Grubmüller, Helmut

[["dc.bibliographiccitation.firstpage","76"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Biophysical Journal"],["dc.bibliographiccitation.lastpage","87"],["dc.bibliographiccitation.volume","107"],["dc.contributor.author","Wolf, Maarten G."],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.author","Groenhof, Gerrit"],["dc.date.accessioned","2018-02-12T09:29:59Z"],["dc.date.available","2018-02-12T09:29:59Z"],["dc.date.issued","2014"],["dc.description.abstract","The cellular energy machinery depends on the presence and properties of protons at or in the vicinity of lipid membranes. To asses the energetics and mobility of a proton near a membrane, we simulated an excess proton near a solvated DMPC bilayer at 323 K, using a recently developed method to include the Grotthuss proton shuttling mechanism in classical molecular dynamics simulations. We obtained a proton surface affinity of −13.0 ± 0.5 kJ mol−1. The proton interacted strongly with both lipid headgroup and linker carbonyl oxygens. Furthermore, the surface diffusion of the proton was anomalous, with a subdiffusive regime over the first few nanoseconds, followed by a superdiffusive regime. The time- and distance dependence of the proton surface diffusion coefficient within these regimes may also resolve discrepancies between previously reported diffusion coefficients. Our simulations show that the proton anomalous surface diffusion originates from restricted diffusion in two different surface-bound states, interrupted by the occasional bulk-mediated long-range surface diffusion. Although only a DMPC membrane was considered in this work, we speculate that the restrictive character of the on-surface diffusion is highly sensitive to the specific membrane conditions, which can alter the relative contributions of the surface and bulk pathways to the overall diffusion process. Finally, we discuss the implications of our findings for the energy machinery."],["dc.identifier.doi","10.1016/j.bpj.2014.04.062"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/12115"],["dc.language.iso","en"],["dc.notes.status","final"],["dc.relation.eissn","1542-0086"],["dc.relation.issn","0006-3495"],["dc.title","Anomalous Surface Diffusion of Protons on Lipid Membranes"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","6812"],["dc.bibliographiccitation.issue","21"],["dc.bibliographiccitation.journal","Journal of the American Chemical Society"],["dc.bibliographiccitation.lastpage","6819"],["dc.bibliographiccitation.volume","129"],["dc.contributor.author","Groenhof, Gerrit"],["dc.contributor.author","Schäfer, Lars V."],["dc.contributor.author","Boggio-Pasqua, Martial"],["dc.contributor.author","Goette, Maik"],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.author","Robb, Michael A."],["dc.date.accessioned","2018-04-23T11:47:47Z"],["dc.date.available","2018-04-23T11:47:47Z"],["dc.date.issued","2007"],["dc.description.abstract","Multiconfigurational ab initio calculations and QM/MM molecular dynamics simulations of a photoexcited cytosine−guanine base pair in both gas phase and embedded in the DNA provide detailed structural and dynamical insights into the ultrafast radiationless deactivation mechanism. Photon absorption promotes transfer of a proton from the guanine to the cytosine. This proton transfer is followed by an efficient radiationless decay of the excited state via an extended conical intersection seam. The optimization of the conical intersection revealed that it has an unusual topology, in that there is only one degeneracy-lifting coordinate. This is the central mechanistic feature for the decay both in vacuo and in the DNA. Radiationless decay occurs along an extended hyperline nearly parallel to the proton-transfer coordinate, indicating the proton transfer itself is not directly responsible for the deactivation. The seam is displaced from the minimum energy proton-transfer path along a skeletal deformation of the bases. Decay can thus occur anywhere along the single proton-transfer coordinate, accounting for the remarkably short excited-state lifetime of the Watson−Crick base pair. In vacuo, decay occurs after a complete proton transfer, whereas in DNA, decay can also occur much earlier. The origin of this effect lies in the temporal electrostatic stabilization of dipole in the charge-transfer state in DNA."],["dc.identifier.doi","10.1021/ja069176c"],["dc.identifier.gro","3142268"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/13396"],["dc.language.iso","en"],["dc.notes.intern","lifescience updates Crossref Import"],["dc.notes.status","final"],["dc.relation.issn","0002-7863"],["dc.title","Ultrafast Deactivation of an Excited Cytosine−Guanine Base Pair in