Theoretical study of the N---H tautomerism in free base porphyrin

The N---H tautomerism of free base porphyrin is investigated at the semiempirical spin-unrestricted AM1 (UAM1) and ab initio RHF/3-21G levels. The UAM1 method provides delocalized geometries for all stationary structures without imposing any symmetry constraint. RHF/3-21G geometry optimizations have to be performed under symmetry restrictions to ensure that realistic delocalized structures are obtained. Both the semiempirical and the ab initio calculations predict that the interconversion between trans tautomers proceeds in an asynchronous two-step process via intermediate cis tautomers. The cis tautomers are characterized as minima in the potential energy surface and are 8–10 kcal mol⁻¹ higher in energy. The activation energy for the trans → cis interconversion is calculated to be approximately 23 kcal mol⁻¹ at the 3-21G level. The activation energy for the synchronous trans → trans interconversion is higher and has a value of 30.5 kcal mol⁻¹. The activation energies obtained at the semiempirical UAM1 level are twice as large as the ab initio values.     

A semiempirical quantum mechanical study of cationically catalyzed homopolymerization and copolymerization of vinyl ethers and epoxides

The purpose of this study was to use the semiempirical quantum mechanical computational method, AM1, to investigate vinyl ether cationic homopolymerization, epoxide homopolymerization, and copolymerization of selected vinyl ethers with a model epoxide (cyclohexene oxide). Homopolymerization studies of 19 vinyl ethers showed that activation enthalpies ranged between 0.0 and 15 kcal/mol, and that the enthalpies of reaction for homopolymerization were nearly all exothermic. Homopolymerization of three epoxides predicted low activation enthalpies, some of which were virtually activationless. All ring-opening epoxide polymerizations were exothermic. Copolymerization of three vinyl ethers with cyclohexene oxide gave activation enthalpies that varied between 2.7 and 4.0 kcal/mol, and the enthalpies of reaction for copolymerization were all exothermic.     

Comparison of SCC-DFTB and NDDO-based semiempirical molecular orbital methods for organic molecules

Extensive testing of the SCC-DFTB method has been performed, permitting direct comparison to data available for NDDO-based semiempirical methods. For 34 diverse isomerizations of neutral molecules containing the elements C, H, N, and O, the mean absolute errors (MAE) for the enthalpy changes are 2.7, 3.2, 5.0, 5.1, and 7.2 kcal/mol from PDDG/PM3, B3LYP/6-31G(d), PM3, SCC-DFTB, and AM1, respectively. A more comprehensive test was then performed by computing heats of formation for 622 neutral, closed-shell H, C, N, and O-containing molecules; the MAE of 5.8 kcal/mol for SCC-DFTB is intermediate between AM1 (6.8 kcal/mol) and PM3 (4.4 kcal/mol) and significantly higher than for PDDG/PM3 (3.2 kcal/mol). Similarly, SCC-DFTB is found to be less accurate for heats of formation of ions and radicals; however, it is more accurate for conformational energetics and intermolecular interaction energies, though none of the methods perform well for hydrogen bonds with strengths under ca. 7 kcal/mol. SCC-DFTB and the NDDO methods all reproduce MP2/cc-pVTZ molecular geometries with average errors for bond lengths, bond angles, and dihedral angles of only ca. 0.01 A, 1.5 degrees , and 3 degrees . Testing was also carried out for sulfur containing molecules; SCC-DFTB currently yields much less accurate heats of formation in this case than the NDDO-based methods due to the over-stabilization of molecules containing an SO bond.     

