The keto→enol photoisomerization of N‐salicilydenemethylfurylamine: Nonadiabatic ab initio dynamics simulation

The photoinduced isomerization of cis‐keto and trans‐keto isomers in N‐salicilydenemethylfurylamine has been studied using the surface‐hopping approach at the CASSCF level of theory. After the cis‐keto or trans‐keto isomer is excited to S₁ state, the molecule initially moves to a excited‐state local minimum. The torsional motion around relative bonds in the chain drives the molecule to approach a keto‐form conical intersection and then nonadiabatic transition occurs. According to our full‐dimensional dynamics simulations, the trans‐keto and enol photoproducts are responsible for the photochromic effect of cis‐keto isomer excited to S₁ state, while no enol isomer was obtained in the photoisomerization of trans keto on excitation. The cis keto to enol and cis keto to trans keto isomerizations are reversible photochemical reactions. It is confirmed that this aromatic Schiff base is a potential molecular switch. Furthermore, the torsion of C N bond occurs in the radiationless decay of trans‐keto isomer, while it is completely suppressed by an intramolecular hydrogen bonding interaction in the dynamics of cis‐keto form. Moreover, the excited‐state lifetime of cis keto is longer than that of trans‐keto form due to the O···H N hydrogen bond.     

Rotational isomeric-state approximation for the unperturbed dimensions of a POLA polyester

Rotational isomeric-state theory has been applied to investigate chain configurations of a polyester prepared from 4′,5-(1,1,3-trimethyl-3-phenylindan) dicarboxylic acid and 2,2-bis(4′-hydroxyphenyl) propane (POLA polyester). Independent conformations for each repeat monomer unit of the chain have been assumed in the calculations of the unperturbed dimensions. Rotations about the oxygen-phenylene-carbon (O? ?? C) bonds are considered to be free with twofold symmetric potentials. The trans and cis conformations of the carbonyl-phenylene-carbon (O?C? ?? C) and the indan-carbonyl residues are assumed to have equal probability. Two rotational states, trans and cis, are assigned to the ester C? O bonds. Calculation of the reduced unperturbed dimensions (〈r₀²〉/M)_∞ with conformations thus assigned for the bonds in the repeat unit, and comparison with experiment (0.72 ± 0.02 Ų/g) indicate that the conformation in the ester C? O bonds is predominantly trans. An equation for the conformational potential as a function of rotational angle about the ester C? O bond has been formulated using data on potential barriers for low molecular weight compounds. This equation, yielding a potential difference between the cis the trans isomers of 2.5–3.0 kcal/mole, is in good agreement with the prediction made from the calculation of the unperturbed dimensions where a cis/trans ratio of 0.01 for the ester C? O bonds was obtained.     

The Shape of the Simplest Non-proteinogenic Amino Acid α-Aminoisobutyric Acid (Aib)

The simplest non-proteinogenic amino acid α-aminoisobutyric acid (Aib), an analogue of glycine and alanine, has been vaporized by laser ablation and probed by high-resolution Fourier transform microwave spectroscopic techniques. Comparison of the experimental rotational and ¹⁴N nuclear quadrupole constants with that predicted ab initio has allowed the identification of three conformers of Aib exhibiting three types of hydrogen-bond interactions I (NH⋅⋅⋅O=C, cis-COOH), II (OH⋅⋅⋅N, trans-COOH), and III (N−H⋅⋅⋅O−H, cis-COOH) within the amino acid backbone. The observation of conformer III, not detected previously for related proteinogenic amino acids with a nonpolar side chain in a supersonic expansion, indicates that the presence of the methyl groups should restrict the conformational relaxation from conformer Aib-III to Aib-I. For conformer Aib-II, the rotational spectra of the ¹³C isotopomers reveal a tunneling motion arising from the two equivalent methyl groups in the molecule. The observation of a single spectrum at the midpoint between those predicted for the two ¹³C of the methyl groups has been explained by considering a double-minimum potential function with a low-energy interconversion barrier for a large amplitude internal motion. This singular fact has been corroborated by the anomalous centrifugal distortion effects determined in conformer Aib-II.     

