Conformational Stability of 1-Butene: An Electron Momentum Spectroscopy Investigation

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.

Adsorption of Olefins at Cupric Ions in Metal-Organic Framework HKUST-1 Explored by Hyperfine Spectroscopy

Metal-organic frameworks (MOFs) represent a promising platform for gas storage and separation. In this work, adsorption of olefins in Zn-doped HKUST-1 metal-organic framework is explored with hyperfine spectroscopy. By means of electron-nuclear double resonance and hyperfine sublevel correlation spectroscopy, we detect the interaction between the electron spins of the Cu²⁺ sites of the MOF and the ¹H nuclear spins of adsorbed C₂H₄ and C₄H₈. Further analysis of the measured spectra allows us to precisely locate the protons in the vicinity of the Cu²⁺ ions and thereby establish ensemble-averaged structural models of the olefin molecules adsorbed at the open metal sites of HKUST-1.

Deeper Insights into Conformational Analysis of cis-Butene and 1-Alkenes as Monomers and Dimers: QTAIM, NCI, and DFT Approach

A few theoretical and experimental studies have been done so far about the properties and the conformational analysis of alkenes as monomers and dimers. Deeper insights into the conformational analysis of monomers and dimers of alkenes and the relation with boiling point are done in this work. In low-lying cis-butene, there is no repulsive interaction between methyl groups but there is an attractive hydrogen-hydrogen bonding. In monomers of 1-alkenes, the most stable conformer has bent-inward geometry which favors the π bond interaction with methyl/methylene hydrogen/carbon atoms. Conversely, each alkene’s molecule in the corresponding most stable alkene’s dimer has a straight, zig-zag geometry. Two straight, zig-zag alkene’s molecules in the corresponding most stable dimer have only one type of intermolecular interaction (hydrogen-hydrogen bonding). As a consequence, very good linear relationships between a physical property (such as boiling point) and theoretical parameters are obtained.

Sequential and direct ionic excitation in the strong-field ionization of 1-butene molecules

We study the Strong-Field Ionization (SFI) of the hydrocarbon 1-butene as a function of wavelength using photoion-photoelectron covariance and coincidence spectroscopy. We observe a striking transition in the fragment-associated photoelectron spectra: from a single Above Threshold Ionization (ATI) progression for photon energies less than the cation D0-D1 gap to two ATI progressions for a photon energy greater than this gap. For the first case, electronically excited cations are created by SFI populating the ground cationic state D0, followed by sequential post-ionization excitation. For the second case, direct sub-cycle SFI to the D1 excited cation state contributes significantly. Our experiments access ionization dynamics in a regime where strong-field and resonance-enhanced processes can interplay.

Electron Momentum Spectroscopy Investigation of Molecular Conformations of Ethanol Considering Vibrational Effects

The interpretation of experimental electron momentum distributions (EMDs) of ethanol, one of the simplest molecules having conformers, has confused researchers for years. High-level calculations of Dyson orbital EMDs by thermally averaging the gauche and trans conformers as well as molecular dynamical simulations failed to quantitatively reproduce the experiments for some of the outer valence orbitals. In this work, the valence shell electron binding energy spectrum and EMDs of ethanol are revisited by the high-sensitivity electron momentum spectrometer employing symmetric noncoplanar geometry at an incident energy of 1200 eV plus binding energy, together with a detailed analysis of the influence of vibrational motions on the EMDs for the two conformers employing a harmonic analytical quantum mechanical (HAQM) approach by taking into account all of the vibrational modes. The significant discrepancies between theories and experiments in previous works have now been interpreted quantitatively, indicating that the vibrational effect plays a significant role in reproducing the experimental results, not only through the low-frequency OH and CH₃ torsion modes but also through other high-frequency ones. Rational explanation of experimental momentum profiles provides solid evidence that the trans conformer is slightly more stable than the gauche conformer, in accordance with thermodynamic predictions and other experiments. The case of ethanol demonstrates the significance of considering vibrational effects when performing a conformational study on flexible molecules using electron momentum spectroscopy.

Vibrational Effects on Electron Momentum Distributions of Outer-Valence Orbitals of Oxetane

Vibrational effects on electron momentum distributions (EMDs) of outer-valence orbitals of oxetane are computed with a comprehensive consideration of all vibrational modes. It is found that vibrational motions influence EMDs of all outer-valence orbitals noticeably. The agreement between theoretical and experimental momentum profiles of the first five orbitals is greatly improved when including molecular vibrations in the calculation. In particular, the large turn-up at low momentum in the experimental momentum profile of the 3b1 orbital is well interpreted by vibrational effects, indicating that, besides the low-frequency ring-puckering mode, C-H stretching motion also plays a significant role in affecting EMDs of outer-valence orbitals of oxetane. The case of oxetane exhibits the significance of checking vibrational effects when performing electron momentum spectroscopy measurements.

