Analysis Of Gas-phase Electron Diffraction Data Research Articles

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.

Molecular structure and conformation of nitrobenzene reinvestigated by combined analysis of gas-phase electron diffraction, rotational constants, and theoretical calculations

The molecular structure and conformation of nitrobenzene has been reinvestigated by gas-phase electron diffraction (GED), combined analysis of GED and microwave (MW) spectroscopic data, and quantum chemical calculations. The equilibrium re structure of nitrobenzene was determined by a joint analysis of the GED data and rotational constants taken from the literature. The necessary anharmonic vibrational corrections to the internuclear distances (re − ra) and to rotational constants (Be(i) − B0(i)) were calculated from the B3LYP/cc-pVTZ quadratic and cubic force fields. A combined analysis of GED and MW data led to following structural parameters (re) of planar nitrobenzene (the total estimated uncertainties are in parentheses): r(C–C)av = 1.391(3) A, r(C–N) = 1.468(4) A, r(N–O) = 1.223(2) A, r(C–H)av = 1.071(3) A, \({\angle}\)C2–C1–C6 = 123.5(6)°, \({\angle}\)C1–C2–C3 = 117.8(3)°, \({\angle}\)C2–C3–C4 = 120.3(3)°, \({\angle}\)C3–C4–C5 = 120.5(6)°, \({\angle}\)C–C–N = 118.2(3)°, \({\angle}\)C–N–O = 117.9(2)°, \({\angle}\)O–N–O = 124.2(4)°, \({\angle}\)(C–C–H)av = 120.6(20)°. These structural parameters reproduce the experimental B0(i) values within 0.05 MHz. The experimental results are in good agreement with the theoretical calculations. The barrier height to internal rotation of nitro group, 4.1±1.0 kcal/mol, was estimated from the GED analysis using a dynamic model. The equilibrium structure was also calculated using the experimental rotational constants for nitrobenzene isotopomers and theoretical rotation–vibration interaction constants.

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.

Conformational analysis. 23: A gas-phase electron-diffraction and ab initio molecular orbital investigation of 3-fluoropropan-1-ol. Is there significant internal hydrogen bonding?

There are 14 possible rotational conformers of 3-fluoropropan-1-ol, based on the assumption of three potential minima for rotation about single bonds. Of these, only the gG−G form (g,G=gauche, a,A=anti) where the sequence indicates rotation around the C–O, the CO–C, and the C–CF bonds, with the minus sign indicating clock-wise rotation has the hydrogen and fluorine atoms in position for formation of a hydrogen bond. Analysis of gas-phase electron-diffraction data obtained at a sample temperature of 20°C indicates the dominant form to be aGG (41 (2σ=19)% of the sample). The hydrogen-bonded form gG−G comprises 2 (19)% of the sample. These values reflect the assumption that the amounts of the remaining components of the system exist in proportions given by the results of ab initio (B3LYP/6-311+G(3d,2p)//B3LYP/6-31G(d)) calculations. Weighted average parameter values (rg/Å, ∠g/deg) for all forms are r(C–C)=1.528(3), r(C1–C2)− r(C2–C3)=0.066(12), r(C–H)=1.115(4), r(C–O)=1.380(8), r(C–F)=1.450(6), ∠(COH)=105.9(assumed), ∠(CCF)=109.7(8), 〈∠(CCC), ∠(CCO)〉=111.8(6), ∠(COH)−∠(COH)=3.1(assumed), ∠(CCH)=109.4(7). Torsion-angle parameters could not be refined. Weighted average theoretical torsion angles for conformers with G or G− orientations are ∠(OCCC)=63.2(3), and ∠(CCCF)=61.0(3). Ab initio calculations at several levels of theory with several basis sets predicted substantially different amounts of the gG−G form. Best agreement with experiment was given by the B3LYP/6311++G(3d,2p)//B3LYP/6-31G(d) calculations.

Gas-Phase Reaction of Tetraborane(10) and Ethyne: Molecular Structure of nido-1,2-C(2)B(3)H(7) in the Gas Phase.

