Prediction of DNA far-IR absorption spectra based on normal mode analysis

 We present a computational method which couples normal mode analysis in internal coordinates of a molecule with very far IR spectroscopy. The analytical expression for the dependence of IR absorption on frequency incorporates frequencies and optical activities of each normal mode. In order to predict far-IR spectra of a molecule we evaluate the optical activity of each normal mode. This optical activity is determined by the vibration amplitude of the dipole moment produced by a normal mode. We calculated normal modes of DNA double-helical fragments (dA)₁₂ · (dT)₁₂ and (dA-dT)₆ · (dA-dT)₆ and evaluated their optical activities. These were found to be very sensitive to the DNA base-pair sequence. The positions of the resonance peaks in the calculated absorption spectrum of (dA)₁₂ · (dT)₁₂ are in a good agreement with those obtained by Fourier transform IR spectroscopy (Powell JW et al. 1987 Phys Rev A 35: 3929–3939). Received: 20 June 2000 / Accepted: 5 January 2001/ Published online: 3 May 2001     

Accurate thermochemistry from corrected Hartree–Fock results: rapid estimation of nearly experimental quality total energy using the small 6-31G(d) basis set

Gaussian-3 ground-state total electronic energies have been approximated using single point 6-31G(d) basis set Harteee–Fock self-consistent-field (HF-SCF) total energies and partial charges based on our earlier rapid estimation of correlation energy from partial charges method. Sixty-five closed-shell neutral molecules (composed of H, C, N, O, and F atoms) of the G2/97 thermochemistry database were selected for the present study. The main feature in this work is that the␣basis set error has been treated by the least squares fit of rapid estimation of basis set error and correlation energy from partial charges (REBECEP) atomic parameters. With these parameters a rather accurate closed-shell ground-state electronic total energy can be obtained from a small basis set HF-SCF calculation in the vicinity of stationary points. The average absolute deviation of the best REBECEP enthalpies of formation from the experimental enthalpies of formation is 1.39 kcal/mol for the test set of 65 enthalpies of neutral molecules. Received: 11 December 2000 / Accepted: 6 February 2001/Published online: 11 October 2001     

Finding transition states using reduced potential-energy surfaces

 We propose a method to locate saddle points that is based on the interplay between the driving coordinate and the restricted quasi-Newton algorithm. The method locates the transition state using a reduced potential-energy surface. The reduced potential-energy surface is characterized by the set of driving coordinates. The proposed algorithm starts at a point on the surface that is slightly perturbed from either reactant or product and, in principle, converges to the transition state. Finally we give a special type of update Hessian matrix formula that should be applied in optimizations carried out on reduced potential-energy surfaces. Received: 29 September 2000 / Accepted: 3 January 2001 / Published online: 3 April 2001     

Fully relativistic correlated benchmark results for uranyl and a critical look at relativistic effective core potentials for uranium

 A complete set of fully-relativistic benchmark results for the bond lengths and vibrational frequencies of uranyl at various levels of correlation treatment are presented. It is shown that the relativistic and correlation effects are of the same magnitude and should be treated on an equal footing. Results of uranyl calculations using various relativistic effective core potentials (RECP) are presented. Appropriate choices for RECPs for use in density functional theory (DFT) calculations in the local density approximation (LDA) and with the gradient-corrected B3LYP exchange-correlation functional are discussed. The conclusion is reached that small-core RECPs need to be used and that the best results as compared to the benchmark values are obtained by using a DFT functional that includes some fraction of Hartree-Fock Exchange. Received: 18 May 2001 / Accepted: 25 July 2001 / Published online: 30 October 2001     

The performance of the rapid estimation of basis set error and correlation energy from partial charges method on new molecules of the G3/99 test set

Experimental enthalpies of formation have been approximated using single-point Hartree–Fock (HF)–self-consistent-field (SCF) total energies plus the rapid estimation of basis set error and correlation energy from partial charges (REBECEP) energy corrections. The energy corrections are calculated from the HF–SCF partial atomic charges and optimized atomic energy parameters. The performance of the method was tested on 51 closed-shell neutral molecules (50 molecules from the G3/99 thermochemistry database plus urea, composed of H, C, N, O, and F atoms). The predictive force of the method is demonstrated, because these larger molecules were not used for the optimization of the atomic parameters. We used the earlier RECEP-3 [HF/6-311+G(2d,p)] and REBECEP [HF/6-31G(d)] atomic parameter sets obtained from the G2/97 thermochemistry database (containing small molecules) together with natural population analysis and Mulliken partial charges. The best results were obtained using the natural population analysis charges, although the Mulliken charges also provide useful results. The root-mean-square deviations from the experimental enthalpies of formation for the selected 51 molecules are 1.15, 3.96, and 2.92 kcal/mol for Gaussian-3, B3LYP/6-11+G(3df,2p), and REBECEP (natural population analysis) enthalpies of formation, respectively (the corresponding average absolute deviations are 0.94, 7.09, and 2.27 kcal/mol, respectively). The REBECEP method performs considerably better for the 51 test molecules with a moderate 6-31G(d) basis set than the B3LYP method with a large 6-311+G(3df,2p) basis set. Received: 10 March 2001 / Accepted: 5 July 2001 / Published online: 11 October 2001     

