Gas-phase properties and Fukui indices of sulfine (CH2SO). Potential energy surface and maximum hardness principle for its protonation process. A density functional study

Gas-phase thermochemical properties of sulfine (CH₂SO) and the potential energy surface of its protonation process were studied by the density functional method employing different exchange-correlation potentials. All calculations showed that the most stable protonated isomer is planar with the proton bonded to the oxygen atom in a trans arrangement of the skeleton. Three transition states were located that allow interconversion between the different isomers. Hardnesses and Fukui indices were calculated to follow the reactivity trend along the protonation path and to explain the preference for a particular protonation site on neutral sulfine. Proton affinity, gas-phase basicity and heat of formation values, obtained for the first time fully quantum mechanically, agree well with those derived by a recent mass spectrometry experimental study. Good agreement between density functional theory and previous high-level theoretical and experimental data was also found for the heat of formation of sulfine and its most stable protonated form. Received: 12 October 1998 / Accepted: 24 November 1998 / Published online: 16 March 1999     

Cyclometalated AuIII Complexes for Cysteine Arylation in Zinc Finger Protein Domains: towards Controlled Reductive Elimination

With the aim of exploiting the use of organometallic species for the efficient modification of proteins through C-atom transfer, the gold-mediated cysteine arylation through a reductive elimination process occurring from the reaction of cyclometalated Au^III C^N complexes with a zinc finger peptide (Cys₂His₂ type) is here reported. Among the four selected Au^III cyclometalated compounds, the [Au(C^CON)Cl₂] complex featuring the 2-benzoylpyridine (C^CON) scaffold was identified as the most prone to reductive elimination and Cys arylation in buffered aqueous solution (pH 7.4) at 37 °C by high-resolution LC electrospray ionization mass spectrometry. DFT and quantum mechanics/molecular mechanics (QM/MM) studies permitted to propose a mechanism for the title reaction that is in line with the experimental results. Overall, the results provide new insights into the reactivity of cytotoxic organogold compounds with biologically important zinc finger domains and identify initial structure–activity relationships to enable Au^III-catalyzed reductive elimination in aqueous media.     

Global geometry optimization of small silicon clusters at the level of density functional theory

By an application to small silicon clusters Si _N (with N = 4,5,7,10) it is shown that truly global geometry optimization on an ab initio or density functional theory level can be achieved, at a computational cost of approximately 1–5 traditional local optimization runs (depending on cluster size). This extends global optimization from the limited area of empirical potentials into the realm of ab initio quantum chemistry. Received: 24 February 1998 / Accepted: 6 March 1998 / Published online: 17 June 1998     

The spin-forbidden reaction CH(2∏) + N2→ HCN + N(4S) revisited I. Ab initio study of the potential energy surfaces

High-level ab initio electronic structure theories have been applied to investigate the detailed reaction mechanism of the spin-forbidden reaction CH(²∏) + N₂ → HCN + N(⁴S). The G2M(RCC) calculations provide accurate energies for the intermediates and transition states involved in the reaction, whereas the B3LYP/6-311G(d,p) method overestimates the stability of some intermediates by as much as about 10 kcal/mol. A few new structures have been found for both the doublet and quartet electronic states, which are mainly involved in the dative pathways. However, due to the higher energies of these structures, the dominant mechanism remains the one involving the C ₂ intersystem-crossing step. The C ₂ minima on the seam of crossing (MSX) structures and the spin-orbit coupling between the doublet and quartet electronic states are rather close to those found in previous studies. Vibrational frequencies orthogonal to the normal of the seam which have been applied in a separate publication to calculate the rate of the CH(²∏) + N₂ → HCN + N(⁴S) reaction with a newly proposed nonadiabatic transition-state theory for spin-forbidden reactions have been calculated at the MSX from first principles. Received: 23 June 1998 / Accepted: 21 September 1998 / Published online: 8 February 1999     

Ab initio quantum chemical study of the formation, decomposition and isomerization of the formaldiminoxy radical (CH2NO): comparison of the Gaussian-2 and CASPT2 techniques in the calculation of potential energy surfaces

