Creating molecular macrocycles for anion recognition

• Amar H. Flood

Beilstein J. Org. Chem. 2016, 12, 611–627, doi:10.3762/bjoc.12.60

• the lines on the notepad for guidance; a hangover from my father’s influence as a builder. If anything, the design got sharper upon redrawing. A few more things happened that same day to benefit the realization of the macrocycle. I tested the idea using simple molecular mechanics to recapitulate the

Dynamic behavior of rearranging carbocations – implications for terpene biosynthesis

• Stephanie R. Hare and
• Dean J. Tantillo

Beilstein J. Org. Chem. 2016, 12, 377–390, doi:10.3762/bjoc.12.41

• the absence of specifically oriented noncovalent interactions with groups in terpene synthase active sites. Molecular dynamics calculations using the full bornyl diphosphate synthase enzyme were also carried out (here using a combination of DFT and molecular mechanics) [21][22]. These simulations

My maize and blue brick road to physical organic chemistry in materials

• Anne J. McNeil

Beilstein J. Org. Chem. 2016, 12, 229–238, doi:10.3762/bjoc.12.24

• solvent interactions are important in gelation. At this point, we wanted to develop a method that could predict solid-state dissolution enthalpies, rationalizing that such an approach could be useful for identifying new gelators. Graduate student Cheryl Moy ambitiously learned molecular mechanics

Physical properties and biological activities of hesperetin and naringenin in complex with methylated β-cyclodextrin

• Waratchada Sangpheak,
• Jintawee Kicuntod,
• Roswitha Schuster,
• Thanyada Rungrotmongkol,
• Peter Wolschann,
• Nawee Kungwan,
• Helmut Viernstein,
• Monika Mueller and
• Piamsook Pongsawasdi

Beilstein J. Org. Chem. 2015, 11, 2763–2773, doi:10.3762/bjoc.11.297

• ) complexes had reached equilibration at 25 ns. The 30 MD snapshots from the last 55 ns of each simulation was selected for binding free energy calculations in accordance with the naringenin/CDs complexes [40]. In this study, we applied a molecular mechanics and continuum solvation method to estimate the

Aggregation behaviour of amphiphilic cyclodextrins: the nucleation stage by atomistic molecular dynamics simulations

• Giuseppina Raffaini,
• Antonino Mazzaglia and
• Fabio Ganazzoli

Beilstein J. Org. Chem. 2015, 11, 2459–2473, doi:10.3762/bjoc.11.267

• = OH), simply denoted in the following as the model aCD. The simulations used molecular mechanics (MM) and molecular dynamics (MD) methods, and were carried out both in vacuo, to mimic a non-polar and weakly interacting solvent, and in explicit water, using a box of water molecules with periodic

• studies based on molecular mechanics and molecular dynamics simulations can yield a most useful “bottom up” approach to model amphiphilic cyclodextrins that may interact in vacuo or in water. The simulation results reported in the present paper show that non-ionic amphiphilic β-CD (aCD) carrying short

Co-solvation effect on the binding mode of the α-mangostin/β-cyclodextrin inclusion complex

• Chompoonut Rungnim,
• Sarunya Phunpee,
• Manaschai Kunaseth,
• Supawadee Namuangruk,
• Kanin Rungsardthong,
• Thanyada Rungrotmongkol and
• Uracha Ruktanonchai

Beilstein J. Org. Chem. 2015, 11, 2306–2317, doi:10.3762/bjoc.11.251

• The gas phase energy, ΔEMM, is a summation of bonded and non-bonded (electrostatic and van der Waals (vdW)) energies obtained from molecular mechanics calculation. The ΔGsolv is solvation free energy. In general, there are several methods for ΔGsolv prediction. Some methods calculate the ΔGsolv using

Structure and conformational analysis of spiroketals from 6-O-methyl-9(E)-hydroxyiminoerythronolide A

• Ana Čikoš,
• Irena Ćaleta,
• Dinko Žiher,
• Mark B. Vine,
• Ivaylo J. Elenkov,
• Marko Dukši,
• Dubravka Gembarovski,
• Marina Ilijaš,
• Snježana Dragojević,
• Ivica Malnar and
• Sulejman Alihodžić

