Structures and stability of N7+ and N7− clusters

Ab initio molecular orbital theory and density functional theory have been used to study nine isomers of N₇ ionic clusters with low spin at the HF/6-31G*, MP2/6-31G*, B3LYP/6-31G*, and B3LYP/6-311(+)G* levels of theory. All stationary points are examined with harmonic vibrational frequency analyses. Four N₇ ⁺ isomers and five N₇ ⁻ isomers are determined to be local minima or very close to the minima on their potential-energy hypersurfaces, respectively. For N₇ ⁺ and N₇ ⁻, the energetically low lying isomers are open-chain structures (C _{2 v} and C _{2 v} or C₂). The results are very similar to those of other known odd-number nitrogen ions, such as N₅ ⁺, N₉ ⁺, and N₉ ⁻, for which the open-chain structures are also the global minima. This research suggests that the N₇ ionic clusters are likely to be stable and to be potential high-energy-density materials if they could be synthesized. Received: 16 July 2001 / Accepted: 8 October 2001 / Published online: 21 January 2002     

Unified analytical treatment of one-electron two-center integrals with noninteger n Slater-type orbitals

A unified treatment of one-electron two-center integrals over noninteger n Slater-type orbitals is described. Using an appropriate prolate spheroidal coordinate system with the two atomic centers as foci, all the molecular integrals are expressed by a single analytical formula which can be readily and compactly programmed. The analysis of the numerical performance of the computational algorithm is also presented. Received: 1 April 1999 / Accepted: 2 July 1999 / Published online: 2 November 1999     

Global cluster geometry optimization by a phenotype algorithm with Niches: Location of elusive minima,and low-order scaling with cluster size

The problem of global geometry optimization of clusters is addressed with a phenotype variant of the method of genetic algorithms, with several novel performance enhancements. The resulting algorithm is applied to Lennard–Jones clusters as benchmark system, with up to 150 atoms. The well-known, difficult cases involving nonicosahedral global minima can be treated reliably using the concept of niches. The scaling of computer time with cluster size is approximately cubic, which is crucial for future applications to much larger clusters. © 1999 John Wiley & Sons, Inc. J Comput Chem 20: 1752–1759, 1999     

Recognition determinants in a T4 ← G4 mutant derived from a 5′-GCGTGGGCGT-3′ oligomer in a zinc finger 268–DNA complex.

The 5′-GCGTGGGCGT-3′ (T4) oligomer found in the zinc finger 268–DNA complex was mutated into the sequence 5′-GCGGGGGCGT-3′ (G4). A 3D model was constructed from the T4 sequence using an X-ray structure as a template. Molecular dynamics simulations were used to test the thermal stability of the model. A 500-ps trajectory was obtained for the fully charged complex in water using GROMOS87. The complex and the G4 sequence are found to have dynamically stationary behavior. Comparisons made with a previous T4 sequence molecular dynamics simulation show both systems have similar thermal stability. The structure of DNA appears to be maintained by its global interactions with the protein although the mutated site does not contribute with its full potential for binding. The protein structure shows some small differences compared to the T4 simulation. The simulation provided evidence for the role of a chloride ion interacting with the protein and helping in the recognition process. Received: 21 June 1999 / Accepted: 19 October 1999 / Published online: 14 March 2000     

Local symmetry and chirality of molecular faces

The concept of local symmetry has been applied to faces of planar sites such as carbon–carbon double bonds and aromatic rings with the principal results being as follows. The two faces of a planar site must have the same local symmetry group. This local symmetry group is limited to the polar point groups. For cyclic compounds, directed cycles must have chirotopic faces although the reverse is not necessarily true: chirotopic faces are possible for both directed and undirected cycles. A number of examples are provided to illustrate these results. Received: 30 June 1999 / Accepted: 4 October 1999 / Published online: 19 April 2000     

Ab initio configuration interaction study on electronically excited 4-dimethylamino-4′-cyanostilbene

Ab initio configuration interaction calculations have been performed to examine the electronic structures of both trans-4-dimethylamino-4′-cyanostilbene (DCS) and four types of perpendicularly twisted DCSs, trans-DCS is predominantly excited into the S₁ state out of low-lying excited states. The S₁ state is an intramolecular charge-transfer (ICT) state in which the dipole moment is about twice as large as that in S₀. The excited DCS at the 4-dimethylanilino twisted conformation, which becomes S₁ in polar solvents, has a very much larger dipole moment than that in S₁ to trans-DCS. This means that the geometrical structure of the twisted ICT (TICT) is the 4-dimethylanilino twisted form, not the dimethylamino twisted one which is well know from the TICT structure of 4-dimethylaminobenzonitrile. Received: 16 December 1998 / Accepted: 19 March 1999 / Published online: 9 September 1999     

