Partitioning of methyl internal rotational barrier energy of thioacetaldehyde

The nature of methyl internal rotational barrier in thioacetaldehyde has been investigated by relaxation effect, natural bond orbital (NBO) analysis and Pauling exchange interactions. The true experimental barrier can be obtained by considering fully relaxed rotation. Nuclear-electron attraction term is a barrier forming term in the fully relaxed rotation, but it appears as an antibarrier for rigid rotation. It is seen that during methyl rotation, the torsional mode is coupled with the aldehydic hydrogen out-of-plane wagging motion. Natural bond orbital analysis shows that the principal barrier forming term originates from the C-C bond. The lengthening of the C-C bond is explained by considering charge transfer interaction between several bonding and antibonding orbitals in the C-C bond region, which leads to higher bonding overlap for the eclipsed conformer compared to the staggered conformer. S-C(σ)/C^me-Hp and C-H_ald/C_me-H_op interactions appear to be the main barrier-forming Pauling exchange terms but have less contribution to make to the barrier compared to the C-C bond interaction.     

Understanding glycine conformation through molecular orbitals

The four most stable C(s) conformers of glycine have been investigated using a variety of quantum-mechanical methods based on Hartree-Fock theory, density-functional theory (B3LYP and statistical average of orbital potential), and electron propagation (OVGF) treatments. Information obtained from these models were analyzed in coordinate and momentum spaces using dual space analysis to provide insight based on orbitals into the bonding mechanisms of glycine conformers, which are generated by rotation of C-O(H) (II), C-C (III), and C-N (IV) bonds from the global minimum structure (I). Wave functions generated from the B3LYP/TZVP model revealed that each rotation produced a unique set of fingerprint orbitals that correspond to a specific group of outer valence orbitals, generally of a' symmetry. Orbitals 14a', 13a', 12a', and 11a' are identified as the fingerprint orbitals for the C-O(H) (II) rotation, whereas fingerprint orbitals for the C-C (III) bond rotation are located as 16a' [highest occupied molecular orbital (HOMO)], 15a' [next highest molecular occupied molecular orbital (NHOMO)], 14a', and 12a' orbitals. Fingerprint orbitals for IV generated by the combined rotations around the C-C, C-O(H), and C-N bonds are found as 16a', 15a', 14a', 13a', and 11a', as well as in orbitals 2a" and 1a". Orbital 14a' is identified as the fingerprint orbital for all three conformational processes, as it is the only orbital in the outer valence region which is significantly affected by the conformational processes regardless rotation of which bond. Binding energies, molecular geometries, and other molecular properties such as dipole moments calculated based on the specified treatments agree well with available experimental measurements and with previous theoretical calculation.     

Thermodynamic functions of conformational changes. 2. Conformational entropy as a measure of information accumulation

Various folded molecular structures contain different amount of information. The relative amount of information may be related to relative entropy or entropy change. The conformational entropy change for n-butane has been computed as the function of rotation around the central C-C bond. It appears that the g+ or g- conformers contain about 16% more information than the anti-structure. Furthermore, the syn conformation with the two groups eclipsed contained about 42% more information than the fully staggered anti orientation. The conformational entropy function calculated from 3N - 7 internal degrees of freedom was found to be a continuous function.     

Pure through‐bond state in organic molecules for analysis of the relationship between intramolecular interactions and total energy

Ab initio configuration interaction through‐space/bond interaction analysis was proposed for the examination of specific intramolecular interactions including the effect of electron correlations. To test the effectiveness of our method, we applied it to rotational barrier in ethane. The results of our test suggest that the insensitivity of the ethane barrier to geometric relaxations is intimately connected with the cancellation of interactions through orbital overlaps and other factors. The orbital overlaps include exchange repulsion and hyperconjugation; other factors include classic Coulomb interaction and changes in bond orbital energy. The rotational state without the barrier (pure through‐bond state) can be achieved by deleting not only the “vicinal” interactions between the C? H bonds that belong to different methyl groups but also the “geminal” interactions within the methyl groups. Our mixing analysis of molecular orbitals supports the superiority of the staggered conformer by hyperconjugation. Moreover, it was demonstrated that our treatment could be applied to excited states as well as to the ground state, including electron correlation effects. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003     

The substituted alkyne 3-heptyne is eclipsed

Although butane exists in staggered anti and gauche conformations, when the ethyl groups are separated by a C[triple bond]C triple bond (3-hexyne), the stable conformation changes to eclipsed, (1)C(2v). Using rotational microwave spectroscopy, we have studied another example, 3-heptyne, the C[triple bond]C elongated analogue of pentane. The most stable conformer of pentane has anti-anti (AA) conformations about the central C-C bonds (C(2v)) and the next most stable has a gauche dihedral angle (GA, C1). This microwave study determines that the extended analogue of the AA form is not staggered about the C[triple bond]C axis but eclipsed (Cs). Also, the elongated analogue of the GA conformer is also not staggered but nearly eclipsed. The conformations of low-polarity substituted acetylenes is determined by dispersion attractions between the end groups. A microwave study of the AA and GA conformers of pentane is also reported.     

