Junmei Wang, Romain M. Wolf, James W. Caldwell, Peter A. Kollman, and David A. Case, "Development and testing of a general amber force field"<i>Journal of Computational Chemistry</i>(2004) 25(9) 1157–1174

Wang, Junmei; Wolf, Romain M.; Caldwell, James W.; Kollman, Peter A.; Case, David A.

doi:10.1002/jcc.20145

Cited by 3,089 publications

(3,676 citation statements)

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“…22 The bonded and nonbonded parameters were adopted from the general Amber force field (GAFF). 23 Preliminary simulations in aqueous solution showed that the coumarin groups of BPC tend to form π-π stacked structures with the naphthol unit, which is in accordance with the NMR observations. Based on this fact we constructed the 1:1 hostguest structure of BPCY for MD simulations in aqueous solution and the final structure of this 1:1 host-guest complex BPCY is shown in Figure 4.…”

Section: Resultssupporting

confidence: 80%

Multicolor Photoluminescence Including White-Light Emission by a Single Host–Guest Complex

et al. 2016

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Achieving multicolor photoluminescence especially white-light emission under mild conditions based on a single fluorescent compound is a great challenge. Herein, we report a novel colorful-emission host-guest complex BPCY, which is composed of a two-arm fluorescent guest molecule (BPC) and γ-cyclodextrin (γ-CD) as the host molecule. BPC bears a unique asymmetrical donor-acceptor-donor (D1-A +~D 2) type structure, where D1, A + , D2 stand for the binaphthol electron donor, pyridinium electron acceptor, and coumarin electron donor, respectively. The luminescence property of BPC shows dual-sensitivity, i.e. toward the excitation wavelength and the cyclodextrin host molecule. Under certain conditions the complex shows three different emission wavelengths allowing the realization of multicolor photoluminescence, including red (R), green (G), blue (B) and the various intermediate colors by orthogonally modulating these two stimuli. In this way, nearly pure white-light emission with CIE coordinates (0.33, 0.34) could be generated. A combination of structural, spectroscopic, and computational simulation studies revealed the occurrence of synergetic mechanistic processes for the stimuli-responsive multicolor luminescence of the BPCY complex, namely host-enhanced intramolecular charge-transfer (ICT) and host-induced restriction of intramolecular rotation (RIR). This new supramolecular complex with superior multicolor emission abilities may find wide applications in the fields of information processing and display media. Furthermore the molecular design rationale presented here may provide a new design strategy for the development of high performance optical materials using a single supramolecular platform.

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Section: Resultssupporting

confidence: 80%

Multicolor Photoluminescence Including White-Light Emission by a Single Host–Guest Complex

et al. 2016

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“…23 In this approach, we used the average induced surface charge density (ISCD), σ i , obtained from a boundary element solution of the Poisson equation to derive a simple linear correction to the van der Waals radius to obtain the Born radius, r i Born , for each atom, i, of a molecule. 23 To obtain the σ i for eq 3, all atoms are initially assigned Born radii equal to the General AMBER Force Field (GAFF) 39 van der Waals radii r i 0 . From the boundary element solution to the Poisson equation, the average ISCDs for each atom are then calculated by assigning the surface patches and their associated charge density to the nearest atom.…”

Section: Theory and Implementationmentioning

confidence: 99%

Rapid Prediction of Solvation Free Energy. 2. The First-Shell Hydration (FiSH) Continuum Model

Corbeil

Sulea

Purisima

2010

J. Chem. Theory Comput.

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Local ordering of water in the first hydration shell around a solute is different from isotropic bulk water. This leads to effects that are captured by explicit solvation models and missed by continuum solvation models which replace the explicit waters with a continuous medium. In this paper, we introduce the First-Shell Hydration (FiSH) model as a first attempt to introduce first-shell effects within a continuum solvation framework. One such effect is charge asymmetry, which is captured by a modified electrostatic term within the FiSH model by introducing a nonlinear correction of atomic Born radii based on the induced surface charge density. A hybrid van der Waals formulation consisting of two continuum zones has been implemented. A shell of water restricted to and uniformly distributed over the solvent-accessible surface (SAS) represents the first solvation shell. A second region starting one solvent diameter away from the SAS is treated as bulk water with a uniform density function. Both the electrostatic and van der Waals terms of the FiSH model have been calibrated against linear interaction energy (LIE) data from molecular dynamics simulations. Extensive testing of the FiSH model was carried out on large hydration data sets including both simple compounds and drug-like molecules. The FiSH model accurately reproduces contributing terms, absolute predictions relative to experimental hydration free energies, and functional class trends of LIE MD simulations. Overall, the implementation of the FiSH model achieves a very acceptable performance and transferability improving over previously developed solvation models, while being complemented by a sound physical foundation.

