A quadratically convergent VBSCF method.

A quadratically convergent valence bond self-consistent field method is described where the simultaneous optimisation of orbitals and the coefficients of the configurations (VB structures) is based on a Newton-Raphson scheme. The applicability of the method is demonstrated in actual calculations. The convergence and efficiency are compared with the Super-CI method. A necessary condition to achieve convergence in the Newton-Raphson method is that the Hessian is positive definite. When this is not the case, a combination of the Super-CI and Newton-Raphson methods is shown to be an optimal choice instead of shifting the eigenvalues of the Hessian to make it positive definite. In the combined method, the first few iterations are performed with the Super-CI method and then the Newton-Raphson scheme is switched on based on an internal indicator. This approach is found computationally a more economical choice than using either the Newton-Raphson or Super-CI method alone to perform a full optimisation of the nonorthogonal orbitals.

Zinc coordination to the bapbpy ligand in homogeneous solutions and at liposomes: zinc detection via fluorescence enhancement.

In this work, the complexation of the bapbpy ligand to zinc dichloride is described (bapbpy = 6,6'-bis(2-aminopyridyl)-2,2'-bipyridine). The water-soluble, colorless complex [Zn(bapbpy)Cl]Cl·2H2O (compound 2·H2O) was synthesized; its X-ray crystal structure shows a mononuclear, pentacoordinated geometry with one chloride ligand in apical position. Upon excitation of its lowest-energy absorption band (375 nm) compound 2 shows intense emission (Φ = 0.50) at 418 nm in aqueous solution, and an excited state lifetime of 5 ns at room temperature. Photophysical measurements, DFT, and TD-DFT calculations prove that emission arises from vibronically coupled Ligand-to-Ligand Charge Transfer singlet excited states, characterized by electron density flowing from the lone pairs of the non-coordinated NH bridges to the π* orbitals of the pyridine rings. Monofunctionalization of the ligand with one long alkyl chain was realized to afford ligand 3, which can be inserted into dimyristoylphosphatidylglycerol (DMPG) or dimyristoylphosphatidylcholine (DMPC) unilamellar vesicles. For negatively charged DMPG membranes the addition of a zinc salt to the vesicles leads to an enhancement of the fluorescence due to zinc coordination to the membrane-embedded tetrapyridyl ligand. No changes were observed for the zwitterionic DMPC lipids, where binding of the Zn ions does not take place. A modest binding constant was found (5 × 10(6) M(−1)) for the coordination of zinc cations to bapbpy-functionalized DMPG membranes, which allows for the detection of micromolar zinc concentrations in aqueous solution. The influence of chloride concentration and other transition metal ions on the zinc binding was evaluated, and the potential of liposome-supported metal chelators such as ligand 3 for zinc detection in biological media is discussed.

Resonance and aromaticity: an ab initio valence bond approach.

Resonance energy is one of the criteria to measure aromaticity. The effect of the use of different orbital models is investigated in the calculated resonance energies of cyclic conjugated hydrocarbons within the framework of the ab initio Valence Bond Self-Consistent Field (VBSCF) method. The VB wave function for each system was constructed using a linear combination of the VB structures (spin functions), which closely resemble the Kekulé valence structures, and two types of orbitals, that is, strictly atomic (local) and delocalized atomic (delocal) p-orbitals, were used to describe the π-system. It is found that the Pauling-Wheland's resonance energy with nonorthogonal structures decreases, while the same with orthogonalized structures and the total mean resonance energy (the sum of the weighted off-diagonal contributions in the Hamiltonian matrix of orthogonalized structures) increase when delocal orbitals are used as compared to local p-orbitals. Analysis of the interactions between the different structures of a system shows that the resonance in the 6π electrons conjugated circuits have the largest contributions to the resonance energy. The VBSCF calculations also show that the extra stability of phenanthrene, a kinked benzenoid, as compared to its linear counterpart, anthracene, is a consequence of the resonance in the π-system rather than the H-H interaction in the bay region as suggested previously. Finally, the empirical parameters for the resonance interactions between different 4n+2 or 4n π electrons conjugated circuits, used in Randic's conjugated circuits theory or Herdon's semi-emprical VB approach, are quantified. These parameters have to be scaled by the structure coefficients (weights) of the contributing structures.

