Conformer Interconversion Processes Research Articles

Twisted and Bent Out of Shape: Symmetry and Chirality Analysis of Substituted Ferrocenes

Ferrocene symmetry is commonly described as either eclipsed (D5h) or staggered (D5d), but this symmetry does not hold when substitution is involved. Here we examine and quantify the effect of substitution on the geometry of the core structure of ferrocene, and provide means to distinguish between its various distortion paths. Continuous symmetry analysis of the core structure of 7418 substituted ferrocenes extracted from the Cambridge Crystallographic Database was used to explore its twisting and bending distortion paths, as well as asymmetric bond stretch that deforms the symmetry of its cyclopentadienyl rings. Gas-phase density functional theory calculations provided a theoretical background to describe these distortion paths and define symmetry profiles for conformer interconversion processes and the interplay between them. Our results show that the distortion of ferrocene can often be substantial. Furthermore, its geometry is highly flexible, and almost always chiral to some degree. Handedness in term...

Isomerization kinetics of AT hook decapeptide solution structures.

The mammalian high mobility group protein HMGA2 contains three DNA binding motifs associated with many physiological functions including oncogenesis, obesity, stem cell youth, human height, and human intelligence. In the present paper, trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) has been utilized to study the conformational dynamics of the third DNA binding motif using the "AT hook" decapeptide unit (Lys(1)-Arg(2)-Prol(3)-Arg(4)-Gly(5)-Arg(6)-Prol(7)-Arg(8)-Lys(9)-Trp(10), ATHP) as a function of the solvent state. Solvent state distributions were preserved during electrospray ion formation, and multiple IMS bands were identified for the [M + 2H](2+) and for the [M + 3H](3+) charge states. Conformational isomer interconversion rates were measured as a function of the trapping time for the [M + 2H](2+) and [M + 3H](3+) charge states. Candidate structures were proposed for all IMS bands observed. Protonation site, proline residue conformation, and side chain orientations were identified as the main motifs governing the conformational interconversion processes. Conformational dynamics from the solvent state distribution to the gas-phase "de-solvated" state distribution demonstrated that ATHP is "structured", and relative abundances are associated with the relative stability between the proposed conformers. The most stable ATHP [M + 2H](2+) conformation at the "de-solvated" state corresponds to the AT hook motif observed in AT-rich DNA regions.

Single Protein Complexes Isomerization and Conformational Dynamics Using Trapped Ion Mobility Spectrometry: From MS to Seconds

In the present work, examples of protein and peptide complexes conformational dynamics, from the solvent state distribution to the gas-phase “de-solvated” state distribution, are characterized for traditionally considered “unstructured” complexes. Conformational motifs and isomerization/conformational dynamics are identified and isomerization kinetics in the ms to few seconds timescale are measured for single molecules using a trapped ion mobility spectrometer - mass spectrometer (TIMS-MS). Theoretical calculations are used to simulate the experimental “TIMS box” single molecule -neutral bath gas phase dynamics and candidate structures are proposed for each conformational state. It is found that, side chain and backbone structural changes are the main motifs governing the conformational inter-conversion processes in the ms-s time scale. Examples will be shown for the case of folded/unfolded protein complexes and DNA-binding proteins.View Large Image | View Hi-Res Image | Download PowerPoint Slide

Theoretical study of the conformational energy hypersurface of cyclotrisarcosyl

Abstract The multidimensional Conformational Potential Energy Hypersurface (PEHS) of cyclotrisarcosyl was comprehensively investigated at the DFT (B3LYP/6-31G(d), B3LYP/6-31G(d,p) and B3LYP/6-311++G(d,p)), levels of theory. The equilibrium structures, their relative stability, and the Transition State (TS) structures involved in the conformational interconversion pathways were analyzed. Aug-cc-pVTZ//B3LYP/6-311++G(d,p) and MP2/6-31G(d)//B3LYP/6-311++G(d,p) single point calculations predict a symmetric cis-cis-cis crown conformation as the energetically preferred form for this compound, which is in agreement with the experimental data. The conformational interconversion between the global minimum and the twist form requires 20.88 kcal mol-1 at the MP2/6-31G(d)//B3LYP/6-311++G(d,p) level of theory. Our results allow us to form a concise idea about the internal intricacies of the PEHSs of this cyclic tripeptide, describing the conformations as well as the conformational interconversion processes in this hypersurface. In addition, a comparative analysis between the conformational behaviors of cyclotrisarcosyl with that previously reported for cyclotriglycine was carried out

