Ab initio investigation of phloroglucinol

All-electron ab initio Hartree–Fock (RHF ) calculations have been carried out to investigate the keto/enol equilibrium of phloroglucinol. The calculations predict that the enol form of phloroglucinol, 1,3,5-benzenetriol, is by far the most stable of the two. This is confirmed by NMR spectra taken on phloroglucinol. A comparison of the keto enol form transformation of phloroglucinol with that of the phenol system shows that the keto form of phloroglucinol, 1,3,5-cyclohexanetrion, is more abundant in the phloroglucinol system, and the keto form of phenol, 2,4-cyclohexadien-1-on, in the phenol system. © 1993 John Wiley & Sons, Inc.     

Ab initio investigation of structure and cohesive energy of crystalline urea

The structure and cohesive energy of crystalline urea have been investigated at the ab initio level of calculation. The performance of different Hamiltonians in dealing with a hydrogen-bonded molecular crystal as crystalline urea is assessed. Detailed calculations carried out by adopting both HF and some of the most popular DFT methods in solid-state chemistry are reported. Local, gradient-corrected, and hybrid functionals have been adopted: SVWN, PW91, PBE, B3LYP, and PBE0. First, a 6-31G(d,p) basis set has been adopted, and then the basis set dependence of computed results has been investigated at the B3LYP level. All calculations were carried out by using a development version of the periodic ab initio code CRYSTAL06, which allows full optimization of lattice parameters and atomic coordinates. With the 6-31G(d,p) basis set, structural features are well reproduced by hybrid methods and GGA. LDA gives lattice parameters and hydrogen-bond distances that are too small relative to experiment, while at the HF level the opposite trend is observed. Results show that hybrid methods are more accurate than HF and both LDA and GGA functionals, with a trend in the computed properties similar to that of hydrogen-bonded molecular complexes. When BSSE and ZPE are taken into account, all methods, except LDA, give computed cohesive energies that are underestimated with respect to the experimental sublimation enthalpy. Dispersion energy, not properly taken into account by DFT methods, plays a crucial role. Such a deficiency also affects dramatically the computed crystalline structure, especially when large basis sets are adopted. We show that this is an artifact due to the BSSE. Indeed, with small basis sets the BSSE gives an extra-binding that compensates for the missing dispersion forces, thus yielding structures in fortuitous agreement with experiment.     

Ab initio stochastic optimization of conformational and many-body degrees of freedom

Moderate to large size molecules in solution have complex energy surfaces due to intramolecular (conformational) and intermolecular (many-body) interactions. The first principles Monte Carlo (FPMC) method, previously shown to effectively locate minimum-energy structures for systems with only many-body complexity, has been extended to address conformational flexibility by adding three new Monte Carlo move types. The primary advantage of the FPMC method is the ability to efficiently locate minimum energy structures of molecules with conformational flexibility in the presence of explicit solvent molecules using highly accurate quantum chemical calculations. The additions to FPMC were validated by studying conformers of glycerol, glyceraldehyde, and a large humic acid monomer unit. The structure of glyceraldehyde in the presence of one and two water molecules was also explored to demonstrate the power of FPMC to study systems with both conformational and many-body degrees of freedom.     

Ab initio investigation of the electronic structure of malonic dialdehyde derivatives

An ab initio quantum chemical investigation is performed for a series of ligands of Β-diketonate metal complexes: neutral and anionic forms of malonic dialdehyde and its nitrous analogs. The nature and sequence of molecular orbitals are established, and the influence of the basis set used on the results of electronic structure calculations of the compounds are analyzed. The electronic effects of oxygen substitution by the NH group are analyzed. The results are compared with the photoelectron spectroscopy data of the ligands. Translated fromZhurnal Strukturnoi Khimii, Vol. 38, No. 6, pp. 1061–1066, November–December, 1997.     

Ab initio calculations of structure and stability of small boron nitride clusters

Clusters of boron nitride B_xN_x (x = 1–4, 12, 15, 30) were investigated by the Hartree-Fock and density functional methods using the 6-31G* basis. It was found that linear, cyclic, and shell structures are stable against minor deformations of the B_xN_x cluster. Inclusion of electron correlation in calculation markedly changes the electron density distribution and the structure of the clusters.     

Ab initio calculations of many-body energy expansion in LiF− clusters

The effects of the basis-set size on many-body energy expansion in LiF^? clusters are investigated and correlated with previously reported values on LiCl^? analogs. Coulomb and non-Coulomb energies in LiF^? at different configurations are also examined. Although at the minimal STO -3G basis V^na(3, 4) and V^na(4, 4) nonadditivity terms were the smallest in the D₃h configuration, they were the largest at the extended 6-311 ++G basis. V(m, n) terms where m = n ≥ 3 were found to be playing a small role in the chemistry and physics of LiF^? clusters compared with V(3, n) terms in LiCl^? clusters.     

