Torsional Barrier Research Articles

Spin-lattice relaxation study of the methyl proton dynamics in solid 9,10-dimethyltriptycene (DMT)

Proton spin-lattice relaxation studies are performed for powder samples of 9,10-dimethyltriptycene (DMT) and its isotopomer DMT- d 12 in which all the non-methyl protons in the molecule are replaced by deuterons. The relaxation data are interpreted in terms of the conventional relaxation theory based on the random jump model in which the Pauli correlations between the relevant spin and torsional states are discarded. The Arrhenius activation energies, obtained from the relaxation data, 25.3 and 24.8 kJ mol −1 for DMT and DMT- d 12, respectively, are very high as for the methyl groups. The validity of the jump model in the present case is considered from the perspective of Haupt theory in which the Pauli principle is explicitly invoked. To this purpose, the dynamic quantities entering the Haupt model are reinterpreted in the spirit of the damped quantum rotation (DQR) approach introduced recently for the purpose of NMR lineshape studies of hindered molecular rotators. Theoretical modelling of the relevant methyl group dynamics, based on the DQR theory, was performed. From these calculations it is inferred that direct assessments of the torsional barrier heights, based on the Arrhenius activation energies extracted from relaxation data, should be treated with caution.

Ether-like Si–Ge hydrides for applications in synthesis of nanostructured semiconductors and dielectrics

Hydrolysis reactions of silyl-germyl triflates are used to produce ether-like Si-Ge hydride compounds including H(3)SiOSiH(3) and the previously unknown O(SiH(2)GeH(3))(2). The structural, energetic and vibrational properties of the latter were investigated by experimental and quantum chemical simulation methods. A combined Raman, infrared and theoretical analysis indicated that the compound consists of an equal mixture of linear and gauche isomers in analogy to the butane-like H(3)GeSiH(2)SiH(2)GeH(3) with an exceedingly small torsional barrier of approximately 0.2 kcal mol(-1). This is also corroborated by thermochemistry simulations which indicate that the energy difference between the isomers is less than 1 kcal mol(-1). Proof-of-principle depositions of O(SiH(2)GeH(3))(2) at 500 degrees C on Si(100) yielded nearly stoichiometric Si(2)Ge(2)O materials, closely reflecting the composition of the molecular core. A complete characterization of the film by RBS, XTEM, Raman and IR ellipsometry revealed the presence of Si(0.30)Ge(0.70) quantum dots embedded within an amorphous matrix of Si-Ge-O suboxide, as required for the fabrication of high performance nonvolatile memory devices. The use of readily available starting materials coupled with facile purification and high yields also makes the above molecular approach an attractive synthesis route to H(3)SiOSiH(3) with industrial applications in the formation of Si-O-N high-k gate materials in high-mobility SiGe based transistors.

Structure and internal rotation in the S0 and S1 states of o-toluidine studied by high resolution UV spectroscopy

The rotationally resolved spectrum of the o-toluidine S(1)<-- S(0) origin was measured using laser induced fluorescence spectroscopy. From the resulting spectrum torsional barriers to internal rotation of the methyl group were derived, which resulted in S(0) state values of V(3) = 699 +/- 11 cm(-1) and V(6) = 64 +/- 11 cm(-1) with an effective rotational constant F of 5.38 +/- 0.04 cm(-1) while for the S(1) state the result was V(3) = 40.87 +/- 0.14 cm(-1) and V(6) = -16.8 +/- 0.8 cm(-1) with F = 5.086 +/- 0.001 cm(-1). The S(1) state structure was found to be severely distorted, with the methyl group making a 7.7 degrees degree angle with the benzene ring. Evidence of an excited state precessional motion of the methyl group was found.