Optimization of parameters for semiempirical methods II. Applications

MNDO/AM1-type parameters for twelve elements have been optimized using a newly developed method for optimizing parameters for semiempirical methods. With the new method, MNDO-PM3, the average difference between the predicted heats of formation and experimental values for 657 compounds is 7.8 kcal/mol, and for 106 hypervalent compounds, 13.6 kcal/mol. For MNDO the equivalent differences are 13.9 and 75.8 kcal/mol, while those for AM1, in which MNDO parameters are used for aluminum, phosphorus, and sulfur, are 12.7 and 83.1 kcal/mol, respectively. Average errors for ionization potentials, bond angles, and dipole moments are intermediate between those for MNDO and AM1, while errors in bond lengths are slightly reduced.     

Proton and sodium cation affinities of harpagide: a computational study

The aim of this work was to estimate the proton and sodium cation affinities of harpagide (Har), an iridoid glycoside responsible for the antiinflammatory properties of the medicinal plant Harpagophytum. Monte Carlo conformational searches were performed at the semiempirical AM1 level to determine the most stable conformers for harpagide and its protonated and Na+-cationized forms. The 10 oxygen atoms of the molecule were considered as possible protonation and cationization sites. Geometry optimizations were then refined at the DFT B3LYP/6-31G level from the geometries of the most stable conformers found. Final energetics were obtained at the B3LYP/6-311+G(2d,2p)//B3LYP/6-31G level. The proton and sodium ion affinities of harpagide have been estimated at 223.5 and 66.0 kcal/mol, respectively. Since harpagide mainly provides HarNa+ ions in electrospray experiments, the DeltarG298 associated with the reaction of proton/sodium exchange between Har and methanol, MeOHNa+ + HarH+ --> MeOH2+ + HarNa+ (1), has been calculated; it has been estimated to be 1.9 kcal/mol. Complexing a methanol molecule to each reagent and product of reaction 1 makes the reaction become exothermic by 1.7 kcal/mol. These values are in the limit of the accuracy of the method and do not allow us to conclude definitely whether the reaction is endo- or exothermic, but, according to these very small values, the cation exchange reaction is expected to proceed easily in the final stages of the ion desolvation process.     

Big macrocyclic assemblies of carboranes (big MACs): synthesis and crystal structure of a macrocyclic assembly of four carboranes containing alternate ortho- and meta-carborane icosahedra linked by para-phenylene units

The macrocyclic compound, [1,2-C₂B₁₀H₁₀-1,4-C₆H₄-1,7-C₂B₁₀H₁₀-1,4-C₆H₄]₂ (5)—a novel cyclooctaphane, was prepared by condensation of the C,C′-dicopper(I) derivative of meta-carborane with 1,2-bis(4-iodophenyl)-ortho-carborane. The X-ray crystal structure of 5·C₆H₆·6C₆H₁₂ was determined at 150 K, revealing an extremely loose packing mode. Molecule 5 has a crystallographic C_s and local C_2v symmetry; the macrocycle adopts a butterfly (dihedral angle 143°) conformation with the ortho-carborane units at the wingtips and the phenylene ring planes roughly perpendicular to the wing planes. Multinuclear NMR spectra suggest that molecule 5 in solution inverts rapidly via the planar D_2h geometry, which (from ab initio HF/6-31G* calculations) is only 1 kcal mol⁻¹ higher in energy than the C_2v one. An attempt to prepare an even larger macrocycle, comprising three para-carborane and three ortho-carborane units linked by six para-phenylene units, was unsuccessful.     

First-principles study of the adsorption of formaldehyde on the clean and atomic oxygen covered Cu(1 1 1) surface

The interaction of formaldehyde with the clean and atomic oxygen-covered Cu(1 1 1) surfaces has been studied by means of cluster model density functional calculations in which Cu₂₂(14,8) is used to represent the perfect Cu(1 1 1) surface. The calculations point towards a η¹-H₂CO---O orientation with the oxygen atom almost on top of a copper surface atom. The formaldehyde adsorption energy is of 22–25 kJ/mol and the internal geometry of adsorbed formaldehyde is almost identical to that of the molecule in the gas-phase. The C---O bond is almost parallel to the surface and the conformation with the molecular plane normal to the surface is slightly preferred to the conformation with the molecular plane nearly parallel to the surface. A Cu₂₂---O model where atomic oxygen is adsorbed on a fcc hollow site was used to study the co-adsorption and reaction of formaldehyde with atomic oxygen. Oxygen co-adsorption has a dramatic effect on the formaldehyde adsorption energy which is increased by 50%. The calculated energy barrier for the formation of the dioxymethylene intermediate species through the H₂CO+O→H₂CO₂ reaction is of 36 kJ/mol.     

