Ab Initio HF-SCF Research Articles

Conformational preferences and structural analysis of hypermodified nucleoside, peroxywybutosine (o2yW) found at 37th position in anticodon loop of tRNAPhe and its role in modulating UUC codon-anticodon interactions

Hypermodified bases present at 3′-adjacent (37th) position in anticodon loop of tRNAPhe are well known for their contribution in modulating codon-anticodon interactions. Peroxywybutosine (o2yW), a wyosine family member, is one of such tricyclic modified bases observed at the 37th position in tRNAPhe. Conformational preferences and three-dimensional structural analysis of peroxywybutosine have not been investigated in detail at atomic level. Hence, in the present study quantum chemical semi-empirical RM1 and multiple molecular dynamics (MD) simulations have been used to study structural significance of peroxywybutosine in tRNAPhe. Full geometry optimizations over the peroxywybutosine base have also been performed using ab-initio HF-SCF (6-31G**), DFT (B3LYP/6-31G**) and semi-empirical PM6 method to compare the salient properties. RM1 predicted most stable structure shows that the amino-carboxy-propyl side chain of o2yW remains ‘distal’ to the five membered imidazole ring of tricyclic guanosine. MD simulation trajectory of the isolated peroxy base showed restricted periodical fluctuations of peroxywybutosine side chain which might be helpful to maintain proper anticodon loop structure and mRNA reading frame during protein biosynthesis process. Another comparative MD simulation study of the anticodon stem loop with codon UUC showed various properties, which justify the functional implications of peroxywybutosine at 37th position along with other modified bases present in ASL of tRNAPhe. Thus, this study presents an atomic view into the structural properties of peroxywybutosine, which can be useful to determine its role in the anticodon stem loop in context of codon-anticodon interactions and frame shift mutations.

Experimental rovibrational constants and equilibrium structure of phosphorus trifluoride

Thanks to recent high-resolution Fourier transform infrared (FTIR) and pure rotational (RF/CM/MMW) measurements, several experimental values of the rotation–vibration parameters of the oblate molecule PF3 have been extracted, contributing thus to the knowledge of the molecular potential of phosphorus trifluoride. The data used are those of the fundamental, overtone and combination bands studied in the 300–1500cm−1 range. The new values are in good agreement with ones determined at low resolution, but significantly more accurate. The agreement is excellent with the available values determined by ab initio HF-SCF calculations employing the TZP/TZ2P triple-zeta basis. From the recent experimental rovibrational interaction constants αC and αB, new accurate equilibrium rotational constants Ce and Be have been derived for the symmetric top molecule PF3, which were used to derive the equilibrium geometry of this molecule: re(F–P)=1.560986 (43)Å; θe(FPF)=97.566657 (64)°.

Structural significance of hypermodified nucleic acid base hydroxywybutine (OHyW) which occur at 37th position in the anticodon loop of yeast tRNAPhe

Conformational preferences of hypermodified nucleic acid base hydroxywybutine (OHyW) have been studied using quantum chemical single point semi-empirical PM3 method. Automated geometry optimization using semi-empirical RM1, molecular mechanics force field (MMFF) along with ab-initio HF-SCF (6-31G** basis set) and DFT (B3LYP/6-31G** basis set) calculations have also been made to compare the salient features. Molecular electrostatic potentials (MEPs) depict the polarities of hydroxywybutine (OHyW) side chain. Another conformational study showed that hydroxywybutosine side chain interacts with adjacent bases within the anticodon loop of tRNAPhe. The solvent accessible surface area (SASA) calculations revealed the structural role of hydroxywybutine in anticodon loop. Explicit molecular dynamics (MD) simulation has been done over the PM3 most stable structure of OHyW. The hydroxywybutine side chain prefers ‘distal’ conformation i.e. spreads away from the cyclic five membered imidazole moiety of modified tricyclic guanine base. The predicted preferred conformation of hydroxywybutine may prevent extended Watson–Crick base pairing during protein biosynthesis process. This conformation of OHyW stabilized by intramolecular interactions between O(6)⋯HO(16), O(6)⋯HC(15) and O(20)⋯HC(17). Further stabilization is also expected from interactions between O(22)⋯HC(16) and O(23)⋯HC(15). Explicit molecular dynamics (MD) simulation over the PM3 most stable structure of OHyW support the preferred geometry by preserving the ‘distal’ orientation of hydroxywybutine side chain and intramolecular hydrogen bonding interactions. MD simulation study revealed the role of hydroxyl group of OHyW to avoid fluctuations and prevent multiple iso-energetic conformations of hydroxywybutine side chain as compared to wybutine (yW).