The reaction between triplet methylene and nitric oxide, producing the formaldiminoxy (CH₂NO) radical, and the subsequent decomposition and isomerization reactions of CH₂NO have been studied using ab␣initio quantum chemical techniques that include the Gaussian-2 (G2), CASSCF and CASPT2 methods. Stationary points on the potential energy surfaces were located at MP2/6-31G(d) and CASSCF/cc-pVDZ levels of theory, while the electronic energies were determined using G2, G2(MP2), QCISD(T)/cc-pVTZ, RCCSD(T)/cc-pVTZ and CASPT2/cc-pVTZ approaches. G2 is believed to be reliable at equilibrium geometries, but the determination of certain transition state geometries and energies requires a MCSCF-based approach. The calculations suggest that CH₂NO (²A^′) forms in a barrierless reaction and could readily decompose to H+HCNO. A subsequent abstraction reaction then results in H₂+CNO. No molecular elimination channel was found. An alternative pathway is the formation of CH₂ON, which readily isomerizes to CH₂NO. Received: 8 May 1998 / Accepted: 11 August / Published online: 9 October 1998     

Ab initio calculations find 2,2-disilylcyclopentane-1,3-diyl is a singlet diradical with a high barrier to ring closure

Ab initio calculations on the lowest singlet and triplet states of 2,2-disilylcyclopentane-1,3-diyl find that the singlet lies well below the triplet. The C ₂ singlet diradical is calculated to be a minimum on the potential energy surface with an enthalpic barrier to ring closure of ΔH ^‡ ₂₉₈ = 13.5 kcal/mol at the CASPT2/6-31G* level of theory. The energy of the 1,3-divinyl-substituted singlet diradical is calculated to be only 0.8 kcal/mol higher than that of 5,5-disilyl-1,3-divinylbicyclo[2.1.0]pentane at this level of theory, but the transition state for their equilibration is computed to be 12.8 kcal/mol above the diradical in energy. Received: 2 July 1998 / Accepted: 4 August 1998 / Published online: 16 November 1998     

The structure and energetics of cryolite melts

A method of solvation energy computation is proposed for ions and molecules in the environment of an ionic melt, based on the approximation of the ionic melt as an ideal conductor. The method is used to compute equilibrium constants of some equilibria in cryolite melt. Theoretically obtained results predict that aluminium is bound in tetrafluorocomplexes AlF₄ ⁻. Received: 16 March 1998 / Accepted: 19 June 1998 / Published online: 7 October 1998     

Different van der Waals radii for organic and inorganic halogen atoms: a significant improvement in IMOMM performance

The discrepancies between X-ray and integrated molecular orbital molecular mechanics computed geometries for Os(H)₂Cl₂(PⁱPr₃)₂ and Ir(H)₂Cl(P^tBu₂ Ph)₂ are explained by the inadequacy of the default molecular mechanics van der Waals radii for halogen elements. A simple procedure is proposed for the calculation of corrected van der Waals radii, and the application of the corrected radius for chloride is shown to improve substantially the results for the systems under test. Received: 25 February 1997 / Accepted: 7 April 1997     

Implementation of the IMOMM methodology for performing combined QM/MM molecular dynamics simulations and frequency calculations

A technique for implementing the integrated molecular orbital and molecular mechanics (IMOMM) methodology developed by Maseras and Morokuma that is used to perform combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations, frequency calculations and simulations of macromolecules including explicit solvent is presented. Although the IMOMM methodology is generalized to any coordinate system, the implementation first described by Maseras and Morokuma requires that the QM and MM gradients be transformed into internal coordinates before they are added together. This coordinate transformation can be cumbersome for macromolecular systems and can become ill-defined during the course of a molecular dynamics simulation. We describe an implementation of the IMOMM method in which the QM and MM gradients are combined in the cartesian coordinate system, thereby avoiding potential problems associated with using the internal coordinate system. The implementation can be used to perform combined QM/MM molecular dynamics simulations and frequency calculations within the IMOMM framework. Finally, we have examined the applicability of thermochemical data derived from IMOMM framework. Finally, we have examined the applicability of thermochemical data derived from IMOMM frequency calculations. Received: 11 May 1998 / Accepted: 14 August 1998 / Published online: 16 November 1998     

