Electronic structures of antiaromatic molecules

The electronic structures of the planar cyclic polymethines with 4n electrons (the so-called antiaromatic molecules) are investigated by the unrestricted Hartree-Fock approximation. The relative stability and spin structures of singlet and triplet states of the above species are discussed.     

Validation of electronic structure methods for isomerization reactions of large organic molecules

In this work the ISOL24 database of isomerization energies of large organic molecules presented by Huenerbein et al. [Phys. Chem. Chem. Phys., 2010, 12, 6940] is updated, resulting in the new benchmark database called ISOL24/11, and this database is used to test 50 electronic model chemistries. To accomplish the update, the very expensive and highly accurate CCSD(T)-F12a/aug-cc-pVDZ method is first exploited to investigate a six-reaction subset of the 24 reactions, and by comparison of various methods with the benchmark, MCQCISD-MPW is confirmed to be of high accuracy. The final ISOL24/11 database is composed of six reaction energies calculated by CCSD(T)-F12a/aug-cc-pVDZ and 18 calculated by MCQCISD-MPW. We then tested 40 single-component density functionals (both local and hybrid), eight doubly hybrid functionals, and two other methods against ISOL24/11. It is found that the SCS-MP3/CBS method, which is used as benchmark for the original ISOL24, has an MUE of 1.68 kcal mol(-1), which is close to or larger than some of the best tested DFT methods. Using the new benchmark, we find ωB97X-D and MC3MPWB to be the best single-component and doubly hybrid functionals respectively, with PBE0-D3 and MC3MPW performing almost as well. The best single-component density functionals without molecular mechanics dispersion-like terms are M08-SO, M08-HX, M05-2X, and M06-2X. The best single-component density functionals without Hartree-Fock exchange are M06-L-D3 when MM terms are included and M06-L when they are not.     

Synthesis of azo-conjugated metalladithiolenes and their photo- and proton-responsive isomerization reactions

A versatile synthetic method of azo-conjugated metalladithiolenes was developed, and new complexes with various central metals and substituent groups were synthesized. Molecular structures of the azo-conjugated metalladithiolenes of Ni(II), Pd(II), and Pt(II) with diphenylphosphinoethane as a co-ligand were determined by X-ray crystallography. While the energy of the reversible trans-to-cis photoisomerization is considerably lower than that of azobenzene, the thermal stability of the cis form is much higher than that of the organic azobenzene derivatives showing similar low-energy trans-to-cis photoisomerization. A novel proton response of the azo group occurs, and the combination of photoisomerization and protonation leads to a novel proton-catalyzed cis-to-trans isomerization, the rate of which correlates with the redox potential of the metalladithiolene moiety. The study including other azo-conjugated metalladithiolenes has indicated that the protonation is a common feature for the azo-conjugated metalladithiolenes, but trans-to-cis photoisomerization is strongly dependent on the electronic structure of the trans form or a steric effect in the cis form.     

Theoretical approach to reactions of polyatomic molecules

A scheme for systematic reduction of the theoretical treatment of elementary reactions involving polyatomic molecules is described; it consists of (1) limitation to the energetically relevant regions of the nuclear configuration space (the reaction path and its near environs) and (2) restriction to the dynamically relevant subspace of the nuclear configuration space (the active modes). Starting from a generalized reaction path Hamiltonian of Nauts and Chapuisat allowing for the use of arbitrary curvilinear coordinates and several large-amplitude modes, the realization of the above-sketched scheme is discussed. A compilation of recent work along these lines, mostly based on the simplified Miller-Handy-Adams reaction path Hamiltonian, is given with particular emphasis on applications of a statistical adiabatic model.     

Method for constructing isomerization reactions

A method is formulated for enumerating and constructing isomerization reactions of molecules exhibiting large amplitude nonrigid motions. This method not only enumerates the isomers of nonrigid molecules and the corresponding rigid molecules but also the symmetry species spanned by the equivalent structures whose representative is an isomer. Consequently, using the method of correlating the symmetry species of a group to the symmetry species of its subgroup the splitting patterns of isomers of nonrigid molecule to those of rigid molecule are obtained. This provides an elegant method for both enumerating and constructing reaction graphs. The method is illustrated with examples.     

Ab initio quality one-electron properties of large molecules: development and testing of molecular tailoring approach

The development of a linear-scaling method, viz. "molecular tailoring approach" with an emphasis on accurate computation of one-electron properties of large molecules is reported. This method is based on fragmenting the reference macromolecule into a number of small, overlapping molecules of similar size. The density matrix (DM) of the parent molecule is synthesized from the individual fragment DMs, computed separately at the Hartree-Fock (HF) level, and is used for property evaluation. In effect, this method reduces the O(N(3)) scaling order within HF theory to an n.O(N'(3)) one, where n is the number of fragments and N', the average number of basis functions in the fragment molecules. An algorithm and a program in FORTRAN 90 have been developed for an automated fragmentation of large molecular systems. One-electron properties such as the molecular electrostatic potential, molecular electron density along with their topography, as well as the dipole moment are computed using this approach for medium and large test chemical systems of varying nature (tocopherol, a model polypeptide and a silicious zeolite). The results are compared qualitatively and quantitatively with the corresponding actual ones for some cases. This method is also extended to obtain MP2 level DMs and electronic properties of large systems and found to be equally successful.     