Vibrational constants of the symmetric top molecule PF3

Interesting relationships linking vibration–rotation band-centres, harmonic wavenumbers and anharmonicity constants of a symmetric top molecule have been established. Using these relationships, several accurate experimental values of the ωi , xij and gij vibrational constants have been extracted from the most recent high-resolution Fourier transform infrared investigation (≈3 × 10−3 cm−1) in the spectra of the PF3 molecule gas. The band-centres used are those of the four fundamental bands, the overtones, the combination and hot bands identified in the region between 300 cm−1 and 1500 cm−1. Taking into account the Fermi resonance established between the fundamental ν 3 and combination ν 2 + ν 4 bands of PF3, with an interaction constant W 234 = 2.86 cm−1 as suggested by ab initio HF-SCF calculations, the band-centres and the anharmonicity constants of the molecular potential of phosphorus trifluoride PF3 have been corrected. Comparison of these constants with those measured previously by infrared spectroscopy at low resolution reveals orders of magnitude higher accuracy of these new values. Comparison with the available ab initio predictions indicates that the deduced values of anharmonicity constants of the pyramid PF3 molecule are in fair agreement with those calculated in the large triple-zeta basis TZP/TZ2P with two sets of polarization function.

New integral transforms for molecular properties and application to a massively parallel GIAO-SCF implementation

We present several new Gaussian integral transforms to be used with the Rys quadrature numerical integration method. These transforms lead to an elegant unified methodology for the calculation of the atomic Gaussian integrals that enter the calculation of many molecular wavefunctions and properties. The unified methodology is highlighted for several types of integrals that are at the heart of other modern electronic structure theoretical developments, including electric and magnetic properties. We make use of these transforms in a massively parallel implementation of the Gauge-Invariant-Atomic-Orbital (GIAO) method for the calculation of chemical shifts at the ab initio HF SCF level of theory. The implementation follows the original GIAO theory that bypasses computational tasks that are not massively scalable. Indeed the response of the wavefunction to the magnetic field is calculated by means of the Derivative Hartree–Fock method (DHF). The DHF method is amenable to high parallel efficiency as it involves only the calculation of Fock-like matrices from density-like matrices. The computationally intensive steps are shown to be highly scalable.

C32: Computations of Low-Energy Cages with Four-Membered Rings

C32 cages built from four-, five-, six-, and seven-membered rings are computed. The computations are primarily performed with semiempirical quantum-chemical methods (AM1, PM3, SAM1), and altogether 199 cages are optimized. The energetics is further checked through ab initio HF SCF computations with the standard 3-21G basis set, and also by density functional theory at the B3LYP level in the standard 6-31G* basis set. All five levels of theory suggest a D4d cage (two four-membered rings, eight pentagons, eight hexagons) as the lowest-energy structure. Temperature effects are treated in the terms of partition functions so that the entropy contributions are considered accordingly. The thermodynamic treatment points out five cages significantly populated at high temperatures. At very high temperatures the structure lowest in energy is not the most abundant isomer. There are just six conventional fullerenes C32, built exclusively from pentagons and hexagons, however, only two of them show significant populations at high temperatures. The remaining three relatively stable cages contain at least one four-membered ring. No structure with a heptagon shows a non-negligible concentration at high temperatures. The study suggests that in the non-IPR region the quasi-fullerene cages with four-membered rings can in some cases be more important than the conventional fullerenes built from pentagons and hexagons only.

Systematic computational study of the geometrical dependence of deuterium quadrupole interaction parameters in an O– 2H⋯OC hydrogen bonded system

A systematic theoretical study of the geometrical dependence of deuterium ( 2H) quadrupole interaction parameters (quadrupole coupling constant and asymmetry parameter) in O– 2H⋯OC hydrogen bonds is reported, using the water–formaldehyde complex as a model system. From ab initio HF–SCF calculations (using 6-31G** basis set), the principal components of the electric field gradient tensor at the 2H nucleus, and hence the quadrupole interaction parameters of the 2H nucleus, have been determined as a function of the intermolecular geometry of the complex. The results provide a systematic understanding of the dependence of quadrupole interaction parameters on hydrogen bonding geometry, and may be applied in order to guide the interpretation of experimental results, for example in the case of solid state 2H-NMR of hydrogen bonded systems.