Electron momentum spectroscopy of dimethyl ether taking account of nuclear dynamics in the electronic ground state

The influence of nuclear dynamics in the electronic ground state on the (e,2e) momentum profiles of dimethyl ether has been analyzed using the harmonic analytical quantum mechanical and Born-Oppenheimer molecular dynamics approaches. In spite of fundamental methodological differences, results obtained with both approaches consistently demonstrate that molecular vibrations in the electronic ground state have a most appreciable influence on the momentum profiles associated to the 2b1, 6a1, 4b2, and 1a2 orbitals. Taking this influence into account considerably improves the agreement between theoretical and newly obtained experimental momentum profiles, with improved statistical accuracy. Both approaches point out in particular the most appreciable role which is played by a few specific molecular vibrations of A1, B1, and B2 symmetries, which correspond to C-H stretching and H-C-H bending modes. In line with the Herzberg-Teller principle, the influence of these molecular vibrations on the computed momentum profiles can be unraveled from considerations on the symmetry characteristics of orbitals and their energy spacing.

Theoretical study of molecular vibrations in electron momentum spectroscopy experiments on furan: an analytical versus a molecular dynamical approach

The influence of thermally induced nuclear dynamics (molecular vibrations) in the initial electronic ground state on the valence orbital momentum profiles of furan has been theoretically investigated using two different approaches. The first of these approaches employs the principles of Born-Oppenheimer molecular dynamics, whereas the so-called harmonic analytical quantum mechanical approach resorts to an analytical decomposition of contributions arising from quantized harmonic vibrational eigenstates. In spite of their intrinsic differences, the two approaches enable consistent insights into the electron momentum distributions inferred from new measurements employing electron momentum spectroscopy and an electron impact energy of 1.2 keV. Both approaches point out in particular an appreciable influence of a few specific molecular vibrations of A1 symmetry on the 9a1 momentum profile, which can be unravelled from considerations on the symmetry characteristics of orbitals and their energy spacing.

Ring-puckering effects on electron momentum distributions of valence orbitals of oxetane

The binding energy spectra and electron momentum distributions for the outer-valence molecular orbitals of oxetane have been measured utilizing (e, 2e) electron momentum spectrometer with non-coplanar asymmetric geometry at the impact energy of 2500 eV. The experimental momentum distributions were compared with the density functional theory calculations employing B3LYP hybrid functional with aug-cc-pVTZ basis set. It was found that the calculation at planar geometry (C2v) completely fails to interpret the large "turn-up" at low momentum region in electron momentum distribution of the highest occupied molecular orbital (HOMO) 3b1, while the calculations considering the thermal abundances of planar (C2v) and bent (Cs) conformers or the thermally populated vibrational states of ring-puckering motion have significantly improved the agreement. The results indicate that the ring-puckering motion of oxetane has a strong effect on the electron density distribution of HOMO.

Electron momentum spectroscopy of 1-butene: a theoretical analysis using molecular dynamics and molecular quantum similarity

The results of experimental studies of the valence electronic structure of 1-butene by means of electron momentum spectroscopy (EMS) have been reinterpreted on the basis of molecular dynamical simulations in conjunction with the classical MM3 force field. The computed atomic trajectories demonstrate the importance of thermally induced nuclear dynamics in the electronic neutral ground state, in the form of significant deviations from stationary points on the potential energy surface and considerable variations of the C-C-C-C dihedral angle. These motions are found to have a considerable influence on the computed spectral bands and outer-valence electron momentum distributions. Euclidean distances between spherically averaged electron momentum densities confirm that thermally induced nuclear motions need to be fully taken into account for a consistent interpretation of the results of EMS experiments on conformationally flexible molecules.