SO2-binding properties of cationic η6,η1-NCN-pincer arene ruthenium platinum complexes: spectroscopic and theoretical studies.

The SO(2)-binding properties of a series of η(6),η(1)-NCN-pincer ruthenium platinum complexes (NCN = 2,6-bis[(dimethylamino)methyl]phenyl anion) have been studied by both UV-visible spectroscopy and theoretical calculations. When an electron-withdrawing [Ru(C(5)R(5))](+) fragment (R = H or Me) is η(6)-coordinated to the phenyl ring of the NCN-pincer platinum fragment (cf. [2](+) and [3](+), see Scheme 1), the characteristic orange coloration (pointing to η(1)- SO(2) binding to Pt) of a solution of the parent NCN-pincer platinum complex 1 in dichloromethane upon SO(2)-bubbling is not observed. However, when the ruthenium center is η(6)-coordinated to a phenyl substituent linked in para-position to the carbon-to-platinum bond, i.e. complex [4](+), the SO(2)-binding property of the NCN-platinum center seems to be retained, as bubbling SO(2) into a solution of the latter complex produces the characteristic orange color. We performed theoretical calculations at the MP2 level of approximation and TD-DFT studies, which enabled us to interpret the absence of color change in the case of [2](+) as an absence of coordination of SO(2) to platinum. We analyze this absence or weaker SO(2)-coordination in dichloromethane to be a consequence of the relative electron-poorness of the platinum center in the respective η(6)-ruthenium coordinated NCN-pincer platinum complexes, that leads to a lower binding energy and an elongated calculated Pt-S bond distance. We also discuss the effects of electrostatic interactions in these cationic systems, which also seems to play a destabilizing role for complex [2(SO(2))](+).

Generation of Kekulé valence structures and the corresponding valence bond wave function.

A new scheme, called "list of nonredundant bonds", is presented to record the number of bonds and their positions for the atoms involved in Kekulé valence structures of (poly)cyclic conjugated systems. Based on this scheme, a recursive algorithm for generating Kekulé valence structures has been developed and implemented. The method is general and applicable for all kinds of (poly)cyclic conjugated systems including fullerenes. The application of the algorithm in generating Valence Bond (VB) wave functions, in terms of Kekulé valence structures, is discussed and illustrated in actual VB calculations. Two types of VBSCF calculations, one involving Kekulé valence structures only and the second one involving all covalent VB structures, were performed for benzene, pentalene, benzocyclobutadiene, and naphthalene. Both strictly local and delocalised p-orbitals were used in these calculations. Our results show that, when the orbitals are restricted to their own atoms, other VB structures (Dewar structures) also have a significant contribution in the VB wave function. When removing this restriction, the other VB structures (Dewar and also the ionic structures) are accommodated in the Kekulé valence structures, automatically. Therefore, at VBSCF delocal level, the ground states of these systems can be described almost quantitatively by considering Kekulé valence structures only at a considerable saving of time.

Assignment of phantom bands in the solid-state infrared and Raman spectra of coronene: The importance of a minute out-of-plane distortion.

The molecular geometry and the normal modes properties of coronene are investigated by means of DFT(B3LYP) and restricted/Hartree-Fock calculations utilizing basis sets of triple zeta+polarization quality. The interpretation of the infrared and Raman spectra of coronene, especially in solid state, is critically revised. The phantom bands in the solid state, previously not understood, are readily assigned after considering a minute out-of-plane molecular distortion from D(6h) to C(2h).

Spin coupling and resonance.

The resonating block localize wave function (RBLW) method is introduced, a resonating modification of the block localized wave functions introduced by Mo et al. [Mo, Y.; Peyerimhoff, S. D. J. Chem. Phys. 1998, 109, 1687].This approach allows the evaluation of resonance energies following Pauling's recipe. The method is tested on two model molecules, hexagonal H(6) and benzene. Calculations have been done with (local) and without local restrictions (delocal). Resonance energies for both molecules have been obtained for each type of calculation, in agreement with Pauling's concept. From a comparison of the resonance energies obtained from RBLW and standard valence bond calculations, the resonating block localize wave functions prove to yield resonance energies close to standard valence bond delocal calculations.