Ab initio polypeptide structure prediction

The biological activity of a polypeptide strongly depends on its 3D structure. Ab initio prediction of the native structure from the sequence of amino acids has long motivated the development of an optimum energy model such that interactions present in the native conformation are stronger than those present in nonnative conformations and of algorithms capable of finding the basin of lowest free energy among an astronomically large number of possible conformations. Despite recent progress in our understanding of the factors responsible for both polypeptide stability and formation, computer simulations of polypeptide models are still far from being practical software tools for biologists. In this work, state-of-the-art computer simulations aimed at ab initio structure prediction in aqueous solution are reviewed and their strengths and weaknesses are highlighted. Received: 23 June 1999 / Accepted: 20 September 1999 / Published online: 15 December 1999     

Ab initio investigations of structure and stability of the LiBeF3 molecule

Ab initio calculations of the potential energy surface of LiBeF₃ have been performed using the basis set of Roos and Siegbahn. The extremum and saddle points were made more precise with Huzinaga-Dunning basis sets in double-and triple-zeta contractions The “bidentate” structure (symmetry group C_2v) is found to have the lowest energy and is much more advantageous than the others, and the LiBeF₃ molecule turns out to be rigid with respect to migration of the cation around the anion. The calculated internuclear distances and the energy of complex formation are in agreement with experimental values within 0.03 Å and 2 kcal/mole. The results are compared with similar ab initio data for LiBeH₃ and LiNO₃.     

Ab initio investigation of the electronic and geometric structure of magnesium diboride, MgB2

Employing multireference variational (MRCI) and coupled cluster (CC) methods combined with quadruple-zeta quality correlation-consistent basis set, we have studied 36 states of the magnesium diboride (MgB(2)) molecule as well as 17 states of the experimentally unknown diatomic MgB. For all states of MgB(2), we report geometries, atomization energies, and dipole moments, while for the first 5 states, potential energy profiles have been also constructed. The ground state is formally of (1)A(1) V-shaped symmetry with an atomization energy of 108.1(109) kcal/mol at the MRCI(MRCI + Davidson correction) level. The first excited state ((3)B(1)) is less than 1 kcal/mol above the X(1)A(1) state, with the next state of linear Mg-B-B geometry (b(3)Sigma(-)) located 10 kcal/mol higher. In all states, bent or linear, the bonding is complicated and unconventional because of the extraordinary bonding agility of the boron atom(s).     

Ab initio study on the stability,geometry and electronic structure of the cyclopropenyl system

Results of an LCAO-MO-SCF investigation into the stability and geometry of the cyclopropenyl cation (C₃H₃⁺), anion (C₃H₃^?) and radical (C₃H₃^o) are presented. By independently varying the two relevant bond angles, the shape of the potential energy curves in the corresponding two-parameter space for these three species has been obtained. It is found that the cation is most stable in the D_3h nuclear configuration, while the anion has minimum energy in the C_s symmetry. In the specific case of the C₃H₃ radical, which exhibits an orbital, as well as spin-degeneracy, in the D_3h configuration, a strong Jahn-Teller effect is observed, leading to estimates for the non-symmetrical equilibrium configuration at C_2v and for the distortion energy of 12 kcal/mole from the D_3h symmetry. In terms of the population analysis and the contour diagrams, the electronic charge distribution has also been studied for these species in their most stable configurations.     

Ab initio investigation of tautomeric stability,molecular structure,and internal rotation of methylphosphonic dicyanide,methoxydicyanophosphine, and their isocyano analogs

The equilibrium geometric parameters and structures of the transition states of internal rotation for MeP(O)(CN)₂, McOP(CN)₂, and their isocyano analogs, MeP(O)(NC)₂ and MeOP(NC)₂, have been calculated by theab initio SCF method and with inclusion of electron correlation effects according to the second-order Muuller-Plesset perturbation theory (MP2). At both levels the 6-31G* basis set has been used. The estimation of relative stability of these tautomeric forms depends largely on the calculation level. The total energies of the cyanides calculated by the MP2 method are 25–30 kcal mol^–1 lower than those of the corresponding isocyanides. The oxo-tautomeric forms containing four-coordinate phosphorus are 15–25 kcal mol^–1 more stable than the three-coordinate phosphorus aci-derivatives. The internal rotation potential curves of the aci-forms are characterized by a deep minimum for thetrans-arrangement of the methoxy group and phosphorus lone electron pair. Two additional less clearly pronounced minima are located symmetrically on both sides of the weak maximum, which corresponds to thecis-arrangement. The equilibrium oxo-form structures have a staggered configuration of the methyl group with respect to the phosphorus atom bonds.Translated from izvestiyaAkademii Nauk. Seriya Khimicheskaya, No. 5, pp. 1104–1115, May, 1996.     