A quantum mechanical study on polymer flexibility: Extended model from monomer to tetramer of 2- and 4-bromostyrenes

DFT Quantum chemical descriptors as dipole and quadrupole momenta as well as molecular volume have been calculated for the monomer, dimer and tetramer of 2- and 4-bromostyrene in order to study the effect of small changes in their molecular structure on the glass transition temperature of the corresponding polymers. In addition, correlation with the chain stiffness has been pursued by analysing torsional barriers both for monomer and oligomers of the title compounds obtained at ab initio and DFT levels of theory. First of all, the performance of the theoretical methods has been checked by optimizing the molecular geometry of the monomer and comparing with experimental data. The internal rotation barrier of the vinyl moiety has been also calculated and a conformational analysis has been afforded in detail through different energy factorization schemes, i.e., the total kinetic and potential scheme and that provided by the NBO theory. In addition, the topological analysis of the electron density provided by the Atom-in-Molecules, AIM, theory has allowed us to rationalize the stable conformers on the basis of bond critical points and ring critical points featuring intramolecular contacts. The most stable conformations of the dimer and tetramer have been determined as models for their respective polymers. The values of the central dihedral angles for the most populated dimer and tetramer of both 2- bromo and 4-bromostyrene indicate that the position of the halogen hardly affects the backbone chain arrangement. Predictive performance of the internal rotation barriers as well as the molecular volume and dipole and quadrupole momenta have been assessed through comparison with the experimental Tg value for the title compounds. As a conclusion, although the internal rotation barrier does not provide conclusive results for the higher chain flexibility in the case of poly-2-bromostyrene, the dipole and quadrupole momenta, as well as the molecular volume calculated for the monomer, dimer and tetramer follow the same trend as the measured Tg for poly-2-bromostyrene and poly-4-bromostyrene demonstrating this way the capability of those descriptors for predicting small variations in glass transition temperatures.

A Quantitative Single-Molecule Study of Thioether Molecular Rotors

This paper describes a fundamental, single-molecule study of the motion of a set of thioethers supported on Au surfaces. Thioethers constitute a simple, robust system with which molecular rotation can be actuated both thermally and mechanically. Low-temperature scanning tunneling microscopy allowed the measurement of the rotation of individual molecules as a function of temperature and the quantification of both the energetic barrier and pre-exponential factor of the motion. The results suggest that movement of the second CH(2) group from the S atom over the surface is responsible for the barrier. Through a series of single-molecule manipulation experiments, we have switched the rotation on and off reversibly by moving the molecules toward or away from one another. Arrhenius plots for individual dibutyl sulfide molecules reveal that the torsional barrier to rotation is approximately 1.2 kJ/mol, in good agreement with the temperature at which the molecule's appearance changes from a linear to a hexagonal shape in the STM images. The thioether backbone constitutes an excellent test bed for studying the details of molecular rotation at the single-molecule level.

Molecular Engineering of Torsional Potentials in Fluorogenic Dyes via Electronic Substituent Effects

Fluorogenic dyes such as thiazole orange (TO) and malachite green have been used in live cellular imaging due to their low quantum yield in solution but large fluorescence enhancements when bound to cellular nucleic acids or to a specific surface-expressed protein partner. Better understanding of the structure-property relationships that establish this fluorogenic behavior could benefit the design of improved dyes. In TO the fluorogenic properties are related to twisting of the dye, following electronic excitation in solution, from an emissive planar structure to a nonemissive twisted structure. Herein we develop a computational approach to identify electron acceptor/donor substitution patterns that impart desirable properties to the dye, such as inducing spectral shifts while maintaining an excited-state torsional surface that will lead to fluorogenic behavior. Additivity of substituent effects, on properties such as spectral shifts and excited-state torsional barriers, is tested and found to be sufficiently accurate that it can be used to identify promising dye candidates. Although additivity suggests an underlying linearity in the substituent effects, additional simplifications stemming from linearity could not be identified. The approach is tested on TO, considering seven different substituents at seven substitution positions, to identify fluorogenic dyes that will span a range of wavelengths. Additivity allows quantum chemical calculations on singly substituted molecules (49 molecules) to be used to make estimates for all substitution patterns (nearly 10(6) molecules).

