Co-reporter:Frank R. Beierlein, Andreas M. Krause, Christof M. Jäger, Piotr Fita, Eric Vauthey, and Timothy Clark
Langmuir September 24, 2013 Volume 29(Issue 38) pp:11898-11907
Publication Date(Web):September 24, 2013
DOI:10.1021/la4021355
Modern spectroscopic techniques such as time-resolved second-harmonic-generation spectroscopy allow molecules to be examined selectively directly at phase interfaces. Two-phase systems formed by glycerol/water and alkane layers have previously been studied by time-resolved second-harmonic-generation spectroscopic measurements. In this molecular dynamics study, a triphenylmethane dye was inserted at the glycerol/water–alkane interface and was used as a probe for local properties such as viscosity. We now show how extensive simulations over a wide range of concentrations can be used to obtain a detailed view of the molecular structure at the glycerol/water–alkane interface. Glycerol is accumulated in a double layer adjacent to the alkane interface, which results in increased viscosity of the glycerol/water phase in the direct vicinity of the interface. We also show that conformational ensembles created by classical molecular-dynamics simulations can serve as input for QM/MM calculations, yielding further information such as transition dipoles, which can be compared with spectroscopic measurements.
Co-reporter:Heike B. Thomas, Matthias Hennemann, Patrick Kibies, Franziska Hoffgaard, Stefan Güssregen, Gerhard Hessler, Stefan M. Kast, and Timothy Clark
Journal of Chemical Information and Modeling August 28, 2017 Volume 57(Issue 8) pp:1907-1907
Publication Date(Web):July 12, 2017
DOI:10.1021/acs.jcim.7b00080
A neglect of diatomic differential overlap (NDDO) Hamiltonian has been parametrized as an electronic component of a polarizable force field. Coulomb and exchange potentials derived directly from the NDDO Hamiltonian in principle can be used with classical potentials, thus forming the basis for a new generation of efficiently applicable multipolar polarizable force fields. The new hpCADD Hamiltonian uses force-field-like atom types and reproduces the electrostatic properties (dipole moment, molecular electrostatic potential) and Koopmans’ theorem ionization potentials closely, as demonstrated for a large training set and an independent test set of small molecules. The Hamiltonian is not intended to reproduce geometries or total energies well, as these will be controlled by the classical force-field potentials. In order to establish the hpCADD Hamiltonian as an electronic component in force-field-based calculations, we tested its performance in combination with the 3D reference interaction site model (3D RISM) for aqueous solutions. Comparison of the resulting solvation free energies for the training and test sets to atomic charges derived from standard procedures, exact solute–solvent electrostatics based on high-level quantum-chemical reference data, and established semiempirical Hamiltonians demonstrates the advantages of the hpCADD parametrization.
Co-reporter:Dr. Noureldin Saleh;Passainte Ibrahim; Dr. Timothy Clark
Angewandte Chemie 2017 Volume 129(Issue 31) pp:9136-9140
Publication Date(Web):2017/07/24
DOI:10.1002/ange.201702468
AbstractProtein nanobodies have been used successfully as surrogates for unstable G-proteins in order to crystallize G-protein-coupled receptors (GPCRs) in their active states. We used molecular dynamics (MD) simulations, including metadynamics enhanced sampling, to investigate the similarities and differences between GPCR–agonist ternary complexes with the α-subunits of the appropriate G-proteins and those with the protein nanobodies (intracellular binding partners, IBPs) used for crystallization. In two of the three receptors considered, the agonist-binding mode differs significantly between the two alternative ternary complexes. The ternary-complex model of GPCR activation entails enhancement of ligand binding by bound IBPs: Our results show that IBP-specific changes can alter the agonist binding modes and thus also the criteria for designing GPCR agonists.
Co-reporter:Dr. Noureldin Saleh;Passainte Ibrahim; Dr. Timothy Clark
Angewandte Chemie International Edition 2017 Volume 56(Issue 31) pp:9008-9012
Publication Date(Web):2017/07/24
DOI:10.1002/anie.201702468
AbstractProtein nanobodies have been used successfully as surrogates for unstable G-proteins in order to crystallize G-protein-coupled receptors (GPCRs) in their active states. We used molecular dynamics (MD) simulations, including metadynamics enhanced sampling, to investigate the similarities and differences between GPCR–agonist ternary complexes with the α-subunits of the appropriate G-proteins and those with the protein nanobodies (intracellular binding partners, IBPs) used for crystallization. In two of the three receptors considered, the agonist-binding mode differs significantly between the two alternative ternary complexes. The ternary-complex model of GPCR activation entails enhancement of ligand binding by bound IBPs: Our results show that IBP-specific changes can alter the agonist binding modes and thus also the criteria for designing GPCR agonists.
