Computational study of the aminolysis of esters. The reaction of methylformate with ammonia

The aminolysis of esters is a basic organic reaction considered as a model for the interaction of carbonyl group with nucleophiles. In the present computational study the different possible mechanistic pathways of the reaction are reinvestigated by applying higher level electronic structure theory, examining the general base catalysis by the nucleophile, and a more comprehensive study the solvent effect. Both the ab initio QCISD/6-31(d,p) method and density functional theory at the B3LYP/6-31G(d) level were employed to calculate the reaction pathways for the simplest model aminolysis reaction between methylformate and ammonia. Solvent effects were assessed by the PCM method. The results show that in the case of noncatalyzed aminolysis the addition/elimination stepwise mechanism involving two transition states and the concerted mechanism have very similar activation energies. However, in the case of catalyzed aminolysis by a second ammonia molecule the stepwise mechanism has a distinctly lower activation energy. All transition states in the catalyzed aminolysis are 10-17 kcal/mol lower than those for the uncatalyzed process.

Cyclopentadiene annulated polycyclic aromatic hydrocarbons: investigations of electron affinities

The adiabatic electron affinities of cyclopentadiene and 10 associated benzannelated derivatives have been predicted with both density functional and Hartree-Fock theory. These systems can also be regarded as benzenoid polycyclic aromatic hydrocarbons (PAHs) augmented with five-membered rings. Like the PAHs, the electron affinities of the present systems generally increase with the number of rings. To unequivocally bind an electron, cyclopentadiene must have at least two conventionally fused benzene rings. 1H-Benz[f]indene, a naphthalene-annulated cyclopentadiene, is predicted to have a zero-point energy corrected adiabatic electron affinity of 0.13 eV. Since the experimental E(A) of naphthalene is negative (-0.19 eV), the five-membered ring appendage contributes to the stability of the naphthalene-derived 1H-benz[f]indene radical anion significantly. The key to binding the electron is a contiguous sequence of fused benzenes, since fluorene, the isomer of 1H-benz[f]indene, with separated six-membered rings, has an electron affinity of -0.07 eV. Each additional benzene ring in the sequence fused to cyclopentadiene increases the electron affinity by 0.15-0.65 eV: the most reliable predictions are cyclopentadiene (-0.63 eV), indene (-0.49 eV), fluorene (-0.07 eV), 1H-benz[f]indene (0.13 eV), 1,2-benzofluorene (0.25 eV), 2,3-benzofluorene (0.26 eV), 12H-dibenzo[b,h]fluorene (0.65 eV), 13H-indeno[1,2-b]anthracene (0.82 eV), and 1H-cyclopenta[b]naphthacene (1.10 eV). In contrast, if the six-membered ring-fusion is across the C(2)-C(3) cyclopentadiene single bond, only a single benzene is needed to bind an electron. The theoretical electron affinity of the resulting molecule, isoindene, is 0.49 eV, and this increases to 1.22 eV for 2H-benz[f]indene. The degree of aromaticity is responsible for this behavior. While the radical anions are stabilized by conjugation, which increases with the size of the system, the regular indenes, like PAHs in general, suffer from the loss of aromatic stabilization in forming their radical anions. While indene is 21 kcal mol(-1) more stable than isoindene, the corresponding radical anion isomers have almost the same energy. Nucleus-independent chemical shift calculations show that the highly aromatic molecules lose almost all aromaticity when an extra electron is present. The radical anions of cyclopentadiene and all of its annulated derivatives have remarkably low C-H bond dissociation energies (only 18-34 kcal mol(-1) for the mono-, bi-, and tricyclics considered). Hydrogen atom loss leads to the restoration of aromaticity in the highly stabilized cyclopentadienyl anion congeners.

The radical anions and the electron affinities of perfluorinated benzene, naphthalene and anthracene

Although benzene and naphthalene do not have electron affinities in the conventional sense, perfluorobenzene and perfluoronaphthalene have nonzero electron affinities. Theoretical methods extensively calibrated with experiment for the prediction of electron affinities (EAs) predict the EAs of perfluorobenzene, perfluoronaphthalene and perfluoroanthracene as 0.69, 1.02 and 1.84 eV, respectively. A rough estimate of 2.39 eV is made for the electron affinity of perfluorotetracene. Thus the perfluoro polycyclic aromatic hydrocarbons (PAHs) are predicted to be effective electron acceptors.

The rule breaking Cr2(CO)10. A 17 electron Cr system or a CrCr double bond?