Torsional barrier and equilibrium structure of ethyl cyanide

The quadratic, cubic and semi-diagonal quartic force field of ethyl cyanide has been calculated at the B3LYP level of theory employing a basis set of triple-ζ quality. A semi-experimental equilibrium structure has been derived from experimental ground state rotational constants and rovibrational interaction parameters calculated from the ab initio force field. This structure is in excellent agreement with the ab initio structure calculated at the CCSD(T) level of theory using a basis set of quadruple-ζ quality and a core correlation correction. The empirical structures are also determined and their accuracy is discussed. The potential barrier V 3 hindering internal rotation of the methyl group has been calculated from 23 rotational transitions of CH 3CH 2C 15N which were found split into doublets, giving V 3 = 3074(27) cal mol −1.

Torsional Barriers and Equilibrium Angle of Biphenyl: Reconciling Theory with Experiment.

The barriers of internal rotation of the two phenyl groups in biphenyl are investigated using a combination of coupled cluster and density functional theory. The experimental barriers are for the first time accurately reproduced; our best estimates of the barriers are 8.0 and 8.3 kJ/mol around the planar and perpendicular conformations, respectively. The use of flexible basis sets of at least augmented quadruple-ζ quality is shown to be a crucial prerequisite. Further, to finally reconcile theory with experiment, extrapolations of both the basis set toward the basis set limit and electron correlation toward the full configuration-interaction limit are necessary. The minimum of the torsional angle is significantly increased by free energy corrections, which are needed to reach an agreement with experiment. The density functional B3LYP approach is found to perform well compared with the highest level ab initio results.

Atomistic Simulation of Poly(dimethylsiloxane) Permeability Properties to Gases and n-Alkanes

A recently developed atomistic force field for poly(dimethylsiloxane) (PDMS) is used to calculate the permeability properties of the polymer to light gases and to n-alkanes. The torsional potential barrier is re-estimated compared to the original force field. Chain dynamics and chain sizes are affected by this change while thermodynamic properties of the melt and of PDMS mixtures remain unaffected. The diffusion coefficients of penetrants to PDMS are calculated at different temperatures based on long molecular dynamics simulations. Subsequently, the permeability coefficients are estimated and ideal mixture selectivities are evaluated for binary hydrocarbon mixtures. In all cases, agreement with literature experimental data ranges from good to excellent. Calculations for mixed penetrant permeation reveal that, in the presence of a second penetrant species, solubility and diffusion coefficients increase, in agreement with recent experimental evidence.

Conformational Analysis of 1-Butyl-3-methylimidazolium by CCSD(T) Level Ab Initio Calculations: Effects of Neighboring Anions

Conformational energies for the butyl group of 1-butyl-3-methylimidazolium (bmim) were calculated by high-level ab initio methods. Estimated relative energies for the TT, GT and G'T rotamers of an isolated bmim cation at the CCSD(T)/cc-pVTZ level are 0.0 -0.02 and -0.50 kcal/mol, respectively. The close contact of a Cl anion to theC(2)-H of imidazolium considerably increases the relative stability of the GT rotamer. Estimated relative energies for the three rotamers of the [bmim]Cl complex, in which the Cl anion exists close to the C(2)-H, are 0.0, -1.61 and -0.25 kcal/mol, respectively. The GT rotamer is favored by the strong attractive electrostatic interaction between the bmim cation and Cl anion. The C(2)-H group in the GT rotamer has a larger positive charge compared with those in the TT and G'T rotamers. The contact of a Br anion to the C(2)-H also stabilizes the GT rotamer. The effects of the Cl anion close to the C(4)-Hand C(5)-Hare small. The anion effects suggest that the GT rotamer is the most stable in ionic liquids. The positive charge on imidazolium ring does not largely change the conformational energies. Estimated relative energies for the three rotamers of N-butylimidazole (0.0, -0.29 and -0.75 kcal/mol, respectively) are not largely different from those for isolated bmim. Calculated MP2/cc-pVTZ level torsional potential for the C im-N im-C-C bond has a minimum when the torsional angle is close to 90 degrees. Coplanar conformation is not a stable structure. Calculated torsional barrier height between the two nonplanar minima is less than 1 kcal/mol.