Symmetry of nonrigid molecules and isomerization processes

Starting from the concept of a totally flexible molecule, rigidity is introduced by restricting progressively the allowed permutations. Each nonrigid isomer is then characterized by its Longuet-Higgins group ? of allowed permutation inversions. For a given ? all nonrigidity types correspond to all possible choices of the symmetry subgroup ? of the skeleton. The structure of ? also allows a characterization of the isomerization processes studied in chemical kinetics. In both situations, isomerization mechanisms may be associated with generators and are, in the simplest situations, represented by Cayley graphs.     

Torsional isomerization of biologically active bicyclic molecules

Rotational isomerization of bipyridines C₅H₄N? C₅H₄N was studied by CNDO /2, PPP /CI , and CNDO /CI methods. It is shown that CNDO /2 overestimates the angle of rotation ? between the pyridine rings ca. two times. The angle ? was determined for 2,2′-bipyridine by means of correlation of the theoretical (CNDO /2) and experimental dipole moment. It was also found from the correlation between the theoretical and experimental UV spectra. It is shown that there is an explicit dependence of the results upon the distance between heteroatoms (PPP /CI ). It has been found that the CNDO /CI method correctly predicts the value of the rotational angles and their sequence in bipyridines.     

An approximate relation between Wigner-Seitz-type one-electron Hamiltonians and complete Hamiltonians for molecules and solids

Summary The relation between the sum of Wigner-Seitz-type one-electron Hamiltonians of all electrons in a system (any molecule or solid) and the complete Hamiltonian for the system is deduced. According to this relation, the total energy for an electronic configuration may be formulated approximately as a quadratic function of the atomic charges defined for the configuration added to the sum of the energies of occupied orbitals. This formula is necessary for evaluating the system's total energy, using the orbital energies calculated from the Wigner-Seitz-type potential (called the linkage of embedded atomic fields (LEAF)), and is also useful for analyzing and understanding electronic structures, reactivities, and other properties of molecules and solids.     

The electronic structure of molecules by a many-body approach : II. Ionization potentials one-electron properties of pyridine and phosphoridine

The valence ionization potential (IPs) of pyridine and phosphoridine are studied by an ab initio many-body approach which includes the effects of electron correlation and reorganization beyond the Hartree-Fock approximation. For pyridine the order of the first three IPs is a₂(π), a₁(n), b₁(π), but the IPs of the a₂ and a₁ orbitals are so close together that they have to be regarded as identical in binding energy, which is also concluded from experiment. Whereas for pyridine the ordering of the IPs calculated in the HF approximation is incorrect, it is correct for phosphoridine. For this latter molecule the first three ionization potentials are due to ionization from the b₁(π), a₂(π), and a₁(n) orbitals. Several one-electron properties are calculated and compared with experimental and other theoretical data. The localized molecular orbitals are discussed as well.     

Properties of nearly one-electron molecules. I. An iterative Green function approach to calculating the reaction matrix

An ab initio R-matrix method for determining the molecular reaction matrix of scattering theory is introduced. The method makes use of a principal-value Green function to compute the collision channel wave functions for the scattered electron, in combination with the Kohn variational scheme for the evaluation of R-matrix eigenvalues on a spherical boundary surface at short range. This technique permits the size of the bounded volume in the variational calculation to be reduced, making the computations fast and efficient. The reaction matrix is determined in a form that minimizes its energy dependence. Thus the procedure does not require modification or an increase in the computational effort to study the electronic structure and dynamics in Rydberg molecules with extremely polar ion cores. The analysis is specialized to examine the bound-state and free-electron scattering properties of nearly one-electron molecular systems, which are characterized by a Rydberg/scattering electron incident on a closed-shell ion core. However, it is shown that the treatment is compatible with all-electron/ab initio representations of open-shell and nonlinear polyatomic ion cores, emphasizing its generality. The introduced approach is used to calculate the electronic spectrum of the calcium monofluoride molecule, which has the extremely polar (Ca+2F-)+e- closed-shell ion-core configuration. The calculation utilizes an effective single-electron potential determined by M. Arif, C. Jungen, and A. L. Roche [J. Chem. Phys. 106, 4102 (1997)] previously. Close agreement with experimental data is obtained. The results demonstrate the practical utility of this method as a viable alternative to the standard variational approaches.     

