Puckering Coordinates Research Articles

Broadband microwave spectroscopy of cyclopentylsilane and 1,1,1-trifluorocyclopentylsilane

The broadband microwave spectra of two related organosilicon molecules, cyclopentylsilane and 1,1,1-trifluorocyclopentylsilane, have been measured and assigned. Both molecules exhibit a Cs-symmetric “envelope” structure, which is confirmed by a determination of the heavy atom backbone rs substitution structures using isotopic substitution in natural abundance, as well as the presence of strong a-type transitions, weaker c-type, and a non-detection of b-type transitions, indicative of a mirror plane perpendicular to the prolate symmetry axis of the molecule. Both molecules appear to have significant zero-point vibrational averaging of their ring twisting and puckering coordinates, which lead to deviations between the ground state experimental structure and the predicted equilibrium structures at the B3LYP-D3/def2-TZVP level of theory. Additionally, we observe an excited vibrational state associated with this large amplitude motion and we use a simple perturbation theory argument to confirm the identity of these excited state carriers.

A Closer Look at the Isomerization of 5-Androstene-3,17-Dione to 4-Androstene-3,17-Dione in Ketosteroid Isomerase

We report a comprehensive investigation of the 5-androstene-3,17-dione to 4-androstene-3,17-dione isomerization in Ketosteroid Isomerase, gas phase and aqueous solution, applying as tools the Unified Reaction Valley Approach (URVA) and the Local Vibrational Mode Analysis. Conformational changes of the steroid rings are monitored via Cremer-Pople puckering coordinates. URVA identifies simultaneous breakage of the C[Formula: see text]–H bond and O–H bond formation with the catalytic acid, leading to an intermediate with the acid positioned over ring [Formula: see text] as the major chemical events of the first reaction step. Via a barrier-less shift, a second intermediate is formed with the acid being positioned over ring [Formula: see text]. Then, according to URVA, breakage of the intermediate O–H bond, the formation of the new C[Formula: see text]–H bond accompanied by a double bond shift in rings [Formula: see text] and [Formula: see text] forms the major chemical events of the second reaction step, which is facilitated by favorable ring puckering. Reactions in protein and gas phase have comparable activation enthalpies, whereas the barrier in aqueous solution is higher, confirming that the major task of the enzyme pocket is to shield the migrating hydrogen atom and the catalyzing acid from interactions with solvent molecules diluting the catalytic power. We do not find exceptional H-bonding with Asp99 and Tyr14, excluding their catalytic activity. There is no strong hydrogen bonding in the TS, which could account for lowering the activation barrier. Our study provides a clear picture of the isomerization process, which will also inspire similar investigations of other important enzymatic reactions.

Solvation Induced Ring Puckering Effect in Fluorinated Prolines and Its Inclusion in Classical Force Fields

Strategic incorporation of fluorinated prolines can accelerate folding and increase thermal stability of proteins. It has been suggested that this behavior emerges from puckering effects induced by fluorination of the proline ring. We use electronic structure calculations to characterize the potential energy surface (PES) along puckering coordinates for a simple dipeptide model of proline and its fluorinated derivatives. Significant shifts in puckering trends between gas phase and implicit solvent calculations shed light on the effect of solvation on electronic structure and conformational preferences of the ring. This solvation induced puckering effect is previously unknown in the context of prolines. The PES based on implicit solvent is then utilized to construct a correction for a classical force field. The corrected force field accurately captures the experimental conformational equilibrium including the coupling between ring puckering and cis-trans isomerism in fluorinated prolines. This method can be extended to other rings and substituents besides fluorine.

Systematic description of molecular deformations with Cremer-Pople puckering and deformation coordinates utilizing analytic derivatives: Applied to cycloheptane, cyclooctane, and cyclo[18]carbon.