Study of chemical bonding in H2 and HF molecules: Wave function and density functional theory (DFT) parameters approach

Balint Kurti's Fourier grid Hamiltonian method is employed to obtain the molecular wave function and equilibrium bond length for H2 and HF molecules. The density functional theory parameter, namely, the chemical hardness (η) value, was determined for some diatomic hydride molecules using this wave function and the results are found to be in good agreement with the values obtained from the ab initio HF–SCF method. A new formula for chemical hardness (η=1/2Dr, where D is the proportionality constant and r is the internuclear distance) is introduced in binding energy and change of hardness equations to determine the chemical hardness and chemical potential values for different bond lengths. The binding energy and change of hardness values are calculated for H2, H, H, HF, HF+, and HF− molecules and the bond stability is discussed. Finally, the concept of an atom in a molecule is examined in the context of DFT parameters and comparison is made between an atom in a molecule and the isolated atom. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 76: 662–669, 2000

Study of chemical bonding in H2 and HF molecules: Wave function and density functional theory (DFT) parameters approach

Balint Kurti's Fourier grid Hamiltonian method is employed to obtain the molecular wave function and equilibrium bond length for H2 and HF molecules. The density functional theory parameter, namely, the chemical hardness (η) value, was determined for some diatomic hydride molecules using this wave function and the results are found to be in good agreement with the values obtained from the ab initio HF–SCF method. A new formula for chemical hardness (η=1/2Dr, where D is the proportionality constant and r is the internuclear distance) is introduced in binding energy and change of hardness equations to determine the chemical hardness and chemical potential values for different bond lengths. The binding energy and change of hardness values are calculated for H2, H, H, HF, HF+, and HF− molecules and the bond stability is discussed. Finally, the concept of an atom in a molecule is examined in the context of DFT parameters and comparison is made between an atom in a molecule and the isolated atom. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 76: 662–669, 2000

Tetrafluoroberrylate(2) Ions as Hydrogen-Bond Proton Acceptors: Quantum Chemical Considerations

The experimentally observed lower proton acceptor ability of the tetrafluorober-rylate(2-) anion, compared to that of the sulphate(2-) and selenate(2-) anions, was explained on the basis of various quantum chemical approaches. The geometries of the above-mentioned XY4 2 anions were fully optimised at the ab initio HF SCF and MP2 levels of theory, as well as within the DFT (BLYP and B3LYP) approach, using the 6-311+G* and LANL2DZ basis sets. The 6-311++G(3df,3pd) basis set was also used within the DFT BLYP approach. The molecular charge distribution was partitioned among the atomic centers using the Mulliken as well as the natural population analysis. All levels of theory (both with and without inclusion of the electron correlation effects), regardless of the basis set employed, predict lower (by absolute value) atomic charge on the fluorine atom in the tetra-ftuoroberrylate(2-) anion than that on oxygen atoms in sulphate(2-) and selenate(2-) anions. The quantum chemical predictions are fully in line with the spec-troscopically observed order of the proton acceptor abilities in these anions.

Quantum-Chemical Study of the Structure, Aggregation, and NMR Shifts of the Lithium Ester Enolate of Methyl Isobutyrate

Ab initio HF-SCF calculations of the equilibrium geometries, energies, and 13C NMR shifts of various monomeric, dimeric, and tetrameric aggregates of the lithium ester enolate of methyl isobutyrate (MIB-Li) were performed. It is shown that an enolate-like nonplanar structure of the MIB-Li monomer, in which a π-interaction between the Li atom and CC double bond is realized, is more stable than the planar enolate-like structure. The energies of the two MIB-Li dimers consisting of the planar and nonplanar MIB-Li monomers, respectively, were found to be nearly the same. However, the experimental 13C NMR shifts for the MIB-Li dimer in THF agree with those calculated for the planar stereoisomer. For the MIB-Li tetramer, two structures were found, namely, a cubic and a nearly flat eight-membered-ring structure. The calculated 13C NMR shifts for the two tetramers are very similar, but the cubic tetramer is considerably more stable than the flat one at the highest level of theory. Semiempirical MNDO and PM-3 calcu...

