Comparison of Methods for Active Orbital Selection in Multiconfigurational Calculations.

Several methods of constructing the active orbital space for multiconfigurational wave functions are compared on typical moderately strongly or strongly correlated ground-state molecules. The relative merits of these methods and problems inherent in multiconfigurational calculations are discussed. Strong correlation in the ground electronic state is found typically in larger conjugated and in antiaromatic systems, transition states which involve bond breaking or formation, and transition metal complexes.

Analytical Energy Gradients for the Cluster-in-Molecule MP2 Method and Its Application to Geometry Optimizations of Large Systems.

An efficient analytical energy gradient algorithm for the cluster-in-molecule (CIM) second order Møller-Plesset perturbation theory (MP2) method is presented. In our algorithm, the gradient contributions from the nonseparable term of the two-body density matrix on a given atom is extracted from calculations on a cluster constructed for this atom. The other terms in the CIM-MP2 energy gradient expression are evaluated by constructing the density matrices of the whole system with the contributions from all clusters constructed.

Automatic Construction of the Initial Orbitals for Efficient Generalized Valence Bond Calculations of Large Systems.

We propose an efficient general strategy for generating initial orbitals for generalized valence bond (GVB) calculations which makes routine black-box GVB calculations on large systems feasible. Two schemes are proposed, depending on whether the restricted Hartree-Fock (RHF) wave function is stable (scheme I) or not (scheme II). In both schemes, the first step is the construction of active occupied orbitals and active virtual orbitals.

Benchmark Relative Energies for Large Water Clusters with the Generalized Energy-Based Fragmentation Method.

The generalized energy-based fragmentation (GEBF) method has been applied to investigate relative energies of large water clusters (HO) (n = 32, 64) with the coupled-cluster singles and doubles with noniterative triple excitations (CCSD(T)) and second-order Møller-Plesset perturbation theory (MP2) at the complete basis set (CBS) limit. Here large water clusters are chosen to be representative structures sampled from molecular dynamics (MD) simulations of liquid water. Our calculations show that the GEBF method is capable of providing highly accurate relative energies for these water clusters in a cost-effective way.

Approximate Force Constants from Uncoupled Self-Consistent Field Perturbation Theory Using Nonhybrid Density Functional Theory.

Second derivatives of the molecular energy with respect to the nuclear coordinates (the nuclear Hessian or force constant matrix) are important for predicting infrared and Raman spectra, for calculating thermodynamic properties, for characterizing stationary states, and for guiding geometry optimization. However, their calculation for larger systems scales with molecular size one power higher than the calculation of the energy and the forces. The step responsible for the steep scaling of the nuclear Hessian is the coupled-perturbed self-consistent field (CP-SCF) iteration.

Finding symmetry breaking Hartree-Fock solutions: The case of triplet instability.

Determining the lowest unrestricted Hartree-Fock (UHF) solution is often difficult in even-electron systems. We have developed a deterministic method for locating approximately the UHF minimum using the restricted Hartree-Fock triplet instability matrix. The current method is truncated to fourth order.

Selection of active spaces for multiconfigurational wavefunctions.

The efficient and accurate description of the electronic structure of strongly correlated systems is still a largely unsolved problem. The usual procedures start with a multiconfigurational (usually a Complete Active Space, CAS) wavefunction which accounts for static correlation and add dynamical correlation by perturbation theory, configuration interaction, or coupled cluster expansion. This procedure requires the correct selection of the active space.

Zundel-type H-bonding in biomolecular ions.

Using quantum chemical calculations and infrared multiphoton dissociation (IRMPD) spectroscopy in the fingerprint and X-H stretching regions, we demonstrate here that the all-Ala (b6) fragment ion features a macrocyclic structure with C(2) symmetry. For this structure, the ionizing proton is equally shared by the Ala(1) and Ala(4) amide oxygens in a Zundel-type symmetric (X…H(+)…X) H-bond.

The accuracy of quantum chemical methods for large noncovalent complexes.

