Ring-puckering Coordinates Research Articles

High-resolution infrared spectroscopy of jet cooled cyclobutyl in the α-CH stretch region: large-amplitude puckering dynamics in a 4-membered ring radical.

Gas-phase cyclobutyl radical (c-C4H7) is generated at a rotational temperature of Trot = 26(1) K in a slit-jet discharge mixture of 70% Ne/30% He and 0.5-0.6% cyclobromobutane (c-C4H7Br). A fully rovibrationally resolved absorption spectrum of the α-CH stretch fundamental band between 3062.9 cm-1 to 3075.7 cm-1 is obtained and analyzed, yielding first precision structural and dynamical information for this novel radical species. The α-CH stretch band origin is determined to be 3068.7887(4) cm-1, which implies only a modest (≈0.8 cm-1) blue shift from rotationally unresolved infrared spectroscopic studies of cyclobutyl radicals in liquid He droplets [A. R. Brown, P. R. Franke and G. E. Douberly, J. Phys. Chem. A, 2017, 121, 7576-7587]. Of particular dynamical interest, a one-dimensional potential energy surface with respect to the ring puckering coordinate is computed at CCSD(T)/ANO2 level of theory and reveals a double minimum Cs puckered geometry, separated by an exceedingly shallow planar C2v transition state barrier (Ebarr ≈ 1 cm-1). Numerical solutions on this double minimum potential yield a zero-point energy for the ground state (Ezero-point ≈ 27 cm-1) greatly in excess of the interconversion barrier. This is indicative of highly delocalized, large amplitude motion of the four-membered ring structure, for which proper vibrationally averaging of the moment of inertia tensor reproduces the experimentally determined inertial defect remarkably well. Finally, intensity alternation in the experimental spectrum due to nuclear spin statistics upon exchange of three indistinguishable H atom pairs (IH = ½) matches Ka + Kc = even : odd = 36 : 28 predictions, implying that the unpaired electron in the radical center lies in an out-of-plane pπ orbital. Thus, high-resolution infrared spectroscopy provides first experimental confirmation of a shallow double minimum ring puckering potential with a highly delocalized ground state wave function peaked at a planar C2v transition state geometry consistent with a cyclobutyl π radical.

Interplay of Rotational and Pseudorotational Motions in Flexible Cyclic Molecules.

Solutions to the time-independent nuclear Schrödinger equation associated with the pseudorotational motion of three flexible cyclic molecules are presented and discussed. Structural relaxations related to the pseudorotational motion are described as functions of a pseudorotation angle ϕ which is formulated according to the definition of ring-puckering coordinates originally proposed by Cremer and Pople (J. Am. Chem. Soc.1975, 97 ( (6), ), 1354−1358). In order to take into account the interplay between pseudorotational and rotational motions, the rovibrational Hamiltonian matrices are formulated for the rotational quantum numbers J = 0 and J = 1. The rovibrational Hamiltonian matrices are constructed and diagonalized using a Python program developed by the authors. Suitable algorithms for (i) the construction of one-dimensional cuts of potential energy surfaces along the pseudorotation angle ϕ and (ii) the assignment of the vibrorotational wave functions (which are needed for the automatic calculation of rotational transition energies J = 0 → J = 1) are described and discussed.

Spectroscopic and Theoretical Study of the Intramolecular π-Type Hydrogen Bonding and Conformations of 2-Cyclopenten-1-ol.