Conformational preferences in methylsilane and disilane. A quantitative non-empirical analysis of the importance of the hyperconjugative interactions

We have investigated the importance of the hyperconjugative interactions in determining the conformational preferences in methylsilane and disilane, and for comparative purposes also in ethane, using a procedure that provides quantitative information about the energy effects associated with orbital interactions. It is found that (1) these interactions are in all cases destabilizing and less destabilizing in the staggered conformation and that (2) in the absence of these interactions, in ethane the staggered conformer is still more stable, while in methylsilane and disilane the eclipsed conformer becomes more stable.We have also investigated the effects of each type of orbital interaction in terms of a quantitative perturbational analysis.     

Van der waals interactions and decrease of the rotational barrier of methyl-sized rotators: a theoretical study

Rotational barriers of methyl-sized molecular rotators are investigated theoretically using ab initio and empirical force field calculations in molecular models simulating various environmental conditions experienced by the molecular rotors. Calculations on neopentane surrounded by methyl groups suggest that the neopentane's methyl rotational potential energy barrier can be reduced by up to an order of magnitude by locating satellite functional groups around the rotator at a geometry that destabilizes the staggered conformation of the rotator through van der Waals repulsive interactions and reduces the staggered/eclipsed relative energy difference. Molecular mechanics and molecular dynamics calculations indicate that this barrier-reducing geometry can also be found in molecular rotators surface mounted on graphite surfaces or carbon nanotube models. In these models, molecular dynamics simulations show that the rotation of methyl-sized functional groups can be catalyzed by van der Waals interactions, thus making very rigid rotators become thermally activated at room temperature. These results are discussed in the context of design of nanostructures and use of methyl groups as markers for microenvironmental conditions.     

Steric strain versus hyperconjugative stabilization in ethane congeners

Rotation barriers in the group IVB ethane congeners H(3)X-YH(3) (X, Y = C, Si, Ge, Sn, Pb) have been systematically studied and deciphered using the ab initio valence bond theory in terms of the steric strain and hyperconjugation effect. Our results show that in all cases the rotation barriers are dominated by the steric repulsion whereas the hyperconjugative interaction between the X-H bond orbitals and the vicinal Y-H antibond orbitals (and vice versa) plays a secondary role, although indeed the hyperconjugation effect favors staggered structures. By the independent estimations of the hyperconjugative and steric interactions in the process of rotations, we found that the structural effect which mainly refers to the central X-Y bond relaxation makes a small contribution to the rotational barriers. Therefore, we conclude that both the rigid and fully relaxed rotations in the group IVB ethane congeners H(3)X-YH(3) observe the same mechanism which is governed by the conventional steric repulsion.     

Toward understanding the nature of internal rotation barriers with a new energy partition scheme: ethane and n-butane

On the basis of an alternative energy partition scheme where density-based quantification of the steric effect was proposed [Liu, S. B. J. Chem. Phys. 2007, 126, 244103], the origin of the internal rotation barrier between the eclipsed and staggered conformers of ethane and n-butane is systematically investigated in this work. Within the new scheme, the total electronic energy is decomposed into three independent components, steric, electrostatic, and fermionic quantum. The steric energy defined in this way is repulsive, exclusive, and extensive and intrinsically linked to Bader's atoms in molecules approach. Two kinds of differences, adiabatic (with optimal structure) and vertical (with fixed geometry), are considered for the molecules in this work. We find that in the adiabatic case the eclipsed conformer possesses a larger steric repulsion than the staggered conformer for both molecules, but in the vertical cases the staggered conformer retains a larger steric repulsion. For ethane, a linear relationship between the total energy difference and the fermionic quantum energy difference is discovered. This linear relationship, however, does not hold for n-butane, whose behaviors in energy component differences are found to be more complicated. The impact of basis set and density functional choices on energy components from the new energy partition scheme has been investigated, as has its comparison with another definition of the steric effect in the literature in terms of the natural bond orbital analysis through the Pauli Exclusion Principle. In addition, profiles of conceptual density functional theory reactivity indices as a function of dihedral angle changes have been examined. Put together, these results suggest that the new energy partition scheme provides insights from a different perspective of internal rotation barriers.     

