Characterization and properties of a polythiophene with a malonic acid dimethyl ester side group

A new polythiophene derivative bearing a malonic acid dimethyl ester substituent attached to the 3-position of the repeat unit has been prepared by chemical oxidative-coupling polymerization. The chemical structure of poly(2-thiophen-3-yl-malonic acid dimethyl ester) has been analyzed by FTIR and ¹H NMR spectroscopy and, additionally, the distribution of the head-to-tail and head-to-head diads arising from polymerization was found to be a 75-25%. The glass transition temperature identified for this polymer was 17.6 °C lower than that recently determined for a closely related polythiophene derivative, in which the ester substituent arose from acrylic acid rather than from malonic acid. On the other hand, the electrical conductivity of the new material, which was soluble in polar solvents but not in water, was higher than that typically found for poly(3-alkylthiophene) derivatives. Ab initio quantum mechanical calculations on simple model compounds were used to predict the regiochemistry of the polymer chain, which was in excellent agreement with the experimental observation, and the conformational preferences of both the inter-ring dihedral angle and the bulky side group. Interestingly, calculations predict that the inter-ring dihedral angles adopt a syn-gauche conformation rather than the anti-gauche arrangement typically found in substituted polythiophenes. Thus, in this case the former conformation reduces the strong repulsive interactions induced by the bulky substituent. The lowest π-π^∗ transition energy derived from calculations on an idealized molecular model is in agreement with the experimental estimation determined using UV-vis spectroscopy. This electronic property is significantly higher for poly(2-thiophen-3-yl-malonic acid dimethyl ester) than for other substituted polythiophene derivatives, which is consequence of the geometrical distortions induced by bulky side group.     

Quantum chemical calculations on thioridazine

Quantum chemical CNDO /2 calculations for the conformational preference of the side chain of thioridazine as a function of angle indicated the crystallographically determined structure gave the lowest energy. There is also a small region of conformational flexibility within the first 90° of rotation of the side chain. This is commensurate with the results which we had obtained previously for our similar calculations for promazine and its Cl and CF₃ derivatives, perazine and its Cl and CF₃ derivatives, and for the hypothetical hitherto unknown N-piperidinopromazine and its Cl and CF₃ derivatives. The conformational profile of thioridazine resembles that of the perazines. The calculated gross atomic populations on the alkyl nitrogen in thioridazine was within the range we had previously found necessary for neuroleptic activity.     

Resonance assignments of diastereotopic CH2 protons in the anomeric side chain of selenoglycosides by means of 2J(Se,H) spin‐spin coupling constants

Unambiguous resonance assignments of diastereotopic CH₂ protons in the anomeric side chain of nine alkyl‐ and aralkylselenoglycosides have been carried out on the basis of experimental CPMG‐HSQMBC measurements and theoretical second order polarization propagator approach (SOPPA) calculations of geminal ⁷⁷Se‐¹H spin‐spin coupling constants involving diastereotopic pro‐R and pro‐S protons. Theoretical conformational analyses have been performed at the MP2/6‐311G** level. The conformational space of each of the selenoglycosides under study could be adequately described as a mixture of six interconverting conformers with the molar fractions depending on the nature of the side chain substituent at the selenium atom. The good agreement observed between measured and the weighted conformational averaged values of the calculated coupling constants provides a basis for reliable diastereotopic assignments in this type of carbohydrate structures. Copyright © 2012 John Wiley & Sons, Ltd.     

Ab initio MO study on [3 + 2] annulation using beta-phenylthio-acryloylsilanes with alkyl methyl ketone enolates and its through-space/bond interaction analysis

Ab initio through-space/bond interaction analysis was applied to [3 + 2] annulation based on Brook rearrangement using beta-phenylthio-acryloylsilanes with alkyl methyl ketone enolates. An uncertain reaction mechanism, wherein a bulky cyclopentenol with large substituents on the same side of the five-membered ring was obtained as a major product, can be explained by the low activation energy of its reaction pathway. Intramolecular orbital interactions related to the carbanion generated by Brook rearrangement preferentially provide the stabilization of the reaction pathway to the bulky cyclopentenol (major product) compared with that provided to the non-bulky cyclopentenol (minor product). In addition, ab initio molecular orbital calculations suggest the existence of an E/Z conformational inversion after Brook rearrangement. This result accurately explains the loss of the E/Z stereochemical integrity in the starting materials of the experiment.     

