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

Vertical ionization and electron capture energies (electron affinities) are obtained for the hypermetallic molecules Al 2 O, Al 3 O, Al 4 O, Al 4 C, CAl 2 Si 2 , NAl 3 Si and BAlSi 3 and some related compounds from ab initio calculations with large basis sets. Many-body effects are taken into account by the Green function technique. The results agree with the photoelectron data on Al 2 O. Koopmans' approximation gives good agreement with the Green function results for the first few ionization energies. However, the one-particle ionization model breaks down for the lower valence levels. Electron correlation and relaxation contributes strongly to the electron capture energies.

Green function calculation of ionization energies of hypermetallic molecules

Carbodications. 6. The ethylene dication: a theoretical study of the ethylene dication (C2H42+) potential-energy surface

Lithiated carbocations. The generation, structure, and stability of CLi5+

Stable Carbonium Ions. X.1 Direct Nuclear Magnetic Resonance Observation of the 2-Norbornyl Cation

Ab-initio-Berechnungen unter Heranziehung isodesmischer Reaktionen zeigen, das σ-Donor- und π-Akzeptorgruppen X in H3P = CHX wie z. B. X. = Li, BeH und BH2 Phosphoniumylide stabilisieren. Der anionische Charakter (π-Elektronendichte) des ylidischen C-Atoms liegt zwischen dem von Olefinen und substituierten Carbanionen. π-Akzeptoren delokalisieren die Ladung. Die Polarisation durch die PH3-Gruppe ermoglicht eine Stabilisierung des Anions H3P = CH− und von Yliden mit elektropositiven Gruppen X wie z. B. Li, die ein planares ylidisches C-Atom bevorzugen, wahrend die Stammverbindung (X = H) nicht planar ist, jedoch eine kleine Inversionsbarriere von 0.8 kcal/mol besitzt. Letztere wird in H3P = CHF auf 2.8 kcal/mol erhoht. Gute π-Donatoren wie OH und NH2, die Singulett-Carbene stabilisieren, destabilisieren Phosphoniumylide, die dadurch eine erhohte Dissoziationstendenz zeigen. Solche Ylide konnen als Komplexe zwischen Phosphanen und Carbenen aufgefast werden. Es wird zwischen Onium- und At- Yliden unterschieden. In letzteren sind die aufgefuhrten Stabilitatseinflusse durch Heterosubstituenten invers.



Phosphine Alkylenes, 47



Ab-initio calculations, evaluated by means of isodesmic equations, show that σ-donor and π-acceptor groups, e.g. X = Li, BeH, and BH2, in H3P = CHX stabilize phosphonium ylides. The anionic character (π-density) of the ylidic carbon is intermediate between that of olefins and of substituted carbanions, and π-delocalization by π-acceptor substituents is effective. Polarization of the PH3 group also leads to stabilization of the anion H3P = CH and of corresponding ylides with electropositive substituents, e. g. Li. These favor planar carbon centers; the parent ylide has a nonplanar PCH2 group with a small (0.8 kcal/mol) inversion barrier. This barrier is enhanced somewhat (to ca. 2.8 kcal/mol) in H3PCHF. Since good π donor substituents like OH and NH2, stabilize singlet carbenes but not the ylides, such ylides have an enhanced tendency to dissociate, in agreement with experimental observations. Indeed, such phosphonium ylides can be considered to be carbene complexes of PR3. One can differentiate between onium and ate ylides; the latter are characterized by inverted substituent stabilization effects.

Paul von Ragué Schleyer

Papers

Green function calculation of ionization energies of hypermetallic molecules

Carbodications. 6. The ethylene dication: a theoretical study of the ethylene dication (C2H42+) potential-energy surface

Lithiated carbocations. The generation, structure, and stability of CLi5+

Stable Carbonium Ions. X.1 Direct Nuclear Magnetic Resonance Observation of the 2-Norbornyl Cation

Phosphinalkylene, 47. Heterosubstituenteneinflüsse auf die Stabilität von Phosphoniumyliden. Eine ab-initio-MO-Studie