Co-reporter:Pavlo O. Dral
Physical Chemistry Chemical Physics 2017 vol. 19(Issue 26) pp:17199-17209
Publication Date(Web):2017/07/05
DOI:10.1039/C7CP02865B
We propose a new approach to the synthesis of AHx@fullerene structures via reactions through the fullerene wall. To investigate the feasibility of the approach, the step-by-step hydrogenation of the template endofullerene N@C60 up to NH4@C60 has been studied using DFT and MP2 calculations. Protonation of the endohedral guest through the fullerene wall is competitive with escape of the guest, whereas reaction with a hydrogen atom is less favorable. Each protonation step is highly exothermic, so that less active acids can also protonate the guest with less accumulation of energy. The final product, NH4@C60 is a novel concentric ion pair NH4+@C60˙− in which the charge-centers of the two ions coincide.
Co-reporter:Noureldin Saleh;Giorgio Saladino;Francesco Luigi Gervasio
Chemical Science (2010-Present) 2017 vol. 8(Issue 5) pp:4019-4026
Publication Date(Web):2017/05/03
DOI:10.1039/C6SC04647A
Signalling by G-protein coupled receptors usually occurs via ternary complexes formed under cooperative binding between the receptor, a ligand and an intracellular binding partner (a G-protein or β-arrestin). While a global rational for allosteric effects in ternary complexes would be of great help in designing ligands with specific effects, the paucity of structural data for ternary complexes with β-arrestin, together with the intrinsic difficulty of characterizing the dynamics involved in the allosteric coupling, have hindered the efforts to devise such a model. Here we have used enhanced-sampling atomistic molecular-dynamics simulations to investigate the dynamics and complex formation mechanisms of both β-arrestin- and Gs-complexes with the β2-adrenergic receptor (ADRB2) in its apo-form and in the presence of four small ligands that exert different allosteric effects. Our results suggest that the structure and dynamics of arrestin–ADRB2 complexes depend strongly on the nature of the small ligands. The complexes exhibit a variety of different coupling orientations in terms of the depth of the finger loop in the receptor and activation states of ADRB2. The simulations also allow us to characterize the cooperativity between the ligand and intracellular binding partner (IBP). Based on the complete and consistent results, we propose an experimentally testable extended ternary complex model, where direction of the cooperative effect between ligand and IBP (positive or negative) and its magnitude are predicted to be a characteristic of the ligand signaling bias. This paves the avenue to the rational design of ligands with specific functional effects.
Co-reporter:Dmitry I. Sharapa, Johannes T. Margraf, Andreas Hesselmann, and Timothy Clark
Journal of Chemical Theory and Computation 2017 Volume 13(Issue 1) pp:
Publication Date(Web):November 29, 2016
DOI:10.1021/acs.jctc.6b00869
The self-assembly of molecular building blocks is a promising route to low-cost nanoelectronic devices. It would be very appealing to use computer-aided design to identify suitable molecules. However, molecular self-assembly is guided by weak interactions, such as dispersion, which have long been notoriously difficult to describe with quantum chemical methods. In recent years, several viable techniques have emerged, ranging from empirical dispersion corrections for DFT to fast perturbation and coupled-cluster theories. In this work, we test these methods for the dimer of the prototypical building block for nanoelectronics, C60-fullerene. Benchmark quality data is obtained from DFT-based symmetry-adapted perturbation theory (SAPT), the adiabatic-connection fluctuation dissipation (ACFD) theorem using an adiabatic LDA kernel, and domain-based local pair natural orbital (DLPNO) coupled-pair and coupled-cluster methods. These benchmarks are used to evaluate economical dispersion-corrected DFT methods, double-hybrid DFT functionals, and second-order Møller–Plesset theory. Furthermore, we provide analytical fits to the benchmark interaction curves, which can be used for a coarse-grain description of fullerene self-assembly. These analytical expressions differ significantly from those reported previously based on bulk data.