DNA"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dc.type.peerReviewed","no"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","2687"],["dc.bibliographiccitation.issue","12"],["dc.bibliographiccitation.journal","ChemPhysChem"],["dc.bibliographiccitation.lastpage","2697"],["dc.bibliographiccitation.volume","14"],["dc.contributor.author","Li, Wenjin"],["dc.contributor.author","Edwards, Scott A."],["dc.contributor.author","Lu, Lanyuan"],["dc.contributor.author","Kubar, Tomas"],["dc.contributor.author","Patil, Sandeep P."],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.author","Groenhof, Gerrit"],["dc.contributor.author","Gräter, Frauke"],["dc.date.accessioned","2018-02-12T11:05:37Z"],["dc.date.available","2018-02-12T11:05:37Z"],["dc.date.issued","2013"],["dc.description.abstract","Internal molecular forces can guide chemical reactions, yet are not straightforwardly accessible within a quantum mechanical description of the reacting molecules. Here, we present a force-matching force distribution analysis (FM-FDA) to analyze internal forces in molecules. We simulated the ring opening of trans-3,4-dimethylcyclobutene (tDCB) with on-the-fly semiempirical molecular dynamics. The self-consistent density functional tight binding (SCC-DFTB) method accurately described the force-dependent ring-opening kinetics of tDCB, showing quantitative agreement with both experimental and computational data at higher levels. Mechanical force was applied in two different ways, namely, externally by a constant pulling force and internally by embedding tDCB within a strained macrocycle-containing stiff stilbene. We analyzed the distribution of tDCB internal forces in the two different cases by FM-FDA and found that external force gave rise to a symmetric force distribution in the cyclobutene ring, which also scaled linearly with the external force, indicating that the force distribution was uniquely determined by the symmetric architecture of tDCB. In contrast, internal forces due to stiff stilbene resulted in an asymmetric force distribution within tDCB, which indicated a different geometry of force application and supported the important role of linkers in the mechanochemical reactivity of tDCB. In addition, three coordinates were identified through which the distributed forces contributed most to rate acceleration. These coordinates are mostly parallel to the coordinate connecting the two CH3 termini of tDCB. Our results confirm previous observations that the linker outside of the reactive moiety, such as a stretched polymer or a macrocycle, affects its mechanochemical reactivity. We expect FM-FDA to be of wide use to understand and quantitatively predict mechanochemical reactivity, including the challenging cases of systems within strained macrocycles."],["dc.identifier.doi","10.1002/cphc.201300252"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/12158"],["dc.language.iso","en"],["dc.notes.status","final"],["dc.title","Force Distribution Analysis of Mechanochemically Reactive Dimethylcyclobutene"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","530"],["dc.bibliographiccitation.issue","4"],["dc.bibliographiccitation.journal","Angewandte Chemie International Edition"],["dc.bibliographiccitation.lastpage","536"],["dc.bibliographiccitation.volume","46"],["dc.contributor.author","Schäfer, Lars V."],["dc.contributor.author","Groenhof, Gerrit"],["dc.contributor.author","Klingen, Astrid R."],["dc.contributor.author","Ullmann, G. Matthias"],["dc.contributor.author","Boggio-Pasqua, Martial"],["dc.contributor.author","Robb, Michael A."],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2017-09-07T11:52:29Z"],["dc.date.available","2017-09-07T11:52:29Z"],["dc.date.issued","2007"],["dc.description.abstract","Molecular light‐switch: Off–on switching of the fluorescence of the protein asFP595 involves a trans–cis isomerization. Mixed quantum/classical simulations elucidate the spectroscopic properties of asFP595 and give detailed insights into the photoswitching mechanism. The conformational trans–cis switching triggers a proton‐transfer cascade between the chromophore and adjacent amino acids."],["dc.identifier.doi","10.1002/ange.200602315"],["dc.identifier.gro","3144945"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/2626"],["dc.language.iso","en"],["dc.notes.intern","Crossref Import"],["dc.notes.status","final"],["dc.publisher","Wiley-Blackwell"],["dc.relation.issn","1433-7851"],["dc.title","Photoswitching of the Fluorescent Protein asFP595: Mechanism, Proton Pathways, and Absorption Spectra"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dc.type.peerReviewed","no"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","2038"],["dc.bibliographiccitation.issue","21"],["dc.bibliographiccitation.journal","Journal of Computational