Molecular structure and conformational composition of 2-chloro-1-phenylethanone, ClH2C-C(=O)Ph, obtained using gas-phase electron-diffraction data and results from theoretical calculations

The structure and conformation of 2-chloro-1-phenylethanone, ClH(2)C-C(=O)Ph (phenacyl chloride), have been determined by gas-phase electron diffraction (GED), augmented by results from ab initio molecular orbital calculations, employing the second-order M?ller-Plesset (MP2) level of theory and the 6-311+G(d) basis set. The molecules may exist as a mixture of different conformers with the C-Cl bond either syn (torsion angle phi = 0 degrees ) or gauche to the carbonyl bond. At 179 degrees C, the majority of the molecules (90 +/- 11%) have the gauche conformation (phi = 112(3) degrees). Torsion is also possible about the C-Ph single bond. Both experimental and theoretical data indicated, however, that the phenyl ring is coplanar or nearly coplanar with the carbonyl group. The results for the principal distances (r(g)) and angles (angle(alpha)) for the gauche conformer from a combined GED/ab initio study (with estimated 2sigma uncertainties) are the following: r(C-C)(phenyl) = 1.394(2) (average value) A, r(C(phenyl)-C(carbonyl)) = 1.484(5) A, r(C(carbonyl)-C(alkyl)) = 1.513(5) A, r(C-Cl) = 1.790(5) A, r(C=O) = 1.218(6) A, r(C-H)(phenyl) = 1.087(9) (average value) A, r(C-H)(alkyl) = 1.090(9) A (average value), angle C(phenyl)-C=O = 119.5(9) degrees, angle C(phenyl)-C(carbonyl)-C(alkyl) = 119.2(10) degrees, angle C-C-Cl = 109.8(12) degrees, angle C(2)-C(1)-C(carbonyl) = 122.8(15) degrees, angle C-C(alkyl)-H = 111.2 degrees (ab initio value).     

Preparation and properties of trifluorothioacetic acid-S-(trifluoromethyl)ester, CF3C(O)SCF3

Trifluorothioacetic acid-S-(trifluoromethyl)ester, CF3C(O)SCF3, was prepared by reacting CF3C(O)Cl and AgSCF3 at 50 degrees C. The compound was characterized by (13)C-, (19)F-NMR, UV, and vibrational spectroscopy as well as by gas electron diffraction (GED) and quantum chemical calculations (HF, MP2, and B3LYP methods 6-31G(d) and 6-311+G(2df) basis sets). GED and vibrational spectroscopy result in the presence of a single conformer with C1 symmetry and synperiplanar orientation of the S-CF3 bond relative to the CO bond. This result is in agreement with quantum chemical calculations which predict the anti conformer to be higher in energy by about 4 kcal/mol. An assignment of the IR (gas) and Raman (liquid) spectra is proposed, and the GED analysis results in the following skeletal geometric parameters (r(a) and angle(a) values with 3sigma uncertainties; these parameters are thermal averages and are not inconsistent with calculated equilibrium values): C=O = 1.202(6) A, C-C = 1.525(10) A, S-C(sp(2)) = 1.774(3) A, S-C(sp(3)) = 1.824 (3) A. O=C-C = 118.7(21) degrees, O=C-S = 127.1(15) degrees, C-S-C = 99.8 (13) degrees.     

Effects of molecular structure on the stability of a thermotropic liquid crystal. Gas electron diffraction study of the molecular structure of phenyl benzoate.

As a model of the core of molecules forming liquid crystals, the molecular structure of phenyl benzoate (Ph-C(=O)-O-Ph) at 409 K was determined by gas electron diffraction, and the relationship between the gas-phase structures of model compounds and the nematic-to-liquid transition temperatures was studied. Structural constraints were obtained from RHF/6-31G ab initio calculations. Vibrational mean amplitudes and shrinkage corrections were calculated from the harmonic force constants given by normal coordinate analysis. Thermal vibrations were treated as small-amplitude motions, except for the phenyl torsion, which was treated as a large-amplitude motion. The potential function for torsion was assumed to be V(phi(1),phi(2)) = V(12)(1 - cos 2phi(1))/2 + V(14)(1 - cos 4phi(1))/2 + V(22)(1 - cos 2phi(2))/2, where phi(1) and phi(2) denote the torsional angles around the C-Ph and O-Ph bonds, respectively. The potential constants (V(ij)()/kcal mol(-)(1)) and the principal structure parameters (r(g)/A, angle(alpha)/deg) with the estimated limits of error (3sigma) are as follows: V(12) = -1.3 (assumed); V(14) = -0.5(9); V(22) = 3.5(15); r(C=O) = 1.208(4); r(C(=O)-O) = 1.362(6); r(C(=O)-O) - r(O-C) = -0.044 (assumed); r(C(=O)-C) = 1.478(10); = 1.396(1); angleOCO = 124.2(13); angleO=CC = 127.3(12); angleCOC = 121.4(22); ( angleOCC(cis) - angleOCC(trans))/2 = 3.0(15); ( angleC(=O)CC(cis) - angleC(=O)CC(trans))/2 = 4.8(17), where < > means an average value and C-C(cis) and C-C(trans) bonds are cis and trans to the C(=O)-O bond, respectively. The torsional angle around the O-Ph bond was determined to be 64(+26,-12) degrees. An apparent correlation was found between the contributions of the cores to the clearing point of liquid crystals and the gas-phase structures of model compounds of the cores of mesogens, i.e., phenyl benzoate, trans-azobenzene (t-AB), N-benzylideneaniline, N-benzylideneaniline N-oxide (NBANO), trans-azoxybenzene (t-AXB), and trans-stilbene. The structures of t-AB, NBANO, and t-AXB have been obtained by our research group.     