Multistep conformational interconversion mechanism of cyclododecane. A simple and fast analysis using potential energy curves

AbstractAn ab initio and Density Functional Theory (DFT) study of the conformational properties of cyclododecane was carried out. The energetically preferred equilibrium structures, their relative stability, and some of the transition state (TS) structures involved in the conformational interconversion pathways were analyzed from RHF/6‐31G(d), B3LYP/6‐31G(d,p) and B3LYP/6311++G(d,p) calculations. Aug‐cc‐pVDZ//B3LYP/6311++G(d,p) single point calculations predict that the multistep conformational interconversion mechanism requires 11.07 kcal/mol, which is in agreement with the available experimental data. These results allow us to form a concise idea about the internal intricacies of the preferred forms of cyclododecane, describing the conformations as well as the conformational interconversion processes in the conformational potential energy hypersurface. Our results indicated that performing an exhaustive analysis of the potential energy curves connecting the most representative conformations is a valid alternate tool to determine the principal conformational interconversion paths for cyclododecane. This methodology represents a satisfactory first approximation for the conformational analysis of medium‐ and large‐size flexible cyclic compounds. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012

Conformation and Self-Assembly of the Transmembrane Peptide Gramicidin A: Insights from ion Mobility Spectrometry and Molecular Dynamics

Gramicidin A which is composed of alternating L- and D-amino acids is a naturally occurring pentadecapeptide from Bacillus brevis known to form monovalent metal ion channels in lipid membranes. The active form is a noncovalently bound dimer. The conformation and self-assembly behavior of gramicidin A highly depends on the solution environment. In this presentation, we report the use of electrospray-ion mobility-mass spectrometry to study the conformation of alkali metals adducts of gramicidin A monomer, as well as the monomerization and conformer interconversion equilibrium of gramicidin A dimer as a function of the solvent. The conformation of gramicidin A monomer vary significantly upon binding different metal adducts. Enhanced sampling molecular dynamics simulations are performed on alkali metals adducts to provide thermodynamics information of different conformers and gain insights of the interaction of different metal ions with the monomer. The kinetics of the monomerization and conformer interconversion processes of dimer in various alcohol solutions (Ethanol, 1-Propanol and, Isobutanol) are monitored by using the ion mobility profile of the monomer and the dimer. The rate constants and the temperature dependence of the rate constants of the monomer compare well with literature values which were obtained by using fluorescence. Furthermore, we found that the water content in the alcohol solution greatly influences the self-assembly process significantly. The role of water in catalyzing the conformer interconversion is being investigated further. Ion mobility spectrometry (IMS) combined with molecular dynamics simulations is a merging technique for conformational analysis of gas-phase low-lying energy level structures of biomolecules. In this study, we will demonstrate that this gas phase technique can also be of utility in studying a solution phase structural dynamics problem.

Ab Initio and DFT Study of the Conformational Energy Hypersurface of Cyclic Gly-Gly-Gly

The multidimensional conformational potential energy hypersurface (PEHS) of cyclic Gly-Gly-Gly (1,4,7-triazonane-2,5,8-trione) was comprehensively investigated at the Hartree-Fock (RHF/6-31G(d)) level of theory. The equilibrium structures, their relative stability, and the transition state (TS) structures involved in the conformational interconversion pathways were analyzed. aug-cc-pVTZ//B3LYP/6-311++G** single point calculations predict a trans-cis-cis conformation as the energetically preferred form for this compound. However, all of the levels of theory employed here predicted that two forms, a trans-cis-cis and a cis-cis-cis (crown), of conformers contribute significantly to the equilibrium mixture at room temperature. The conformational interconversion between the global minimum and the symmetric cis-cis-cis crown form requires 12.49 kcal/mol at the RHF 6-31G(d) level of theory, whereas the conformational interconversion between the cis-cis-cis crown and cis-cis-cis boat form requires 18.70 kcal/mol. An exploratory topological analysis of the PEHS was also carried out. Our results allow us to form a concise idea about the internal intricacies of the PEHSs of these cyclic tripeptides, describing the conformations as well as the conformational interconversion processes in these hypersurfaces.

