Semi-experimental Equilibrium Structure Research Articles

Experimental values of the rotational and vibrational constants of deuterated silyl fluoride

ABSTRACTAccurate experimental values of the αA and αB rotation–vibration interaction, and ωi, xij and gij vibrational constants have been extracted from the most recent high-resolution Fourier transform infrared and millimetre-wave measurements in the spectra of the prolate symmetric top SiD3F, between 400 and 2000 cm−1. From the experimental values of the ground state rotational and rovibrational interaction parameters, accurate equilibrium rotational constants have been derived: Ae = 1.432326 (12) cm−1 and Be = 0.4112012 (45) cm−1 for silyl fluoride. The effective ground state structure has also been determined from the observed moments of inertia of SiD3F: r0(Si-D) = 1.4755 (29) Å; r0(Si-F) = 1.5931 (26) Å; θ0(DSiD) = 110.47 (32)° and θ0(DSiF) = 108.45 (56)°. A merge of equilibrium moments of 28SiH3F and 28SiD3F yielded an experimental equilibrium structure of silyl fluoride. This geometry has been found in good agreement with semi-experimental median values, as well as with the recent semi-experimental ab initio equilibrium structure obtained using all data available of the various isotopic species of silyl fluoride.

Semi-experimental equilibrium structure of pyrazinamide from gas-phase electron diffraction. How much experimental is it?

A semi-experimental equilibrium structure of free molecules of pyrazinamide has been determined for the first time using gas electron diffraction method. The refinement was carried using regularization of geometry by calculated quantum chemical parameters. It is discussed to which extent is the final structure experimental. A numerical approach for estimation of the amount of experimental information in the refined parameters is suggested.The following values of selected internuclear distances were determined (values are in Å with 1σ in the parentheses): re(Cpyrazine—Cpyrazine)av = 1.397(2), re(Npyrazine—Cpyrazine)av = 1.332(3), re(Cpyrazine—Camide) = 1.493(1), re(Namide—Camide) = 1.335(2), re(Oamide—Camide) = 1.219(1). The given standard deviations represent pure experimental uncertainties without the influence of regularization.

Correction to Semiexperimental Equilibrium Structures for Building Blocks of Organic and Biological Molecules: The B2PLYP Route

ADVERTISEMENT RETURN TO ISSUEPREVErratumNEXTORIGINAL ARTICLEThis notice is a correctionCorrection to Semiexperimental Equilibrium Structures for Building Blocks of Organic and Biological Molecules: The B2PLYP RouteEmanuele Penocchio, Matteo Piccardo, and Vincenzo Barone*Cite this: J. Chem. Theory Comput. 2016, 12, 6, 3001Publication Date (Web):May 27, 2016Publication History Published online27 May 2016Published inissue 14 June 2016https://doi.org/10.1021/acs.jctc.6b00520Copyright © 2016 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views429Altmetric-Citations2LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (109 KB) Get e-Alerts Get e-Alerts

Correction to Semi-Experimental Equilibrium Structure Determinations by Employing B3LYP/SNSD Anharmonic Force Fields: Validation and Application to Semirigid Organic Molecules.

This work aims at extending the semi-experimental (SE) approach for deriving accurate equilibrium structures to large molecular systems of organic and biological interest. SE equilibrium structures are derived by a least-squares fit of the structural parameters to the experimental ground-state rotational constants of several isotopic species corrected by vibrational contributions computed by quantum mechanical (QM) methods. A systematic benchmark study on 21 small molecules (CCse set) is carried out to evaluate the performance of hybrid density functionals (in particular B3LYP) in the derivation of vibrational corrections to rotational constants. The resulting SE equilibrium structures show a very good agreement with the corresponding geometries obtained employing post-Hartree–Fock vibrational corrections. The use of B3LYP in conjunction with the double-ζ SNSD basis set strongly reduces the computational costs, thus allowing for the evaluation of accurate SE equilibrium structures for medium-sized molecul...