1,2-Dibromoethyl-trichlorosilane (CH2BrCHBrSiCl3): conformational structure and vibrational properties by gas-phase electron diffraction, infrared and Raman spectroscopy, and ab initio molecular orbital and density functional theory calculations

The molecular structure and conformational properties of 1,2-dibromoethyl-trichlorosilane (CH2BrCHBrSiCl3) have been investigated using gas-phase electron diffraction (GED) data recorded at a temperature of 100 degrees C, together with ab initio molecular orbital (MO) and density functional theory (DFT) calculations, infrared (IR) and Raman spectroscopy in the liquid and solid phases, and normal coordinate analysis (NCA). The molecule exists in the gas- and liquid phases as a mixture of three conformers, gauche(-) [G(-)], with a refined torsion angle phi(BrCCBr)=-71(6) degrees, anti [A], with a torsion angle phi(BrCCBr) approximately -170 degrees , and gauche(+) [G(+)], with a torsion angle phi(BrCCBr) approximately +70 degrees . The second torsion angle of importance, the rotation about the CSi bond, has been refined to a value of +175(13) degrees . Torsion angles were only refined for the more abundant G(-) conformer. In the solid phase, only the G(-) conformer was observed. The temperature-dependent Raman spectra have provided an estimate of the relative conformational entropies, DeltaS. The obtained composition from GED refinements was (%) G(-)/A/G(+)=64(27)/23(13)/13(18) (values with estimated 2sigma uncertainties), giving a conformational stability order in agreement with both the Raman enthalpy measurements and the ab initio MO and DFT calculations using the 6-311G(d) basis set and scaled zero-point energies. Relevant structural parameter values obtained from the GED refinements (with the ab initio HF values used as constraints) were as follows (G(-) values with estimated 2sigma uncertainties): bond lengths (r(g)):r(C-C)=1.501(18)A, r(SiC)=1.865(15)A, r(CBr)=1.965(8)A (average), r(SiCl)=2.028(3)A (average). Bond angles ( anglealpha):angleCCSi=114.1(33) degrees , angleC1C2Br=114.0(21) degrees , angleCSiCl=109.6(7) degrees (average). Experimental IR/Raman and obtained vibrational wavenumbers based on both the unscaled, fixed-scaled as well as the scale-refined quantum-mechanical force fields [HF/6-311G(d)] are presented. The results are discussed and compared with some similar molecules from the literature.     

Molecular structure and conformational composition of 1,3-dihydroxyacetone studied by combined analysis of gas-phase electron diffraction data, rotational constants, and results of theoretical calculations. Ideal gas thermodynamic properties of 1,3-dihydroxyacetone

The molecular structure of 1,3-dihydroxyacetone (DHA) has been studied by gas-phase electron diffraction (GED), combined analysis of GED and microwave (MW) data, ab initio, and density functional theory calculations. The equilibrium re structure of DHA was determined by a joint analysis of the GED data and rotational constants taken from the literature. The anharmonic vibrational corrections to the internuclear distances (re-ra) and to the rotational constants (B(i)e-B(i)0) needed for the estimation of the re structure were calculated from the B3LYP/cc-pVTZ cubic force field. It was found that the experimental data are well reproduced by assuming that DHA consists of a mixture of three conformers. The most stable conformer of C2v symmetry has two hydrogen bonds, whereas the next two lowest energy conformers (Cs and C1 symmetry) have one hydrogen bond and their abundance is about 30% in total. A combined analysis of GED and MW data led to the following equilibrium structural parameters (re) of the most abundant conformer of DHA (the uncertainties in parentheses are 3 times the standard deviations): r(C=O)=1.215(2) A, r(C-C)=1.516(2) A, r(C-O)=1.393(2) A, r(C-H)=1.096(4) A, r(O-H)=0.967(4) A, angleC-C=O=119.9(2) degrees, angleC-C-O=111.0(2) degrees, angleC-C-H=108.2(7) degrees, angleC-O-H=106.5(7) degrees. These structural parameters reproduce the experimental B(i)0 values within 0.05 MHz. The experimental structural parameters are in good agreement with those obtained from theoretical calculations. Ideal gas thermodynamic functions (S degrees (T), C degrees p(T), and H degrees (T)-H degrees (0)) of DHA were calculated on the basis of experimental and theoretical molecular parameters obtained in this work. The enthalpy of formation of DHA, -523+/-4 kJ/mol, was calculated by the atomization procedure using the G3X method.     

