Molecular orbital study on the OH stretching frequency of the phenol dimer and its cation

Ab initio calculations were performed to investigate the structure and bonding of the phenol dimer and its cation, especially the OH stretching frequencies. Some stable structures of the phenol dimer and its cation were obtained at the Hartree–Fock level and were found to be in agreement with predictions based on spectroscopic investigations. In these dimers the phenol moieties are bound by a single OH⋯O hydrogen bond. The hydrogen bond is much stronger in the dimer cation than in the neutral dimer. The calculated binding energy of the phenol dimer in the most stable structure was 6.5–9.9 kcal/mol at various levels of calculation, compared with the experimental value of 5 kcal/mol or greater. The binding energy of the phenol dimer cation is more than 3 times (24.1–30.6 kcal/mol) as large as that of the neutral dimer. For the phenol dimer the OH stretching frequency of the proton-accepting phenol (PAP) is 3652 cm⁻¹ and that of the proton-donating phenol (PDP) is 3516 cm⁻¹; these are in agreement with observed values of 3654 and 3530 cm⁻¹, respectively. For the phenol dimer cation the OH stretching frequency of the PAP is 3616–3618 cm⁻¹ in comparison with an observed value of 3620 ± 3 cm⁻¹. That of the PDP in the dimer cation is calculated to be 2434–2447 cm⁻¹, which is 1210–1223 cm⁻¹ lower than that of the bare phenol. The large reduction in the OH stretching frequency of the PDP in the phenol dimer cation is attributed to the formation of a stronger hydrogen bond in the cation than in the neutral dimer. Received: 24 March 2000 / Accepted: 26 April 2000 / Published online: 11 September 2000     

Pseudopotential study of the rare earth monohydrides,monoxides and monofluorides

Nonrelativistic and quasirelativistic energy-adjusted pseudopotentials for fixed 4f subconfigurations of the rare earth elements La through Lu together with corresponding optimized valence basis sets have been used in SCF and CI(SD) calculations to determine the spectroscopic constants for the energetically low lying superconfigurations of the lanthanide monohydrides, monoxides and monofluorides. The experimentally observed trends in dissociation energies, bond lengths and vibrational frequencies for the ground states of the calculated superconfigurations of the monoxides and monofluorides are well reproduced. The results for the monohydrides are mainly predictions.     

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     

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     

Density functional theory gas- and solution-phase study of nucleophilic substitution at di- and trisulfides

 Density functional calculations indicate that nucleophilic substitution in the thiolate–disulfide and thiolate–trisulfide exchange reactions proceeds by an addition–elimination pathway. Solution calculations were performed using B3LYP/6-31+G* and the polarized continuum method. These solution-phase calculations indicate that for the reactions where the sulfur under attack bears a hydrogen atom, the substitution proceeds via an addition–elimination mechanism; however, when a methyl group is attached to the sulfur under attack, the S_N2 mechanism is predicted. Received: 12 October 2001 / Accepted: 28 November 2001 / Published online: 8 April 2002     

Theoretical study on structures and stability of HC2P isomers

 The structures and isomerization pathways of various HC₂P isomers in both singlet and triplet states are investigated at the B3LYP/6-311G(d,p), QCISD/6-311G(d,p) (for isomers only) and single-point CCSD(T)/6-311G(d,p)//B3LYP/6-311G(d,p) levels. At the CCSD(T)/6-311G(d,p)//B3LYP/6-311G(d,p) level, the lowest-lying isomer is a linear HCCP structure ³ 1 in the ³∑⁻ state. The second low-lying isomer has a CPC ring with exocyclic CH bonding ¹ 5 in a singlet state at 10.5 kcal/mol. The following third and fourth low-lying isomers are a singlet bent HCCP structure ¹ 1 at 20.9 kcal/mol and a bent singlet HPCC structure ¹ 3 at 35.8 kcal/mol, respectively. Investigation of the HC₂P potential-energy surface indicates that in addition to the experimentally known isomer ³ 1, the other isomers ¹ 1, ¹ 3 and ¹ 5 also have considerable kinetic stability and may thus be observable. However, the singlet and triplet bent isomers HCPC ¹ 2 and ³ 2 as well as the triplet bent isomer HPCC ³ 3 are not only high-lying but are also kinetically unstable, in sharp contrast to the situation of the analogous HCNC and HNCC species that are both kinetically stable and that have been observed experimentally. Furthermore, the reactivity of various HC₂P isomers towards oxygen atoms is briefly discussed. The results presented here may be useful for future identification of the completely unknown yet kinetically stable HC₂P isomers ¹ 1, ¹ 3 and ¹ 5 either in the laboratory or in interstellar space. Received: 5 November 2000 / Accepted: 25 November 2001 / Published online: 8 April 2002     