The conformations of 2-cyclopenten-1-ol (2CPOL) have been investigated by high-level theoretical computations and infrared spectroscopy. The six conformational minima correspond to specific values of the ring-puckering and OH internal rotation coordinates. The conformation with the lowest energy possesses intramolecular π-type hydrogen bonding. A second conformer with weaker hydrogen bonding has somewhat higher energy. Ab initio coupled-cluster theory with single and double excitations (CCSD) was used with the cc-pVTZ (triple-ζ) basis set to calculate the two-dimensional potential energy surface (PES) governing the conformational dynamics along the ring-puckering and internal rotation coordinates. The two conformers with the hydrogen bonding lie about 300 cm−1 (0.8 kcal/mole) lower in energy than the other four conformers. The lowest energy conformation has a calculated distance of 2.68 Å from the hydrogen atom on the OH group to the middle of the C=C double bond. For the other conformers, this distance is at least 0.3 Å longer. The infrared spectrum in the O-H stretching region agrees well with the predicted frequency differences between the conformers and shows the conformers with the hydrogen bonding to have the lowest values. The infrared spectra in other regions arise mostly from the two hydrogen-bonded species.

Spectroscopic and Theoretical Study of the Intramolecular π-Type Hydrogen Bonding and Conformations of 3-Cyclopentene-1-amine.

The infrared and Raman spectra of 3-cyclopentene-1-amine (3CPAM) have been recorded and analyzed, and the experimental investigations have been complemented by theoretical calculations. Ab initio coupled cluster theory with single and double excitations (CCSD) was used with the cc-pVTZ (triple-ζ) basis set to calculate the conformational energy and geometrical parameters for each of the six conformers of this molecule. MP2/cc-pVTZ and B3LYP/cc-pVTZ computations were utilized to calculate the vibrational frequencies of the conformers. Both the spectra and theoretical calculations verify the presence of the conformers and show that the conformer at the lowest energy has intramolecular π-type hydrogen bonding involving the NH2 group. The hydrogen bonded conformer is about 2 kJ/mol lower in energy than the other conformers. The potential energy topographical contour map for the ring-puckering and NH2 internal rotation coordinates has been calculated, and this shows how the different conformers can interconvert into each other. The far-infrared spectrum in the 190 to 280 cm-1 region shows several NH2 internal rotation bands for each of the different conformers, and these are consistent with one-dimensional representations for their torsional motions.

Potential-Energy Surfaces for Ring-Puckering Motions of Flexible Cyclic Molecules through Cremer-Pople Coordinates: Computation, Analysis, and Fitting.

Ring-puckering motion in 12 flexible cyclic molecules is investigated by calculation and analysis of two-dimensional potential-energy surfaces (PESs) using the so-called ring-puckering coordinates proposed by Cremer and Pople. The PESs are calculated by means of density-functional theory using a B2PLYP-D3BJ exchange-correlation functional with a maug-cc-pVTZ basis set, and results are compared to the available experimental and theoretical data. Special care is devoted to the aspect of symmetry in such two-dimensional PESs, which are here reported for the first time also for molecules whose planar form has symmetry lower than D5 h or C2 v. The issue of PES fitting and that of solving the nuclear dynamics using ring-puckering coordinates are also addressed. Analytical formulations of the computed PESs using suitable functional forms with a limited set of parameters are provided.

Theoretical Study of Structures and Ring-Puckering Potential Energy Functions of Bicylo[3.1.0]hexane and Related Molecules.

Ab initio computations using the MP2/cc-pVTZ method have been carried out to calculate the structures and relative energies of the different conformations of five bicyclic molecules including bicyclo[3.1.0]hexane, 3-oxabicyclo[3.1.0]hexane, 6-oxabicyclo[3.1.0]hexane, 3,6-oxabicyclo[3.1.0]hexane, and bicyclo[3.1.0]hexan-3-one. Theoretical ring-puckering potential energy functions (PEFs) in terms of the ring-puckering coordinate have been calculated for each of the molecules and these were compared to those determined experimentally from spectroscopic data. Each potential function is asymmetric and has an energy minimum corresponding to where the five-membered ring is puckered in the same direction as the attached three-membered ring. In contrast to the experimental result, the calculations predict that bicyclo[3.1.0]hexane has a second shallow energy minimum. All of the other molecules have a single conformational minimum and their experimental and theoretical PEFs agree very well. The wave functions for the lower ring-puckering energy levels have been computed.