Chalcogenide-halides of niobium (V). 1. Gas-phase structures of NbOBr(3), NbSBr(3), and NbSCl(3). 2. Matrix infrared spectra and vibrational force fields of NbOBr(3), NbSBr(3), NbSCl(3), and NbOCl(3)

The molecular structures of NbOBr(3), NbSCl(3), and NbSBr(3) have been determined by gas-phase electron diffraction (GED) at nozzle-tip temperatures of 250 degrees C, taking into account the possible presence of NbOCl(3) as a contaminant in the NbSCl(3) sample and NbOBr(3) in the NbSBr(3) sample. The experimental data are consistent with trigonal-pyramidal molecules having C(3)(v)() symmetry. Infrared spectra of molecules trapped in argon or nitrogen matrices were recorded and exhibit the characteristic fundamental stretching modes for C(3)(v)() species. Well resolved isotopic fine structure ((35)Cl and (37)Cl) was observed for NbSCl(3), and for NbOCl(3) which occurred as an impurity in the NbSCl(3) spectra. Quantum mechanical calculations of the structures and vibrational frequencies of the four YNbX(3) molecules (Y = O, S; X = Cl, Br) were carried out at several levels of theory, most importantly B3LYP DFT with either the Stuttgart RSC ECP or Hay-Wadt (n + 1) ECP VDZ basis set for Nb and the 6-311G basis set for the nonmetal atoms. Theoretical values for the bond lengths are 0.01-0.04 A longer than the experimental ones of type r(a), in accord with general experience, but the bond angles with theoretical minus experimental differences of only 1.0-1.5 degrees are notably accurate. Symmetrized force fields were also calculated. The experimental bond lengths (r(g)/A) and angles ( 90 degree angle (alpha)()/deg) with estimated 2sigma uncertainties from GED are as follows. NbOBr(3): r(Nb=O) = 1.694(7), r(Nb-Br) = 2.429(2), 90 degree angle (O=Nb-Br) = 107.3(5), 90 degree angle (Br-Nb-Br) = 111.5(5). NbSBr(3): r(Nb=S) = 2.134(10), r(Nb-Br) = 2.408(4), 90 degree angle (S=Nb-Br) = 106.6(7), 90 degree angle (Br-Nb-Br) = 112.2(6). NbSCl(3): r(Nb=S) = 2.120(10),r(Nb-Cl) = 2.271(6), 90 degree angle (S=Nb-Cl) = 107.8(12), 90 degree angle (Cl-Nb-Cl) = 111.1(11).     

Molecular structure, conformation, and potential to internal rotation of 2,6- and 3,5-difluoronitrobenzene studied by gas-phase electron diffraction and quantum chemical calculations

3,5-Difluoronitrobenzene (3,5-DFNB) and 2,6-difluoronitrobenzene (2,6-DFNB) have been studied by gas-phase electron diffraction (GED), MP2 ab initio, and by B3LYP density functional calculations. Refinements of r h1 and r e static and r h1 dynamic GED models were carried out for both molecules. Equilibrium r e structures were determined using anharmonic vibrational corrections to the internuclear distances ( r e - r a) calculated from B3LYP/cc-pVTZ cubic force fields. 3,5-DFNB possesses a planar structure of C 2 v symmetry with the following r e values for bond lengths and bond angles: r(C-C) av = 1.378(4) A, r(C-N) = 1.489(6) A, r(N-O) = 1.217(2) A, r(C-F) = 1.347(5) A, angleC6-C1-C2 = 122.6(6) degrees , angleC1-C2-C3 = 117.3(3) degrees , angleC2-C3-C4 = 123.0(3) degrees , angleC3-C4-C5 = 116.9(6) degrees , angleC-C-N = 118.7(3) degrees , angleC-N-O = 117.3(4) degrees , angleO-N-O = 125.5(7) degrees , angleC-C-F = 118.6(7) degrees . The uncertainties in parentheses are three times the standard deviations. As in the case of nitrobenzene, the barrier to internal rotation of the nitro group in 3,5-DFNB, V 90 = 10 +/- 4 kJ/mol, is substantially lower than that predicted by quantum chemical calculations. The presence of substituents in the ortho positions force the nitro group to rotate about the C-N bond, out of the plane of the benzene ring. For 2,6-DFNB, a nonplanar structure of C 2 symmetry with a torsional angle of phi(C-N) = 53.8(14) degrees and the following r e values for structural parameters was determined by the GED analysis: r(C-C) av = 1.383(5) A, r(C-N) = 1.469(7) A, r(N-O) = 1.212(2) A, r(C-F) = 1.344(4) A, angleC6-C1-C2 = 118.7(5) degrees , angleC1-C2-C3 = 121.2(2) degrees , angleC2-C3-C4 = 119.0(2) degrees , angleC3-C4-C5 = 121.1(4) degrees , angleC-C-N = 120.6(2) degrees , angleC-N-O = 115.7(4) degrees , angleO-N-O = 128.6(7) degrees , angleC-C-F = 118.7(5) degrees . The refinement of a dynamic model led to barriers V 0 = 16.5 +/- 1.5 kJ/mol and V 90 = 2.2 +/- 0.5 kJ/mol, which are in good agreement with values predicted by B3LYP/6-311++G(d,p) and MP2/ cc-pVTZ calculations. The values of C-F bond lengths are similar in both molecules. This is in contrast to the drastic shortening of the C-F bond in the ortho position in 2-fluoronitrobenzene compared to the C-F bond length in the meta and para position in 3- and 4-fluoronitrobenzene observed in an earlier GED study.     