Vibrational dependence of the NH3 (v2)+NO and NO(v)+NH3 charge transfer cross sections

A tandem quadrupole mass spectrometer is used to study the charge transfer reactions NH₃⁺ + NO and NO⁺ + NH₃ over a collision energy range 1.5–13 eV. The vibrational state of the reagent ions is selected by resonance-enhanced multiphoton ionization. For the 0.9 eV exothermic process NH₃⁺ + NO → NH₃ + NO⁺ excitation of the v₂ umbrella bending mode (v₂ = 0–12) causes no marked change in the charge transfer cross section, while in the reverse process NO⁺ + NH₃ → NO + NH₃⁺ excitation of the NO⁺ vibration (v = 0–6) strongly enhanced the charge transfer cross section.     

Solvent-mediated tautomerization of purine: single to quadruple proton transfer

We present calculations for the structures and the tautomerization reaction of purine and purine – (H₂O)_n (n=1–3) clusters. We find two pathways (via the carbene and the sp³-type intermediate) for the 9 ↔ 7 tautomerization of bare purine. The barrier heights for the 9 → 3 and 9 → 7 tautomerization of bare purine are calculated to be large (60–70 kcal/mol). Hydrogen bonding with the water molecule(s), however, dramatically lowers the 9 → 3 barrier by the concerted multiple proton transfer mechanism, favoring the formation of the conformer 3(H)- relative to the 7(H)-purine in the microsolvated environment, in contrast to the gas phase or the aqueous solution.     

A semiempirical study of the optimized ground and excited state potential energy surfaces of retinal and its protonated Schiff base.

The electronic ground and first excited states of retinal and its Schiff base are optimized for the first time using the semiempirical AM1 Hamiltonian. The barrier for rotation about the C(11)-C(12) double bond is characterized by variation of both the twist angle delta(C(10)-C(11)-C(12)-C(13)) and the bond length d(C(11)-C(12)). The potential energy surface is obtained by varying these two parameters. The calculated ground state rotational barrier is equal to 15.6 kcal/mol for retinal and 20.5 kcal/mol for its Schiff base. The all-trans conformation is more stable by 3.7 kcal/mol than the 11-cis geometry. For the first excited state, S(1,) the 90 degrees twisted geometry represents a saddle point for retinal with the rotational barrier of 14.6 kcal/mol. In contrast, this conformation is an energy minimum for the Schiff base. It can be easily reached at room temperature from the planar minima since it is separated from them by a barrier of only 0.6 kcal/mol. The 90 degrees minimum conformation is more stable than the all-trans by 8.6 kcal/mol. We are thus able to present a reaction path on the S(1) surface of the retinal Schiff base with an almost barrier-less geometrical relaxation into a twisted minimum geometry, as observed experimentally. The character of the ground and first excited singlet states underscores the need for the inclusion of double excitations in the calculations.     

ortho-Mercuration of ferrocenylimines

The mercuration of a series of aryliminomethylferrocenes occurred predominantly in an ortho-position of the substituted ferrocenyl ring to yield 2-mercurated ferrocenylimines. The regiospecificity of this reaction suggests that the mercury is directed into the ortho-position by coordination of the mercury to imino nitrogen with subsequent electrophilic substitution. The chromatographic and spectral properties of the 2-mercurated products show the presence of an intramolecular N → Hg coordination via the five-membered ring in these molecules, which was further confirmed by the single-crystal structure analysis of 2-chloromercuro-1-[(4-methoxyphenylimino)methyl]ferrocene.     

