An improved force field (MM4) for saturated hydrocarbons

Allinger, Norman L.; Chen, Kuohsiang; Lii, Jenn‐Huei

doi:10.1002/(sici)1096-987x(199604)17:5/6<642::aid-jcc6>3.0.co;2-u

Cited by 329 publications

(218 citation statements)

References 49 publications

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“…MM2 was parameterised for a lot of functional groups while MM3 [Allinger & Durkin, 2000;Allinger & Yan, 1993] is probably one of the most accurate ways of modelling hydrocarbons. MM4 is the latest version with several improvements [Allinger et al, 1996]. Halgren [1996] is also a general purpose force field mainly for organic molecules.…”

Section: Most Used Existing Force Fieldsmentioning

confidence: 99%

Using Molecular Modelling to Study Interactions Between Molecules with Biological Activity

Yunta¹

2012

Bioinformatics

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Section: Most Used Existing Force Fieldsmentioning

confidence: 99%

Using Molecular Modelling to Study Interactions Between Molecules with Biological Activity

Yunta¹

2012

Bioinformatics

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“…There are primarily two types of empirical force fields that are used for molecular simulations, which are referred to as class I force fields ͓e.g, AMBER, 50 [58][59][60] CFF, 61 PCFF, [62][63][64] COMPASS ͑Refs. 65-67͔͒.…”

Section: Empirical Force Field Parametrizationmentioning

confidence: 99%

Molecular simulation of protein-surface interactions: Benefits, problems, solutions, and future directions (Review)

2008

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While the importance of protein adsorption to materials surfaces is widely recognized, little is understood at this time regarding how to design surfaces to control protein adsorption behavior. All-atom empirical force field molecular simulation methods have enormous potential to address this problem by providing an approach to directly investigate the adsorption behavior of peptides and proteins at the atomic level. As with any type of technology, however, these methods must be appropriately developed and applied if they are to provide realistic and useful results. Three issues that are particularly important for the accurate simulation of protein adsorption behavior are the selection of a valid force field to represent the atomic-level interactions involved, the accurate representation of solvation effects, and system sampling. In this article, each of these areas is addressed and future directions for continued development are presented.

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“…The lateral manipulation was performed by reducing the tunnel resistance during scanning by increasing the tunneling current (up to ~1.5 nA) while reducing the tunneling voltage (down to ~200 mV) [11]. Theoretical simulations of the STM images were performed using extended Hückel molecular orbital-elastic scattering quantum chemistry (EHMO-ESQC) [27] after having relaxed the molecule on the surface using the molecular mechanics MM4 (2003) code [28]. The STM image simulations were carried out on Cu(110) under the same tunneling conditions as those for the result in Fig.…”

Section: Nano Researchmentioning

confidence: 99%

STM manipulation of molecular moulds on metal surfaces

Wang

Benjalal

et al. 2009

Nano Res.

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Molecular Landers are a class of compounds containing an aromatic board as well as bulky side groups which upon adsorption of the molecule on a surface may lift the molecular board away from the substrate. Different molecular Landers have extensively been studied as model systems for nanomachines and the formation of molecular wires, as well as for their function as "molecular moulds", i.e., acting as templates by accommodating metal atoms underneath their aromatic board. Here, we investigate the adsorption of a novel Lander molecule 1,4-bis(4-(2,4-diaminotriazine)phenyl)-2,3,5,6-tetrakis(4-tert-butylphenyl)benzene (DAT, C 64 H 68 N 10 ) on Cu(110) and Au(111) surfaces under ultrahigh vacuum (UHV) conditions. By means of scanning tunneling microscopy (STM) imaging and manipulation, we characterize the morphology and binding geometries of DAT molecules at terraces and step edges. On the Cu(110) surface, various contact confi gurations of individual DAT Landers were formed at the step edges in a controlled manner, steered by STM manipulation, including lateral translation, rotation, and pushing molecules to an upper terrace. The diffusion barrier of single DAT molecules on Au(111) is considerably smaller than on Cu(110). The DAT Lander is specially designed with diamino-triazine side groups making it suitable for future studies of molecular self-assembly by hydrogen-bonding interactions. The results presented here are an important guide to the choice of substrate for future studies using this compound.

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An improved force field (MM4) for saturated hydrocarbons

Cited by 329 publications

References 49 publications

Using Molecular Modelling to Study Interactions Between Molecules with Biological Activity

Using Molecular Modelling to Study Interactions Between Molecules with Biological Activity

Molecular simulation of protein-surface interactions: Benefits, problems, solutions, and future directions (Review)

STM manipulation of molecular moulds on metal surfaces

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