Role of twisting and sliding on the solvation of a stacked cytosine dimer: an ab initio study

Ab initio calculations with inclusion of correlation effects at the MP2/6-31G* level have been used to predict the interaction energy of stacked cytosine dimer (C/C) as a function of twisting and sliding in the gas phase. Systematic calculations have also been carried out on the solvation free energies of various rotated and translated C/C dimers using a polarized continuum model approach at the HF/6-31G* level with a view to probe the role of various degrees of freedom on the free energy of solvation of the C/C dimer. The interaction energy of the C/C dimer decreases upon changing from a parallel to an antiparallel conformation in the gas phase. The 180°-rotated conformation has been found to be the most stable arrangement when compared to other rotated positions. The rotated and translated dimers exhibit lower solvation free energy than the parallel conformation. The decrease in the dipole moment upon rotation from the parallel to the antiparallel conformation indicates the cancellation of charge distribution upon rotation in the z direction of one cytosine base with respect to the other. The calculation reveals that the present approach could not yield association energy, ΔΔG _Asso, in a solvent medium. This may be due to the fact that in the case of floppy molecules the contribution from translational, rotational and vibrational free energies plays a significant role in the calculation of ΔΔG _Asso. Received: 13 December 2001 / Accepted: 25 March 2002 / Published online: 13 June 2002     

Ab initio calculations with effective core potentials on trivalent lanthanide–terpyridine complexes

 The electronic structures of complexes of terpyridine (tpy) with trivalent lanthanides (Ln) were calculated using ab initio methods with effective core potentials at Hartree–Fock and post-Hartree–Fock levels of theory. The quasirelativistic large-core (with 4f electrons included in the core) pseudopotentials of the Stuttgart group were chosen for the Ln atoms. The variation of several properties of the Ln(tpy)³⁺ complexes was studied for the whole Ln series. It was shown that there was a monotonous variation for all properties (geometrical and energetic) along the Ln series, except for Mulliken charges on the metal atom. Calculations were performed on three complexes of known solid-state structure. The difference between experimental and calculated geometries is discussed; for all structures, it is found to be lower than 0.2 ?. In all cases, the relative order from one complex to another is conserved. Received: 13 September 1999 / Accepted: 3 February 2000 / Published online: 19 April 2000     

Recent applications of density functional theory calculations to biomolecules

The purpose of this overview is to highlight the broad scope and utility of current applications of density functional theory (DFT) methods for the study of the properties and reactions of biomolecules. This is illustrated using examples selected from research carried out within our research group and in collaboration with others. The examples include the hyperfine coupling constants of amino acid radicals, the use of an amino acid as a chiral catalyst for the formation of carbon–carbon bonds in the aldol reaction, hydrogen-bond mediated catalysis of an aminolysis reaction, radiation-induced protein–DNA cross-links, and the mechanism by which an antitumor drug cleaves DNA. We demonstrate that DFT-based methods can be applied successfully to a broad range of problems that remain beyond the scope of conventional electron-correlation methods. Furthermore, we show that contemporary computational quantum chemistry complements experiment in the study of biological systems. Received: 19 December 2001 / Accepted: 8 April 2002 / Published online: 4 July 2002     

A DFT study of pyramidalized alkenes: 7-oxasesquinorbornenes and 7,7′-dioxasesquinorbornenes

  DFT calculations of 7′–oxasesquinorbornenes and 7,7′-dioxasesquinorbornenes using the B3LYP/6–31G* method are reported. All the investigated structures (syn- and anti- derivatives) showed significant non-planarity of the central double bond, with the exception of those anti-derivatives possessing symmetrical structures. The influence of the replacement of the methylene groups at position 7- of the norbornene fragment with oxygen and the introduction of second and third (peripheral) double bonds and benzene rings on the molecular and electronic structures of these molecules have also been investigated. Received: 11 November 2002 / Accepted: 6 June 2002 / Published online: 29 April 2003     

A theoretical study of photoinduced electron transfer between tetracyanoethylene and arene

