as well as enzymatic activity are theoretically more challenging to assess, as no energy decomposition scheme is available to date for such interactions. The parameterization of accurate and transferable repulsive potentials is a The presented theoretical scheme fills the gapand proposes an intramolecular keyingredient for the density functional tight-binding method (DFTB). In variant of the SAPT formalism, which enables the analysis of intramolecular the conventional parameterization scheme the balanced description of differ- interactions. ent chemical environments involves significant human effort and chemical The suggested formalism is based on azeroth-order reference energy state, intuition. The present work aims at an in situ parameterization scheme with corresponding to an artificial molecular state in which no interaction is present limited transferability butmaximal accuracyfor the chemical and physical between the twofragments of interest. The orbitals are absolutely localized environment under investigation. In acomparative study we tested the perfor- on the fragments and optimized for this state prior to the construction of a mance and practical features of twoalternative schemes: Force matching and suitable zeroth-order wavefunction, from which the different energetic terms the iterative Boltzmann inversion method. We applied thetwo schemes to liq- of SAPT can be derived. uid water at ambient conditions, apathological case for conventional DFTB. Our newly determined parameters significantly improvedthe structural prop- [1] Jeziorski, B.; Moszynski, R.; Szalewicz, K., Chem. Rev. 1994, 94,1887. erties of liquid water.

Computational Chemistry ComputationalChemistry Computational Chemistry,Talk 169 Computational Chemistry,Talk 170 Understanding the impact of entropy on the structureand properties of AMorphological StudyofMagnetiteNanoparticles:influence of the

ScFeO3 from first principle simulations structureonthe magnetic dead layer

Florian Schiffmann1,2,Furio Cora2,Ben Slater2 Andrea Barbiero1,AlkeFink1,2,Claude Daul1

1 1ETH Zurich/Department¨ of Materials, ETH Zurich,¨ HIT G33.2, UniversityofFribourg, Chemin du Musée9,1700 Fribourg Wolfgang-Pauli-Strasse 27, 8093 Zurich,¨ Switzerland 2Adolph Merkle Institute, Routedel'ancienne PapeterieCP209, CH-1723 2UCL London/ Department of Chemistry,University College London, 20 Marly1,Fribourg Gordon Street,London WC1H 0AJ Nanomaterialscomposedbyoxidesoftransitionelementspossess interest- Combining long-range magnetic order with polarity in the same structure is ingand tunablepropertiesthatjustify thesynthetic, analytical andtheoreti- aprerequisite for the design of (magnetoelectric) multiferroic materials. Re- calefforts of thelastyears,towards thecomprehension of theirnature. Ob- taining magnetic order above room temperature still remains adifficult target. jectsbetween molecularand bulk state, they requiregreat open-mindedness

Recently,Lietal. presented apolar corundum phase of FeScO3 exposing a to treat both from theexperimentaland thecomputational [1]point of view. weak ferromagnetic ground state up to 356K. The obtained material shows Our research is focusedonmodelingFe3O4magnetitenanoparticles,which, extended disorder,which prevents adetailed insight in the microscopic struc- as SuperparamagneticIronOxide Nanoparticles, areinteresting forseveral ture and properties by experimental methods. applications,notably in thebio-medical field[2].The empirical interatomic In this study we will present insight from computational chemistry which potentialsusedinthisstudy [3], give thepossibilitytomodel particlesof givesamore detailed understanding of the material. In the first step, we will thousandsofatoms andtodoMolecularDynamicssimulations of theeffect use results from hybrid to showhow the stability of the material is effected of thesolvent on thestructure.Our scopeistostudy,through structural and magnetic calculations, therelationshipbetween themorphology of particles by entropy. Afterwards, these results will be used to derive an extended Ising (diameter,surface ligands)and thesocalled‘magnetic dead layer’,alsopre- model which is used in Monte-Carlo simulations. The results of these simula- sent on othernanoparticles[4]: asurface region of notdefined depth, which tions reveal astrong interconnection between the magnetic structure, entropy givesnullorverysmall contribution to themacroscopic magnetization. and polarization in the material. [1] BromleyS.T., MoreiraI.deP.R.,Neymanab K. M.,IllasF., Chem. [1] MR Li, UAdem, SRC. McMitchell, ZXu, CI Thomas, JE Warren, DV Soc.Rev., 2009, 38,2657-2670. Giap, HNiu, XWan, RG Palgrave,FSchiffmann, FCora, BSlater,TL [2] LaurentS., ForgeD., Port M., Roch A.,Robic C.,VanderElstL., Burnett, MG Cain, AM Abakumov, Gvan Tendeloo, MF Thomas, MJ MullerR.N., Chemical Reviews, 2008, 108(6),2064–2110; Petri-Fink, A., Rosseinsky, and JB Claridge, JACS 2012, 134(8),3737. Hofmann, H., IEEE Transactions on NanoBioscience, 2007, 6(4),289–297. [3]ReaxFFfromADF program; AryanpourM., vanDuinA.C.T., Ku- bickiJ.D., Journal of Physical ChemistryA,2010, 114,6298-6307 [4]Curiale J.,Granada M.,Troiani H. E.,SánchezR.D., Leyva A. G.,Levy P.,SamwerK., Appl.Phys. Lett., 2009, 95,04310 522 CHIMIA 2012, 66, No. 7/8 Computational Chemistry

Computational Chemistry Computational Chemistry Computational Chemistry,Talk 171 Computational Chemistry 172

First-principles structureprediction of LiBHx,x=2 DFTModelling of Ru/ActiveCarbon Catalyst

Riccarda Caputo1 I. Czekaj,J.Wambach, F. Vogel

1ETH Zurich,¨ Wolfgang-Pauli Strasse 10, CH-8093 Zurich¨ Paul ScherrerInstitute,Villigen, Switzerland [email protected]

The partial thermal decomposition of LiBH4(s),with evolution of H2(g), might lead to the formation of aternary phase formed by lithium-boron- Ruthenium/active carboncatalystisusedfor Haber-Boschammonia synthe- hydrogen, with astoichiometry LiBHx,x<4,ascomputationally suggested [1]. Therein the proposed crystal structures for x =2.5 and x =2.0 were sis as well as supercritical-water gasification of wet biomassfor methana- tion processes. Both reactionsare structuresensitiveand requires specific characterized by the formation of boron-hydrogen anionic chains, 1 [BH ]. ∞ 2 activesitesatthe catalyst. It has been found experimentally that mainly B5 We extended our investigation of the phase space of the ternary system Li-B- sites are present and actively taking part in catalysis [1]. H, searching for other possible stable configurations, in particular for x =2.0. The general methodological approach combines cluster modelling, simulated Themain task of our DFT studies is findingstableRunanoparticleatgraph- annealing (contributed by Prof Adem Tekin, Istanbul Technical University, ite using cluster model. Different Ru nanoparticles have been tested starting Informatics Institute, Istanbul, Turkey)and density functional total energy from3up to 17 atoms. The graphite hasbeenmodeled by single and double calculations, as successfully applied in structure prediction of complexboro- layer. Theepitaxial growth of Ru at graphite follows two locations [2]. hydrides [2,3,4]. In addition to chain-structures, ring-structures, in particular However our DFT resultssuggest that only one of themisstable. Basing on with butterflyand square topologies, are found to be local minima with lattice such preliminary results we were able to buildand stabilize at carbonsup- stability ascertained by phonon calculations. The enthalpies of formation, the port Ru nanoparticle with threeB5activesites.SuchaC-supportedRu- nanoparticle with B5-sites gives potentialfor further molecule adsorption calculated XRD patterns and the IR spectra are reported for stable structures and reaction mechanism studies. The all investigated structures and configu- representative of found family groups: monoclinic, orthorhombic and tetrag- rations for different Ru-nanoparticles will be presented. onal.

[1] R. Caputo, et al., Mol. Phys. 2010, 108,1236. [1] S.B. Vendelbo, M. Johansson, J.H. Nielsen, Ib Chorkendorff [2] R. Caputo, A. Tekin, et al., Chem. Phys. Lett. 2009, 480,203. Phys. Chem. Chem. Phys. 2011, 13, 10333. [3] A. Tekin, R. Caputo, Phys. Rev. Lett. 2010, 104,215501. [2] Z. Song et al., J. Am.Chem.Soc. 2004, 126, 8576. [4] R. Caputo, A. Tekin, J. Solid State Chem. 2011, 184,1622.

Computational Chemistry Computational Chemistry Computational Chemistry 173 Computational Chemistry 174 Howmany Chiral Centers can Raman Optical Activity Spectroscopy MOVIPAC:Vibrational Spectroscopy with aRobust Meta-Program for Distinguish in aMolecule? Massively Parallel Standard and Inverse Calculations