Conformations and CH/π interactions in aliphatic alkynes and alkenes

The carbon 1s photoelectron spectra of a series of aliphatic alkynes and alkenes that have the possibility of possessing two or more conformers have been recorded with high resolution. The two conformers of 2-hexyne and 4-methyl-1-pentyne, anti and gauche, have been identified and quantified from an analysis of their carbon 1s photoelectron spectra, yielding 30 ± 5% and 70 ± 6% anti conformers, respectively. In the case of 1-hexyne, the photoelectron spectrum is shown to provide partial information on the distribution of conformers. Central to these analyses is a pronounced ability of the C1s photoemission process to distinguish between conformers that display weak γ-CH/π hydrogen bonding and those that do not. For the corresponding alkene analogs, similar analyses of their C1s photoelectron spectra do not lead to conclusive information on the conformational equilibria, mainly because of significantly smaller chemical shifts and higher number of conformers compared with the alkynes.

Thermodynamic study of simple molecular glasses: universal features in their heat capacity and the size of the cooperatively rearranging regions

We have obtained some universal thermodynamic properties on glass transitions of molecular liquids. The heat capacity C(p) of glassy propene, which was vitrified by using a vapor-deposition technique, was measured with a newly developed adiabatic calorimeter. Propene has the lowest glass transition temperature (T(g)=56 K), the largest C(p) jump at T(g) (C(p)(lq)/C(p)(gl)~2.5), and the lowest residual entropy (S(res)~Rln2) compared with glass-forming molecules measured before. We have analyzed the present data with other hydrocarbon molecules vitrified by liquid quenching and obtained the following results: (1) The excess heat capacities are scaled well by using a Kauzmann temperature T(K), (2) The size of the cooperative rearrangement region (CRR) frozen at T(g) increases with decreasing the temperature difference between T(g) and T(K) (Kauzmann temperature), and (3) The simpler the molecule is, the larger the frozen CRR becomes. These are all supporting the validity of the Adam-Gibbs theory.

Large Amplitude Motions in Cyclopentene and 1-Butene: Quantum Chemical Insights into the Ground- and Excited State Potential Energy Surfaces

The ring-puckering motion in cyclopentene as well as the hindered internal rotation around the central C–C bond in 1-butene have been studied by high-level quantum chemical calculations. Relevant potential energy surfaces of these molecules along these large-amplitude motions are provided as well as rotational constants are given allowing for thorough comparison with recent results from time-resolved femtosecond degenerate four-wave mixing (fs DFWM) spectroscopy. Emphasis is put on the performance of various post-Hartree Fock methods, the required level of electron correlation as well as the basis set quality.

Isotope effects and the temperature dependences of the hyperfine coupling constants of muoniated sec-butyl radicals in condensed phases

Reported here is the first μSR study of the muon (A(μ)) and proton (A(p)) β-hyperfine coupling constants (Hfcc) of muoniated sec-butyl radicals, formed by muonium (Mu) addition to 1-butene and to cis- and trans-2-butene. The data are compared with in vacuo spin-unrestricted MP2 and hybrid DFT/B3YLP calculations reported in the previous paper (I), which played an important part in the interpretation of the data. The T-dependences of both the (reduced) muon, A(μ)′(T), and proton, A(p)(T), Hfcc are surprisingly well explained by a simple model, in which the calculated Hfcc from paper I at energy minima of 0 and near ±120° are thermally averaged, assuming an energy dependence given by a basic 2-fold torsional potential. Fitted torsional barriers to A(μ)′(T) from this model are similar (~3 kJ/mol) for all muoniated butyl radicals, suggesting that these are dominated by ZPE effects arising from the C−Mu bond, but for A(p)(T) exhibit wide variations depending on environment. For the cis- and trans-2-butyl radicals formed from 2-butene, A(μ)′(T) exhibits clear discontinuities at bulk butene melting points, evidence for molecular interactions enhancing these muon Hfcc in the environment of the solid state, similar to that found in earlier reports for muoniated tert-butyl. In contrast, for Mu−sec-butyl formed from 1-butene, there is no such discontinuity. The muon hfcc for the trans-2-butyl radical are seemingly very well predicted by B3LYP calculations in the solid phase, but for sec-butyl from 1-butene, showing the absence of further interactions, much better agreement is found with the MP2 calculations across the whole temperature range. Examples of large proton Hfcc near 0 K are also reported, due to eclipsed C−H bonds, in like manner to C−Mu, which then also exhibit clear discontinuities in A(p)(T) at bulk melting points. The data suggest that the good agreement found between theory and experiment from the B3LYP calculations for eclipsed bonds in the solid phase may be fortuitous. For the staggered protons of the sec-butyl radicals formed, no discontinuities are seen at all in A(p)(T), also demonstrating no further effects of molecular interactions on these particular proton Hfcc.