The conformational properties of ring compounds such as cycloalkanes determine to a large extent their stability and reactivity. Therefore, the investigation of conformational processes such as ring inversion and/or ring pseudorotation has attracted a lot of attention over the past decades. An in-depth conformational analysis of ring compounds requires mapping the relevant parts of the conformational energy surface at stationary and also at non-stationary points. However, the latter is not feasible by a description of the ring with Cartesian or internal coordinates. We provide in this work, a solution to this problem by introducing a new coordinate system based on the Cremer-Pople puckering and deformation coordinates. Furthermore, analytic first- and second-order derivatives of puckering and deformation coordinates, i.e., B-matrices and D-tensors, were developed simplifying geometry optimization and frequency calculations. The new coordinate system is applied to map the potential energy surfaces and reaction paths of cycloheptane (C7H14), cyclooctane (C8H16), and cyclo[18]carbon (C18) at the quantum chemical level and to determine for the first time all stationary points of these ring compounds in a systematic way.

Describing Polytopal Rearrangements of Fluxional Molecules with Curvilinear Coordinates Derived from Normal Vibrational Modes: A Conceptual Extension of Cremer-Pople Puckering Coordinates.

In this work a new curvilinear coordinate system is presented for the comprehensive description of polytopal rearrangements of N-coordinate compounds (N = 4-7) and systems containing an N-coordinate subunit. It is based on normal vibrational modes and a natural extension of the Cremer-Pople puckering coordinates ( J. Am. Chem. Soc. 1975, 97, 1354) together with the Zou-Izotov-Cremer deformation coordinates ( J. Phys. Chem. A 2011, 115, 8731) for ring structures to N-coordinate systems. We demonstrate that the new curvilinear coordinates are ideal reaction coordinates describing fluxional rearrangement pathways by revisiting the Berry pseudorotation and the lever mechanism in sulfur tetrafluoride, the Berry pseudorotation and two Muetterties' mechanisms in pentavalent compounds, the chimeric pseudorotation in iodine pentafluoride, Bailar and Ray-Dutt twists in hexacoordinate tris-chelates as well as the Bartell mechanism in iodine heptafluoride. The results of our study reveal that this dedicated curvilinear coordinate system can be applied to most coordination compounds opening new ways for the systematic modeling of fluxional processes.

Equivalence properties of the Cremer & Pople puckering coordinates for N-membered rings

The Cremer & Pople puckering coordinates are an invaluable tool in the conformational mapping and classification of rings fragments, especially for medium size rings. However, because of the topological symmetries that many chemical fragments exhibit, it is important to be aware of which values of the puckering coordinates should be considered equivalent because they correspond to the same fragments, up to a permutation of the atoms labels or a coordinates inversion. In this paper a precise description of the action of the relevant permutational operators and coordinate inversion is given for a ring of any size. The results are then specialized to the case of medium rings (6–8 atoms) for which on one hand, the symmetry equivalents of the puckering coordinates are obtained and on the other hand, in the case of structurally equivalent atoms, simple algorithms are derived to compute the representative puckering coordinates that fall into the representative asymmetric unit.

New Way of Describing Static and Dynamic Deformations of the Jahn–Teller Type in Ring Molecules

A new method is presented to describe deformations of an N-membered planar ring (N-ring) molecule in terms of deformation vectors that can be expressed by a set of 2N-3 deformation amplitudes and phase angles. The deformation coordinates are directly derived from the normal vibrational modes of the N-ring and referenced to a regular polygon (N-gon) of unit length. They extend the conceptual approach of the Cremer-Pople puckering coordinates (J. Am. Chem. Soc. 1975, 97, 1354) to the planar ring and make it possible to calculate, e.g., a planar ring of special deformation on a Jahn-Teller surface. It is demonstrated that the 2N-3 deformation parameters are perfectly suited to describe the pseudorotation of a bond through the ring as it is found in cyclic Jahn-Teller systems. In general, an N-membered planar ring can undergo N-2 different bond pseudorotations provided the energetics of such a process is feasible. The Jahn-Teller distortions observed in ring compounds correspond either directly to the basic pseudorotation modes or to linear combinations of them. Any deformed ring molecule can be characterized in terms of the new ring deformation coordinates, which help to identify specific electronic effects. The usefulness of the ring deformation coordinates is demonstrated by calculating the Jahn-Teller surfaces for bond pseudorotation in the case of the cyclopropyl radical cation and cyclobutadiene as well as the ring deformation surfaces of disulfur dinitride and its dianion employing multireference averaged quadratic coupled cluster (MR-AQCC) theory, equation-of-motion coupled cluster theory in form of EOMIP-CCSD, and single determinant coupled cluster theory in form of CCSD(T).