Energetics, structures, bonding, and kinetics of the HSCl–HClS system

The [H,S,Cl] potential-energy surface has been investigated at the self-consistent field (SCF), complete active space self-consistent field (CASSCF), second-order M?ller–Plesset, coupled-cluster single-double and perturbative triple excitation, [CCSD(T)]/6-31G(d,p), 6-31G(2df,2pd), and correlation-consistent polarized valence triple zeta (cc-pVTZ) levels of theory. CCSD(T)/ cc-pVTZ results predict a very stable HSCl species, an isomer HClS, 51.84 kcal/mol higher in energy, and a transition state 57.68 kcal/mol above HSCl. Independent of the level of theory, results with the smaller 6-31G(d,p) basis set turned out to be poor, especially for HClS. Vibrational analysis indicates that both species can be easily differentiated if isolated. Bonding differences between these molecules are illustrated by contour plots of valence orbitals. Viewed classically, bonding in HClS involves a dative bond. Transition-state rate constants, and equilibrium constants for the HSCl ↔ HClS isomerization have been estimated for various temperatures (200–1000 K). At 298.15 K, the forward rate is predicted to be 7.95 × 10⁻²⁹ s⁻¹, and the equilibrium constant to be 2.31 × 10⁻³⁸. Tunneling corrections vary from 1.57 at 298.15 K to 1.05 at 1000 K. Activation energies have been obtained by a two-points linear fit to the Arrhenius equation. Received: 7 May 1999 / Accepted: 22 July 1999 / Published online: 4 October 1999     

A study of DNA tethered to a surface by an all-atom molecular dynamics simulation

 In order to understand the structure of DNAs and their interactions when on microarray surfaces, we performed the first all-atom molecular dynamics simulation of DNA tethered to a surface. On the surface, the binding of the DNA was enhanced, and its average equilibrium conformation was the B form. The DNA duplex spontaneously tilted towards its nearest neighbor and settled in a leaning position with a interaxial distance of 2.2 nm. This close packing of the DNAs, which affects both in situ synthesis and deposition of probes on microarray surfaces, can thus be explained by salted-induced colloidlike DNA–DNA attractions. Received: 30 November 2000 / Accepted: 7 February 2001 / Published online: 22 May 2001     

Study of association of 2-methoxyethanol in the aqueous phase

 Monte Carlo simulations have been carried out for 2-methoxyethanol in an isothermal–isobaric ensemble (NPT) at 298.15 K and 1 atm pressure. The optimized potential for liquid simulation force field parameters has been used for modeling 2-methoxyethanol and the TIP4P model for water. Intramolecular rotations are described by an analytical potential function fitted to ab initio energies. It has been shown that the water molecules can form hydrogen bonds between adjacent O atoms of CH₃OCH₂CH₂OH in aqueous media. The self-association of 2-methoxyethanol in aqueous media has been studied by statistical perturbation theory. Received: 9 October 2000 / Accepted: 5 January 2001 / Published online: 3 May 2001     

Localized Orbitals vs. Pseudopotential-Plane Waves Basis Sets: Performances and Accuracy for Molecular Magnetic Systems

 Density functional theory, in combination with a) a careful choice of the exchange-correlation part of the total energy and b) localized basis sets for the electronic orbitals, has become the method of choice for calculating the exchange-couplings in magnetic molecular complexes. Orbital expansion on plane waves can be seen as an alternative basis set especially suited to allow optimization of newly synthesized materials of unknown geometries. However, little is known on the predictive power of this scheme to yield quantitative values for exchange coupling constants J as small as a few hundredths of eV (50–300 cm⁻¹). We have used density functional theory and a plane waves basis set to calculate the exchange couplings J of three homodinuclear Cu-based molecular complexes with experimental values ranging from +40 cm⁻¹ to −300 cm⁻¹. The plane waves basis set proves as accurate as the localized basis set, thereby suggesting that this approach can be reliably employed to predict and rationalize the magnetic properties of molecular-based materials. Corresponding author. E-mail: Carlo.Massobrio@ipcms.u-strasbg.fr Received August 5, 2002; accepted August 9, 2002     