Binding of DNA purine sites to dirhodium compounds probed by mass spectrometry

The adducts formed between the antitumor active compounds [Rh(2)(O(2)CCH(3))(2)(CH(3)CN)(6)](BF(4))(2), Rh(2)(O(2)CCH(3))(4), and Rh(2)(O(2)CCF(3))(4) with DNA oligonucleotides have been assessed by matrix-assisted laser desorption ionization (MALDI) and nanoelectrospray (nanoESI) coupled to time-of-flight mass spectrometry (TOF MS). A series of MALDI studies performed on dipurine (AA, AG, GA, and GG)-containing single-stranded oligonucleotides of different lengths (tetra- to dodecamers) led to the establishment of the relative reactivity cis-[Pt(NH(3))(2)(OH(2))(2)](2+) (activated cisplatin) approximately Rh(2)(O(2)CCF(3))(4) > cis-[Pt(NH(3))(2)Cl(2)] (cisplatin) > [Rh(2)(O(2)CCH(3))(2)(CH(3)CN)(6)](BF(4))(2) > Rh(2)(O(2)CCH(3))(4) approximately Pt(C(6)H(6)O(4))(NH(3))(2) (carboplatin). The relative reactivity of the complexes is associated with the lability of the leaving groups. The general trend is that an increase in the length of the oligonucleotide leads to enhanced reactivity for Rh(2)(O(2)CCH(3))(2)(CH(3)CN)(6)](BF(4))(2) and Rh(2)(O(2)CCH(3))(4) (except for the case of [Rh(2)(O(2)CCH(3))(2)(CH(3)CN)(6)](2+), which reacts faster with the GG octamers than with the dodecamers), whereas the reactivity of Rh(2)(O(2)CCF(3))(4) is independent of the oligonucleotide length. When monitored by ESI, the dodecamers containing GG react faster than the respectiveAA oligonucleotides in reactions with Rh(2)(O(2)CCF(3))(4) and Rh(2)(O(2)CCH(3))(2)(CH(3)CN)(6)](BF(4))(2), whereas AA oligonucleotides react faster with Rh(2)(O(2)CCH(3))(4). The mixed (AG, GA) purine sequences exhibit comparable rates of reactivity with the homopurine (AA, GG) dodecamers in reactions with Rh(2)(O(2)CCH(3))(4). The observation of initial dirhodium-DNA adducts with weak axial (ax) interactions, followed by rearrangement to more stable equatorial (eq) adducts, was achieved by electrospray ionization; the Rh-Rh bond as well as coordinated acetate or acetonitrile ligands remain intact in these dirhodium-DNA adducts. MALDI in-source decay (ISD), collision-induced dissociation (CID) MS-MS, and enzymatic digestion studies followed by MALDI and ESI MS reveal that, in the dirhodium compounds studied, the purine sites of the DNA oligonucleotides interact with the dirhodium core. Ultimately, both MALDI and ESI MS proved to be complementary, valuable tools for probing the identity and stability of dinuclear metal-DNA adducts.     

Gas electron diffraction analysis on S-methyl thioacetate, CH3C(O)SCH3

The molecular structure of S-methyl thioacetate, CH3C(O)SCH3, was determined by gas electron diffraction (GED) with the assistance of quantum chemical calculations (B3LYP/6-31G and MP2/6-31G). Experimental and theoretical methods result in a structure with syn conformation (C=O double bond syn with respect to the S-C(H3) single bond). The following skeletal geometric parameters were derived from the GED analysis (ra values with 3sigma uncertainties): C=O = 1.214(3), C-C = 1.499(5), S-C(sp2) = 1.781(6), S-C(sp3) = 1.805(6) angstroms, O=C-C = 123.4(8) degrees, O=C-S = 122.8(5) degrees and C-S-C = 99.2(9) degrees.     

Matrix isolation and low temperature solid state FTIR spectroscopic study of alpha-furil

