Focal-Point Conformational Analysis of Ethanol, Propanol, and Isopropanol

Tracing Photoinduced Hydrogen Migration in Alcohol Dications from Time-Resolved Molecular-Frame Photoelectron Angular Distributions

The recent implementation of attosecond and few-femtosecond X-ray pump/X-ray probe schemes in large-scale free-electron laser facilities has opened the way to visualize fast nuclear dynamics in molecules with unprecedented temporal and spatial resolution. Here, we present the results of theoretical calculations showing how polarization-averaged molecular-frame photoelectron angular distributions (PA-MFPADs) can be used to visualize the dynamics of hydrogen migration in methanol, ethanol, propanol, and isopropyl alcohol dications generated by X-ray irradiation of the corresponding neutral species. We show that changes in the PA-MFPADs with the pump-probe delay as a result of intramolecular photoelectron diffraction carry information on the dynamics of hydrogen migration in real space. Although visualization of this dynamics is more straightforward in the smaller systems, methanol and ethanol, one can still recognize the signature of that motion in propanol and isopropyl alcohol and assign a tentative path to it. A possible pathway for a corresponding experiment requires an angularly resolved detection of photoelectrons in coincidence with molecular fragment ions used to define a molecular frame of reference. Such studies have become, in principle, possible since the first XFELs with sufficiently high repetition rates have emerged. To further support our findings, we provide experimental evidence of H migration in ethanol-OD from ion-ion coincidence measurements performed with synchrotron radiation.

New Aspects of Alcohol-Alcohol and Alcohol-Water Interactions: Crystallographic and Quantum Chemical Studies of Antiparallel O-H/O-H Interactions

New modes of interaction, antiparallel O-H/O-H interactions of alcohol-alcohol dimers and alcohol-water dimers, were studied by analyzing data in the Cambridge Structural Database (CSD) and by calculating potential energy surfaces at a very accurate quantum chemical CCSD(T)/CBS level. The data reveal the existence of antiparallel interactions in crystal structures and significant interaction energies. Data from the CSD for alcohol-alcohol dimers show 49.2% of contacts with classical hydrogen bonds and 10.1% of contacts with antiparallel interactions, while for alcohol-water dimers, 59.4% of contacts are classical hydrogen bonds and only 0.6% of contacts are antiparallel interactions. The calculations were performed on methanol, ethanol, and n-propanol dimers. Classical hydrogen-bonded alcohol-alcohol and alcohol-water dimers have interaction energies of up to -6.2 kcal/mol and up to -5.5 kcal/mol, respectively. Antiparallel interactions in alcohol-alcohol and alcohol-water dimers have interaction energies of up to -4.7 kcal/mol and up to -4.4 kcal/mol, respectively. Symmetry-adapted perturbation theory analysis for antiparallel interactions shows their electrostatic nature.

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.

DFT-Based Calculation of Molecular Hyperpolarizability and SFG Intensity of Symmetric and Asymmetric Stretch Modes of Alkyl Groups

Vibrational sum frequency generation (SFG) spectroscopy has been extensively used for obtaining structural information of molecular functional groups at two-dimensional (2D) interfaces buried in the gas or liquid medium. Although the SFG experiment can be done elegantly, interpreting the measured intensity in terms of molecular orientation with respect to the lab coordinate is quite complicated. One of the main reasons is the difficulty of determining the hyperpolarizability tensors of even simple molecules that govern their SFG responses. The single-bond polarizability derivative model has been proposed to estimate the relative magnitude of SFG-active hyperpolarizability by assuming that the perturbation associated to each vibration is negligible. In this study, density functional theory was used to calculate the polarizability and dipole derivative tensors of the CH3 stretch mode of CH3I, CH3CH2I, CH3OH, and CH3CH2OH. Then, the hyperpolarizability tensors of symmetric and asymmetric vibration modes were calculated considering the Boltzmann distribution of representative conformers, which allowed us to theoretically calculate their SFG intensities at all polarization combinations as a function of the tilt angle of the CH3 group with respect to the surface normal direction. Then, the ratios of the calculated SFG intensities for the CH3 symmetric and asymmetric stretch peaks used in experimental studies for the CH3 tilt angle determination were compared. This comparison clearly showed that the effect of vibrational coupling among neighboring functional groups is significant and cannot be assumed to be negligible. This study presents new parameters that can be used in determining the average tilt angle of the CH3 group at the 2D interface with SFG measurements as well as limitations of the method.