 Ab initio calculations have been performed to investigate the state transition in photoinduced electron transfer reactions between tetracyanoethylene and biphenyl as well as naphthalene. Face-to-face conformations of electron donor–acceptor (EDA) complexes were selected for this purpose. The geometries of the EDA complexes were determined by using the isolated optimized geometries of the donor and the acceptor to search for the maximum stabilization energy along the center-to-center distance. The correction of interaction energies for basis set superposition error was considered by using counterpoise methods. The ground and excited states of the EDA complexes were optimized with complete-active-space self-consistent-field calculations. The theoretical study of the ground state and excited states of the EDA complex in this work reveals that the S₁ and S₂ states of the EDA complexes are charge–transfer (CT) excited states, and CT absorption which corresponds to the S₀→S₁ and S₀→S₂ transitions arise from π−π^* excitation. On the basis of an Onsager model, CT absorption in dichloromethane was investigated by considering the solvent reorganization energy. Detailed discussions on the excited state and on the CT absorptions were made. Received: 30 April 2001 / Accepted: 18 October 2001 / Published online: 9 January 2002     

Density functional theory study of the mechanism of the proline-catalyzed intermolecular aldol reaction

Transition structures associated with the C-C bond-formation step of the proline-catalyzed intermolecular aldol reaction between acetone and isobutyraldehyde have been studies using density functional theory methods at the B3LYP/6-31G** computational level. A continuum model has been selected to represent solvent effects. For this step, which is the stereocontrolling and rate-determining step, four reactive channels corresponding to the syn and anti arrangement of the active methylene of the enamine relative to the carboxylic acid group of l-proline and the re and si attack modes to both faces of the aldehyde carbonyl group have been analyzed. The B3LYP/6-31G** energies are in good agreement with experiment, allowing us to explain the origin of the catalysis and stereoselectivity for these proline-catalyzed aldol reactions. Received: 2 April 2002 / Accepted: 18 July 2002 / Published online: 11 October 2002 Acknowledgements. This work was supported by research funds provided by the Ministerio de Educación y Cultura of the Spanish Government by DGICYT (project PB98–1429). All the calculations were performed on a Cray–Silicon Graphics Origin 2000 of the Servicio de Informática de la Universidad de Valencia. We are most indebted to this center for providing us with computer capabilities. Correspondence to: L. R. Domingo e-mail: domingo@utopia.uv.es     

A density functional theory study of bridging and terminal oxotitanium(IV) oligomeric and polymeric linear titanoxanes

 This work deals with theoretical investigations on the oxygen–transition metal bond in systems containing linear chains of Ti–O units. From an experimental point of view, in the recent past a number of systems containing linearly arranged Ti–O units were synthesized, in which the Ti atom is complexed with Schiff bases such as acacen and salen. The theoretical study presented here has been carried out applying the density functional theory to model compounds of these systems, in order to shed light on the interactions between the transition metal and oxygen. Calculations have been performed on Ti–O oligomers (dimers, trimers and tetramers) by means of density functional theory at the gradient-corrected level of theory, optimizing the molecular geometries. Calculations have also been performed on linear polymers of the same systems, applying periodic boundary conditions, in order to compare the results with those of oligomeric analogues. Received: 12 January 2002 / Accepted: 16 April 2002 / Published online: 5 July 2002     

Prediction of the Raman spectrum of the aqueous formate anion by a combined density functional theory and self-consistent-reaction-field study

Formate, HCOO⁻, is a small ion that can be used as a convenient model to represent general carboxylic acids as well as the terminal side chains of glutamic and aspartic amino acids in biological systems. Several ab initio techniques (Hartree–Fock and density functional theory methods) were used to study the formate anion in aqueous solution, where the solvent was treated as an electrostatic influence by means of a self-consistent-reaction-field (SCRF) method. The comparison of calculated frequencies with Raman experimental data constitutes a good test for the solvation model employed in this work. The results showed that the application of a SCRF method not only produced smaller errors but also improved the linear correlation between predicted and experimental values. This latter characteristic enables a more efficient application of a linear scaling factor, λ, which corrects the calculated frequencies. In fact, the application of λ to the values calculated for the continuum, when compared to those obtained for a vacuum, resulted in smaller root-mean-square errors of the deviations from the experimental data. Received: 15 May 2000 / Accepted: 19 June 2000 / Published online: 11 September 2000     

A thermodynamic and kinetic study of the formation of C<Subscript>20</Subscript> compounds encapsulating H,He and Ne atoms

 Binding energies of helium, neon and atomic hydrogen encapsulated inside a C₂₀ cage were calculated using an ab initio method at the B3LYP/6-31+G⋆ level of theory. The standard equilibrium constants for the reactions of noble-gas atoms going into the C₂₀ molecular cage have also been studied. The transition states for the reactions of C₂₀ with hydrogen and helium were further obtained with an ab initio method at the B3LYP/6-31+G⋆ level and the rate constants were estimated by using conventional transition-state theory. It was found that the hydrogen and helium atoms are extremely difficult to put into the C₂₀ cage. Once inside the cage, a helium atom can hardly get out, while a hydrogen atom can easily escape from the cage. The results are expected to enrich fullerene science and be helpful for fullerene applications such as storage. Received: 2 November 2002 / Accepted: 19 December 2002 / Published online: 30 April 2003 Correspondence to: R. Q. Zhang, e-mail: aprqz@cityu.edu.hk Acknowledgements. The work described in this paper was jointly supported by a grant from the City University of Hong Kong (project no. 7001222) and a grant from the Research Grants Council of the Hong Kong Special Administrative Region, China (project no. 9040633/CityU, 1011/01P].     

