Molecular structure of ethynylbenzene from electron diffraction and ab initio molecular orbital calculations

The molecular structure and benzene ring distortions of ethynylbenzene have been investigated by gas-phase electron diffraction and ab initio MO calculations at the HF/6-31G^* and 6-3G^** levels. Least-squares refinement of a model withC _2v, symmetry, with constraints from the MO calculations, yielded the following important bond distances and angles:r _g(C _i -C _o )=1.407±0.003 Å,r _g(C _o -C _m )=1.397±0.003 Å,r _g(C _m -C _p )=1.400±0.003 Å,r _g(Cr _i -CCH)=1.436 ±0.004 Å,r _g(C=C)=1.205±0.005 Å, C _o -C _i -C _o =119.8±0.4°. The deformation of the benzene ring of ethynylbenzene given by the MO calculations, including o-C_i-C_o=119.4°, is insensitive to the basis set used and agrees with that obtained by low-temperature X-ray crystallography for the phenylethynyl fragment, C₆H₅-CC-, in two different crystal environments. The partial substitution structure of ethynylbenzene from microwave spectroscopy is shown to be inaccurate in the ipso region of the benzene ring.     

Molecular structure of phenylsilane: a study by gas-phase electron diffraction and ab initio molecular orbital calculations

The molecular structure of phenylsilane has been determined accurately by gas-phase electron diffraction and ab initio MO calculations at the MP2(f.c.)/6-31G* level. The calculations indicate that the perpendicular conformation of the molecule, with a Si–H bond in a plane orthogonal to the plane of the benzene ring, is the potential energy minimum. The coplanar conformation, with a Si–H bond in the plane of the ring, corresponds to a rotational transition state. However, the difference in energy is very small, 0.13 kJ mol⁻¹, implying free rotation of the substituent at the temperature of the electron diffraction experiment (301 K). Important bond lengths from electron diffraction are: <r_g(C–C)>=1.403±0.003 Å, r_g(Si–C)=1.870±0.004 Å, and r_g(Si–H)=1.497±0.007 Å. The calculations indicate that the C_ipso–C_ortho bonds are 0.010 Å longer than the other C–C bonds. The internal ring angle at the ipso position is 118.1±0.2° from electron diffraction and 118.0° from calculations. This confirms the more than 40-year old suggestion of a possible angular deformation of the ring in phenylsilane, in an early electron diffraction study by F.A. Keidel, S.H. Bauer, J. Chem. Phys. 25 (1956) 1218.     

A molecular orbital study of nitrogen inversion in aniline with extensive geometry optimization

The geometry and energy of aniline have been calculated using the 6-31G and 6-31G^*(5D) basis sets for the planar structure and various pyramidal structures, assuming that the ring and the N-atom bonded to it lie in the same plane, but otherwise with full geometry optimization. With the 6-31G basis set the planar structure is predicated to be the most stable, whereas the inclusion of polarization functions in the 6-31G^*(5D) basis set finds a pyramidal structure with the out-of-plane angle =42.3° to be most stable and the energy barrier to inversion via the planar transition state to be 1.59±0.02 kcal mol^–1, in close agreement with experiment. Completing the optimization, allowing the N-atom and the C- and H-atoms of the ring to take up equilibrium out-of-plane positions increases the calculated energy carrier to inversion by less than 0.1 kcal mol^–1 to 1.66 kcal mol^–1. The ring adopts a very shallow inverted boat-type conformation with N₇-C₁C₄ = 2.0°.     

Molecular structure and conformational composition of 1-Chlorobutane, 1-Bromobutane,and 1-Iodobutane as determined by gas-phase electron diffraction and ab initio calculations