Reactivity of Cl–P+–Cl toward cyclic organic ethers

The dichlorophosphenium ion (Cl-P(+)-Cl) undergoes a variety of reactions with cyclic organic ethers in the gas phase in a Fourier-transform ion cyclotron resonance mass spectrometer. Most of the reactions are initiated by Cl-P(+)-Cl-induced heterolytic C-O bond cleavage. However, the observed final products depend on the exact structure of the ether. For saturated ethers, e.g., tetrahydropyran, tetrahydrofuran, and 2-methyltetrahydrofuran, the most abundant ionic product corresponds to hydroxide abstraction by Cl-P(+)-Cl. This unexpected reaction is rationalized by a multistep mechanism that involves an initial heterolytic C-O bond cleavage accompanied by a 1,2-hydride shift, and that ultimately yields a resonance-stabilized allyl cation and HOPCl2. The process is estimated to be highly exothermic (AM1 calculations yield delta H = -(33-38) kcal mol(-1) for the ethers mentioned above). However, the adducts formed from most of the unsaturated ethers are unable to undergo hydride shifts and hence cannot react via this pathway. In some of these cases, e.g., for 2,5-dihydrofuran and 2,5-dihydro-3,4-benzofuran, the C-O bond heterolysis is followed by oxygen/chlorine exchange to yield the O=PCl radical and a resonance-stabilized carbocation (AM1 calculations yield delta H = -14 kcal mol(-1) for the reaction of 2,5-dihydro-3,4-benzofuran). Hydride abstraction by Cl-P(+)-Cl also yields an abundant product for these two ethers. On the other hand, the ethers with low ionization energies, such as 2,3-dihydrofuran and 2,3-dihydrobenzofuran, react with Cl-P(+)-Cl by electron transfer. Finally, a unique pathway, addition followed by elimination of HCl, dominates the reaction with furan. The observed reactions are rationalized by thermochemical data obtained from semiempirical molecular orbital calculations.     

Water clusters in a confined nonpolar environment

The stability and structure of water clusters in a confined nonpolar environment is investigated theoretically by examining the encapsulation of water molecules inside a fullerene (C₆₀) cage. While the Hartree–Fock (6-31G) calculations suggest H₂O@C₆₀ to be marginally more stable (−0.5 kcal/mol) than the isolated water and C₆₀ molecules, second order Møller–Plesset perturbation theory suggests it to be much more stable (−9.9 kcal/mol). It is shown that encapsulation results in the breaking of hydrogen bonds and rearrangement of water clusters. The tetramer inside the cage, for example, is tetrahedral in arrangement, in contrast to a square planar geometry observed in the gas phase.     

Solution structure, mutagenesis, and NH exchange studies of the MutT enzyme–Mg-8-oxo-dGMP complex

