L. Van Den Enden

Ab initio studies of structural features not easily amenable to experiment: Part 31. Conformational analysis and molecular structures of ethylene glycol

Abstract The geometries of ten conformations of ethylene glycol have been refined without any geometrical constraints by the ab initio gradient method on the 4-21G level. The two most stable forms found are tGg′ and gGg′ , both of which are stabilized by internal hydrogen bonding. A number of conformationally dependent structural trends are apparent in the optimized local geometries. Bond distances and bond angles in different conformations can vary by up to 0.01–0.02 A and 5°, respectively. The results are found to be consistent with most of the previous investigations of the system.

The molecular structure of gaseous methyl vinyl ether at room temperature, studied by molecular orbital constrained electron diffraction and microwave spectroscopy

Abstract The gas phase molecular structure of methyl vinyl ether at room temperature has been studied by joint analysis of electron diffraction and microwave data. Constraints on geometrical and thermal parameters were derived from the geometry and force field of the s-cis form, obtained by ab-initio calculations (4–21 G basis set) after complete geometry relaxation. A range of models was investigated that fits all available data (infrared, microwave and electron diffraction). The following r g / r α -parameters were obtained: CC: 1.337 A, C( sp 2 )O: 1.359 A, C( sp 3 )O: 1.427 A, : 1.102 A ∠CCO : 127.3° and ∠COC: 116.8°. Experimental r g  r e (ab initio) corrections are given for CC, C( sp 2 )O and C sp 3 )O. This investigation demonstrates that molecular orbital constrained electron diffraction is sufficiently reliable and in such a manner that it can be applied to more complicated problems.

Structure determination of propanal by joint analysis of gas electron diffraction, microwave and infrared spectroscopy, including constraints and a valence force field from geometry relaxed ab-initio calculations

Abstract The structure and conformational equilibrium of CH 3 -SYN and CH 3 -SKEW conformers of propanal were studied by joint analysis of gas electron diffraction, microwave and infrared data, including constraints obtained after ab-initio relaxations (4-21G basis set) of the molecule. A valence force field was calculated for both conformers and scaled upon experimental IR frequencies; theoretical frequencies and band intensities are compared to experimental ones. Rotamer populations of CH 3 -SYN and CH 3 -SKEW were found to be 81 and 19%, respectively, at 300 K. The following best-fitting r g / r α parameters were obtained as: r (OC) = 1.209(4) A, r (C2C3) = 1.515(9) A, r (C3C4) = 1.521(9) A for CH 3 -SYN and (with lower reliability) 1.569(45) A for CH 3 -SKEW, = 1.127(4) A, ∠O=CC = 124.5(3)°(SYN) and 125.1(3)° (SKEW), ∠CCC = 113.8(4)° (SYN) and 110.2(4)° (SKEW), torsion angle around C2C3 = 123.7(2.6)° for CH 3 -SKEW.

The molecular structure of gaseous allyl alcohol determined from electron diffraction, microwave, infrared and geometry-relaxed ab-initio data

The structure of allyl alcohol was determined in the gas phase from electron diffraction, microwave and infrared data in combination with constraints obtained from ab-initio calculations (4-21G basis set). At 300 K the rotamer composition consists of 57(6)% (sp, sc) and 43% (ac,—sc) forms. The molecular orbital constrained joint analysis yields the following geometries (rg-distances, rα-angles): (sp, sc) conformer r(CC) = 1.334(5) A, r(CC) = 1.500(8) A, r(CO) = 1.425(5) A, ∠(CCC) = 124.7 (1.5)°, /o<(CCO) = 113.6(1.1)° and torsion (CCCO) = 22(9). (ac,—sc) conformer r(CC) = 1.335(5) A, r(CC) = 1.496(8) A, r(CO) = 1.431(5) A, ∠(CCC) = 125.3(1.5)°, ∠(CCO) = 112.2(1.1)° and torsion (CCCO) = 1.222(1.5)°. The average r(〈CH〉) = 1.096(6) A and r(OH) = 1.028(27) A in both rotamers.

The molecular orbital constrained electron diffraction (moced) structural model of quadricyclane determined by electron diffraction combined with ab initio calculations of potential and geometrical parameters

Abstract The gas electron diffraction (GED) data of quadicyclane (previously recorded by the University of Tokyo group) were reinvestigated using constraints taken from ab inito (4–21G) gradient geometry and force field calculations. It was the purpose of this study to determine the MOCED structural model for this compound that is obtained when the differences between some unrasolved bond distances and angles in the GED data analysis are constrained to the calculated values. In addition, a novel procedure was tested, in which a scale factor for the ab initio calculated vibrational amplitudes was refined from the diffraction data together with the variable structural parameters. This novel procedure greatly reduces parameter correlation in the least-squares analysis and is expected to be useful whenever extraneous constraints of unresolved parameters are needed for fitting molecular models to the diffraction data. Subject to the ab initio constraints, the analysis yields the following model ( r g -distances, r α -angles; numbers in parentheses are six times the standard deviations of the least-squares intensitv refinements): (CH) = 1.109(1) A, (CC) = 1.526(2) A 1 C 1 C 2 = 1.525(24) A, C 2 C 6 = 1.525(12) A 1 C 2 C 3 = 1.543(24) A 1 C 1 C 7 = 1.514(42) A 1 and C 1 C 7 C 4 = 98.7(6)°. With these parameters, the dependent angles are C 1 C 2 C 3 = 104.3°, C 1 C 2 - C 4 = 60°, C 2 C 1 C 6 = 60 °, and C 2 C 1 C 7 = 110.6°.