We evaluate the performance of the most widely used wavefunction, density functional theory, and semiempirical methods for the description of noncovalent interactions in a set of larger, mostly dispersion-stabilized noncovalent complexes (the L7 data set). The methods tested include MP2, MP3, SCS-MP2, SCS(MI)-MP2, MP2.5, MP2.

A benchmark comparison of σ/σ and π/π dispersion: the dimers of naphthalene and decalin, and coronene and perhydrocoronene.

The stacking interaction between π systems is a well-recognized structural motif, but stacking between σ systems was long considered of secondary importance. A recent paper points out that σ stacking can reach the energy of chemical bonds and concludes that "σ/σ and π/π interactions are equally important" (Fokin, A. F.

The Ethidium-UA/AU Intercalation Site: Effect of Model Fragmentation and Backbone Charge State.

We report a systematic analysis of the intermolecular interactions of cationic ethidium intercalated into a UA/AU step of RNA for a single conformation based on crystallographic coordinates. Interaction energies at the MP2/6-31G** level were partitioned into electrostatic, exchange, delocalization, and correlation components. Various pairwise interaction models built from chemically intuitive fragments reproduce within a few percent values obtained when treating the intercalation site as a whole.

A reliable and efficient first principles-based method for predicting pK(a) values. 2. Organic acids.

In part 1 of this series, we developed a protocol for the large-scale calculation of pK(a) values in aqueous solutions from first principles calculations, with the goal of striking a compromise between accuracy and computational efficiency. Following previous workers in the field, pK(a) values are calculated from a linear regression fit to deprotonation energies: pK(a)(f) = alpha(f)(E(A)(-) - E(HA)) + beta(f), where f denotes a family of functional groups. In this paper, we derive (alpha(f), beta(f)) values for the acidic functional groups -COOH, -POOH, alcoholic and phenolic -OH, -SH, -NHOH/ horizontal lineNOH, and -NROH, using a data set of 449 experimental pK(a) values.

A reliable and efficient first principles-based method for predicting pK(a) values. 1. Methodology.

We have developed an efficient and reliable protocol for the calculation of pK(a) values in aqueous solution from density functional calculations. We establish a standard linear regression fit using only calculated energies of deprotonation and experimental pK(a) values; all other factors, including most entropic effects, are absorbed into the fitting constants. In this article we fit a small training set of 34 experimentally well-characterized molecules to determine the best level of theory among those tested (i.

Efficient Parallel Implementation of the CCSD External Exchange Operator and the Perturbative Triples (T) Energy Calculation.

A new, efficient parallel algorithm is presented for the most expensive step in coupled cluster singles and doubles (CCSD) energy calculations, the external exchange operator (EEO). The new implementation requires much less input/output than our previous algorithm and takes better advantage of integral screening. It is formulated as a series of matrix multiplications.

Comments on the molecular geometry of ferrocene: The dangers of using quantum chemistry programs as black boxes.

The dangers of using standard quantum chemistry programs as black boxes is illustrated by analyzing some results in a recent paper published in this journal (Zhang et al., J Comput Chem 2007, 28, 2260). The main danger is that nonlinear optimizations of both the wavefunction and the molecular geometry may converge to higher local minima or to saddle points, producing misleading results.

Quantum chemistry in parallel with PQS.

This article describes the capabilities and performance of the latest release (version 4.0) of the Parallel Quantum Solutions (PQS) ab initio program package. The program was first released in 1998 and evolved from the TEXAS program package developed by Pulay and coworkers in the late 1970s.

Parallel Calculation of Coupled Cluster Singles and Doubles Wave Functions Using Array Files.

A new parallel implementation of the Coupled Cluster Singles and Doubles (CCSD) and related wave functions (e.g Quadratic Configuration Interaction, QCI, and Coupled Electron Pair, CEPA) is described, based on the Array Files middleware. The program can handle large basis sets, even without utilizing symmetry, on modest distributed memory workstation clusters.