Effect of free volume fluctuations on polymer relaxation in the glassy state. II. Calculated results

The relaxation following a change in temperature of amorphous polymers near the glass transition has been calculated. The calculation uses a chain model consisting of cis and trans backbone rotational states. The relaxation is assumed to proceed by localized conformational changes whose rates are controlled by the fractional free volume in small enough regions of the polymer that thermal fluctuations need to be considered. The relaxation is treated as a stochastic process, and an approximate solution is obtained for a finite set of relaxation environments. Using what is believed to be the most plausible set of parameters for polystyrene, relaxation curves are computed for the internal energy that are very similar to the curves obtained by Kovacs and others for the volumetric relaxation of poly(vinyl acetate) and polystyrene.     

Relaxation–structure relationship in bulk and plasticized polyamide 11

A series of blends of high molecular weight polyamide 11 (PA11) and three different polar molecules [i.e., N-butyl benzene sulfonamide (BBSA), δ-valerolactam, and ω-laurolactam] have been studied by differential scanning calorimetry (DSC), Fourier transform infrared microscopy (FTIR), differential mechanical thermal analysis (DMTA), and wide- and small-angle X-ray scattering (WAXS and SAXS) experiments. FTIR analysis shows that the concentration of free NH groups in bulk or plasticized PA11 is lower than 15% up to 260°C and less than 1% at room temperature. DMTA data show a β relaxation for dry PA11 but not for dry PA6 and PA12. On the other hand, when ω-laurolactam, which allows trans conformation of amide groups, is added to PA11 the intensity of the α relaxation increases and a strong antiplasticizing effect is observed. This effect is associated with a decrease of the PA11 free volume by increasing the chains packing. On the contrary, when δ-valerolactam, which allows cis amide groups conformations, and BBSA are blended with PA11, the α relaxation temperature and β peak intensity decrease as a function of added molecules concentration. This is associated with a plasticizing effect. It is suggested to attribute the bulk β relaxation to segmental motions involving H-bonded CONH in a cis conformation in amorphous domains of the PA11. In turn, the α relaxation is related to segmental motions involving CONH groups in a trans conformation. Therefore, antiplasticizing and plasticizing effects depend upon the ability of the additive molecule to change the initial conformational structure of polyamide (i.e., the ratio cis over trans H-bonding of the amide group conformations). Overall, a point of interest to note seems to be the difference between the trans and cis conformations of the amide groups in term of bonding with each other in a PA11 chain and additives such as BBSA. In addition, the limited influence of BBSA on the crystalline microstructure of PA11 is explained by the fact that 85% of the PA11 amorphous phase is intraspherulitic and that a great part of the plasticizer is located in these domains. © 1996 John Wiley & Sons, Inc.     

The role of the torsional potential in relaxation dynamics: a molecular dynamics study of polyethylene

The role of the torsional potential in bulk polymer chain dynamics is investigated via molecular dynamics simulation using polyethylene as a model system. A number of three-fold barrier values, both greater and less than the standard one, were invoked. The one-fold potential that determines the gauche vs trans energy difference was also varied. For each of the selected torsional potentials, the MD volumetric glass transition temperature, T_g, was located. It was found that T_g is quite sensitive to the three-fold barrier magnitude, moving from below 100 K to nearly 400 K as the barrier goes from zero to twice the standard value. However T_g was found to be quite insensitive to the gauche trans energy difference. Details of the conformational dynamics were studied for the case of a zero torsional potential. This included the rate and location of conformational transitions, the decay of the torsional angle autocorrelation function (ACF) and the cooperativity of conformational transitions, all as a function of temperature. The temperature dependence of the conformational transition rate remains Arrhenius at all temperatures. The relaxation time characterizing the torsional angle ACF decay exhibits WLF temperature behavior. The conformational transitions are randomly distributed over the bonds at high temperature, but near T_g they become spatially heterogeneous and localized. The transitions show next-neighbor correlation as well as self-correlated forward-backward transitions. All of these features are similar to those found in previous simulations under the standard torsional potential.     

Conformational study of fosinopril sodium in solution using NMR and molecular modeling

Two conformers of fosinopril sodium in methanol were unambiguously established using 2D NMR methods and variable‐temperature NMR experiments. Differences in their conformational structure were shown to be related to the rotational energy barrier about the amide bond and hydrophobic interaction. The relationship between the 3D structure and activity is discussed. It is suggested that the trans‐conformer may be more biologically active owing to its stacking structure and strong hydrophobic interaction and the cis‐conformer could be more easily hydrolyzed because of its extended structure. Copyright © 2003 John Wiley & Sons, Ltd.     