3D superposition of chemical fragments for N‐membered rings: application to conformational analysis

AbstractIn this paper a procedure is suggested for the 3D superposition of chemical fragments, which is specifically designed for rings molecules and can be combined with statistical multivariate procedures to extract useful conformational information. The procedure relies on the plane introduced by Cremer and Pople ‘A general definition of ring puckering coordinates. J. Am. Chem. Soc. 1975; 97(6): 1354–1358’ to define the celebrated puckering coordinates, and provides a measure of distance between two geometrical conformations. Real datasets are analyzed to illustrate how it can be used as input to agglomerative clustering methods, multidimensional scaling analysis and allows to compute the centroid of a group of fragments. Copyright © 2010 John Wiley & Sons, Ltd.

Puckering free energy of pyranoses: A NMR and metadynamics-umbrella sampling investigation

We present the results of a combined metadynamics-umbrella sampling investigation of the puckered conformers of pyranoses described using the GROMOS 45a4 force field. The free energy landscape of Cremer-Pople puckering coordinates has been calculated for the whole series of α and β aldohexoses, showing that the current force field parameters fail in reproducing proper puckering free energy differences between chair conformers. We suggest a modification to the GROMOS 45a4 parameter set which improves considerably the agreement of simulation results with theoretical and experimental estimates of puckering free energies. We also report on the experimental measurement of altrose conformer populations by means of NMR spectroscopy, which show good agreement with the predictions of current theoretical models.

The Conformational Free Energy Landscape of β-d-Glucopyranose. Implications for Substrate Preactivation in β-Glucoside Hydrolases

Using ab initio metadynamics we have computed the conformational free energy landscape of beta-D-glucopyranose as a function of the puckering coordinates. We show that the correspondence between the free energy and the Stoddard's pseudorotational itinerary for the system is rather poor. The number of free energy minima (9) is smaller than the number of ideal structures (13). Moreover, only six minima correspond to a canonical conformation. The structural features, the electronic properties, and the relative stability of the predicted conformers permit the rationalization of the occurrence of distorted sugar conformations in all the available X-ray structures of beta-glucoside hydrolase Michaelis complexes. We show that these enzymes recognize the most stable distorted conformers of the isolated substrate and at the same time the ones better prepared for catalysis in terms of bond elongation/shrinking and charge distribution. This suggests that the factors governing the distortions present in these complexes are largely dictated by the intrinsic properties of a single glucose unit.

Proline Zwitterion Dynamics in Solution, Glass, and Crystalline State

Raman and Raman optical activity spectra of L- and D-proline zwitterionic (PROZW) forms were recorded for H(2)O and D(2)O solutions in a wide frequency range and analyzed with respect to the motion of the proline ring and rotation of the carbonyl group. The solution spectra were additionally compared to Raman scattering of glass and crystalline powder proline. Solution and glass spectral band broadenings are similar and reveal information about the extent of internal molecular motion. Two distinct but equally populated flexible forms were found in the glass and the solution. The equal population is consistent with NMR data, temperature, and concentration dependencies. The molecular flexibility is reduced significantly in the crystal, however, where only one conformer is present. Consequently, the crystal bands are narrow and exhibit minor frequency shifts. The spectra were interpreted with the aid of density functional theory computations involving both continuum and explicit solvent. A two-dimensional potential energy surface pertaining to the five-member ring puckering coordinates was constructed and used for dynamical averaging of spectral properties. Comparison of the computed and experimental bandwidths suggests that the puckering is strongly correlated with the carbonyl rotation. An averaging over these two motions produces similar results. The interpretation of the Raman experiments with the aid of the simulation techniques also indicates that the environment modulates properties of the hydrophobic part of the molecule indirectly by interacting with the ionic group. Such behavior may be important for the reactivity and biological activity of proline-containing peptides and proteins.