Beilstein J. Org. Chem. 2015, 11, 1447–1457, doi:10.3762/bjoc.11.157

• Determining the structure of the thermodynamically stable product 4 proved to be more challenging. Our initial hypothesis was that it was an anomerically stabilised 8C5 conformer of 3 with the 6-methoxy group in the more stable equatorial position. Molecular mechanics calculations, however, showed that such a

• calculations as distance and angle constraints. Various conformations of the proposed structure were analysed by molecular mechanics calculations, but only one structure (Figure 5), with inverted stereochemistry at the 8-C position (8S) was consistent with all measured nOe contacts and vicinal coupling

Mechanical stability of bivalent transition metal complexes analyzed by single-molecule force spectroscopy

• Manuel Gensler,
• Christian Eidamshaus,
• Maurice Taszarek,
• Hans-Ulrich Reissig and
• Jürgen P. Rabe

Beilstein J. Org. Chem. 2015, 11, 817–827, doi:10.3762/bjoc.11.91

• intermediate alone. A possible explanation is the release of geometrical folding after breakage of the first bond. A purely geometrical molecular mechanics estimation of a possible ortho-complex of both Cu2+ metal centers results in a 0.61 nm length increase after rupture of the first bond due to the applied

• the molecular mechanics tool based on CHARMM force fields included in ChemSketch (v 14.01, ACD/Labs, Toronto, Canada). Most probable rupture forces at a logarithmic loading rate of 8.5 in relation to the corresponding rupture lengths of monovalent and all three bivalent interactions. Continuous lines

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

• . An explicit treatment of at least some solvent molecules would be desirable but is computationally not feasible at the required quantum mechanical level. A combined molecular mechanics/quantum mechanics treatment could be a solution to this problem in the future. Nevertheless, concerning the

Binding mode and free energy prediction of fisetin/β-cyclodextrin inclusion complexes

• Bodee Nutho,
• Wasinee Khuntawee,
• Chompoonut Rungnim,
• Piamsook Pongsawasdi,
• Peter Wolschann,
• Alfred Karpfen,
• Nawee Kungwan and
• Thanyada Rungrotmongkol

Beilstein J. Org. Chem. 2014, 10, 2789–2799, doi:10.3762/bjoc.10.296

• of the two individual molecules upon complexation process was taken from the normal mode analysis. Therefore, Equation 2 can be rewritten as: where ΔEMM is the energy of molecular mechanics composed of bonded and non-bonded energies. The latter one contains the electrostatic (ΔEele) and van der Waals

• in Table 2, where the decomposition binding free energies from the A- and B-rings are shown in Table S1 of Supporting Information File 1. By molecular mechanics (MM) calculation in gas phase, the attractive electrostatic contributions (∆Eele) between fisetin and β-CD were similar in all three

Macrocyclic bis(ureas) as ligands for anion complexation

• Claudia Kretschmer,
• Gertrud Dittmann and
• Johannes Beck

Beilstein J. Org. Chem. 2014, 10, 1834–1839, doi:10.3762/bjoc.10.193

• is manifested in longer N−H∙∙∙O bonds of 2.09(1) and 2.18(2) Å in the 2·2DMSO adduct. Since immediate experimental data for the structure of the unsolvated macrocyclic bis(ureas) were not obtainable, we used molecular mechanics calculations as implemented in the SPARTAN program suite [17] to

Why a diaminopyrrolic tripodal receptor binds mannosides in acetonitrile but not in water?

• Diogo Vila-Viçosa,
• Oscar Francesconi and
• Miguel Machuqueiro

Beilstein J. Org. Chem. 2014, 10, 1513–1523, doi:10.3762/bjoc.10.156

• complementarity between molecular mechanics/molecular dynamics (MM/MD) simulations, that correctly samples the conformational space of a system according to a classic potential energy function, and Poisson–Boltzmann/Monte Carlo methods, that can efficiently treat multiple protonation equilibria on rigid

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

• computational energy profile [22]. The formation of α-cyclodextrin-based [3]pseudorotaxanes in the gas phase was studied by means of density functional calculations [23]. Molecular mechanics calculations were used for a free energy calculation of an α-cyclodextrin rotaxane system and for the investigation of

Synthesis of chiral N-phosphoryl aziridines through enantioselective aziridination of alkenes with phosphoryl azide via Co(II)-based metalloradical catalysis

