Far infrared and low frequency gas phase Raman spectra and conformational stability of the 1‐halopropanes

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.

Probing self-associated intermolecular H-bonding using low-frequency SERS coupled with mid-IR SERS and DFT study: a case study of 2-MBA adsorbed on ZnO nanoparticles

In the present study, low-frequency SERS is reported for the first time to investigate intermolecular interactions. Low-frequency SERS in the THz region (>50 cm-1) and the mid-IR region is used to probe the H-bonding interaction in 2-mercaptobenzoic acid (2-MBA) molecules adsorbed on the surface of ZnO nanoparticles. The self-association due to H-bonding leads to dimer formation of 2-MBA through carboxylic acid groups. The characteristic Raman bands of the 2-MBA dimer, H-bonded O-H stretching and out-of-plane O-H bending modes, are observed. Subsequently, this dimer formation causes the evolution of two new low-frequency modes at 90 cm-1 (shear dimer in-plane bending) and 110 cm-1 (shear dimer stretching) of intermolecular H-bonding and a blue-shift of the torsional mode of (-COOH) + (-SH). In the THz region (50-200 cm-1) the vibrational modes are blue-shifted, while in the mid-IR region the symmetric out-of-plane O-H bending is red-shifted. The present work shows that SERS can be used to study intermolecular H-bonding of molecules at very low concentrations.

Conformational stability from variable temperature FT-IR spectra of krypton solutions, r0 structural parameters, vibrational assignment, and ab initio calculations of 4-fluoro-1-butene

Variable temperature (-115 to -155 degrees C) studies of the infrared spectra (3200-400 cm-1) of 4-fluoro-1-butene, CH2=CHCH2CH2F, dissolved in liquid krypton have been carried out. The infrared spectra of the gas and solid as well as the Raman spectra of the gas, liquid, and solid have also been recorded from 3200 to 100 cm-1. From these data, an enthalpy difference of 72 +/- 5 cm-1 (0.86 +/- 0.06 kJ x mol-1) has been determined between the most stable skew-gauche II conformer (the first designation refers to the position of the CH2F group relative to the double bond, and the second designation refers to the relative positions of the fluorine atom to the C-C(=C) bond) and the second most stable skew-trans form. The third most stable conformer is the skew-gauche I with an enthalpy difference of 100 +/- 7 cm-1 (1.20 +/- 0.08 kJ x mol-1) to the most stable form. Larger enthalpy values of 251 +/- 12 cm-1 (3.00 +/- 0.14 kJ x mol-1) and 268 +/- 17 cm-1 (3.21 +/- 0.20 kJ x mol-1) were obtained for the cis-trans and cis-gauche conformers, respectively. From these data and the relative statistical weights of one for the cis-trans conformer and two for all other forms, the following conformer percentages are calculated at 298 K: 36.4 +/- 0.9% skew-gauche II, 25.7 +/- 0.1% skew-trans, 22.5 +/- 0.2% skew-gauche I, 10.0 +/- 0.6% cis-gauche, and 5.4 +/- 0.2% cis-trans. The potential surface describing the conformational interchange has been analyzed and the corresponding two-dimensional Fourier coefficients were obtained. Nearly complete vibrational assignments for the three most stable conformers are proposed and some fundamentals for the cis-trans and the cis-gauche conformers have been identified. The structural parameters, dipole moments, conformational stability, vibrational frequencies, infrared, and Raman intensities have been predicted from ab initio calculations and compared to the experimental values when applicable. The adjusted r0 structural parameters have been determined by combining the ab initio predicted parameters with previously reported rotational constants from the microwave data. These experimental and theoretical results are compared to the corresponding quantities of some similar molecules.

Effects of molecular conformation on inner-shell ionization energies

Experimental evidence for an effect of molecular conformation on inner-shell ionization energies has been observed for the first time. Examples are seen in the carbon 1s spectra of butyronitrile, 1-fluoropropane, and propanal, and other similar molecules. At room temperature these exist in two different conformations, with different distances and, hence, different Coulombic interactions between the negatively charged electronegative group and the methyl carbon. The experimental results are in accord with theoretical predictions with respect to both ionization energies and populations of the different conformers.

Unimolecular Rate Constants for HX or DX Elimination (X = F, Cl) from Chemically Activated CF3CH2CH2Cl, C2H5CH2Cl, and C2D5CH2Cl: Threshold Energies for HF and HCl Elimination

Vibrationally activated CF(3)CH(2)CH(2)Cl molecules were prepared with 94 kcal mol(-1) of vibrational energy by the combination of CF(3)CH(2) and CH(2)Cl radicals and with 101 kcal mol(-1) of energy by the combination of CF(3) and CH(2)CH(2)Cl radicals at room temperature. The unimolecular rate constants for elimination of HCl from CF(3)CH(2)CH(2)Cl were 1.2 x 10(7) and 0.24 x 10(7) s(-1) with 101 and 94 kcal mol(-1), respectively. The product branching ratio, k(HCl)/k(HF), was 80 +/- 25. Activated CH(3)CH(2)CH(2)Cl and CD(3)CD(2)CH(2)Cl molecules with 90 kcal mol(-1) of energy were prepared by recombination of C(2)H(5) (or C(2)D(5)) radicals with CH(2)Cl radicals. The unimolecular rate constant for HCl elimination was 8.7 x 10(7) s(-1), and the kinetic isotope effect was 4.0. Unified transition-state models obtained from density-functional theory calculations, with treatment of torsions as hindered internal rotors for the molecules and the transition states, were employed in the calculation of the RRKM rate constants for CF(3)CH(2)CH(2)Cl and CH(3)CH(2)CH(2)Cl. Fitting the calculated rate constants from RRKM theory to the experimental values provided threshold energies, E(0), of 58 and 71 kcal mol(-1) for the elimination of HCl or HF, respectively, from CF(3)CH(2)CH(2)Cl and 54 kcal mol(-1) for HCl elimination from CH(3)CH(2)CH(2)Cl. Using the hindered-rotor model, threshold energies for HF elimination also were reassigned from previously published chemical activation data for CF(3)CH(2)CH(3,) CF(3)CH(2)CF(3), CH(3)CH(2)CH(2)F, CH(3)CHFCH(3), and CH(3)CF(2)CH(3). In an appendix, the method used to assign threshold energies was tested and verified using the combined thermal and chemical activation data for C(2)H(5)Cl, C(2)H(5)F, and CH(3)CF(3).

Ab Initio calculations of the stabilization energies of the conformational and the structural isomers of C(3)H(7)X where X = F, Cl, and Br

HF, MP2, and B3LYP calculations with different basis sets have been used in the computation of the stabilization energies of C(3)H(7)X isomers, where X is F, Cl, and Br. The experimental stabilization energies of the structural isomers of C(3)H(7)Cl and C(3)H(7)Br have been reproduced via B3LYP calculations. However, the calculated stabilization energies of fluoropropane isomers from their reported enthalpies of formation have been reproduced in all methods of calculations in present work. The experimental relative stabilities of the gauche conformers of 1-fluoro-, 1-chloro-, and 1-bromopropanes have been also reproduced via some of the used calculations in the present work. The effect of the geminal interactions on X atomic charges and on the C-X and C-C bond lengths in halopropane isomers are also discussed.