On the interpretation of valence bond wavefunctions.

Valence bond wavefunctions are naturally geared to the chemist's idea of chemical bonding. In a structure one may distinguish different electron pair bonds and possible radical character. A structure may correspond to a covalent bond, where all electrons are equally divided over the atoms, or may describe an excess charge on a discrete part of the molecule, which indicates ionic bond character. From the weights of the structure in a variationally optimised multi-structure valence bond wavefunction one may derive the importance of the different bonding types. The individual structures could be considered to represent the different physical situations. We explore this concept for simple diatomic molecules and for polyatomics, and we discuss the relation to Lewis structures. We show that the assumption of individual properties for the individual structures leads to inconsistencies.

Weak distance dependence of through-bond interactions in tetrahydro-4H-thiopyran-4-ylidene end-capped oligo(cyclohexylidenes); a computational survey.

Calculations on members of the oligo(cyclohexylidene) series [(n), n = 1-5)] and related tetrahydro-4H-thiopyran end-capped analogues [(n), n = 1-4)] show a strong through-bond coupling between their pi bonds and sulfur lone pairs (Lp(pi)S). This coupling is mediated by an interaction between the H(ax)-C-C-H(ax) structural sub-units and the pi bonds connecting the cyclohexyl moieties. A comparison of the length dependency of the through-bond coupling via an oligo(cyclohexylidene) and an alkane bridge [divinyl alkanes (n)] shows that oligo(cyclohexylidenes) are more efficient in mediating through-bond couplings over large distances. Oligo(cyclohexylidene) bridges exhibit molecular wire characteristics.

Ab initio calculation of the NH(3sigma-)-NH(3sigma-) interaction potentials in the quintet, triplet, and singlet states.

We present the ab initio potential-energy surfaces of the NH-NH complex that correlate with two NH molecules in their 3sigma- electronic ground state. Three distinct potential-energy surfaces, split by exchange interactions, correspond to the coupling of the S(A) = 1 and S(B) = 1 electronic spins of the monomers to dimer states with S = 0, 1, and 2. Exploratory calculations on the quintet (S = 2), triplet (S = 1), and singlet (S = 0) states and their exchange splittings were performed with the valence bond self-consistent-field method that explicitly accounts for the nonorthogonality of the orbitals on different monomers. The potential surface of the quintet state, which can be described by a single Slater determinant reference function, was calculated at the coupled cluster level with single and double excitations and noniterative treatment of the triples. The triplet and singlet states require multiconfiguration reference wave functions and the exchange splittings between the three potential surfaces were calculated with the complete active space self-consistent-field method supplemented with perturbative configuration interaction calculations of second and third orders. Full potential-energy surfaces were computed as a function of the four intermolecular Jacobi coordinates, with an aug-cc-pVTZ basis on the N and H atoms and bond functions at the midpoint of the intermolecular vector R. An analytical representation of these potentials was given by expanding their dependence on the molecular orientations in coupled spherical harmonics, and representing the dependence of the expansion coefficients on the intermolecular distance R by the reproducing kernel Hilbert space method. The quintet surface has a van der Waals minimum of depth D(e) = 675 cm(-1) at R(e) = 6.6a0 for a linear geometry with the two NH electric dipoles aligned. The singlet and triplet surfaces show similar, slightly deeper, van der Waals wells, but when R is decreased the weakly bound NH dimer with S = 0 and S = 1 converts into the chemically bound N2H2 diimide (also called diazene) molecule with only a small energy barrier to overcome.

Hydrogen storage in magnesium clusters: quantum chemical study.