Benjamin Simmen,Thomas Weymuth, Markus Reiher1 T. Weymuth1,M.P.Haag1,K.Kiewisch1,2,S.Luber1,3,S.Schenk1,4, Ch. R. Jacob5,C.Herrmann6,J.Neugebauer7,M.Reiher1 1ETH Zurich,¨ Laboratorium fur¨ Physikalische Chemie, Wolfgang-Pauli-Str.10, 8093 Zurich,¨ Switzerland 1 ETH Zurich, Wolfgang-Pauli-Str.10, 8093 Zurich,¨ CH 2 VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, NL 3 To study the capabilities and limitations of Raman Optical Activity, (−)- Yale University,P.O. Box 208107, NewHaven, CT 06520-8107, USA 4 (M)σ-[10]Helicene and (−)-(M)σ-[4]Helicene serveasscaffold molecules BASF SE, B001, 67056 Ludwigshafen, DE 5 on which newchiral centers are introduced by substitution of hydrogen atoms KIT,Wolfgang-Gaede-Str.1a, 76131 Karlsruhe, DE 6 with other functional groups. These functional groups are deuterium atoms, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, DE 7 fluorine atoms, and methyl groups. Multiply deuterated species are compared. Technical University Braunschweig, Hans-Sommer-Str.10, 38106 Then, results of singly deuterated derivativesare compared against results ob- Braunschweig, DE tained from singly fluorinated and methylated derivatives. The analysis re- quired the calculation of atotal of 2433 Raman Optical Activity spectra. The The calculation of vibrational spectra for large molecules is achallenge, as the method we propose for the comparison of the various Raman Optical Activ- computational cost increases sharply with system size. The program package ity spectra is based on the total intensity of squared difference spectra. This MOVIPAC [1] is designed for such massively parallelized calculations imple- allows aqualitative comparison of pairs of Raman Optical Activity spectra menting efficient subsystem approaches such as Mode-Tracking [2], Intensity- and the extraction of the pair of most similar Raman Optical Activity spectra Tracking [3], and the Cartesian Tensor Transfer Method [4,5] which allowfor for each group of stereoisomers. Different factors were accounted for,such aconsiderable decrease in computational cost while offering the desired prop- as the spectral resolution (modeled by line broadening) and the range of vi- erties at high accuracy. M OV I PAC unites improvedand extended versions of brational frequencies considered. In the case of σ-[4]Helicene all generated the programs SNF [6] and AKIRA [2] yielding acomprehensive tool for the stereoisomers in each group can be distinguished from one another by Raman calculation of vibrational spectra. As the analysis of such spectra is challeng- Optical Activity spectroscopy. For σ-[10]Helicene this holdsexcept for the ing due to the huge amount of data, MOVIPAC includes the LOCVIB package lower one of the tworesolutions considered. Here, the group consisting of for interpreting the data in an intuitive wayemploying localized modes [7]. stereoisomers with five chiral centers contains at least one pair of derivatives [1] T. Weymuth, et al., J. Comput. Chem. 2012,submitted. whose Raman Optical Activity spectra cannot be distinguished from one an- [2] M. Reiher,J.Neugebauer, J. Chem. Phys. 2003, 118,1634. other.This indicates that an increased molecular size has anegative effect on [3] K. Kiewisch, et al., Chimia 2009, 63,270. the number of chiral centers which can be distinguished by Raman Optical [4] P. Bour,ˇ et al., J. Comput. Chem. 1997, 18,646. Activity spectroscopy. Regarding the different substituents, stereoisomers are [5] N. S. Bieler, et al., J. Chem. Theory Comput. 2011, 7,1867. distinguishable in Raman Optical Activity spectroscopythe better,the more [6] J. Neugebauer, et al., J. Comput. Chem. 2002, 23,895. distinct the signals of the substituent are from the rest of the spectrum. [7] Ch. R. Jacob, M. Reiher, J. Chem. Phys. 2009, 130,084106. Computational Chemistry CHIMIA 2012, 66, No. 7/8 523

Computational Chemistry Computational Chemistry Computational Chemistry 175 Computational Chemistry 176 Analysis of the Cartesian Tensor Transfer Method forCalculating Exact decoupling of the relativistic Fock operator Vibrational Spectra of Polypeptides Daoling Peng1,Markus Reiher1 Moritz P. Haag1,Noah S. Bieler1,Christoph R. Jacob2,Markus Reiher1 1Laboratorium fur¨ Physikalische Chemie, ETH Zurich,¨ 1ETH Zurich, Laboratorium fur¨ Physikalische Chemie, Wolfgang-Pauli-Strasse 10, CH-8093 Zurich, Switzerland Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland 2 Karlsruhe Institute of Technology (KIT), Center for Functional It is generally acknowledged that the inclusion of relativistic effects is cru- Nanaostructures, Wolfgang-Gaede-Str.1a, 76131 Karlsruhe, Germany cial for the theoretical description of heavy-element-containing molecules. Four-component Dirac-operator-based methods serveasthe relativistic refer- The Cartesian Tensor Transfer Method (CTTM) [1] wasproposed as an effi- ence for molecules and highly accurate results can be obtained — provided cient waytocalculate infrared, Raman, and Raman Optical Activity (ROA) that asuitable approximation for the electronic wave function is employed. spectra for large molecules from the Hessian matrix and property tensor deriv- However, four-component methods applied in astraightforward manner suffer ativescalculated for smaller molecular fragments. Although this approach has from high computational cost and the presence of pathologic negative-energy been widely used, its reliability has not been analyzed in depth yet. Especially solutions. To remove these drawbacks, arelativistic electron-only theory is for ROAspectra, such an analysis became only recently possible because of desirable for which the relativistic Fock operator needs to be exactly decou- methodological advances that allowfor the calculation of full ROAspectra of pled. Recent developments in the field of relativistic two-component meth- fairly large molecules with large basis sets. In this work[2], we investigate an ods demonstrated that exact decoupling can be achievedfollowing different α-helical polypeptide of 20 alanine amino acids, for which we reported the strategies. Three different approaches — DKH [1], X2C [2], and BSS [3] — full ROAspectra earlier,inorder to study the CTTM for protein subunits. By exist for this purpose and theyare all intimately related. The theoretical for- comparing the full first-principles calculation of the vibrational spectra with malism of these exact-decoupling approaches is reviewed in this presentation spectra reconstructed with the CTTM from different fragment sizes, we find followed by acomparison of efficiencyand results [4]. Alocal approach for that infrared and Raman spectra are mostly well reproduced. However, this is these exact-decoupling methods is proposed to reduce the computational cost not the case for the ROAspectrum. The results of this work might have im- of large molecules [5]. plications for peptide and protein CTTM ROAspectra that have already been published in the literature. [1] B. A. Hess, Phys. Rev. A 1986, 33,3742; M. Reiher and A. Wolf, J. Chem. Phys. 2004, 121,2037. [1] P. Bour,ˇ J. Sopkova,´ L. Bednaro´ va,´ P. Malon,ˇ T. A. Keiderling, J. Comput. [2] W. Kutzelnigg and W. Liu J. Chem. Phys. 2005, 123,244102; W. Liu Chem. 1997, 18,646. and D. Peng J. Chem. Phys. 2006, 125,044102. [2] N. S. Bieler,M.P.Haag, C. R. Jacob, M. Reiher, J. Chem. Theory Com- [3] M. Barysz, A. Sadlej and J. G. Snijders Int. J. Quantum Chem. 1997, 65, put. 2011, 7,1867. 225; D. Ke¸dziera and M. Barysz Chem. Phys. Lett. 2007, 446,176. [4] D. Peng and M. Reiher, Theor.Chem. Acc. 2012, 131,1081. [5] D. Peng and M. Reiher, In preparation.

Computational Chemistry Computational Chemistry Computational Chemistry 177 Computational Chemistry 178 Accurate ab initio spin densities Theoretical Studies into the Mechanism of [Fe] and [FeFe] Hydrogenases Katharina Boguslawski1,Konrad H. Marti1, Ors¨ Legeza2,Markus Reiher1 Arndt R. Finkelmann1,Martin T. Stiebritz1,Markus Reiher1 1ETH Zurich, Laboratorium fur¨ Physikalische Chemie, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland 1Laboratorium fur¨ Physikalische Chemie, ETH Zurich,¨ 2Wigner Research Centre, P.OBox 49, H-1525 Budapest, Hungary Wolfgang-Pauli-Strasse 10, CH-8093 Zurich,¨ Switzerland Forlarge molecular systems such as transition metal complexes, density- functional theory (DFT) became instrumental in theoretical studies of mech- Enzymes which catalyze the reversible oxidation or formation of molecu- anisms in metal-mediated catalysis. Yet, the treatment of open-shell systems lar hydrogen are called hydrogenases and grouped into three classes, namely remains achallenge for DFT [1]. In addition to the difficult prediction of [FeFe], [NiFe] and [Fe] hydrogenases. Theyare of interest as potential cata- ground states from states of different spin, spin density distributions consid- lysts in renewable energy technologies. [FeFe] hydrogenases, which have the erably depend on the approximate exchange–correlation density functional highest hydrogen formation turnoverrates, are irreversibly inhibited by O2 if transition metal complexescontaining noninnocent ligands are considered. which is amajor drawback for their technical applicability [1]. [Fe] hydroge- Especially,nitric oxide as an open-shell molecule endows acorresponding nase is, however, not inhibited by O2. transition metal nitrosyl complexwith acomplicated electronic structure for To relate both active sites, we construct cluster models of [Fe] and [FeFe] which qualitatively correct spin densities are difficult to obtain within the stan- hydrogenases active sites by mutual ligand exchange [2]. The influence of dard Kohn–Sham formalism [2]. the first-shell ligand sphere on the catalytic cycle of these models is inves- We present highly accurate spin densities for an iron nitrosyl complexwhich tigated with density functional theory calculations. Crucial reaction steps of we have identified as achallenging system for DFT and standard electron [Fe] hydrogenase’scatalytic mechanism are strongly affected by the change to correlation methods [3]. Our approach is based on the density-matrix renor- [FeFe] hydrogenase-like first-shell ligands [3] and the reactivity is biased to- malization group (DMRG) algorithm [4] and allows the treatment of active wards [FeFe] hydrogenase-likereactivity.For [FeFe] hydrogenase we present orbital spaces beyond the current limit of 18 electrons correlated in 18 molec- afull reaction mechanism based on alarge model of the active site which in- ular orbitals. Furthermore, the explicit reconstruction of acomplete-active- cludes interactions of important residues with the Hcluster.Adetailed picture space configuration-interaction-type wave function [5] provides insights into of apossible catalytic cycle provides answers to the question if abridging or chemically interesting features of the studied molecules such as the distribu- terminal-bound hydride species is the central catalytic intermediate [3]. tion of α-and β-electrons in terms of Slater determinants, CI coefficients, and natural orbitals. The DMRG reference spin densities can be used to validate [1] M.T.Stiebritz, M. Reiher, Chem. Sci. 2012, doi:10.1039/C2SC01112C; the accuracyofDFT spin densities and assess the quality of the restricted M.T.Stiebritz, M. Reiher, Inorg. Chem. 2009, 48,7127; C. Lambertz, N. active orbital spaces. Leidel, K.G.V.Havelius, J. Noth, P. Chernev, M. Winkler,T.Happe, M.