Co-reporter:Elke Haensele, Nawel Mele, Marija Miljak, Christopher M. Read, David C. Whitley, Lee Banting, Carla Delépée, Jana Sopkova-de Oliveira Santos, Alban LepailleurRonan Bureau, Jonathan W. Essex, Timothy Clark
Journal of Chemical Information and Modeling 2017 Volume 57(Issue 2) pp:
Publication Date(Web):January 5, 2017
DOI:10.1021/acs.jcim.6b00706
Conformation and dynamics of the vasoconstrictive peptides human urotensin II (UII) and urotensin related peptide (URP) have been investigated by both unrestrained and enhanced-sampling molecular-dynamics (MD) simulations and NMR spectroscopy. These peptides are natural ligands of the G-protein coupled urotensin II receptor (UTR) and have been linked to mammalian pathophysiology. UII and URP cannot be characterized by a single structure but exist as an equilibrium of two main classes of ring conformations, open and folded, with rapidly interchanging subtypes. The open states are characterized by turns of various types centered at K8Y9 or F6W7 predominantly with no or only sparsely populated transannular hydrogen bonds. The folded conformations show multiple turns stabilized by highly populated transannular hydrogen bonds comprising centers F6W7K8 or W7K8Y9. Some of these conformations have not been characterized previously. The equilibrium populations that are experimentally difficult to access were estimated by replica-exchange MD simulations and validated by comparison of experimental NMR data with chemical shifts calculated with density-functional theory. UII exhibits approximately 72% open:28% folded conformations in aqueous solution. URP shows very similar ring conformations as UII but differs in an open:folded equilibrium shifted further toward open conformations (86:14) possibly arising from the absence of folded N-terminal tail-ring interaction. The results suggest that the different biological effects of UII and URP are not caused by differences in ring conformations but rather by different interactions with UTR.
Co-reporter:Elke Haensele, Noureldin Saleh, Christopher M. Read, Lee Banting, David C. Whitley, and Timothy Clark
Journal of Chemical Information and Modeling 2016 Volume 56(Issue 9) pp:1798-1807
Publication Date(Web):September 1, 2016
DOI:10.1021/acs.jcim.6b00344
Arginine vasopressin (AVP) has been suggested by molecular-dynamics (MD) simulations to exist as a mixture of conformations in solution. The 1H and 13C NMR chemical shifts of AVP in solution have been calculated for this conformational ensemble of ring conformations (identified from a 23 μs molecular-dynamics simulation). The relative free energies of these conformations were calculated using classical metadynamics simulations in explicit water. Chemical shifts for representative conformations were calculated using density-functional theory. Comparison with experiment and analysis of the results suggests that the 1H chemical shifts are most useful for assigning equilibrium concentrations of the conformations in this case. 13C chemical shifts distinguish less clearly between conformations, and the distances calculated from the nuclear Overhauser effect do not allow the conformations to be assigned clearly. The 1H chemical shifts can be reproduced with a standard error of less than 0.24 ppm (<2.2 ppm for 13C). The combined experimental and theoretical results suggest that AVP exists in an equilibrium of approximately 70% saddlelike and 30% clinched open conformations. Both newly introduced statistical metrics designed to judge the significance of the results and Smith and Goodman’s DP4 probabilities are presented.
Co-reporter:Noureldin Saleh;Dr. Giorgio Saladino;Dr. Francesco L. Gervasio;Elke Haensele;Dr. Lee Banting;Dr. David C. Whitley;Dr. Jana Sopkova-deOliveiraSantos; Ronan Bureau;Dr. Timothy Clark
Angewandte Chemie 2016 Volume 128( Issue 28) pp:8140-8144
Publication Date(Web):
DOI:10.1002/ange.201602729
Abstract
Molecular-dynamics simulations with metadynamics enhanced sampling reveal three distinct binding sites for arginine vasopressin (AVP) within its V2-receptor (V2R). Two of these, the vestibule and intermediate sites, block (antagonize) the receptor, and the third is the orthosteric activation (agonist) site. The contacts found for the orthosteric site satisfy all the requirements deduced from mutagenesis experiments. Metadynamics simulations for V2R and its V1aR-analog give an excellent correlation with experimental binding free energies by assuming that the most stable binding site in the simulations corresponds to the experimental binding free energy in each case. The resulting three-site mechanism separates agonists from antagonists and explains subtype selectivity.
Co-reporter:Noureldin Saleh;Dr. Giorgio Saladino;Dr. Francesco L. Gervasio;Elke Haensele;Dr. Lee Banting;Dr. David C. Whitley;Dr. Jana Sopkova-deOliveiraSantos; Ronan Bureau;Dr. Timothy Clark
Angewandte Chemie International Edition 2016 Volume 55( Issue 28) pp:8008-8012
Publication Date(Web):
DOI:10.1002/anie.201602729
Abstract
Molecular-dynamics simulations with metadynamics enhanced sampling reveal three distinct binding sites for arginine vasopressin (AVP) within its V2-receptor (V2R). Two of these, the vestibule and intermediate sites, block (antagonize) the receptor, and the third is the orthosteric activation (agonist) site. The contacts found for the orthosteric site satisfy all the requirements deduced from mutagenesis experiments. Metadynamics simulations for V2R and its V1aR-analog give an excellent correlation with experimental binding free energies by assuming that the most stable binding site in the simulations corresponds to the experimental binding free energy in each case. The resulting three-site mechanism separates agonists from antagonists and explains subtype selectivity.