High resolution spectroscopy of six SOCl2 isotopologues from the microwave to the far-infrared.

Despite its potential role as an atmospheric pollutant, thionyl chloride, SOCl2, remains poorly characterized in the gas phase. In this study, the pure rotational and ro-vibrational spectra of six isotopologues of this molecule, all detected in natural abundance, have been extensively studied from the cm-wave band to the far-infrared region by means of three complementary techniques: chirped-pulse Fourier transform microwave spectroscopy, sub-millimeter-wave spectroscopy using frequency multiplier chain, and synchrotron-based far-infrared spectroscopy. Owing to the complex line pattern which results from two nuclei with non-zero spins, new, high-level quantum-chemical calculations of the hyperfine structure played a crucial role in the spectroscopic analysis. From the combined experimental and theoretical work, an accurate semi-experimental equilibrium structure (r(e)(SE)) of SOCl2 has been derived. With the present data, spectroscopy-based methods can now be applied with confidence to detect and monitor this species, either by remote sensing or in situ.

Semiexperimental equilibrium structures for building blocks of organic and biological molecules: the B2PLYP route.

The B2PLYP double hybrid functional, coupled with the correlation-consistent triple-ζ cc-pVTZ (VTZ) basis set, has been validated in the framework of the semiexperimental (SE) approach for deriving accurate equilibrium structures of molecules containing up to 15 atoms. A systematic comparison between new B2PLYP/VTZ results and several equilibrium SE structures previously determined at other levels, in particular B3LYP/SNSD and CCSD(T) with various basis sets, has put in evidence the accuracy and the remarkable stability of such model chemistry for both equilibrium structures and vibrational corrections. New SE equilibrium structures for phenylacetylene, pyruvic acid, peroxyformic acid, and phenyl radical are discussed and compared with literature data. Particular attention has been devoted to the discussion of systems for which lack of sufficient experimental data prevents a complete SE determination. In order to obtain an accurate equilibrium SE structure for these situations, the so-called templating molecule approach is discussed and generalized with respect to our previous work. Important applications are those involving biological building blocks, like uracil and thiouracil. In addition, for more general situations the linear regression approach has been proposed and validated.

Benchmark study of molecules with large-amplitude ring-twisting motion: accurate equilibrium structure of succinic anhydride from gas electron diffraction data and coupled-cluster computations

The gas electron diffraction (GED) study of succinic anhydride (dihydro-2,5-furandione) is used as a benchmark example for the reliable determination of the structure of floppy molecules with saturated non-rigid ring. According to results of B3LYP calculations, the molecule has a planar skeleton (C2v total symmetry), whereas the MP2 optimized structure has a non-planar ring with the torsional angle φ(C–C–C–C) of up to 11° (C2 symmetry). It has been revealed that the increase in the quality of ab initio calculations up to CCSD(T) level and the enlargement of basis set up to quadruple-ζ size decrease the non-planarity of the molecular skeleton, which is approximated to be planar in the best-estimated ab initio structure. The semiexperimental equilibrium structure ( $$r_{\text{e}}^{\text{se}}$$ ) has been determined from the GED data with the application of the so-called dynamic (pseudo-conformer) model describing the large-amplitude ring-twisting motion. Vibrational corrections Δ(r a − r e) to the experimental internuclear distances have been calculated from the B3LYP/cc-pVTZ quadratic and cubic force constants. The best-estimated ab initio structure agrees well with the $$r_{\text{e}}^{\text{se}}$$ structure. This fact points to the reliability and a high accuracy of both experimental data and applied theory.

CC/DFT Route toward Accurate Structures and Spectroscopic Features for Observed and Elusive Conformers of Flexible Molecules: Pyruvic Acid as a Case Study.

