Spectral multitude and spectral dynamics reflect changing conjugation length in single molecules of oligophenylenevinylenes

Single-molecule study of phenylenevinylene oligomers revealed distinct spectral forms due to different conjugation lengths which are determined by torsional defects. Large spectral jumps between different spectral forms were ascribed to torsional flips of a single phenylene ring. These spectral changes reflect the dynamic nature of electron delocalization in oligophenylenevinylenes and enable estimation of the phenylene torsional barriers.     

First-principles prediction and interpretation of propagation and transfer rate coefficients

Propagation and transfer rate coefficients in free-radical polymerizations are calculated from first principles, using quantum calculations (both ab initio and semi-empirical) to determine geometries, frequencies, torsional potentials and energies of reactants and transition state, after which transition state theory yields the Arrhenius parameters. While activation energies can only be calculated for small species and with large computational resources, acceptable frequency factors (A) are obtained with relative ease provided that lower frequencies corresponding to torsions are treated as hindered rotors, not harmonic oscillators; this entails finding the torsional potential and exact evaluation of the corresponding partition function. Simple theory can be used to find A because this involves a ratio of partition functions of reactant and transition state, and because torsions (which are dominated by geometrical considerations) dominate A. A is determined by three modes in the transition state: rotation of the monomer about the forming bond, rotation of a “propylene”-group about the terminal C–C bond in the radical, and simultaneous bending of the two angles associated with the forming bond. Calculations on ethylene and acrolein give agreement with experiment. These studies explain some experimental observations. (i) Changing the penultimate unit gives a small but significant change in the torsion of two of the three modes dominating A, leading to a penultimate-unit effect of ca. a factor of 1–10. (ii) Deuteration affects the moments of inertia of the torsions, leading to changes in A in accord with experiment. (iii) A, but not the activation energy, changes predictably along a homologous series (e.g., methyl, butyl methacrylate). (iv) For a given monomer, A's for transfer to monomer and propagation are similar.     

Structure of Isolated 1,4-Butanediol: Combination of MP2 Calculations, NBO Analysis, and Matrix-Isolation Infrared Spectroscopy

Theoretical calculations at the MP2 level, NBO and AIM analysis, and matrix-isolation infrared spectroscopy have been used to investigate the structure of the isolated molecule of 1,4-butanediol (1,4-BDO). Sixty-five structures were found to be minima on the potential energy surface, and the three most stable forms are characterized by a folded backbone conformation leading to the formation of an intramolecular H-bond. To better characterize the intramolecular interactions and particularly the hydrogen bonds, natural bond orbital analysis (NBO) was performed for the four most stable conformers, and was further complemented with an atoms-in-molecules (AIM) topological analysis. Infrared spectra of 1,4-BDO isolated in low-temperature argon and xenon matrixes show a good agreement with a population-weighted mean theoretical spectrum, and the spectral features of the conformers expected to be trapped in the matrixes were observed experimentally. Annealing the xenon matrix from 20 to 60 K resulted in significant spectral changes, which were interpreted based on the barriers to intramolecular rotation. An estimation of the intramolecular hydrogen bond energy was carried out following three different methodologies.     

Microwave spectrum and rotational isomers of ethyl fluoroformate

The microwave spectrum of ethyl fluoroformate displays strong a-type R branch transitions from two rotameric forms. One species (extended form) has rotational constants A₀ = 9191.3(9) MHz, B₀ = 2112.61(1) MHz, C₀ = 1756.73(1) MHz which are consistent with a syn-anti (τ₁(OCOC) = 0°, r₂(cocc) = 180°) planar heavy atom structure. The second species (compact form) has rotational constants A₀ = 7760(3) MHz, B₀ = 2388.38(4) MHz, C₀ = 2102.47(3) MHz which are consistent with a syn-gauche (τ₁(ococ) = 0°, τ₂(cocc) ˜ 90°) structure. The two conformational forms have approximately equal energy (0 ± 40 cm⁻¹). Four vibrational satellites of the extended species have been analyzed yielding a torsional frequency around the O-ethyl bond of 70(10) cm⁻¹. Three vibrational satellites attributed to the O-ethyl torsion of the compact species have been analyzed yielding a vibrational frequency of 90(10) cm⁻¹. Approximate Fourier coefficients of a three term potential function for internal rotation about the O-ethyl bond have been determined. Vibrational satellites attributed to the first excited states of the O-ester torsion have been analyzed for both conformers. The torsional vibrational frequency around the O-ester bond is 110(15) cm⁻¹ for the extended conformers and 120(20) cm⁻¹ for the compact.     