Chemistry"],["dc.bibliographiccitation.lastpage","2038"],["dc.bibliographiccitation.volume","37"],["dc.contributor.author","Wolf, Maarten G."],["dc.contributor.author","Hoefling, Martin"],["dc.contributor.author","Aponte-Santamaría, Camilo"],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.author","Groenhof, Gerrit"],["dc.date.accessioned","2021-03-05T08:58:22Z"],["dc.date.available","2021-03-05T08:58:22Z"],["dc.date.issued","2016"],["dc.identifier.doi","10.1002/jcc.24386"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/80104"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.iserratumof","/handle/2/80104"],["dc.relation.issn","0192-8651"],["dc.title","Corrigendum: g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dc.type.subtype","erratum_ja"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","3250"],["dc.bibliographiccitation.issue","11"],["dc.bibliographiccitation.journal","Journal of the American Chemical Society"],["dc.bibliographiccitation.lastpage","3251"],["dc.bibliographiccitation.volume","130"],["dc.contributor.author","Groenhof, Gerrit"],["dc.contributor.author","Schäfer, Lars V."],["dc.contributor.author","Boggio-Pasqua, Martial"],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.author","Robb, Michael A."],["dc.date.accessioned","2018-02-13T12:55:37Z"],["dc.date.available","2018-02-13T12:55:37Z"],["dc.date.issued","2008-03-19"],["dc.description.abstract","We have performed excited-state dynamics simulations of the Arg52Gln (R52Q) mutant of photoactive yellow protein (PYP). The results of these simulations demonstrate that in the mutant the primary events after photoexcitation are different from those in the wild-type. In the mutant, the chromophore predominantly undergoes single bond photoisomerization, whereas in the wild-type, photoisomerization of the double bond occurs. Furthermore, the excited-state lifetime is around three times longer than in wild-type PYP, which agrees well with recent transient absorption measurements. In 20% of the trajectories, we observe the formation of a photoproduct that has the carbonyl oxygen atom of the chromophore flipped by almost 180°, disrupting the hydrogen bond between the chromophore and the backbone amino group of Cys69. This observation, in combination with the fact that the mutant is photoactive, suggests that the break of the hydrogen bond is the key step in the photoactivation process rather than the double bond trans-to-cis isomerization."],["dc.identifier.doi","10.1021/ja078024u"],["dc.identifier.pmid","18293978"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/12226"],["dc.language.iso","en"],["dc.notes.status","final"],["dc.relation.eissn","1520-5126"],["dc.title","Arginine52 controls the photoisomerization process in photoactive yellow protein"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","069904"],["dc.bibliographiccitation.issue","6"],["dc.bibliographiccitation.journal","The Journal of Chemical Physics"],["dc.bibliographiccitation.volume","141"],["dc.contributor.author","Inhester, L."],["dc.contributor.author","Burmeister, C. F."],["dc.contributor.author","Groenhof, Gerrit"],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2021-03-05T08:58:43Z"],["dc.date.available","2021-03-05T08:58:43Z"],["dc.date.issued","2014"],["dc.identifier.doi","10.1063/1.4892982"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/80222"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.eissn","1089-7690"],["dc.relation.iserratumof","/handle/2/12189"],["dc.relation.issn","0021-9606"],["dc.title","Erratum: “Auger spectrum of a water molecule after single and double core ionization” [J. Chem. Phys. 136, 144304 (2012)]"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dc.type.subtype","erratum_ja"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","3261"],["dc.bibliographiccitation.issue","7"],["dc.bibliographiccitation.journal","Journal of Chemical Theory and Computation"],["dc.bibliographiccitation.lastpage","3261"],["dc.bibliographiccitation.volume","9"],["dc.contributor.author","Donnini, Serena"],["dc.contributor.author","Tegeler, Florian"],["dc.contributor.author","Groenhof, Gerrit"],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2021-03-05T08:58:22Z"],["dc.date.available","2021-03-05T08:58:22Z"],["dc.date.issued","2013"],["dc.identifier.doi","10.1021/ct400439g"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/80110"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.eissn","1549-9626"],["dc.relation.iserratumof","/handle/2/80110"],["dc.relation.issn","1549-9618"],["dc.title","Correction to Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dc.type.subtype","erratum_ja"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","381"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Journal of Chemical Theory and