[1] M. Reiher, Chimia 2009 63,140. Haumann, J. Biol. Chem. 2011, 286,40614. [2] K. Boguslawski, C. R. Jacob and M. Reiher, J. Chem. Theory Comput. 2011, 7,2740. [3] K. Boguslawski, K. H. Marti, O.¨ Legeza and M. Reiher, J. Chem. Theory Comput. submitted. [2] M.T.Stiebritz, M. Reiher, Inorg. Chem. 2010, 49,5818. [4] S. R. White Phys. Rev. Lett. 1992, 69,2863.; K. H. Marti, M. Reiher, Z. Phys. Chem. 2010, 224,583. [5] K. Boguslawski, K. H. Marti and M. Reiher, J. Chem. Phys. 2011, 134,224101. [3] A.R. Finkelmann, M.T.Stiebritz, M. Reiher, in preparation 524 CHIMIA 2012, 66, No. 7/8 Computational Chemistry

Computational Chemistry Computational Chemistry Computational Chemistry 179 Computational Chemistry 180

4Fe-4S Clusters: Reactivity vs. Cluster Geometry Dioxygen induced degradation of [Fe4S4]cubane clusters: aquantum chemical perspective. MaikeBergeler1,Martin T. Stiebritz1,Markus Reiher1 Bruska, M.K.1,Stiebritz M.T.1,Reiher M.1 1Laboratorium fur¨ Physikalische Chemie, ETH Zurich,¨ Wolfgang-Pauli-Str. 10, 8093 Zurich,¨ Switzerland 1Laboratory of Physical Chemistry,ETH Zurich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland Iron-sulfur clusters play akey role in electron transfer processes, metabolism, Lifetimes and decomposition products of the [Fe4S4]clusters exposed to oxy- signal transduction and activation of low-reactivity molecules likeN2/H2 [1]. Despite the same type of ligation of the 4Fe-4S cluster by four cysteines in gen range from rapid and complete degradation of the Fe-S cluster for en- several proteins, the 4Fe-4S clusters feature arecognizably different reactivity zymes like[FeFe]-hydrogenases [1] to O2 stable cubanes harbored by the towards reactive oxygen species (ROS) [2], which can lead to an irreversible Escherichia coli DinG helicase [2]. Aquestion not fully resolved is howand damage of the protein [1, 3]. One reason for the varying reactivities towards whysome of the solvent accessible Fe-S cubane clusters survive longer in ROScould be the effect of the protein environment on the first ligand sphere aerobic environment.

due to the inflexibility of the protein backbone. Here, we address the problem of oxygen sensitivity of the [Fe4S4]cubane clusters with density functional theory (DFT) calculations on several O2 addi- Here, we studied D2d-symmetric cubane type 4Fe-4S cluster models ligated by four cysteines with constraints on the ligands to mimic the spatial con- tion and decomposition reactions at [Fe4S4]cubanes. The presented work is a straints imposed by the protein environment using Density Functional The- continuation of the research recently published by our group [3] and discusses ory.Spin couplings within the cubane were treated by employing the broken- the general principles of decomposition pathways for the structural model of symmetry approach. We investigated the reactivity towards ROSdepending an isolated [Fe4S4]cubane and refers them to the study on a800 atoms model on spin state and symmetry of the cluster by systematic distortions of the ge- of [FeFe]-hydrogenase active site in order to discuss the influence of aprotein ometric constraints. We conclude that both spin coupling and reactivity of environment. In particular,wediscuss coordination energetics of dioxygen 4Fe-4S clusters are determined by deviations from the ideal cluster geometry adducts of the [Fe4S4]cubane, possibility of ROSformation, transition state as givenbythe anchoring in the particular protein in which theyoccur. structures and activation barriers for the oxygen-induced destruction of the Fe-S cluster,and the role of different spin-coupling schemes at iron centers. [1] J. A. Imlay, Mol. Microbiol. 2006, 59,1073; I. R. Tsaneva,B.Weiss, The theoretical investigation of the decomposition pathways of Fe-S cubanes J. Bacteriol. 1990, 172,4197; K. A. Vincent, A. Parkin, O. Lenz, S. P. opens apossibility for in silico mutation studies not only for Fe-only hydro- J. Albracht, J. C. Fontecilla-Camps, R. Cammack, B. Friedrich and F. A. genases butalso other enzymes harboring [Fe4S4]cubanes. Armstrong, J. Am. Chem. Soc. 2005, 127,18179. [2] M. T. Stiebritz and M. Reiher, Chem. Sci. 2012, 10.1039/c2sc01112c. [1] Vincent, K.A. et al., J. Am. Chem. Soc. 2005, 127,18179. [3] K. A. Vincent, A. Parkin and F. A. Armstrong, Chem. Rev. 2007, 107, [2] Ren, B., Duan, X., Ding, H., J. Biol. Chem. 2009, 284,4829. 4366; M. K. Bruska, M. T. Stiebritz and M. Reiher, J. Am. Chem. Soc. [3] Bruska, M.K., Stiebritz, M.T., Reiher,M., J. Am. Chem. Soc. 2011, 133, 2011, 133,20588. 20588.

ComputationalChemistry Computational Chemistry Computational Chemistry 181 Computational Chemistry 182 2+/3+ Afirst-principles studyofthe redoxpropertiesof[Ru(bpy)3] Perfomance of Dispersion-Corrected Atom-Centered Potentials: Non-equilibrium gas phase geometries and condensed matter systems. Polydefkis Diamantis,Ivano Tavernelli, Ursula Rothlisberger* A. Laktionov,M.Doemer,I.Tavernelli, and U. Rothlisberger Ecole Polytechnique Fédérale de Lausanne(EPFL), Av. Forel2,CH-1015 Lausanne,Switzerland Ecole Polytechnique Fed´ erale´ de Lausanne, Lausanne, Switzerland

Van-der-Waals interactions play acrucial role in biological and pharmaceu- Car-Parrinello moleculardynamicssimulations basedonDFT/BP86were tically relevant systems. Unfortunately,standard density functional theory performed, in ordertostudy the redox reaction: (DFT) calculations within generalized gradient approximations (GGA) fail

2+ 3+ to account for these weak interactions. In recent works, dispersion-corrected [Ru(bpy)3] → [Ru(bpy)3] ,for both thesinglet andthe triplet state. atom-centered potentials (DCACPs) have been developed to account for long- range dispersion forces between molecules within aDFT/GGA framework. Forthe calculation of theredox free energydifference(ΔAR→O)and the re- organizationfreeenergy(λ)ofboth reactions, awellknown method was DCACP are based on the idea of representing anon-local dispersion interac- applied [1][2], one that assumes Marcustheoryfor electron transfer, andin tion potential as asum of atom-centered semilocal potentials. which ΔA =<ΔE> +<ΔE> (theaverage ionization potential of the extended DCACP � R→O R O vxc = vxc + I vI (r, r ) (1) reduced state andthe averageelectron affinity of the oxidizedstate respec- DCACP � �max +� I I I � I ∗ � tively). The method provided reasonable resultsfor both ΔAR→O (5.37 eV vI (r, r )= �=0 m=−� Y�m(ˆr ) p � ( r ) σ 1 p � ( r ) Y �m(ˆr ) (2) and3.60 eV for singlet andtriplet statesrespectively)and λ (1.19eVsinglet where r = r−R is the distance from the electron to the position of nucleus I, and1.25 eV forsinglet andtriplet statesrespectively),ingood agreement I and pI (r) is the normalized projector,embraced by spherical harmonics. Such with existing experimental andcalculatedvalues (singlet ΔA =5.60 eV, � R→O achoice of sets of functions has several advantages. First, separating variables λ =1.21 eV)[3].Inorder to further check the validityofMarcusTheory, reduces the computational cost of the non-local dispersion term from N 6 to the free energycurvesof[Ru(bpy) ]2+ and[Ru(bpy) ]3+ were also plotted 3 3 N 3.Second, the exponential decay of projectors allows to introduce acutoff for both reactions, as functions of ΔE –ΔAR→O.Inboth cases,the two free energy curves were parabolas to averygood approximation, aproof that on the radial grid, making calculations cheaper.Thirdly,asDCACP use only Marcustheorycan apparentlydescribe quiteaccuratelythese two reactions. unoccupied channels in the Goedecker-Teter-Hutter (GTH) pseudopotentials, there is no necessity to modify the code, when planewave calculations are per- [1]M.Cascella,A.Magistrato, I. Tavernelli,P.Carloni, U. Rothlisberger, formed. Within this approach dispersion interactions can nowbeaccurately Proc.Natl. Acad.Sci.USA, 2006, 102,19641 described by DFT at the cost of roughly astandard GGA functional. [2]J.Blumberger,I.Tavernelli, M.L. Klein, M. Sprik, J. Chem.Phys., Here, we demonstrate that by adding more terms to the expansion (2) one 2006, 124,64507 can retrieve the correct R−6 asymptotics of the tail of the interaction curve. [3]R.Seidel, M. Faubel, B. Winter,J.Blumberger, J. Am.Chem. Soc., Additionally,wepresent results on the physisorption of organic molecules 2009, 131, 16127 on gold and silicon surfaces and on the influence of halogen bonding on the molecular structure in gas-phase clusters up to molecular crystals. Computational Chemistry CHIMIA 2012, 66, No. 7/8 525

ComputationalChemistry ComputationalChemistry Computational Chemistry 183 Computational Chemistry 184 Ab Initio Based Methodologies for Investigation of Charge Transfer Sector model scheme for placement of explicit water molecules for pKa Through Organic Molecules prediction Laura Berstis1,Kim Baldridge1 Rebecca AAbramson, Kim KBaldridge

