Ab initio Hartree-Fock/6-31G** calculation on 9-beta-D-arabinofuranosyladenine-5'-monophosphate molecule: application to the analysis of its IR and Raman spectra

9-beta-D-arabinofuranosyaldenine-5'-monophosphate (5'-ara-AMP) is an arabinonucleotide that has antiviral and antitumor activity. The accurate knowledge of the nature of its vibrational modes is a valuable step for the forthcoming elucidation of drug-nucleotide and drug-enzyme interactions. The FTIR and FT Raman spectra (4000-30 cm(-1)) of 5'ara-AMP and two deuterated derivatives ara-AMP-d(C8) (deuteration in C8) and ara-AMP-d7 (deuteration in C8, amino and hydroxyl groups) are reported. Theoretical vibrational calculations were performed using the Hartree-Fock/6-31G** method. An assignment of the observed spectra is proposed considering the scaled potential energy distribution of the vibrational modes of the 5'ara-AMP molecule and the observed band shifts by deuteration. The scaled ab initio frequencies are in good agreement with the experimental data (<3 cm(-1) SD).     

Quantum chemical investigations on the complexes of Ca2+ and Zn2+ with aliphatic dipeptides

Several 1:1 complexes of Zn²⁺ with glycylglycine and of Ca²⁺ and Zn²⁺ with prolylglycine and glycylproline have been calculated within the Hartree-Fock method using a minimal GLO basis set. It was found that in spite of the fact that there are large differences in complex binding energy the relative stabilities of the different binding sites are the same in the case of Ca²⁺ and Zn²⁺ ions. Electronic density diagrams have been produced to illustrate the changes in electronic distribution caused by complex formation.     

Application of a universal solvation model to nucleic acid bases: comparison of semiempirical molecular orbital theory, ab initio Hartree-Fock theory, and density functional theory

The free energies of solvation of six nucleic acid bases (adenine, cytosine, hypoxanthine, guanine, thymine, and uracil) in water and chloroform are calculated using CM2 class IV charges and SM5.42R atomic surface tensions. Using any of three approximations to the electronic wave function (AM1, Hartree-Fock, or DFT), we obtain good agreement with experiment for five cases where the experimental results are known for the partition coefficients between the two solvents. Decomposition of the solvation effects into bulk electrostatic contributions and first-solvation-shell effects shows that the partitioning is dominated by the former, and this illustrates the importance of using accurate partial atomic charges for modeling these molecules in aqueous solution.     

Theoretical study of the NMR chemical shift of Xe in supercritical condition

In this work we investigate the level of theory necessary for reproducing the non-linear variation of the ¹²⁹Xe nuclear magnetic resonance (NMR) chemical shift with the density of Xe in supercritical conditions. In detail we study how the ¹²⁹Xe chemical shift depends under supercritical conditions on electron correlation, relativistic and many-body effects. The latter are included using a sequential-QM/MM methodology, in which a classical MD simulation is performed first and the chemical shift is then obtained as an average of quantum calculations of 250 MD snapshots conformations carried out for Xe _n clusters (n =?2 ? 8 depending on the density). The analysis of the relativistic effects is made at the level of 4-component Hartree-Fock calculations (4c-HF) and electron correlation effects are considered using second order Møller-Plesset perturbation theory (MP2). To simplify the calculations of the relativistic and electron correlation effects we adopted an additive scheme, where the calculations on the Xe _n clusters are carried out at the non-relativistic Hartree-Fock (HF) level, while electron correlation and relativistic corrections are added for all the pairs of Xe atoms in the clusters. Using this approach we obtain very good agreement with the experimental data, showing that the chemical shift of ¹²⁹Xe in supercritical conditions is very well described by cluster calculations at the HF level, with small contributions from relativistic and electron correlation effects.     

Quantum chemical modeling of perovskite: An investigation of piezoelectricity in ferrite of yttrium

In a previous article, we used Hartree-Fock (HF) theory to study the piezoelectricity in BaTiO₃. In this paper, we applied the Douglas-Kroll-Hess second order scalar relativistic method to investigate the possible piezoelectric properties in the perovskite YFeO₃ structure, which has not yet been studied experimentally. The 30s20p13d and 31s21p17d Gaussian basis sets for the Fe (⁵D) and Y (²D) atoms, respectively, were built with the Generator Coordinate HF method. After contraction to [13s7p5d] and [13s8p7d], in combination with the 20s14p/6s4p basis set for the O (³P) atom from literature, they had their quality evaluated using calculations of the total and the orbital energies for the ²FeO⁺¹ and ¹YO⁺¹ fragments. The dipole moment, the total energy, and the total atomic charges in YFeO₃ in C_s space group were calculated. The results and the analysis lead us to believe that the perovskite YFeO₃ does not present piezoelectric properties.     