Co-reporter:Germán Zango, Johannes Zirzlmeier, Christian G. Claessens, Timothy Clark, M. Victoria Martínez-Díaz, Dirk M. Guldi and Tomás Torres
Chemical Science 2015 vol. 6(Issue 10) pp:5571-5577
Publication Date(Web):17 Jun 2015
DOI:10.1039/C5SC01709B
Unsymmetrical subphthalocyanine fused dimers have been prepared from appropriate ortho-dinitrile SubPc precursors. In particular, either electron-donating or electron-accepting substituents have been introduced on each SubPc constituent unit, resulting in unprecedented push–pull π-extended curved aromatic macrocycles. From fluorescence experiments in solvents of different polarity we conclude a dual fluorescence, namely a delocalized singlet excited state (1.73 eV) and a polarized charge transfer state (<1.7 eV). Pump probe experiments corroborate the dual nature of the fluorescence. On one hand, the delocalized singlet excited state gives rise to a several nanosecond lasting intersystem crossing yielding the corresponding triplet excited state. On the other hand, the polarized charge transfer state deactivates within a few picosesonds. Visualization of the charge transfer state was accomplished by means of molecular modeling with a slight polarization of the HOMO towards the electron donor and of the LUMO towards the electron acceptor.
Co-reporter:Frank R. Beierlein, Timothy Clark, Björn Braunschweig, Kathrin Engelhardt, Lena Glas, and Wolfgang Peukert
The Journal of Physical Chemistry B 2015 Volume 119(Issue 17) pp:5505-5517
Publication Date(Web):March 31, 2015
DOI:10.1021/acs.jpcb.5b01944
We report a combined experimental and computational study of the whey protein β-lactoglobulin (BLG) in different electrolyte solutions. Vibrational sum-frequency generation (SFG) and ellipsometry were used to investigate the molecular structure of BLG modified air–water interfaces as a function of LiCl, NaCl, and KCl concentrations. Molecular dynamics (MD) simulations and thermodynamic integration provided details of the ion pairing of protein surface residues with alkali-metal cations. Our results at pH 6.2 indicate that BLG at the air–water interface forms mono- and bilayers preferably at low and high ionic strength, respectively. Results from SFG spectroscopy and ellipsometry are consistent with intimate ion pairing of alkali-metal cations with aspartate and glutamate carboxylates, which is shown to be more effective for smaller cations (Li+ and Na+). MD simulations show not only carboxylate–alkali-metal ion pairs but also ion multiplets with the alkali-metal ion in a bridging position between two or more carboxylates. Consequently, alkali-metal cations can bridge carboxylates not only within a monomer but also between monomers, thus providing an important dimerization mechanism between hydrophilic surface patches.
Co-reporter:Dmitry Sharapa; Andreas Hirsch; Bernd Meyer; Timothy Clark
ChemPhysChem 2015 Volume 16( Issue 10) pp:2165-2171
Publication Date(Web):
DOI:10.1002/cphc.201500230
Abstract
Ab initio and DFT calculations are used to investigate the structure, electronic properties, spectra and reactivity of cubic C8, which is predicted to be aromatic according to Hirsch′s rule. Although highly strained and with a small amount of diradical character, the carbon cube represents a surprisingly deep minimum and should therefore be observable as an isolated molecule. It is, however, predicted to be very reactive, both with itself and triplet oxygen. Calculated IR, Raman, and UV/Vis spectra are provided to aid identification of cubic C8 should it be synthesized.
Co-reporter:Johannes T. Margraf, Volker Strauss, Dirk M. Guldi, and Timothy Clark
The Journal of Physical Chemistry B 2015 Volume 119(Issue 24) pp:7258-7265
Publication Date(Web):March 3, 2015
DOI:10.1021/jp510620j
We have studied hydrogen-passivated amorphous carbon nanostructures with semiempirical molecular orbital theory in order to provide an understanding of the factors that affect their electronic properties. Amorphous structures were first constructed using periodic calculations in a melt/quench protocol. Pure periodic amorphous carbon structures and their counterparts doped with nitrogen and/or oxygen feature large electronic band gaps. Surprisingly, descriptors such as the elemental composition and the number of sp3-atoms only influence the electronic structure weakly. Instead, the exact topology of the sp2-network in terms of effective conjugation defines the band gap. Amorphous carbon nanodots of different structures and sizes were cut out of the periodic structures. Our calculations predict the occurrence of localized electronic surface states, which give rise to interesting effects such as amphoteric reactivity and predicted optical band gaps in the near-UV/visible range. Optical and electronic gaps display a dependence on particle size similar to that of inorganic colloidal quantum dots.
