A Critical Analysis on the Rotation Barriers in Butane

Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory

We selected 145 reference organic molecules that include model fragments used in computer-aided drug design. We calculated 158 conformational energies and barriers using force fields, with wide applicability in commercial and free softwares and extensive application on the calculation of conformational energies of organic molecules, e.g. the UFF and DREIDING force fields, the Allinger's force fields MM3-96, MM3-00, MM4-8, the MM2-91 clones MMX and MM+, the MMFF94 force field, MM4, ab initio Hartree-Fock (HF) theory with different basis sets, the standard density functional theory B3LYP, the second-order post-HF MP2 theory and the Domain-based Local Pair Natural Orbital Coupled Cluster DLPNO-CCSD(T) theory, with the latter used for accurate reference values. The data set of the organic molecules includes hydrocarbons, haloalkanes, conjugated compounds, and oxygen-, nitrogen-, phosphorus- and sulphur-containing compounds. We reviewed in detail the conformational aspects of these model organic molecules providing the current understanding of the steric and electronic factors that determine the stability of low energy conformers and the literature including previous experimental observations and calculated findings. While progress on the computer hardware allows the calculations of thousands of conformations for later use in drug design projects, this study is an update from previous classical studies that used, as reference values, experimental ones using a variety of methods and different environments. The lowest mean error against the DLPNO-CCSD(T) reference was calculated for MP2 (0.35 kcal mol-1), followed by B3LYP (0.69 kcal mol-1) and the HF theories (0.81-1.0 kcal mol-1). As regards the force fields, the lowest errors were observed for the Allinger's force fields MM3-00 (1.28 kcal mol-1), ΜΜ3-96 (1.40 kcal mol-1) and the Halgren's MMFF94 force field (1.30 kcal mol-1) and then for the MM2-91 clones MMX (1.77 kcal mol-1) and MM+ (2.01 kcal mol-1) and MM4 (2.05 kcal mol-1). The DREIDING (3.63 kcal mol-1) and UFF (3.77 kcal mol-1) force fields have the lowest performance. These model organic molecules we used are often present as fragments in drug-like molecules. The values calculated using DLPNO-CCSD(T) make up a valuable data set for further comparisons and for improved force field parameterization.

Theoretical and X-ray evidence of electrostatic phosphonium anti and gauche effects

Sulfur, not phosphorus, is the only known third-row element capable of experiencing an electrostatic gauche effect with fluorine. Some six-membered rings containing an endocyclic phosphorus atom and a β-fluorine substituent that can interconvert to axial ( gauche relative to phosphorus) and equatorial positions were then analysed. While phosphines do not establish an electrostatic attraction between fluorine and phosphorus, some oxidised forms exhibit surprising stability for the sterically disfavoured axial orientation. Because the nature of this behaviour was not obvious, since an intramolecular hydrogen bond can appear, a phosphonium derivative was further studied and its axial conformation was found to be highly stable. A preference for the gauche arrangement appears even for the acyclic and sterically hindered (2-fluoroethyl)triphenylphosphonium cation. On the other hand, (ethane-1,2-diyl)bis(phosphonium) cations are exclusively in anti conformation due to an (+/+)-electrostatic repulsion between the positively charged phosphonium groups.

Combined spectroscopic and computational study for optimising catalyst design in hydrocarbon transformations

Molecular interactions of hydrocarbons within the confined pores of heterogeneous catalysts can influence reaction pathways, which play a crucial role in determining the overall efficacy of catalytic transformations. We probe...

Substrate Specific Metal-Ligand Cooperative Binding: Considerations for Weak Intramolecular Lewis Acid/Base Pairs

Metal-ligand cooperative binding modes were interrogated in a series of zinc bis(thiophenoxide) complexes. A weak B-S binding interaction is observed in solution between the weakly Lewis basic thiophenoxide ligands and an appended trialkylborane. The energy of this binding event is dependent upon the strength of the Lewis acid and its proximity to the zinc thiophenoxide.