The MM3 force field for amides,polypeptides and proteins

The potential functions for simple amides, several peptides and a small protein have been worked out for the MM3 force field. Structures and energies were fit as previously with MM2, but additionally, we fit the vibrational spectra of the simple amides (average rms error over four compounds, 34 cm^?1), and examined more carefully electrostatic interactions, including charge-charge and charge-dipole interactions. The parameters were obtained and tested by examining four simple amides, five electrostatic model complexes, two dipeptides, six crystalline cyclic peptides, and the protein Crambin. The average root-mean-square deviation from the X-ray structures for the six cyclic peptide crystals was only 0.10 Å for the nonhydrogen atomic positions, and 0.011 Å, 1.0°, and 4.9° for bond lengths, bond angles, and torsional angles, respectively. The parameter set was then further tested by minimizing the high resolution crystal structure of the hydrophobic protein Crambin. The resultant root-mean-square deviations for the non-hydrogen atomic data, in the presence of the crystal lattice, are 0.22 Å, 0.023 Å, 2.0°, and 6.4° for coordinates, bond lengths, bond angles, and torsional angles, respectively.     

Beiträge zur Chemie der Pyrrolpigmente, 24. Mitt. Über die Beziehung zwischen Lichtabsorption und Struktur von Bilatrienen-abc

Using the recently established solution structure of a bilatriene-abc derivative the parameter set of thePPP-SCF-LCAO-MO-Cl model was refined. The general trend, that molecular configuration itself does not so much determine the absorption spectra as was deduced by investigation of partial bile pigment structures, was confirmed for the bilatrienes-abc. Instead, the configuration at a particular double bond induces a certain torsional angle at the adjacent single bond which leads to dramatic spectral changes on isomerization of this double bond. Isomerization without this torsional effect brings about different relative intensities of the two main spectral bands. Comparing measured spectra of several bilatrienes-abc and calculated spectra a helicalsyn, syn, syn-conformation with three torsional angles at the methine fragments of appr. 20° was deduced for systems with (Z, Z, Z)-configuration. For a recently prepared (E, Z, Z)-derivative a nearly helicalsyn, syn, syn-conformation with torsional angles of 40°, 20° and 20° at the methine single bonds is the most probable.

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23. Mitt.:H. Falk, K. Grubmayr undK. Thirring, Z. Naturforsch.33b, 924 (1978).     

Structural Aspects of Nucleosides: Protonated and Complexed Adenosines

To gain insight into the structural changes exerted by protonation or complexation of the adenine in nucleosides, the X‐ray structures of adenosines were compared with their protonated or complexed congeners. Comparison of a variety of bond angles, bond lengths, and torsional angles in and around the ribose ring revealed only small differences. The specific case of the 5′‐deoxy‐5′‐adenosyl moiety covalently bonded to the Co‐atom in coenzyme B₁₂ is discussed.     

The experimental determination of the torsional barrier and shape for disilane

The torsional spectrum of disilane was recorded for the first time under high-pressure-pathlength conditions and at a spectral resolution of 0.007 cm(-1) using a Bruker IFS-120 HR Fourier transform spectrometer. The spectrum shows six distinct Q branches. The most prominent Q branch is near 130 cm(-1) which is a blend of four components of the torsional fundamental. Of the remaining five, four were assigned to the first torsional hot band (v(4)=2<--1) and one to the second torsional hot band (v(4)=3<--2). Over 350 transitions were identified. An analysis of the torsional fundamental, the first torsional hot band, and the lower state combination differences from frequencies of the vibrational bands nu(9) and nu(9)+nu(4)-nu(4) was made to characterize the torsion-rotation Hamiltonian in the ground vibrational state. The barrier height, barrier shape, and the rotational constant about the Si-Si bond were determined to be 404.344(83) cm(-1), 2.255(65) cm(-1), and 43208(28) MHz, respectively. Comparison of simulated and the experimental spectra yielded (mu||-mu(perpendicular))/mu(perpendicular)= -4(1) for the torsional dipole moments. This ratio compares well with -3.39(6) for ethane. A comparison of molecular parameters obtained here is made with those for methyl silane and ethane.     

