Ab initio studies of NMR chemical shifts for calix[4]arene and its derivatives

Ab initio calculations are performed for the calix[4]arene (1) and its derivatives (2 and 3), in this study. ¹H and ¹³C NMR measured spectral data given in our previous work are used to elucidate the structures of the prepared calix[4]arenes (1–3). The molecular geometry and chemical shift are calculated by using ab initio calculations based on the Hartree-Fock (HF) and the density functional theory (DFT) in the ground state. The results obtained from both methods are in agreement with the experimental results. The results of molecular geometry and chemical shifts show that DFT approach is closer to the experimental data than HF method.     

Pentapnictogen heterocyclic monoanions: Structure,stability, and aromaticity

Inorganic planar ring-shape molecules with 4n + 2 π electrons are always the focus of experimental synthesis and theoretical research due to their potential aromaticity and stability. In this work, the whole series of five-membered heterocycle monoanions X _nY_5-n⁻ (X, Y = group 15 elements; n = 1-4) were thoroughly investigated by means of density functional theory calculations. They all have large formation energies and HOMO-LUMO gap energies, suggesting the potential thermodynamic and kinetic stability. Their aromaticities are comparable to that of typical aromatic hydrocarbons. Their thermal stabilities were firmly established by the ab initio molecular dynamics simulations. As most of them are predicted for the first time, their various spectra were simulated for experimental characterization. Furthermore, we demonstrate that these five-membered cyclic anions can be employed as η⁵-ligand to construct novel all-inorganic metallocenes, which may serve as the building blocks of low-dimensional nanomaterials.     

The Gaussian and augmented-plane-wave density functional method for ab initio molecular dynamics simulations

A new algorithm for density-functional-theory-based ab initio molecular dynamics simulations is presented. The Kohn–Sham orbitals are expanded in Gaussian-type functions and an augmented-plane-wave-type approach is used to represent the electronic density. This extends previous work of ours where the density was expanded only in plane waves. We describe the total density in a smooth extended part which we represent in plane waves as in our previous work and parts localised close to the nuclei which are expanded in Gaussians. Using this representation of the charge we show how the localised and extended part can be treated separately, achieving a computational cost for the calculation of the Kohn–Sham matrix that scales with the system size N as O(NlogN). Furthermore, we are able to reduce drastically the size of the plane-wave basis. In addition, we introduce a multiple-cutoff method that improves considerably the performance of this approach. Finally, we demonstrate with a series of numerical examples the accuracy and efficiency of the new algorithm, both for electronic structure calculations and for ab initio molecular dynamics simulations. Received: 15 December 1998 /Accepted: 18 February 1999 /Published online: 14 July 1999     

Maximum hardness in P6 isomers

Parr and Chattaraj proposed a principle of maximum hardness for stable molecular structures. Pearson and Palke used ab initio SCF MO calculations for ammonia and ethane to demonstrate the operation of the principle. In this paper, we present ab initio SCF MO results for five isomeric forms of the homoatomic P⁶ cluster as further support for the principle of maximum hardness. © 1994 John Wiley & Sons, Inc.     

Novel pentacoordinated bridged silicon anions

Both ab initio and semiempirical electronic structure calculations are used to investigate the molecular and electronic structures and eneregetic stabilities of an unusual bridged compound with the general formula [Y? SiH₃? X? SiH₃? Y]^?, with Y = H or F and X = H, CH₃, NH₂, OH, F, or Cl. Most of these bridged anions are quite stable relative to YSiH₃ + XSiH₃Y^?, and the stability is predicted to increase considerably when Y = H is replaced with Y = F.     

Ab initio model potential and molecular dynamics simulation of Ag6 clusters

We present an approach to generate a model potential with parameters fitted to ab initio energetic surfaces. The potential includes two-, three- and four-body terms. Each of them consists of an exponential exchange and dispersion terms. The analytical form of the latter was taken from perturbation theory up to fourth order. We illustrate the present approach by constructing an ab initio model potential for the Ag₆ cluster. A molecular dynamics simulation using this potential reveals interesting features in the isomerization of the C _2v structure. A two step isomerization transition is observed: First, at temperatures around 350 K, the cluster structures fluctuate between two-dimensional isomers. At higher temperatures (450 K), fast transitions occur between two- and three-dimensional cluster configurations.     