Conformational analysis of N-arachidonylethanolamide (anandamide) using nuclear magnetic resonance and theoretical calculations

The conformational properties of cis-5,8,11,14-eicosatetraenoylethanolamide (anandamide) were analysed by the combined use of NMR experimental results plus molecular simulations. The structure of anandamide was found to be a predominantly linear with a seven-atom ring of the ethanolamine group having a hydrogen bond which stabilizes the molecule. The vinylic group present has a cis conformation in solution. The terminal chain has a linear conformation and undergoes isotropic fast motion typical of this structure. Copyright © 2001 John Wiley & Sons, Ltd.     

Study of <Emphasis Type="Italic">cis</Emphasis>–<Emphasis Type="Italic">trans</Emphasis> isomerization mechanism of 3,3′-azobenzene disulphonate in the lowest singlet and triplet electronic states by density functional theory

Abstract  

The cis–trans isomerization pathways of 3,3′-azobenzene disulphonate in the S₀ and T₁ states are studied by DFT method at the B3LYP/6-31G(d,p) level. In the S₀ state, the cis–trans isomerization concerns the complex pathway that is characterized by the inversion of one NNC angle combined with rotation around the NC bond, and the three sequential transition states are also found on the potential energy profile. Therefore, the cis–trans isomerization of 3,3′-azobenzene disulphonate can be understood in terms of a pathway involving successive rotation, inversion, and rotation processes. The energy barrier of the S₀ state is 22.79 kcal mol⁻¹. In the T₁ state, the isomerization mainly concerns the rotational pathway around the NN double bond, and the two isomers are connected through only one transition state. The isomerization of the T₁ state is related to a lower energy barrier, 5.02 kcal mol⁻¹, but requires a change in spin-multiplicity.     

Solvent influence on the rotational isomerism in terephthalaldehyde

Experimental and theoretical studies were carried out in order to investigate the rotational isomerism of terephthalaldehyde. The dipole moment measurements and infrared spectroscopy in Ar matrix and using various solvents were performed experimentally. In order to supplement the experimental study, both static and dynamical theoretical calculations were performed. IR spectra and potential energy distribution (PED) were calculated for both cis and trans isomers of terephthalaldehyde in gas phase using B3LYP/6-31G(d,p) level of theory. Further calculations consisted of conformational analysis were performed in order to estimate the rotational barrier and relative stabilities of isomers. The DFT theory with B3LYP functional and four double-zeta and triple-zeta basis sets served as framework for this part of calculations. Semiempirical AM1 and PM3 methods were also used for gas-phase modeling. Molecular dynamics using MM3 force field was applied to study the preferences of solvent molecules’ orientation around the studied molecule. Additionally, the effect of solvent polarity on the Gibbs energy of the trans ⇌ cis equilibrium was analyzed in terms of the continuum dielectric medium models.     

Theoretical Study of Rotational Isomerism in Ethyl Pseudohalides

The structure and conformational stability of ethyl pseudohalides CH₃CH₂ — XCN (X = O, S, Se) were investigated using ab initiocalculations at the MP2 level of theory with a triple- basis set augmented with polarization and diffusion functions. Full optimization was performed on the minimum energy structures as well as on the transition state forms. The relative stabilities of rotational conformers were calculated at the MP4 level using MP2 optimized reference geometries. The nature of all considered stationary points was verified by calculation of the harmonic vibrational frequencies. The calculated bond lengths, bond angles, dipole moments, and rotational constants of optimized global minima structures agree very well with the corresponding experimental data obtained from microwave spectroscopic studies. Also, available experimental frequencies are in good accord with the theoretical values. For ethyl cyanate CH₃CH₂ — OCN, the antiperiplanar (trans) form is predicted to be more stable than the synclinal (gauche) form, and the synperiplanar (cis) form corresponds to the transition state. For both ethyl thiocyanate CH₃CH₂ — SCN and ethyl selenocyanate CH₃CH₂ — SeCN, the gaucheform is the global minimum while the trans-conformer is a local minimum and the cis-form is a transition state.     