Collision-induced conformational changes in glycine

We present quantum dynamical calculations on the conformational changes of glycine in collisions with the He, Ne, and Ar rare-gas atoms. For two conformer interconversion processes (III-->I and IV-->I), we find that the probability of interconversion is dependent on several factors, including the energy of the collision, the angle at which the colliding atom approaches the glycine molecule, and the strength of the glycine-atom interaction. Furthermore, we show that attractive interactions between the colliding atom and the glycine molecule catalyze conformer interconversion at low collision energies. In previous infrared spectroscopy studies of glycine trapped in rare-gas matrices and helium clusters, conformer III has been consistently observed, but conformer IV has yet to be conclusively detected. Because of the calculated thermodynamic stability of conformer IV, its elusiveness has been attributed to the IV-->I conformer interconversion process. However, our calculations present little indication that IV-->I interconversion occurs more readily than III-->I interconversion. Although we cannot determine whether conformer IV interconverts during experimental Ne- and Ar-matrix depositions, our evidence suggests that the conformer should be present in helium droplets. Anharmonic vibrational frequency calculations illustrate that previous efforts to detect conformer IV may have been hindered by the overlap of its IR-absorption bands with those of other conformers. We propose that the redshifted symmetric -CH(2) stretch of conformer IV provides a means for its conclusive experimental detection.

A p-tert-butylcalix[6]arene bearing phosphinoyl pendant arms for the complexation and sensitisation of lanthanide ions

The new lower rim functionalised macrocycle 5,11,17,23,29,35-hexa-tert-butyl-37,38,39,40,41,42-hexakis(dimethylphosphinoylmethoxy)calix[6]arene (B6bL6) has been synthesised. Temperature dependent 1H and 31P NMR studies indicate a mixture of conformers with a time-averaged C6v symmetry at 405 K in dmso-d6; ΔG≠ values for conformational interconversion processes are equal to 68(1) and 75(2) kJ mol−1 and reveal a semi-flexible macrocycle with alternate in-out cone conformation, a fact confirmed by molecular mechanics and dynamics calculations. B6bL6 crystallises as a dimer where the two calixarenes are linked through hydrogen bonding and surrounded by water and toluene molecules in the lattice. UV-Vis spectrophotometric titration of B6bL6 with La(III) in acetonitrile yields stability constants logβ1 = 9.8 and logβ2 = 19.6 for the 1 ∶ 1 and 1 ∶ 2 (Ln ∶ B6bL6) species, respectively. The corresponding complexes with La, Eu, Gd and Tb have been isolated and characterised. Lifetime determinations of the Eu(III) and Tb(III) complexes in acetonitrile solution are consistent with no or little interaction of water molecules in the inner co-ordination sphere. The new ligand sensitises reasonably well the luminescence of the Tb(III) (Qabs = 4.8% , τf = 2.1 ms, 1 ∶ 1 complex) and Eu(III) (Qabs = 2.5%, τ = 2.0 ms, 1 ∶ 2 complex) ions.

NMR spin relaxation methods for characterization of disorder and folding in proteins

The flexibility and dynamics of proteins directly influence the processes of protein folding, recognition, and function. NMR spin relaxation methods are used to assess the dynamics and mobility of proteins, for fast ps and ns motions as well as slower μs and ms events. The degree of protein flexibility and disorder as well as the changes in protein flexibility can be assessed by NMR spin relaxation methods at individual residues within the protein. In addition to probing protein dynamics, the changes in the NMR-derived order parameters can be used to estimate the entropic contributions of order–disorder transitions. Furthermore, kinetic processes in the ms time regime may be directly investigated to extract the rates of conformational interconversion, ligand binding, and protein folding processes. We show how a variety of dynamical information can be obtained from NMR relaxation measurements. We present examples that illustrate the use of NMR spin relaxation analysis for investigation of folding and disorder in proteins. © 2001 by Elsevier Science Inc.

Vibrational levels connected with reaction coordinate in conformer interconversion processes: application of the phase integral method to torsional energy levels

A procedure for calculation of torsional vibrational energy levels for oscillators and rotors around single bonds by the phase integral method is described. The procedure is easy to use and very informative. As input, only the potential funcition governing the vibration required, while the numerical and graphical output of the computer code yield accurate energy levels for all states of the system as well as degeneracies associated with the torsional states. There are no restrictions for the form or symmetry of the potential function. The procedure, which is a valuable tool at modelling the mechanisms for IR-interconversion processes, is applied to study rotamerization of 1-fluoropropane and nitrous acid and torsional frequencies of three molecules with different symmetries known to interconvert due to IR excitation in cryogenic matrices. The results are compared with experimental data, where available, and with previous computational methods.