Density functional theory (DFT) has been used to investigate the conformations and thermochemistry on the singlet and triplet potential energy surfaces (PES) of Cr2(CO)10. The global minimum energy structure for the lowest singlet state of C2h symmetry is consistent with a model of two interacting Cr(CO)5 fragments in which one carbonyl in each fragment acts as an asymmetric four-electron donor bridging carbonyl, with chromium-chromium distances of 2.93 A (B3LYP) or 2.83 A (BP86). Avoiding a Cr...Cr bond by incorporating four-electron donor CO groups in this way allows each chromium atom in singlet Cr(CO)10 to attain the favored 18-electron configuration by using, in a simple picture of the bonding, only the six octahedral sp3d2 hybrids. The dissociation energy to two Cr(CO)5 fragments or to Cr(CO)6 + Cr(CO)4 fragments is predicted to be 10 kcal mol(-1). The lowest triplet state of Cr2(CO)10 is predicted to lie approximately 10 kcal mol(-1) above the singlet global minimum. In the case of triplet Cr2(CO)10 the lowest energy minima were found to be of C2 and C2h symmetry, with similar energies. The chromium-chromium distances in triplet Cr2(CO)10 were found to be shorter than those in the corresponding singlet structures, namely 2.81 (B3LYP) or 2.68 A (BP86) suggesting a sigma + 2(1/2) pi Cr=Cr double bond similar to the O=O bond in O2 or the Fe=Fe bond in the experimentally observed triplet state (Me5C5)2Fe2(mu-CO)3.

2-Pyridinethiol/2-pyridinethione tautomeric equilibrium. A comparative experimental and computational study

The gas phase and solvent dependent preference of the tautomerization between 2-pyridinethiol (2SH) and 2-pyridinethione (2S) has been assessed using variable temperature Fourier transform infrared (FTIR) experiments, as well as ab initio and density functional theory computations. No spectroscopic evidence (nu(S)(-)(H) stretch) for 2SH was observed in toluene, C(6)D(6), heptane, or methylene chloride solutions. Although, C(s)() 2SH is 2.61 kcal/mol more stable than C(s)() 2S (CCSD(T)/cc-pVTZ//B3LYP/6-311+G(3df,2p)+ZPE), cyclohexane solvent-field relative energies (IPCM-MP2/6-311+G(3df,2p)) favor 2S by 1.96 kcal/mol. This is in accord with the FTIR observations and in quantitative agreement with the -2.6 kcal/mol solution (toluene or C(6)D(6)) calorimetric enthalpy for the 2S/2SH tautomerization favoring the thione. As the intramolecular transition state for the 2S, 2SH tautomerization (2TS) lies 25 (CBS-Q) to 30 kcal/mol (CCSD/cc-pVTZ) higher in energy than either tautomer, tautomerization probably occurs in the hydrogen bonded dimer. The B3LYP/6-311+G(3df,2p) optimized C(2) 2SH dimer is 10.23 kcal/mol + ZPE higher in energy than the C(2)(h)() 2S dimer and is only 2.95 kcal/mol + ZPE lower in energy than the C(2) 2TS dimer transition state. Dimerization equilibrium measurements (FTIR, C(6)D(6)) over the temperature range 22-63 degrees C agree: K(eq)(298) = 165 +/- 40 M(-)(1), DeltaH = -7.0 +/- 0.7 kcal/mol, and DeltaS = -13.4 +/- 3.0 cal/(mol deg). The difference between experimental and B3LYP/6-311+G(3df,2p) [-34.62 cal/(mol deg)] entropy changes is due to solvent effects. The B3LYP/6-311+G(3df,2p) nucleus independent chemical shifts (NICS) are -8.8 and -3.5 ppm 1 A above the 2SH and 2S ring centers, respectively, and the thiol is aromatic. Although the thione is not aromatic, it is stabilized by the thioamide resonance. In solvent, the large 2S dipole, 2-3 times greater than 2SH, favors the thione tautomer and, in conclusion, 2S is thermodynamically more stable than 2SH in solution.

Molecules for materials: germanium hydride neutrals and anions. Molecular structures, electron affinities, and thermochemistry of GeHn/GeHn- (n = 0-4) and Ge2Hn/Ge2Hn(-) (n = 0-6)

