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The Dalton quantum chemistry program system

Dalton is a powerful general‐purpose program system for the study of molecular electronic structure at the Hartree–Fock, Kohn–Sham, multiconfigurational self‐consistent‐field, Møller–Plesset, configuration‐interaction, and coupled‐cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic‐structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge‐origin‐invariant manner. Frequency‐dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one‐, two‐, and three‐photon processes. Environmental effects may be included using various dielectric‐medium and quantum‐mechanics/molecular‐mechanics models. Large molecules may be studied using linear‐scaling and massively parallel algorithms. Dalton is distributed at no cost from http://www.daltonprogram.org for a number of UNIX platforms.

Ab initio classical trajectories on the Born–Oppenheimer surface: Updating methods for Hessian-based integrators

For the integration of the classical equations of motion in the Born–Oppenheimer approach, each time the energy and gradient of the potential energy surface are needed, a properly converged wave function is calculated. If Hessians (second derivatives) can be calculated, significantly larger steps can be taken in the numerical integration of the equations of motion without loss of accuracy. Even larger steps can be taken with a Hessian-based predictor–corrector algorithm. Since updated Hessians are used successfully in quasi-Newton methods for geometry optimization, it should be possible to improve the performance of trajectory calculations using updated Hessians. The Murtagh–Sargent (MS) update, the Powell-symmetric–Broyden (PSB) update and Bofill’s update (a weighted combination of MS and PSB) were tested, and Bofill’s update was found to be the best. Slightly smaller step sizes were needed with Hessian updating to maintain good conservation of the energy, but this was more than compensated by the reduction in total computational cost. An overall factor of 3 in speed-up was obtained for trajectories of systems containing 4 to 6 heavy atoms computed at the HF/3-21G level.

The efficient optimization of molecular geometries using redundant internal coordinates

The optimization of ab initio molecular geometries is discussed. Based on comparisons of 30 minimizations and 15 saddle-point optimizations, the most efficient combination of coordinate system, approximate and exact Hessians, and step control is determined. Use of a proposed set of extra-redundant internal coordinates is shown to reduce the number of geometry steps significantly relative to the use of redundant coordinates. Various update schemes are tested for minimum and saddle-point optimizations, including combination formulas. The complete expressions for the first and second derivatives of the Wilson B matrix are presented, thereby avoiding the need to calculate this by finite-difference methods. The presented scheme appears to be the most efficient, robust and generally applicable scheme to date.

Models of fragmentations induced by electron attachment to protonated peptides

Invoking a number of theoretical levels ranging from HF/STO-3G to CCSD(T)/aug-cc-pVQZ, we have made a detailed survey of six potential energy surfaces (NH4+, NH4•, [CH3CONHCH3]H+, [CH3CONHCH3]H•, [HCONHCH2CONH2]H+ and [HCONHCH2CONH2]H•). In conjunction with this, ab inito direct dynamics calculations have been conducted, tracing out several hundred reaction trajectories to reveal details of the electron-capture dissociation mechanism. The model calculations suggest the possibility of a bimodal pattern where some of the radicals, formed upon recombination, dissociate almost directly within one picosecond, the remaining radicals being subject to complete energy redistribution with a subsequent dissociation occurring at the microsecond timescale. Both processes give rise to c and z backbone fragments, resulting from cleavage of N?Cα bonds of the peptide chain.

Experimental and theoretical studies of gas phase NO3 and OH radical reactions with formaldehyde, acetaldehyde and their isotopomers

The vapour phase reactions of formaldehyde, formaldehyde-d2, 13C-formaldehyde, acetaldehyde, acetaldehyde-1-d1, acetaldehyde-2,2,2-d3, and acetaldehyde-d4 with NO3 and OH radicals were studied at 298 ± 2 K and 1013 ± 10 mbar using long-path FTIR detection. The values of the kinetic isotope effects at 298 K, as determined by the relative rate method, were: kNO3+HCHO/kNO3+DCDO = 2.97 ± 0.14, kNO3+HCHO/kNO3+H13CHO = 0.97 ± 0.02, kOH+HCHO/kOH+DCDO = 1.62 ± 0.08, and kOH+H13CHO/kOH+DCDO = 1.64 ± 0.12, kOH+HCHO/kOH+H13CHO = 0.97 ± 0.11, kNO3+CH3CHO/kNO3+CD3CHO = 1.19 ± 0.11, kNO3+CH3CHO/kNO3+CD3CDO = 2.51 ± 0.09, kOH+CH3CHO/kOH+CH3CDO = 1.42 ± 0.10, kOH+CH3CHO/kOH+CD3CHO = 1.13 ± 0.04, and kOH+CH3CHO/kOH+CD3CDO = 1.65 ± 0.08. Quoted errors represent 3σ from the statistical analyses. These errors do not include possible systematic errors. The reactions of NO3 and OH radicals with formaldehyde and acetaldehyde were studied by quantum chemical methods on the MP2 and CCSD(T) levels of theory using the aug-cc-pVDZ and aug-cc-pVTZ basis sets which include diffuse functions. The calculations indicate the existence of weak adducts in which the radicals are bonded to the aldehydic oxygen. Transition states of the reactions X + HCHO → products, and X + CH3CHO → products (X = OH, NO3) were located. Energy level diagrams for reactants, intermediates and products in the OH reactions are presented and discussed in relation to the observed product distribution. Reaction rate coefficients and kinetic isotope effects calculated from different models of the reaction rate theory are compared to experimental data.