Modeling ring puckering in strained systems: application to 3,6-anhydroglycosides

Different conformations of methyl 3,6-anhydroglycosides with the β- d- galacto, α- d- galacto, and β- d- gluco configurations were studied by molecular mechanics (using the program mm3) and by quantum mechanical (QM) methods at the HF/- and B3LYP/6-31+G** levels, with and without solvent emulation. Using molecular mechanics, the energies were plotted against the ϕ, θ puckering coordinates of Cremer and Pople. In such strained systems, only two extreme conformations of the six-membered ring are likely: 1 C 4 and B 1,4, or any one close to either of them. Results show the preponderance of a distorted chair conformation over that of the distorted boat, though the energy difference is lower and the distortions are larger for the compound with the β- d- galacto configuration. For derivatives of this compound, experimental data in solution indicate both chair and boat forms, depending on the compound and the solvent, whereas for the remaining compounds, experimental data always show the preponderance of the chair conformation. The more accurate DFT calculations lead to the lower energy differences, suggesting that HF and mm3 underestimate the stability of the boat-like conformations. Similar studies on model compounds depict the importance of the anomeric effect in the conformational preferences.

Diphenyl (3,3-diphenoxycyclohexyl)phosphonate

The solid-state structure of the title compound, C30H29O5P, has been determined at 100 K. The generalized puckering coordinates, Q2 (0.587), φ2 (286.82°) and θ2 (178.9°), confirm that the cyclo­hexane ring is in the chair conformation 2C5. The phosphine ligand is equatorial to the ring, with the P atom in a slightly distorted tetrahedral configuration.

Conforma: a program for determining ring conformations and puckering coordinates

A program (CONFORMA) was developed to calculate ring puckering coordinates using Cremer and Pople's (J. Am. Chem. Soc. 1975, 97, 1354) methodology, which quantifies the conformation of five or more atom rings. The program performs, also, a conformational analysis based on these results.

Self-assembly of frame structures. 10. Stereochemistry of 2,5-dioxabicyclo [2.2.1]heptane-3,6-digne

By optimization of the geometry of 2, 5-dioxabicyclo[2. 2.1]heptane-3.6-dione (1) with an ab initio (RHF/6-31 G') calculation, we have found that a single synchro(+, +)-twist form (A) corresponds to the (1 R,4R)-enantiomer (the dihedral angles of the lactone bridges areϕ0 = 2.6°). According to MM2(91) and MM3(92) calculations, (1R,4R)-1 exists as the s-ynchro(+, +)-A-twist (ϕ0 = 3.9°) and the synchro(-, -)-B-twist (ϕ = -3.8°) forms, respectively. Investigating the torsional energy surface of the dilactone 1 (MM2(91)), we found only the (1R,4R,P)-diastereomeric form (A), which is stabilized compared with the (1R,4P,M) form (B) (probably as a result of the more preferred dipole-dipole interaction of the carbonyl groups). According to the calculated puckering coordinates, the five-membered and six-membered moieties of the bicycle 1 are flattened compared with norbornane.

Modeling of aldopyranosyl ring puckering with MM3 (92)

The molecular mechanics algorithm MM3 was used to compute energy surfaces for aldopyranosyl rings having a full range of shapes. Energies were plotted against the ΦΘ puckering coordinates of Cremer and Pople. The 4 C 1 conformations of the model pyranosyl rings are dominant for both anomers of d-allose, d-galactose, d-glucose, d-mannose, and d-talose, as are the 4 C 1 conformations of β- d-altropyranose, β- d-gulopyranose, and β- d-idopyranose. α- d-Altropyranose is predicted to exist as an equilibrium of 1 C 4 and 4 C 1, α- d-idopyranose as an equilibrium among O S 2, 1 C 4, and 4 C 1, and α- d-gulopyranose is predominately 4 C 1 but has some contribution from 1 C 4 (18%) and O S 2 (9%). The calculated and measured hydrogen-hydrogen coupling constants agree well, although the energies for the β anomers in water are systematically low by an average of 0.4 kcal/mol. Because the errors in the predicted anomeric ratios are small and are similar for the eight hexoses, and because the only concession to the solvent was a dielectric constant of 3.0, specific solvent effects are apparently small.