The influence of monovalent cations on the stability of electrochemically formed nickel fluoride films

The stability of electrochemically formed NiF₂ film in 1.0 M perchloric acid containing monovalent fluorides namely, NH₄F, HF, NaF, KF and LiF, is investigated using cyclic voltammetry, chronoamperometry, atomic absorption spectroscopy and scanning electron microscopy. In addition to direct dissolution of nickel and dissolution through the oxide layer, a new mode of dissolution of NiF₂ film as NiF₃ ⁻ and NiF₄ ²⁻ through complex formation is proposed. This process is significantly influenced by the alkali metal fluorides. On a comparative basis the stability of NiF₂ decreases in the order NH₄F > HF > KF > LiF. Received: 29 July 1998 / Accepted: 3 November 1998     

The effect of the protein environment on the structure and charge distribution of the retinal Schiff base in bacteriorhodopsin

The effects of the amino acid side chains of the binding pocket of bacteriorhodopsin (bR) and of a water molecule on the structure of the retinal Schiff base have been studied using Becke3LYP/6-31G* level of density functional theory. A model protonated Schiff base structure including six conjugated double bonds and methyl substituents was optimized in the presence of several amino acid side chains and of a water molecule, separately. The Schiff base structure was also calculated in the form of a neutral species. At each optimized complex geometry the atomic charges of the model Schiff base were calculated using Mulliken population analysis. In agreement with previously proposed counterion(s) of the protonated retinal Schiff base in bR, the results show that Asp₈₅ and Asp₂₁₂, which are present in the form of negatively charged groups, have significantly large effects on the structure and electronic configuration of both unprotonated and protonated model Schiff bases. The presence of a water molecule in the vicinity of the Schiff base demonstrates significant effects which are comparable to those of aspartate groups. Other side chains studied did not show any significant effect in this direction. Apart from the aspartate groups and the water molecule, in none of the other complexes studied are the atomic charges and the bond alternation of the model Schiff base significantly influenced by the presence of the neighboring amino acids. Received: 24 March 1998 / Accepted: 3 September 1998 / Published online: 10 December 1998     

Determination of a set of parameters for the molecular modelling of phosphorothioate DNA

Phosphorothioate DNAs, have emerged as a new class of potent drugs. They are obtained by the replacement of the anionic oxygens of the phophodiester backbone by sulphur. A set of parameters has been developed for the FLEX force field implemented in JUMNA 10.0 to take into account the influence of sulphur on the structure of the DNA double helix. The consistency of our parameters was tested by modelling a phosphorothioate oligomer namely d(GC)8. d(GC)8. Results, obtained on both R-p_S and S-p_S diastereoisomers, were compared to the phosphodiester counterpart and are in agreement with available experimental data. Thus, our set of parameters seems suitable for further molecular modelling of other phosphorothioate oligomers. Received: 15 July 1998 / Accepted: 8 September 1998 / Published online: 10 December 1998     

Periodic orbits and vibrational wave functions for DCP: nonlinear resonances in isotopically substituted molecules

We investigate, by means of classical and quantum mechanics, how isotopic substitution (H/D) affects the vibrational dynamics of HCP. The analysis of periodic orbits, including the location of the principal families as well as saddle node bifurcations, reveals a totally different picture for the phase-space resonance structure for HCP and DCP. While HCP is characterized by a 1:2 resonance between the CP stretch and the bending mode, DCP shows a 1:2 resonance between the two stretching degrees of freedom. Saddle node bifurcations, which are associated with large-amplitude motion of H/D moving from the C- to the P-end, appear at considerably higher energies in DCP than in HCP. These results are in accord with exact quantum mechanical calculations of the vibrational levels. Received: 24 June 1998 / Accepted: 10 August 1998 / Published online: 9 October 1998     

Possible long-lived quartet resonance states of CO−

Two states of CO⁻ which are expected to live longer than the well-known ²Π shape resonance are examined and the results obtained are compared with the analogous states of the isoelectronic N₂ ⁻ system. The ⁴Σ⁻ and ⁴Π states are found to be stable with respect to dissociation. The latter state is also stable with respect to single-electron loss to its parent neutral state. The lifetime of this state is supposed to be long, but not necessarily long enough to allow detection in a mass spectrometer. Received: 28 May 1998 / Accepted: 23 July 1998 / Published online: 9 October 1998     