Molecular structure and vibrational and chemical shift assignments of 5-(2-Hydroxyphenyl)-4-(p-tolyl)-2,4-dihydro-1,2,4-triazole-3-thione by DFT and <Emphasis Type="Italic">ab initio</Emphasis> HF calculations

The molecular geometry, vibrational frequencies, gauge including atomic orbital (GIAO) ¹H and ¹³C chemical shift values and several thermodynamic parameters of 5-(2-Hydroxyphenyl)-4-(p-tolyl)-2,4-dihydro-1,2,4-triazole-3-thione in the ground state have been calculated by using the Hartree-Fock (HF) and density functional method (DFT/B3LYP) with 6–31G(d), 6–31 + G(d,p) and LANL2DZ basis sets. The results of the optimized molecular structure are presented and compared with the experimental X-ray diffraction. The computed vibrational frequencies are used to determine the types of molecular motions associated with each of the experimental bands observed. Also, calculated ¹H chemical shift values compared with the experimental ones. The data of the title compound display significant molecular structure and IR, NMR analysis provide the basis for future design of efficient materials having the of 1,2,4-triazole core.     

Application of the change in partition coefficient with pH to the structure determination of alkyl substituted guanosines.

A versatile method for the determination of the ionization of guanosine is described. Suitably derivatized alkyl-guanosines are partitioned between organic solvents and aqueous buffer solutions at various pH values. Ionization is revealed by a change in partition coefficient with pH. The method is ideally suited for application to micro samples since any quantitative method can be used to determine the partition coefficient. A procedure for distinguishing N¹ or O⁶, N², and C⁸ alkylation of guanosine is described.     

Ab initio self-consistent field study of deoxyguanosine

The rotational energy of deoxyguanosine around the C₁–N₉ bond is calculated using the Hartree-Fock method with an STO-3G basis set.     

Studies of NAD(H) conformations in solution: A new method using the PMR spectra of cobalt ion—dinucleotide complexes

In aqueous solutions of NAD(H), there is an equilibrium between two different conformations : a “folded” conformation in which adenine and nicotinamide are staked together and an “unfolded” conformation in which the two rings are without interaction.The folded conformation is the more stable in aqueous solution whereas in organic solution it is the unfolded one.As we have previously shown, the PMR spectra of Co²⁺—NAD(H) complexes may be related with the coenzyme conformation giving suggest to a new method for NAD(H) conformational analysis.The results of this method applied to methanol ²H₂O and dioxane/²H₂O solutions are reported in this paper: they are in good accordance with those of spectrofluorimetric analysis.     

Ab initio prediction of optical rotation: comparison of density functional theory and Hartree-Fock methods for three 2,7,8-trioxabicyclo[3.2.1]octanes

We report ab initio calculations of the frequency-dependent electric dipole-magnetic dipole polarizabilities, beta(nu), at the sodium D line frequency and, thence, of the specific rotations, [alpha](D), of 2,7,8-trioxabicyclo[3.2.1]octane, 1, and its 1-methyl derivative, 2, using the Density Functional Theory (DFT) and Hartree-Fock/Self-Consistent Field (HF/SCF) methodologies. Gauge-invariant (including) atomic orbitals (GIAOs) are used to ensure origin-independent [alpha](D) values. Using large basis sets which include diffuse functions DFT [alpha](D) values are in good agreement with experimental values (175.8 degrees and 139.2 degrees for (1S,5R)-1 and -2, respectively); errors are in the range 25-35 degrees. HF/SCF [alpha](D) values, in contrast, are much less accurate; errors are in the range 75-95 degrees. The use of small basis sets which do not include diffuse functions substantially lowers the accuracy of predicted [alpha](D) values, as does the use of the static limit approximation: beta(nu) approximately beta(o). The use of magnetic-field-independent atomic orbitals, FIAOs, instead of GIAOs, leads to origin-dependent, and therefore nonphysical, [alpha](D) values. We also report DFT calculations of [alpha](D) for the 1-phenyl derivative of 1, 3. DFT calculations find two stable conformations, differing in the orientation of the phenyl group, of very similar energy, and separated by low barriers. Values of [alpha](D) predicted using two different algorithms for averaging over phenyl group orientations are in good agreement with experiment. In principle, the absolute configuration (AC) of a chiral molecule can be assigned by comparison of the optical rotation predicted ab initio to the experimental value. Our results demonstrate the critical importance of the choice of ab initio methodology in obtaining reliable optical rotations and, hence, ACs, and show that, at the present time, DFT constitutes the method of choice.     

Tube gel isotachophoresis: A method for quantitative isolation of nucleic acids from diluted solutions

The technique of isotachophoresis is intended for separation of molecules having different electrophoretic mobilities in a nonhomogeneous electric field. Since the mobility of nucleic acids in water solutions is uniform and does not depend on their size (because of a uniform distribution of negatively charged phosphate groups along the molecule), isotachophoresis will concentrate rather than separate them in the mobile borderline zone between the rapid (Cl⁻) and the slow (β-alanine⁻) anions. This idea served as the basis for elaboration of a novel method for isolation of nucleic acids from diluted solutions. Advantages of the method include quantitative yield (regardless of molecule size), high degree of concentration, and the ability to visually monitor the process. The method may find applications in nucleic acid isolation from highly degraded forensic and clinical samples, from bodily fluids in particular, and thereby promote development of this important direction of diagnostics.     

