Understanding molecular structure from molecular mechanics

Allinger, Norman L.

doi:10.1007/s10822-011-9422-4

Cited by 31 publications

(36 citation statements)

References 33 publications

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“…There are various molecular mechanics packages with specific force fields, such as the MM3-MM4 force field, 91,92 Dreiding, 93 PCFF, 94,95 Amber, 96,97 and CHARMM. 98 In the MM3-MM4…”

Section: Hydrogen Bondingmentioning

confidence: 99%

Bicomponent Supramolecular Architectures at the Vacuum–Solid Interface

et al. 2017

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This review aims at giving the readers the basic concepts needed to understand two-dimensional bimolecular organizations at the vacuum–solid interface. The first part describes and analyzes molecules–molecules and molecules–substrates interactions. The current limitations and needs in the understanding of these forces are also detailed. Then, a critical analysis of the past and recent advances in the field is presented by discussing most of the key papers describing bicomponents self-assembly on solid surface in an ultrahigh vacuum environment. These sections are organized by considering decreasing molecule–molecule interaction strengths (i.e. starting from strong directional multiple H bonds up to weaker nondirectional bonds taking into account the increasing fundamental role played by the surface). Finally, we conclude with some research directions (predicting self-assembly, multi-components systems, and nonmetallic surfaces) and potential applications (porous networks and organic surfaces).

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“…There are various molecular mechanics packages with specific force fields, such as the MM3-MM4 force field, 91,92 Dreiding, 93 PCFF, 94,95 Amber, 96,97 and CHARMM. 98 In the MM3-MM4…”

Section: Hydrogen Bondingmentioning

confidence: 99%

Bicomponent Supramolecular Architectures at the Vacuum–Solid Interface

et al. 2017

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“…According to Hendrickson [7] and separately Allinger [8] the total strain of a conformation is the sum of: Any cyclic molecule tends to assume such a conformation in which the sum of the four types of strain is minimal. Since bond strain is considerably higher than the rest, it is relatively rare in cyclic compounds.…”

Section: Types Of Strainmentioning

confidence: 99%

Conformational analysis of cycloalkanes

Dragojlović

2015

ChemTexts

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Conformational analysis is a comparatively new area of organic chemistry that has been developed well after the theories of organic reactions, bonding in organic compounds and stereochemistry. It was only in the second half of twentieth century that its importance was fully recognized and its central role with respect to bonding, reactivity and stability of organic compounds was appreciated. Fundamental concepts of conformational analysis, a deeper discussion of the conformational analysis of small and common rings and an introduction into the conformational analysis of medium and large rings are presented at a level suitable for an introductory organic chemistry course. This discussion aims to provide a better understanding of the complex relationship among different types of strain, while also discussing the factors that determine stability of a particular conformation. Finally, the unique nature of each class of cycloalkanes is explored.

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“…We have checked this property by calculating STM images of a single HBC molecule in the constant-height mode: At a fixed tip height (z tip ) and for each (x,y) position of the probe during the scanning, we have calculated the total potential energy of the HBC molecule, that is to say the tipmolecule energy E MT + the molecule-substrate energy E MS . The E MT energy is evaluated by a standard MM4 force-field parametrization for van der Waals interactions [63][64][65]: (the slow scanning direction), until the top right point is reached. One can observe that the molecule is gently attracted and repelled by the tip around its central position.…”

Section: B Influence Of the Stm Tip: Molecular Manipulationmentioning

confidence: 99%

Adsorption and STM imaging of polycyclic aromatic hydrocarbons on graphene

et al. 2015

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The structural characterization of polycyclic aromatic hydrocarbon molecules adsorbed on graphene is of fundamental importance in view of the use of graphene or graphene nanoribbons for electronic applications. Before reaching this point, one has to determine the structure of the adsorbed molecules. Here, we study the case of benzene, coronene, and hexabenzocoronene on a graphene layer. First, the adsorption properties of single molecules are calculated using first-principles calculations at the level of density functional theory. We benefit from a recent scheme, particularly adapted for weakly adsorbed molecules, allowing us to precisely calculate the van der Waals contribution. Then, scanning tunneling microscopy (STM) is used to produce images of self-assembled molecules comparing different theoretical approaches to experimental observations. Finally, we consider the imaging of isolated molecules, and we show how the STM tip influences the molecule position by soft mechanical interaction during the scanning process.

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Understanding molecular structure from molecular mechanics

Cited by 31 publications

References 33 publications

Bicomponent Supramolecular Architectures at the Vacuum–Solid Interface

Bicomponent Supramolecular Architectures at the Vacuum–Solid Interface

Conformational analysis of cycloalkanes

Adsorption and STM imaging of polycyclic aromatic hydrocarbons on graphene

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