Peptide–polymer ligands for a tandem WW-domain, an adaptive multivalent protein–protein interaction: lessons on the thermodynamic fitness of flexible ligands

• Katharina Koschek,
• Vedat Durmaz,
• Oxana Krylova,
• Marek Wieczorek,
• Shilpi Gupta,
• Martin Richter,
• Alexander Bujotzek,
• Christina Fischer,
• Rainer Haag,
• Christian Freund,
• Marcus Weber and
• Jörg Rademann

Beilstein J. Org. Chem. 2015, 11, 837–847, doi:10.3762/bjoc.11.93

• substantially different values for the three carrier materials. With −913 kJ/mol dextran yielded the by far lowest energy compared with those peptides attached to the two high-stoichiometry polymers (−515 kJ/mol and −783 kJ/mol). Since lower energies correspond to preferential states, the interaction energy can

Probing multivalency in ligand–receptor-mediated adhesion of soft, biomimetic interfaces

• Stephan Schmidt,
• Hanqing Wang,
• Daniel Pussak,
• Simone Mosca and
• Laura Hartmann

Beilstein J. Org. Chem. 2015, 11, 720–729, doi:10.3762/bjoc.11.82

• deformation is a measure of the sum over all specific interactions between the carbohydrate ligand and the protein receptor layer. Detection of the interaction energy is straight forward using the contact area of the SCP with the protein layer via reflection interference contrast microscopy (RICM) (Figure 1

First principle investigation of the linker length effects on the thermodynamics of divalent pseudorotaxanes

• Andreas J. Achazi,
• Doreen Mollenhauer and
• Beate Paulus

Beilstein J. Org. Chem. 2015, 11, 687–692, doi:10.3762/bjoc.11.78

• ; Gibbs energy; pseudorotaxanes; solvent effects; COSMO-RS; Introduction If two or more binding sites of a molecular system are involved in the association process, the interaction energy can be significantly increased compared to the sum of the individual binding energies. This effect is called

• investigation. A more detailed analysis of the accuracy of the TPSS-D3(BJ) functional has been performed for the crown-6/ammonium complex in [25]. Another point to remark is that even for the monovalent system about 36% of the electronic interaction energy is due to the dispersion correction. 2) The finite

Substitution effect and effect of axle’s flexibility at (pseudo-)rotaxanes

• Friedrich Malberg,
• Jan Gerit Brandenburg,
• Werner Reckien,
• Oldamur Hollóczki,
• Stefan Grimme and
• Barbara Kirchner

Beilstein J. Org. Chem. 2014, 10, 1299–1307, doi:10.3762/bjoc.10.131

• close relationship between the strength of the hydrogen bond and the charge of the acceptor oxygen was detected [32]. Substitution with electron-withdrawing groups weakens the twofold hydrogen bond, whereas substitution with electron-donating groups led to an increase of interaction energy. In the

• theory (MP2) calculations [29]. The contribution of the London dispersion interaction to the total interaction energy in the gas phase is of the same magnitude as the hydrogen bonding interaction (about −14 kcal/mol). The molecular functionality of rotaxanes is solely based on the interplay of different

Metal and metal-free photocatalysts: mechanistic approach and application as photoinitiators of photopolymerization

• Jacques Lalevée,
• Sofia Telitel,
• Pu Xiao,
• Marc Lepeltier,
• Frédéric Dumur,
• Fabrice Morlet-Savary,
• Didier Gigmes and
• Jean-Pierre Fouassier

Beilstein J. Org. Chem. 2014, 10, 863–876, doi:10.3762/bjoc.10.83

• and C are the oxidation potential of Ir(piq)2(tmd), the reduction potential of Ph2I+, the excited triplet state energy of Ir(piq)2(tmd), and the electrostatic interaction energy for the initially formed ion pair, generally considered as negligible in polar solvents) [69]. This favorable 3PIC/Ph2I

Direct alkenylation of indolin-2-ones by 6-aryl-4-methylthio-2H-pyran-2-one-3-carbonitriles: a novel approach

• Sandeep Kumar,
• Ramendra Pratap,
• Abhinav Kumar,
• Brijesh Kumar,
• Vishnu K. Tandon and
• Vishnu Ji Ram

Beilstein J. Org. Chem. 2013, 9, 809–817, doi:10.3762/bjoc.9.92

• interaction energy in the crystal structures of 8yc by means of the dimer unit bound by C–H…π, C–H…O and Ar–H…π interactions at the DFT level of theory yields interaction energies of 22.33, 14.92 and 15.45 kJ·mol−1, respectively. To confirm further the presence of these weak interactions, bond critical points

• calculations were performed using the Gaussian 03 program [50]. The intermolecular interaction energies were estimated at the MP2 level of theory. For the interaction energy calculations, the C–H…π, Ar–H…π and Ar–H…O distances were fixed for the dimer while all other degrees of freedom were relaxed in the