Potential energy scans and vibrational assignments of cyclopropanecarboxylic acid and cyclopropanecarboxamide

The structural stability and internal rotations in cyclopropanecarboxylic acid and cyclopropanecarboxamide were investigated by the DFT-B3LYP and the ab initio MP2 calculations using 6-311G** and 6-311+G** basis sets. The computations were extended to the MP4//MP2/6-311G** and CCSD(T)//MP2/6-311G** single-point calculations. From the calculations the molecules were predicted to exist predominantly in the cis (C O group eclipses the cyclopropane ring) with a cis– trans barrier of about 4–6 kcal/mol. The OCOH torsional barrier in the acid was estimated to be about 12–13 kcal/mol while the corresponding OCNH torsional barrier in the amide was calculated to be about 20 kcal/mol. The equilibrium constant k for the cis ⇔ trans interconversion in cyclopropanecarboxylic acid was calculated to be 0.1729 at 298.15 K that corresponds to an equilibrium mixture of about 85% cis and 15% trans. The vibrational frequencies were computed at the DFT-B3LYP level. Normal coordinate calculations were carried out and potential energy distributions were calculated for the low energy cis conformer of the molecules. Complete vibrational assignments were made on the basis of normal coordinate calculations and comparison with experimental data of the molecules.

Origin of threefold methyl torsional potential in methylindoles

In this article, we present a systematic study on mono-methylindoles to investigate the electronic origin of the threefold symmetric component (V3) of the methyl torsional potential barrier in the ground electronic state (S0). The structures and the torsional potential parameters of these molecules were evaluated from ab initio calculation using Hartree-Fock (HF), second order Mollar Plesset perturbation (MP2) and B3LYP density functional level of theories and Gaussian type basis set 6-31G(d, p). Natural bond orbital (NBO) analysis of these molecules were carried out using B3LYP/6-31G(d, p) level of calculation to understand the formation of the threefold V3 term arising from the changes of various non-covalent interactions during methyl rotation. Our analysis reveals that the contributions from π orbitals play a dominant role in the barrier height determination in this class of molecules. The threefold term in the barrier arises purely from the interactions non-local to the methyl group in case when the methyl group has two single bonds vicinal to it. On the other hand, it is the local interaction that determines the potential energy barrier when the methyl group has one single bond and one double bond vicinal to it. However, in all these cases, the magnitude of the energy barrier depends on the resonance structure formation in the benzene ring frame upon rotation of the methyl group and, therefore, the energetics of the barrier cannot be understood without considering the molecular flexing during methyl rotation.

Spectroscopy and Photophysics of 1,4-Bis(phenylethynyl)benzene: Effects of Ring Torsion and Dark πσ* State

A combination of supersonic-jet laser spectroscopy and quantum chemistry calculation was applied to 1,4-bis(phenylethynyl)benzene, BPEB, to study the role of the dark pisigma* state on electronic relaxation and the effect of ring torsion on electronic spectra. The result provides evidence for fluorescence break-off in supersonic jet at high S1(pi pi*) <-- S0 excitation energies, which can be attributed to the pi pi*-pi sigma* intersection. The threshold energy for the fluorescence break-off is much larger in BPEB (approximately 4000 cm(-1)) than in diphenylacetylene (approximately 500 cm(-1)). The high-energy barrier in BPEB accounts for the very large fluorescence quantum yield of the compound (in solution) relative to diphenylacetylene. The comparison between the experimentally derived torsional barrier and frequency with those from the computation shows overall good agreement and demonstrates that the low-energy torsional motion involves the twisting of the end ring in BPEB. The torsional barrier is almost an order of magnitude greater in the pi pi* excited state than in the ground state. The finding that the twisting of the end ring in BPEB is relatively free in the ground state, but strongly hindered in the excited state, provides rationale for the well-known temperature dependence of the spectral shape of absorption and the lack of mirror symmetry relationship between the absorption and fluorescence at elevated temperatures.