Liquid–Liquid Equilibria of Oxygenate Fuel Additives with Water: Two Quaternary Aqueous Systems of Diisopropyl Ether + 2,2,4-Trimethylpentane with Methyl <Emphasis Type="Italic">tert</Emphasis>-Butyl Ether or Toluene

Experimental tie-line data for two quaternary systems, water + diisopropyl ether + 2,2,4-trimethylpentane + methyl tert-butyl ether or toluene, were investigated at 298.15 K and atmospheric pressure. The experimental liquid–liquid equilibrium data were correlated using a modified UNIQUAC activity coefficient model with ternary and quaternary parameters, in addition to the binary ones. The calculated results were further compared with those obtained with an extended UNIQUAC model from Nagata [Fluid Phase Equilib. 54, 191–206 (1990)].     

Compacting local protein folds with a “hybrid protein model”

 The “hybrid protein model” is a fuzzy model for compacting local protein structures. It learns a nonredundant database encoded in a previously defined structural alphabet composed of 16 protein blocks (PBs). The hybrid protein is composed of a series of distributions of the probability of observing the PBs. The training is an iterative unsupervised process that for every fold to be learnt consists of looking for the most similar pattern present in the hybrid protein and modifying it slightly. Finally each position of the hybrid protein corresponds to a set of similar local structures. Superimposing those local structures yields an average root mean square of 3.14 ?. The significant amino acid characteristics related to the local structures are determined. The use of this model is illustrated by finding the most similar folds between two cytochromes P450. Received: 13 June 2000 / Accepted: 18 September 2000 / Published online: 19 January 2001     

Hydrogen Bonding Properties of the Complexes of Formaldehyde and its Derivatives with HF and HCl

Summary.  The complexes of formaldehyde and some of its derivatives with HF and HCl were investigated at HF/6-311 + +G^** and MP2/6-311 + +G^** levels of theory. Interaction energies were corrected for the basis set superposition error (BSSE). The full optimizations of dimers and monomers were performed during calculations. The Bader theory of atoms-in-molecules (AIM) was also applied for the localization of bond critical points (BCP) and for the calculation the electron densities and their Laplacians at these points. The relationships between H-bond energy and parameters obtained from calculations were also studied. Received June 29, 2001. Accepted (revised) October 29, 2001     

Gas phase and water solution conformational analysis of the herbicide diuron (DCMU): an ab initio study

In the present work, the conformational equilibrium for the herbicide diuron (DCMU) has been investigated using high level ab initio calculations. The solvent effect was included through two different continuum models: (1) the real cavity IPCM method and (2) the standard dipole Onsager model SCRF. The effect due to solute-solvent hydrogen-bond interactions was analyzed considering a hybrid discreet-continuum model. At the Hartree-Fock level, the gas phase results showed that only the trans forms (A and B) are present in the equilibrium mixture, with the relative concentrations found to be 33% (A) and 67% (B) (HF/6-311+G**//6-31G**). When the electronic correlation effect is included (MP2/6-31G*//HF/6-31G*), a relative stabilization of the cis forms was observed, with the conformational distribution calculated as 38% (A), 50% (B), 6% (C) and 6% (D). The trans conformations were found to be completely planar, which has been considered to be a prerequisite for the herbicide binding. In water solution, the trans conformation A should be the most abundant conformer, the IPCM and SCRF values being ca. 100% and ca. 85% respectively. The IPCM calculations with the isodensity level set to 0.0005 present a conformational distribution close to that obtained from the hybrid model [92% (A) and 8% (B)], which has been considered our best solvent approach. Regarding the biological action of urea-type herbicides, the results presented here are important, because some QSAR studies have suggested that the partition coefficient is related to the herbicide activity, so the conformational equilibrium may play a role in the biological action. Received: 23 February 1998 / Accepted: 28 May 1998 / Published online: 19 August 1998     

A theoretical study on the ionization of OCS with an analysis of vibrational structures of the photoelectron spectrum

 Ab initio calculations have been performed to study the molecular structures and vibrational levels of the four low-lying ionic states (1, 2²Π, and 1, 2²Σ⁺) of carbonyl sulfide. The global regions of the potential-energy surfaces have been obtained by multireference single and double excitation configuration interaction calculations. Vibrational calculations using explicit vibrational Hamiltonians have been used for vibrational analysis. The equilibrium molecular structures and a vibrational analysis of the four ionic states are presented. The theoretical ionization intensity curves including the vibrational structures of the ionic states are also presented and are compared with the photoelectron spectrum. Received: 20 January 2001 / Accepted: 22 August 2001 / Published online: 30 October 2001     