Roles of hydrogen bonding interactions and hydrophobic effects on enhanced water structure in aqueous solutions of amphiphilic organic molecules

Insights into the solute-induced water structural transformations are essential to understand the role of water in biological and chemical reaction processes. Herein, the structural changes in water induced by amphiphilic organic molecules were investigated using concentration-dependent derivative Raman spectroscopy (DRS) combined with two-dimensional Raman correlation spectroscopy (2D Raman-COS). We shall restrict our attention in this work to binary mixtures of water with dimethyl sulfoxide (DMSO), acetone, and isopropanol (IPA), all of which have similar chemical structures. The spectral changes in O:H and OH stretching modes illustrate that the solute molecules induce an enhancement of the water structure in dilute solutions, where the enhanced degree of water structure is closely related to the size of the dipole moment of organic molecules. In addition, the transformations of solute-induced water-specific structures were evaluated by 2D Raman-COS, which shows that the strong hydrogen bond (H-bond) structure of water is more sensitive to organic molecules and induces a transition to the weak H-bond structure of water.

Conformer-Specific Desorption in Propanol Ices Probed by Chirped-Pulse Millimeter-Wave Rotational Spectroscopy

We present a new technique for the detection of molecules desorbed from an ice surface using broad-band millimeter-wave rotational spectroscopy. The approach permits interrogation of molecules that have undergone the slow warmup process of temperature-programmed desorption (TPD), analogous to the warmup phase of icy grains in the interstellar medium as they approach the central protostar. The detection is conformer- and isomer-specific and quantitative, as afforded by chirped-pulse rotational spectroscopy. To achieve this, we combine ice TPD with buffer gas cooling, followed by detection in the millimeter-wave regime. In this report we examine the TPD profiles of n- and i-propanol, the former of which may be in five different conformational isomeric forms, and which display distinct desorption profiles. The limited conformational isomerization and temperature-dependent relative yields of n-propanol conformers observed show that the desorption is highly conformer-specific.

Theoretical Investigation into a Possibility of Formation of Propylene Oxide Homochirality in Space

The preferential synthesis or destruction of a single enantiomer by ultraviolet circularly polarized light (UV-CPL) has been proposed as a possible triggering mechanism for the extraterrestrial origin of homochirality. Herein, we investigate the photoabsorption property of propylene oxide (c-C3H6O) for UV-CPL in the Lyman-α region. Our calculations show that c-C3H6O was produced by CH3+ and CH3CH(OH)CH3 or C3H7• and O (triplet). The computed electronic circular dichroism spectra show that c-C3H6O and the intermediate (CH3CH(OH)CH2+) could absorb the UV-CPL originating from the Lyman-α emitter spectrum, suggesting that the photolysis of c-C3H6O or CH3CH(OH)CH2+ upon irradiation could induce chiral symmetry breakage.

Quantum Calculations on a New CCSD(T) Machine-Learned Potential Energy Surface Reveal the Leaky Nature of Gas-Phase Trans and Gauche Ethanol Conformers

Ethanol is a molecule of fundamental interest in combustion, astrochemistry, and condensed phase as a solvent. It is characterized by two methyl rotors and trans (anti) and gauche conformers, which are known to be very close in energy. Here we show that based on rigorous quantum calculations of the vibrational zero-point state, using a new ab initio potential energy surface (PES), the ground state resembles the trans conformer, but substantial delocalization to the gauche conformer is present. This explains experimental issues about identification and isolation of the two conformers. This “leak” effect is partially quenched when deuterating the OH group, which further demonstrates the need for a quantum mechanical approach. Diffusion Monte Carlo and full-dimensional semiclassical dynamics calculations are employed. The new PES is obtained by means of a Δ-machine learning approach starting from a pre-existing low level density functional theory surface. This surface is brought to the CCSD(T) level of theory using a relatively small number of ab initio CCSD(T) energies. Agreement between the corrected PES and direct ab initio results for standard tests is excellent. One- and two-dimensional discrete variable representation calculations focusing on the trans–gauche torsional motion are also reported, in reasonable agreement with experiment.