Ab initio HF-SCF studies of the equilibrium structures and vibrational spectra of the Be(NO 3) 2, Mg(NO 3) 2 and Ca(NO 3) 2 molecules

HF-SCF calculations have been performed for the Mg(NO 3) 2, Ca(NO 3) 2 and Be(NO 3) 2 molecules to determine their stable equilibrium structures and vibrational spectra. Bidentate and monodentate structures have been taken into account and the calculations suggest that non-planar D 2 d is the most stable equilibrium structure for all the species considered in the work. The infrared spectra of the D 2 d and D 2 h structures of Mg(NO 3) 2 have been simulated on the basis of the HF/6–31G ∗ frequency and intensity calculations, and the 18O isotope shifts have been predicted in the stretching region of the NO 3 − modes. The conclusions of the calculations have been used to assign the FT-IR spectra of molecular Cu(NO 3) 2. The paper includes calculations for the [BeNO 3] +H 2O, [MgNO 3] +H 2O, [CaNO 3] +H 2O, [AlNO 3] 2+H 2O, [BeNO 2] +H 2O, [MgNO 2] +H 2O, [CaNO 2] +H 2O, and [AlNO 2] 2+H 2O hydrated species.

Ab initio HF-SCF study of naphthazarin: Geometries, isomerism, hydrogen bonding, and vibrational spectrum

The structural properties and intramolecular hydrogen bonding of a series of structures of naphthazarin molecule were investigated by ab initio HF-SCF methods. The geometries of theC2v,C2h,D2h, andCs symmetry structures were optimized using split-valence basis sets. MP2/6-31G*// HF/6-31G single-point energy calculations indicate that theC2v isomer (5,8-dihydroxy-1,4-naphthoquinone) is the lowest energy structure of the molecule and that theC2h symmetry one (4,8-dihydroxy-1,5-naphthoquinone), lying 37 kJ/mol above theC2v form, is the other stable isomer of naphthazarin. At the HF/6-31G level, the intramolecular proton exchange between two equivalentC2v structures is a two-step process where each proton can be independently transferred through an unsymmetrical potential having a 1,5-quinone intermediate, theC2h symmetry structure, and two equivalent transition states ofCs symmetry, with a barrier height equal to 38 kJ/ mol (MP2/6-31G*//HF/6-31G). The study of naphthazarin molecule is flanked by a theoretical investigation on theC2v andC2h isomers of the parent naphthoquinone and dihydroxynaphthalene molecules. The SCF vibrational spectrum of the ground state of naphthazarin, harmonic frequencies, and infrared and Raman band intensities were computed at the HF/6-31G level. The results of the calculations are compared with the matrix isolation FT-IR spectroscopy measurements and with the infrared and Raman spectra of the crystal molecule.

An ab initio HF-SCF and MP2 study of hydrogen bonding and van der Waals interactions: Low frequency vibrations of bimolecular complexes

HF-SCF and {BDMP2} calculations were carried out to investigate hydrogen bonding interactions in a series of bimolecular complexes. Calculations are reported at different levels of theory to examine the structural and vibrational effects of bimolecular interaction of molecules such as N 2, CO, C 2H 2, CH 3CN, HC 3N, NH 2OH, NH 3, pyrrole, pyridine, pyrazine and benzene with HF, HCl, HCN, H 2O and NH 3. The van der Waals complexes He… HF, He…HCl, Ne…HF, Ne…HCl, Ar…HF, Ar…HCl, He…CO, Ne…CO, Ar…CO, HF…He, HCl… He, CO… He, HF… Ne, HCl…Ne, CO…Ne, HF… Ar, HCl… Ar and CO… Ar are also discussed.

HF-SCF study of the ground state geometry and harmonic vibrational frequencies of borazine derivatives

The results of ab initio HF-SCF calculations of the B-monosubstituted borazine derivatives B 3N 3H 5X (X = NH 2, NO 2, F, Cl, CN, NC, OH, N 2 +, CCH, CHO, CH 3, NH 3 + and SiH 3) are reported. The equilibrium geometries of the molecules were determined from gradient optimizations carried out employing the 6-31G ∗ and 6-31G ∗∗ basis sets. HF/6-31G ∗ level calculations of disubstituted and trisubstituted F and Cl borazine derivatives and of trimethylborazine are included. The effects of the substituents on the geometry of the borazine ring were investigated. Vibrational frequencies were calculated for some B-monosubstituted molecules and the splittings of the degenerate modes of borazine due to symmetry lowering occurring in the B-monosubstituted molecules were examined.