Anodic oxidation of 2-aminofluorene in CH2Cl2 + 0.2 M Bu4NBF4: electrochemical behaviour of the derived oxidation products

The physicochemical properties and electrochemical behaviour of products obtained by anodic oxidation of 2-aminofluorene in CH₂Cl₂ + 0.2 M Bu₄NBF₄ are presented together with the oxidation conditions. Received: 8 January 1998 / Accepted: 21 September 1998     

SAC-CI general-R study of the ionization spectrum of HCl

The valence ionization spectrum of HCl is studied by symmetry-adapted-cluster configuration-interaction general-R and SD-R methods. The general-R method describes well the peak positions and intensities of seven satellite lines observed below the double ionization threshold. The twinning shake-up states due to the (4σ)⁻¹ state and the Rydberg states of HCl⁺ are correctly reproduced. Received: 26 June 1998 / Accepted: 9 September 1998 / Published online: 8 February 1999     

Hydration of platinum(II) complexes: a molecular mechanics study using atom-based force-field parameters

 This work is related to the interaction of water with two platinum(II) complexes, [Pt(NH₃)₄]²⁺ (denoted 1) and trans-[Pt(OH)₂(NH₃)₂] (denoted 2). We have considered two approaches of a water molecule to complexes 1 and 2 along the z-axis normal to the platinum(II) coordination plane: approach I, with the water oxygen oriented towards Pt, and approach II, with one water hydrogen directed towards Pt. Calculations have been performed within a molecular mechanics method based upon the interaction potentials proposed earlier by Claverie et al. and subsequently adjusted to results obtained with symmetry – adapted perturbational theory as well as with supermolecule (up to second-order M?ller–Plesset, MP2) methods. We discuss some possible simplifications of the potentials mentioned. The results relative to the hydration of Pt complexes 1 and 2 following approach I or II are discussed and compared to recent (MP2) ab initio energy–distance curves that we have recently determined. The MP2 calculations have shown that besides exchange–repulsion contributions, which are very similar in all hydrated complexes, approach I is mainly governed by electrostatics, whereas for approach II both electrostatic and dispersion contributions are important. Received: 16 September 1999 / Accepted: 3 February 2000 / Published online: 5 June 2000     

Nafion-based solid-state gas sensors: Pt / Nafion electrodes prepared by an impregnation-reduction method in sensing oxygen

The influences of the reductant concentration of NaBH₄ and the quantity of Pt loading on the active surface area and the sensitivity of the Pt/Nafion electrodes prepared by an impregnation-reduction method in detecting oxygen were investigated in this study. The Pt/Nafion electrodes with a Pt loading of 4.99 mg/cm², obtained at 0.0107 M Pt(NH₃)₄Cl₂ and 0.06 M NaBH₄, show maximum sensitivities of 0.0528 A/ppm and 0.0538 A/ppm obtained in O₂ concentration regions of 0–5000 and 5000–50 000 ppm, respectively. A sensing model was also proposed to illustrate the sensing phenomenon. Received: 21 January 1998 / Accepted: 10 March 1998     

Molecular modeling study of an abasic DNA undecamer duplex: d(GCGTGOGTGCG) · d(CGCACTCACGC)

Molecular mechanics calculations were performed with the JUMNA program on d(GCGTGOGTGCG) · d(CGCACTCACGC) where “O” is a modified abasic site: 3-hydroxy-2-(hydroxymethyl)tetrahydrofuran. From energy minimizations, for intrahelical or extrahelical positions of the unpaired thymine, various structures with different curvatures were obtained. Dynamical properties of this abasic sequence were also investigated through the controlled studies of DNA bending. Poisson-Boltzmann calculations were used to mimic the electrostatic effect of solvent on this sequence. The lowest energy structures show an acceptable agreement with experimental data. Received: 1 June 1998 / Accepted: 17 September 1998 / Published online: 10 December 1998