The conventional view that the σCC and σCH bonds in alkanes and unsaturated hydrocarbons are so highly localized that their non-steric interactions are negligible is scrutinized by the block-localized wavefunction (BLW) method. Even molecules considered conventionally to be "strain free" and "unperturbed" have surprisingly large and quite significant total σ-BLW-delocalization energies (DEs) due to their geminal and vicinal hyperconjugative interactions. Thus, the computed BLW-DEs (in kcal mol(-1)) for the antiperiplanar conformations of the n-alkanes (C(N)H(2N+2), N = 1-10) range from 11.6 for ethane to 82.2 for n-decane and are 50.9 for cyclohexane and 91.0 for adamantane. Although σ-electron delocalization in unsaturated hydrocarbons usually is ignored, the σ-BLW-DEs (in kcal mol(-1)) are substantial, as exemplified by D2h ethylene (9.0), triplet D2d ethylene (16.4), allene (19.3), butadiene (19.0), hexatriene (28.3), benzene (28.1), and cyclobutadiene (21.1). While each individual geminal and vicinal hyperconjugative interaction between hydrocarbon σ-bonding and σ-antibonding orbitals tends to be smaller than an individual π conjugative interaction (e.g., 10.2 kcal mol(-1) in anti-1,3-butadiene, the presence of many σ-hyperconjugative interactions (e.g., a total of 12 in anti-1,3-butadiene, see text), result in substantial total σ-stabilization energies (e.g., 19.0 kcal mol(-1) for butadiene), which may surpass those from the π interactions. Although large in magnitude, σ-electron delocalization energies often are obscured by cancellation when two hydrocarbons are compared. Rather than being strain-free, cyclohexane, adamantane, and diamantane suffer from their increasing number of intramolecular 1,4-C…C repulsions resulting in elongated C-C bond lengths and reduced σ-hyperconjugation, compared to the (skew-free) antiperiplanar n-alkane conformers. Instead of being inconsequential, σ-bond interactions are important and merit consideration.

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00894-014-2228-2DOI Listing

Publication Analysis

Top Keywords

kcal mol-1
16
unsaturated hydrocarbons
8
geminal vicinal
8
vicinal hyperconjugative
8
σ-electron delocalization
8
interactions
5
large σ-hyperconjugation
4
σ-hyperconjugation alkanes
4
alkanes alkenes
4
alkenes conventional
4

Similar Publications

Using methods of DFT, we investigated the effect of electron withdrawing and electron donating groups on the relative stability of tentative glycosyl donor reaction intermediates. The calculation shows that by changing the stereoelectronic properties of the protecting group, we can influence the stability of the dioxolenium type of intermediates by up to 10 kcal mol, and that by increasing nucleophillicity of the 4--Bz group, the dioxolenium intermediate becomes more stable than a triflate-donor pair. We exploited this mechanism to design galactosyl donors with custom protecting groups on O2 and O4, and investigated the outcome of the reaction with cyclohexanol.

View Article and Find Full Text PDF

Predicting reaction barriers for arbitrary configurations based on only a limited set of density functional theory (DFT) calculations would render the design of catalysts or the simulation of reactions within complex materials highly efficient. We here propose Gaussian process regression (GPR) as a method of choice if DFT calculations are limited to hundreds or thousands of barrier calculations. For the case of hydrogen atom transfer in proteins, an important reaction in chemistry and biology, we obtain a mean absolute error of 3.

View Article and Find Full Text PDF

Molecular modelling and optimization of a high-affinity nanobody targeting the nipah virus fusion protein through in silico site-directed mutagenesis.

Comput Biol Chem

January 2025

Virology and Vaccine Research and Development Program, Department of Science and Technology-Industrial Technology Development Institute, Taguig City, Metro Manila 1631, Philippines; S&T Fellows Program, Department of Science and Technology, Taguig City, Metro Manila 1631, Philippines; Department of Biology, College of Arts and Sciences, University of the Philippines - Manila, Metro Manila 1000, Philippines. Electronic address:

Nipah virus (NiV) is a re-emerging zoonotic pathogen with a high mortality rate and no effective treatments, prompting the search for new antiviral strategies. While conventional antiviral drugs are often limited by issues such as poor specificity, off-target effects, and resistance development, nanobodies offer distinct advantages. These small, single-domain antibodies exhibit high specificity and stability, making them ideal candidates for antiviral therapy.

View Article and Find Full Text PDF

Understanding the chemistry of the inert actinide oxo bond in actinyl ions AnO22+ is important for controlling actinide behavior in the environment, during separations, and in nuclear waste (An = U, Np, Pu). The thioether calixarene TC4A (4-tert-butyltetrathiacalix[4]arene) binds equatorially to [AnO2]n+ (An = U, Np) forming a conical pocket that differentiates the two trans-oxo groups. The 'ate' complexes, [A]2[UO2(TC4A)] (A = [Li(DME)2], HNEt3) and [HNEt3]2[NpO2(TC4A)], enable selective oxo chemistry.

View Article and Find Full Text PDF

Context: Cation-π and cation-lone pair interactions between 3d-metal (II) ions [Fe(II), Co(II), Ni(II) and Cu(II)] and furan are explored in the formation of 1:1 and 1:2 type complexes. Both cation-π (IE = -192.27 to -312.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!