The role of isomerism and medium effects on stability of anions of formo- and thioformohydroxamic acid

The anionic forms of formo- and thioformohydroxamic acids have been analyzed for their relative stabilities and barriers for interconversion between the tautomeric forms employing ab initio and DFT methods. The deprotonation affinities and pK_a values are evaluated to differentiate the various deprotonation processes. The effect of medium on deprotonation behavior is analysed using Tomasi’s PCM model and examining free energy changes of deprotonation from isolated molecules, molecule–water aggregates and subsequently from anion–water aggregates in the gas phase and aqueous phase respectively. Variation of geometrical parameters, charges, electron delocalizations, intramolecular H-bonding and relative stabilities upon water aggregation of the anions all point towards NH deprotonation as the most favored process.     

Comparative Study of the Structure of Rhodanine, Isorhodanine, Thiazolidine-2,4-dione, and Thiorhodanine

Ab initio (HF and MP2 level) and semiempirical (AM1, PM3, MNDO) calculations on the relative stabilities and structures of the potential tautomeric forms of rhodanine, isorhodanine, thiazolidine-2,4-dione, and thiorhodanine are reported. Ab initio calculations predict that the thiooxo, oxothio, dioxo, and dithio tautomers are the most stable. These results correspond to the known experimental data. Infrared spectra of the investigated compounds were recorded for the region 4000-150 cm^-1, and the characteristic bands were compared with ab initio calculated frequencies at the HF/3-21G^(*)* level.     

The isomeric structures of SiH2LiF

The structures of four isomeric forms of the model “silylenoid” SiH₂LiF have been investigated by ab initio molecular orbital theory. The two most stable forms are suggested to be the SiH₂Li⁺F^? ion pair and the H₂Si : FLi complex, analogous to the similar structures previously found for carbenoids. Two further species, a H₂Si : LiF complex and the “classical” (tetrahedral) SiH₂LiF, are also local minima on the potential energy surface, but are higher in energy.     

C36填充单壁碳纳米管的结构和电子性质

The structures and electronic properties for C36 encapsulated in four single-wall armchair carbon nanotubes (C36@(n,n), n=6-9) were calculated using ab initio self-consistent field crystal orbital method based on density functional theory. The calculations show that the interwall spacing between the carbon nanotube and C36 plays an important role in the stabilities of resultant structures. The optimum interwall spacing is about 0.30 nm and the tubes can be considered as inert containers for the encapsulated C36. The Fermi levels and relative position of energy bands also have something to do with the interwall spacing. The shifts of Fermi level and C36-derived electron states modulate the electron properties of these structures. The extra electrons fill the bands of C36@(8,8) with the optimum interwall spacing almost in a rigid-band manner.     

Molecular orbital study of the bridge bonding in an electron deficient molecule [(CH3)2ALH]2

The electronic distribution in the AlH₂Al bridge of the dimethyl aluminium hybride dimer was computed through ab initio SCF calculation. Comparison with diborane shows an increased role of the ionic Al⁺H ₂ ^2– Al⁺ structures with respect to the usual covalent three-center bonds.     

Quantum mechanic study of hydrogen chemisorptions on nanocluster vanadium surface

In the present investigation, we have employed the adsorption of H-H at the bcc site of V (100) with use of an ab initio method. The most stable adsorption configuration has been found on transition metal surface with chemisorption energies. Although similar in type and energy, the adsorption on the V (100) surface shows a markedly different optimized geometry. The calculations have performed for small clusters representing three adjacent metal sites. Upon the adsorption, the molecule forms strong covalent bonds with the surface, whereupon the structure of nearby single H-H and H-V bonds change at various positions of top, bridge, and center sites in this model. We have predicted the existence of a new ordered structure comparable in stability to one proposed previously. We confirm the preference of the top approach of adsorption configuration suggested by experiment. Adsorption of H₂ from the top site goes through the same from the bridge and center sites, but the former has a higher energy.     

Linear Free‐Energy Relationships between a Single Gas‐Phase Ab Initio Equilibrium Bond Length and Experimental pKa Values in Aqueous Solution

Remarkably simple yet effective linear free energy relationships were discovered between a single ab initio computed bond length in the gas phase and experimental pK_a values in aqueous solution. The formation of these relationships is driven by chemical features such as functional groups, meta/para substitution and tautomerism. The high structural content of the ab initio bond length makes a given data set essentially divide itself into high correlation subsets (HCSs). Surprisingly, all molecules in a given high correlation subset share the same conformation in the gas phase. Here we show that accurate pK_a values can be predicted from such HCSs. This is achieved within an accuracy of 0.2 pK_a units for 5 drug molecules.     