Molecular mechanics force-field parameterization procedures

A set of procedures and guidelines are presented for the estimation of bond length, bond angle, and torsional potential constants for molecular mechanics force fields. The force field constants are ultimately derived by “subtracting” nonbonded molecular mechanics energies from corresponding molecular orbital energies using a model compound containing the chemical structure to be parameterized. Case study examples of bond length, bond angle, and torsional rotation force field parameterizations are presented. A general discussion of molecular mechanics force field parameterization strategy is included for reference and completeness. Finally, a curve-fitting program to generate force field parameters from raw data is given in Appendix I.     

Intra and intermolecular hydrogen bonding in formohydroxamic acid

The presence of hydrogen bonding interactions in several tautomeric forms of formohydroxamic acid (FHA) and 1:1 association among the tautomeric forms and water‐coordinated tautomeric forms of FHA is explored theoretically. Out of the seven equilibrium structures, four tautomeric forms have been selected for aggregation with single water molecule and dimer formation. Fifteen aggregates of FHA with H₂O have been optimized at MP2/AUG‐cc‐PVDZ level and analyzed for intramolecular and intermolecular H‐bond interactions. Twenty‐seven dimers of the four tautomeric forms have been obtained at MP2/6‐31+G* level. The stabilization energies associated with dimerization and adduct formation with water are the result of H‐bond interactions and range from very weak to medium. The atomic charges and NBO analysis indicate that the electrostatic and the charge transfer are the important components favoring H‐bond formation. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Origin of trans-bent geometries in maximally bonded transition metal and main group molecules

Recent crystallographic data unambiguously demonstrate that neither Ar'GeGeAr' nor Ar'CrCrAr' molecules adopt the expected linear (VSEPR-like) geometries. Does the adoption of trans-bent geometries indicate that Ar'MMAr' molecules are not "maximally bonded" (i.e., bond order of three for M = Ge and five for M = Cr)? We employ theoretical hybrid density functional (B3LYP/6-311++G) computations and natural bond orbital-based analysis to quantify molecular bond orders and to elucidate the electronic origin of such unintuitive structures. Resonance structures based on quintuple M-M bonding dominate for the transition metal compounds, especially for molybdenum and tungsten. For the main group, M-M bonding consists of three shared electron pairs, except for M = Pb. For both d- and p-block compounds, the M-M bond orders are reflected in torsional barriers, bond-antibond splittings, and heats of hydrogenation in a qualitatively intuitive way. Trans-bent structures arise primarily from hybridization tendencies that yield the strongest sigma-bonds. For transition metals, the strong tendency toward sd-hybridization in making covalent bonds naturally results in bent ligand arrangements about the metal. In the p-block, hybridization tendencies favor high p-character, with increasing avidity as one moves down the Group 14 column, and nonlinear structures result. In both the p-block and the d-block, bonding schemes have easily identifiable Lewis-like character but adopt somewhat unconventional orbital interactions. For more common metal-metal multiply bonded compounds such as [Re2Cl8]2-, the core Lewis-like fragment [Re2Cl4]2+ is modified by four hypervalent three-center/four-electron additions.     

The effect of electronegative atoms on the structures of hydrocarbons. ab initio calculations on molecules containing fluorine or (carbonyl) oxygen

A series of ab initio calculations have been carried out, using the 4-21G basis set. Ethane and propane were first studied to obtain reference points. The effect of adding an electronegative atom (fluorine, or carbonyl oxygen) onto the framework was then studied as a function of the torsional angle about the single bond. Some pronounced trends in structural changes were observed, and these can in part be correlated with hyperconjugative effects. For example, fluoroethane has bond lengths which are shorter than those in ethane itself, by 0.024 Åin the C C bond, and 0.003 Åin the α C H bonds. These changes are essentially torsionally independent. On the other hand, in propionaldehyde, the C C bond length of the methyl group and the C H bond lengths of the hydrogens attached to the alpha carbon vary as a function of the torsion angle. If the methyl C C bond in the carbonyl plane is taken as a reference, the bond stretches .016 Åwhen the torsion angle is increased to 90°, an α C H bond similarly stretches up to .007 Å. Many of these geometric changes are large, well beyond the experimental errors in modern measurements.     