The MutT pyrophosphohydrolase from E. coli (129 residues) catalyzes the hydrolysis of nucleoside triphosphates (NTP), including 8-oxo-dGTP, by substitution at Pβ, to yield NMP and pyrophosphate. The product, 8-oxo-dGMP is an unusually tight binding, slowly exchanging inhibitor with a K_D=52 nM, (ΔG°=−9.8 kcal/mol) which is 6.1 kcal/mol tighter than the binding of dGMP (ΔG°=−3.7 kcal/mol). The higher affinity for 8-oxo-dGMP results from a more favorable ΔH_binding (−32 kcal/mol) despite an unfavorable −TΔS°_binding (+22 kcal/mol). The solution structure of the MutT–Mg²⁺-8-oxo-dGMP complex shows a narrowed, hydrophobic nucleotide-binding cleft with Asn-119 and Arg-78 among the few polar residues. The N119A, N119D, R78K and R78A single mutations, and the R78K+N119A double mutant all showed largely intact active sites, on the basis of small changes in the kinetic parameters of dGTP hydrolysis and in ¹H–¹⁵N HSQC spectra. However, the N119A mutation profoundly weakened the active site binding of 8-oxo-dGMP by 4.3 kcal/mol (1650-fold). The N119D mutation also weakened 8-oxo-dGMP binding but only by 2.1 kcal/mol (37-fold), suggesting that Asn-119 functioned both as a hydrogen bond donor to C8=O, and a hydrogen bond acceptor from N7H of 8-oxo-dGMP, while aspartate at position −119 functioned as an acceptor of a single hydrogen bond. Much smaller weakening effects (0.3–0.4 kcal/mol) on the binding of dGMP and dAMP were found, indicating specific hydrogen bonding of Asn-119 to 8-oxo-dGMP. While formation of the wild type MutT–Mg²⁺-8-oxo-dGMP complex slowed the backbone NH exchange rates of 45 residues distributed throughout the protein, the same complex of the N119A mutant slowed the exchange rates of only 11 residues at or near the active site, indicating an increase in conformational flexibility of the N119A mutant. The R78K and R78A mutations weakened the binding of 8-oxo-dGMP by 1.7 and 1.1 kcal/mol, respectively, indicating a lesser role of Arg-78 than of Asn-119 in the selective binding of 8-oxo-dGMP, likely donating a single hydrogen bond to its C6=O. The R78K+N119A double mutant weakened the binding of 8-oxo-dGMP (K_I^slope=3.1 mM) by 6.5±0.2 kcal/mol which overlaps, within error with the sum of the effects of the two single mutants (6.0±0.3 kcal/mol). Such additive effects of the two single mutants in the double mutant are most simply explained by the independent functioning of Asn-119 and Arg-78 in the binding of 8-oxo-dGMP. Independent functioning of these two residues in nucleotide binding is consistent with their locations in the MutT–Mg²⁺-8-oxo-dGMP complex, on opposite sides of the active site cleft, with a distance of 8.4±0.5 Å between their side chain nitrogens.     

Conformational analysis of N-benzyl-N-o-tolyl-p-methylbenzene-sulfonamides from dynamic H NMR experiments and theoretical calculations

Theoretical studies of molecular conformations of four N-benzyl-N-o-tolyl-p-methylbenzenesulfonamides, by means of semiempirical PM3, ab initio (RHF and MP2) methods, and DFT approach, are presented and discussed in comparison with the experimental data. The free energy (ΔG^#) of rotation obtained by the dynamic shape analysis of the ¹H NMR spectra is ca. 16 kcal/mol for those systems for which the barrier has been probed experimentally. Failure to determine the barrier in the experimental spectra in the case of one system is attributed to the chiral conformation of the global minimum. The rotational profile was established at the PM3 level and verified at the DFT level of theory. The solvent effect, the 0th-order vibrational corrections, and the temperature dependence of the Boltzman distribution of conformers and kinetic equilibrium are discussed.     

Potential energy surface of 1,6-Methano

The potential energy surface of 1,6-methano[10]annulen-11-ylidene and its isomers has been investigated by density functional (BLYP and B3LYP) molecular orbital methods. These calculations indicate the lowest energy annulene structure to be 56.9 kcal mol(-)(1) higher in energy than triplet 1-naphthylcarbene. These calculations, together with calculations on transition states connecting possible rearrangement products derived from this carbene, indicate that the trapping products reported by Carlton et al. J. Am. Chem. Soc. 1976, 98, 6068-6070 arise from rearrangement of the annulene-carbene to a tricyclic isomer.     