Synthesis, structure, and antimycobacterial activity of 6-[1(3H)-isobenzofuranylidenemethyl]purines and analogs

6-Benzofuryl-, styryl, benzyl, and furfurylpurines as well as 6-[1(3H)-isobenzofuranylidenemethyl]purines have been synthesized and their activities against Mycobacterium tuberculosis (Mtb) determined. Several compounds displayed profound antimycobacterial activity in combination with low toxicity towards mammalian cells. NMR and X-ray crystallography were employed to determine the detailed structures and the results were supported by quantum chemical calculations.

An efficient density-functional-theory force evaluation for large molecular systems

An efficient, linear-scaling implementation of Kohn-Sham density-functional theory for the calculation of molecular forces for systems containing hundreds of atoms is presented. The density-fitted Coulomb force contribution is calculated in linear time by combining atomic integral screening with the continuous fast multipole method. For higher efficiency and greater simplicity, the near-field Coulomb force contribution is calculated by expanding the solid-harmonic Gaussian basis functions in Hermite rather than Cartesian Gaussians. The efficiency and linear complexity of the molecular-force evaluation is demonstrated by sample calculations and applied to the geometry optimization of a few selected large systems.

Experimental and theoretical study of the F, Cl and Br reactions with formaldehyde and acetaldehyde

The vapour phase reactions of formaldehyde, formaldehyde-d2, 13C-formaldehyde, acetaldehyde, acetaldehyde-1-d1, acetaldehyde-2,2,2-d3, and acetaldehyde-d4 with Cl and Br atoms were studied at 298±2 K and 1013±10 hPa using long-path FTIR detection. For formaldehyde the only products observed were HCl, HBr and CO; for acetaldehyde the product distribution suggests one dominant channel: CH3CHO+X→CH3CO+HX. The kinetic isotope effects at 298 K were determined by the relative rate method as: kCl+HCHO/kCl+DCDO=1.302±0.014, kCl+H13CHO/kCl+DCDO=1.217±0.025, kBr+HCHO/kBr+DCDO=7.5±0.4 and kBr+H13CHO/kBr+DCDO=6.8±0.4, kCl+CH3CHO/kCl+CH3CDO=1.343±0.023, kCl+CH3CHO/kCl+CD3CDO=1.323±0.018, kCl+CD3CHO/kCl+CH3CDO=1.345±0.015, kCl+CD3CHO/kCl+CD3CDO=1.394±0.021, kBr+CH3CHO/kBr+CH3CDO=3.98±0.26, kBr+CH3CHO/kBr+CD3CDO=3.79±0.29, kBr+CD3CHO/kBr+CH3CDO=4.02±0.10 and kBr+CD3CHO/kBr+CD3CDO=3.96±0.20. Quoted errors represent 3σ from the statistical analyses and do not include possible systematic errors. The reactions of F, Cl and Br atoms with formaldehyde and acetaldehyde were studied by quantum chemical methods on the MP2 level of theory using the cc-pVDZ basis sets. The calculations indicate the existence of a weak adduct in which the halogen atoms are bonded to the aldehydic oxygen. Transition states of the reactions X+HCHO→HX+CHO and X+CH3CHO→HX+CH3CO (X=F, Cl, Br) were located. Reaction rate coefficients and kinetic isotope effects, calculated from conventional transition state theory are compared to experimental data and the deviations are tentatively attributed to adduct formation.

Calculation of electric dipole hypershieldings at the nuclei in the Hellmann-Feynman approximation.

The third-rank electric hypershieldings at the nuclei of four small molecules have been evaluated at the Hartree-Fock level of theory in the Hellmann-Feynman approximation. The nuclear electric hypershieldings are closely related to molecular vibrational absorption intensities and a generalization of the atomic polar tensors (expanded in powers of the electric field strength) is proposed to rationalize these intensities. It is shown that the sum rules for rototranslational invariance and the constraints imposed by the virial theorem provide useful criteria for basis-set completeness and for near Hartree-Fock quality of nuclear shieldings and hypershieldings evaluated in the Hellmann-Feynman approximation. Twelve basis sets of different size and quality have been employed for the water molecule in an extended numerical test on the practicality of the proposed scheme. The best results are obtained with the R12 and R12+ basis sets, designed for the calculation of electronic energies by the explicitly correlated R12 method. The R12 basis set is subsequently used to investigate three other molecules, CO, N2, and NH3, verifying that the R12 basis consistently performs very well.

Insights into the dynamics of evaporation and proton migration in protonated water clusters from Large‐scale Born–Oppenheimer direct dynamics

Large‐scale on‐the‐fly Born–Oppenheimer molecular dynamics simulations using recent advances in linear scaling electronic structure theory and trajectory integration techniques have been performed for protonated water clusters around the magic number (H2O)nH+, for n = 20 and 21. Besides demonstrating the feasibility and efficiency of the computational approach, the calculations reveal interesting dynamical details. Elimination of water molecules is found to be fast for both cluster sizes but rather insensitive to the initial geometry. The water molecules released acquire velocities compatible with thermal energies. The proton solvation shell changes between the well‐known Eigen and Zundel motifs and is characterized by specific low‐frequency vibrational modes, which have been quantified. The proton transfer mechanism largely resembles that of bulk water but one interesting variation was observed.