Rotational Spectroscopy of 2-Furoic Acid and Its Dimer: Conformational Distribution and Double Proton Tunneling

Structural and tunneling properties of the 2-furoic acid (FA) monomer and dimer were investigated using rotational spectroscopy and DFT calculations. CREST, a conformational ensemble space exploration tool, was used to identify all possible low-energy conformations of the FA monomer and dimer, followed by the DFT geometry optimization and harmonic frequency calculations. Broadband rotational spectra in the 2–6 and 8–12 GHz regions were recorded in a supersonic jet expansion. The monomeric FA was found to exist dominantly as three different conformers: I , II , and III in a jet, with I and II taking on the cis-COOH configuration while III having the trans-COOH configuration. For the FA dimer, only the I – II conformer was observed experimentally, whereas the symmetric I – I and II – II conformers were not observed because of their zero dipole moments. The analysis of the splittings in the rotational transitions of I – II allowed one to extract the tunneling splitting to be 1056.0(12) MHz. The barrier height was determined to be ∼442 cm⁻¹ using the scaled potential energy scans at several different levels of theory.     

Disulfide conformational analysis: The nature of the S-S rotation barrier

Previous DNMR measurements for a series of bulky disulfides led to the conclusion that rotation about the S-S bond occurs preferentially through the cis transition state. To investigate this conclusion and to study the conformational properties of disulfides in general, we have applied Allinger's force field to a series of dialkyl disulfides generated by homologating dimethyl disulfide to di-t-butyl disulfide. The optimized ground state geometries evidence a gradual increase in the CS-CS dihedral angle from 83 to 114° and indicate that increased substituent bulk drives the disulfide system in the direction of the trans rotational maximum. Explicit calculation of barrier heights yields ΔE(trans) < ΔE(cis) in every case. Furthermore the energy gap, ΔΔE(cis-trans), increases sharply as substituent size grows. This trend results from a rapid rise in the cis barrier and a small drop in the trans one. A rotation-inversion pathway is ruled out and it is concluded that disulfide conformational isomerization occurs by way of the trans transition state. p ]Torsion about the S-C bonds for several t-Bu substituted disulfides is considered. A strongly coupled alkyl-t-Bu rotation is observed computationally in accord with Nelander and Sunner's speculations concerning a “cogwheel effect.” ΔG2 trends for S-S rotation are discussed in connection with the latter. p ]Finally a ΔH(S-S) parameter is derived. Heats of formation and strain energies for dialkyl disulfides are calculated.     

Rotational isomers of small molecules in noble-gas solids: From monomers to hydrogen-bonded complexes

Molecular conformation, quantum tunneling, and hydrogen bonding play important roles in various photochemical processes. We have studied a number of small molecules possessing rotational isomerism (HONO, formic acid, acetic acid, etc.) isolated in noble-gas solid matrices. Selective vibrational excitation efficiently promotes the conformational change in the excited molecule, which allows preparation of higher-energy conformers. Stability of the higher-energy conformers is often limited by quantum tunneling of hydrogen as observed for some carboxylic acids (formic, acetic, etc.). The tunneling mechanism is supported by the strong H/D isotope effect and characteristic temperature dependence with a clear low-temperature limit. The reaction barrier height is an important factor in a tunneling process; however, other factors also play an essential role. The energy mismatch between the initial state of the higher-energy conformer and accepting state of the ground-state conformer is probably important. Hydrogen bonding can change tunneling decay rate of unstable conformers. The trans–cis formic acid dimer was prepared by vibrational excitation of the trans–trans form in neon and argon matrices. Tunneling decay of cis formic acid is substantially slower in the dimeric form compared to monomer, especially in solid neon. This stabilization effect is explained by a complexation-induced increase of reaction barrier, which is confirmed computationally. The complex between cis formic acid and water was prepared in an argon matrix and found to be stable at low-temperatures. These results show that intrinsically unstable conformational structures can be thermodynamically stabilized in asymmetrical hydrogen-bonded network. This effect occurs when the energy difference between conformers is smaller than the hydrogen bond interaction energy, which allows chemistry of unstable conformers to be studied.     

Configurational-conformational entropy of 1,4-polydienes

A method based on matrix algebra and on the rotational isomeric state scheme to study the configurational- conformational entropy of 1,4-polydienes with geometrical isomerism has been developed. Bernoullian and first-and second-order Markovian statistics for the sequences of cis and trans units along the chains have been considered, and the explicit relation between entropy and mole fraction of cis units has been derived. Calculations performed by using available experimental data for the configurational parameters and the conformational partition functions of 1,4-polybutadiene and 1,4-polyisoprene show that entropy is a monotonic function of the geometrical isomer composition. While the entropy of polybutadiene increases with the content of cis units, the reverse is true for polyisoprene.     