The molecular structure of a curl-shaped retinal isomer

Computational studies of retinal protonated Schiff base (PSB) isomers show that a twisted curl-shaped conformation of the retinyl chain is a new low-lying minimum on the ground-state potential energy surface. The curl-shaped isomer has a twisted structure in the vicinity of the C(11)=C(12) double bond where the 11-cis retinal PSB isomerizes in the rhodopsin photoreaction. The twisted configuration is a trapped structure between the 11-cis and all-trans isomers. Rotation around the C(10)-C(11) single bond towards the 11-cis structure is prevented by steric interactions of the two methyl groups on the retinyl chain and by the torsion barrier of the C(10)-C(11) bond in the other direction. Calculations of spectroscopic properties of the 11-cis, all-trans, and curl-shaped isomers provide useful data for future identification of the new retinal PSB isomer. Circular dichroism (CD) spectroscopy might be used to distinguish between the retinal PSB isomers. The potential energy surface for the orientation of the beta-ionone ring of the 11-cis retinal PSB reveals three minima depending on the torsion angle of the beta-ionone ring. Two of the minima correspond to 6-s-cis configurations and one has the beta-ionone ring in 6-s-trans position. The calculated CD spectra for the two 6-s-cis configurations differ significantly indicating that the sign of the beta-ionone ring torsion angle could be determined using CD spectroscopy. Calculations of the CD spectra suggest that a flip of the beta-ionone ring might occur during the first 1 ps of the photoreaction. Rhodopsin has a negative torsion angle for the beta-ionone ring, whereas the change in the sign of the first peak in the experimental CD spectrum for bathorhodopsin could suggest that it has a positive torsion angle for the beta-ionone ring. Calculated nuclear magnetic resonance (NMR) shielding constants and infrared (IR) spectra are also reported for the retinal PSB isomers.

Acyl chain conformations in phospholipid bilayers: a comparative study of docosahexaenoic acid and saturated fatty acids

A variety of experimental methods indicate unique biophysical properties of membranes containing the highly polyunsaturated ω-3 fatty acid, docosahexaenoic acid (DHA). In the following we review the atomically detailed picture of DHA acyl chains structure and dynamics that has emerged from computational studies of this system in our lab. A comprehensive approach, beginning with ab-initio quantum chemical studies of model compounds representing segments of DHA and ending with large scale classical molecular dynamics simulations of DHA-containing bilayers, is described with particular attention paid to contrasting the properties of DHA with those of saturated fatty acids. Connection with experiment is made primarily through comparison with Nuclear Magnetic Resonance (NMR) studies, particularly those that probe details of the chain structure and dynamics. Our computational results suggest that low torsional energy barriers, comparable to kT at physiological conditions, for the rotatable bonds in the DHA chain are the key to the differences observed between polyunsaturated and saturated acyl chains.

Microwave spectroscopy and structures of two conformers of 6-methyl-3-heptyne and three of 2-methylpentane

From its microwave rotational spectrum, 6-methyl-3-heptyne (MHept, ethyl isobutyl acetylene) has been characterized in two conformations of C s and C 1 symmetry with the opposing alkyl groups arranged syn-eclipsed or nearly so about the C C axis. The dominant interaction determining the dihedral angle about the C C axis is the small dispersion attraction between the separated ethyl and isobutyl groups. The three lowest energy conformers of 2-methylpentane (MPane), MHept without C C, have been characterized from their microwave spectra. MPane has more conformations than MHept because the C 3 C 4 bond in MPane has a substantial ethane-like barrier supporting gauche and anti conformations while MHept’s tiny C 2 (C 3 C 4) C 5 torsional barrier has only a single minimum. Ab initio calculations of both compounds at the MP2/6-311+G(d,p) level agree with the experimental results.