The structures and relative stabilities as well as the rotational and vibrational spectra of the three low-energy conformers of pyruvic acid (PA) have been characterized using a state-of-the-art quantum-mechanical approach designed for flexible molecules. By making use of the available experimental rotational constants for several isotopologues of the most stable PA conformer, Tc-PA, the semiexperimental equilibrium structure has been derived. The latter provides a reference for the pure theoretical determination of the equilibrium geometries for all conformers, thus confirming for these structures an accuracy of 0.001 Å and 0.1 deg for bond lengths and angles, respectively. Highly accurate relative energies of all conformers (Tc-, Tt-, and Ct-PA) and of the transition states connecting them are provided along with the thermodynamic properties at low and high temperatures, thus leading to conformational enthalpies accurate to 1 kJ mol(-1). Concerning microwave spectroscopy, rotational constants accurate to about 20 MHz are provided for the Tt- and Ct-PA conformers, together with the computed centrifugal-distortion constants and dipole moments required to simulate their rotational spectra. For Ct-PA, vibrational frequencies in the mid-infrared region accurate to 10 cm(-1) are reported along with theoretical estimates for the transitions in the near-infrared range, and the corresponding infrared spectrum including fundamental transitions, overtones, and combination bands has been simulated. In addition to the new data described above, theoretical results for the Tc- and Tt-PA conformers are compared with all available experimental data to further confirm the accuracy of the hybrid coupled-cluster/density functional theory (CC/DFT) protocol applied in the present study. Finally, we discuss in detail the accuracy of computational models fully based on double-hybrid DFT functionals (mainly at the B2PLYP/aug-cc-pVTZ level) that avoid the use of very expensive CC calculations.

Semi-experimental equilibrium structure determinations by employing B3LYP/SNSD anharmonic force fields: validation and application to semirigid organic molecules.

This work aims at extending the semi-experimental (SE) approach for deriving accurate equilibrium structures to large molecular systems of organic and biological interest. SE equilibrium structures are derived by a least-squares fit of the structural parameters to the experimental ground-state rotational constants of several isotopic species corrected by vibrational contributions computed by quantum mechanical (QM) methods. A systematic benchmark study on 21 small molecules (CCse set) is carried out to evaluate the performance of hybrid density functionals (in particular B3LYP) in the derivation of vibrational corrections to rotational constants. The resulting SE equilibrium structures show a very good agreement with the corresponding geometries obtained employing post-Hartree-Fock vibrational corrections. The use of B3LYP in conjunction with the double-ζ SNSD basis set strongly reduces the computational costs, thus allowing for the evaluation of accurate SE equilibrium structures for medium-sized molecular systems. On these grounds, an additional set of 26 SE equilibrium structures including the most common organic moieties has been set up by collecting the most accurate geometries available in the literature together with new determinations from the present work. The overall set of 47 SE equilibrium structures determined using B3LYP/SNSD vibrational corrections (B3se set) provides a high quality benchmark for validating the structural predictions of other experimental and/or computational approaches. Finally, we present a new strategy (referred to as the template approach) to deal with the cases for which it is not possible to fit all geometrical parameters due to the lack of experimental data.

Electron delocalization in polyenes: a semiexperimental equilibrium structure for (3E)-1,3,5-hexatriene and theoretical structures for (3Z,5Z)-, (3E,5E)-, and (3E,5Z)-1,3,5,7-octatetraene.

Electronic structure theory reveals that π-electron delocalization increases with the chain length in polyenes. To analyze quantitatively this effect a semiexperimental equilibrium structure has been determined for trans-hexatriene by the mixed estimation method. For this fit rotational constants for a number of carbon and hydrogen isotopologues as well as a high-level ab initio structure have been used. The accuracy is 0.001 Å for bond lengths and 0.1° for bond angles. For the three isomers of octatetraene, high-level ab initio calculations have given a comparably accurate structure. These structures have been used in comparison with the structure of s-trans-butadiene to show that "C═C" bonds increase in length and "C-C" bonds decrease in length as the polyene chain lengthens. These structural effects of π-electron delocalization increase toward the center of polyenes. Most likely, π-π conjugation in the molecules studied plays a large part in their planarity that, in turn, forces the hydrogen atoms of cis fragments in bay regions to be in a close contact. Their distance is indeed shorter than the sum of their van der Waals radii, and they seem to participate in a six-membered ring.