1University of Zürich, Winterthurerstrasse 190, 8057 Zürich Organic Chemistry Institute, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich Switzerland The study of charge transfer (CT) reactivity through organic molecules pre- sents vast opportunities to understand and design materials with desirable Accurate prediction of the properties associated with proton transfer reac- electronic properties. In the current work, afirst principles methodology has tions, in particular the acidity dissociation constant (Ka), are abenchmark been developed for the evaluation of CT properties in nonadiabatic systems, challenge for theory. Considerable efforts have been made in the last decade and implemented into the widely used ab initio computational suite towards prediction within 0.5 units,1 which is the minimum level of accura- GAMESS. In this implementation abroad range of levels of theory, includ- cy for many problems such as structure based drug design2.Hybrid ap- ing semiempirical, Hartree-Fock, DFT, or MP2, may be applied to the sys- proaches, referred to as continuum cluster (CC), are the most recent and tem studied, to achieve the highest possible accuracy for the size and com- promising development in pKa prediction.1,3,4,5 They attempt to capture plexity of the CT system at hand. The calculation of the electronic coupling some of the missing first solvation shell effects by adding asmall number between an electron donor and acceptor utilizes alocalized molecular orbital (<4) solvent molecules explicitly around the solute embedded in the solvent effective Hamiltonian1,relating the coupling between the donor and accep- cavity. However, anumber of practical challenges arise in application of tor through the remaining bridge localized orbitals. Furthermore the possible this method due to the need to have aconsistent framework for determina- tunneling pathways available are calculated by means of aGreens function tion of optimal number and position of solvent molecules surrounding the matrix of the bridge localized atomic or molecular orbitals.2 These evalua- solute. We propose asector model approach to investigate in greater detail tions shed new light on discussions of through-bond and through-space cou- the role of explicit first-shell solvationofaset of carboxylic acids and their pling effects.The electronic coupling and pathway analyses enable aquanti- conjugate bases. This model offers the possibility of systematizing the study fication of the magnitude of through-space or through-bond coupling, and of these effects according to the degree of solvation (SD)and the configura- clarify through which molecular orbitals these interactions are made possi- tion of solvation (SC), which allows anumber of rules for future prediction ble. Additionally the impact of solvent to these CT characteristicsiscon- to be elucidated. sidered in the present work. Through these investigations, an understanding [1] Ho, J., Coote, M.L., 2011, Wires Comput. Mol. Sci., 2011, 1(5), 649- is gained of the impacts of structure,and presence of functional groups on 660 the donor, acceptor or bridge, on the probability and mechanism of the CT [2] Klicic, J.J. Friesner, R.A., Liu, S., Guida, W., J. Phys. Chem. A, 2002, reactions, contributing greatly towards the design of materials, which will 106, 1327-1335 offer desirable properties. [3] Pliego, J.R., Riveros, J.M., J. Phys. Chem. A, 106, 2002, 7434-7439 [1] Teklos A, Skourtis S.S. 2006, J. Chem. Phys. 125, 244103. [4] Eckert, F., Diedenhofen, M., Klamt, A., Molecular Physics, 2010, 108 (3), 229-241 [2] C. Kobayashi, K. Baldridge, J.N. Onuchic. 2003, J. Chem. Phys. Vol. [5] Kelly, C.P., Cramer, C.J., Truhlar, D.G., J. Phys. Chem. A, 2006, 110 119, No. 6. (7), 2493-9

Computational Chemistry Computational Chemistry Computational Chemistry 185 Computational Chemistry 186 Direct Second-Order Møller-Plesset Perturbation Energy Dielectric constant calculations: ANew Implementation Based on aTwo-LevelParallelization of Integral DFT approach using Tree Monte Carlo Computation and Transformation Mandes Schonherr¨ 1,Joost VandeVondele2,Jur¨ gHutter2 Mauro Del Ben1,Jur¨ gHutter1 and Joost VandeVondele2 1Institute of Physical Chemistry,University of Zurich 1Institute of Physical Chemistry,University of Zurich¨ 2Department of Materials, ETH Zurich 2Department of Materials, ETH Zurich¨ The development of high performance computers significantly increase the Aconventional implementation of the Second-Order Møller-Plesset (MP2) computing power available. To use this potential, novelalgorithms have to theory consists in three steps: the two-electron integrals calculation in the be adopted to the increase of parallelization. In the case of molecular simula- atomic orbitals (AOs) basis; the integrals transformation into molecular or- tions, the scalability of Molecular Dynamics (MD) is ultimately limited, and bitals (MOs) and the integrals contraction into the MP2 energy.The most time the step-by-step integration essentially serializes the procedure. We present a demanding step is the integrals transformation, that scales formally O(N 5), Tree Monte Carlo (TMC) algorithm which permits the simultaneous calcula- while the other twosteps scale as O(N 4),where N is the size of the system. tion of manymolecular configurations. Using aspeculative approach, various Based on this different scaling behavior,anewparallel direct MP2 energy pathways, accounting for both rejection and acceptance of proposed moves, algorithm is presented for which the total number of processes is divided into can be computed in parallel. Keytothis approach is the fact that generating groups: the occupied orbitals pairs, in the integrals transformation step, are configurations for the Monte Carlo algorithm is cheap and can be performed distributed overall processes, while the integrals overAOs are recomputed for without computing forces. The TMC procedure respects detailed balance, and each group. In this way, the communication is restricted to the members of the in fact the sequence of Monte Carlo movesused is independent of the number group, avoiding aglobal message-passing scheme that involves all processes. of simultaneously computed tasks. The parallel efficiencyofthe TMC algo- Test calculations demonstrate scalability up to thousands of processes and rithm depends on the acceptance probabilities of the moves. Various config- ability to handle systems containing thousands of basis functions. The pro- urational changes are implemented, varying from standard MC moves, such posed algorithm outperforms other parallel MP2 implementations with com- as atom and molecule translation or molecule rotation, to more intelligent putational savig of 50% achivedbytuning the number of processes within movessuch as proton reordering, twopotential moves(Nested Monte Carlo), agroup. The developed algorithm is promising for extending the range of hybrid Monte Carlo, parallel tempering and Nested Monte Carlo. Calculation applications of the MP2 method. costs are significantly reduced using approximate potentials. Sub-box meth- ods increase the acceptance rate and hence the efficiency. Further efficiency gains will come through dynamic process termination and acceptance estima- tion. Using this algorithm, we were able to calculate the dielectric constant, a property with long relaxation time, of ice Ih structures using PBE and PBE0. The PBE model overestimates the dielectric constant compared to experimen- tal values. In contrast to that, the value using PBE0 is in good agreement with the experimental results. The results of both methods were converged. 526 CHIMIA 2012, 66, No. 7/8 Computational Chemistry

Computational Chemistry Computational Chemistry Computational Chemistry 187 Computational Chemistry 188 Hexagonal Boron Nitride on Nickel and Copper Surfaces Implementation of the image charge method in QM/MM

Ralph Koitz,Marcella Iannuzzi, Ari P. Seitsonen, Jur¨ gHutter Dorothea Golze,Marcella Iannuzzi, Jur¨ gHutter

University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich¨ University of Zurich, Winterthurerstr.190, CH-8057 Zurich, Switzerland

Numerous transition metals have been studied as substrates for the adsorption Amethod for including polarization effects within hybrid quantum mechan- of monolayers of hexagonal boron nitride (h-BN), and promising applications ics/molecular mechanics (QM/MM) simulations of physisorbed adsorbate- have been suggested for these materials [1]. We studied the structural, elec- metal systems is presented. In astandard QM/MM description, the adsorbed tronic, and magnetic properties of h-BN on the (111) surfaces of Ni and Cu. molecules are treated by QM and the metal by MM. The interactions be- While the lattice-matching of h-BN and Ni is near-perfect, we observethat tween adsorbate and metal are usually described by apair potential where the adsorption registry plays an important role for the metal–h-BN interac- electrostatic interactions are neglected. However, polar adsorbates can in- tion. Configurations with Natoms atop Ni positions are bound with signifi- duce charges in the metal and interact with these charges. This classical phe- cantly higher energies and smaller interlayer distances. We also find aclear nomenon is referred to as image effect. It wasshown that image charges are dependence of the surface magnetic moment on the interlayer distance. important for determining the assembling behavior of organic molecules on metal surfaces [1]. Image charges are also needed for acomprehensive de- Cu has been studied less extensively as asubstrate, buthas recently seen in- scription of processes at electrode interfaces [2]. creasing interest. Small slabs of Cu showadsorption characteristics with com- In this work, the image charge method wasimplemented in the QM/MM mod- paratively little differentiation between surface registries and lowadsorption ule [3, 4] of the CP2K program package. The implementation is based on energies. In contrast, larger systems, such as a24x24 rotated h-BN layer on the Siepmann-Sprik scheme [5], where the image charge distribution in the a23x23 Cu cell, form moirep´ atterns resulting in astructural as well as elec- metal is modeled by aset of Gaussian charges centered at the metal atoms. tronic corrugation of the surface (see figure). The image charges are determined self-consistently by imposing the constant- potential condition within the metal. The image charge method wasapplied to simple nitro-substituted aromatic molecules at Au(111) interfaces and the results were compared to full DFT.

[1] G. Tomba et al., ACSNano 2010, 4,7545. [2] S. K. Reed, O. J. Lanning, P. A. Madden, J. Chem. Phys. 2007, 126, 084704. [3] T. Laino, F. Mohamed, A. Laio, M. Parrinello, J. Chem. Theory Comput. 2005, 1,1176. [4] T. Laino, F. Mohamed, A. Laio, M. Parrinello, J. Chem. Theory Comput. 2006, 2,1370. [1] R. Laskowski et al. Phys RevB2008, 78,045409. [5] J. I. Siepmann, M. Sprik, J. Chem. Phys. 1995, 102,511.