Co-reporter:Tatyana E. Shubina ; Dmitry I. Sharapa ; Christina Schubert ; Dirk Zahn ; Marcus Halik ; Paul A. Keller ; Stephen G. Pyne ; Sreenu Jennepalli ; Dirk M. Guldi
Journal of the American Chemical Society 2014 Volume 136(Issue 31) pp:10890-10893
Publication Date(Web):July 22, 2014
DOI:10.1021/ja505949m
Density functional theory calculations indicate that van der Waals fullerene dimers and larger oligomers can form interstitial electron traps in which the electrons are even more strongly bound than in isolated fullerene radical anions. The fullerenes behave like “super atoms”, and the interstitial electron traps represent one-electron intermolecular σ-bonds. Spectroelectrochemical measurements on a bis-fullerene-substituted peptide provide experimental support. The proposed deep electron traps are relevant for all organic electronics applications in which non-covalently linked fullerenes in van der Waals contact with one another serve as n-type semiconductors.
Co-reporter:Nico Fritsch, Christian R. Wick, Thomas Waidmann, Pavlo O. Dral, Johannes Tucher, Frank W. Heinemann, Tatyana E. Shubina, Timothy Clark, and Nicolai Burzlaff
Inorganic Chemistry 2014 Volume 53(Issue 23) pp:12305-12314
Publication Date(Web):November 13, 2014
DOI:10.1021/ic501435a
The synthesis and structural characterization of new coordination polymers with the N,N-donor ligand trans-1,2-bis(N-methylimidazol-2-yl)ethylene (trans-bie) are reported. It was found that the acetate-bridged paddlewheel metal(II) complexes [M2(O2CCH3)4(trans-bie)]n with M = Rh, Ru, Mo, and Cr are linked by the trans-bie ligand to give a one-dimensional alternating chain. The metal–metal multiple bonds were analyzed with density functional theory and CASSCF/CASPT2 calculations (bond orders: Rh, 0.8; Ru, 1.7; Mo, 3.3).
Co-reporter:Tim Clark
Journal of Cheminformatics 2014 Volume 6( Issue 1 Supplement) pp:
Publication Date(Web):2014 March
DOI:10.1186/1758-2946-6-S1-O19
Co-reporter:Ahmed El Kerdawy, Christofer S. Tautermann, Timothy Clark, and Thomas Fox
Journal of Chemical Information and Modeling 2013 Volume 53(Issue 12) pp:3262-3272
Publication Date(Web):December 1, 2013
DOI:10.1021/ci4006222
A series of density functional/basis set combinations and second-order Møller–Plesset calculations have been used to test their ability to reproduce the trends observed experimentally for the strengths of hydrogen-bond acceptors in order to identify computationally efficient techniques for routine use in the computational drug-design process. The effects of functionals, basis sets, counterpoise corrections, and constraints on the optimized geometries were tested and analyzed, and recommendations (M06-2X/cc-pVDZ and X3LYP/cc-pVDZ with single-point counterpoise corrections or X3LYP/aug-cc-pVDZ without counterpoise) were made for suitable moderately high-throughput techniques.
Co-reporter:Johannes T. Margraf, Andrés Ruland, Vito Sgobba, Dirk M. Guldi, and Timothy Clark
Langmuir 2013 Volume 29(Issue 49) pp:15450-15456
Publication Date(Web):2017-2-22
DOI:10.1021/la403633e
We present a series of non-stoichiometric cadmium sulfide quantum-dot (QD) models. Using density functional theory (DFT) and semi-empirical molecular orbital (MO) calculations, we explore the ligand binding and exchange chemistry of these models. Their surface morphology allows for these processes to be rationalized on the atomic scale. This is corroborated by ultraviolet–visible (UV–vis), infrared (IR), and inductively coupled plasma–optical emission spectroscopy (ICP–OES).
Co-reporter:Frank R. Beierlein, Andreas M. Krause, Christof M. Jäger, Piotr Fita, Eric Vauthey, and Timothy Clark
Langmuir 2013 Volume 29(Issue 38) pp:11898-11907
Publication Date(Web):2017-2-22
DOI:10.1021/la4021355
Modern spectroscopic techniques such as time-resolved second-harmonic-generation spectroscopy allow molecules to be examined selectively directly at phase interfaces. Two-phase systems formed by glycerol/water and alkane layers have previously been studied by time-resolved second-harmonic-generation spectroscopic measurements. In this molecular dynamics study, a triphenylmethane dye was inserted at the glycerol/water–alkane interface and was used as a probe for local properties such as viscosity. We now show how extensive simulations over a wide range of concentrations can be used to obtain a detailed view of the molecular structure at the glycerol/water–alkane interface. Glycerol is accumulated in a double layer adjacent to the alkane interface, which results in increased viscosity of the glycerol/water phase in the direct vicinity of the interface. We also show that conformational ensembles created by classical molecular-dynamics simulations can serve as input for QM/MM calculations, yielding further information such as transition dipoles, which can be compared with spectroscopic measurements.