The semi-experimental equilibrium structures of AlCCH and AlNC

Based on experimental rotational constants available in the literature (Walker and Gerry, Chem. Phys. Lett. 278, 9 (1997); Walker et al., J. Mol. Spectrosc. 209, 178 (2001); Sun et al., Chem. Phys. Lett. 553, 11 (2012)) [14,17,19] for five isotopologues of AlCCH and three isotopologues of AlNC as well as quantum-chemical computations for the vibrational corrections to rotational constants, the semi-experimental structures of these two aluminum compounds are determined. These empirical equilibrium structures (AlCCH: re(AlC)=1.957Å, re(CC)=1.222Å, re(CH)=1.065Å; AlNC: re(AlN)=1.850Å, re(NC)=1.181Å) compare favorably with theoretical best-estimate structures obtained using highly accurate coupled-cluster calculations in combination with sophisticated extrapolation and additivity schemes, i.e., the deviations are smaller than 0.002Å, but significant deviations are noted in comparison with previously determined experimental structures. Good agreement is also reached between calculations and experimental values for the relevant spectroscopic parameters of AlCCH and AlNC, indicating the predictive power of state-of-the-art high-level quantum-chemical calculations.

Vibrational spectrum and gas-phase structure of disulfur dinitride (S2N2).

Gas-phase FTIR spectra of the ν6 (B-type) and the ν4 (C-type) fundamental bands of S2 N2 (D2h ) were recorded with a resolution of ≤0.004 cm(-1) and the vibrational spectrum of S2 N2 (D2h ) in solid Ar has been revisited. All IR-active fundamentals and four combination bands were assigned in excellent agreement with calculated values from anharmonic VPT2 and VCI theory based on (explicitly correlated) coupled-cluster surfaces. Accurate experimental vibrational ground- and excited-state rotational constants of (32) S2 (14) N2 are obtained from a rovibrational analysis of the ν6 and ν4 fundamental bands, and precise zero-point average rz (Rz (SN)=1.647694(95) Å, αz (NSN)=91.1125(33)°) and semi-experimental equilibrium structures (Re (SN)=1.64182(33) Å, αe (NSN)=91.0716(93)°) of S2 N2 have been established. These are compared to the solid-state structure of S2 N2 and structural properties of related sulfur nitrogen compounds and to results of ab initio structure calculations.

Accurate equilibrium structures of fluoro- and chloroderivatives of methane

This work is a systematic study of molecular structure of fluoro-, chloro-, and fluorochloromethanes. For the first time, the accurate ab initio structure is computed for 10 molecules (CF4, CClF3, CCl2F2, CCl3F, CHClF2, CHCl2F, CH2F2, CH2ClF, CH2Cl2, and CCl4) at the coupled cluster level of electronic structure theory including single and double excitations augmented by a perturbational estimate of the effects of connected triple excitations [CCSD(T)] with all electrons being correlated and Gaussian basis sets of at least quadruple-ζ quality. Furthermore, when possible, namely for the molecules CH2F2, CH2Cl2, CH2ClF, CHClF2, and CCl2F2, accurate semi-experimental equilibrium (rSEe) structure has also been determined. This is achieved through a least-squares structural refinement procedure based on the equilibrium rotational constants of all available isotopomers, determined by correcting the experimental ground-state rotational constants with computed ab initio vibration–rotation interaction constants and electronic g-factors. The computed and semi-experimental equilibrium structures are in excellent agreement with each other, but the rSEe structure is generally more accurate, in particular for the CF and CCl bond lengths. The carbon–halogen bond length is discussed within the framework of the ligand close-packing model as a function of the atomic charges. For this purpose, the accurate equilibrium structures of some other molecules with alternative ligands, such as CH3Li, CF3CCH, and CF3CN, are also computed.