Gas-phase electron diffraction (ED), together with ab initio molecular orbital calculations, have been used to determine the structure and conformational composition of 1-chlorobutane, 1-bromobutane, and 1-iodobutane. These molecules may in principle exist as mixtures of five different conformers, but only three or four of these were observed in gas phase at temperatures of the ED experiments, 18C, 18C, and 23C, respectively. The observed conformational compositions (1-chlorobutane, 1-bromobutane, and 1-iodobutane) were AA (13 ± 12%, 21 ± 14%, 19 ± 17%), GA (60±13%, 33±32%, 17±31%), AG (12±16%, 8±12%, <1%), and GG (12 ±16%, 38± 34%, 64±31%). A and G denotesanti andgauche positions for the X-C₁-C₂-C₃ (X=Cl, Br, I), and the C₁-C₂-C₃-C₄ torsion angles. The results for the most important distances (r _g) and angles () from the combined ED/ab initio study for the GA conformer of 1-chlorobutane, with estimated 2 uncertainties, arer(C₁-C₂)=1.519(3)å,r (C₂-C₃)=1.530(3) å,r (C₃-C₄)=1.543(3) å,r (C₁-Cl)=1.800(4) å, <C₁C₂C₃=114.3(6), <C₂C₃C₄=112.0(6), <CCCl=112.3(5). The results for the GA conformer of 1-bromobutane arer (C₁-C₂)=1.513(4) å,r (C₂-C₃)=1.526(4) å,r (C₃-C₄)=1.540(4) å,r(C₁-Br)=1.959(8) å, <C₁C₂C₃=115.3(11), <C₂C₃C₄=112.8(11),<CCBr=112.1(14). The results for 1-chlorobutane and 1-bromobutane are compared with those from earlier electron diffraction investigations. The results for the GA conformer of 1-iodobutane arer (C₁-C₂)=1.506(5) å,r (C₂-C₃)=1.518(5) å,r (C₃-C₄)=1.535(5) å,r (C₁-I)=2.133(11) å, <C₁C₂C₃=116.8(15), <C₂C₃C₄=115.3(15), <CCI=110.2(14). Differences in length between the different C-H bonds in each molecule, between the different C-C bonds, between the different CCH angles, and between the different CCC angles were kept constant at the values obtained from the ab initio calculations.     

The molecular structure and the puckering potential function of silacyclobutane as determined by gas electron diffraction and relaxation constraints from ab initio calculations

Gas electron diffraction is applied to determine the geometric parameters of the silacyclobutane molecule using a dynamic model where the ring puckering was treated as a large amplitude motion. The structural parameters and the parameters of the potential function were refined taking into account the relaxation of the molecular geometry estimated from ab initio calculations at the MP2/6-311+G(d, p) level of theory. The potential function has been described as V() = V₀[(/_e)² − 1]² with the following parameters V₀ = 0.82 ± 0.60 kcal/mol and _e = 33.5 ± 2.7°, where is a puckering angle of the ring.

The geometric parameters at the minimum V() (r_a in Å, in degrees and uncertainties given as three times the standard deviations including a scale error) are: r(Si–H_ax) = 1.467(96), r(Si–H_eq) = 1.468(96), r(Si–C) = 1.885(2), r(C–C) = 1.571(3), r(C–H) = 1.100(3), CSiC = 77.2(9), HSiH = 108.3, SiCH_eq = 123.5(16), SiCH_ax = 111.9(16), CC₅H_eq = 118.4(24), CC₅H_ax = 112.3(24), HC₃H = 107.7, δ(HSiH) = 6.6, δ(HC₃H) = 7.0, where the tilts δ, HSiH, and HC₃H are estimated from ab initio constraints. The structural parameters are compared with those obtained for related compounds.     

Unimolecular isomerization/decomposition of cyclopentadienyl and related bimolecular reverse process: ab initio MO/statistical theory study

The cyclopentadienyl radical decomposition has been studied in detail by high‐level correlation MO methods combined with multichannel RRKM rate constant calculations. The product channels of the reaction were examined by calculating their pressure‐dependent branching rate constants. The overall reaction rate has been shown to be controlled by the first transition state corresponding to 1,2‐hydrogen atom migration. Also, the reverse bimolecular reactions (C₃H₃ + C₂H₂ → products) have been included in the study. We provide a summary of pressure dependent rate constant expressions for the 1000–3000 K temperature range that may be useful for kinetic modeling of relevant combustion systems. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 415–425, 2000     

Molecular structure of 1,2,3-triethyldiaziridine: Gas-phase electron diffraction and theoretical calculations

For the first time, the equilibrium molecular structure and conformational composition (6 to 8 conformers) of 1,2,3-triethyl-diaziridine in the gas phase were determined by gas-phase electron diffraction. Using 1D and 2D ¹H and ¹³C NMR spectro-scopy, it was shown that in a CDCl₃ solution under normal conditions on the NMR time scale, the molecule exists only as one conformer. The enthalpy of formation Δ_fH ⁰₂₉₈ of the studied molecule in the gas phase was calculated by the method of atomization reactions and is equal to 92.2 ± 1.7 kJ mol⁻¹.     

Spectroscopic properties in the liquid phase: combining high-level ab initio calculations and classical molecular dynamics.

We present an integrated computational tool, rooted in density functional theory, the polarizable continuum model, and classical molecular dynamics employing spherical boundary conditions, to study the spectroscopic observables of molecules in solution. As a test case, a modified OPLS-AA force field has been developed and used to compute the UV and NMR spectra of acetone in aqueous solution. The results show that provided the classical force fields are carefully reparameterized and validated, the proposed approach is robust and effective, and can also be used by nonspecialists to provide a general and powerful complement to experimental techniques.     