• Jingran Tao,
• Li-Mei Jin and
• X. Peter Zhang

Beilstein J. Org. Chem. 2014, 10, 1282–1289, doi:10.3762/bjoc.10.129

• metalloradical catalysis (MRC). (A) Potential H-bonding interaction in postulated nitrene radical complex of [Co(D2-Por*)]. R* represents a chiral unit. (B) Geometry corresponding to the minimum energy from simplified computer modeling by molecular mechanics with Spartan 10. The P=O…H–N distance of (1.87 Å

Plakilactones G and H from a marine sponge. Stereochemical determination of highly flexible systems by quantitative NMR-derived interproton distances combined with quantum mechanical calculations of ¹³C chemical shifts

• Simone Di Micco,
• Angela Zampella,
• Maria Valeria D’Auria,
• Carmen Festa,
• Simona De Marino,
• Raffaele Riccio,
• Craig P. Butts and
• Giuseppe Bifulco

Beilstein J. Org. Chem. 2013, 9, 2940–2949, doi:10.3762/bjoc.9.331

• the conformational space of 1 and 2 by using the MMFFs [24] force field. All molecular mechanics calculations were performed in chloroform (continuum model, MacroModel software package [25]). We found 254 major conformers for 1a, 285 for 1b, 574 for 1c and 146 for 1d. We found 209 major conformers for

• geometries of 1a–d and 2a–h presenting an energy difference ≤13 kJ/mol from the global minimum were retained and used for QM calculations. All the obtained geometries of 1a–d and 2a–h from molecular mechanics methods, were further refined in vacuo at the DFT theoretical level by using MPW1PW91 functional and

Structure elucidation of β-cyclodextrin–xylazine complex by a combination of quantitative ¹H–¹H ROESY and molecular dynamics studies

• Syed Mashhood Ali,
• Kehkeshan Fatma and
• Snehal Dhokale

Beilstein J. Org. Chem. 2013, 9, 1917–1924, doi:10.3762/bjoc.9.226

• clear. Thus, two geometries for the β-CD-xylazine complex can be assumed (Figure 5). We established the structure of the complex using this ROESY data and molecular dynamics simulation studies in vacuum. Earlier, we established the structure of a fexofenadine-α-CD complex [20] on the basis of molecular

• mechanics and ROESY data recorded with 0.5 s mixing time, but intermolecular peaks on both sides of the diagonal were clear in that case. Molecular dynamics Molecular dynamics simulations for only aromatic ring were performed. All the calculations were performed using CS Chem3D Pro (Cambridge Soft Corp.) in

True and masked three-coordinate T-shaped platinum(II) intermediates

• Manuel A. Ortuño,
• Salvador Conejero and
• Agustí Lledós

Beilstein J. Org. Chem. 2013, 9, 1352–1382, doi:10.3762/bjoc.9.153

• water molecule. Indeed, quantum mechanics/molecular mechanics (QM/MM) calculations on the cisplatin–hen egg white lysozyme adduct confirmed the facile inclusion of a solvent water molecule in the first coordination shell of the platinum complex (Figure 13) [94]. NMR coupling constants to 195Pt as

Utilizing the σ-complex stability for quantifying reactivity in nucleophilic substitution of aromatic fluorides

• Magnus Liljenberg,
• Tore Brinck,
• Tobias Rein and
• Mats Svensson

Beilstein J. Org. Chem. 2013, 9, 791–799, doi:10.3762/bjoc.9.90

• fulfill the requirements 1 and 2 but fail 3 and 4. There are approaches reported where successful attempts have been made to strike a compromise between generality/accuracy and throughput/robustness. One example is the so-called Q2MM method, which is designed to apply molecular mechanics calculations to

The diketopiperazine-fused tetrahydro-β-carboline scaffold as a model peptidomimetic with an unusual α-turn secondary structure

• Francesco Airaghi,
• Andrea Fiorati,
• Giordano Lesma,
• Manuele Musolino,
• Alessandro Sacchetti and
• Alessandra Silvani

Beilstein J. Org. Chem. 2013, 9, 147–154, doi:10.3762/bjoc.9.17

• were submitted to an unconstrained Monte Carlo (MC) conformational search combined with Molecular Mechanics (MM) minimization (see Table 1 for results). As a main indication of a stable secondary structure, the presence of intramolecular hydrogen bonds was first evaluated. Two H-bonds have been