ComputationalChemistry Computational Chemistry Computational Chemistry 189 Computational Chemistry 190 Influence of Donor-AcceptorSubstitutiononthe Molecular Quantum Chemical Investigation of the Solvent Effect on Two PropertiesofLinearlyConjugated Oligomers Competing Trifluoromethylation Reaction Mechanisms Involving λ3-Iodane Reagents: At the Limit of the PCM Model? Elizabeth Chirackal Varkey1,2,Peter Andreas Limacher1,HansPeter Lüthi1, 2 Jürg Hutter OliverSala,Hans Peter Luthi,¨ Halua Pinto de Magalhaes,˜ Antonio Togni 1 2 LaboratoryofPhysical Chemistry, ETH Zurich, Institute of Physical ETH Zurich,¨ Wolfgang-Pauli-Strasse 10, CH-8093 Zurich,¨ Switzerland Chemistry, UniversityofZurich. We performed asystematic investigationofthe impact of different Hypervalent iodines are important reagents for the trifluoromethylation of nu- donor-acceptor substitutionpatternsasafunctionofbackbone type andsize. cleophiles such as N-heterocyclic compounds[1]. Twocompeting reaction The typesofbackbones investigated are trans-polyacetylene(PA), polyyne mechanisms for the trifluoromethylation were found based on DFT calcula-

(PY) andpolythiophene (PT).All calculations were performed using density tions: areductive elimination (RE) and an SN 2. The solvent effect on these functionaltheory(CAM-B3LYP).Toinvestigatethe response of theprop- twocompeting reaction mechanisms wasinvestigated using aPCM model.

ertiesonelectrondelocalization, we evaluatedthe BLA, polarizability, Whereas the barrier of the SN 2reaction pathway is raised by the solvent, the hyperpolarizabilityand rotationalbarrier. The studies revealedthatBLA barrier of the RE is lowered. However, not enough, to become the lowest androtationalbarrier followanexponentialbehaviour (intermsofchain energy pathway as one would expect from chemical intuition. Using explicit length andsubstituents)whereas,polarizabilitiesand hyperpolarizabilities solvent molecules, we found that their interaction with the hypervalent bond is followapower law. TheSuperpositionModel[1] wasappliedtoexplore the too complextobeadequately described by apure electrostatic solvent model. cooperativeeffect of substituents in bothhomoand hetero end-cappedoli- gomerchains. We observed that thecooperativeeffect of BLA, polarizabili-

ty,hyperpolarizabilityand rotationalbarrierdecaysexponentiallyasthe oli- N H N F3C I O gomerchain length,regardlessofthe donor-acceptorstrength. H F3C I O R DMTI-H-MeCN (1) 2 TS-2 R1 Polyacetylenes (PA) n reductive Polythiophenes(PT) MeCN elimination (RE) R R 1 S 2 R1 R2 Polyynes(PY) n N CF3 4 n n=4, 6, 8, 10 &12 N H SN2 N F3C I O R1,R2=H,NH2,NO2,CN&OH -MeCN I OH Figure 1: Oligomers investigated TS-3 5 [1]S.Borini, P. A. Limacher, H. P. Lüthi, J. Phys.Chem. A, 2010, 114, 2221. [1] K. Niedermann, N. Fruh, E. Vinogradova,M.S. Wiehn, A. Moreno, A. Togni, Angew. Chem. Int. Ed. 2011, 50,1059-1063. Computational Chemistry CHIMIA 2012, 66, No. 7/8 527

Computational Chemistry Computational Chemistry Computational Chemistry 191 Computational Chemistry 192 Akey weak point of the prion protein Non-bonded Interactions in Solution: InterplaybetweenTheory and Experiment Julian Garrec1,co-authors1 Stephan N. Steinmann and ClemenceCorminboeuf 1Ecole´ Polytechnique Fed´ erale´ de Lausanne, Laboratory of Computational Chemistry and Biochemistry,Institute of Chemical Sciences and Laboratoryfor Computational Molecular Design, Institute of Chemical Sci- Engineering, CH-1015 Lausanne, Switzerland ences and Engineering, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland

The characteristic misfolding of the prion protein (PrP) observed in trans- Non-bonded interactions are responsible for many structural and energetical missible spongiform encephalopathies (TSE) is favored by acidic pH in vitro, phenomena, which are difficulttoassess experimentally. Thepresent com- which represent relevant conditions insofar as endosome organelles have been putational approach aimsatproviding acomprehensivepicture of these pro- proposed as possible location for PrP aggregation. Recent experiments have cesses that complementsexperimental data. We here specifically decipher shown that the protonation of H187 in the prion protein (PrP) at endosomal the origin of the selectivity of chemosensors and provide details regarding pH induces aconformational transition of the protein that could be linked to thepositionofindividualmoleculesinself-assembled softmatter. Achiev- characteristic misfolding of prion diseases. Using molecular dynamics sim- ing good agreement with experiment relies on considering both explicit sol- ulations, we have explored the mechanism of the early stages of this desta- vent effects and intermolecular flexibility. bilization process. Our results suggest amodel in which the protonation of We estimate the selectivity of molecular receptors for caffeine1 accounting H187 induces an electrostatic repulsion with the nearby guanidinium group forexplicit solvent and entropy effects by combining the quantum mechani- of R136. The system responds to this perturbation by pushing either H187 or cal treatment of the intermolecular complex with molecular mechanics sim- R136 away from their native cavity.This triggers acascade of conformational ulationsinaqueous solution. Similarly, key structural parameters of transitions in different regions of the protein, some of which are located far supramolecular assembliesare extracted from classical trajectories. Those from H187. The finding that the H187 interaction with R136 is aweak point structures, which combine bioinspired building blocks and π-conjugated moieties are promising precursors to organic electronics. Information on of mammalian PrP is supported by the absence of the {H187,R136} residue relative arrangements between adjacent π-functionalunits helps identifying pair in non-mammalian species that are known to be resistant to TSE. The the most promising candidate structures. imidazole ring of H187 and the guanidinium group of R136 form asolvent- accessible site that represent an alternative or complementary target for drug design.

[1]S.Rochat,S.N.Steinmann, C. Corminboeuf, K. Severin, Chem. Commun. 2011, 47,10584.

Computational Chemistry Computational Chemistry Computational Chemistry 193 Computational Chemistry 194 Density Dependent Dispersion Correction Scheme forLarge Scale Investigating the natureofthe charge carriers in conducting organic Systems polymers using DMRG

Riccardo Petraglia,Stephan N. Steinmann and Clemence Corminboeuf L. Bomble,J.Gonthier,R.Petraglia, C. Corminboeuf 1

Institut des Sciences st Ingenierie´ Chimiques, Ecole Polytechnique Fed´ erale´ 1 Laboratory for Computational Molecular Design, EPFL, Switzerland de Lausanne, CH-1015 Lausanne The Density Matrix Renormalization Group (DMRG) ansatz has been devel- The self-consistent charge density functional tight-binding (SCC-DFTB) sche- oped in the 1990‘s by the solid state physics community to enable the study of me [1] can provide highly valuable insights for large molecular systems. Fur- large-scale systems with strong electronic interactions. DMRG has recently ther development and validation of such methods could strongly benefitthe emerged as asolution to challenging quantum chemistry problems [1]. The investigation of organic based functional nanostructures. Akin to DFT,SCC- DMRG protocol [2] defines an effective Hamiltonian that focuses on the most DFTB also suffers from the neglect of long-range correlation effects, which important correlation interactions and iteratively approaches the full CI (Con- would lead to the erroneous descriptions of structural and energetic properties. figuration Interaction) solution. The approach produces very accurate results We here takeadvantage of our recent density dependent dispersion correction for large systems (up to 100 π electrons in 100 orbitals) [3-4] butisstill at a (dDsC) [2] for DFT and present aDFTB scheme (DFTB-dDMC) that incor- development stage. Our goal is to implement and use the DMRG protocol to porates the density dependent treatment of dispersion, while still enabling the investigate the polaron-bipolaron nature of conductive organic polymers with treatment of over1000 atoms. Our correction relies on “aposteriori”at- increasing chain size [5]. These molecules, which are keyplayers in the field tractive energy term: Molecular dispersion coefficients are obtained using a of organic electronics, are very challenging for standard electronic structure simple derivation starting from arescaling of free atomic C6 coefficients de- methods. Long polymer chains are indeed characterized by strong multirefer- pending on atomic Mulliken charges. As these charges are necessary to com- ence character butare too large to be treated using high-levelmultireference pute the SCC-DFTB energy,the coefficients are obtained for no extra cost. ab initio methodologies (up to 20 monomers, i.e. 120 pi electrons). Alter- The robustness of our SCC-DFTB-dDMC scheme also depends on the damp- natively,Kohn Sham Density Functional Theory (DFT) has been extensively ing function used: the universal Tank and Toennies damping function [3] with used butthere exists no accurate reference to validate the diverse performance one parameter fitted on an extended S22 test set. Preliminary results indicates of standard and modern functionals. Our aim is to use DMRG to benchmark that the scheme clearly outperforms other classical schemes with aMAD be- the accuracyofdensity functional computations and determine the nature of low0.75 Kcal/mol and aMAPE neverabove 30%. The performance of the the charge carriers in conductive organic polymers. scheme is further demonstrated on abroad range of molecular precursors to organic electronics. [1] S. R. White and R. L. Martin J. Chem. Phys,110, 4127. [2] G. K.-L. Chan [1] M. Elstner et al., Phys. Rev. B 1998, 58,11. and M. Head-Gordon J. Chem. Phys,116, 4462. [3] K. H. Marti ,I.M.Ondik, [2] Stephan N. Steinmann and Clemence Corminboeuf, J. Chem. Teory Com- G. Moritz and M. Reiher J. Chem. Phys,128, 014105. [4] J. Hachmann, W. put. 2011, 7,3567. Cardoen, and G. K.-L. Chan J. Chem. Phys,125,14410. [5] T. Nishinaga, M. [3] K. T. Tang and J. P. Tonnies, J. Chem. Phys. 1984, 80,3726. Tateno, M. Fujii, W. Fujita, M. Takase, M. IyodaOrg. Let.,12,5374. 528 CHIMIA 2012, 66, No. 7/8 Computational Chemistry

ComputationalChemistry ComputationalChemistry Computational Chemistry 195 Computational Chemistry 196 Unraveling the Mechanism of theUnusual Topochemical Mutationsand DeletionstoInvestigate the Dynamics of GroupIIIntrons by smFRET Dimerization of Bromodiacetylene Fiorini,E.;Cardo, L.;Kowerko, D. andSigel,R.K.O.