Alpha-furil [C(4)H(3)O-C(=O)-C(=O)-C(4)H(3)O] has been isolated in argon and xenon matrices and studied by FTIR spectroscopy, supported by DFT(B3LYP)/6-311++G(d,p) calculations. The obtained spectra were fully assigned and revealed the presence in the matrices of three different conformers, all of them exhibiting skewed conformations around the intercarbonyl bond with the two C(4)H(3)O-C(=O) fragments nearly planar. The three conformers differ in the orientation of the furan rings relative to the carbonyl groups: the most stable conformer, I (C(2) symmetry; O=C-C=O intercarbonyl dihedral equal to 153.1 degrees), has both furan rings orientated in such a way that one of their beta-hydrogen atoms approaches the oxygen atom of the most distant carbonyl group, forming two H-C=C-C-C=O six-membered rings; the second most stable conformer, II (C(1) symmetry; O=C-C=O intercarbonyl dihedral equal to 126.9 degrees ), has one furan ring orientated as in I, while the second furan group is rotated by ca. 180 degrees (resulting in an energetically less favourable H-C=C-C=O five-membered ring); in the third conformer, III (C(2) symmetry; O=C-C=O dihedral equal to 106.2 degrees ), both furan rings assume the latter orientation relative to the dicarbonyl group. The theoretical calculations predicted the two higher energy forms being 5.85 and 6.22 kJ mol(-1) higher in energy than the most stable form, respectively, and energy barriers for conformational interconversion higher than 40 kJ mol(-1). These barriers are high enough to prevent observation of conformational isomerization for the matrix isolated compound. The three possible conformers of alpha-furil were also found to be present in CCl(4) solution, as well as in a low temperature neat amorphous phase of the compound prepared from fast condensation of its vapour onto a suitable 10 K cooled substrate. On the other hand, in agreement with the available X-ray data [S. C. Biswas, S. Ray and A. Podder, Chem. Phys. Lett., 1987, 134, 541], the IR spectra obtained for the neat low temperature crystalline state reveals that, in this phase, alpha-furil exists uniquely in its most stable conformational state, I.     

Molecular structure of 2,2,4,4,6,6-hexamethyl-1,3,5-trimethylenecyclohexane as determined by gas-phase electron diffraction

The molecular structure of 2,2,4,4,6,6-hexamethyl-1,3,5-trimethylenecyclohexane has been determined in the gas phase at a nozzle tip temperature of 340 K. The electron diffraction data were found to be consistent with a model where the cyclohexane ring adopts a distorted twist-boat conformation. The averaged geometrical parameters (r(g) and 90 degree angle (alpha)) obtained from least squares analysis are r(C=C) = 1.346(4) A, r(C-C)(ring) = 1.537(1) A, r(C-C)(Me) = 1.543(1) A, 90 degree angle C(6)C(1)C(2) = 117.5(11) degrees, 90 degree angle C(1)C(2)C(3) = 113.1(12) degrees, and 90 degree angle MeCMe = 108.2(13) degrees. The experimental results are consistent with the results from HF/6-311G(d) and MP2/6-311G(d) calculations where the distorted twist-boat form is found to be lower in energy than the chair form by 9.85 and 10.7 kcal/mol, respectively.     

Copper(II) complexes of a series of alkoxy diazine ligands: mononuclear, dinuclear, and tetranuclear examples with structural, magnetic, and DFT studies

Picolyl hydrazide ligands have two potentially bridging functional groups (micro-O, micro-N-N) and consequently can exist in different coordination conformers, both of which form spin-coupled polynuclear coordination complexes, with quite different magnetic properties. The complex [Cu(2)(POAP-H)Br(3)(H(2)O)] (1) involves a micro-N-N bridge (Cu-N-N-Cu 150.6 degrees ) and exhibits quite strong antiferromagnetic coupling (-2J = 246(1) cm(-)(1)). [Cu(2)(PZOAPZ-H)Br(3)(H(2)O)(2)] (2) has two Cu(II) centers bridged by an alkoxide group with a very large Cu-O-Cu angle of 141.7 degrees but unexpectedly exhibits quite weak antiferromagnetic exchange (-2J = 91.5 cm(-)(1)). This is much weaker than anticipated, despite direct overlap of the copper magnetic orbitals. Density functional calculations have been carried out on compound 2, yielding a similar singlet-triplet splitting energy. Structural details are reported for [Cu(2)(POAP-H)Br(3)(H(2)O)] (1), [Cu(2)(PZOAPZ-H)Br(3)(H(2)O)(2)] (2), [Cu(2)(PAOPF-2H)Br(2)(DMSO)(H(2)O)].H(2)O (3), [Cu(4)(POMP-H))(4)](NO(3))(4).2H(2)O (4), and PPOCCO (5) (a picolyl hydrazide ligand with a terminal oxime group) and its mononuclear complexes [Cu(PPOCCO-H)(NO(3))] (6) and [Cu(PPOCCO-H)Cl] (7). Compound 1 (C(12)H(13)Br(3)Cu(2)N(5)O(4)) crystallizes in the monoclinic system, space group P2(1)/c, with a = 15.1465(3) A, b = 18.1848(12) A, c = 6.8557(5) A, beta = 92.751(4) degrees, and Z = 4. Compound 2 (C(10)H(13)Br(3)Cu(2)N(7)O(4)) crystallizes in the triclinic system, space group P, with a = 9.14130(1) A, b = 10.4723(1) A, c = 10.9411(1) A, alpha = 100.769(1), beta = 106.271(1) degrees, gamma = 103.447(1) degrees, and Z = 2. Compound 3 (C(23)H(22)Br(2)Cu(2)N(7)O(5.5)S) crystallizes in the monoclinic system, space group P2(1)/c, with a = 12.406(2) A, b = 22.157(3) A, c = 10.704(2) A, beta = 106.21(1) degrees, and Z = 4. Compound 4(C(52)H(48)Cu(4)N(20)O(18)) crystallizes in the monoclinic system, space group P2(1)/n, with a = 14.4439(6) A, b = 12.8079(5) A, c = 16.4240(7) A, beta = 105.199(1) degrees, and Z = 4. Compound 5 (C(15)H(14)N(4)O(2)) crystallizes in the orthorhombic system, space group Pna2(1), with a = 7.834(3) A, b = 11.797(4) A, c = 15.281(3) A, and Z = 4. Compound 6(C(15)H(13)CuN(5)O(5)) crystallizes in the monoclinic system, space group P2(1)/c, with a = 8.2818(9) A, b = 17.886(2) A, c = 10.828(1) A, beta = 92.734(2) degrees, and Z = 4. Compound 7 (C(15)H(13)CuClN(4)O(2)) crystallizes in the orthorhombic system, space group Pna2(1), with a = 7.9487(6) A, b = 14.3336(10) A, c = 13.0014(9) A, and Z = 4. Density functional calculations on PPOCCO are examined in relation to the anti-eclipsed conformational change that occurs on coordination to copper(II).     