Ab initio studies of structural features not easily amenable to experiment: Part 26. Conformational analysis and study of the self-induced molecular asymmetry of glycerol

Abstract The structures of ten conformations of glycerol have been refined without any geometrical constraints by ab initio gradient relaxation on the 4-21G level. The compound can exist in forms which possess a symmetry plane, and in forms in which asymmetry is induced by intramolecular interactions. The two most stable forms are of type αγ (Fig. 1) and γγ (Fig. 9). The latter is characterized by a chair-type six-membered ring closed by hydrogen bonding. The calculations make it possible to estimate the positions of the hydrogen atoms which are not known from experimental work. Intramolecular hydrogen bonds are approximately oriented along the directions conventionally defined for σ-,π-and sp 3 -type electron lone pairs on oxygen. The results also make it possible to describe the differences in local geometry which can cause the central carbon atom to be chiral. This is in contrast to presentations in which the chemical equivalence of the terminal CH 2 OH groups in glycerol is correlated with the assumption that the central carbon atom is symmetric. It is postulated that, rather, the chemical equivalence of the terminal groups can involve the rapidly interconverting equilibrium of asymmetric, enantiomeric forms. The results thus demonstrate that details of molecular local geometries can be important in interpretations of chemical reactivity.

The molecular structure of 1,1-dichloro-1-silacyclo-hexane and of 1,1-dimethoxy-1-silacyclohexane in the gas phase, an electron diffraction study

Abstract The molecular structure of 1,1-dichloro-1-silacyclohexane (DCSC) and of 1,1-dimethoxyl-silacyclohexane (DMSC) has been determined by gas phase electron diffraction. Starting values for the vibrational parameters were obtained from force field calculations. Both molecules are in the chair conformation with a flattening in the vicinity of the silicon atom, which is most pronounced in the dichloro-compound. Disregarding the substituents the title compounds show C s -symmetry. In DMSC the gem -dimethoxy grouping is in the sc , sc conformation in accordance with the anomeric effect. A comparison is made between the experimentally found geometries with predictions of molecular mechanics calculations based on two available force fields.

The molecular structures of cis-3-hexene and trans-3-hexene in the gas phase by electron diffraction and molecular mechanical calculations

Abstract The molecular structures of cis -3-hexene and of trans -3-hexene in the gas phase have been determined by electron diffraction combined with molecular mechanical calculations. For cis -3-hexene the data indicate the presence of the (+ac, +ac) and the (−ac, +ac) forms. In trans -3 -hexene three rotamers were observed, with an energy sequence E (+ac, +ac) ≈ E (−ac, +ac) E (ac, sp). The refined r α 0 -structural parameters are: cis -3-hexene: C-H = 1.073 A, CC = 1.330 A, C( sp 2 )-C( sp 3 ) = 1.505 A, ∠CCH(in CH 2 ) = 111.1°, ∠CCC = 111.4°, ∠(CC-C) = 129.1° trans -3-hexene: C-H = 1.078 A, CC = 1.342 A, C( sp 2 )-C( sp 3 ) = 1.506 A, ∠CCH(in CH 2 ) = 109.3°, ∠CCC = 112.8, ∠CC—C = 124.1° The agreement between calculated and experimental geometries and vibrational amplitudes is good.

Ab initio studies of structural features not easily amenable to experiment: Part 28. Comparison of the observed ground state rotational constants of the methyl ester of glycine with the rotational constants calculated for some planar and non-planar gradient geometries

The rotational constants calculated for the ab initio gradient optimized geometries (4–21G) of several conformations of the methyl ester of glycine are compared with the observed ground state rotational constants of the system. Conformations with a symmetry plane containing all the heavy atoms and non-planar conformations (0° < NCCO < 180°) are considered. The analysis clearly confirms the interpretation of the observed rotational constants in terms of the stretched form, I, of the methyl ester of glycine. In I, which is also the most stable conformation in 4–21G space, the NCCO arrangement is syn-planar and the amino group chelates the carbonyl oxygen. Rotational constants calculated with the unmodified ab initio geometry of I reproduce the constants observed with an absolute error of approximately 30 MHz, corresponding to relative errors of 0.3–1.8%. The calculations also make it possible to discuss the changes in bond distances and bond angles encountered in geometries refined for different values of the NCCO torsional angle.

Ab-initio studies of structural features not easily amenable to experiment: Part 29. Conformational analysis of glycine aldehyde

Abstract The geometries of ten conformations of glycine aldehyde have been determined by ab initio gradient refinements on the 4-21G level. The potential energy curve of the NCCO torsion is very similar to that of the methyl ester of glycine. The energy minimum is at 0° ; the barrier to rotation is at approximately 75° ; and there is an energy plateau between approximately 150° and 210°. The possibility of large-amplitude motions in the 180° region is a significant property of the NCCO torsion because it supports the flexibility of φ-angles (NC(α)C′N) in the helical forms of peptide systems. By comparing the glycine aldehyde with the recently investigated dipeptide N-acetyl N′-methyl glyeyl amide, it is possible to establish the following conformational trends in the monomer, dimer and polymer states of the glycine moiety: The C7 form of the glycine residue, which corresponds to a high energy region of the monomer but is low energy in the dipeptide, is relatively infrequently encountered in proteins. The α-helical form of the glycine residue, which corresponds to a relatively low energy region in the monomer but is high energy in the dipeptide, is frequently encountered in proteins. The extended form (C5) of the glycine residue is relatively low energy both in the monomer and in the dipeptide and is frequent in proteins.