Influence of steric and electronic effects of substituents on the molecular structures and conformational flexibility of 1,8-naphthalenedicarboximides

A series of 1,8-naphthalenedicarboximide derivatives containing substituents of different steric and electronic nature were studied by X-ray diffraction analysis.Ab initio quantumchemical calculations in the HF/3–21G approximation demonstrated the high conformational flexibility of the imide tetrahydro ring in the molecules of these compounds. The electronic nature of the substituents has no effect on the geometry and conformational flexibility of naphthalenedicarboximides due to weak conjugation between the imide and naphthalene fragments in the molecules. However, the steric effects of the bulky substituents noticeably affect the equilibrium geometry of the imide ring by increasing its conformational flexibility. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 68–73, January, 2000.     

Influence of steric and electronic effects of substituents on the molecular structures and conformational flexibility of 1,8-naphthalenedicarboximides

A series of 1,8-naphthalenedicarboximide derivatives containing substituents of different steric and electronic nature were studied by X-ray diffraction analysis.Ab initio quantumchemical calculations in the HF/3–21G approximation demonstrated the high conformational flexibility of the imide tetrahydro ring in the molecules of these compounds. The electronic nature of the substituents has no effect on the geometry and conformational flexibility of naphthalenedicarboximides due to weak conjugation between the imide and naphthalene fragments in the molecules. However, the steric effects of the bulky substituents noticeably affect the equilibrium geometry of the imide ring by increasing its conformational flexibility. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 68–73, January, 2000.     

AM1 molecular orbital studies of the structures,conformations, protonation energies,and electronic properties of triazine dihydrofolate reductase inhibitors

The structural, conformational, and electronic properties of three triazine antifolates were determined by AM1 molecular orbital calculations, and the results were compared with other theoretical studies and with X-ray crystallographic studies of these and similar triazines both in the crystalline state and as complexes bound to dihydrofolate reductase. Calculated protonation energies confirm crystal structure data indicating N-protonation analogous to that reported for MTX in similar environments. Overall, the calculated structural and conformational properties are in good agreement with X-ray crystallographic results for these and similar triazines as found in the crystalline state and in enzymebound ternary complexes. However, for one triazine AM1 predicts a conformation with the bulky aromatic substituent twisted about 60° away from coplanarity with the triazine ring, in contrast to the nearly coplanar conformation found in the crystalline state. Intermolecular interactions favoring the coplanar conformation may thus be operative in the crystalline environment. The unique conformational preferences and greater conformation flexibility of triazines in general and of this triazine in particular may provide a key to understanding their biological activity.     

A Theoretical and Experimental Study of the Effects of Silyl Substituents in Enantioselective Reactions Catalyzed by Diphenylprolinol Silyl Ether

The effect of silyl substituents in diphenylprolinol silyl ether catalysts was investigated. Mechanistically, reactions catalyzed by diphenylprolinol silyl ether can be categorized into three types: two that involve an iminium ion intermediate, such as for the Michael‐type reaction (type A) and the cycloaddition reaction (type B), and one that proceeds via an enamine intermediate (type C). In the Michael‐type reaction via iminium ions (type A), excellent enantioselectivity is realized when the catalyst with a bulky silyl moiety is employed, in which efficient shielding of a diastereotopic face of the iminium ion is directed by the bulky silyl moiety. In the cycloaddition reaction of iminium ions (type B) and reactions via enamines (type C), excellent enantioselectivity is obtained even when the silyl group is less bulky and, in this case, too much bulk reduces the reaction rate. In other cases, the yield increases when diphenylprolinol silyl ethers with bulky substituents are employed, presumably by suppressing side reactions between the nucleophilic catalyst and the reagent. The conformational behaviors of the iminium and enamine species have been determined by theoretical calculations. These data explain the effect of the bulkiness of the silyl substituent on the enantioselectivity and reactivity of the catalysts.     