Study of the thymine molecule: equilibrium structure from joint analysis of gas-phase electron diffraction and microwave data and assignment of vibrational spectra using results of ab initio calculations

Thymine is one of the nucleobases which forms the nucleic acid (NA) base pair with adenine in DNA. The study of molecular structure and dynamics of nucleobases can help to understand and explain some processes in biological systems and therefore it is of interest. Because the scattered intensities on the C, N, and O atoms as well as some bond lengths in thymine are close to each other the structural problem cannot been solved by the gas phase electron diffraction (GED) method alone. Therefore the rotational constants from microvawe (MW) studies and differences in the groups of N-C, C=O, N-H, and C-H bond lengths from MP2 (full)/cc-pVQZ calculations were used as supplementary data. The analysis of GED data was based on the C(s) molecular symmetry according to results of the structure optimizations at the MP2 (full) level using 6-311G (d,p), cc-pVTZ, and cc-pVQZ basis sets confirmed by vibrational frequency calculations with 6-311G (d,p) and cc-pVTZ basis sets. Mean-square amplitudes as well as harmonic and anharmonic vibrational corrections to the internuclear distances (r(e)-r(a)) and to the rotational constants (B(e)(k)-B(0)(k), where k = A, B, C) were calculated from the quadratic (MP2 (full)/cc-pVTZ) and cubic (MP2 (full)/6-311G (d,p)) force constants (the latter were used only for anharmonic corrections). The harmonic force field was scaled using published IR and Raman spectra of the parent and N1,N3-dideuterated species, which were for the first time completely assigned in the present work. The main equilibrium structural parameters of the thymine molecule determined from GED data supplemented by MW rotational constants and results of MP2 calculations are the following (bond lengths in Angstroms and bond angles in degrees with 3sigma in parentheses): r(e) (C5=C6) = 1.344 (16), r(e) (C5-C9) = 1.487 (8), r(e) (N1-C6) = 1.372 (3), r(e) (N1-C2) = 1.377 (3), r(e) (C2-N3) = 1.378 (3), r(e) (N3-C4) = 1.395 (3), r(e) (C2=O7) = 1.210 (1), r(e) (C4=O8) = 1.215 (1), angle e (N1-C6=C5) = 123.1 (5), angle e (C2-N1-C6) = 123.7 (5), angle e (N1-C2-N3) = 112.8 (5), angle e (C2-N3-C4) = 128.0 (5), angle e (N3-C4-C5) = 114.8 (5), angle e (C6=C5-C9) = 124.4 (9). The experimental structural parameters are in good agreement with those from MP2 (full) calculations with use of cc-pVTZ and cc-pVQZ basis sets.     

The interaction of water and dibromine in the gas phase: an investigation of the complex H(2)O...Br(2) by rotational spectroscopy and ab initio calculations

The ground-state rotational spectra of eight isotopomers of a complex formed by water and dibromine in the gas phase were observed by pulsed-jet, Fourier transform microwave spectroscopy. The spectroscopic constants B(0), C(0), delta(J), delta(JK), chi(aa)(Br(x)) (x=i for inner, o for outer), [chi(bb)(Br(x))-chi(cc)(Br(x))] and M(bb)(Br(x)) were determined for H(2)O...(79)Br(79)Br, H(2)O...(81)Br(79)Br, H(2)O...(79)Br(81)Br, H(2)O...(81)Br(81)Br, D(2)O...(79)Br(81)Br and D(2)O...(81)Br(81)Br. For the isotopomers HDO...(79)Br(81)Br and HDO...(81)Br(81)Br, only (B(0) + C(0))/2, delta(J), the chi(aa)(Br(x)) and M(bb)(Br(x)) were determinable. The spectroscopic constants were interpreted on the basis of several models of the complex to give information about its geometry, binding strength and the extent of electronic rearrangement on complex formation. The molecule H(2)O...Br(2) has C(s) symmetry with a pyramidal configuration at O. The zero-point effective quantities r(O...Br(i))=2.8506(1) A and phi(0)=46.8(1), where phi is the angle between the C(2) axis of H(2)O and the O...Br-Br internuclear axis, were obtained under the assumption of monomer geometries unchanged by complexation. Ab initio calculations, carried out at the aug-cc-pVDZ/MP2 level of theory, gave the equilibrium values r(e)(O...Br(i))=2.7908 A and phi(e)=45.7 degrees and confirmed the collinearity of the O...Br-Br nuclei. The potential energy function V(phi), also determined ab initio, showed that the wavenumber required for inversion of the configuration at O in the zero-point state is only 9 cm(-1). By interpreting the Br nuclear quadrupole coupling constants, the fractions delta(O-->Br(i))=0.004(5) and delta (Br(i)-->Br(o))=0.050(2) of an electron were determined to be transferred from O to Br(i) and Br(i) to Br(o), respectively, when the complex is formed. The complex is relatively weak, as indicated by the small value k(sigma)=9.8(2) N m(-1) of the intermolecular stretching force constant obtained from delta(J). A comparison of the properties, similarly determined, of H(2)O...F(2), H(2)O...Cl(2), H(2)O...Br(2), H(2)O...BrCl, H(2)O...ClF and H(2)O...ICl is presented.     