Pseudorotational landscape of seven-membered rings: the most stable chair and twist-boat conformers of ε-caprolactone.

The conformational landscape and ring-puckering properties of ε-caprolactone have been analyzed by using microwave spectroscopy and quantum chemical calculations. Two conformers were detected in a supersonic jet expansion, the most stable form being a chair containing the ester group in its rectangular flap. This conformation benefits from reduced CH2 bond eclipsing and angle strain, while π-electron delocalization in the ester group is increased. The derived effective structure of the chair form satisfactorily agrees with the calculated near-equilibrium structure. A twist-boat conformer was also identified (9.4 kJ mol(-1) higher in energy at CCSD(T)/aug-cc-pVTZ level), and was located in the boat-twist-boat pseudorotation cycle of the seven-membered ring. Three other low-energy conformers were investigated and characterized in terms of the four puckering coordinates of the seven-membered ring. Potential interconversions in the four-dimensional conformation space are also discussed.

Theoretical calculations and vibrational potential energy surface of 4-silaspiro(3,3)heptane

Theoretical computations have been carried out on 4-silaspiro(3,3)heptane (SSH) in order to calculate its molecular structure and conformational energies. The molecule has two puckered four-membered rings with dihedral angles of 34.2° and a tilt angle of 9.4° between the two rings. Energy calculations were carried out for different conformations of SSH. These results allowed the generation of a two-dimensional ring-puckering potential energy surface (PES) of the form V = a(x1 (4) + x2 (4)) - b(x1 (2) + x2 (2)) + cx1 (2)x2 (2), where x1 and x2 are the ring-puckering coordinates for the two rings. The presence of sufficiently high potential energy barriers prevents the molecule from undergoing pseudorotation. The quantum states, wave functions, and predicted spectra resulting from the PESs were calculated.

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.

Conformational Free Energy Surface of α-N-Acetylneuraminic Acid: An Interplay Between Hydrogen Bonding and Solvation

The conformational free energy surface of alpha-N-acetylneuraminic acid (Neu5Ac, sialic acid) in the space of ring-puckering coordinates was calculated using the metadynamics method. Free energy surfaces in vacuum and with an explicit solvent were calculated in GLYCAM 06 force field. In vacuum three structures are almost equivalently populated, namely, the (2)C(5) chair and the B(3,6)/(2)S(6) and (O)S(3) boat/skew-boat conformations. The B(3,6)/(2)S(6) structure is stabilized by an ionic hydrogen bond between the amide N-H bond and the carboxylic group. However, this structure is unfavorable in a water environment in which the experimentally observed (2)C(5) chair conformation is predicted to be more stable than the other structures. These results indicate that environment significantly influences conformation of Neu5Ac and that Neu5Ac-processing enzymes might modify a conformation of their substrates solely by a changing polarity of the environment. The structure of Neu5Ac bound in influenza neuraminidase ((4)S(2)/B(2,5)) belongs to conformations preferred in a water environment. The free energy penalty of this conformational change was calculated (relative to (2)C(5)) as 10.2 +/- 2.0 and 17.3 +/- 2.0 kJ/mol for (4,O)B/(O)S(3) and (4)S(2), respectively. This result indicates that mimicking of the enzyme-bound conformation is likely to be a viable strategy for the design of neuraminidase inhibitors.

Jet-cooled vibronic spectroscopy and asymmetric torsional potentials of phenylcyclopentene