Gas‐Phase Structure Determination of Dihydroxycarbene, One of the Smallest Stable Singlet Carbenes

Carbenes are reactive molecules of the form R(1)-:C-R(2) that play a role in topics ranging from organic synthesis to gas-phase oxidation chemistry. We report the first experimental structure determination of dihydroxycarbene (HO-:C-OH), one of the smallest stable singlet carbenes, using a combination of microwave rotational spectroscopy and high-level coupled-cluster calculations. The semi-experimental equilibrium structure derived from five isotopic variants of HO-:C-OH contains two very short CO single bonds (ca. 1.32 Å). Detection of HO-:C-OH in the gas phase firmly establishes that it is stable to isomerization, yet it has been underrepresented in discussions of the CH2O2 chemical system and its atmospherically relevant isomers: formic acid and the Criegee intermediate CH2OO.

Semiexperimental equilibrium structure of the oblate-top molecules dimethyl sulfoxide and cyclobutene

A semiexperimental equilibrium structure is derived for dimethyl sulfoxide and cyclobutene from experimental ground-state rotational constants and rovibrational interaction parameters calculated from the ab initio cubic force field. In the case of dimethyl sulfoxide, the presence of several small Cartesian coordinates as well large rotations of the principal axis system upon isotopic substitution hamper an accurate determination of the structure. To achieve an accurate structure, the mixed estimation method is used. In this method, internal coordinates of good quality quantum chemical calculations (with appropriate uncertainty) are fitted simultaneously with the semiexperimental moments of inertia of all isotopomers. On the other hand, there was no difficulty to get an accurate semiexperimental structure for cyclobutene because there are neither small coordinates nor large rotations of the principal axis system.

Interplay of Experiment and Theory: Determination of an Accurate Equilibrium Structure of 1-Methyluracil by the Gas Electron Diffraction Method and Coupled-Cluster Computations

As far as fundamental knowledge is concerned, the methyl derivatives of uracil can be considered as the simplest objects for studying the structural effects due to the substitution in the pyrimidyne nucleobases. From this point of view, 1-methyluracil is of special importance in biochemistry because uracil attaches ribose in ribonucleic acid (RNA) just precisely at the N1 atom. The semi-experimental equilibrium structure (r(e)(se)) of 1-methyluracil has been determined for the first time by the gas electron diffraction (GED) method taking into account rovibrational corrections to the thermal-average internuclear distances calculated with harmonic and anharmonic (cubic) MP2/cc-pVTZ force constants with consideration of the methyl torsion as a large-amplitude motion. For the first time, the structure of the molecule has been optimized by the very time-consuming coupled-cluster method with single and double excitations and perturbative treatment of connected triples using the correlation-consistent polarized weighted core-valence triple-ζ basis set with all electrons being correlated (CCSD(T)(all)/cc-pwCVTZ) and extrapolated to the complete basis set (CBS) with the help of the MP2 calculations. Small differences between similar bond lengths of equilibrium configurations were assumed in the GED analysis at the CCSD(T)(all)/CBS values. A remarkable agreement between the semi-experimental and computed equilibrium structures points out the high accuracy of both the GED determination and the coupled-cluster computations. The effect of methylation on the structure of uracil has been analyzed.

