Gaussian basis sets of quadruple zeta valence quality for Rb-Rn are presented, as well as bases of split valence and triple zeta valence quality for H-Rn. The latter were obtained by (partly) modifying bases developed previously. A large set of more than 300 molecules representing (nearly) all elements-except lanthanides-in their common oxidation states was used to assess the quality of the bases all across the periodic table. Quantities investigated were atomization energies, dipole moments and structure parameters for Hartree-Fock, density functional theory and correlated methods, for which we had chosen Moller-Plesset perturbation theory as an example. Finally recommendations are given which type of basis set is used best for a certain level of theory and a desired quality of results.

Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy

CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a highly flexible computer program which uses empirical energy functions to model macromolecular systems. The program can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations. The operations that CHARMM can perform are described, and some implementation details are given. A set of parameters for the empirical energy function and a sample run are included.

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solvent−solvent, solvent−solute, and solute−solute interactions. Optimization of the internal parameters used experimental gas-phase geometries, vibrational spectra, and torsional energy surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized with respect to data for N-methylacetamide and the alanine dipeptide. The interaction parameters, particularly the atomic charges, were determined by fitting ab initio interaction energies and geometries of complexes between water and model compounds that represented the backbone and the various side chains. In addition, dipole moments, experimental heats and free energies of vaporization, solvation and sublimation, molecular volume...

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All-atom empirical potential for molecular modeling and dynamics studies of proteins.

We present the theoretical and technical foundations of the Amsterdam Density Functional (ADF) program with a survey of the characteristics of the code (numerical integration, density fitting for the Coulomb potential, and STO basis functions). Recent developments enhance the efficiency of ADF (e.g., parallelization, near order-N scaling, QM/MM) and its functionality (e.g., NMR chemical shifts, COSMO solvent effects, ZORA relativistic method, excitation energies, frequency-dependent (hyper)polarizabilities, atomic VDD charges). In the Applications section we discuss the physical model of the electronic structure and the chemical bond, i.e., the Kohn–Sham molecular orbital (MO) theory, and illustrate the power of the Kohn–Sham MO model in conjunction with the ADF-typical fragment approach to quantitatively understand and predict chemical phenomena. We review the “Activation-strain TS interaction” (ATS) model of chemical reactivity as a conceptual framework for understanding how activation barriers of various types of (competing) reaction mechanisms arise and how they may be controlled, for example, in organic chemistry or homogeneous catalysis. Finally, we include a brief discussion of exemplary applications in the field of biochemistry (structure and bonding of DNA) and of time-dependent density functional theory (TDDFT) to indicate how this development further reinforces the ADF tools for the analysis of chemical phenomena. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 931–967, 2001

Chemistry with ADF

A method of ‘‘natural population analysis’’ has been developed to calculate atomic charges and orbital populations of molecular wave functions in general atomic orbital basis sets. The natural analysis is an alternative to conventional Mulliken population analysis, and seems to exhibit improved numerical stability and to better describe the electron distribution in compounds of high ionic character, such as those containing metal atoms. We calculated ab initio SCF‐MO wave functions for compounds of type CH3X and LiX (X=F, OH, NH2, CH3, BH2, BeH, Li, H) in a variety of basis sets to illustrate the generality of the method, and to compare the natural populations with results of Mulliken analysis, density integration, and empirical measures of ionic character. Natural populations are found to give a satisfactory description of these molecules, providing a unified treatment of covalent and extreme ionic limits at modest computational cost.

Natural population analysis

Einblicke in die Struktur kleiner cyclischer Carbo-Kationen durch MO-Berechnungen

Cumulenic amines R1CHCC(R3)NR22(R1 and R2H or alkyl, R3H or Me) are converted rapidly at 20 °C into enyne amines R1CC–CHC(R3)NR22 with methanol or water under neutral conditions.

Proton-catalysed isomerization of cumulenic amines

Can the H2+4 dication exist?

The orbital deletion procedure is introduced, which is suited to quantitatively investigating the electronic delocalization effect in carbocations and boranes. While the routineab initio molecular orbital methods can generate wavefunctions for real systems where all electrons are delocalized, the present orbital deletion procedure can generate wavefunctions for hypothetical reference molecules where electronic delocalization effect is deactivated. The latter wave-function normally corresponds to the most stable resonance structure in terms of the resonance theory. By comparing and analyzing the delocalized and the localized wavefunctions, one can obtain a quantitative and instinct picture to show how electronic delocalization inside a molecule affects the molecular structure, energy as well as other physical properties. Two examples are detailedly discussed. The first is related to the hyperconjugation of alkyl groups in carbocations and a comparison of the order of stability of carbocations is made. The second concerns the Lewis acidity of boron trihalides where the conjugation effect among the doubly-occupied π atomic orbitals on the halide atoms and the vacant π atomic rbital on the boron atom plays a dominant role in determining the relative acceptor properties. The results demonstrate that the orbital deletion procedure can be used to very successfully interpret some traditional chemical intuitions and concepts in a quantitative way.

Paul von Ragué Schleyer

Papers

Einblicke in die Struktur kleiner cyclischer Carbo-Kationen durch MO-Berechnungen

Proton-catalysed isomerization of cumulenic amines

Can the H2+4 dication exist?

Orbital deletion procedure and its applications

3-Ethynylcyclopropene: a highly suspicious crystal structure