V.J. Klimkowski

Normal coordinate ab initio force relaxation

Abstract A procedure for optimization of molecular geometries is presented, combining ab initio calculations with vibrational molecular data from spectroscopy or empirical force fields. Theoretical cartesian forces are transformed to vibrational normal coordinate forces from which geometry increments are calculated. Test results indicate that the method saves considerable effort compared to other optimization schemes.

Ab initio studies of structural features not easily amenable to experiment: Part 39. Conformational analysis of glycine and alanine

Abstract The NCCO torsional potential energies of glycine and alanine were determined by 4-21G ab initio calculations with geometry gradient optimization at each point. The potential energy of glycine is characterized by minima at 0 and 180°, and by a barrier at approximately 75°. The 180° local minimum is part of an energy plateau extending from approximately 150 to 210°. The alanine NCCO potential is characterized by minima at 0 and 150°, and by asymmetric barriers in the 60–90° and 270–300° regions. The 150° minimum is part of an asymmetrically stepped energy plateau extending from approximately 120 to 240°. It is shown that the qualitative features of the alanine potential can be simulated from the CCCO and NCCO torsions of propanoic acid and glycine. Some quantitative differences between the simulated and the actual potentials may point to cooperative effects in the total system. A similar, qualitative prediction is made for the NCCO potential of α-aminoisobutyric acid from glycine and 2-methyl propanoic acid.

Local geometry maps and conformational transitions between low-energy conformers of N-acetyl-N′-methyl glycine amide: An ab initio study at the 4–21g level with gradient relaxed geometries

Abstract Energy pathways between the α R , β′, C 7 eq and β-regions of the conformational energy surface of N -acetyl N ′-methyl glycine amide were obtained by SCF ab initio calculations on the 4–21G level with gradient geometry optimization at each point. The calculations point to the possibility that no barrier exists at this computational level between α R and β′. The variation of geometry (bond distances and bond angles) with conformation is analyzed in detail and the geometrical parameters which should be treated as variables in both empirical energy calculations and, possibly, in the fitting of polypeptide chains in proteins by X-ray methods, are identified. The study shows that, in general, Local Geometry Maps (of conformationally dependent structural trends) are as important as Local Energy Maps for the characterization of peptide systems.

Ab initio studies of structural features not easily amenable to experiment: Part 37. Structural and conformational investigations of the dicarbonyls glyoxal, biacetyl and oxalic acid

Abstract The geometries of glyoxal, oxalic acid and biacetyl were determined by the ab initio gradient procedure on the 4-21G level, and the conformational energies of glyoxal and biacetyl were calculated as functions of the OC CO torsional angles. In the case of biacetyl, the results are in agreement with previous observations that, even at elevated temperatures, and in somewhat surprising contrast to oxalyl halides, only the trans form is detected in its vapors by gas electron diffraction. Empirical corrections, rg — re (ab initio), are determined for some bond distances and compared to previous estimates. CC rg bond distances, calculated for the CH3CO and C(O)C(O) bonds in biacetyl from the ab initio results with empirical corrections, agree within the experimental error estimates with the more sophisticated of two contradictory electron diffraction models, and the predicted mean CC bond (rg, 1.520 A) is close to the reported experimental means (rg, 1.522(3) and 1.526(2) A).

Ab initio studies of structural features not easily amenable to experiment: Part 41. Molecular geometries of hydrogen-bonded six-membered ring structures of glycerol

Abstract The geometries of eight conformations of glycerol, which contain hydrogen-bonded six-membered ring structures, were refined by the ab initio gradient method on the 4-21G level. The two most stable forms in 4-21G space are both of type γγ; the energy difference between them is 1 kcal mol −1 , and the barrier to conversion is 1.3 kcal mol −1 . In this and a previous study four conformations were found, including α-γ-forms, whose energies are within approximately 2 kcal mol −1 . The results suggest that the system represents a complex dynamic process. In addition to the interconversion of different conformers, which differ both in HOCC and OCCO torsional arrangements the dynamic equilibrium of glycerol can involve the concerted exchange of the conformational arrangements of inequivalent CH 2 OH-groups within a given conformer.