TanyaK.Todorova andClemenceCorminboeuf University of Zurich, Institute of InorganicChemistry,Winterthurerstrasse Laboratoryfor ComputationalMolecular Design, Ecole Polytechnique 190, 8057, Zurich (Switzerland), +41446354652, [email protected] Fédérale de Lausanne, CH-1015 Lausanne, Switzerland Group II introns belongtothe class of self-splicing ribozymes, aremobile Topochemical reactions of organic molecules in the crystalline stateoften geneticelements andare found withinthe genesofbacteria andlowereu- proceedwith unrivalled selectivityand sometimes allowfor reactions not karyotes [1]. We designedaderivative of S. Cerevisiae ai5γ group II intron conceivableinsolution.1 Upon exposure to light, bromodiacetyleneunder- (~900 nts), named D135-L14, whichislabeled with the Cy3-Cy5fluoropho- goes an unusualdimerizationreaction, whichproceedsunderdrasticdis- res. Constructallows for adetailed characterisation of the folding pathways placements andrearrangements of the reacting molecular fragments.2 An by smFRETusingTIRFmicroscopysince it is able to preserve the dynam- investigation of the underlying mechanism by meansofDFT computations ics andthe catalytic activityofthe parent ribozymeare preserved[2].The suggests that therate-determining initial step is a[2+1] photocycloaddition group II intron ribozymefolds sequentially in three steps from the unfolded that appearstobepredeterminedbythe nature of short contacts between to the native state with distinguishablestructuralconformations,whose re- pairs of molecules in the crystalline state.2 Insight intothe electronic struc- latedrateconstants depend on concentrationand the type of metalions in ture of allthe stationary is provided by thelocalized orbital locator (LOL), the system [2,3]. We nowintroduced point mutations and/or domain dele- proventobeavery useful tool in assigning chemical bonding patterns in tions in those positions responsible for inter-domain docking.Subsequent complex systems.3 smFRETanalysis of these derivativesallowedustoassign the specific structurestoeachFRETstate of the folding process. [1]L.R.MacGillivray, G. S. Papaefstathiou, T. Friscic, T. D. Hamilton, D.- K. Bucar, Q. Chu, D. B. Varshney, I. G. Georgiev, Acc. Chem.Res. 2008, 41,280. [2]T.N.Hoheisel, S. Schrettl,R.Marty,T.K.Todorova,C.Corminboeuf, R. Scopelliti, W. B. Schweizer, H. Frauenrath,Natur. Chem.(submitted). [3]S.N.Steinmann, Y. Mo, C. Corminboeuf, Phys.Chem. Chem.Phys. 2011, 13,20584.

References [1] A.M.Pyle, Crit. Rev. Biochem.Mol.Biol., 2010,45, 215. [2] M. Steiner,K.S.Karunatilaka,R.K.O.Sigel, D. Rueda, PNAS, 2008, 105, 13853. [3] L. Cardo, K. Karunatilaka,D.Rueda andR.K.O.Sigel (2012) Methods Mol. Bio.l, 2012, 848,227.

Computational Chemistry Computational Chemistry Computational Chemistry 197 Computational Chemistry 198 Insight of trHbN: quantitative analysis of the network and Sampling RareEvents with Spatial Averaging: Implementation and gate-trapping forO2uptake. Application to RareGas Clusters and Biomolecules

Pierre-AndreC´ azade1,Florent Hedin1,Markus Meuwly1∗ Florent Hédin1,Nuria Plattner2,Markus Meuwly3*

1Department of Chemistry,University of Basel, Klingelbergstrasse 80, 123Department of Chemistry,University of Basel, Klingelbergstrasse 80, CH-4056 Basel CH-4056 Basel

Truncated hemoglobin (trHbN) is aprotein involved in NO dioxygenation Spatial averaging [1] is an efficient Monte Carlo method which can be ap-

[1, 2] by converting nitric oxide to harmless nitrates (Fe(II)O2 + NO → plied to problems where important regions (e.g. minima) of the energy land- + − Fe (III)+NO3 ). The tunnel system of trHbN plays an important role scape may be difficult to sample with astandard random walk method, such as in determining and controlling ligand entrance, migration, and rebinding.[2] Metropolis sampling. At the heart of the method is the realisation that from

Due to agreater affinity of Fe(II) for NO than for O2,the first step of dioxy- the equilibrium density arelated, modified probability density can be con- genation is expected to be the substitution of NO ligated to the heme group by structed through asuitable transformation. This newdensity is more highly

free O2 (Fe(II)NO+O2 → Fe(II)O2 +NO). O2 dynamics and migration connected which increases the chances for transitions between neighbouring in the protein network has already been analyzed [3], providing the ligand states which in turn speeds up the sampling. In order to transform the equi- docking sites and their connectivity together with the free energy barriers be- librium density,Gaussian distributions with variable widths are used. tween them. The network can be further analyzed by means of aTransition First successful investigations included the diffusion of small molecules in Network Analysis (TNA) which provides acomprehensive picture of the lig- condensed phase environments [2] and localisation of lowest energy struc- and migration dynamics and kinetics in the network from several independent tures of Lennard-Jones clusters [3]. Amore general implementation in CHA- trajectories [4]. It provestypically the time-resolved connectivity network in RMM allowed us to study the conformational space of small biomolecules. the protein, the half-livesofthe docking sites, the transition timescales, and the extent of population transfer among different docking sites. Furthermore, [1] JD Doll, JE Gubernatis, NPlattner,MMeuwly,PDupuis, and HWang, aclose attention at the coupling between ligand and protein dynamics reveals JOURNAL OF CHEMICAL PHYSICS 2009, 10,131. agate-trapping mechanism for the ligand uptake. The protein conformation [2] NPlattner,JDDoll, and MMeuwly, JOURNAL OF CHEMICAL PHY- changes are studied by means of MD and MC simulations. SICS 2010, 4,133. [3] F. Hédin, Master Thesis, University of Basel 2011 [1] Hausladen, A., Gow, A., Stamler,J.S., Proc. Natl. Acad. Sci. U.S.A. 2001, 98,10108–10112. [2] Mishra, S., Meuwly,M., J. Am. Chem. Soc., 2010, 132,2968. [3] Cazade, P.-A., Meuwly,M., Oxygen Migration Pathways in Truncated Hemoglobin, submitted, 2012. [4] Mishra, S., Meuwly,M., Biophysical J., 2010, 99,3969. Computational Chemistry CHIMIA 2012, 66, No. 7/8 529

ComputationalChemistry ComputationalChemistry Computational Chemistry 199 Computational Chemistry 200 DFT study of the Jahn-Tellerand Pseudo-Jahn-Tellereffects in the ex- Theoretical InvestigationtoStudy Organic Photosensitizers dyes

cited states of CO3 SofianeMoussi1,2,Claud Daul2,OuridaOuamerali1 Ramanantoanina Harry1,Daul Claude1 University of Fribourg,Chemindumusée9,1700 Fribourg / 1University of Fribourg, Chemin du Musée 9, 1700 Fribourg 2University of Scienceand Technology Houari Boumedienne/El alia Po- box32Bebezzouar, 16111 Algiers, Algeria The electronic structure and the geometry of CO3 have been the subject of tremendous interest [1], since the experimental evidence of the confor- mation of this molecule in D [2]point group was reported, in addition to 3h Anovelclass of organicphoto sensitizersissought[1,2].Thisorganic the well-known C symmetry [3]. The CO molecule is involved as inter- 2v 3 dyes Pyrenoimidazole-πbridge-Cyanoacrylic acid show charge migration mediate reagentinthe atmospheres of Earth and Mars for quenching elec- 18 from thedonor to theacceptorthrough theπ-bridge (Donor-πbridge- tronically excited oxygen atoms and in contributing to the Oisotope en- Acceptor). Theintensity andthe position of thechargetransfertransition richment of stratospheric carbon dioxide[2]. Herein, we report adiscussion canbetuned by simple structural modification (variation of donorstrength about the ground state configuration and the geometry of the CO molecule: [3] 3 andnatureofthe conjugationpathway . C2v versus D3h by means of the Density Functional Theory (DFT). The pres- ence of the C2v conformation, which is the global minimum, lower in energy -1 about 500 cm than the D3h local minimum is reported, and the correspond- ing Adiabatical Potential Energy Surface of the descent in symmetry is ana- lyzed. The combination of the Jahn-Teller Effect and the Pseudo-Jahn- Teller Effect, which are involved in the twofold degenerate 1E' excited states

of the conformation in the D3h point group are mainly responsible of the dis- tortion. Our Density Functional Theory analysis of this small molecule with acomplicated electronic structure is efficient and in agreement with the pre- In this study we usebothTDDFT andMulti determinantalDFT calculation vious work reported by Liu, Bersuker et al., [4] based on avery high level to tune the π→π*energygap in ordertocover thewhole spectral range of quantum chemistry ab initio method. sunlight. [1] (a) Mebel, A.M.; Hayashi, M.; Kislov, V.V.; Lin, S.H.; J. Phys. Chem. A 2004,108, 7983; (b) Benett, C.J.; Jamieson, C.; Mebel, A.M.; Kaiser, [1]ChenyiYi, Carmen Blum,Mario Lehmann, StephanKeller, Shi-Xia R.I.; Phys. Chem. Chem. Phys., 2004,6,735. Liu,GabrielaFrei, AntoniaNeels,JurgHauser, Stefan Schurch, Sil [2] Jamieson, C.A.; Mebel, A.M.; Kaiser, R.I.; ChemPhysChem. 2006,7, vioDecurtins, J.Org.Chem. 2010, 75,3350. 2508. [2]DhirendraKumar,K.R.JustinThomas,Chuan PeiLee,Kuo-Chuan [3] (a) Moll, N.G.; Clutter, D.R.; Thompson, W.E.; J. Chem. Phys., 1966, Ho, journal Org.Lett, 2011, Vol13, No.10, 2622. 45, 4469; (b) Jacox, M.E.; Milligan, D.E.; J. Chem. Phys., 1971,54, 919. [3]Mishra,A.;Fisher,M. K. R.;Bauerel,P. Angew. Chem., Int. Ed, 2009, [4] Liu, Y.; Bersuker, I.B.; Zou, W.; Boggs, J.E.; J. Chem. Theory Com- put., 2009,5,2679. 48,2474