Co-reporter:Timothy Clark
Perspectives in Science (December 2015) Volume 6() pp:58-65
Publication Date(Web):1 December 2015
DOI:10.1016/j.pisc.2015.06.003
Systems in which movements occur on two significantly different time domains, such as organic electronic components with flexible molecules, require different simulation techniques for the two time scales. In the case of molecular electronics, charge transport is complicated by the several different mechanisms (and theoretical models) that apply in different cases. We cannot yet combine time scales of molecular and electronic movement in simulations of real systems. This review describes our progress towards this goal.
Co-reporter:Noureldin Saleh, Giorgio Saladino, Francesco Luigi Gervasio and Timothy Clark
Chemical Science (2010-Present) 2017 - vol. 8(Issue 5) pp:NaN4026-4026
Publication Date(Web):2017/03/24
DOI:10.1039/C6SC04647A
Signalling by G-protein coupled receptors usually occurs via ternary complexes formed under cooperative binding between the receptor, a ligand and an intracellular binding partner (a G-protein or β-arrestin). While a global rational for allosteric effects in ternary complexes would be of great help in designing ligands with specific effects, the paucity of structural data for ternary complexes with β-arrestin, together with the intrinsic difficulty of characterizing the dynamics involved in the allosteric coupling, have hindered the efforts to devise such a model. Here we have used enhanced-sampling atomistic molecular-dynamics simulations to investigate the dynamics and complex formation mechanisms of both β-arrestin- and Gs-complexes with the β2-adrenergic receptor (ADRB2) in its apo-form and in the presence of four small ligands that exert different allosteric effects. Our results suggest that the structure and dynamics of arrestin–ADRB2 complexes depend strongly on the nature of the small ligands. The complexes exhibit a variety of different coupling orientations in terms of the depth of the finger loop in the receptor and activation states of ADRB2. The simulations also allow us to characterize the cooperativity between the ligand and intracellular binding partner (IBP). Based on the complete and consistent results, we propose an experimentally testable extended ternary complex model, where direction of the cooperative effect between ligand and IBP (positive or negative) and its magnitude are predicted to be a characteristic of the ligand signaling bias. This paves the avenue to the rational design of ligands with specific functional effects.
Co-reporter:Pavlo O. Dral and Timothy Clark
Physical Chemistry Chemical Physics 2017 - vol. 19(Issue 26) pp:NaN17209-17209
Publication Date(Web):2017/06/14
DOI:10.1039/C7CP02865B
We propose a new approach to the synthesis of AHx@fullerene structures via reactions through the fullerene wall. To investigate the feasibility of the approach, the step-by-step hydrogenation of the template endofullerene N@C60 up to NH4@C60 has been studied using DFT and MP2 calculations. Protonation of the endohedral guest through the fullerene wall is competitive with escape of the guest, whereas reaction with a hydrogen atom is less favorable. Each protonation step is highly exothermic, so that less active acids can also protonate the guest with less accumulation of energy. The final product, NH4@C60 is a novel concentric ion pair NH4+@C60˙− in which the charge-centers of the two ions coincide.
Co-reporter:Germán Zango, Johannes Zirzlmeier, Christian G. Claessens, Timothy Clark, M. Victoria Martínez-Díaz, Dirk M. Guldi and Tomás Torres
Chemical Science (2010-Present) 2015 - vol. 6(Issue 10) pp:NaN5577-5577
Publication Date(Web):2015/06/17
DOI:10.1039/C5SC01709B
Unsymmetrical subphthalocyanine fused dimers have been prepared from appropriate ortho-dinitrile SubPc precursors. In particular, either electron-donating or electron-accepting substituents have been introduced on each SubPc constituent unit, resulting in unprecedented push–pull π-extended curved aromatic macrocycles. From fluorescence experiments in solvents of different polarity we conclude a dual fluorescence, namely a delocalized singlet excited state (1.73 eV) and a polarized charge transfer state (<1.7 eV). Pump probe experiments corroborate the dual nature of the fluorescence. On one hand, the delocalized singlet excited state gives rise to a several nanosecond lasting intersystem crossing yielding the corresponding triplet excited state. On the other hand, the polarized charge transfer state deactivates within a few picosesonds. Visualization of the charge transfer state was accomplished by means of molecular modeling with a slight polarization of the HOMO towards the electron donor and of the LUMO towards the electron acceptor.