Combined molecular mechanical and quantum mechanical potential study of a nucleophilic addition reaction in solution

The procedure of combined semiempirical quantum mechanical (AM1) and molecular mechanical potential⁷ was used to study the nucleophilic addition of hydroxide to formaldehyde in solution. The gas phase AM1 potential surface is approximately 26 kcal/mol more exothermic than the corresponding ab initio 6-31 + G* calculation results. The free energy profile for the reaction in solution was determined by means of molecular dynamic simulations. The resulting free energy of activation is approximately 5 kcal/mol. The difference of the free energy of solvation between the reactant and the product states is about 38 kcal/mol. As the reaction goes on, the number of hydrogen bonds formed by the hydroxide oxygen with the surrounding water molecules decreases, whereas the number of hydrogen bonds formed by the carbonyl oxygen increases. There is no significant change in the total number of hydrogen bonds between the solute and the solvent molecules, and the average number of these hydrogen bonds is between five and six during the entire reaction process. These results are consistent with previous studies using a model based on ad initio 6-31 + G* calculations in the gas phase. The reaction path in solution is different from the gas phase minimum energy reaction path. When the two reactants are at a large distance, the attack route of the hydroxide anion in solution is close to perpendicular to the formaldehyde plane, whereas in the gas phase the route is collinear with the carbonyl group. These results suggests that although AM1 does not yield accurate energies in the gas phase, valuable insights into the solvent effects can be obtained through computer simulations with this combined potential. This combined procedure could be applied to chemical reactions within macromolecules, in which a quantitative estimation of the effects of the environment would not be easily attainable by another technique. © 1994 by John Wiley & Sons, Inc.     

The structure of intermediate products of ‘fragmentation’ of 10-bromodihydrocinchonine

10-Bromodihydrocinchonine 1d, similarly to analogical derivatives of other main cinchona alkaloids, transforms into nicinquine and isonicinquine 2d formally loosing its C2 carbon atom in a form of formaldehyde. This reaction was found to proceed via the so-far unstudied intermediate compounds (5a) 4-S-(Z-propenyl)- and (5 4-S-(E-propenyl)-6-R-7-S-(quinolyl-4)-8-oxa-1-R-azabicyclo[4.3.0]nonane which at the same time are products of a novel rearrangement of the parent cinchonine. The stereostructure of these compounds was determined using, mainly, NMR techniques. The energy minima of conformers 5 and 5a were supported by molecular mechanics calculations. The mechanisms for the 1d → 5 → 2d sequence have been discussed. The alkaloid 5 is sterically preferred to its Z-isomer. The accompanying nucleophilic substitution (1d → 6) and elimination (1d → 7) are also stereospecific.     

DFT and CASPT2 study of two thermal reactions of nitromethane: C–N bond cleavage and nitro-to-nitrite isomerization. An example of the inverse symmetry breaking deficiency in density functional calculations of an homolytic dissociation

The reaction paths of nitromethane leading to the dissociation products or isomerization to methyl nitrite have been computationally investigated at the CAS-SCF and DFT levels of theory. Additionally, the CAS-SCF wave functions were used as reference in a second-order perturbation treatment, CASPT2, in order to obtain a good estimate for the activation energy of each reaction path. Both methods predict the isomerization as a concerted reaction. However, the behavior of the two approximations with respect to dissociation is rather different; while CASPT2 predicts a barrier height of (≈59 kcal/mol) in good accordance with the experimental activation energy (59.0 kcal/mol), B3-LYP/6-31G^* calculations overestimate the barrier for more than 30 kcal/mol. The DFT prediction of the dissociation channel exhibits inverse symmetry breaking, dissociating to the unphysical absurd CH₃^δ+ plus NO₂^δ−.     

Isomerization of substituted biphenyls by superacid. A remarkable confluence of experiment and theory

Acid-catalyzed isomerization of dimethylbiphenyls is determined by the relative stability of intermediate carbocations, rather than the neutral products, and may be predicted by a simple semiempirical method (AM1). A general kinetic model for such isomerizations is suggested in which the rearrangement of an intermediate cation is the rate-limiting step. Control of regiochemistry of dialkylbiphenyls provides a useful entry into high-purity monomers for high-polymer synthesis.