The ultraviolet spectroscopy of the S(1) <-- S(0) transition of 1-phenylcyclopentene (PCP) was studied by resonant-two-photon ionization (R2PI), laser-induced fluorescence (LIF) and single vibronic level fluorescence (SVLF). UV-UV hole-burning (UVHB) spectroscopy was used to determine that there is only one spectroscopically distinct conformer in the supersonic expansion. The excitation spectrum shows extensive vibronic structure extending to over 1000 cm(-1) above the electronic origin (34,646 cm(-1)). Much of the vibronic structure is similar to that of styrene and other singly substituted benzene derivatives, with Franck-Condon (FC) activity predominantly in substituent-sensitive benzene modes. Sizeable FC progressions were also found in the inter-ring torsion, reflecting a large displacement in the inter-ring angle upon electronic excitation. No evidence for FC activity in the ring-puckering coordinate is observed. The torsional potentials of the ground and excited states were determined from the experimental transition frequencies by fitting the calculated to the experimental torsional frequency spacings in an automated least-squares fitting procedure. The S(1) torsional potential is a symmetric single-well potential centered around a locally planar equilibrium geometry at a torsional angle of varphi = 0 degrees . The energy levels are reproduced by a cosine term potential function with torsional parameters V(2) = 3765 cm(-1) and V(4) = -183 cm(-1). The S(0) torsional potential possesses a twisted equilibrium geometry that is strongly asymmetric about varphi = 0 degrees due to the non-planarity of the cyclopentene ring. The best-fit potential parameters uses a sin/cos potential function (odd/even), with V = 948 cm(-1), V = -195 cm(-1), V = -162 cm(-1) and V = -268 cm(-1). The shape of the potentials are similar to those predicted by relaxed potential energy scans calculated at the DFT, CIS and TDDFT//CIS levels of theory. The change in the torsional angle varphi upon electronic excitation was determined to be approximately 15 degrees from fits of the displacement delta of the S(0) torsional potential with respect to the S(1) potential. The simulated shift of the S(0) potential with respect to the S(1) potential of approximately 15 degrees is in very good agreement with that obtained from B3LYP calculations.

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.

Internal dynamics in azetidine: A microwave and ab initio study

The internal dynamics of interconversion between equivalent conformations due to the coupling between ring puckering and NH inversion in azetidine has been investigated by rotational spectroscopy and ab initio computations. Analysis of the rotational spectra in the 8–220 GHz region has been completed for the ground state and first four excited states of the ring-puckering vibration. Rotational transitions exhibit a characteristic doubling originated by tunneling between equivalent conformations through a C2v barrier, which is related to symmetric (A1) and antisymmetric (B1) inversion states. Additionally, nuclear quadrupole hyperfine structure arising from the N nucleus could be resolved for low-J transitions. Accurate rotational and centrifugal distortion parameters together with the energy difference between inversion states derived from μc-type inversion transitions have been derived for each ring-puckering state using a two-state Hamiltonian. An effective monodimensional reduced potential function for the ring-puckering vibration V(X)=10.82(X4+14.29X−8.93X2−0.28X3) has been found consistent with the observed experimental variation of the rotational and centrifugal distortion constants with ring-puckering. This asymmetric single minimum potential function supports the existence of only one stable equatorial form. The barrier to interconversion between equivalent equatorial conformers, related to the C2v conformation of azetidine in which the ring atoms and the NH group are coplanar, has been estimated to range between 1900 and 2600 cm−1. The strong dependence of the dipole moment and quadrupole coupling constants with ring-puckering vibrational state evidence structural changes that occur along the ring-puckering coordinate.

Far-Infrared and Raman Spectra and Vibrational Potential Energy Surface for the Ring-Puckering and Ring-Flapping of Coumaran

The far-infrared and Raman spectra of coumaran vapor have been recorded and analyzed. Single, double, and triple quantum jump transitions (ΔvP = 1, 2, 3) were observed in the 60−270 cm-1 region for the ring-puckering vibration in both the ground and first excited states of the ring-flapping vibration. These were utilized to assign the ring-puckering quantum states for both flapping states, allowing both one- and two-dimensional potential energy functions to be determined. The one-dimensional function in terms of the ring-puckering coordinate (x1) has the form V (cm-1) = (7.92 × 105)x14 − (2.99 × 104)x12 and has a barrier to planarity of 279 cm-1 (3.32 kJ/mol) with energy minima corresponding to dihedral angles of ±30°. The two-dimensional surface in terms of the puckering and flapping coordinates shows that there is extensive interaction between these two vibrations. The barrier for the two-dimensional surface is 275 cm-1, and the dihedral angle is 37°. The coumaran barrier is considerably higher than that for 2,3-dihydrofuran (83 cm-1), which does not have the attached benzene ring.