The GeH(n) (n = 0-4) and Ge(2)H(n) (n = 0-6) systems have been studied systematically by five different density functional methods. The basis sets employed are of double-zeta plus polarization quality with additional s- and p-type diffuse functions, labeled DZP++. For each compound plausible energetically low-lying structures were optimized. The methods used have been calibrated against a comprehensive tabulation of experimental electron affinities (Chemical Reviews 102, 231, 2002). The geometries predicted in this work include yet unknown anionic species, such as Ge(2)H(-), Ge(2)H(2)(-), Ge(2)H(3)(-), Ge(2)H(4)(-), and Ge(2)H(5)(-). In general, the BHLYP method predicts the geometries closest to the few available experimental structures. A number of structures rather different from the analogous well-characterized hydrocarbon radicals and anions are predicted. For example, a vinylidene-like GeGeH(2) (-) structure is the global minimum of Ge(2)H(2) (-). For neutral Ge(2)H(4), a methylcarbene-like HGë-GeH(3) is neally degenerate with the trans-bent H(2)Ge=GeH(2) structure. For the Ge(2)H(4) (-) anion, the methylcarbene-like system is the global minimum. The three different neutral-anion energy differences reported in this research are: the adiabatic electron affinity (EA(ad)), the vertical electron affinity (EA(vert)), and the vertical detachment energy (VDE). For this family of molecules the B3LYP method appears to predict the most reliable electron affinities. The adiabatic electron affinities after the ZPVE correction are predicted to be 2.02 (Ge(2)), 2.05 (Ge(2)H), 1.25 (Ge(2)H(2)), 2.09 (Ge(2)H(3)), 1.71 (Ge(2)H(4)), 2.17 (Ge(2)H(5)), and -0.02 (Ge(2)H(6)) eV. We also reported the dissociation energies for the GeH(n) (n = 1-4) and Ge(2)H(n) (n = 1-6) systems, as well as those for their anionic counterparts. Our theoretical predictions provide strong motivation for the further experimental study of these important germanium hydrides.

From "parasitic" association reactions toward the stoichiometry controlled gas phase synthesis of nanoparticles: a theoretically driven challenge for experimentalists

In the present record a model for the gas-phase reactions during the chemical vapor deposition (CVD) processes of group 13-15 materials is presented, based on the results of extensive quantum-chemical modeling. Thermodynamic criteria have been introduced to evaluate the importance of a range of association reactions. For the organometallic and hydride derivatives, association processes are found to be favorable both thermodynamically and kinetically. Formation of high mass association products takes place under CVD conditions, including laser-assisted CVD. Structural and thermodynamic properties of the most important ring and cluster intermediates have been predicted. The stoichiometry-controlled synthesis of the 13-15 ternary alloys and nanoparticles using cluster compounds as single-source precursors is predicted to be viable. The association pathway described may be generalized to the CVD reactions of many binary materials (12-16, 13-16, 13-15, 14-15, 14-16).

Electron affinity of the guanine-cytosine base pair and structural perturbations upon anion formation

The adiabatic electron affinity (AEA) for the Watson-Crick guanine-cytosine (GC) DNA base pair is predicted using a range of density functional methods with double- and triple-zeta plus polarization plus diffuse (DZP++ and TZ2P++) basis sets in an effort to bracket the true electron affinity. The methods used have been calibrated against a comprehensive tabulation of experimental electron affinities (Chem.Rev. 2002, 102, 231). Optimized structures for GC and the GC anion are compared to the neutral and anionic forms of the individual bases as well as Rich's 1976 X-ray structure for sodium guanylyl-3',5'-cytidine nonahydrate, GpC.9H(2)O. Structural distortions and natural population (NPA) charge distributions of the GC anion indicate that the unpaired electron is localized primarily on the cytosine moiety. Unlike treatments using second-order perturbation theory (MP2), density functional theory consistently predicts a substantial positive adiabatic electron affinity for the GC pair (e.g., TZ2P++/B3LYP: +0.48 eV). The stabilization of C(-) via three hydrogen bonds to guanine is sufficient to facilitate adiabatic binding of an electron to GC and is also consistent with the positive experimental electron affinities obtained by photoelectron spectroscopy of cytosine anions incrementally microsolvated with water molecules. The pairing (dissociation) energy for GC(-) (35.6 kcal/mol) is determined with inclusion of electron correlation and shows the anion to have greater thermodynamic stability; the pairing energy for neutral GC (TZ2P++/B3LYP 23.9 kcal/mol) compares favorably to previous MP2/6-31G (23.4 kcal/mol) results and a debated experiment (21.0 kcal/mol).

What is the nature of polyacetylene neutral and anionic chains HC(2n)H and HC(2n)H(-) (n = 6-12) that have recently been observed?

The optimized geometries, adiabatic electron affinities, and IR-active vibrational frequencies have been predicted for the long linear carbon chains HC(2n)H. The B3LYP density functional combined with the DZP basis set was used in this theoretical study. The computed physical properties are discussed. The predicted electron affinities form a remarkably regular sequence: 1.78 (HC(12)H), 2.08 (HC(14)H), 2.32 (HC(16)H), 2.53 (HC(18)H), 2.69 (HC(20)H), 2.83 (HC(22)H), and 2.95 eV (HC(24)H). The predicted structures display an alternating triple and very short single bond pattern, with the degree of bond alternation significantly less for the radical anions.