Intrinsic conformational characteristics of alpha,alpha-diphenylglycine

Quantum mechanical calculations at the B3LYP/6-31+G(d,p) level have been used to investigate the intrinsic conformational preferences of alpha,alpha-diphenylglycine, a simple alpha,alpha-dialkylated amino acid bearing two phenyl substituents on the alpha-carbon, in both the gas phase and aqueous solution. Nine minimum energy conformations have been characterized for the N-acetyl-N'-methylamide derivative within a relative energy range of about 9 kcal/mol. The relative stability of these structures is largely influenced by specific backbone...side chain and side chain...side chain interactions that can be attractive (N-H...pi and C-H...pi) or repulsive (C=O...pi). On the other hand, comparison with the minimum energy conformations calculated for alpha-aminoisobutyric acid, in which the two phenyl substituents are replaced by methyl groups, revealed that the bulky aromatic rings of alpha,alpha-diphenylglycine induce strain in the internal geometry of the peptide. Finally, a set of force-field parameters for classical Molecular Mechanics calculations was developed for the investigated amino acid. Molecular Dynamics simulations in aqueous solutions have been carried out to validate the parameters obtained.     

Experimental anomalies and the conformational theory of polymers

The influence of the size and shape of the torsional potential upon the theoretical temperature coefficient (T? ln 〈r₀²〉/?T) of a polymeric chain was studied. The uncorrelated end-to-end distance equations for isotactic, syndiotactic, and completely atactic chains were differentiated with respect to temperature and the integrals in the resulting equations were evaluated by the method of Gaussian quadrature. The calculated coefficients were found to be nonlinear functions of the energy ratio U_max/KT, where U_max is the maximum potential barrier and possess real roots which critically depend upon the size and shape of the potential. Qualitative anomalies between experiment and theory disappeared when the entire torsional potential was used in the conformational theory. It appears that quantitative agreement between theory and experiment can be established for polymeric materials if the entire potential is used, rotations within bulky side groups are included, and the potential is determined by the method of minimum conformational energy.     

Anionic polymerization of 2,7‐di‐t‐butyldibenzofulvene: Synthesis,structure, and photophysical properties of the oligomers with a π‐stacked conformation

2,7‐Di‐t‐butyldibenzofulvene (tBu₂DBF), a bulky dibenzofulvene derivative, was polymerized using n‐butyllithium as initiator in tetrahydrofuran at ?78 °C and in toluene at 0 °C. tBu₂DBF afforded mainly oligomers up to trimer even at [monomer]₀/[initiator]₀ = 20 ([monomer]₀ = 0.2 M) at ?78 °C and 0 °C, indicating that this monomer is much less reactive than dibenzofulvene (DBF), its parent compound. The reaction at the same [monomer]₀/[initiator]₀ ratio at an elevated [monomer]₀ gave a small amount of insoluble polymer. The oligomers indicated a hypochromic effect in the absorption spectra and only monomer emission in the fluorescent spectra. The conformation of the trimer and the dimer was examined by means of NOESY NMR spectra and semiempirical calculations. In the trimer conformation, the fluorene moieties of the central and the initiation‐side monomeric units were found to be closely stacked on top of each other, while the termination‐side monomeric unit appeared to be in a faster conformational dynamics compared with the other monomeric units. Although the dimer seemed to have a relatively flexible conformation, a π‐stacked structure appeared to be involved in the conformational dynamics to show hypochromicity. The results of this study suggest that the reported intramolecular excited dimer (excimer) formation of the poly‐ and oligo(DBF)s [J Am Chem Soc 2003, 125, 15474] is based on a slight, local conformational change upon photo absorption, leading to a closer π‐stacked alignment of two neighboring fluorene units than that in the ground state. Such a local conformational transition may be difficult for the tBu₂DBF trimer because of steric repulsion of the t‐butyl groups. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 561–572, 2006     

Quantum chemical studies on the conformational structure of bacterial peptidoglycan. V. PCILO Calculations on β(1 → 4) linked disaccharide of N-acetyl-glucosamine and N-acetyl muramic acid

The glycan moiety of the bacterial peptidoglycan consists of alternatingly β(1 → 4) linked disaccharides of N-acetylglucosamine (NAG) and its 3-O-D lactic derivative, N-acetyl β-D-muramic acid (NAM). PCILO conformational energy calculations have been carried out for NAG–NAM and NAM–NAG disaccharides to see whether or not the glycan strands possess a chitinlike structure as suggested by earlier workers. In agrement with recent experimental findings, the present results also suggest that the chitinlike structure is energetically disallowed. Furthermore, the bulky N-acetyl substituents at C₂ positions of the two sugar molecules are found to be relatively less important in stabilizing mutual orientations of the two pyranosyl rings.     