Hybrid-DFT Study and NBO Interpretation of the Configurational Behavior of 2-Halotetrahydrothiopyran S-Oxides

Abstract

Natural bond orbital (NBO) interpretation and hybrid density functional theory (hybrid-DFT: B3LYP/Def2-TZVPP)-based methods were used to investigate the impacts of the generalized anomeric effects (GAE), electrostatic, and steric interactions on the conformational properties of cis and trans isomers of 2-fluoro-, 2-chloro-, and 2-bromotetrahydrothiopyran S-oxide (1–3). The results obtained showed that the trans-axial configurations are the most stable forms of compounds 1–3. Based on the results obtained, the instability of the second lowest energy-minimum (cis-equatorial configuration, with axial S?O and equatorial C?X bonds, X = halogen atoms) increases from compound 1 to compound 3. This trend is also observed for the third lowest energy-minimum (i.e., the trans-equatorial configuration). Contrary to the trend observed for the cis- and trans-equatorial forms, the instability of the cis-axial form compared to the trans-axial form, increases from 1 to 2 but decreases slightly from 2 to 3. The correlations between the GAE, bond orders, steric effects, ΔG, Δμ, structural parameters, and conformational and configurational behaviors of compounds 1–3 have been investigated.

Supplemental materials are available for this article. Go to the publisher's online edition of Phosphorus, Sulfur, and Silicon and the Related Elements to view the free supplemental file.     

A CGenFF-based force field for simulations of peptoids with both cis and trans peptide bonds

Peptoids, or poly-n-substituted glycines, are peptide-like polymers composed of a flexible backbone decorated with diverse chemical side chains. Peptoids can form a variety of self-assembling structures based on the type and sequence of the side chains attached to their backbones. All-atom molecular dynamics simulations have been useful in predicting the conformational structures of proteins and will be valuable tools for identifying combinations of peptoid side chains that may form interesting folded structures. However, peptoid models must address a major degree of freedom not common in proteins – the cis/trans isomerization of the peptide bond. This work presents CHARMM general force field (CGenFF) parameters developed to accurately represent peptoid conformational behavior, with an emphasis on a correct representation of both the cis and trans isomers of the peptoid backbone. These parameters are validated against experimental and quantum mechanics data and used to simulate three peptoid side chains in explicitly solvated systems. © 2019 Wiley Periodicals, Inc.     

Local chain motions of poly(β-hydroxyoctanoate) in the bulk. 13C NMR relaxation study

Variable-temperature ¹³C NMR spin-lattice relaxation times (T₁) and Nuclear Overhauser Enhancements (NOE) at two magnetic fields have been used to study the dynamics of the amorphous part of a semicrystalline sample (33% of crystallinity) of poly(β-hydroxyoctanoate) (PHO). The interpretation of the relaxation data of the backbone carbons was made by employing a number of motional models. Among these, the DLM model offered the best interpretation of the relaxation data in terms of conformational transitions and librational motions of the backbone C? H vectors, and proved to be superior to unimodal distribution functions. The interpretation of temperature- and frequency-dependent T₁ and NOE data of the carbon nuclei in the n-pentyl side chain was made by employing a newly developed composite spectral density function for multiple internal C? C bond rotations of restricted amplitude and chain segmental motion. The temperature dependence of the linewidths of the various protonated carbon resonances of PHO has been discussed in terms of the semicrystalline character of this polymer. © 1995 John Wiley & Sons, Inc.     

cis–trans Isomerisation of Substituted Aromatic Imines: A Comparative Experimental and Theoretical Study

The cis–trans isomerisation of N‐benzylideneaniline (NBA) and derivatives containing a central C?N bond has been investigated experimentally and theoretically. Eight different NBA molecules in three different solvents were irradiated to enforce a photochemical trans${{\mathop \rightarrow \limits ^{h\nu }_{}}}$ cis isomerisation and the kinetics of the thermal backreaction cis${{\mathop \rightarrow \limits ^{\Delta }_{}}}$ trans were determined by NMR spectroscopy measurements in the temperature range between 193 and 288 K. Theoretical calculations using density functional theory and Eyring transition‐state theory were carried out for 12 different NBA species in the gas phase and three different solvents to compute thermal isomerisation rates of the thermal back reaction. While the computed absolute rates are too large, they reveal and explain experimental trends. Time‐dependent density functional theory provides optical spectra for vertical transitions and excitation energy differences between trans and cis forms. Together with isomerisation rates, the latter can be used to identify “optimal switches” with good photochromicity and reasonable thermal stability.