Small Alcohols Revisited: CCSD(T) Relative Potential Energies for the Minima, First- and Second-Order Saddle Points, and Torsion-Coupled Surfaces

The elucidation of conformations and relative potential energies (rPEs) of small molecules has a long history across a diverse range of fields. Periodically, it is helpful to revisit what conformations have been investigated and to provide a consistent theoretical framework for which clear comparisons can be made. In this paper, we compute the minima, first- and second-order saddle points, and torsion-coupled surfaces for methanol, ethanol, propan-2-ol, and propanol using consistent high-level MP2 and CCSD(T) methods. While for certain molecules more rigorous methods were employed, the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pV5Z theory level was used throughout to provide relative energies of all minima and first-order saddle points. The rPE surfaces were uniformly computed at the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVTZ level. To the best of our knowledge, this represents the most extensive study for alcohols of this kind, revealing some new aspects. Especially for propanol, we report several new conformations that were previously not investigated. Moreover, two metrics are included in our analysis that quantify how the selected surfaces are similar to one another and hence improve our understanding of the relationship between these alcohols.

A spectroscopic and theoretical study in the near-infrared region of low concentration aliphatic alcohols

The near-infrared (NIR) spectra of low-concentration (5 × 10⁻³ M) solutions in CCl₄ of basic aliphatic alcohols, methanol, ethanol, and 1-propanol were, for the first time, calculated by second-order vibrational perturbation theory computations and were compared with the corresponding experimental data.

Cβ–H stretching vibration as a new probe for conformation of n-propanol in gaseous and liquid states

The CH₂ symmetric stretching mode at the β-carbon position can be used as a new probe for the five conformations of n-propanol.

Bracketing subtle conformational energy differences between self-solvated and stretched trifluoropropanol

The interconversion landscape between stretched and folded trifluoropropanol conformations is characterized by Raman jet spectroscopy and theory.

Gas-phase structures, rotational barriers, and conformational properties of hydroxyl and mercapto derivatives of cyclohexa-2,5-dienone and cyclohexa-2,5-dienthione

The rotational barriers and conformational properties of the hydroxyl and mercapto groups attached to the alpha and beta positions of cyclohexa-2,5-dione and cyclohexa-2,5-dienthione have been studied at the B3LYP/ 6-311++G(d,p) level of theory. The results show that the conformational preferences of these studied systems are the result of a subtle interplay between different competing effects (conjugation, hyperconjugation, and steric repulsions). The applicability of the density functional theory reactivity indices and the maximum hardness principle for the present systems has been analyzed.

Convergence of third order correlation energy in atoms and molecules

We have investigated the convergence of third order correlation energy within the hierarchies of correlation consistent basis sets for helium, neon, and water, and for three stationary points of hydrogen peroxide. This analysis confirms that singlet pair energies converge much slower than triplet pair energies. In addition, singlet pair energies with (aug)-cc-pVDZ and (aug)-cc-pVTZ basis sets do not follow a converging trend and energies with three basis sets larger than aug-cc-pVTZ are generally required for reliable extrapolations of third order correlation energies, making so the explicitly correlated R12 calculations preferable.

Conformational effects in inner-shell photoelectron spectroscopy of ethanol

The carbon 1s photoelectron spectrum of ethanol shows two peaks, one for the methyl carbon and one for the functionalized carbon. While the peak shape for the functionalized carbon is readily understood, the shape for the methyl carbon requires that there be comparable contributions from both the anti and gauche conformers of ethanol and that the torsional motion in the HOCC dihedral angle be strongly excited upon core ionization. An accurate description of the peak shape requires a high level of electronic-structure theory together with consideration of anharmonicity and coupling of the torsional motion with other vibrational modes.