Calculation of molecular geometries,relative conformational energies,dipole moments,and molecular electrostatic potential fitted charges of small organic molecules of biochemical interest by density functional theory

Density functional theory is tested on a large ensemble of model compounds containing a wide variety of functional groups to understand better its ability to reproduce experimental molecular geometries, relative conformational energies, and dipole moments. We find that gradient-corrected density functional methods with triple-ζ plus polarization basis sets reproduce geometries well. Most bonds tend to be approximately 0.015 Å longer than the experimental results. Bond angles are very well reproduced and most often fall within a degree of experiment. Torsions are, on average, within 4 degrees of the experimental values. For relative conformational energies, comparisons with Hartree-Fock calculations and correlated conventional ab initio methods indicate that gradient-corrected density functionals easily surpass the Hartree-Fock approximation and give results which are nearly as accurate as MP2 calculations. For the 35 comparisons of conformational energies for which experimental data was available, the root mean square (rms) deviation for gradient-corrected functionals was approximately 0.5 kcal mol^?1. Without gradient corrections, the rms deviation is 0.8 kcal mol^?1, which is even less accurate than the Hartree-Fock calculations. Calculations with extended basis sets and with gradient corrections incorporated into the self-consistent procedure generate dipole moments with an rms deviation of 5%. Dipole moments from local density functional calculations, with more modest basis sets, can be scaled down to achieve roughly the same accuracy. In this study, all density functional geometries were generated by local density functional self-consistent calculations with gradient corrections added in a perturbative fashion. Such an approach generates results that are almost identical to the self-consistent gradient-corrected calculations, which require significantly more computer time. Timings on scalar and vector architectures indicate that, for moderately sized systems, our density functional implementation requires only slightly less computer resources than established Hartree-Fock programs. However, our density functional calculations scale much better and are significantly faster than their MP2 counterparts, whose results they approach. © 1995 John Wiley & Sons, Inc.     

Randomizing the Unfolded State of Peptides (and Proteins) by Nearest Neighbor Interactions between Unlike Residues

To explore the influence of nearest neighbors on conformational biases in unfolded peptides, we combined vibrational and 2D NMR spectroscopy to obtain the conformational distributions of selected “GxyG” host–guest peptides in aqueous solution: GDyG, GSyG, GxLG, GxVG, where x/y=A, K, L, V. Large changes of conformational propensities were observed due to nearest‐neighbor interactions, at variance with the isolated pair hypothesis. We found that protonated aspartic acid and serine lose their above‐the‐average preference for turn‐like structures in favor of polyproline II (pPII) populations in the presence of neighbors with bulky side chains. Such residues also decrease the above‐the‐average pPII preference of alanine. These observations suggest that the underlying mechanism involves a disruption of the hydration shell. Thermodynamic analysis of ³J(H^N,H^α) (T) data for each x,y residue reveals that modest changes in the conformational ensemble masks larger changes of enthalpy and entropy governing the pPII?β equilibrium indicating a significant residue dependent temperature dependence of the peptides’ conformational ensembles. These results suggest that nearest‐neighbor interactions between unlike residues act as conformational randomizers close to the enthalpy–entropy compensation temperature, eliminating intrinsic biases in favor of largely balanced pPII/β dominated ensembles at physiological temperatures.     

DFT‐GIAO 1H and 13C NMR prediction of chemical shifts for the configurational assignment of 6β‐hydroxyhyoscyamine diastereoisomers

¹H and ¹³C NMR chemical shift calculations using the density functional theory–gauge including/invariant atomic orbitals (DFT–GIAO) approximation at the B3LYP/6‐311G++(d,p) level of theory have been used to assign both natural diastereoisomers of 6β‐hydroxyhyoscyamine. The theoretical chemical shifts of the ¹H and ¹³C atoms in both isomers were calculated using a previously determined conformational distribution, and the theoretical and experimental values were cross‐compared. For protons, the obtained average absolute differences and root mean square (rms) errors for each comparison showed that the experimental chemical shifts of dextrorotatory and levorotatory 6β‐hydroxyhyoscyamines correlated well with the theoretical values calculated for the (3R,6R,2′S) and (3S,6S,2′S) configurations, respectively, whereas for ¹³C atoms the calculations were unable to differentiate between isomers. The nature of the relatively large chemical shift differences observed in nuclei that share similar chemical environments between isomers was asserted from the same calculations. It is shown that the anisotropic effect of the phenyl group in the tropic ester moiety, positioned under the tropane ring, has a larger shielding effect over one ring side than over the other one. Copyright © 2009 John Wiley & Sons, Ltd.     

