Exact method for the calculation of pseudorotation parametersP, τmand their errors. A comparison of the Altona–Sundaralingam and Cremer–Pople treatment of puckering of five-membered rings

Rao, S.T.; Westhof, Éric; Sundaralingam, M.

doi:10.1107/s0567739481000892

Cited by 224 publications

(143 citation statements)

References 6 publications

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“…The phase of pseudorotation, P, and the amplitude of pucker, r,,, (Rao, Westof & Sundaralingam, 1981), for (I) and (II) are P (I)= 197.7 (3), e(II)= 187.2 (5) ° and Zm(I) = 31.9 (1), Zm(II) = 40.0 (3) °. Thus, the conformation of (I) is sE (the ideal value of P is 198 ° for 3E), while (II) exhibits a conformation between ~T and 3E (the ideal value of P is 180 ° for 32T).…”

Section: Commentmentioning

confidence: 99%

D-glycero-D-gulo-Heptono- (I) and 2,7-ditosyl-D-glycero-D-gulo-heptono-1,4-lactone (II)

Søtofte¹

1994

Acta Crystallogr C

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Section: Commentmentioning

confidence: 99%

D-glycero-D-gulo-Heptono- (I) and 2,7-ditosyl-D-glycero-D-gulo-heptono-1,4-lactone (II)

Søtofte¹

1994

Acta Crystallogr C

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“…It is desired to use simplified parameters that can describe the movements of the ring atoms. Phase angle and amplitude are such parameters that can describe the five-membered ring puckering very well, [18][19][20]30 and they are widely utilized nowadays. (Note additional parameters are needed to describe more than fivemembered ring puckering).…”

Section: Theorymentioning

confidence: 99%

“…Usually, the pyrrolidine ring puckering is symbolized with two parameters-the pseudorotation phase angle and amplitude-that can be calculated either by the five ring-atom positions 18 or by the five endocyclic torsion angles χ j . 19,20 Quite often, the five χ j values are calculated for each puckering state and are listed as part of the puckering parameters in the results. 12,15,16 It is easy to see that the sign of several χ j switches at the UP and DOWN puckering states, respectively.…”

Section: Introductionmentioning

confidence: 99%

The puckering free-energy surface of proline

2013

AIP Advances

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Proline has two preferred puckering states, which are often characterized by the pseudorotation phase angle and amplitude. Although proline's five endocyclic torsion angles can be utilized to calculate the phase angle and amplitude, it is not clear if there is any direct correlation between each torsion angle and the proline-puckering pathway. Here we have designed five proline puckering pathways utilizing each torsion angle χj (j = 1∼5) as the reaction coordinate. By examining the free-energy surfaces of the five puckering pathways, we find they can be categorized into two groups. The χ2 pathway (χ2 is about the Cβ—Cγ bond) is especially meaningful in describing proline puckering: it changes linearly with the puckering amplitude and symmetrically with the phase angle. Our results show that this conclusion applies to both trans and cis proline conformations. We have also analyzed the correlations of proline puckering and its backbone torsion angles ϕ and ψ. We show proline has preferred puckering states at the specific regions of ϕ, ψ angles. Interestingly, the shapes of ψ-χ2 free-energy surfaces are similar among the trans proline in water, cis proline in water and cis proline in the gas phase, but they differ substantially from that of the trans proline in the gas phase. Our calculations are conducted using molecular simulations; we also verify our results using the proline conformations selected from the Protein Data Bank. In addition, we have compared our results with those calculated by the quantum mechanical methods

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“…Pseudorotational parameters (°)for all published muscarine ions and compounds (1) and (2) The pseudorotational parameters were calculated by PLATON (Spek, 1991) according to the method described by Rao, Westhof & Sundaralingam (1981 Notes: (a) musearine iodide (Jellinek, 1957); (b) muscarine chloride (Frydenvang & Jensen, 1990); (c) muscarine picrate (Frydenvang & Jensen, 1993); (at) musearine tetraphenylborate (Frydenvang & Jensen, 1993).…”

mentioning

confidence: 99%

Structure of the charge-transfer complexes 2,4,5,7-tetranitro-9-fluorenone–1-ethylnaphthalene (1/1) (I) and 2,4,5,7-tetranitro-9-fluorenone–3,6-dimethylphenanthrene (1/1) (II)

Baldwin¹,

Baughman²

1993

Acta Crystallogr C

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Exact method for the calculation of pseudorotation parametersP, τ_mand their errors. A comparison of the Altona–Sundaralingam and Cremer–Pople treatment of puckering of five-membered rings

Cited by 224 publications

References 6 publications

D-glycero-D-gulo-Heptono- (I) and 2,7-ditosyl-D-glycero-D-gulo-heptono-1,4-lactone (II)

D-glycero-D-gulo-Heptono- (I) and 2,7-ditosyl-D-glycero-D-gulo-heptono-1,4-lactone (II)

The puckering free-energy surface of proline

Structure of the charge-transfer complexes 2,4,5,7-tetranitro-9-fluorenone–1-ethylnaphthalene (1/1) (I) and 2,4,5,7-tetranitro-9-fluorenone–3,6-dimethylphenanthrene (1/1) (II)

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