Catalyst Control over Twofold and Higher-Order Stereogenicity by Atroposelective Arene Formation

Contradictory to the first intuitive impression that forging putatively flat aromatic rings evades stereoisomerism, a striking variety of atropisomeric compounds are conceivable by the formation of arenes, offering captivating avenues for catalyst-controlled stereoselective strategies. Since the assembled atropisomeric products that contain one or several rotationally restricted single bonds are characterized by especially well defined molecular architectures, they are distinctly suitable for numerous pertinent applications. In view of the fascinating arene-forming aldol condensation pathways taking place in polyketide biosynthesis (cyclases/aromatases (CYC/ARO)), the versatile small-molecule-catalyzed aldol reaction appeared as an exceptionally appealing synthetic means to prepare various unexplored atropisomeric compounds in our efforts presented herein. In our initial studies, the use of secondary amine organocatalysts provided excellent selectivities in stereoselective arene-forming aldol condensations for a broad range of atropisomeric products, such as biaryls and rotationally restricted aromatic amides. In further analogy to polyketide biosynthesis, it was also conceivable that several aromatic rings are formed in catalytic cascade reactions. The use of small-molecule catalysts thereby enabled us to transfer this concept to the conversion of unnatural and noncanonical polyketide substrates, thus giving access to atropisomers with particular value for synthetic applications. The versatility of the stereoselective aldol reactions with numerous catalytic activation modes further provided a strategy to individually control several stereogenic axes, similar to the various methodologies developed for controlling stereocenter configurations. By the use of iterative building block additions combined with catalyst-controlled aldol reactions to form the aromatic rings, stereodivergent pathways for catalyst-substrate-matched and -mismatched products were obtained. Besides secondary amines, cinchona-alkaloid-based quaternary ammonium salts also proved to be highly efficient in overcoming severe substrate bias. The obtained atropisomeric multiaxis systems, with all of the biaryl bonds suitably restricted in rotation even at high temperatures, are spatially distinctly defined. The helical secondary structure is therefore excellently suited for several captivating applications.While previous catalyst-controlled stereoselective methods distinguish two stereoisomers for each stereogenic unit, catalyst control beyond the realms of this dualistic stereoisomerism remained unexplored. By the selective preparation of O̅ki atropisomers characterized by their sixfold stereogenicity in Rh-catalyzed [2 + 2 + 2] cyclotrimerizations, one out of the six possible stereoisomers resulting from the restricted rotation of a single bond was shown to be catalytically addressable. Catalyst control over higher-order stereogenicity therefore further interconnects conformational analysis and stereoselective catalysis and offers captivating avenues to explore uncharted stereochemical space for creating a broad range of unprecedented molecular motifs.

Internal- and rho-axis systems of molecules with one large amplitude internal motion: The geometry of rho

The internal-axis system (IAS) of molecules with a large amplitude internal motion (LAM) is determined by integrating the kinematic equation of the IAS by Lie-group and Lie-algebraic methods. Numerical examples on hydrogen peroxide, nitrous acid, and acetaldehyde demonstrate the methods. By exploiting the special product structure of the solution matrix, simple methods are devised for calculating the transformation to the rho-axis system (RAS) along with the value of the parameter ρ characterizing a RAS rotational-LAM kinetic energy operator. The parameter ρ so calculated agrees exactly with that one obtained by the Floquet method as shown in the example of acetaldehyde. Geometrical interpretation of ρ is given. The advantageous property of the RAS over the IAS in retaining simple periodic boundary conditions is numerically demonstrated.

Crystallization of lysozyme with (R)-, (S)- and (RS)-2-methyl-2,4-pentanediol

Chiral control of crystallization has ample precedent in the small-molecule world, but relatively little is known about the role of chirality in protein crystallization. In this study, lysozyme was crystallized in the presence of the chiral additive 2-methyl-2,4-pentanediol (MPD) separately using the R and S enantiomers as well as with a racemic RS mixture. Crystals grown with (R)-MPD had the most order and produced the highest resolution protein structures. This result is consistent with the observation that in the crystals grown with (R)-MPD and (RS)-MPD the crystal contacts are made by (R)-MPD, demonstrating that there is preferential interaction between lysozyme and this enantiomer. These findings suggest that chiral interactions are important in protein crystallization.