Computation"],["dc.bibliographiccitation.lastpage","390"],["dc.bibliographiccitation.volume","10"],["dc.contributor.author","Hub, Jochen S."],["dc.contributor.author","Groot, Bert L. de"],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.author","Groenhof, Gerrit"],["dc.date.accessioned","2017-09-07T11:46:56Z"],["dc.date.available","2017-09-07T11:46:56Z"],["dc.date.issued","2014"],["dc.description.abstract","Ewald summation, which has become the de facto standard for computing electrostatic interactions in biomolecular simulations, formally requires that the simulation box is neutral. For non-neutral systems, the Ewald algorithm implicitly introduces a uniform background charge distribution that effectively neutralizes the simulation box. Because a uniform distribution of counter charges typically deviates from the spatial distribution of counterions in real systems, artifacts may arise, in particular in systems with an inhomogeneous dielectric constant. Here, we derive an analytical expression for the effect of using an implicit background charge instead of explicit counterions, on the chemical potential of ions in heterogeneous systems, which (i) provides a quantitative criterium for deciding if the background charge offers an acceptable trade-off between artifacts arising from sampling problems and artifacts arising from the homogeneous background charge distribution, and (ii) can be used to correct this artifact in certain cases. Our model quantifies the artifact in terms of the difference in charge density between the non-neutral system with a uniform neutralizing background charge and the real neutral system with a physically correct distribution of explicit counterions. We show that for inhomogeneous systems, such as proteins and membranes in water, the artifact manifests itself by an overstabilization of ions inside the lower dielectric by tens to even hundreds kilojoules per mole. We have tested the accuracy of our model in molecular dynamics simulations and found that the error in the calculated free energy for moving a test charge from water into hexadecane, at different net charges of the system and different simulation box sizes, is correctly predicted by the model. The calculations further confirm that the incorrect distribution of counter charges in the simulation box is solely responsible for the errors in the PMFs."],["dc.identifier.doi","10.1021/ct400626b"],["dc.identifier.gro","3142219"],["dc.identifier.isi","000330142400036"],["dc.identifier.pmid","26579917"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/5854"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.eissn","1549-9626"],["dc.relation.issn","1549-9618"],["dc.title","Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net Charge"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1962"],["dc.bibliographiccitation.issue","6"],["dc.bibliographiccitation.journal","Journal of Chemical Theory and Computation"],["dc.bibliographiccitation.lastpage","1978"],["dc.bibliographiccitation.volume","7"],["dc.contributor.author","Donnini, Serena"],["dc.contributor.author","Tegeler, Florian"],["dc.contributor.author","Groenhof, Gerrit"],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2018-02-13T09:46:16Z"],["dc.date.available","2018-02-13T09:46:16Z"],["dc.date.issued","2011-06-14"],["dc.description.abstract","pH is an important parameter in condensed-phase systems, because it determines the protonation state of titratable groups and thus influences the structure, dynamics, and function of molecules in solution. In most force field simulation protocols, however, the protonation state of a system (rather than its pH) is kept fixed and cannot adapt to changes of the local environment. Here, we present a method, implemented within the MD package GROMACS, for constant pH molecular dynamics simulations in explicit solvent that is based on the λ-dynamics approach. In the latter, the dynamics of the titration coordinate λ, which interpolates between the protonated and deprotonated states, is driven by generalized forces between the protonated and deprotonated states. The hydration free energy, as a function of pH, is included to facilitate constant pH simulations. The protonation states of titratable groups are allowed to change dynamically during a simulation, thus reproducing average protonation probabilities at a certain pH. The accuracy of the method is tested against titration curves of single amino acids and a dipeptide in explicit solvent."],["dc.identifier.doi","10.1021/ct200061r"],["dc.identifier.pmid","21687785"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/12197"],["dc.language.iso","en"],["dc.notes.status","final"],["dc.relation.eissn","1549-9626"],["dc.title","Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]