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“…All initial structures were taken from molecular docking. Force field parameters for the nonprotein atoms (dienophiles and diene) were generated from the general Amber force field (gaff), [62] using the Antechamber program. The generation of gaff-parameters was based on AM1 geometries, and the AM1-BCC approach was used for partial charges.…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

Computational design of a lipase for catalysis of the Diels-Alder reaction

et al. 2010

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Combined molecular docking, molecular dynamics (MD) and density functional theory (DFT) studies have been employed to study catalysis of the Diels-Alder reaction by a modified lipase. Six variants of the versatile enzyme {\em Candida Antarctica} lipase B (CALB) have been rationally engineered {\em in silico} based on the specific characteristics of the pericyclic addition. A kinetic analysis reveals that hydrogen bond stabilization of the transition state and substrate binding are key components of the catalytic process. In the case of substrate binding, which has the greater potential for optimization, both binding strength and positioning of the substrates are important for catalytic efficiency. The binding strength is determined by hydrophobic interactions and can be tuned by careful selection of solvent and substrates. The MD simulations show that substrate positioning is sensitive to cavity shape and size, and can be controlled by a few rational mutations. The well-documented S105A mutation is essential to enable sufficient space in the vicinity of the oxyanion hole. Moreover, bulky residues on the edge of the active site hinders the formation of a sandwich-like near-attack conformer (NAC), and the I189A mutation is needed to obtain enough space above the face of the $\alpha$,$\beta$-double bond on the dienophile. The double mutant S105A/I189A performs quite well for two of three dienophiles. Based on binding constants and NAC energies obtained from MD simulations combined with activation energies from DFT computations, relative catalytic rates ($v_{cat}/v_{uncat}$) of up to $10^3$ are predicted.Response to Reviewers: We are happy with the favorable comments by the reviewers. We have have corrected the manuscript as suggested by reviewer 1 1. A sentence explaining catalytic promiscuity has been added. 2. A paragraph discussing the relationship between the NAC concept and the Reaction Force has been added.We have shortened the manuscript as suggested by reviewer 2. In particular, we have moved information regarding the structural relaxation of protein structure in MD simulations to the supplementary material. Abstract Combined molecular docking, molecular dynamics (MD) and density functional theory (DFT) studies have been employed to study catalysis of the DielsAlder reaction by a modified lipase. Six variants of the versatile enzyme Candida Antarctica lipase B (CALB) have been rationally engineered in silico based on the specific characteristics of the pericyclic addition. A kinetic analysis reveals that hydrogen bond stabilization of the transition state and substrate binding are key components of the catalytic process. In the case of substrate binding, which has the greater potential for optimization, both binding strength and positioning of the substrates are important for catalytic efficiency. The binding strength is determined by hydrophobic interactions and can be tuned by careful selection of solvent and substrates. The MD simulations show that substrate positioning is sensitive to cavity s...

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Junmei Wang, Romain M. Wolf, James W. Caldwell, Peter A. Kollman, and David A. Case, "Development and testing of a general amber force field"Journal of Computational Chemistry(2004) 25(9) 1157–1174

Abstract: In the online and published versions, equation (5) appeared incorrectly. The correct version appears below. We would like to extend our sincere apologies for any confusion this may have caused.

Cited by 3,089 publications

References 0 publications

Multicolor Photoluminescence Including White-Light Emission by a Single Host–Guest Complex

Multicolor Photoluminescence Including White-Light Emission by a Single Host–Guest Complex

Rapid Prediction of Solvation Free Energy. 2. The First-Shell Hydration (FiSH) Continuum Model

Computational design of a lipase for catalysis of the Diels-Alder reaction

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