An investigation of the molecular geometry and electronic structure of nitryl chloride by a combination of rotational spectroscopy and ab initio calculations

The ground-state rotational spectra of the six isotopomers (16)O(2) (14)N(35)Cl, (16)O(2) (14)N(37)Cl, (18)O(16)O(14)N(35)Cl, (18)O(2) (14)N(35)Cl, (16)O(2) (15)N(35)Cl, and (16)O(2) (15)N(37)Cl of nitryl chloride were observed with a pulsed-jet, Fourier-transform microwave spectrometer to give rotational constants, Cl and (14)N nuclear quadrupole coupling, and spin-rotation coupling constants. These spectroscopic constants were interpreted to give r(0), r(s), and r(m) ((2)) versions of the molecular geometry and information about the electronic redistribution at N when nitryl chloride is formed from NO(2) and a Cl atom. The r(m) ((2)) geometry has r(N-Cl)=1.8405(6) A, r(N-O)=1.1929(2) A, and the angle ONO=131.42(4) degrees , while the corresponding quantities for the r(s) geometry are 1.8489 A, 1.1940 A, and 131.73 degrees , respectively. Electronic structure calculations at CCSD(T)cc-pVXZ (X=T, Q, or 5) levels of theory were carried out to give a r(e) geometry, vibration-rotation corrections to equilibrium rotational constants, and values of the (35)Cl and (14)N nuclear hyperfine (quadrupole and spin-rotation) coupling constants in good agreement with experiment. The equilibrium geometry at the CCSD(T)/cc-pV5Z level of theory has r(N-Cl)=1.8441 A, r(N-O)=1.1925 A and the angle ONO=131.80 degrees . The observed rotational constants were corrected for the vibration-rotation effects calculated ab initio to yield semiempirical equilibrium constants which were then fitted to give the following semiempirical equilibrium geometry: r(N-Cl)=1.8467(2) A, r(N-O)=1.1916(1) A, and the angle ONO=131.78(3) degrees .     

S-(fluoroformyl)O-(trifluoroacetyl) thioperoxide, FC(O)S-OC(O)CF3: gas-phase structure and conformational properties

The geometric structure and conformational properties of S-(fluoroformyl)O-(trifluoroacetyl) thioperoxide, FC(O)S-OC(O)CF3, were investigated by gas electron diffraction, matrix isolation infrared spectroscopy, and quantum chemical calculations (B3LYP with the 6-31G and aug-cc-pVTZ basis sets and MP2 with the 6-31G basis set). The experimental methods result in a mixture of two conformers with gauche conformation around the S-O bond. In the main conformer (82(7)% according to GED at 298 K), the C=O bond of the FC(O) group is oriented syn with respect to the S-O bond and phi(C-S-O-C) = 75(3) degrees . In the minor conformer (18(7)%), this C=O is oriented anti. Both conformers possess syn orientation of the C=O bond of the CF3C(O) group. The conformational properties and geometric parameters are reproduced reasonably well by the quantum chemical calculations, except for the S-O bond length, which is predicted too long by 0.04 A (B3LYP/aug-cc-pVTZ).     

1-Phenyl-1,2-dicarba-closo-dodecaborane, 1-Ph-1,2-closo-C(2)B(10)H(11). Synthesis, Characterization, and Structure As Determined in the Gas Phase by Electron Diffraction, in the Crystalline Phase at 199 K by X-ray Diffraction, and by ab Initio Computations