The arene–alkene photocycloaddition

• Ursula Streit and
• Christian G. Bochet

Beilstein J. Org. Chem. 2011, 7, 525–542, doi:10.3762/bjoc.7.61

• enthalpy of the radical ion pair formation, ΔEexcit = excitation energy of the chromophore, ΔEcoul = coulomb interaction energy of the radical ions and = half wave potential of donor and acceptor. If electron transfer pathways dominate, substitution reactions are found to prevail. However, if the electron

Anion–π interactions influence pK_a values

• Christopher J. Cadman and
• Anna K. Croft

Beilstein J. Org. Chem. 2011, 7, 320–328, doi:10.3762/bjoc.7.42

• and is accompanied by a ring critical point from the 6-membered ring made from the additional atoms of the naphthalene moiety. The ρ value is, as can be surmised from the lower interaction energy, lower for the bond critical point between H and C for 2(a) (0.0193 e·bohr−3) than for that between H and

Catalysis: transition-state molecular recognition?

• Ian H. Williams

Beilstein J. Org. Chem. 2010, 6, 1026–1034, doi:10.3762/bjoc.6.117

• ΔGRdist and the interaction energy ΔGRint is equal to the apparent binding energy ΔGRbind. The magnitude of the enzyme catalytic power ΔG‡aq − ΔG‡enz = 38 kJ mol−1 is equal to the difference in binding energies ΔGTbind − ΔGRbind of the enzyme with the TS and the solvent-separated ion-pair, neither of

• in enzyme catalysis has been that the TS need not be the same for both the catalysed and uncatalysed reactions [8]. Consequently, the previous analysis [17] should be modified by recognising that the apparent binding energy ΔGTbind is the sum of distortion energy ΔGTdist and interaction energy ΔGTint

Symmetry breaking and structure of a mixture of nematic liquid crystals and anisotropic nanoparticles

• Marjan Krasna,
• Matej Cvetko and
• Milan Ambrožič

Beilstein J. Org. Chem. 2010, 6, No. 74, doi:10.3762/bjoc.6.74

• interaction energy with respect to all the spins. Therefore, we neglect thermal fluctuations. Consequently, our approach is sensible, deep in the nematic LC phase region, i.e. well below the isotropic–nematic phase transition. In order to satisfy the normalization of the spin vectors, = 1, the “operational

• ” total interaction energy must be rewritten as: where: with Lagrange multipliers λijk, which must also be evaluated in order to solve the system. From the obtained spin configurations, we calculate various quantities which reflect the structural properties of the system. One of these is the equilibrium

The subtle balance of weak supramolecular interactions: The hierarchy of halogen and hydrogen bonds in haloanilinium and halopyridinium salts

• Kari Raatikainen,
• Massimo Cametti and
• Kari Rissanen

Beilstein J. Org. Chem. 2010, 6, No. 4, doi:10.3762/bjoc.6.4

• of the halogen atom, localized along the extension of the Y–X···A covalent bond. The existence and magnitude of this positive region, known as σ-hole [25], depends on the polarizability of the halogen atom, and by no surprise the interaction energy is found to increase in by the order Cl < Br < I [26

Competition between local disordering and global ordering fields in nematic liquid crystals

• Matej Cvetko,
• Milan Ambrožič and
• Samo Kralj

Beilstein J. Org. Chem. 2010, 6, No. 2, doi:10.3762/bjoc.6.2

• structural details are averaged out via relatively fast molecular rotations) or nanotubes. The corresponding interaction energy of the system can be expressed as [6][8][23] The parameter J > 0 describes the ordering interaction among neighbouring molecules tending to orient directors parallel. The index α in

• directors or from completely disordered configuration. For a given set of control parameters we calculate a configuration of the system by minimizing the interaction energy. The configuration reflects the interplay among elastic, external ordering field and surface disordering tendencies. The external

• ). Conclusions We have studied the influence of external ordering electric or magnetic field B on systems of rod-like objects (e.g. nematic liquid crystals or a dispersion of nano-rods in a liquid environment [20][21]) in the presence of random anisotropic type of disorder. We express the interaction energy F of

Inversion symmetry and local vs. dispersive interactions in the nucleation of hydrogen bonded cyclic n-mer and tape of imidazolecarboxamidines

• Sihui Long,
• Venkatraj Muthusamy,
• Peter G. Willis,
• Sean Parkin and
• Arthur Cammers

Beilstein J. Org. Chem. 2008, 4, No. 23, doi:10.3762/bjoc.4.23

• upper right corner of the graph in Figure 11. The C1 dimer also suffers due to high-energy hydrogen bonds (right side of Figure 11) but this dimer can optimize one of the two structures in the asymmetric unit as in 8b, or both fairly well as in 8a, thereby minimizing the average local interaction energy