Radiometric determination of cytidine 5′-triphosphate in biological materials

A simple and sensitive radioenzymic method is described for the direct determination of cytidine 5′-triphosphate (CTP) in the range of 1 to 9 nmol in perchloric acid extracts of tissue. The method involves a specific conversion of CTP and [1,2-¹⁴C]phosphorylethanolamine to labeled CDP-ethanolamine using purified CTP:phosphorylethanolamine cytidylyltransferase (EC 2.7.7.14). The [¹⁴C]CDP-ethanolamine formed is isolated on a Dowex 1-formate column taking advantage of the selectivity of borate complexing. A spectrophotometric method for determining CTP in standard solutions is also described.     

An ab initio study of valence isomerization in the HOCl-HClO system

Hartree-Fock level and post Hartree-Fock level molecular orbital calculations have been completed for HOCl and its valence isomer, HClO. Ground state geometries have been determined for each molecule. The energy change for the reaction HOCl→HClO is estimated to be 67±5 kcal/mol endothermic and the activation energy for the process is 74±5 kcal/ mol. The transition state for the reaction is identified and discussed. A vibrational analysis has been carried out for both HOCl and HClO. The calculated photoelectron spectrum is discussed for each of the molecules.     

Structural and energetic aspects of spin pairing in lanthanides

Numerical Hartree-Fock calculations on the lanthanide ions confirm the earlier results of Marcantonatos and coworkers, by showing that the excitation from the ground state of a given fⁿ- configuration to a state with lower spin multiplicity is accompanied by a change in size and shape of the orbitals. This orbital change is also shown to be at the basis of a new interpretation of the spin pairing phenomenon in lanthanides. This interpretation is significantly different from the picture offered by conventional multiplet theory; indeed, the spin pairing energy, calculated on the basis of Hartree- Fock theory is accompanied by a decrease in interelectronic repulsion.Although the relevant energetic (repulsion) effects are obviously quite large, the underlying size effects are very much smaller. Therefore, it seems highly unlikely that they are responsible for the change in coordination number of Gd(H₂O)₈³⁺ upon excitation, as suggested by Marcantonatos.     

Novel spectral-kinetic methods for investigation of ligand exchange in labile metal complexes in solutions

The luminescent spectral-kinetic method using selective complex excitation with short light pulse compared to relaxation reactions is described. The method makes it possible to obtain direct information on the rates of fast chemical reactions of dissociation or addition of ligands to Ln³⁺ ions in solutions. Data are presented on the rates and mechanisms of dissociation reactions for phenanthroline, bipyridile, salicylate, acetate, naphthoate and other complexes of Ln³⁺ ions in water and alcohols.     

Simple GC-FID method development and validation for determination of α-tocopherol (vitamin E) in human plasma

This paper describes the development and validation of a novel GC-FID method for the determination of α-tocopherol concentration in human plasma which does not requires derivatization. The standard solutions and the plasma working solutions were prepared in absolute ethanol. To determine the concentration of α-tocopherol in human plasma, an aliquot of the plasma sample was deproteinized with ethanol. α-tocopherol was extracted with a mixture of hexane and dichloromethane (9:1). GC separation was performed using a HP-5 capillary column. Nitrogen was used as carrier gas at a flow-rate of 2 ml min^− 1. Calibration curves were linear over the concentration range 1–30 μg ml^− 1 (for standard solutions and solutions without endogenous α-tocopherol in plasma) and 5–34 μg ml^− 1 (for solutions with endogenous α-tocopherol in plasma). Absolute recovery, precision, sensitivity and accuracy assays were carried out. The analytical recovery of α-tocopherol from plasma averaged 97.44%. The limit of quantification (LOQ) and the limit of detection (LOD) of method for standard samples were 0.35 μg.ml^− 1 and 0.30 μg.ml^− 1, respectively. Within-day and between-day precision, expressed as the relative standard deviation (RSD) were less than 4%, and accuracy (relative error) was better than 8%. This novel method, developed and validated in our laboratory, could be successfully applied to the in-vivo determination of α-tocopherol. The endogenous α-tocopherol amounts in blood of twelve healthy volunteers with no vitamin drug usage were measured with this method.     

Theoretical conformational studies on unsaturated aldehydes,I. Alkenals

Conformational analyses (using the PCILO method) and structural analyses (using the Hartree-Fock method with the STO-3G and 3-21G basis sets) have been performed on the fives-trans-2-alkenals from acrolein to 2-heptenal. This series of molecules were found to be very similar both structurally and electronically.     

High-efficiency liquid-scintillation counting of 14C-labelled material in aqueous solution and determination of specific activity of labelled proteins

1. Inexpensive scintillation mixtures are described which enable the detection of as little as 40μμc of ¹⁴C in aqueous solution with an efficiency of counting of over 80%. 2. A rapid method for the counting of alkaline, acidic and neutral aqueous solutions of up to 1ml. volume is described. Ethanol or 2-ethoxyethanol is used as blending agent. 3. The scintillation counting of alkaline solutions is applied to the accurate determination of the specific activity of ¹⁴C-labelled proteins from plant tissues. 4. Attention has been paid to the importance of a standardized washing procedure for the removal of all traces of radioactive material from glassware.