The compound 1-phenyl-1,2-dicarba-closo-dodecaborane(12), 1-C(6)H(5)-1,2-closo-C(2)B(10)H(11) (1), has been synthesized and characterized by a complete assignment of its (11)B NMR spectrum via (11)B{(1)H}/(11)B{(1)H} (COSY), (1)H{(11)B(selective)} and (1)H{(11)B}/(1)H{(11)B} (COSY) spectroscopy. An electron- and X-ray diffraction investigation of 1, complemented by ab initio calculations, has been undertaken. The gas-phase electron-diffraction (GED) data can be fitted by several models describing conformations which differ in the position of the phenyl ring with respect to the carborane cage. Local symmetries ofC(2)(v)() and D(6)(h)() for the 1,2-C(2)B(10) and C(6) moieties, respectively, were adopted in the GED model in order to simplify the problem. In addition, constraints among the close-lying C-C and B-B bonds were employed. However, even though such simplifications led to satisfactory refinements (R(G) = 0.069-0.071), a unique, definitive solution could not be gained. The (C-C)(mean), (C-B)(mean) and (B-B)(mean) bond lengths,r(a), are ca. 1.44, 1.72, and 1.78 ?, respectively. The C(6) hexagon, with r(a)(C-C) = ca. 1.394 ?, either eclipses the C(1)-C(2) vector (overall C(s)() symmetry) or more or less eclipses the C(1)-B(4) cluster bond (overall C(1) symmetry). In contrast, in the solid at 199 K, the ring lies at a position intermediate between the two GED positions, as determined by X-ray crystallography [C(8)H(16)B(10), monoclinic P2(1)/a: a = 12.047(3) ?, b = 18.627(4) ?, c = 12.332(5) ?, beta = 110.09(4) degrees, Z = 8]. The C-B distances span the range 1.681(6)-1.743(5) ?, and B-B lengths lie between 1.756(6) and 1.795(6) ?. A similar conformation was found for the theoretical (RHF/6-31G level) structure which was fully optimized in C(1) symmetry. The r(e) distances are consistent with the dimensions derived in the experimental studies. IGLO calculations of the (11)B chemical shifts, in addition to SCF single-point energies of the GED structures, further support these observations.     

The substituted alkyne 3-heptyne is eclipsed

Although butane exists in staggered anti and gauche conformations, when the ethyl groups are separated by a C[triple bond]C triple bond (3-hexyne), the stable conformation changes to eclipsed, (1)C(2v). Using rotational microwave spectroscopy, we have studied another example, 3-heptyne, the C[triple bond]C elongated analogue of pentane. The most stable conformer of pentane has anti-anti (AA) conformations about the central C-C bonds (C(2v)) and the next most stable has a gauche dihedral angle (GA, C1). This microwave study determines that the extended analogue of the AA form is not staggered about the C[triple bond]C axis but eclipsed (Cs). Also, the elongated analogue of the GA conformer is also not staggered but nearly eclipsed. The conformations of low-polarity substituted acetylenes is determined by dispersion attractions between the end groups. A microwave study of the AA and GA conformers of pentane is also reported.     

Triangular,ferromagnetically-coupled CuII 3-pyrazolato complexes as possible models of particulate methane monooxygenase (pMMO)

Magnetic susceptibility and EPR studies show that trinuclear Cu(II)-pyrazolato complexes with a Cu(3)(mu3-X)2 core (X = Cl, Br) are ferromagnetically coupled: J(Cu-Cu) = +28.6 cm(-1) (X = Cl), +3.1 cm(-1) (X = Br). The orderly transition from an antiferromagnetic to a ferromagnetic exchange among the Cu centers of Cu(3)(mu3-X) complexes, X = O, OH, Cl, Br, follows the change of the Cu-X-Cu angle from 120 degrees to approximately 80 degrees. The crystal structures of [Bu4N]2"[Cu3(mu3-Br)2(mu-pz*)3Br3] (pz* = pz (1a) or 4-O2N-pz (1b), pz = pyrazolato anion, C(3)H(3)N(2)(1-)) are presented.     

Molecular structure and conformations of para-methylbenzene sulfonamide and ortho-methylbenzene sulfonamide: gas electron diffraction and quantum chemical calculations study

The molecular structure and conformational properties of para-methylbenzene sulfonamide (4-MBSA) and ortho-methylbenzene sulfonamide (2-MBSA) have been studied by gas electron diffraction (GED) and quantum chemical methods (B3LYP/6-311+G** and MP2/6-31G**). Quantum chemical calculations predict the existence of two conformers for 4-MBSA with the S-N bond perpendicular to the benzene plane and the NH2 group either eclipsing or staggering the S-O bonds of the SO2 group. Both conformers possess CS symmetry. The eclipsed form is predicted to be favored by DeltaE = 0.63 kcal/mol (B3LYP) or 1.00 kcal/mol (MP2). According to the calculations, the S-N bond in 2-MBSA can possess planar direction opposite the methyl group (phi(C2C1SN) = 180 degrees ) or nonplanar direction (phi(C2C1SN) approximately 60 degrees ). In both cases, the NH2 group can adopt eclipsed or staggered orientation, resulting in a total of four stable conformers. The nonplanar eclipsed conformer (C1 symmetry) and the planar eclipsed form (CS symmetry) are predicted to be favored. According to the GED analysis, the saturated vapor over solid 4-MBSA at T = 151(3) degrees C consists as mixture of the eclipsed (78(19) %) and staggered (22(19) %) forms. The saturated vapor over solid 2-MBSA at T = 157(3) degrees C consists as a mixture of the nonplanar eclipsed (69(11) %) and planar eclipsed (31(11) %) forms.