Molecular structures and ab initio molecular orbital calculations of the optically active derivatives of 1-aminocyclopropane-1-carboxylic acid

The novel optically active derivatives of 2,2′-disubstituted-1-aminocyclopropane-1-carboxylic acid (−)-2 and (+)-3 were synthesised from the spiro-azlactone (+)-1. Oxidation of the diol moiety of (+)-3 gave by ring enlargement the racemic mixture of 2,3-dihydrofuran derivative (±)-6. This conversion is explained by stepwise rearrangement of the initially formed tetrasubstituted cyclopropanecarbaldehyde 4 through zwitterionic's reactive intermediate 5. The formation of (±)-6 is preferred energetically as established by ab initio calculations of the ground states and possible intermediates for that rearrangement. The crystal structure and absolute configuration of the compounds (+)-1, (−)-2, (+)-3 and (−)-7 were determined by single-crystal X-ray diffraction method. All four compounds possess Z-configuration of the cyclopropane ring. The dioxolane ring in the structures (+)-1 and (−)-2 adopts half-chair conformation, while the cyclopropane ring and geminally substituted groups in the structures (−)-2, (+)-3 and (−)-7 possess the anticlinal conformation. The molecules of the compound (+)-1 are connected by very weak intermolecular hydrogen bond of C-H?O type. In the compounds (−)-2, (+)-3 and (−)-7inter- and intramolecular hydrogen bonds of N-H?O type were observed. The spiro-compound (+)-1 exhibited a more pronounced inhibitory activity against the proliferation of murine leukemia and human T-lymphocytes cells than other type of tumor cell lines and normal human fibroblast cells.     

Molecular Structure and Conformation of p-Bis(trimethylsilyl)benzene: A Study by Gas-Phase Electron Diffraction and Theoretical Calculations

The molecular structure and conformation of p-bis(trimethylsilyl)benzene have been investigated by gas-phase electron diffraction, ab initio MO calculations at the HF/6-31G*, MP2(f.c.)/6-31G*, and B3LYP/6-31G* levels, and MM3 molecular mechanics calculations. The calculations indicate the syn- and anti-coplanar conformations, with two bonds in the plane of the benzene ring, to be energy minima. The perpendicular conformations, with two bonds in a plane orthogonal to the ring plane, are transition states. The two coplanar conformers have nearly the same energy with a low interconversion barrier, 0.3–0.5 kJ mol^–1. The calculated lengths of the and bonds differ by only a few thousandths of an angstrom, in agreement with electron diffraction results from molecules containing either or bonds. The geometrical distortion of the benzene ring in p-bis(trimethylsilyl)-benzene may be described by superimposing independent distortions from each of the two SiMe₃ groups. The electron diffraction intensities from a previous study (Rozsondai, B.; Zelei, B.; Hargittai, I. J. Mol. Struct. 1982, 95, 187) have been reanalyzed, imposing constraints from the theoretical calculations, and using a model based on a 1:1 mixture of the two coplanar conformers. The effective torsion angles of the SiMe₃ groups may indicate nearly free rotation. Important geometrical parameters from the present electron diffraction analysis are , and . While the mean bond lengths are virtually the same from the previous and present analyses, the new ipso angle is in better agreement with the MO calculations [HF, 116.9° MP2(f.c.), 117.1° B3LYP, 116.9°].     

Molecular structure of 5-fluorouracil from gas-phase electron diffraction data and quantum-chemical calculations

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Lithium hydroxide phase transition under high pressure: an ab initio molecular dynamics study.

The high-pressure phase transition in the deuterated lithium hydroxide crystalline state has been studied by Car-Parrinello molecular dynamics simulations, in the constant-pressure, constant-temperature ensemble. The recently developed metadynamics approach has been applied to encourage the system to transform into different phases in an affordable simulation time. A previously not completely characterized high-pressure phase has been obtained. The structural and spectroscopic properties have been studied and compared with the neutron scattering, infrared and Raman measurements. It has been found that the calculated structure differs slightly from the experimental hypothesis, and that the presence of strong hydrogen bonds is the source of the red shift and of the characteristic features of the OD-stretching bands in both IR and Raman spectra.     