Ab initio structural and vibrational investigation of sulfuric acid monohydrate

We employ ab initio methods to find stable geometries and to calculate potential energy surfaces and vibrational wavenumbers for sulfuric acid monohydrate. Geometry optimizations are carried out with the explicitly correlated coupled-cluster approach that includes single, double, and perturbative triple excitations (CCSD(T)-F12a) with a valence double-ζ basis set (VDZ-F12). Four different stable geometries are found, and the two lowest are within 0.41 kJ mol(-1) (or 34 cm(-1)) of each other. Vibrational harmonic wavenumbers are calculated at both the density-fitted local spin component scaled second-order M?ller-Plesset perturbation theory (DF-SCS-LMP2) with the aug-cc-pV(T+d)Z basis set and the CCSD-F12/VDZ-F12 level. Water O-H stretching vibrations and two highly anharmonic large-amplitude motions connecting the three lowest potential energy minima are considered by limiting the dimensionality of the corresponding potential energy surfaces to small two- or three-dimensional subspaces that contain only strongly coupled vibrational degrees of freedom. In these anharmonic domains, the vibrational problem is solved variationally using potential energy surfaces calculated at the CCSD(T)-F12a/VDZ-F12 level.     

Ab initio investigation of ammonia-borane complexes for hydrogen storage

The structural, electronic, and thermodynamic properties of ammonia-borane complexes with varying amounts of hydrogen have been characterized by first principles calculations within density functional theory. The calculated structural parameters and thermodynamic functions (free energy, enthalpy and entropy) were found to be in good agreement with experimental and quantum chemistry data for the crystals, dimers, and molecules. The authors find that zero-point energies change several H2 release reactions from endothermic to exothermic. Both the ammonia-borane polymeric and borazine-cyclotriborazane cycles show a strong exothermic decomposition character (approximately -10 kcal/mol), implying that rehydrogenation may be difficult to moderate H2 pressures. Hydrogen bonding in these systems has been characterized and they find the N-H bond to be more covalent than the more ionic B-H bond.     

Ab initio investigation of the electron structure in bis-Cu+ acetylene and vinylidene complexes

[Cu(-C₂H₂)₂]⁺, [Cu(-CCH₂)₂]⁺ and [Cu(-C₂H₂) (-CCH₂]⁺ complexes have been studied by the ab initio double-zeta basis set method. It has been established that all calculated compounds are stable to decomposition into two C₂H₂ molecules and Cu⁺ cation and into one C₂H₂ molecules and the respective monocomplex. Calculation results suggest the possibility of intramolecular acetylene-vinylidene rearrangement in the coordination sphere of Cu⁺.

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ab initio : [Cu(-C₂H₂)₂]⁺, [Cu(-CCH₂)₂]⁺, [Cu(-C₂H₂) (-CCH₂)]⁺. C₂H₂ Cu⁺ C₂H₂ . - Cu⁺.

     

Ab initio SCF structure investigation of β-hydroxypropionic acid and 3-aminopropionamide

The potential energy surfaces of β-hydroxypropionic acid and 3-aminopropionamide have been investigated by means of RHF /4-31G calculations. Structures, reaction paths for internal rotations, and the respective energy barriers are reported. The influence of the various intramolecular interactions on structural and energetical properties is shown and compared to the results previously obtained for β-alanine. © 1996 John Wiley & Sons, Inc.     

Ab initio investigation of the stability of Si3C3 clusters and their structural and bonding features

Various structural possibilities for Si₃C₃ clusters are investigated by ab initio calculations employing basis sets of double- and triple-zeta quality augmented by d polarization functions. Correlation effects are included by a second-order Moeller Plesset perturbation treatment. For the two lowest-lying structures higher-order correlation corrections and multi-reference effects are also included. Bonding features are investigated by two different types of population analyses to obtain insight into the nature of chemical bonding. A total of 17 stationary points were investigated, 14 of which correspond to local minima and three being transition states. The energetically lowest-lying structures are: A “pyramidlike” structure with various multicenter bonds, followed by a C_s symmetric isomer closely related to the ground state Si₆ structure. Planar structures, favoured in small carbon clusters, lie higher in energy and are transition states. The lowest-lying triplet system is found to be the linear nonsymmetric Si-C-C-C-Si-Si structure, which is calculated to lie about 38 kcal/mole above the singlet ground state. A building-up principle based on bonding criteria is suggested for the occurence of the various structural possibilities.     

Ab initio investigation of the hydration of deprotonated amino acids

The complexation of five deprotonated anionic amino acids (glycine, L-alanine, L-valine, L-Aspartic acid, and L-glutamine) with one water molecule, has been investigated using a MP2/63-11++G(d,p) approach fully accounting for the basis set superposition errors. For each amino acid, several energetic minima have been identified, and we provide spectroscopic information allowing to discriminate them. Our results strongly suggest that two complexes should coexist under the experimental conditions for [Ala − H]⁻, [Val − H]⁻, and [Asp − H]⁻. Comparisons with the experimental enthalpies, entropies, and Gibbs free energies recently obtained by Wincel [J. Am. Soc. Mass Spectrom. 2008, 19, 1091–1097] show that our simulation reproduces the most significant structure/energy experimental trends, though the entropic changes induced by hydration are slightly overestimated.