Ab initio conformational analysis of cyclooctane molecule

Rocha, Willian R.; Pliego, Josefredo R.; Resende, Stella M.; Santos, Hélio F. Dos; Oliveira, Marcos Antônio de; Almeida, Wagner B. De

doi:10.1002/(sici)1096-987x(19980415)19:5<524::aid-jcc5>3.0.co;2-o

Cited by 35 publications

(25 citation statements)

References 22 publications

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“…A total of 10 different conformations have been identified [24,25]. In fact, an additional conformation was reported [26], but it was apparently identical to the one already known [27]. Complexities of conformational analysis of cyclooctane are a very good illustration of the challenges encountered when dealing with medium and large rings.…”

Section: Cyclooctanementioning

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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Section: Cyclooctanementioning

confidence: 99%

Conformational analysis of cycloalkanes

Dragojlović

2015

ChemTexts

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“…43 Of these, eight-membered rings have been the most popular subject due to the existence of multiple conformers of similar energy, a complicated potential energy surface resulting from the ring closure constraint, and significant steric influence from hydrogen atoms on preferred molecular conformations. [43][44][45][46] For these same reasons, eight-membered rings pose an interesting challenge for dimensionality reduction algorithms. In Cartesian space, a saturated 8-ring requires 72 dimensions to represent a conformation.…”

Section: A Eight-membered Ringsmentioning

confidence: 99%

Algorithmic dimensionality reduction for molecular structure analysis

Brown

Martin

Pollock

et al. 2008

The Journal of Chemical Physics

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Dimensionality reduction approaches have been used to exploit the redundancy in a Cartesian coordinate representation of molecular motion by producing low-dimensional representations of molecular motion. This has been used to help visualize complex energy landscapes, to extend the time scales of simulation, and to improve the efficiency of optimization. Until recently, linear approaches for dimensionality reduction have been employed. Here, we investigate the efficacy of several automated algorithms for nonlinear dimensionality reduction for representation of trans, trans-1,2,4-trifluorocyclo-octane conformation-a molecule whose structure can be described on a 2-manifold in a Cartesian coordinate phase space. We describe an efficient approach for a deterministic enumeration of ring conformations. We demonstrate a drastic improvement in dimensionality reduction with the use of nonlinear methods. We discuss the use of dimensionality reduction algorithms for estimating intrinsic dimensionality and the relationship to the Whitney embedding theorem. Additionally, we investigate the influence of the choice of high-dimensional encoding on the reduction. We show for the case studied that, in terms of reconstruction error root mean square deviation, Cartesian coordinate representations and encodings based on interatom distances provide better performance than encodings based on a dihedral angle representation.

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“…The second molecule used in the experiments is the cyclooctane, a cyclic molecule including eight carbon and sixteen hydrogen atoms. This molecule has received significant attention [16,33,50,20,4,11,47,46,39] because it has a complex energy landscape, despite its structural simplicity. The third test case is the loop formed by the residues 74 to 77 of the FTSJ of escherichia coli (PDB code 1EJ0).…”

Section: Methodsmentioning

confidence: 95%

Exploring the energy landscapes of flexible molecular loops using higher‐dimensional continuation

Porta

Jaillet

2012

J Comput Chem

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The conformational space of a flexible molecular loop includes the set of conformations fulfilling the geometric loop-closure constraints and its energy landscape can be seen as a scalar field defined on this implicit set. Higher-dimensional continuation tools, recently developed in Dynamical Systems and also applied to Robotics, provide efficient algorithms to trace out implicitly defined sets. This paper describes these tools and applies them to obtain full descriptions of the energy landscapes of short molecular loops that, otherwise, can only be partially explored, mainly via sampling. Moreover, to deal with larger loops, this paper exploits the higher-dimensional continuation tools to find local minima and minimum energy transition paths between them, without deviating from the loop-closure constraints. The proposed techniques are applied to previously studied molecules revealing the intricate structure of their energy landscapes. This paper introduces the use of higher-dimensional continuation tools to explore the energy landscapes of the implicitly-defined conformational spaces of flexible molecular loops. These tools produce an atlas composed by coordinated charts that parametrize the conformational space. The atlas captures the structure of this space, which determines the motion of the loop and the transition paths between conformations, something that is hard to obtain using existing approaches.

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Ab initio conformational analysis of cyclooctane molecule

Cited by 35 publications

References 22 publications

Conformational analysis of cycloalkanes

Conformational analysis of cycloalkanes

Algorithmic dimensionality reduction for molecular structure analysis

Exploring the energy landscapes of flexible molecular loops using higher‐dimensional continuation

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