Exploring the hydration of Pb2+: ab initio studies and first-principles molecular dynamics

Even though lead is a well-known toxicant widely scattered throughout the world since antiquity, its chemistry is poorly documented at the molecular level. Here we investigate the hydration of the Pb(2+) ion by means of first-principles molecular dynamics (Car-Parrinello molecular dynamics, CPMD). We found that the hydrated cation is heptacoordinated in a dynamically holodirected arrangement roughly corresponding to a fluxional distorted pentagonal bipyramid. The time-averaged Pb-O bond length is especially large and amounts to 2.70 A with an associated root-mean-square deviation of 0.26 A. This results from a dynamic exchange between short (<2.6 A), intermediate (2.6-3.0 A) and long (>3.0 A) Pb-O bonds. The latter very long Pb-O distance implies that the determination of the coordination number n(c) from experimental work may not necessarily yield values directly comparable to the theoretical value of n(c)=7, since not all experimental techniques would recognize such a long distance as a bond to the metal cation. Pronounced disorders are evidenced in the second shell, characteristic of a chaotropic cation, and exchanges between the first and second shells cannot be excluded on a timescale of a few tens of picoseconds.     

On the bond-stretch isomerism in the benzo[1,2:4,5]dicyclobutadiene system--an ab initio MR-AQCC study.

Bond-stretch isomerism in benzo[1,2:4,5]dicyclobutadienle (BDCB) has been investigated using the MR-AQCC/6-31G(d) method, a high-level multireference ab initio approach including size-extensivity corrections. The applied theoretical approach includes both nondynamical and dynamical electron correlation effects. Full MR-AQCC geometry optimizations of localized (1) and delocalized (3) isomers as well as the transition structure (TS) have been determined using D2h, symmetry restriction. The calculations show that both isomers are approximately of equal stability separated by a barrier with a height of about 5 kcal mol(-1). Thus, the present results strongly indicate that benzof[1,3:4,5]dicyclobutadiene is a very good candidate for an organic compound exhibiting bond-stretch isomerism, since isomers 1 and 3 correspond to true minima on the double-well potential energy surface, which are separated by a sufficiently high barrier. It is particularly important to emphasize that isomer 3 represents a realization of the highly elusive quasi-[10]annulene.     

Molecular structure and vibrational spectra of phenobaraitone by density functional theory and ab initio hartree-Fock calculations

Quantum chemistry calculations have been performed using Gaussian03 program to compute optimized geometry, harmonic vibrational frequency along with intensities in IR and Raman spectra at RHF/6-31++G** and B3LYP/6-31++G** levels for phenobarbitone (C₁₂H₁₂N₂O₃) in the ground state. The scaled harmonic vibrational frequencies have been compared with experimental FT-IR and FT-Raman spectra. Theoretical vibrational spectra of the title compound were interpreted by means of potential energy distributions (PEDs) using MOLVIB program. A detailed interpretation of the infrared spectra of the title compound is reported. On the basis of the agreement between the calculated and observed results, the assignments of fundamental vibrational modes of phenobarbitone were examined and some assignments were proposed. The theoretical spectrograms for FT-IR and FT-Raman spectra of the title compound have been constructed.     

Evaluation of the electron momentum density of crystalline systems from ab initio linear combination of atomic orbitals calculations

Alternative techniques are presented for the evaluation of the electron momentum density (EMD) of crystalline systems from ab initio linear combination of atomic‐orbitals calculations performed in the frame of one‐electron self‐consistent‐field Hamiltonians. Their respective merits and drawbacks are analyzed with reference to two periodic systems with very different electronic features: the fully covalent crystalline silicon and the ionic lithium fluoride. Beyond one‐electron Hamiltonians, a post‐Hartree–Fock correction to the EMD of crystalline materials is also illustrated in the case of lithium fluoride. © 2012 Wiley Periodicals, Inc.     

A hybrid ab initio/free electron computational model for conjugated dye molecules: Simple cyanines and oxonols

Justifications developed for the application the free electron model to the π‐orbitals of conjugated molecules suggest that the optical properties of these molecules would be well described by a one‐dimensional free electron model with a potential chosen to reproduce the energy level spacing of the ground state occupied π‐orbitals. Such a hybrid ab initio/free electron modeling approach, where the free electron potential parameters are optimized on a molecule‐by‐molecule basis, is developed, and applied to a series of simple cyanine and oxonol dyes. The ensuing predictions for λ_max, oscillator strengths, and redox properties compare well to available experimental information. Two important strengths of this approach are that no explicit calculations of the excited electronic state are required, and that the ab initio determination of the occupied π‐orbital level spacing considers all the electrons (π and σ) of the entire molecule in a specified geometry, environment, etc. This second characteristic gives the ability to efficiently model modifications of the optical properties of conjugated molecules resulting from chemical and/or physical modifications occuring within and remote to the conjugated region of the molecule. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 943–953, 2000