Conformational preferences of Ac-Gly-NHMe in solution

The conformational behaviour of Ac-Gly-NHMe and its fluorinated [CF₃-C(O)-Gly-NHMe] and N-methyl[Ac-Gly-N(Me)₂] derivatives is investigated in nonpolar, polar and polar protic solutions by NMR and IR spectroscopies and theoretical calculations.

Stretching and folding of 2-nanometer hydrocarbon rods

Linear alkanes CnH2n+2 in vacuum isolation are finite models for an infinite polyethylene chain. Using spontaneous Raman scattering in supersonic jet expansions for n = 13-21 in different spectral ranges, we determine the minimal chain length nh for the cohesion-driven folding of the preferred extended all-trans conformation into a hairpin structure. We treat fully stretched all-trans alkanes as molecular "nanorods" and derive Young's modulus E for the stretching of an isolated single-strand polyethylene fibre by extrapolating the longitudinal acoustic mode to infinite chain length. Two key quality parameters for accurate intra- and intermolecular force fields of hydrocarbons (nh = 18 ± 1, E = 305 ± 5 GPa) are thus derived with high accuracy from experimental spectroscopy.

On the origin of internal rotation in ammonia borane

The internal rotation in ammonia borane (AB) was studied on the basis of natural orbitals for chemical valence (NOCV) and eigenvectors for Pauli repulsion (NOPR). We found that the total hyperconjugation stabilization (ca. 5 kcal mol⁻¹), based on the charge transfer from the occupied σ (B–H) orbitals into the empty σ*(N–H), slightly favors the staggered conformation over the eclipsed one; however, the barrier to internal rotation in ammonia borane can be understood predominantly in a ‘classical’ way, as originating from the steric (Pauli) repulsion contributions (of the kinetic origin) that act solely between N–H and B–H bonds. Repulsion between the lone pair of ammonia and the adjacent B–H bonds was found to be dominant in absolute terms; however, it does not determine the rotational barrier. Similar conclusions on the role of CH↔HC repulsion appeared to be valid for isoelectronic ethane.

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The Construction and Validation of All-Atom Bulk-Phase Models of Amorphous Polymers Using the TIGER2/TIGER3 Empirical Sampling Method

A new empirical sampling method termed "temperature intervals with global exchange of replicas and reduced radii" (TIGER3) is presented and demonstrated to efficiently equilibrate entangled long-chain molecular systems such as amorphous polymers. The TIGER3 algorithm is a replica exchange method in which simulations are run in parallel over a range of temperature levels at and above a designated baseline temperature. The replicas sampled at temperature levels above the baseline are run through a series of cycles with each cycle containing four stages - heating, sampling, quenching, and temperature level reassignment. The method allows chain segments to pass through one another at elevated temperature levels during the sampling stage by reducing the van der Waals radii of the atoms, thus eliminating chain entanglement problems. Atomic radii are then returned to their regular values and re-equilibrated at elevated temperature prior to quenching to the baseline temperature. Following quenching, replicas are compared using a Metropolis Monte Carlo exchange process for the construction of an approximate Boltzmann-weighted ensemble of states and then reassigned to the elevated temperature levels for additional sampling. Further system equilibration is performed by periodic implementation of the previously developed TIGER2 algorithm between cycles of TIGER3, which applies thermal cycling without radii reduction. When coupled with a coarse-grained modeling approach, the combined TIGER2/TIGER3 algorithm yields fast equilibration of bulk-phase models of amorphous polymer, even for polymers with complex, highly branched structures. The developed method was tested by modeling the polyethylene melt. The calculated properties of chain conformation and chain segment packing agreed well with published data. The method was also applied to generate equilibrated structural models of three increasingly complex amorphous polymer systems: poly(methyl methacrylate), poly(butyl methacrylate), and DTB-succinate copolymer. Calculated glass transition temperature (T(g)) and structural parameter profile (S(q)) for each resulting polymer model were found to be in close agreement with experimental T(g) values and structural measurements obtained by x-ray diffraction, thus validating that the developed methods provide realistic models of amorphous polymer structure.