ComputationalChemistry ComputationalChemistry Computational Chemistry 201 ComputationalChemistry 202 Correlationbetween thevibrational properties of borohydridecom- Visualizationand RapidSearch of Chemical Spacewith Scalar Finger- - pounds andthe localenvironment of BH4 :atheoreticalanalysis prints

Vincenza D’Anna,LatéviMax Lawson Daku, Hans Hagemann Julian Schwartz1 andJean-LouisReymond1

Université de Genève 30, Quai Ernest-Ansermet 1Department of Chemistryand Biochemistry,UniversityofBerne CH-1211 Genève 4

Due to theirhighgravimetric andvolumetrichydrogencontent,inorganic Binary substructure fingerprints in combination with theTanimotocoeffi- borohydridesare considered as potentialsolid hydrogenstorage material for cientasdistancemetricare commonlyusedtoperform in silico similarity mobile applications. searchesinvirtualchemical databases. Forthisreason it is necessary to achieveanin-depthunderstandingofthe We have recentlyshownthatscalar fingerprints of molecules, like the42 relationshipbetween theirbonding propertiesand theirstructures. MolecularQuantum Numbers (MQN)[3] descriptorset,can be used forrapid [1] From this point of view,vibrationalspectroscopycan be considered avalu- Nearest-Neighbor searchesinlarge databases. Moreover,the MQNset is - able to retrieve annotated bioactivecompounds from PubChemwith signifi- able approach because thevibrationalspectra of BH4 aresensitive to itslo- [2] cal environment. cant enrichment factors. - Herein, we demonstrate theusefulness of scalar fingerprints,inparticular, of Here we trytorelatethe vibrationalpropertiesofBH4 to its local symme- try, fromthe analysis of acomprehensive database of experimental infrared asimple 34 dimensionalscalar descriptor set that can be readilyderived andRaman spectra basedonthe FG method [1]and on molecularand pe- from SMILES,and allows forrapid similarity searchesand significanten- riodical calculations performedwithin Density FunctionalTheory[2,3]. richmentsofbioactivecompounds from largechemicaldatabases.Assuch, thechemical universedatabaseGDB-13[1],(975 million molecules) canbe searchedwithinseconds. [1]E.B.Wilson, J. Chem.Phys. 1939,7,1047 Additionally, an n-dimensionalscalarmoleculardescriptorset,asopposed [2]P.Hohenberg andW.Kohn, Phys. Rev. 1964,136, B864 to binary molecular descriptor sets(usually1024 dimensional),can be inter- preted as an n-dimensionalChemicalSpace wheremolecules with similar [3]W.Khon andL.J.Sham, Phys. Rev. 1965,140,A1133 descriptors, andthus similarstructuresand presumably similarbioactivities, clusterinthe same region of thechemicalspace.Due to thesmall numberof dimensions,the resultingpropertyspace is chemically meaningful andcan be visually inspected, afterapplicationofprinciple componentanalysis, as a two-dimensionalprojectionofthe 34-dimensionalspace. [1]L.C.Blum et.al., J. Comput.Aided Mol. Des. 2011, 25,637. [2]R.v.Deursen et.al., J. Comput.Aided Mol. Des. 2011, 25,649. [3]K.T.Nguyen et.al., ChemMedChem 2009, 4,1803. 530 CHIMIA 2012, 66, No. 7/8 Computational Chemistry

Computational Chemistry ComputationalChemistry Computational Chemistry 203 Computational Chemistry 204 Effects of the finite length of the pump laser pulse in nonadiabatic Ultrafast time-resolved electronic spectra with on-the-fly ab initio semi- quantum dynamics simulations of ultrafast time-resolved spectroscopy classical methods for many-dimensional systems

Aurelien´ Patoz,Marius Wehrle, and Jiri Vanicek M. Wehrle, J. Vaníček*

Ecole Polytechnique Fed´ erale´ de Lausanne Laboratory of TheoreticalPhysical Chemistry, Institut des Sciences et Ingé- nierie Chimiques, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland We have implemented ageneral split-operator algorithm for exact nonadi- abatic quantum dynamics of amolecule interacting with atime-dependent electromagnetic field. This algorithm enables evaluation of the accuracyof Semiclassical methods allow to capture quantum effects approximately but the assumption of ultrashort pulse length as well as of other approximations they are usually difficult to apply to high-dimensional systems because of frequently used in theoretical treatments of such systems. We compare the main two reasons: First, the number of trajectoriesrequired often scales ex- usual approximate treatments with the exact solution for the ultrafast nonadi- ponentially with the number of degrees of freedom. Second, semiclassical abatic dynamics of afour-dimensional model of pyrazine. algorithms typically require the Hessian of the potential in addition to the force, which makes the calculation more expensive than classical calcula- tions. It has been showed that the required number of trajectories is inde- pendent of dimensions for the dephasing representation of quantum fidelity [1,2]. The capability of the dephasing representation for ”on-the-fly” quan- tum simulations of large systems is demonstrated by calculating the time- resolved stimulated emission spectrum of the 54-dimensional azulene mole- cule.

[1] J. Vaníček, Phys. Rev. E 2006, 73,046204. [2] C. Mollica, J. Vaníček, Phys. Rev. Lett. 2011, 107,014101.

*[email protected]

Computational Chemistry Computational Chemistry Computational Chemistry 205 Computational Chemistry 206 Understanding the nucleation of the microRNA-mRNApairing by using Accelerating the calculation of time-resolved electronic spectra of CLIP-Seq and RNAfolding data many-dimensional systems with the cellular dephasing representation

Ray Mar´ın1,Jirˇ´ıVan´ıcekˇ 1 Miroslav Sulcˇ ,Jirˇ´ıVan´ıcekˇ ∗

1Laboratory of Theoretical Physical Chemistry,Institut des Sciences et Institut des Sciences et Ingenierie´ Chimiques, Ingnierie Chimiques, cole Polytechnique Fdrale de Lausanne, CH-1015 Ecole Polytechnique Fed´ erale´ de Lausanne, CH-1015, Switzerland Lausanne, Switzerland Dephasing representation (DR) of fidelity [1], also known as the phase av- To find out whether the AGO-miRNAcomplexismore sensitive to the acces- eraging method, can be considered as aspecial case of Miller’slinearised sibility of aparticular region inside the seed match, we analyze in detail the semiclassical initial value representation and belongs among the most effi- accessibility of awide set of miRNAbinding sites validated by PAR-CLIP cient approximate semiclassical approaches for the calculation of ultrafast experiments [1]. Our analysis reveals that nucleotides at the 3’-end of bound time-resolved electronic spectra. seed matches are significantly more accessible than nucleotides at the 5’-end, It has been shown [2] that the number of trajectories required for convergence and also more accessible than nucleotides at anypositions in the unbound of the DR is independent of the dimensionality.Here we propose [3] afurther seed matches. We showthat the accessibility of asingle nucleotide at the accelerated version of the dephasing representation in the spirit of Heller’s 3’-end is more effective than the accessibility of several nucleotides at the cellular dynamics. The basic idea of the “cellular dephasing representation” 5’-end in discriminating between functional and non-functional sites. Analy- is to decompose the Wigner transform of the initial state into aphase space sis of mRNAand protein fold changes induced by miRNAover-expression, Gaussian basis and then evaluate the contribution of each Gaussian to the demonstrated that genes with accessible nucleation regions at the 3’-end are relevant correlation function approximately analytically,using numerically more strongly downregulated than genes whose accessible nucleation regions acquired information only along the trajectory of the Gaussian’scentre. are located elsewhere within the seed match. The pronounced sensitivity of the AGO-miRNAcomplextothe accessibility of the 3’-end of the seed match The proposed method turns out to be sufficiently accurate wheneverthe inter- suggests that, in most cases, nucleation occurs in this region. It is shown that action with the environment diminishes the importance of recurrences in the our conclusions are consistent with previous experimental studies [2-4]. correlation functions of interest. Numerical tests on acollinear NCO molecule and on a48-dimensional azulene model indicate that even 1-trajectory results [1] M. Hafner,M.Landthaler,L.Burger,M.Khorshid, J. Hausser,P.Berninger, are in good agreement with the fully converged DR (104 trajectories). A. Rothballer,M.Ascano Jr,etal., Cell 2010, 141,129. [2] Y. Wang, G. Sheng, S. Juranek, T. Tuschl, and D.J. Patel, Nature 2010, [1] J. Van´ıcek,ˇ Phys. Rev. E 2006, 73,046204. 456,209. [2] C. Mollica, J. Van´ıcek,ˇ Phys. Rev. Lett. 2011, 107,214101. [3] S.L. Ameres, J. Martinez, and R. Schroeder, Cell 2007, 130,101. [3] M. Sulc,ˇ J. Van´ıcek,ˇ Mol. Phys. 2012, published online [4] S.W.Chi, G.J. Hannon, and R.B. Darnell, Nat. Struct. Mol. Biol. 2012, DOI: 10.1080/00268976.2012.668971. 19,321. ∗E-mail: jiri.vanicek@epfl.ch Computational Chemistry CHIMIA 2012, 66, No. 7/8 531