Ab initio studies of structural features not easily amenable to experiment: Part 36. Structural investigation of the relative stability of trans and gauche acetylcholine and comparison with methyl acetate

Abstract The geometries of the trans and gauche forms of acetylcholine have been determined by geometrically unconstrained ab initio gradient relaxation on the 4-21G level. In this space the optimized gauche form is 3.0 kcal mol −1 more stable than the trans . The stability of this somewhat crowded form has in the past often been interpreted in terms of a CH⋯O hydrogen bond (involving C4H10⋯O20 in our notation, see Fig. 1) in which the CH bond is activated by the quaternary nitrogen atom. The calculated geometrical trends are consistent with the existence of a special, but weak, interaction between H10 and O20 in gauche acetylcholine. It is therefore proposed that other factors, such as those which normally favour the gauche conformations of 1,2-disubstituted ethanes and, for example, the closer proximity of the quaternary nitrogen to the ester oxygen in the gauche form (3.03 A) than in the trans (3.73 A), may contribute significantly to the stability of the system. Among the geometrical differences between trans and gauche acetylcholine, an unusually small OCC angle of 101.2° is found in the trans form, but not in the gauche . The carbonyl CO and ester CO bond distances in acetylcholine are found to be 0.008 A shorter and 0.032 A longer, respectively, than in methyl acetate. This structural feature can be rationalized in terms of less resonance stabilization in the choline than in the methyl ester. Possible correlations with the enhanced reactivity of the acetyl group of the choline in acylation reactions as compared to aliphatic acetates are discussed.

Ab initio structural investigation of methyl and ethyl carbamate, and carbamyl choline

The molecular structures of four conformations of methylcarbamate, three forms of ethylcarbamate, four forms of ethylacetate, and of the trans-form of carbamylcholine, were determined by ab initio gradient geometry refinement on the 4-21G level, and the results are compared with the geometries of homologous systems. Significant changes in bond distances and angles are observed with torsional changes, but, barring long-range non-bonded interactions, they are to a large extent localized in that part of the system which is directly involved with the torsional transition; i.e., through-bond effects in a bond distance chain begin to be insignificant after a sequence of three bonds.

Ab initio studies of structural features not easily amenable to experiment: Part 43. Basis set dependence of CO single bonds and comment on the microwave substitution structure of mthyl-ethyl-ether

Abstract The geometries of CH 3 OH, CH 3 OCH 3 , C 2 H 5 OCH 3 , and ethylene oxide were refined by Pulays ab initio gradient method on the 6-513G** level, in order to comment on a previously noted irregularity in the differences between the 4-21G and r s CO bond distances of C 2 H 5 OCH 3 and ethylene oxide. It is concluded that, in the case of ethylene oxide, the unusually large difference of 0.049 A between the 4-21G and the r s CO bond lengths is mainly due to deficiencies of the 4-21G basis in predicting the structures of strained cyclic organic systems containing hetero-atoms. In the case of C 2 H 5 OCH 3 , however, the most credible interpretation of the currently available data is that experimental uncertainties contribute significantly to the relatively large difference of 0.040 A between the 4-21G and r s C(methylene)O bonds, and the r s parameters very likely are not a true measure of the relative extension of the C(methyl)O and C(methylene)O bond distances in this compound. An r g CO bond distance of 1.428(9) A is tentatively predicted for ethylene oxide. Furthermore it is found that, in agreement with previous studies, differences between CH bond distances within a methyl group adjacent to electron lone pairs are practically independent of the basis set. The study confirms that, in general, ab initio gradient geometries can be a useful supplement in critical evaluations of experimental structural information.

Predictions of structural trends from standard geometry functions: The modelling of some parameters of 2-methyl- and 2,2′-dimethyl-propanal from propanal and acethaldehyde

Abstract Seven structures of 2-methylpropanal (MPRO) and three structures of 2,2′-dimethyl-propanal (DMPRO) were refined by ab initio gradient calculations on the 4-21G level. For both systems the geometries calculated represent a full scan, at approximately 30° intervals, of the CCCO torsional space. Thus, it is possible to give a detailed description of the conformationally dependent trends exhibited by the bond distances and angles in these systems. It is found that, for some parameters of MPRO and DMPRO, these trends can be predicted approximately by combining phase-adjusted, corresponding 4-21G trends previously obtained for the smaller systems, propanal and acetaldehyde.

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.