Jet-cooled fluorescence excitation spectra and carbonyl wagging and ring-puckering potential energy functions of cyclobutanone and its 2,2,4,4-d4 isotopomer in the S1(n,π*) electronic excited state

The jet-cooled fluorescence excitation spectra of cyclobutanone and its 2,2,4,4-d4 isotopomer have been recorded in the 305–335 nm region. The electronic band origin of the d0 molecule for the S1(n,π*) state of A2 symmetry occurs at 30 292 cm−1 (30 265 cm−1 for the d4 molecule). The observed spectra consisting of more than 50 bands for each isotopomer involve ν7, ν8, and ν9 (the three A1 ring vibrations) as well as ν20(C=O in-plane wag), ν26 (C=O out-of-plane wag), and ν27 (ring puckering). Five bands associated with the excited vibrational states of ν26 in the S1(n,π*) electronic state were observed for each isotopic species, and these were used to determine the one-dimensional potential energy functions for the C=O out-of-plane wagging. The C=O wagging angle was determined to be 39° and the barrier to inversion is 2149 cm−1 (2188 cm−1 for the deuteride). For the ring-puckering in the S1 state the lowest three vibrational energy spacings were found to be 106, 166, and 185 cm−1 as compared to values of 35, 57, and 65 cm−1 in the S0 ground state. Several ring-puckering potential energy functions with varying degrees of asymmetry are capable of reproducing the observed results. In all cases, however, the v=0 puckering state lies above any barrier to planarity. A two-dimensional potential function which fits the observed data was also determined in terms of the wagging and puckering coordinates.

Conformational analysis of six-membered rings in solution: ring puckering coordinates derived from vicinal NMR proton-proton coupling constants

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTConformational analysis of six-membered rings in solution: ring puckering coordinates derived from vicinal NMR proton-proton coupling constantsC. A. G. HaasnootCite this: J. Am. Chem. Soc. 1993, 115, 4, 1460–1468Publication Date (Print):February 1, 1993Publication History Published online1 May 2002Published inissue 1 February 1993https://doi.org/10.1021/ja00057a034RIGHTS & PERMISSIONSArticle Views317Altmetric-Citations30LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (1 MB) Get e-Alerts Get e-Alerts

A two-dimensional ring puckering potential energy surface for ethylene carbonate from ab initio and flexible model computations

A two-dimensional ring puckering potential energy surface has been derived for ethylene carbonate using ab initio and flexible model computations. The surface is expressed as a mixed Taylor—Fourier series expansion of the generalized ring puckering coordinates ( q, φ). The ab initio molecular energies have been used to determine the degree of truncation of the series which gives an accurate representation of the surface in the region of q, φ space spanned by data from microwave spectroscopy. The ab initio geometries have been used for the kinetic energy part of the flexible model computations. By scaling the coefficients of the ab initio potential it is possible to obtain reasonably good agreement with the observed inversion splitting, fundamental puckering vibrational frequencies and most of the variation in the rotational constants with excitation of the ring puckering vibrations. This potential function has a twisted C 2 symmetry equilibrium conformation with a puckering amplitude of 27 pm. The lowest energy path to ring inversion passes through the planar ring conformation where there is a barrier of 2.7 kJ mol − (229 cm −1).

Conformation and ring inversion in γ-butyrolacetone. Part 2.—Ab initio and flexible model computations

The conformation and ring inversion of γ-butyrolactone have been studied using ab initio and flexible model computations. The potential energy surface has been computed using STO-3-21G orbitals and complete geometry optimization as a function of the ring puckering coordinates. The computed equilibrium geometry has a ring in which all of the atoms with the exception of the β carbon are nearly coplanar. The computed inversion barrier is 6.1 kJ mol–1. Analytical expressions, as functions of the correct symmetry of the ring puckering coordinates, have been obtained for the potential energy surface and internal coordinates by least-squares fits to the computed molecular energies and geometries. These data have been used as the input for flexible model computations of the vibrational frequencies, inversion splittings and rotational constants. By using a simple uniform scaling of the potential energy surface good agreement with the observed vibrational frequencies and inversion splittings is obtained for a barrier to ring inversion of 7.9 kJ mol–1. The changes in the rotational constants are reasonably well reproduced for excitation of the vibration which is associated with a double minimum potential and less successfully for the other ring puckering vibration.