Magnesium hydride is cheap and contains 7.7 wt % hydrogen, making it one of the most attractive hydrogen storage materials. However, thermodynamics dictate that hydrogen desorption from bulk magnesium hydride only takes place at or above 300 degrees C, which is a major impediment for practical application. A few results in the literature, related to disordered materials and very thin layers, indicate that lower desorption temperatures are possible. We systematically investigated the effect of crystal grain size on the thermodynamic stability of magnesium and magnesium hydride, using ab initio Hartree-Fock and density functional theory calculations. Also, the stepwise desorption of hydrogen was followed in detail. As expected, both magnesium and magnesium hydride become less stable with decreasing cluster size, notably for clusters smaller than 20 magnesium atoms. However, magnesium hydride destabilizes more strongly than magnesium. As a result, the hydrogen desorption energy decreases significantly when the crystal grain size becomes smaller than approximately 1.3 nm. For instance, an MgH2 crystallite size of 0.9 nm corresponds to a desorption temperature of only 200 degrees C. This predicted decrease of the hydrogen desorption temperature is an important step toward the application of Mg as a hydrogen storage material.

The electronic structure of inorganic benzenes: valence bond and ring-current descriptions.

Valence bond (VB) theory and ring-current maps have been used to study the electronic structure of inorganic benzene analogues X(6)H(6) (X = C (1), Si (2)), X(6) (X = N (3), P (4)), X(3)Y(3)H(6) (X,Y = B,N (5), B,P (6), Al,N (7), Al,P (8)), and B(3)Y(3)H(3) (Y = O (9), S (10)). It is shown that the homonuclear compounds possess benzene-like character, with resonance between two Kekulé-like structures and induced diatropic ring currents. Heteronuclear compounds typically show localization of the lone pairs on the electronegative atoms; Kekulé-like structures do not contribute. Of the heteronuclear compounds, only B(3)P(3)H(6) (6) has some benzene-like features with a significant contribution of two Kekulé-like structures to its VB wave function, an appreciable resonance energy, and a discernible diatropic ring current in planar geometry. However, relaxation of 6 to the optimal nonplanar chair conformation is accompanied by the onset of localization of the ring current.

An ab initio valence bond study on cyclopenta-fused naphthalenes and fluoranthenes.

To probe the effect of external cyclopenta-fusion on a naphthalene core, ab initio valence bond (VB) calculations have been performed, using strictly atomic benzene p-orbitals and p-orbitals that are allowed to delocalize, on naphthalene (1), acenaphthylene (2), pyracylene (3), cyclopenta[b,c]acenaphthylene (4), fluoranthene (5), and cyclopenta[c,d]fluoranthene (6). For the related compounds 1-4 and 5,6 the total resonance energies (according to Pauling's definition) are similar. Partitioning of the total resonance energy in contributions from the possible 4n + 2 and 4n pi-electron conjugated circuits shows that only the 6pi-electron conjugated circuits (benzene-like) contribute to the resonance energy. The results show that cyclopenta-fusion does not extend the pi system in the ground state; the five-membered rings act as peri-substituents. As a consequence, the differences in (total) resonance energy do not coincide with the differences in thermodynamic stability. Notwithstanding, the relative energies of the Kekule structures can be estimated using Randic's conjugated circuits model.

A unified orbital model of delocalised and localised currents in monocycles, from annulenes to azabora-heterocycles.

Why are some (4n+2)pi systems aromatic, and some not? The ipsocentric approach to the calculation of the current density induced in a molecule by an external magnetic field predicts a four-electron diatropic (aromatic) ring current for (4n+2)pi carbocycles and a two-electron paratropic (antiaromatic) current for (4n)pi carbocycles. With the inclusion of an electronegativity parameter, an ipsocentric frontier-orbital model also predicts the transition from delocalised currents in carbocycles to nitrogen-localised currents in alternating azabora-heterocycles, which rationalises the differences in (magnetic) aromaticity between these isoelectronic pi-conjugated systems. Ab initio valence-bond calculations confirm the localisation predicted by the naive model, and coupled-Hartree-Fock calculations give current-density maps that exhibit the predicted delocalised-to-localised/carbocycle-heterocycle transition.

SYNOPSIS: SYNthesize and OPtimize System in Silico.