Infrared Induced Conformer Interconversion Processes in Low-Temperature Matrices

Molecules embedded in low-temperature matrices experience conformer interconversion processes due to IR- (or UV-)irradiation. This paper summarizes the known IR-induced conformational changes, of which the majority has been studied by using broad-band sources provided with filters. We focus at the thermal and IR-photochemical methods in obtaining information of conformational energetics of matrix isolated molecules, at the usefulness of ab initio calculations in assigning the spectra of conformers involved and in finding the reaction path on the ground state surface. The data obtained from a number of molecules is used to discuss possible mechanisms in both intramolecularly hydrogen-bonded and non-bonded molecules. Also possible indications of mode-selective phenomena in these processes are dealt with. In addition, common trends found for photorotamerization in different hosts are discussed.

IR-induced conformer interconversion processes of glycolaldehyde in low-temperature matrices, and ab initio calculations on the energetics and vibrational frequencies of the conformers

Both IR-induced and thermal conformer interconversion processes of glycolaldehyde (CHOCH 2OH) were studied in low-temperature Ar, Kr and Xe matrices. The observed photochemical reaction induced by broad-band IR irradiation is interpreted to proceed from the lowest-energy conformer Cc which prevails after deposition to conformer Tt. In Xe and Kr the photochemical steady state (ratio [Tt]/[Cc]) depends on the matrix temperature; two conformers, Tg and Tt, seem to be in thermal equilibrium, and at elevated temperatures species Tg is enriched, and then the reverse photoprocess Tg → Cc occurs more rapidly than the competing reverse process, Tt → Cc which prevails at 13 K. Because of the thermal equilibrium the routes of the forward and reverse photoprocesses are considered to be different. A thermal reverse process, Tt → Tg → Cc, is observed at temperatures above 30 K in Xe and Kr. The role of the torsional barrier heights in determining the rates of the photoprocesses is emphasized. To aid in the interpretation of the experimental results, ab initio calculations were carried out. Geometries and energies of all conformers of glycoaldehyde as well as the geometries of the most important saddle points were fully optimized at the HF/6-31G** level, and vibrational spectra were calculated on the HF/4-31G level; the latter conformed to the experimental conformer assignment.

Infrared-induced conformer interconversion processes for allylamine in argon matrices: Wavelength dependence on the kinetics

Infrared photoisomerization of allylamine trapped in solid argon is studied by irradiation either at specific wavelengths emitted by a CO 2 laser in coincidence with bands of the three conformers (S + G + , ST and CT) or in several mid- or near-IR domains using broad band filters. Upon irradiation with broad band filters the CT → ST process is mainly observed whatever the frequency domain, with only a slight intensity increase of the S + G + bands. Upon irradiation with CO 2 lines in coincidence with CT bands the conversion CT → ST is observed; the reverse process is evidenced by irradiation at ST frequencies. Irradiation at S + G + frequency shows no effect on the conformational equilibrium. Kinetic rate constants are measured and normalized to constant light power absorbed by the sample. They are compared with those calculated by the RRKM theory of first-order processes, assuming the same torsional barrier around the CC bond as in the gas phase. The good agreement between experimental and calculated values suggests the absence of vibrational selectivity in this photoisomerization process.

ChemInform Abstract: Thermal und IR‐Induced Conformer Interconversion Processes for 2‐Fluoroethylamine in Several Low‐Temperature Matrix Media und ab initio 4‐3lG, 4‐31G(N*), und 6‐31G** Calculations

Chemischer InformationsdienstVolume 16, Issue 28 Physical Organic Chemistry ChemInform Abstract: Thermal und IR-Induced Conformer Interconversion Processes for 2-Fluoroethylamine in Several Low-Temperature Matrix Media und ab initio 4-3lG, 4-31G(N*), und 6-31G** Calculations T. LOTTA, T. LOTTASearch for more papers by this authorJ. MURTO, J. MURTOSearch for more papers by this authorM. + RAESAENEN, M. + RAESAENENSearch for more papers by this authorA. ASPIALA, A. ASPIALASearch for more papers by this authorP. + SAERKKAE, P. + SAERKKAESearch for more papers by this author T. LOTTA, T. LOTTASearch for more papers by this authorJ. MURTO, J. MURTOSearch for more papers by this authorM. + RAESAENEN, M. + RAESAENENSearch for more papers by this authorA. ASPIALA, A. ASPIALASearch for more papers by this authorP. + SAERKKAE, P. + SAERKKAESearch for more papers by this author First published: July 16, 1985 https://doi.org/10.1002/chin.198528065Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat No abstract is available for this article. Volume16, Issue28July 16, 1985 RelatedInformation