Parallel DFT gradients using the Fourier Transform Coulomb method.

The recently described Fourier Transform Coulomb (FTC) algorithm for fast and accurate calculation of Density Functional Theory (DFT) gradients (Füsti-Molnar, J Chem Phys 2003, 119, 11080) has been parallelized. We present several calculations showing the speed and accuracy of our new parallel FTC gradient code, comparing its performance with our standard DFT code. For that part of the total derivative Coulomb potential that can be evaluated in plane wave space, the current parallel FTC gradient algorithm is up to 200 times faster in total than our classical all-integral algorithm, depending on the system size and basis set, with essentially no loss in accuracy.

New parallel algorithm for MP2 energy gradient calculations.

A new parallel algorithm has been developed for calculating the analytic energy derivatives of full accuracy second order Møller-Plesset perturbation theory (MP2). Its main projected application is the optimization of geometries of large molecules, in which noncovalent interactions play a significant role. The algorithm is based on the two-step MP2 energy calculation algorithm developed recently and implemented into the quantum chemistry program, GAMESS.

Accuracy of the three-body fragment molecular orbital method applied to Møller-Plesset perturbation theory.

The three-body energy expansion in the fragment molecular orbital method (FMO) was applied to the 2nd order Møller-Plesset theory (MP2). The accuracy of both the two and three-body expansions was determined for water clusters, alanine n-mers (alpha-helices and beta-strands) and one synthetic protein, using the 6-31G* and 6-311G* basis sets. At the best level of theory (three-body, two molecules/residues per fragment), the absolute errors in energy relative to ab initio MP2 were at most 1.

Array files for computational chemistry: MP2 energies.

A simple message-passing implementation for distributed disk storage, called array files (AF), is described. It is designed primarily for parallelizing computational chemistry applications but it should be useful for any application that handles large amounts of data stored on disk. AF allows transparent distributed storage and access of large data files.

Ligand redox effects in the synthesis, electronic structure, and reactivity of an alkyl-alkyl cross-coupling catalyst.

The ability of the terpyridine ligand to stabilize alkyl complexes of nickel has been central in obtaining a fundamental understanding of the key processes involved in alkyl-alkyl cross-coupling reactions. Here, mechanistic studies using isotopically labeled (TMEDA)NiMe(2) (TMEDA = N,N,N',N'-tetramethylethylenediamine) have shown that an important catalyst in alkyl-alkyl cross-coupling reactions, (tpy')NiMe (2b, tpy' = 4,4',4' '-tri-tert-butylterpyridine), is not produced via a mechanism that involves the formation of methyl radicals. Instead, it is proposed that (terpyridine)NiMe complexes arise via a comproportionation reaction between a Ni(II)-dimethyl species and a Ni(0) fragment in solution upon addition of a terpyridine ligand to (TMEDA)NiMe(2).

The interpretation of compliance constants and their suitability for characterizing hydrogen bonds and other weak interactions.

Compliance constants (or their inverses, relaxed force constants) have frequently been proposed as replacements for internal coordinate force constants because of their invariance properties. Recently, Grunenberg and co-workers have proposed using compliance constants as bond strength descriptors, particularly for weak bonds. In this paper, we critically assess this claim and conclude that the use of compliance constants in this regard is inappropriate.

H2, Ne, and N2 Energies of Encapsulation into C60 Evaluated with the MPWB1K Functional.

The recently suggested MPWB1K functional is tested on H2@C60, Ne@C60, and N2@C60 as a tool for evaluations of stabilization energies upon encapsulation of nonmetallic species into fullerenes. It is found that the MPWB1K (modified Perdew-Wang and Becke functionals) values can be within a few kilocalories per mole from the MP2 or SCS-MP2 (spin-component scaled MP2) values so that further applications of the functional are clearly encouraged. The best estimates of the encapsulation-energy gains found for H2@C60, Ne@C60, and N2@C60 are at least 4 kcal/mol, slightly less than 4 kcal/mol, and about 9 kcal/mol, respectively.