Unitary perturbation theory: a generalization of two-by-two rotations

A generalization of the two-by-two rotation technique is proposed, permitting a whole row (column) of the matrix to be treated simultaneously. The method is based on the explicit analytical evaluation of the matrix exponent representing a symmetric combination of the individual rotations. Besides constructing the unitary transformation matrices, a new orthogonalization algorithm is also proposed. The resulting “unitary perturbation theory” and orthogonalization method may be useful in different areas. Received: 15 November 1999 / Accepted: 30 January 2000 / Published online: 19 April 2000     

Structure and stability of gold-substituted diborane, boranes, and borohydride ions

Pseudopotential ab initio calculations were performed for species of the type BH _n (AuPH₃) _m ^k , where n+m=3 or 4, and the charge k is −2,…,+1. Some derivatives of these and diaurated diboranes were also studied. The structural data agree well with the available experimental evidence. Factors affecting the stability of these systems, including the role of aurophilic attraction, are discussed. The singly charged anions and the diaurated diboranes are predicted to be the most stable members of these series. Received: 22 January 1999 / Accepted: 2 June 1999 / Published online: 4 October 1999     

A small-core multiconfiguration Dirac–Hartree–Fock-adjusted pseudopotential for Tl – application to TlX (X = F, Cl, Br, I)

 A relativistic pseudopotential of the energy-consistent variety simulating the Tl²¹⁺ (1s– 4f) core has been generated by adjustment to multiconfiguration Dirac–Hartree–Fock data based on the Dirac–Coulomb–Breit Hamiltonian. Valence ab initio calculations using this pseudopotential have been performed for atomic excitation energies and for spectroscopic constants of the X0⁺ and A0⁺ states of TlX (X = F, Cl, Br, I). Comparison is made to experiment and to four-component density functional results. Received: 22 June 1999 / Accepted: 5 August 1999 / Published online: 15 December 1999     

MRINDO/S-CI calculation of the electronic spectra of azines

An MRINDO/S calculation completed by singly excited configuration interaction was performed on the azines vic-triazine, as-triazine, vic-tetrazine, and as-tetrazine. The importance of outer (Rydberg) atomic orbitals is stressed and it is found that a few transitions of these azines lead to an excited state with considerable Rydberg character. Ionization potentials of the azines are also interpreted. Received: 23 June 1998 / Accepted: 27 July 1999 / Published online: 15 December 1999     

Non adiabatic vibrational resonances in molecules containing low barrier moieties: a classical dynamics study

 We discuss the classical dynamics of a CH-stretching and an OH-stretching vibration coupled to a hindered rotation around a CC (OC) bond of a CH₃ group or an OH group. Our model is based on a two-dimensional system, in which zero angular momentum is assumed. The model is further simplified by considering only kinetic coupling between the CH (OH) stretching and the hindered rotation. Through numerical calculations, a new set of states is found, which originates from n:1 resonances between the internal rotation frequency and the stretching frequency, n being associated to the order of symmetry (n = 3 and 6 for the cases investigated). We also present a perturbative approach based on the Lie series method, which provides insight into these nonadiabatic states. Received: 28 April 1999 / Accepted: 21 September 1999 / Published online: 15 December 1999     

Structure and stability of hypervalent NLi n Na2 (n = 1–4) and related species at density functional theory level

A number of configurations of NLi _n Na₂ (n = 1–4) species were optimized using the B3LYP–density functional theory method; the 6-31G^* basis set was used in this calculation. In order to study all possible dissociation energies, some related species such as NLi₂Na, NLi _n (n = 1–4), Li _n (n = 1, 2) and Na _n (n = 1, 2) were also considered. Optimizations of these species were followed by fundamental frequency calculations at the same level. Global minima of these species were shown to adopt C _{2 v} (NLi₄Na₂, NLi₂Na₂), D _{3 h} (NLi₃Na₂) and C _s (NLiNa₂ and NLi₂Na) configurations. All possible dissociation energies were obtained. Received: 30 November 1998 / Accepted: 15 October 1999 / Published online: 14 March 2000     

Plane-wave calculations applied to conjugated polymers

Density functional calculations using pseudopotentials and a plane-wave basis set are applied to study the geometry and the electronic structure of conjugated polymers consisting of heterocyclic aromatic rings. This article focuses on the computational methods. The influence of the pseudopotentials on the structural and electronic properties is studied. The rates of convergence of these properties with respect to the basis set size and the density of sampling points for the Brillouin zone integration are considered. The effects of using different exchange–correlation potentials (local density or generalized gradient approximations) are examined. It is shown that smooth norm-conserving pseudopotentials used for calculations on conjugated polymers lead to converged results with a moderately sized basis set. Received: 20 August 1999 / Accepted: 23 November 1999 / Published online: 19 April 2000     