Modeling the H5+ potential-energy surface: a first attempt

 Ab initio molecular electronic structure calculations are performed for H₅ ⁺ at the QCISD(T) level of theory, using a correlation-consistent quadruple-zeta basis set. Structures, vibrational frequencies and thermochemical properties are evaluated for ten stationary points of the H₅ ⁺ hypersurface and are compared with previous calculations. The features of the H₃ ⁺…H₂ interaction at intermediate and large intermolecular distances are also investigated. Furthermore, an analytical functional form for the potential-energy surface of H₅ ⁺ is derived using a first-order diatomics-in-molecule perturbation theory approach. Its topology is found to be qualitatively correct for the short-range interaction region. Received: 15 March 2001 / Accepted: 5 July 2001 / Published online: 11 October 2001     

Quaternary Liquid–Liquid Equilibria for Fuel Additive Systems Containing Diethyl Carbonate or 1,1-Dimethylethyl Methyl Ether at 298.15 K and Atmospheric Pressure

Liquid–liquid equilibrium tie line data were determined for three quaternary systems water + ethanol + diethyl carbonate+n-heptane, water + ethanol + 1,1-dimethylethyl methyl ether + diethyl carbonate, and water + 1,1-dimethylethyl methyl ether + diethyl carbonate+n-heptane at 298.15 K and atmospheric pressure. The experimental liquid–liquid equilibria results have been correlated using a modified UNIQUAC model and an extended UNIQUAC model, both with multicomponent interaction parameters in addition to the binary ones.     

Theoretical study of the role of low-barrier hydrogen bonds in enzyme catalysis: a model of proton transfer in serine protease

 A model of low-barrier hydrogen bonds (LBHBs) in enzymes has been studied by ab initio quantum mechanical calculations including the self-consistent reaction field solvent model. The hydrogen-bond strengths and the deprotonation energies for the hydrogen-bonded and non-hydrogen-bonded cis-urocanic acid were calculated at the HF/6-31 + G(d,p) level at various dielectric constants. The same calculations were performed for the α,β-dihydrourocanic acid to model the catalytic dyad of serine protease. The deprotonation energy of N^ɛ2 in α,β-dihydrourocanic acid is increased by formation of LBHBs and depends very much on the dielectric constant. This study suggests that the formation of LBHBs increases the basicity of the dyad, and the polarity change near the reaction center in the active site could help the proton abstraction from Ser 195 and the donation to the leaving group. Both the LBHBs and the environment can play crucial roles in the enzyme catalysis. Received: 8 March 2000 / Accepted: 3 January 2001 / Published online: 3 May 2001     

Formulas and numerical table for the radial part of overlap integrals with the same screening parameters of Slater-type orbitals

 The numerical properties of the radial part of overlap integrals with the same screening parameters in the form of polynomials in p = ξR over Slater-type orbitals have been studied and obtained by using three different methods. For that purpose, the characteristics of auxiliary functions were used first, then Fourier transform convolution theorem, and recurrence relations for the basic coefficients of A ^s _{n l λ, n ′ l ′λ} were used. The calculations of the radial part of overlap integrals with the same screening parameters were made in the range 1 ≤ n ≤ 75, 1 ≤ n′ ≤ 75, and 10⁻⁶ ≤ p. Received: 18 January 2001 / Accepted: 5 April 2001 / Published online: 27 June 2001     

Spectrophotometric micro-method for the determination of ethanol in commercial beverages

 A sensitive spectrophotometric method for the determination of ethanol with potassium dichromate was developed. Chromium(VI), in 7 mol L^-1 perchloric acid, reacts quantitatively with ethanol to form chromium(III) and acetic acid. The reaction is complete in about 15 min at room temperature and the chromium(VI) consumed may be determined by the decrease of the absorbance at 267 nm. The analytical working parameters (such as acidity and ionic strength of the solution, temperature and time of the reaction, chromium(VI) concentration, matrix interferences) were optimized. The apparent molar absorptivities of chromium(VI), in the monomer and dimer form, and the equilibrium quotient for the dimerization reaction were determined in 3 mol L^-1 perchloric acid solution. The method was applied to the analysis of micro samples of commercial beverages (beers, wines and spirits) without the previous distillation of ethanol. Received: 9 April 1996/Revised: 3 June 1996/Accepted: 11 June 1996