Molecular orbital studies on the model compounds of doped polyacetylene

The electronic structures of model compounds of doped polyacetylene are investigated by the molecular orbital method. The structures of charge transfer complexes between short polymethine with Na or Cl atoms are optimized by the ab initio HF SCF MO calculation. It is found that the allyl group in the polymethine chain acts as a bidentate ligand to the dopant and it forms a stable closed shell unit which shields the conjugation of double bonds. The polyene with such units at the trans position is assigned to the charged soliton-antisoliton. The polymethine chain which consists of two coordinated allyl groups and a short radical chain between them is called the polson. These structures are used in the calculation of the energy levels of doped long chains by the P-P-P method. The mid gap state is found with the charged soliton lattice and the metallic state is obtained with the polson lattice.

Molecular and Electronic Structures of Model Compounds of Doped Polyacetylene

Abstract Using the ab initio HF SCF MO method optimized molecular structures were calculated on twenty five model compounds of doped polyacetylene, which were charge-transfer complexes between dopants (Na, Li, and Cl atoms) and trans-polyenes (C6H8, C8H10, C12H14, C14H16, and C16H18) or trans-odd polyene radicals (C3H5·, C5H7·, C7H9·, C9H11·, C11H13·, and C13H15·). In alkali metal-doped complexes, each alkali atom is located at the vertex of the trigonal pyramid, whose basal triangle consists of an allylic group, (CH)3. On the other hand, each chlorine atom is coplanar with the (CH)n chain and is connected with an allylic group by hydrogen bonding. The allylic group acts as a bidentate or tridentate ligand, forming an ionic closed-shell structure with the dopants. The molecular orbitals of the singly doped complexes are correlated with those of parent trans-polyene or odd polyene radical chains. The molecular orbitals of doubly doped complexes are analyzed on the basis of those of singly doped complexes. The molecular structure of the polson unit is presented, which is important for heavily doped polyacetylene to be metallic.

Zn(H 2O) 2+6 is very stable among aqua-Zn(II) ions

Ab initio HF-SCF and MP2 calculations have been performed on Zn(H 2O) 2+ n , where 4⩽ n⩽8. The calculation with the Zn(8s4p2d)/O(4s2p1d)/H(2s) basis set shows that the fifth water molecule hydrating Zn(II) tends to have one more water molecule in the first hydration shell, while the seventh water molecule tends to be in the second hydration shell. Thus, we have provided evidence from ab initio calculations that hexaaqua-Zn(II) is very stable among aqua-Zn(II) ions, unless unusual thermodynamic conditions apply. The structure of the hexaaqua-Zn(II) has T h symmetry. The solvation energy contribution due to the primary hydration accounts for more than 50% of the experimental solvation energy of Zn(II). We also discuss the structure, hydration energy and spectra, comparing with experimental data.

Ab initio calculations on the AsO 2− anion and LiAsO 2, NaAsO 2, KAsO 2 and RbAsO 2 molecules

Ab initio HF-SCF and non-empirical Pseudopotential calculations are reported for the bent anion AsO 2 − and the bidentate cyclic molecules LiAsO 2, NaAsO 2, KAsO 2 and RbAsO 2. The molecular geometries have been optimized employing split-valence basis sets including polarization functions on all atoms. Vibrational frequencies of the anion and molecules are calculated in the harmonic approximation and the spectroscopic data are compared with experimental results. This work has been extended to the study of the radical anion SiO 2 − and to the LiSiO 2 and NaSiO 2 charge transfer complexes.

Theoretical treatment of the chemisorption of hydrogen on a beryllium monolayer

The aim of this paper is to contribute to the mathematical description of chemisorption by using the Green matrix formalism to treat the adsorption of a hydrogen molecule on a monolayer of beryllium. This is done at a rigorous ab initio HF SCF level with correlation corrections of the Be surface, a posteriori. It is shown that, at a certain geometrical arrangement of the hydrogen molecule, a binding occurs whose parameters (length, strength) turn out to be quite reasonable. Thus, we believe that our formalism is capable of describing perturbed quantum-mechanical systems in general, on a level comparable to the accuracy of standard quantum-chemical calculations of molecules and solids.