On the Nanoaggregated Emitter of All sp2-Hybridized Bistriphenylenyl in the Device Layout of Organic Light-Emitting Diodes

Atomic force microscopy (AFM) is employed to unveil the film morphology of 2,2‘-bistriphenylenyl (BTP), an all sp2-hybridized polyaromatic blue emitter derived from two triphenylenes (TP) in the OLED layout (organic light-emitting diode). It is generally believed that molecules with such planar cores require derivatization or steric hindrance to hamper intermolecular π−π stacking and reduce self-absorption. X-ray crystallographic results of BTP crystals show that the two triphenylenyls are coplanar, indicative of a likely tendency toward self-quenching. Surprisingly, AFM reveals grainy nanoaggregates of the BTP layer in the device, yet BTP films exhibit excellent performance for OLED applications. To correlate luminescent spectra with the molecular structure, BTP films of crystalline, nanoaggregated, and amorphous features are prepared and subjected to spectroscopic studies. These AFM and spectroscopic results in conjunction with simulation results of a small torsion barrier to rotate the TP rings suggest...

Towards the complete analysis of the rotational spectrum of (CH 3) 3SnCl

The rotational spectrum of the symmetric top trimethyl tin chloride (CH 3) 3SnCl has been studied using a pulsed molecular beam Fourier transform microwave spectrometer in the frequency range from 3 to 24 GHz. The spectrum is exceedingly complicated by the internal rotation motions of the three equivalent methyl tops, the high number of Sn- and Cl-isotopes and the quadrupole hyperfine structure of the chlorine nucleus. In this paper, we present the microwave spectrum, ab initio calculations, permutation inversion (PI) group-theoretical considerations, Stark-effect measurements and finally the K = 0 assignments and fits of the different torsion–rotation species. Based on the Stark-effect measurements, the dipole moment is μ = 3.4980(30) D. Due to Δ K = ± 1 -mixing effects we observe linear Stark-effect behavior and additional quadrupole splitting for some K = 0 torsion–rotation transitions in (CH 3) 3SnCl, which can be group-theoretically explained. The symmetric rotor fit of A 1 and A 2 torsion-rotation states leads to an effective B-constant of 1680.040124(92) MHz for the main isotopologue (CH 3) 3 120Sn 35Cl. A global fit of 182 K = 0 torsion–rotation transitions yields a V 3 torsional barrier of 1.774(6) kJ.

Water trimer torsional spectrum from accurate ab initio and semiempirical potentials

The torsional levels of (H2O)3 and (D2O)3 were calculated in a restricted dimensionality (three-dimensional) model with several recently proposed water potentials. Comparison with the experimental data provides a critical test, not only of the pair interactions that have already been probed on the water dimer spectra, but also of the nonadditive three-body contributions to the potential. The purely ab initio CC-pol and HBB potentials that were previously shown to yield very accurate water dimer levels, also reproduce the trimer levels well when supplemented with an appropriate three-body interaction potential. The TTM2.1 potential gives considerably less good agreement with experiment. Also the semiempirical VRT(ASP-W)III potential, fitted to the water dimer vibration-rotation-tunneling levels, gives substantial disagreement with the measured water trimer levels, which shows that the latter probe the potential for geometries other than those probed by the dimer spectrum. Although the three-body nonadditive interactions significantly increase the stability of the water trimer, their effect on the torsional energy barriers and vibration-tunneling frequencies is less significant.

An optimized force field for crystalline phases of resorcinol

The two known crystalline phases of resorcinol and their phase transitions are of considerable interest. The crystals exhibit pyro- and piezo-electricity and, remarkably, the higher temperature β phase is the denser phase. Furthermore, crystals of the α phase, by virtue of having a polar axis, have played a crucial role in investigating fundamental issues of crystal growth. We report an optimized force field for the molecular simulation of crystalline phases of resorcinol. The hydroxyl groups of the resorcinol molecule have a torsional degree of freedom and the molecule adopts a different conformation in each of the two phases of resorcinol. The torsional barrier, therefore, was considered to be critical and has been characterized using ab initio methods. Although the atomic partial charges showed some dependence on the molecular conformation, a single set of partial charges was found to be sufficient in describing the electrostatic potential for all conformations. The parameters for the van der Waals interactions were optimized using sensitivity analysis. The proposed force field reproduces not only the static structures but also the stability of the crystalline phases in extended molecular dynamics simulations.