Theoretical Methods for Supramolecular Chemistry

Kirchner, Barbara; Reiher, Markus

doi:10.1002/9783527644131.ch16

Cited by 3 publications

(5 citation statements)

References 251 publications

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“…It should be stressed that point charges entering eqn (9) are never optimized by the JOYCE procedure and the electrostatic term remains constant at the value it was assigned. In such a way, the assigned point charges can remain consistent between the inter-and the intra-molecular terms of eqn (1). Conversely, intramolecular LJ parameters can be either assigned to literature values or optimized by JOYCE2.0.…”

Section: Intramolecular Force Field Expressionmentioning

confidence: 99%

“…The JOYCE protocol derives all parameters that define the intramolecular E intra term from the information contained in the energies, gradients and Hessian matrices computed at the QM level on the isolated target molecule. Once parameterized, E intra is coupled to its inter-molecular counterpart through eqn (1), thus yielding a complete FF, suitable for condensed phase computer simulations. The parameters defining E inter (i.e.…”

Section: Basicsmentioning

confidence: 99%

“…Computer simulation techniques can nowadays exploit recent advances in computer hardware to allow for detailed investigations of large systems and complex phenomena, such as supramolecular assembly, 1 biomolecular functions in solution, [2][3][4] soft matter structural and dynamic properties. [5][6][7][8] However the computational effort becomes useless if not complemented by a reliable and physically sound description of the molecular details which specify the chemical identity of the simulated systems.…”

Section: Introductionmentioning

confidence: 99%

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Joyce and Ulysses: integrated and user-friendly tools for the parameterization of intramolecular force fields from quantum mechanical data

Barone

Cacelli

Mitri

et al. 2013

Phys. Chem. Chem. Phys.

101

195

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The Joyce program is augmented with several new features, including the user friendly Ulysses GUI, the possibility of complete excited state parameterization and a more flexible treatment of the force field electrostatic terms. A first validation is achieved by successfully comparing results obtained with Joyce2.0 to literature ones, obtained for the same set of benchmark molecules. The parameterization protocol is also applied to two other larger molecules, namely nicotine and a coumarin based dye. In the former case, the parameterized force field is employed in molecular dynamics simulations of solvated nicotine, and the solute conformational distribution at room temperature is discussed. Force fields parameterized with Joyce2.0, for both the dye's ground and first excited electronic states, are validated through the calculation of absorption and emission vertical energies with molecular mechanics optimized structures. Finally, the newly implemented procedure to handle polarizable force fields is discussed and applied to the pyrimidine molecule as a test case.

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Section: Intramolecular Force Field Expressionmentioning

confidence: 99%

Section: Basicsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Joyce and Ulysses: integrated and user-friendly tools for the parameterization of intramolecular force fields from quantum mechanical data

Barone

Cacelli

Mitri

et al. 2013

Phys. Chem. Chem. Phys.

101

195

View full text Add to dashboard Cite

show abstract

“…Additionally, theoretical chemistry provides efficient and accurate methods for the structural and physicochemical characterization of molecular aggregates that complement insights obtained by experimental techniques …”

Section: Introductionmentioning

confidence: 99%

Dispersion and Halogen-Bonding Interactions: Binding of the Axial Conformers of Monohalo- and (±)-trans-1,2-Dihalocyclohexanes in Enantiopure Alleno-Acetylenic Cages

et al. 2017

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Enantiopure alleno-acetylenic cage (AAC) receptors with a resorcin[4]arene scaffold, from which four homochiral alleno-acetylenes converge to shape a cavity closed by a four-fold OH-hydrogen-bonding array, form a highly ordered porous network in the solid state. They enable the complexation and co-crystallization of otherwise non-crystalline small molecules. This paper analyzes the axial conformers of monohalo- and (±)-trans-1,2-dihalocyclohexanes, bound in the interior cavity of the AACs, on the atomic level in the solid state and in solution, accompanied by accurate calculations. The dihedral angles ϑ (X-C(1)-C(2)-X/H) of the axial/diaxial conformers deviate substantially from 180°, down to 144°, accompanied by strong flattening of the ring dihedral angles. Structure optimization of the isolated guest molecules demonstrates that the non-covalent interactions with the host hardly affect the dihedral angles, validating that the host is an ideal means to study the elusive axial/diaxial conformers. X-ray co-crystal structures of AACs further allowed for a detailed investigation, both experimentally and theoretically, on the interplay between space occupancy, guest conformation, and chiral recognition based purely on dispersion forces and weak C-X···π (X = Cl, Br, I) and C-X···||| (acetylene) contacts (X = Cl, Br). The theoretical analysis of the non-covalent interactions between host and guest confirmed the high shape complementarity with fully enveloping dispersive interactions between the binding partners, rationalizing the high degree of enantioselectivity in the previously communicated complexation of (±)-trans-1,2-dimethylcyclohexane. This study also showed that (±)-trans-1,2-dihalocyclohexanes (X = Cl, Br) engage in significant halogen bonding (XB) interactions C-X···||| with the hosts. Slow host-guest exchange on the NMR time scale enabled the characterization of the encapsulated guests in solution, demonstrating that the complexes have identical geometries to those seen in the solid state, with the guests bound in axial/diaxial conformations.

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“…Thanks to the massive increase of computational resources in the past two decades, computer simulation techniques,[1, 2] as molecular dynamics (MD) or Monte Carlo, have nowadays become powerful tools in many different fields of supramolecular chemistry,[3] as the study of soft matter structural and dynamic properties[4–7] or the investigation of biomolecular functions in solution. [8–10] Indeed, it is now possible to perform MD atomistic simulations on bulk phases up to thousands of medium sized molecules for several tenths of nanoseconds,[6, 7, 11–13] whereas large biomolecules can be studied in solution up to the microsecond regime.…”

Section: Introductionmentioning

confidence: 99%

An automated approach for the parameterization of accurate intermolecular force‐fields: Pyridine as a case study

et al. 2012

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An automated protocol is proposed and validated, which integrates accurate quantum mechanical calculations with classical numerical simulations. Intermolecular force fields, (FF) suitable for molecular dynamics (MD) and Monte Carlo simulations, are parameterized through a novel iterative approach, fully based on quantum mechanical data, which has been automated and coded into the PICKY software, here presented. The whole procedure is tested and validated for pyridine, whose bulk phase, described through MD simulations performed with the specifically parameterized FF, is characterized by computing several of its thermodynamic, structural, and transport properties, comparing them with their experimental counterparts.

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Theoretical Methods for Supramolecular Chemistry

Cited by 3 publications

References 251 publications

Joyce and Ulysses: integrated and user-friendly tools for the parameterization of intramolecular force fields from quantum mechanical data

Joyce and Ulysses: integrated and user-friendly tools for the parameterization of intramolecular force fields from quantum mechanical data

Dispersion and Halogen-Bonding Interactions: Binding of the Axial Conformers of Monohalo- and (±)-trans-1,2-Dihalocyclohexanes in Enantiopure Alleno-Acetylenic Cages

An automated approach for the parameterization of accurate intermolecular force‐fields: Pyridine as a case study

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