![4-Thia-1-azabicyclo[3.2.0]heptane-2-carboxylicacid, 6-(acetylamino)-3,3-dimethyl-7-oxo-, (2S,5R,6R)-](http://img.cochemist.com/ccimg/15500/15493-53-5.png)
![4-Thia-1-azabicyclo[3.2.0]heptane-2-carboxylicacid, 6-(acetylamino)-3,3-dimethyl-7-oxo-, (2S,5R,6R)-](http://img.cochemist.com/ccimg/15500/15493-53-5_b.png)
![Ferrate(1-),[[N,N'-1,2-ethanediylbis[N-[(carboxy-kO)methyl]glycinato-kN,kO]](4-)]-, (OC-6-21)-](http://img.cochemist.com/ccimg/15300/15275-07-7.png)
![Ferrate(1-),[[N,N'-1,2-ethanediylbis[N-[(carboxy-kO)methyl]glycinato-kN,kO]](4-)]-, (OC-6-21)-](http://img.cochemist.com/ccimg/15300/15275-07-7_b.png)
![Nickel, [5,10,15,20-tetraphenyl-21H,23H-porphinato(2-)-κN21,κN22,κN23,κN24]-, (SP-4-1)- (9CI)](/data/chemimg/478900/14172-92-0.png)
![Nickel, [5,10,15,20-tetraphenyl-21H,23H-porphinato(2-)-κN21,κN22,κN23,κN24]-, (SP-4-1)- (9CI)](/data/chemimg/478900/14172-92-0_b.png)
![Zinc, [5,10,15,20-tetraphenyl-21H,23H-porphinato(2-)-κN21,κN22,κN23,κN24]-, (SP-4-1)-](/data/chemimg/478800/14074-80-7.png)
![Zinc, [5,10,15,20-tetraphenyl-21H,23H-porphinato(2-)-κN21,κN22,κN23,κN24]-, (SP-4-1)-](/data/chemimg/478800/14074-80-7_b.png)
![Zincate(2-), [7,12-bis(1-hydroxyethyl)-3,8,13,17-tetramethyl-21H,23H-porphine-2,18-dipropanoato(4-)-κN21,κN22,κN23,κN24]-, hydrogen (1:2), (SP-4-2)-](/data/chemimg/472300/13939-11-2.png)
![Zincate(2-), [7,12-bis(1-hydroxyethyl)-3,8,13,17-tetramethyl-21H,23H-porphine-2,18-dipropanoato(4-)-κN21,κN22,κN23,κN24]-, hydrogen (1:2), (SP-4-2)-](/data/chemimg/472300/13939-11-2_b.png)
![Manganese,tricarbonyl[(1,2,3,4,5-h)-2,4-cyclohexadien-1-yl]-](http://img.cochemist.com/ccimg/12200/12108-14-4.png)
![Manganese,tricarbonyl[(1,2,3,4,5-h)-2,4-cyclohexadien-1-yl]-](http://img.cochemist.com/ccimg/12200/12108-14-4_b.png)
![5'-(2,4,6-Triphenylpyridin-1-ium-1-yl)-[1,1':3',1''-terphenyl]-2'-olate](http://img.cochemist.com/ccimg/10100/10081-39-7.png)
![5'-(2,4,6-Triphenylpyridin-1-ium-1-yl)-[1,1':3',1''-terphenyl]-2'-olate](http://img.cochemist.com/ccimg/10100/10081-39-7_b.png)
![methyl 3-[(dimethylamino)methyl]-4-hydroxybenzoate](http://img.cochemist.com/ccimg/6300/6279-52-3.png)
![methyl 3-[(dimethylamino)methyl]-4-hydroxybenzoate](http://img.cochemist.com/ccimg/6300/6279-52-3_b.png)
![2,5-CYCLOHEXADIENE-1,4-DIONE, MONO[(1-METHYL-4(1H)-PYRIDINYLIDENE)HYDRAZONE]](http://img.cochemist.com/ccimg/6100/6068-47-9.png)
![2,5-CYCLOHEXADIENE-1,4-DIONE, MONO[(1-METHYL-4(1H)-PYRIDINYLIDENE)HYDRAZONE]](http://img.cochemist.com/ccimg/6100/6068-47-9_b.png)
![4-[(2S)-2-CYANO-2-({[(4-METHOXYBENZYL)OXY]CARBONYL}AMINO)ETHYL]PH<WBR />ENYL 4-METHOXYBENZYL CARBONATE](http://img.cochemist.com/ccimg/3500/3475-07-8.png)
![4-[(2S)-2-CYANO-2-({[(4-METHOXYBENZYL)OXY]CARBONYL}AMINO)ETHYL]PH<WBR />ENYL 4-METHOXYBENZYL CARBONATE](http://img.cochemist.com/ccimg/3500/3475-07-8_b.png)
![Tricyclo[8.2.2.24,7]hexadeca-4,6,10,12,13,15-hexaene,5-bromo-](http://img.cochemist.com/ccimg/2000/1908-61-8.png)