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

An 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     

Direct identification of conformational isomers of adsorbed oligothiophene on Cu100

A direct conformational analysis using scanning tunneling microscopy (STM) has been performed for individual adsorbed alpha-octithiophene molecules on Cu(100). s-cis and s-trans conformational isomers are induced by the rotational flexibility of individual thiophene rings. By adding bulky N-silyl substituents to octithiophene, we successfully identify the s-cis and s-trans conformational isomers using STM. The obtained relative abundances of the s-cis and s-trans conformations are analyzed using ab initio molecular orbital calculations.     

DFT‐Aided Vibrational Circular Dichroism Spectroscopy Study of (−)‐S‐cotinine

The implementation of a strategy comprising the use of vibrational circular dichroism spectroscopy and DFT calculations allows determination of the solution‐state conformational distribution in (?)‐S‐cotinine, giving further proof of the extra conformer‐discriminating potential of this experimental technique, which may offer unique molecular fingerprints of subtly dissimilar molecular conformers of chiral samples. Natural bond orbital electronic structure calculations of the rotational barrier height between the two main conformers of the species indicate that hyperconjugative effects are the key force governing the conformational equilibrium. The negligible effect of the solvent’s polarity over both structure and conformational energy profile supports this result.     

MCCE2: Improving protein pKa calculations with extensive side chain rotamer sampling

Multiconformation continuum electrostatics (MCCE) explores different conformational degrees of freedom in Monte Carlo calculations of protein residue and ligand pK_as. Explicit changes in side chain conformations throughout a titration create a position dependent, heterogeneous dielectric response giving a more accurate picture of coupled ionization and position changes. The MCCE2 methods for choosing a group of input heavy atom and proton positions are described. The pK_as calculated with different isosteric conformers, heavy atom rotamers and proton positions, with different degrees of optimization are tested against a curated group of 305 experimental pK_as in 33 proteins. QUICK calculations, with rotation around Asn and Gln termini, sampling His tautomers and torsion minimum hydroxyls yield an RMSD of 1.34 with 84% of the errors being <1.5 pH units. FULL calculations adding heavy atom rotamers and side chain optimization yield an RMSD of 0.90 with 90% of the errors <1.5 pH unit. Good results are also found for pK_as in the membrane protein bacteriorhodopsin. The inclusion of extra side chain positions distorts the dielectric boundary and also biases the calculated pK_as by creating more neutral than ionized conformers. Methods for correcting these errors are introduced. Calculations are compared with multiple X‐ray and NMR derived structures in 36 soluble proteins. Calculations with X‐ray structures give significantly better pK_as. Results with the default protein dielectric constant of 4 are as good as those using a value of 8. The MCCE2 program can be downloaded from http://www.sci.ccny.cuny.edu/～mcce . © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

The effect of electron correlation on the conformational space of melatonin

The pineal gland hormone melatonin regulates several physiological processes including circadian rhythm and also alleviates oxidative stress‐induced degenerative diseases. In spite of its important biological roles, no high level ab initio conformational study has been conducted to reveal its structural features. In this work, the conformational flexibility of melatonin was investigated using correlated ab initio calculations. Conformers, obtained previously at the Hartree‐Fock level (HF/6‐31G*), were fully optimized using second order Møller‐Plesset perturbation theory applying the frozen core approximation (MP2(FC)/6‐31G*). Furthermore, single‐point MP4(SDQ,FC)/6‐31G*//MP2(FC)/6‐31G* computations were performed to investigate the effect of higher order perturbation terms. The HF and MP2 conformational spaces are considerably different: the initial 128 structures converged into 102 different local minima as confirmed by frequency calculations; 28 new minima appeared and 26 previous HF local minima disappeared; no “all‐trans” C3 side chain conformations are seen at the MP2(FC) level. The MP2 global minimum conformation is stabilized by an aromatic‐side chain interaction. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008