Conformational profile of 1-aminocyclopropanecarboxylic acid

1-Aminocyclopropanecarboxylic acid (Ac₃c) is a constrained α amino acid residue that exhibits peculiar conformational characteristics. The aim of the present study is to provide a deeper understanding of these features to be used as guidance to decide when to choose Ac₃c as a building block for the design of peptide and protein surrogates. The whole Ramachandran plot of the Ace-Ac₃c-NCH₃ dipeptide was investigated at the Hartree–Fock level using a 6-31G(d) basis set and the most favorable structures were assessed on this surface by energy minimization. These results were subsequently used as a reference to generate specific molecular mechanics parameters for Ac₃c compatible with the parm94 set of the AMBER force field. The effect of water as a solvent on the conformational profile of the dipeptide was also assessed using the Miertus–Scrocco–Tomasi self-consistent reaction-field model at the Hartree–Fock level using a 6-31G(d) basis set and using the AM1 semiempirical method. The conformational profile of the Ac₃c dipeptide can be characterized by two symmetric low-energy regions for values of φ around ±80° with a wide range of values for ψ ranging from −40 to 180°, with the lower areas located at low values of ψ. Solvent effects do not alter the features of the conformational map, but a shift of the two absolute minima to (φ, ψ) values near (±90°, 0°) can be observed. These results are in accord with all experimental evidence and with the known tendency of Ac₃c to induce β-turn conformations in peptides. Received: 19 March 1999 / Accepted: 10 June 1999 / Published online: 9 September 1999     

Computation of the influence of chemical substitution on the pK a of pyridine using semiempirical and ab initio methods

The physical properties of chemicals are strongly influenced by their protonation state, affecting, for example, solubility or hydrogen-bonding characteristics. The ability to accurately calculate protonation states in the form of pK _as is, therefore, desirable. Calculations of pK _a changes in a series of substituted pyridines are presented. Computations were performed using both ab initio and semiempirical approaches, including free energies of solvation via reaction-field models. The selected methods are readily accessible with respect to both software and computational feasibility. Comparison of calculated and experimental pK _as shows the experimental trends to be reasonably reproduced by the computations with root-mean-square differences ranging from 1.22 to 4.14 pK _a units. Of the theoretical methods applied the best agreement occurred using the second-order M?ller–Plesset/6-31G(d)/isodensity surface polarized continuum solvation model, while the more computationally accessible Austin model 1/Solvent model 2 (SM2) approach yielded results similar to the ab initio methods. Analysis of component contributions to the calculated pK _as indicates the largest source of error to be associated with the free energies of solvation of the protonated species followed by the gas-phase protonation energies; while the latter may be improved via the use of higher levels of theory, enhancements in the former require improvements in the solvation models. The inclusion of alternate minimum in the computation of pK _as is also indicated to contribute to differences between experimental and calculated pK _a values. Received: 27 April 1999 / Accepted: 27 July 1999 / Published online: 2 November 1999     

Model studies of the chemisorption of hydrogen and oxygen on the Au (1 0 0) surface

 The convergence of chemisorption energy for hydrogen and oxygen on gold clusters is studied. Two theoretical approaches have been employed; wavefunction methods at the self-consistent-field second–order M?ller–Plesset level and density functional theory and the two methods are compared. Relativistic effective core potentials exploited in the former approach were developed in this work. Received: 25 October 1999 / Accepted: 21 February 2001 / Published online: 11 October 2001     

Cation π interaction between acetylcholine and the benzene ring

 Ab initio self-consistent-field second-order M?ller–Plesset perturbation theory computations including basis set superposition error and zero-point vibrational energy corrections have been performed on the complexation of benzene with the polar head of acetylcholine (ACh). The ACh–benzene complex is about 0.5 kcal/mol less stable than the corresponding tetramethylammonium (TMA)–benzene complex, with a structure a little distorted with respect to the latter. The electronic structure of ACh is little modified by the ligand. Overall, the replacement of one methyl group of TMA by the acetyl tail of ACh does not affect strongly the complexation to benzene, as far as the main interaction is concerned. Received: 1 April 1999 / Accepted: 19 October 1999 / Published online: 14 March 2000     

Does the topological approach characterize the hydrogen bond?

 The topological analysis of the electron localization function has been applied to complexes representative of the weak, medium and strong hydrogen bond. For both the weak and the medium hydrogen bonds, the number of basins in the complexes is the sum of those of the moieties. In this case, the formation of a weak or a medium hydrogen-bonded complex does not involve a chemical reaction. In the weak hydrogen bond case, the reduction of the localization domain yields two domains in the first step, which can be partitioned afterwards into valence and core domains. In contrast, for medium complexes the core–valence separation is the first event which occurs during the reduction process and therefore the complex should be considered as a single molecular species. Moreover, the analysis of the basin population variance indicates in this case a noticeable delocalization between the V(A, H) and V(B) basins. Finally, the symmetrical strong hydrogen bond has a protonated basin V(H) at the bond midpoint. Such a topology corresponds to an incomplete proton transfer and to a rather covalent bond. Received: 19 April 1999 / Accepted: 22 July 1999 / Published online: 17 January 2000