The molecular structure of nido-1,2-C(2)B(3)H(7), 1, the principal volatile carborane generated in the quenched gas-phase reaction of B(4)H(10) and ethyne at 70 degrees C, has been determined by a combined analysis of gas-phase electron-diffraction data and rotation constants restrained by ab initio computations at the CCSD(T)/TZP' level. The structure is consistent with a geometry having C(s)() symmetry, similar to that of pentaborane(9). The apical position is occupied by a carbon atom, displaced toward B(4) from a position directly above the B(5).B(3) vector, and hydrogen atoms asymmetrically bridge the B-B bonds. The basal atoms are almost coplanar, C(2) lying ca. 2 degrees below the B(3)-B(4)-B(5) plane. Important experimental structural parameters (r(alpha) degrees /pm, angle(alpha)/ degrees ) are r[C(1)-C(2)] = 162.6(6); r[C(1)-B(3)] = 161.4(3); r[C(2)-B(3)] = 154.3(2); r[C(1)-B(4)] = 157.4(5); r[B(3)-B(4)] = 185.7(3); <B(3)-B(4)-B(5) = 80.9(1). In addition to this and the other previously reported carboranes, 2,3-C(2)B(4)H(8), 2-Me-2,3,4-C(3)B(3)H(6), and 4-Me-2-CB(5)H(8), several new derivatives have been identified among the volatile products. These include the dicarbahexaboranes 2,4-Me(2)-2,3-C(2)B(4)H(6) and 5-Et-2,3-C(2)B(4)H(7) (the major volatile products obtained when the reaction is allowed to go to completion, previously reported as tricarbahexaboranes) and the derivatives 2,5-Me(2)-2,3-C(2)B(4)H(6), 4-Et-2,3-C(2)B(4)H(7), 1-Me-2,3,4-C(3)B(3)H(6), 2-Me-2-CB(5)H(8), 3-Me-2-CB(5)H(8), and 2,3,4,5-C(4)B(2)H(6). The complex mechanism of the reaction is discussed in light of these new results.

Synthesis of Volatile Cyclic Silylamines and the Molecular Structures of Two 1-Aza-2,5-disilacyclopentane Derivatives.

An optimized synthetic procedure for alpha,omega-bis(bromosilyl)alkanes, BrH(2)Si(CH(2))(n)()SiH(2)Br (with n = 2 and 3), is proposed. 1,2-Bis(bromosilyl)ethane reacts with ammonia to give 1,4-bis(1-aza-2,5-disilacyclopentane-1-yl)-1,4-disilabutane, traces of 1,6-diaza-2,5,7,10,11,14-hexasilabicyclo[4.4.4]tetradecane and nonvolatile products. The primary reaction products undergo slow redistribution reactions whereby (1-aza-2,5-disilacyclopentane-1-yl)-1,4-disilabutane is formed as the major product. Reactions of alpha,omega-bis(bromosilyl)alkanes, BrH(2)Si(CH(2))(n)()SiH(2)Br (with n = 2 and 3), with isopropylamine afford the heterocycles 1-isopropyl-1-aza-2,5-disilacyclopentane and 1-isopropyl-1-aza-2,6-disilacyclohexane, whereas the analogous reaction with bis(bromosilyl)methane gives 1,5-diisopropyl-1,5-diaza-2,4,6,8-tetrasilacyclooctane rather than a four-membered ring compound. All compounds have been characterized by elemental analysis, mass spectrometry, and IR and NMR spectroscopy [(1)H, (13)C, (15)N and (29)Si including the measurement of (1)J((29)Si(15)N) coupling constants]. The molecular structure of 1-isopropyl-1-aza-2,5-disilacyclopentane, determined by analysis of gas-phase electron-diffraction data augmented by restraints derived from ab initio calculations, is compared with the molecular structure of the isoelectronic 1-(dimethylamino)-1-aza-2,5-disilacyclopentane. The latter also was determined by gas-phase electron-diffraction (supported by ab initio calculations) and by low-temperature crystallography. The presence of a beta-donor Si.N interaction in the latter compound, leading to a narrow Si-N-N angle, is apparent from a significant distortion of the molecular structure as compared with the isoelectronic reference compound.