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...

/pdf/all-atom-empirical-potential-for-molecular-modeling-and-2nds0dxw12.pdf

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

Computational predictions of planar tetracoordinate carbon R1R2CαLi2 arrangements in the cyclopropenyllithium dimer have now been realized experimentally in derivatives with additional chelating ligands. The dimer structures of two substituted cyclopropenyllithiums bearing lithium alkoxide and lithium amide side arms, Cα and O dilithiated 1-(di-tert-butylhydroxymethyl)-3,3-dimethylcyclopropene (8) as well as Cα and N dilithiated 1-(tert-butylaminodimethylsilyl)-3,3-dimethylcyclopropene (9), were characterized by single-crystal X-ray diffraction. The complexes of 8 with tetramethylethylenediamine (TMEDA), (8·TMEDA)2, and with THF, (8·2THF)2, show ladder-type dimeric aggregation. The tetracoordinate R1R2CαLi2 carbon environments in both crystal structures have a high degree of planarization (with 35−39° twist angles), partly due to chelation of one of the lithiums by the O- moiety. Compound 9 crystallizes as a dimeric THF solvate, (9·2THF)2, with a puckered ladder structure. Chelation of one of the lithiums...

Toward Planar Tetracoordinate Carbon in the Puckered Ladder Structures of Chelated Cyclopropenyllithium Aggregates

CNDO [complete neglect of differential overlap] calculations on isomeric cyclopentadienyl(1+) cations

Participation by neighboring aryl groups. I. Determination of assisted and nonassisted solvolysis rates by Hammett correlation

In accordance with predictions based on molecular orbital calculations, the crystal structure of 2,2′-dilithiobiphenyl consists of monomeric units units containing a planar biphenyl unit symmetrically bridged by two tweda-complexed lithium atoms (tmeda = Me2NCH2CH2NMe2).

Paul von Ragué Schleyer

Papers

Toward Planar Tetracoordinate Carbon in the Puckered Ladder Structures of Chelated Cyclopropenyllithium Aggregates

CNDO [complete neglect of differential overlap] calculations on isomeric cyclopentadienyl(1+) cations

Participation by neighboring aryl groups. I. Determination of assisted and nonassisted solvolysis rates by Hammett correlation

Symmetrical double lithium bridging in 2,2′-di(lithium-tmeda)biphenyl (tmeda = MeNCH2CH2NMe2): experimental confirmation of theoretical predictions

Die π-Donorfähigkeit schwerer Elemente ist nicht geringer