Computational Chemistry ComputationalChemistry Computational Chemistry 207 Computational Chemistry 208 Measuring nonadiabaticity and importance of spin orbit couplings in StudyofTh(IV) hydration structure by theoretical methods the quantum molecular dynamics using the quantum fidelity and its 1 2 3 efficient semiclassical approximation BeuchatCésar ,SpeziaRiccardo andGagliardi Laura 1UniversityofGeneva, Department of PhysicalChemistry, Quai Ernest Toma´ sZˇ immermann, Jirˇ´ıVan´ıcekˇ � Ansermet30, CH-1211 Geneva, 2CNRS,LAMBE UMR 8587, Université d'EvryVal d'Essonne, Evry, Laboratory of Theoretical Physical Chemistry,Institut des Sciences et France, 91025, France Ingenierie´ Chimiques, Ecole Polytechnique Fed´ erale´ de Lausanne, CH-1015, 3UniversityofMinnesota,DepartmentofChemistryand Supercomputing Switzerland Institute, 207 Pleasant St.SE,

We propose to measure nonadiabaticity of molecular quantum dynamics rig- The understandingofhydrationproperties of ions is the first step to study orously by the quantum fidelity between the Born-Oppenheimer quantum dy- their reactivityinwater.Inparticular, properties like ion-water distances namics and the full nonadiabatic quantum dynamics. In addition to nonadia- andcoordination numberofsolvation shells areatthe centre of both theo- baticity,the quantum fidelity may be used to evaluate the importance of the retical1,2 andexperimentalstudies. spin orbit couplings and other coupling terms. The quantum fidelity is esti- mated efficiently with the multiple-surface dephasing representation (MSDR) Thorium is of particularinterestbecause it can be used as acombustible for [1], which is the generalization of the dephasing representation (DR) [2] of nuclearpowerplants. This could in principle leadtonuclearenergybased on amoreabundantcombustible andwith less radioactivewastes. Tho- quantum fidelity to several potential energy surfaces (PESs). In contrast to rium(IV)hydration hasbeen studied experimentallyand theoretically,but quantum dynamics the cost of the MSDR does not scale exponentially with manyquestions arestill unanswered. In particular,while it is well estab- the number of degrees of freedom. Being asemiclassical method, it still ap- lished that the Th-water first shell distance is 2.45-2.46 Å,the coordination proximately includes quantum effects on the motion of nuclei through in- number is not yetuniquelydefined. EXAFS andHEXSexperiments have terference without the need for the Hessian of PESs. Twomixed quantum- provided values in the8-12range. classical dynamics methods are currently used to propagate the nuclei: the locally mean field method (LMFD), which turns out to be nothing else than Given the interestinthe topic, we have undertakenacomputationalstudy the Ehrenfest dynamics of an ensemble of trajectories and the fewest switches aimedatadeeper understanding of the Th(IV) hydrationstructure andthe surface hopping dynamics (FSSH). The method is compared to the numeri- differences between ThCl4 andThBr4 saltsatdifferentconcentrations. Sev- cally exact quantum results using several model problems. Subsequently,itis eral theoretical methods were employed: densityfunctionaltheory, classical molecular dynamics basedonboth semi-empirical polarisable potentialsand applied on-the-flytoevaluate the nonadiabaticity and the importance of spin ab initioderivedpolarisable potentials.The resultsofthe computations were orbit couplings in the dynamics on the second excited state of azulene and + combinedwith EXAFS experimentaldata. CH2NH2 and in the collision of F+H2. [1] C.Beuchat, D.Hagberg, R.Spezia, L.Gagliardi, J. Phys.Chem. B. 2010,114 [1] T. Zimmermann and J. Van´ıcek,ˇ J. Chem. Phys. 2012, 136,094196. (47), 15590. [2] J. Van´ıcek,ˇ Phys. Rev. E 2004, 70,055201; J. Van´ıcek,ˇ Phys. Rev. E [2] M.Duvail, P.Vitorgeand R.Spezia, J. Chem.Phys. 2009,130, 104501. 2006, 73,046204.

Computational Chemistry 31487%7-32%0 ,)1-675< Computational Chemistry 209 Computational Chemistry 210 Evaluation of ParityViolating Energy Differencesfor Cyanoaziridine,               Cyano-and Fluorooxiranes with Highly Correlated Wavefunctions. %52%= )-(%5 "%(),%80  <)56 Ľuboš Horný and Martin Quack Physical Chemistry, ETH Hönggerberg, CH-8093 Zürich, Switzerland '%67)5 2-9)56-7<)4%571)273*,)1-675< %2(,)1-'%0 -303+<   %-275))7 )67%1-0732 27%5-3%2%(% Possible experiments on molecular parity violationand its possible implications for the origin of molecular chirality andbiomolecular )7)51-2-2+ 7,) 4534)57-)63*130)'80)6,%6%0:%<6 &))2 32) 3* 7,) 1%.35 homochiralityare of fundamentalinterest1,2.Ithas been established3 howto 7%6/6 3*',)1-'%05)6)%5', ,)2 32) -6 6)%5',-2+ *35 %2 );-67-2+ 130)'80) include the electroncorrelationeffectsincomputation of molecular parity- :-7, %()6-5)( 4534)57< 35 75<-2+ 73 ()6-+2 %2):130)'80) :-7, %()6-5)( violationpotentials Epv using nonrelativistic highlycorrelated coupled 4534)57< 32) 3*7)2 2))(673'326-()57,386%2(63*4366-&0)'314382(6 cluster wavefunctions withinalinearresponse framework4.This ,-61%/)67,));4)5-1)27%0 %2('31487%7-32%01%7)5-%04534)57< ()7)51- complementsprevious developments in the precise theoretical description of 2%7-32 3* -2281)5%&0) 4366-&-0-7-)6 '3670< %2( -145%'7-'%0-21367 '%6)62 molecular-parity violation5,6.Recently, high resolution spectroscopic 7,) 37,)5,%2( 7,)5)%5)1%2<4534)57-)67,%7%5)237 (-5)'70<1)%685%&0) analysis of chiral compounds becamefeasible1,2,7.Wereport structure and );4)5-1)27%00<35'31487%&0) 7,)35)7-'%00<35 );%140) 32) '%2 033/ %7 energetics for someofsuch species – cis-/trans-cyanoaziridine, cyano-and 7,) 73;-'-7<3*130)'80)6 -7 :380(&)82)7,-'%0737)67 7,)6) 130)'80)6 );4) fluorooxirane,and comparethem to previous results2,8.Using CC2and 5-1)27%00<%2( -7 -6 '31487%7-32%00<-275%'7%&0) 73 6-180%7) 7,) -2+)67-32 CCSD wavefunctions, we find (R)-configurations of cyanoaziridine, and (-+)67-32 %2(&-3',)1-'%05)64326) 3*%130)'80) fluorooxirane, and (S)-configurationofcyanooxiranetobeenergetically more stablethan theircounterparts. 3:)9)5&<);4035-2+ 7,) 1%',-2) 0)%52-2+ 1)7,3(6 :)'%2 )**-'-)270< [1] M. Quack, “FundamentalSymmetries and SymmetryViolations from %2( :-7, '3275300)( )55356)67-1%7) 7,) 4534)57-)63*%',)1-'%068&67%2') High Resolution Spectroscopy” In HandbookofHigh Resolution &<0)9)5%+-2+ 7,) 5)68076 *53145)9-386 );4)5-1)276 35 %''85%7)'%0'80% Spectroscopy, M. Quack and F. Merkteds. 2011, 659. 7-326,)/)<-26-+,7 -6 7,%76-1-0%5130)'80)67)2( 73 ,%9) 6-1-0%54534)5 [2] M. Quack, J. Stohner, M. Willeke, Ann. Rev. Phys. Chem. 2008, 59,741. 7-)63-*7,) 4534)57-)63*%(-9)56)>5)*)5)2') 6)7? 3* 130)'80)6-6/23:2 [3] Ľ. Horný and M. Quack, Faraday Discussions 2011, 150, 152. 7,)2 32) '%2 45)(-'77,)4534)57-)63*82/23:2 130)'80)6
7,)>7)67 6)7? &< [4] T. Helgaker,S.Coriani, P. Jørgensen, K. Kristensen, J. Olsen, K. Ruud, ()7)51-2-2+ 7,) 5)0%7-326,-4 &)7:))2 7,) 82/23:2 130)'80)6 %2( 7,) 5)*)5 Chem.Rev. 2012, 112, )2') 130)'80)6 #$ ,)%4453%',:)%5)()9)034-2+ *35 130)'80%56-1-0%5- [5]A.Bakasov, T. K. Ha,M.Quack,J.Chem. Phys. 1998, 109,7263. 7< -6 &%6)( 32 /5-+-2+%43:)5*80 )67-1%7-32 7330 35-+-2%00<86)( -2+)367% [6]R.Berger and M. Quack, J. Chem. Phys. 2000,112,3148. 7-67-'6 #$ 2 7,-6 45)6)27%7-32 7,-6 1)7,3( -6 %440-)( 73 45)(-'79%5-386 13 [7]AlbertS.and M. Quack, ChemPhysChem 2007,8,1271. 0)'80%5 %2( 1%7)5-%04534)57-)6 [8]R.Berger,M.Quack, G. S. Tschumper, Helv. Chim. Acta, 2000, 83, #$85+)5 -8 <)56   
  1919.   [9] R. Berger,M.Quack, J. Stohner, Angew. Chem. Intl. Ed. 2001, 40,1667. #$ %'/)52%+)0 45-2+)5 )50%+ ):!35/