We present a de novo design program called SYNOPSIS, that includes a synthesis route for each generated molecule. SYNOPSIS designs novel molecules by starting from a database of available molecules and simulating organic synthesis steps. This way of generating molecules imposes synthetic accessibility on the molecules. In addition to a starting database, a fitness function is needed that calculates the value of a desired property for an arbitrary molecule. The values obtained from this function guide the design process in optimizing the molecules toward an optimal value of the calculated property. Two applications are described. The first uses an electric dipole moment calculation to generate molecules possessing a strong dipole moment. The second makes use of the three-dimensional structure of a viral enzyme in order to generate high affinity ligands. Twenty eight compounds designed with the program resulted in 18 synthesized and tested compounds, 10 of which showed HIV inhibitory activity in vitro.

1H,1H,2H,2H-perfluoroalkyl-functionalization of Ni(II), Pd(II), and Pt(II) mono- and diphosphine complexes: minimizing the electronic consequences for the metal center.

A series of fluorous derivatives of group 10 complexes MCl(2)(dppe) and [M(dppe)(2)](BF(4))(2) (M = Ni, Pd or Pt; dppe = 1,2-bis(diphenylphosphino)ethane) and cis-PtCl(2)(PPh(3))(2) was synthesized. The influence of para-(1H,1H,2H,2H-perfluoroalkyl)dimethylsilyl-functionalization of the phosphine phenyl groups of these complexes, as studied by NMR spectroscopy, cyclovoltammetry (CV), XPS analyses, as well as DFT calculations, points to a weak steric and no significant inductive electronic effect. The steric effect is most pronounced for M = Ni and leads in the case of NiCl(2)(1c) (3c) and [Ni(1c)(2)](BF(4))(2) (7c) (1c = [CH(2)P[C(6)H(4)(SiMe(2)CH(2)CH(2)C(6)F(13))-4](2)](2)) to a tetrahedral distortion from the expected square planar geometry. The solubility behavior of NiCl(2)[CH(2)P[C(6)H(4)(SiMe(3-b)(CH(2)CH(2)C(x)F(2x+1)b)-4](2)](2) (3: b = 1-3; x = 6, 8) in THF, toluene, and c-C(6)F(11)CF(3) was found to follow the same trends as those observed for the free fluorous ligands 1. A similar correlation between the partition coefficient (P) of complexes 3 and free 1 was observed in fluorous biphasic solvent systems, with a maximum value obtained for 3f (b = 3, x = 6, P = 23 in favor of the fluorous phase).

Magnetic properties and aromaticity of o-, m-, and p-benzyne.

The relative aromaticities of the three singlet benzyne isomers, 1,2-, 1,3-, and 1,4-didehydrobenzenes have been evaluated with a series of aromaticity indicators, including magnetic susceptibility anisotropies and exaltations, nucleus-independent chemical shifts (NICS), and aromatic stabilization energies (all evaluated at the DFT level), as well as valence-bond Pauling resonance energies. Most of the criteria point to the o-benzyne

Stability and aromaticity of the cyclopenta-fused pyrene congeners.

The aromaticity of all possible cyclopenta-fused pyrene congeners has been investigated at various levels of theory. On the basis of the calculated resonance energies and magnetic properties (delta(1)H data, magnetic susceptibility anisotropies, and NICS values), the overall aromaticity of these compounds is found to decrease gradually with increasing number of externally fused five-membered rings. The relatively small differences (<5 kcal/mol) in thermodynamic stability of the isomeric dicyclopentapyrenes (E(tot): dicyclopenta[cd,fg]- > dicyclopenta[cd,jk]- > dicyclopenta[cd,mn]pyrene), which differs from the aromaticity order based on the magnetic criteria (dicyclopenta[cd,mn]- > dicyclopenta[cd,fg]- > dicyclopenta[cd,jk]pyrene), is shown by model calculations to be dominated by sigma-strain imposed on the pyrene skeleton by sequential cyclopenta-fusion. This is supported by the computed homodesmotic reaction energies and aromatic stabilization energy (ASE(isom)) from isodesmic aromatic-nonaromatic isomerization, and by the model calculations on "distorted" cyclopenta[cd]pyrenes. The elusive tetracyclopenta[cd,fg,jk,mn]pyrene is computed to be bowl-shaped; its corresponding planar geometry is the transition state for bowl-bowl interconversion.