Thermal and IR-induced conformer interconversion processes for 2-fluoroethylamine in several low-temperature matrix media and ab initio 4-31G, 4-31G(N*), and 6-31G** calculations

IR-induced conformer interconversion processes have been found to occur for 2-fluoroethylamine in solid Ar, Kr, Xe, and N2 matrices but not in solid CH4. Using information obtained from the photoprocesses as well as from thermal processes and ab initio calculations, it was possible to find out the conformers present, to evaluate the conformer energies and torsional barrier heights, and to unravel the occurring processes. The total IR process consists of two parallel first-order C–C rotations, Gg→Tg and Gt→Tt. The influence of the host molecules upon the rates and barrier heights, the efficiency of different spectral regions in initiating the process, and the thermal processes were studied. The latter occur as C–C rotations opposite to the photoprocesses and as conformational equilibria involving rotations around the C–N bond. Extensive ab initio calculations were carried out on the 4-31G, 4-31G(N*), and 6-31G** levels. Geometries of the conformers were fully optimized at these levels, and torsional potential energy barrier heights and vibrational frequencies [at the 4-31G(N*) level] were calculated; the latter confirmed the experimental conformer assignment. IR-induced conformer changes were observed also for 2-chloro- ethylamine in Ar. The mechanism of the photorotamerizations of alcohols and amines is discussed and the importance of C–C torsional barriers is emphasized. A linear relationship between the logarithm of the first-order rate constant and the ab initio 4-31G calculated barrier height of the C–C torsion has been found (including several alcohols, 2-fluoroethylamine, and two aldehydes).

Gas—phase high resolution NMR as a potential tool for conformational studies

Gas—phase high resolution NMR is a potentially useful new tool for the study of rotational isomerism. The methods of measurement are explained, with the care necessary for sample preparations. The main areas of application at present are a) dynamic NMR study of conformational interconversion processes and b) conformational analysis for populations and energies through coupling constants. For the latter, our recent results on 1,2-disubstituted propanes such as 1,2-dichloropropane, 1,2-di(methoxy- d 3)propane and 1-methoxy-2-propanol are discussed.

Thermal and IR-induced conformer interconversion processes for 2-chloroallyl alcohol in Low-temperature matrices: Wavelength-dependent conformer steady states

2-chloroallyl alcohol has been studied in low-temperature Ar, Kr, Xe, N 2 and CH 4 matrices. An IR-induced process was found in all media except CH 4 and resulted in a steady state dependent on the Wavelength of the irradiation. At elevated temperatures thermal conformer interconversions occurred. The energetics of the processes are discussed and their potential barriers determined. No mode selectivity was found.

Thermal and infrared-induced conformer interconversion processes for 2-fluoroethylamine in solid Xe

Four conformers, Gg, Gt, Tg and Tt, of 2-fluoroethylamine were found to be present in Xe matrices at temperatures between 15 and 65 K. Two parallel CC rotations, Gg → Tg and Gt → Tt, were induced by infrared irradiation. At temperatures above 35 K reverse thermal processes occurred. The species Gg and Gt are at thermal equilibrium at temperatures above ≈33 K and their energy difference is ≈400 J mol −1.

Ab initio calculations on ethanol and 2-substituted fluorine and chlorine containing mono-, di- and tri-haloethanols, with reference to conformer interconversions at low temperatures

All conformers of ethanol and of several 2-substituted mono-,di- and trihalogenated (halogen = F and/or Cl) ethanols have been optimized, mostly at the 4–31G level. Semirigid torsional energy curves have been constructed for these compounds. For 2-fluoroethanol, calculations were carried out also using polarization functions, as well as on the MP and CID levels. The results are discussed with special reference to conformer interconversion processes in low-temperature matrices, and it is concluded that ab initio calculations help essentially in interpreting the experimental results. It is concluded that 4–31G is the most suitable level for calculating the torsional potential energy barriers for such processes (the minimal basis STO-3G giving much too high CO barriers and too low CC barriers). The CO barriers seem to be quite low for many conformational processes (or even non-existent); thus the only “stable” conformers at the low temperatures in question (10–30 K) seem to be Gg′ and Tt for monohaloethanols, Gg and Tg for 2,2-difluoroethanol and g for 2,2,2-trihaloethanols. The CC barrier between the Gg and Tg conformers of 2,2-difluoroethanol is quite high. The trans-angle rule proposed earlier is found to be independent of the basis set used.