Force-field parametrization of retro-inverso modified residues: Development of torsional and electrostatic parameters

Summary Torsional and the electrostatic parameters for molecular mechanics studies of retro-inverso modified peptides have been developed using quantum mechanical calculations. The resulting parameters have been compared with those calculated for conventional peptides. Rotational profiles, which were obtained spanning the corresponding dihedral angle, were corrected by removing the energy contributions associated to changes in interactions different from torsion under study. For this purpose, the torsional energy associated to each point of the profiles was estimated as the corresponding quantum mechanical energy minus the bonding and nonbonding energy contributions produced by the perturbations that the variation of the spanned dihedral angle causes in the bond distances, bond angles and the other dihedral angles. These energies were calculated using force-field expressions. The corrected profiles were fitted to a three-term Fourier expansion to derive the torsional parameters. Atomic charges for retro-inverso modified residues were derived from the rigorously calculated quantum mechanical electrostatic potential. Furthermore, the reliability of electrostatic models based on geometry-dependent charges and fixed charges has been examined.     

Structural relaxation upon internal rotation in cis-methyl nitrite,CH3 ONO

The ab initio SCF gradient method has been used to obtain changes of bond lengths and valence angles upon internal rotation of CH₃ and NO groups in cis-methyl nitrite. The data for methyl torsion are confirmed by comparison of calculated and observed shifts of rotational constants in the first methyl torsional state.     

Bond angle versus torsional deformation in an overcrowded alkene: 9-(2,2,2-triphenylethylidene)fluorene

Competition between bond angle and torsional strain in sterically crowded alkenes generally causes twisting in tetrasubstituted alkenes, while most structurally characterized trisubstituted alkenes are planar. To investigate structural effects of steric repulsion between a planar aromatic ring and a vicinal triphenylmethyl (trityl) group, 9-(2,2,2-triphenylethylidene)fluorene (1 a) was synthesized by reaction of 9-bromomethylenefluorene with triphenylmethyllithium. For comparison with a less strained analogue, 9-ethylidenefluorene (1 b) was prepared by reaction of fluorenone with ethylmagnesium bromide. The X-ray crystal structures show that the difference between bond angles at the 9-fluorenyl carbon atom is much larger for 1 a (12.9 degrees) than 1 b (2.6 degrees). Bond angle and torsional deformations were compared theoretically (HF/6-31+G*) with the tert-butyl analogue (1 c), 1,2,2-tri-tert-butylethene (7), and 2,4,4-trimethyl-2-pentene (8) and crystallographically with six known 1,1-diaryl-2-tert-alkylethenes (2). The trisubstituted alkenes formed three groups with 1) large angle distortion with moderate twisting (1 a, 1 b, and 7), 2) moderate bending with a large range of torsional angles (2), and 3) little bending or twisting (1 b and 8). For the entire series, there appears to be a delicate balance between angle and torsional deformation, but twisting appears to produce smaller relief from steric strain than angle bending. In the crystallographically characterized trisubstituted alkenes, the choice between the two is mainly determined by more subtle packing forces.     

DIFFERENTIAL EFFECTS OF A DNA-SYNTHESIS MUTATION ON UV-INDUCED MUTATION YIELDS IN VEGETATIVE CELLS AND SPORES OF BACILLUS SUBTILIS

Abstract— The absorption and emission properties of the photochemically produced dipyrimidine adducts are analyzed at 300 and 77K. Those adducts which have a saturated C(5)—C(6) bond in the pyrimidin-2,4-dione (Pyr) ring and a pyrimidin-2-one (Pyo) ring behave spectroscopically as a substituted Pyo. However, those consisting of one Pyr and one Pyo moiety can be considered as bichromophoric molecules and their spectral properties can be understood in terms of the relative torsional angle between the two rings. The adduct with the most bulky substituents ortho to the torsional bond bears the largest torsional angle and exhibits relatively independent absorption and emission phenomenon. At the other extreme, those adducts with no substituents at this position exist as almost planar molecules and exhibit considerable overlap of absorption bands as well as room temperature fluorescence which, in certain cases, is characteristic of intramolecular exciplex interaction. Using inter-ring torsional angles of ortho-substituted biphenyl molecules as a basis for comparative calculation, quantitative estimates of the torsional angles in dipyrimidine adducts at 300K have been made.     