Resonant Ionic,Covalent Bond,and Steric Characteristics Present in 1Σu+ States of Li2

The molecular bonding in the excited states of the alkali dimers involves the resonant ionic, covalent bond and steric interactions. We show here the case of the ¹Σ_u⁺ states of Li₂ by ab initio calculation. These interactions as functions of the internuclear distance lead to complex potential energy curves, providing an important application for high resolution laser spectroscopy. The spectroscopic constants for the 4 and 5 ¹Σ_u⁺ states are obtained for the first time.     

A theoretical study of spin level crossing induced by an external magnetic field of ring molecule magnet models

The dependence of the magnetization of model systems on an external magnetic field has been investigated. An ab initio path integral Monte Carlo method is used to study the spin level crossing phenomena of molecules with ring structures such as those in the ferric wheel [Fe(OMe)₂(O₂CCH₂Cl)]₁₀. The ab initio treatment is essential to calculate the magnetization in a system with a large contribution from next-neighbor interactions. A possible use as a molecular device for switching or molecular recognition is suggested.     

Electronic transition moment with spin‐orbit coupling of the molecular ion KRb+

By using the electronic wave functions obtained from an ab initio calculation, including the spin‐orbit coupling, the electronic transition moments have been investigated for two bound states of symmetry Ω = 1/2 and Ω = 3/2 of the molecular ion KRb⁺. Based on a canonical functions approach for the determination of the vibrational wave functions, the matrix elements have been calculated for the bound states considered for v = 0, 10, 20 with v′‐ v = 0, 1, 2, …, 6; by using the same canonical approach, the eigenvalues and abscissas of the corresponding turning points (r_min and r_max) have been investigated for these states that obtained from a theoretical ab initio calculation up to v = 105. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Soft Scorpionate Anions as Platforms for Novel Heterocycles

Soft scorpionates have thus far been seen mainly as a family of ligands. Their chemistry is extended here to the production of novel cationic macrocycles using dihaloalkanes. By replacing the dihaloalkanes with mild oxidising agents (NO⁺, I₂) we obtain two unique polycyclic heterocycles. The mechanism which leads to the formation of these polycyclic heterocycles is investigated using ab initio DFT calculations.     

Toward ab initio refinement of protein X-ray crystal structures: interpreting and correlating structural fluctuations

The refinement of protein crystal structures currently involves the use of empirical restraints and force fields that are known to work well in many situations but nevertheless yield structural models with some features that are inconsistent with detailed chemical analysis and therefore warrant further improvement. Ab initio electronic structure computational methods have now advanced to the point at which they can deliver reliable results for macromolecules in realistic times using linear-scaling algorithms. The replacement of empirical force fields with ab initio methods in a final refinement stage could allow new structural features to be identified in complex structures, reduce errors and remove computational bias from structural models. In contrast to empirical approaches, ab initio refinements can only be performed on models that obey basic qualitative chemical rules, imposing constraints on the parameter space of existing refinements, and this in turn inhibits the inclusion of unlikely structural features. Here, we focus on methods for determining an appropriate ensemble of initial structural models for an ab initio X-ray refinement, modeling as an example the high-resolution single-crystal X-ray diffraction data reported for the structure of lysozyme (PDB entry “2VB1”). The AMBER force field is used in a Monte Carlo calculation to determine an ensemble of 8 structures that together embody all of the partial atomic occupancies noted in the original refinement, correlating these variations into a set of feasible chemical structures while simultaneously retaining consistency with the X-ray diffraction data. Subsequent analysis of these results strongly suggests that the occupancies in the empirically refined model are inconsistent with protein energetic considerations, thus depicting the 2VB1 structure as a deep-lying minimum in its optimized parameter space that actually embodies chemically unreasonable features. Indeed, density-functional theory calculations for one specific nitrate ion with an occupancy of 62% indicate that water replaces this ion 38% of the time, a result confirmed by subsequent crystallographic analysis. It is foreseeable that any subsequent ab initio refinement of the whole structure would need to locate a globally improved structure involving significant changes to 2VB1 which correct these identified local structural inconsistencies.