• (2C), 126.9, 122.2, 119.8, 118.7, 112.0, 108.1, 66.7, 55.4, 55.3, 53.5, 46.7, 44.7, 22.7, 25.9, 14.5; HRMS–EI (m/z): [M+] calcd for C27H29N5O5, 503.2169; found, 503.2186. Computational details An unconstrained Monte Carlo (MC) conformational search combined with Molecular Mechanics (MM) minimization

Theoretical study on β-cyclodextrin inclusion complexes with propiconazole and protonated propiconazole

• Adrian Fifere,
• Narcisa Marangoci,
• Stelian Maier,
• Adina Coroaba,
• Dan Maftei and
• Mariana Pinteala

Beilstein J. Org. Chem. 2012, 8, 2191–2201, doi:10.3762/bjoc.8.247

• orientation of the guest molecules toward the β-CD cavity remains the same in the presence of water molecules. In this respect, the geometries of the complexes were optimized in aqua, by combining techniques of molecular mechanics and quantum mechanics [23]. The results given in Table 5 shows that, as solvent

Exploring chemical diversity via a modular reaction pairing strategy

• Joanna K. Loh,
• Sun Young Yoon,
• Thiwanka B. Samarakoon,
• Alan Rolfe,
• Patrick Porubsky,
• Benjamin Neuenswander,
• Gerald H. Lushington and
• Paul R. Hanson

Beilstein J. Org. Chem. 2012, 8, 1293–1302, doi:10.3762/bjoc.8.147

• have been sketched and optimized in SYBYL [44], according to default molecular mechanics settings, and the resulting optimized structures were then all mutually aligned in order to minimize the total pairwise RMSD among conserved scaffold core atoms. The pairwise RMSD values reported in Figure 5 also

Similarity analysis, synthesis, and bioassay of antibacterial cyclic peptidomimetics

• Workalemahu M. Berhanu,
• Mohamed A. Ibrahim,
• Girinath G. Pillai,
• Alexander A. Oliferenko,
• Levan Khelashvili,
• Farukh Jabeen,
• Bushra Mirza,
• Farzana Latif Ansari,
• Ihsan ul-Haq,
• Said A. El-Feky and
• Alan R. Katritzky

Beilstein J. Org. Chem. 2012, 8, 1146–1160, doi:10.3762/bjoc.8.128

• program [52] and preoptimized using the molecular mechanics utility (MM2) [53] in Chem3D Ultra 12.0 software [54]. Final geometry optimization of the compounds was carried out by using the semiempirical quantum-mechanical AM1 parameterization [55]. Molecular descriptors The optimized geometries of the

Synthesis of a library of tricyclic azepinoisoindolinones

• Bettina Miller,
• Shuli Mao,
• Kara M. George Rosenker,
• Joshua G. Pierce and
• Peter Wipf

Beilstein J. Org. Chem. 2012, 8, 1091–1097, doi:10.3762/bjoc.8.120

• steric bulk of the adamantyl group: molecular mechanics calculations indicate that the aminolysis of 5 to regioisomer 10 proceeds with minimal isomerization of the seven-membered ring geometry in the lowest-energy product conformer, whereas the formation of 9 requires a substantial ring flip [41

Enantioselective supramolecular devices in the gas phase. Resorcin[4]arene as a model system

• Caterina Fraschetti,
• Matthias C. Letzel,
• Antonello Filippi,
• Maurizio Speranza and
• Jochen Mattay

Beilstein J. Org. Chem. 2012, 8, 539–550, doi:10.3762/bjoc.8.62

• reaction carried out in a nano ESI-FT-ICR instrument, supported by a thermodynamic MS-study and molecular-mechanics and molecular-dynamics (MM/MD) computational techniques. The noncovalent ion–molecule complexes are ideal for the study of chiral recognition in the absence of complicating solvent and

Self-assembly of Ru₄ and Ru₈ assemblies by coordination using organometallic Ru(II)₂ precursors: Synthesis, characterization and properties

• Sankarasekaran Shanmugaraju,
• Dipak Samanta and
• Partha Sarathi Mukherjee

Beilstein J. Org. Chem. 2012, 8, 313–322, doi:10.3762/bjoc.8.34

• structural characteristics of the newly designed macrocycle, the energy-minimized structure of the macrocycle 2c was obtained by means of molecular mechanics universal-force-field simulation (MMUFF) [13]. A perspective view of the energy-minimized structure of the macrocycle 2c is depicted in Figure 5. The