Internal rotation study of some sixfold barrier molecules

Molecular orbital calculations of sixfold barriers in nitromethane, methyl boron difluoride, and trifluoronitromethane were performed by various Hartree-Fock and electron correlation methods. In those calculations, staggered and eclipsed conformations are of primary concern. These results indicated that for CH₃NO₂ and CH₃BF₂ the staggered conformations are more stable, while CF₃NO₂ has a more stable conformation in an eclipsed form. Both conformations do not differ significantly, which may account for the low internal rotational barrier of each molecule. Values of the barrier calculated by the Møller-Plesset perturbation and the quadratic configuration interaction methods did not match the experimental results. However, better internal rotational barrier values of each molecule were observed when the improved better basis sets and the Hartree-Fock method were selected. © 1997 John Wiley & Sons, Inc.     

A study of the ethane internal rotation barrier

In an effort to deduce the source of the ethane internal rotation barrier, we have investigated the contributions of exchange energy and orthogonality: two effects that are required by the Pauli principle. Fully antisymmetrized, partially antisymmetrized and non-antisymmetrized optimized orbital product wavefunctions were determined. Results show that the exchange energy contribution to the barrier is negligible only when it is evaluated from energy-localized orbitals; even in this case the small total results from cancellation of large contributions. The barrier is apparently caused by the orthogonality that is required between CH orbitals on opposite ends of the molecule. The CC bond has insignificant participation in this effect.     

A theoretical study of the staggered and eclipsed forms of the dinuclear complex Mn Re(CO)10

Two possible conformers of the dinuclear complex Mn Re(CO)10, each of C(4v) symmetry, with eclipsed and staggered conformations, have been analyzed theoretically. Using both the B3LYP and BP86 density functionals we find that the staggered form is lower in energy. A determination of the B3LYP potential energy surface as a function of the Mn-Re distance is presented for both conformers. The computed bond lengths, bond angles, and rotational constant for the staggered conformation compare favorably with the results from microwave experiments. The harmonic frequencies for the staggered structure have been determined using several basis sets, with both analytical and finite difference methods. These unscaled vibrational frequencies, together with their intensities for both infrared and Raman activity, are used to assign the three most intense experimental IR and Raman bands, and in particular, the nu(CO) region. The lowest A(2) vibration was calculated to occur at 41 cm(-1) in the staggered conformer; this frequency becomes imaginary in the (saddle point) eclipsed form. Several fundamentals remain to be observed experimentally.     

Monte carlo simulation of ethane in dilute aqueous solution

A Monte Carlo simulation of a dilute aqueous solution of ethane both fixed and flexible conformation runs shows that energetically and entropically the eclipsed conformation of ethane is preferred to the staggered conformation in solution which is a reversal in the gas phase.     

Highly stereoselective grignard addition to cis-substituted C-cyclopropylaldonitrones. The bisected s-trans transition state can be stabilized effectively by the Lewis acid-coordination

We previously found that Grignard addition to a C-cyclopropylaldonitrone, C-[cis-2-(N,N-diethylcarbamoyl)-trans-2-phenylcyclopropyl]-N-benzylaldonitrone (1), stereoselectively gave the anti-product 3, in which the stereoselectivity was particularly high when MgBr(2) was the additive. In this study, the reaction pathway was investigated in detail. The stereoselective addition was initially thought to occur via either a 1,5-chelation-controlled or a bisected s-trans conformation-controlled pathway. However, Grignard addition to a nonchelating silyl ether-type substrate, C-[cis-2-(tert-butyldiphenylsilyloxymethyl)-trans-2-phenylcyclopropyl]-N-benzylaldonitrone (7), also gave the anti-product 9 with high stereoselectivity suggesting that chelation is not important in the reaction. Theoretical calculations of C-cyclopropylaldonitrones showed that the coordination of Mg(2+) at the nitrone oxygen significantly stabilizes the bisected s-trans conformer due to the effective hyperconjugation between the pi* of the nitrone C=N bond and the electron-donating cyclopropane orbitals. This kind of orbital interaction is able to stabilize the transition state of the nucleophilic addition and is maximized in the bisected conformation, in which the orbitals of the forming bond and the cyclopropane C-C bond are in an almost planar arrangement. Thus, the high stereoselectivity can be explained by nucleophilic attack on the less hindered side of the C=N bond of the substrates in the Mg(2+)-coordinated bisected s-trans conformation.     