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.

Profiles of the far-infrared modes of 2,5-dihydrofuran and cyclopentanone in the liquid state

The ring-puckering vibration of 2,5-dihydrofuran in solution is studied. A relation between the second moment M(2) of the ring-puckering absorption band and the mean square value of the force acting on the ring during the motion is deduced: M(2) = 〈F 2〉 m 0kT where m 0 and kT are respectively the reduced mass of the motion and the Boltzmann factor. The far-infrared spectra of the liquid at different temperatures are presented and the second moment M(2) of the ring-puckering vibration is obtained. Finally, the experimental value of M(2) is compared to the calculated value using the relation M(2) = 〈 dV Q dQ ) 2 liq 〉 m 0kT where V( Q) liq is a possible potential function for the ring-puckering vibration in the liquid state and Q is the ring-puckering coordinate. The same treatment is also applied to the intense band observed in the far-infrared spectra of cyclopentanone in hexane assigned to the pseudorotational mode in the liquid state.

Relationships between Torsional Angles and Ring-Puckering Coordinates. 5. Application to Six-Membered Rings

Relationships between Torsional Angles and Ring-Puckering Coordinates. 5. Application to Six-Membered Rings

Far-infrared spectra and ring--puckering potential energy function of 4H-pyran. Conformations and bonding of 1,4-cyclohexadiene and its oxygen analogs

The far-infrared, mid-infrared, and Raman spectra of 4H-pyran have been recorded and analyzed. The far-infrared gas-phase spectrum of this molecule shows a series of 12 bands between 115 and 128 cm -1 arising from the ring-puckering vibration. The kinetic energy (reciprocal reduced mass) expansion was calculated for this mode and utilized in the determination of the potential energy function, which was found to be V (cm -1 )=(1.21×10 5 )x 4 +(2.24×10 4 )x 2 , where x is the ring-puckering coordinate in angstroms. This shows the ring to be planar. The corresponding potential energy functions for the analogous 1,4-cyclohexadiene and 1,4-dioxin are respectively nearly harmonic and nearly quartic

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

Spectra and structure of small ring compounds. LIX

The Raman (3200 to 10 cm−1) and far infrared (380 to 60 cm−1) spectra of gaseous fluorocyclobutane,c-C4H7F, have been recorded. A series of Q-branches observed in both of these spectra beginning at 166 cm−1 with successive transitions falling to lower frequencies have been assigned to the ring puckering vibrations of both the low energy equatorial and high energy axial conformers. These data have been fit to an asymmetric potential function of the form:V (cm−1)=(1.76±0.05)103X+(4.88±0.28)104X2+(2.12 ±0.16)103 exp(−5.66±0.41)10X2 with a reduced mass function ofg44= 0.00386−0.00295X+0.03485X2+0.1228X3 +0.3459X4, whereX is the ring puckering coordinate. Utilizing this potential, the difference between the puckering angles for the two conformers was calculated to be 4° with the equatorial conformer having the larger value of 28°. This potential function is consistent with an energy difference between the equatorial and axial forms of 447 cm−1 (1.28 kcal/mol) and a barrier to ring inversion from the equatorial to the axial conformation of 713 cm−1 (2.04 kcal/mol). Experimental values for the enthalpy difference between the two conformers have been determined for both the liquid (400±30 c−1) and gas (413±43 cm−1) from investigations of the Raman spectra at variable temperatures. The conformational stability, enthalpy difference, structural parameters, and fundamental vibrational frequencies, which have been determined experimentally, are compared to those obtained from ab initio Hartree-Fock calculations employing the 3-21G, 6-31 G*, and 6-31 G** basis sets.