Dimerization and isomerization reactions of alpha-lithiated terminal aziridines

The scope of dimerization and isomerization reactions of alpha-lithiated terminal aziridines is detailed. Regio- and stereoselective deprotonation of simple terminal aziridines with lithium 2,2,6,6-tetramethylpiperidide (LTMP) or lithium dicyclohexylamide (LiNCy2) generates trans-alpha-lithiated terminal aziridines. These latter species can then undergo dimerization or isomerization reactions depending on the nature of the N-protecting group. alpha-Lithiated terminal aziridines bearing N-alkoxycarbonyl (Boc) protection undergo N- to C-[1,2] migration to give N-H trans-aziridinylesters. In contrast, aziridines bearing N-organosulfonyl [tert-butylsulfonyl (Bus)] protection undergo rapid dimerization to give 2-ene-1,4-diamines or, if a pendant alkene is present, diastereoselective cyclopropanation to give 2-aminobicyclo[3.1.0]hexanes. All of these reactions were used as key steps in the preparation of synthetically and biologically important targets.     

Nonlinear organic reactions to proliferate acidic and basic molecules and their applications

Acid amplifiers derived from a certain class of sulfonates suffer from autocatalytic decomposition in the presence of a strong acid to give corresponding sulfonic acids, which catalyze the decomposition of the parent sulfonates, leading to the liberation of more of the same sulfonic acids in an exponential manner. Five types of acid amplifiers displaying acid proliferation reactions are presented. A certain type of carbamate exhibits autocatalytic fragmentation to give the corresponding aliphatic amine and olefin together with carbon dioxide, whereas the generated amine is able to act as a catalyst for the fragmentation so that the carbamates are referred to as base amplifiers. Applications of acid and base amplifiers to photofunctional materials, including photoresists, are described as a consequence of the combination of the molecular amplifiers with photoacid as well as photobase generators. Practical applications of acid proliferation reactions in polymer films are discussed.     

Computational modeling of enzymatic keto-enol isomerization reactions

Catalysis of proton abstraction from nonacidic carbon atoms adjacent to a carbonyl or carboxylate group is a fundamental reaction in enzymology that has been extensively studied during the last few decades. Enzymes catalyzing these reactions, which normally involve labile enolic intermediates, need to overcome large pK _a differences between the reacting groups as well as high intrinsic free-energy barriers. Here, we present an overview of results from recent computer simulation studies of keto-enol isomerization reactions catalyzed by the enzymes glyoxalase I, triosephopsphate isomerase and ketosteroid isomerase. For all three enzymes it is found that electrostatic stabilization of the transient enolate intermediates, either by charge–charge interactions or by hydrogen bonding, accounts for the main part of the activation free-energy barrier reduction. Another catalytic effect observed in all cases is the reduction of the reorganization energy by the enzyme active site. Some other factors that have been proposed to be important for these reactions are also discussed and evaluated. Received: 3 January 2002 / Accepted: 13 May 2002 / Published online: 29 July 2002     

Some one-electron oxidation reactions of biheteroorganic derivatives with Ge-Hg and Ge-Li groupings

Conclusions 4-Bromo-2,4,6-tri-tert-butylcyclohexadien-2,5-one and the 2,4,6-tri-tert-butylphenoxyl radical function as a one-electron oxidizing agent in reactions with biheteroorganic compounds that contain the Ge-Hg and Ge-Li bonds.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 3, pp. 685–688, March, 1978.     

The induced current strengths and aromatic pathways of heteroporphyrins and their antiaromatic derivatives

The magnetically induced current strengths as well as nucleus independent chemical shifts of aromatic heteroporphyrins and antiaromatic 22,24‐dideazaheteroporphyrins have been studied using the density functional theory method. The induced current strengths and pathways are obtained by numerical integration of the induced current densities following the specific chemical bonds. The total induced current strengths of antiaromatic 22,24‐dideazaheteroporphyrins is about 6 nA/T weaker than the one for the heteroporphyrins in absolute value. The substitution of pyrrole NH groups by O and S atoms does not change the total induced current strengths. The induced currents around the molecular macroring split at the heterocycles (pyrrole, furan, and thiophene) into the inner and outer routes. The heteroatoms (N, O, and S) have high resistance and consequently lead to a weaker induced current strength than the one passing the outer route in aromatic heteroporphyrins. For antiaromatic 22,24‐dideazaheteroporphyrins, the heteroatoms enhance the current strength and change the main current pathway into the inner route. The induced current strength following the NH moiety is stronger than the one passing the oxygen moiety of furan ring and the sulfur moiety of the thiophene ring in both heteroporphyrins and 22,24‐dideazaheteroporphyrins. © 2015 Wiley Periodicals, Inc.