![Tricyclo[8.2.2.24,7]hexadeca-4,6,10,12,13,15-hexaene,5-bromo-](http://img.cochemist.com/ccimg/2000/1908-61-8_b.png)
![Tetracyclo[3.2.0.02,7.04,6]heptane](http://img.cochemist.com/ccimg/300/278-06-8.png)
![Tetracyclo[3.2.0.02,7.04,6]heptane](http://img.cochemist.com/ccimg/300/278-06-8_b.png)
![Pentacyclo[4.2.0.02,5.03,8.04,7]octane](http://img.cochemist.com/ccimg/300/277-10-1.png)
![Pentacyclo[4.2.0.02,5.03,8.04,7]octane](http://img.cochemist.com/ccimg/300/277-10-1_b.png)
![L-Aspartic acid,N-[4-[[(2,4-diamino-6-pteridinyl)methyl]methylamino]benzoyl]-](http://img.cochemist.com/ccimg/200/154-24-5.png)
![L-Aspartic acid,N-[4-[[(2,4-diamino-6-pteridinyl)methyl]methylamino]benzoyl]-](http://img.cochemist.com/ccimg/200/154-24-5_b.png)
![4'-Chloro-[1,1'-biphenyl]-4-amine](http://img.cochemist.com/ccimg/200/135-68-2.png)
![4'-Chloro-[1,1'-biphenyl]-4-amine](http://img.cochemist.com/ccimg/200/135-68-2_b.png)
![Methyl (3s,4r)-3-benzoyloxy-8-methyl-8-azabicyclo[3.2.1]octane-4-carboxylate](http://img.cochemist.com/ccimg/100/50-36-2.png)
![Methyl (3s,4r)-3-benzoyloxy-8-methyl-8-azabicyclo[3.2.1]octane-4-carboxylate](http://img.cochemist.com/ccimg/100/50-36-2_b.png)
![Thiourea, N-[(1S,2S)-2-aminocyclohexyl]-N'-[(1R)-1-phenylethyl]-](/data/chemimg/1372000/874662-43-8.png)
![Thiourea, N-[(1S,2S)-2-aminocyclohexyl]-N'-[(1R)-1-phenylethyl]-](/data/chemimg/1372000/874662-43-8_b.png)
![Heptanedioic acid, 4-(2-carboxyethyl)-4-[(1-oxotetradecyl)amino]-](http://img.cochemist.com/ccimg/870700/870675-57-3.png)
![Heptanedioic acid, 4-(2-carboxyethyl)-4-[(1-oxotetradecyl)amino]-](http://img.cochemist.com/ccimg/870700/870675-57-3_b.png)
![Bicyclo[4.1.0]hept-2-yl](http://img.cochemist.com/ccimg/87100/87087-55-6.png)
![Bicyclo[4.1.0]hept-2-yl](http://img.cochemist.com/ccimg/87100/87087-55-6_b.png)
![2-Propanol,1-(9H-carbazol-4-yloxy)-3-[(1-methylethyl)amino]-](http://img.cochemist.com/ccimg/57800/57775-29-8.png)
![2-Propanol,1-(9H-carbazol-4-yloxy)-3-[(1-methylethyl)amino]-](http://img.cochemist.com/ccimg/57800/57775-29-8_b.png)
![Poly[imino(1-oxo-1,2-ethanediyl)]](http://img.cochemist.com/ccimg/25800/25734-27-4.png)
![Poly[imino(1-oxo-1,2-ethanediyl)]](http://img.cochemist.com/ccimg/25800/25734-27-4_b.png)
![Lithium, μ-[1,1'-biphenyl]-2,2'-diyldi-](/data/chemimg/1753500/16291-32-0.png)
![Lithium, μ-[1,1'-biphenyl]-2,2'-diyldi-](/data/chemimg/1753500/16291-32-0_b.png)
![Benzene, [2-(phenylmethyl)-2-propen-1-yl]-](/data/chemimg/512500/14213-80-0.png)
![Benzene, [2-(phenylmethyl)-2-propen-1-yl]-](/data/chemimg/512500/14213-80-0_b.png)
![3,5,9-Trioxa-4-phosphapentacosan-1-aminium,4-hydroxy-N,N,N-trimethyl-10-oxo-7-[(1-oxohexadecyl)oxy]-, inner salt, 4-oxide](http://img.cochemist.com/ccimg/2700/2644-64-6.png)
![3,5,9-Trioxa-4-phosphapentacosan-1-aminium,4-hydroxy-N,N,N-trimethyl-10-oxo-7-[(1-oxohexadecyl)oxy]-, inner salt, 4-oxide](http://img.cochemist.com/ccimg/2700/2644-64-6_b.png)