Deformation of the benzene ring upon fluorination: equilibrium structures of all fluorobenzenes

Born−Oppenheimer equilibrium structure (r BO e) estimates are reported for benzene and all 12 possible fluorobenzenes, based on geometry optimizations performed at the coupled cluster level of electronic structure theory including single and double excitations augmented by a perturbational estimate of the effects of connected triple excitations [CCSD(T)] and Gaussian basis sets of at least triple zeta quality. Furthermore, accurate semiexperimental equilibrium (r SE e) structures are determined for C6H6, C6H5F, and 1,2- and 1,3-difluorobenzene. They are obtained through a least-squares structural refinement procedure based on equilibrium rotational constants of as many isotopologues as feasible, determined by correcting experimental vibrationally averaged ground-state rotational constants with computed ab initio vibration–rotation interaction constants and electronic g-factors, and using a few structural constraints based on the best r BO e estimates. The r BO e and r SE e equilibrium structures are in excellent agreement with each other for the four semirigid molecules but in almost all cases they differ significantly from previously determined equilibrium structure estimates based on rotational spectroscopy or gas electron diffraction. The nature of deformations of the benzene ring induced by a single fluorine substitution can be characterized as follows: (a) the strongest effect is the pushing of the ipso carbon atom toward the ring center resulting in a deformation at the ipso [by +2.7(1)°] and ortho [−1.7(1)°] CCC angles, (b) a simultaneous decrease in the ortho CC bond length of the benzene ring by 0.009 Å and (c) a decrease of all the CH bond lengths. Additivity relations concerning the F substitution effects are obtained based on the equilibrium structures of all possible fluorobenzenes.

Analysis of the rotational structure in the high-resolution infrared spectra of cis,cis- and trans,trans-1,4-difluorobutadiene-1-d1 and trans,trans-1,4-difluorobutadiene-1,4-d2

Samples of cis,cis- and trans,trans-1,4-difluorobutadiene-1-d1 and of trans,trans-1,4-difluorobutadiene-1,4-d2 have been synthesized, and high-resolution (⩽0.0018cm−1) infrared spectra of these substances have been recorded in the gas phase. Analysis of the rotational structure, mostly in C-type bands, has yielded ground state rotational constants. For the two 1-d1 species more than one band has been analyzed. For the 1,4-d2 species only one band was available for analysis. However, good agreement between the experimental centrifugal distortion constants and those predicted with a B3LYP/cc-pVTZ model give strong support to the analysis of the very dense spectrum. The ground state rotational constants are a contribution to finding semiexperimental equilibrium structures of the two nonpolar isomers of 1,4-difluorobutadiene.

Accurate Semiexperimental Structure of 1,3,4-Oxadiazole by the Mixed Estimation Method

In order to determine an accurate equilibrium structure for 1,3,4-oxadiazole, microwave transitions and ground-state rotational constants are reported for the parent species and for the (18)O isotopologue measured in natural abundance. These rotational constants along with those of the (13)C, (15)N, and D1 species were used together with vibration-rotation constants calculated from a cubic force field calculated at the B3LYP/6-311+G(3df,2pd) level of theory to derive a semiexperimental equilibrium structure. However, the results of this fit were not satisfactory; therefore, the structure was later significantly improved by the mixed estimation method. In this method, internal coordinates from good-quality quantum chemical calculations (with appropriate uncertainties) are fitted simultaneously with moments of inertia of the full set of isotopologues. The accuracy of this structure has been confirmed by using an extrapolation technique. All elements of the (14)N nuclear quadrupole coupling tensor have been determined.

Semiexperimental Equilibrium Structure of the Lower Energy Conformer of Glycidol by the Mixed Estimation Method

Rotational constants were determined for (18)O-substituted isotopologues of the lower energy conformer of glycidol, which has an intramolecular inner hydrogen bond from the hydroxyl group to the oxirane ring oxygen. Rotational constants were previously determined for the (13)C and the OD species. These rotational constants have been corrected with the rovibrational constants calculated from an ab initio cubic force field. The derived semiexperimental equilibrium rotational constants have been supplemented by carefully chosen structural parameters, including those for hydrogen atoms, from medium level ab initio calculations. The combined data have been used in a weighted least-squares fit to determine an equilibrium structure for the glycidol H-bond inner conformer. This work shows that the mixed estimation method allows us to determine a complete and reliable equilibrium structure for large molecules, even when the rotational constants of a number of isotopologues are unavailable.