Conformation-specific Raman bands and electronic conjugation in substituted thioanisoles

Nonresonant Raman spectra and conformational stability are studied for thioanisole (TA) and substituted analogues [4-XTA, X = NO(2) (1), CN (2), H (3), CH(3) (4), and NH(2) (5)] at the 4-position. The ring-substituent (SCH(3)) vibrational modes of out-of-plane bending and torsional types are calculated to have strong Raman scattering activities only for the vertical conformers. Agreement between observed and calculated Raman spectra is analyzed numerically. The conformational stability of the SCH(3) rotation changes systematically to the electron-withdrawing character of the substituents. The rotational barrier is calculated satisfactorily by B3LYP/6-31++G(d,p) calculations, whereas the second- to fourth-order M?ller-Presset perturbation theory and coupled-cluster with single- and double-excitation calculations tend to overestimate conformational energy barriers with respect to coplanar forms. The coplanar form is obtained for 1 and 2, whereas the vertical conformer is favorable for 4 and 5. The origin of the conformational energy difference, DeltaE, is demonstrated on the basis of canonical molecular orbitals and natural bond orbitals (NBOs) of the ground state. The natural bond orbital interaction between a nonbonding n(S) orbital of the S atom and a pi orbital of the benzene ring is shown to stabilize the coplanar form predominantly. A linear relationship is obtained between the energy of the highest occupied molecular orbitals and DeltaE. The n(S)-pi interaction energy, E(2), based on the NBO representation and the Hammet constants also change linearly with respect to DeltaE.     

On the stability and structure of β-fluoro-substituted radical anions of acetamides. An EPR study at 3 K

An EPR study at 3 K of X-ray irradiated monofluoroacetamide does not reveal a radical anion species, despite the fact that the radical anion in trifluoroacetamide is stable at 77 K. This difference in stability has been found to be dependent on the conformation of the -CF₃ group (eclipsed) versus the -CFH₂ group (staggered). The eclipsed conformation permits effective σ-π hyperconjugation in stabilizing the radical anion. An INDO calculation of CF₃CONH₂^? suggests that the radical site is pyramidal rather than planar with a non-planar angle of 32° and a dihedral angle for the eclipsed fluorine, relative to the nearly π-like orbital, of 30°.     

Electronic control of the stereochemistry of electrophilic and nucleophilic attack on double bonds in 6-membered rings

CNDO and ab initio MO calculations reveal a deformation of the π^* and π orbitals of cyclohexene in the axial directions, thus providing a reasonable explanation for the axial attack on cyclohexene either by electrophiles or by nucleophiles. It is shown in the case of 1-butene by an ab initio calculation that this orbital deformation is a result of the mixing of the π and σ orbitals of the double bond under the influence of the allylic C-C bond.     

Structure and bonding energy analysis of cationic metal-ylyne complexes of molybdenum and tungsten, [(MeCN)(PMe3)4M≡EMes]+ (M = Mo, W; E = Si, Ge, Sn, Pb): a theoretical study

The molecular and electronic structures and bonding analysis of terminal cationic metal-ylyne complexes (MeCN)(PMe(3))(4)M≡EMes](+) (M = Mo, W; E = Si, Ge, Sn, Pb) were investigated using DFT/BP86/TZ2P/ZORA level of theory. The calculated geometrical parameters for the model complexes are in good agreement with the reported experimental values. The M-E σ-bonding orbitals are slightly polarized toward E except in the complex [(MeCN)(PMe(3))(4)W(SnMes)](+), where the M-E σ-bonding orbital is slightly polarized toward the W atom. The M-E π-bonding orbitals are highly polarized toward the metal atom. In all complexes, the π-bonding contribution to the total M≡EMes bond is greater than that of the σ-bonding contribution and increases upon going from M = Mo to W. The values of orbital interaction ΔE(orb) are significantly larger in all studied complexes I-VIII than the electrostatic interaction ΔE(elstat). The absolute values of the interaction energy, as well as the bond dissociation energy, decrease in the order Si > Ge > Sn > Pb, and the tungsten complexes have stronger bonding than the molybdenum complexes.     

Conformational behavior of ethane molecule encapsulated in a nanotube

Investigation of conformation transformations of ethane molecule in single-wall carbon nanotubes by the hybrid DFT method PBE/3z showed that the parameters and the character of the nanotube (length, diameter, open, closed, or semiopened) affect the conformational behavior of the encapsulated molecule leveling the difference in the energy or even resulting in the inversion of the relative stability of the staggered and eclipsed forms.