A density functional theory study of the conformational properties of 1,2-ethanediamine: protonation and solvent effects

 The structures and the conformational energies of nonprotonated, monoprotonated and diprotonated 1,2-ethanediamine have been investigated through density functional theory. The relative performance of local and gradient-corrected functionals is discussed. The existence of hydrogen-bond formation has been determined with electron localisation function calculations. Proton affinities for nonprotonated and monoprotonated 1,2-ethanediamine have been calculated and are in agreement with experimental data. The influence of solvation has been accounted for through the self-consistent isodensity polarisable continuum model. The results for the nonprotonated conformers show that solvation stabilises those conformers which have the lone pair in an antiperiplanar conformation. Solvation of the monoprotonated conformer stabilises significantly the “anti” conformation, which is unstable in the gas phase. For the di-protonated species, solvation stabilises slightly the gauche conformer, which is unstable in the gas phase. Received: 28 September 1999 / Accepted: 2 May 2000 / Published online: 27 September 2000     

Aconityl-derived polymers for biomedical applications. Modeling study of cis–trans isomerisation

 Soluble polymers have been prepared that are designed to undergo enhanced rates of hydrolysis at pH values less than that observed in blood circulation. The degradable element in the polymer mainchain is derived from cis-aconityl acid and is defined by a carboxylic acid pendent functionality (C-4) that is cis across a double bond to an amide at C-1 in the polymer mainchain. While degradation studies in vitro have confirmed these polymers do undergo enhanced rates of degradation at acidic pH values, there is also increasing evidence that during the degradation process the double bond isomerises to the trans configuration and thus prevents the full degradation of a polymer. From a molecular modelling perspective we are seeking to understand the propensity for this cis–trans isomerisation and the mechanism of this cis–trans isomerisation is discussed. Received: 29 April 2002 / Accepted: 6 September 2002 / Published online: 14 February 2003     

Molecular dynamics study of the tautomeric equilibrium in the 4-nitro- and 2,4,6-trichloro derivatives of 2-(N,N-dialkyloaminomethyl)phenol

 Molecular dynamics thermodynamic integration (MDTI) method and quantum chemical calculations at the density functional theory B3LYP 6-31+(d,p) level, which included the Tomasi model of the solvent reaction field, were applied to study the tautomeric equilibrium of Mannich base in methanol solution. The values obtained for the free-energy difference are in good agreement with experimental data. However, the results from quantum mechanical calculations were not as good as the results of MDTI simulations owing to inappropriate treatment of intermolecular hydrogen bonds between the solute molecule and the first shell of solvent molecules in the Tomasi model of the solvent reaction field. The radial distribution functions between solute atoms and solvent atoms confirmed the formation of hydrogen bonds between the solute molecule and surrounding methanol molecules and indicated that the zwitterionic form is associated more with an organized solvent structure at the level of the first solvation shell than is the molecular form. Received: 26 April 2002 / Accepted: 9 September 2002 / Published online: 31 March 2003     

A density functional theory study of a concerted mechanism for proton exchange between amino acid side chains and water

 A concerted mechanism for proton exchange between water and the amino acid side chains of cysteine, serine, arginine and glutamic acid has been investigated with hybrid density functional theory. The models used include, besides the amino acid side chain, a number of water molecules ranging from one to five in some cases. The modeling of the amino acids without their backbones is shown to be an excellent approximation. Long-range polarization effects were incorporated through a dielectric cavity method allowing a better comparison to existing measurements for free amino acids in water. The barriers converge rather fast with the number of water molecules for all the present amino acids and the converged values are in reasonable agreement with experiments with discrepancies in the range 2–6 kcal/mol. The dielectric effects were found to be small for all systems except cysteine, where there is a lowering of the barrier by 3–5 kcal/mol. The transition states for these concerted pathways form rings in which the separated charges can be stabilized. Received: 25 October 1999 / Accepted: 5 April 2000 / Published online: 21 June 2000