The effect of protonation on the thermal isomerization of stilbazolium betaines

MINDOC calculations have been carried out on the protonated and unprotonated forms of a stilbazolium betaine. The results show (1) a strong increase by 24 kcal/mol of the torsional barrier around the central bond upon protonation, (2) polar structures for the protonated as well as the unprotonated forms, and (3) strong alterations of the polar structure of the latter during isomerization, and predict a higher pK value for the cis isomer, particularly, in the case of less polar and less protonic solvents.     

A new method for fast and accurate derivation of molecular conformations

During molecular simulations, three-dimensional conformations of biomolecules are calculated from the values of their bond angles, bond lengths, and torsional angles. In this paper we study how to efficiently derive three-dimensional molecular conformations from the values of torsional angles. This case is of broad interest as torsional angles greatly affect molecular shape and are always taken into account during simulations. We first review two widely used methods for deriving molecular conformations, the simple rotations scheme and the Denavit-Hartenberg local frames method. We discuss their disadvantages which include extensive bookkeeping, accumulation of numerical errors, and redundancies in the local frames used. Then we introduce a new, fast, and accurate method called the atomgroup local frames method. This new method not only eliminates the disadvantages of earlier approaches but also provides lazy evaluation of atom positions and reduces the computational cost. Our method is especially useful in applications where many conformations are generated or updated such as in energy minimization and conformational search.     

Conformational polymorphism in bicalutamide: a quantum chemical study

Bicalutamide is an anti-neoplastic drug widely used for the treatment of prostate cancer and it exhibits conformational polymorphism. Three crystal structures of bicalutamide are reported as racemic mixtures, two of which are polymorphs. In addition, three co-crystals are also reported—two with organic coformers and one with adrenoreceptor (the macromolecular target). All the reported structures show significant conformational differences. Quantum chemical B3LYP/6-31+G(d,p) analysis has been carried out to understand the interplay of intra- and intermolecular interactions leading to the conformational preferences in this molecule. The difference between the two polymorphic forms has been traced to the C5–S8–C11–C12 torsional angle. Inside the cavity of androgen receptor, a completely different conformation is found but it does not correspond to any local minima on the potential energy surface of the drug. A relatively rigid torsional angle C11–C12–C15–N17 is also expected due to a strong five-membered ring intramolecular hydrogen bond (H–O13–C12–C15–O16), which has been reported to be desirable; quantum chemical analysis revealed that this rigidity is of the order of 11 kcal/mol. Ab initio calculations demonstrate that polymorphs and polymorphic co-crystals differ in the extent of intra- and intermolecular hydrogen bonding interactions. The strength of the intermolecular interactions associated with these structures is analyzed in terms of energy release due to dimerization.     

Conformational analysis and kinetics of ring inversion for methylene- and dimethylsilyl-bridged dicyclooctatetraene

Dicyclooctatetraenylmethane (1) and dicyclooctatetraenyldimethylsilane (2) in THF-d(8) at 272 K exist as mixtures of diastereomers in ratios of 1:0.8 and 1:1, respectively. Nine energy minima (four meso and five racemic conformers) were located for each compound by geometry optimization at the HF/6-31G level of theory. The effects of torsional strain, steric interactions and dynamic electron correlation were analyzed. The diastereomeric ratios for 1 and 2 were reproduced reasonably well from the total energy calculated for each conformer corrected for its conformational enthalpy and entropy contributions. The ratio of rate constants for bond shift (BS) (k(BS)(1)/k(BS)(2)) is three times greater than the corresponding ratio for ring inversion. This suggests that additional substituent effects, such as pi interactions, are operative in the transition state for BS.