Structure Analysis Restrained byab InitioCalculations:  The Molecular Structure of 2,5-Dichloropyrimidine in Gaseous and Crystalline Phases

Abstract

A new method to obtain improved structural parameters by supplementing gas-phase electron diffraction (GED) data with restraints based on the results of ab initio calculations is proposed. The procedure involves the use of ab initio parameters with estimated uncertainties as additional observations; this allows previously fixed parameters to refine, with all geometrical parameters included in the final refinement. The refinement of the molecular structure of 2,5-dichloropyrimidine is used as an example to illustrate the principle of this technique. In this simple case, the effects are not very great, but this new approach allowed refinement of all structural parameters. The nine independent structural parameters (r R structure) were found to be: 6)-H( 10)] ) 109.9(12) pm, ∠[N(1)C( 2)N(3)] ) 127.9(4)°, ∠[C(2)N(3)C( 4)] ) 116.3(7)°, and ∠[N(3)C(4)H( 8)] ) 117.2(5)°. All structural parameters were found to be in good agreement with both ab initio and crystallographic values, which are presented for comparison.

Structures of Tetrasilylmethane Derivatives (XMe2Si)2C(SiMe3)2 (X = H, Cl, Br) in the Gas Phase, and their Dynamic Structures in Solution

“…The SARACEN [58][59][60] method was used for the refinement of experimental data, with the required restraints based upon comparison of calculations at the MP2, B3LYP, and M06-2X levels of theory, and with 6-31G(d) and aug-cc-pVDZ basis sets (using aug-cc-pVDZ-PP as a pseudopotential for Br in 4). Vibrational corrections were based upon data from SHRINK [51,52], calculated using force constants obtained from GAUSSIAN. As is common, because they are not particularly well defined from the GED data, restraints were placed upon the distance difference parameters, as well as parameters associated with hydrogen atoms.…”

Molecular Structure of 1,2-Bis(trifluoromethyl)-1,1,2,2-tetramethyldisilane in the Gas, Liquid, and Solid Phases: Unusual Conformational Changes between Phases

“…17,18 All independent geometric parameters were refined using a least-squares method and restraints were applied, using the SARACEN method, [5][6][7] to five parameters that could otherwise not be refined (Table 4). The restraints were based on values calculated at the MP2/6-311++G** level.…”

“…[5][6][7] The structure of 1,2-ditert-butyldisilane 1 was found to be anti with C 2 symmetry at room temperature, while 1,2-ditert-butyltetrachlorodisilane 2 returned a transoid conformation by both GED and ab initio methods. Both of these systems displayed evidence of steric crowding, with larger than average bond angles observed about the silicon atoms.…”

Structures of Energetic Acetylene Derivatives HC≡CCH2ONO2, (NO2)3CCH2C≡CCH2C(NO2)3 and Trinitroethane, (NO2)3CCH3

“…The refinement was performed according to the SARACEN method [49,50], which places flexible restraints on parameters that are not well resolved from the GED experiment, with the value of the restraint and the uncertainty estimated from calculated values.…”