Study of direction of cyclization of malonodithioamides as a method of investigation of reactivity of α-diazothioacetamides

The reaction of malonothioamides with benzene-sulfonyl azide and 2-azido-3-ethylbenzthiazolium tetrafluoroborate gave amides of 2-diazothiomalonic acid, which underwent cyclization to a mixture of 5-N-R-amino-1,2,3-thiadiazole-4-carbothioamides and 5-amino-1,2,3-thiadiazole-4-N-R-carbothioamides. The ratio of the isomeric thiadiazoles formed in this reaction is the same as in the reactions of 2-diazo-2-cyanoacetamides, 5-amino-1,2,3-thiadiazole- and 5-mercapto-1,2,3-triazole-4-carboxamides with P₄S₁₀ and of 5-amino-1, 2,3-thiadiazole-4-carbonitriles with H₂S; it is characteristic of the influence of substituents on the reactivity of -diazothioacetamides. It was found that the cyclization of the diazo compounds is accelerated when electron-acceptor substituents are attached to the nitrogen atom of the carbothioamide group.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 8, pp. 1106–1112, August, 1992.     

Synthesis of a Pair of Derivatives of N-Methylpyrrole Polyamide

A pair of derivatives of tetrameric N-methylpyrrole polyamide were synthesized in order to develop a new method for the study of interaction of the polyamide derivatives with DNA. Indole acetic acid and nicotinic acid were introduced to the polyamide in the synthesized compound, which showed an expected red shift in the UV spectrum. These compounds may function as a potential tool in the detection of the polyamide binding to DNA.     

Structure of Potassium of Undecatungstomononickelosilicate

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Kinetics of tautomerization of 1,3,4,7-tetramethylisoindole

The kinetics of transformation of 1,3,4,7-tetramethylisoindole(1)to 1,3,4,7-tetramethyl-1H-isoindole(2)in water or in deuterium oxide at various pH or pD at 25℃ were measuredspectrophotometricalty.The results indicated that the transformation of 1 to 2 could be promotedby acid and base.From the solvent isotope effects and the fact that the 1-position of isoindole nucleusis electron-rich,the mechanism of this transformation is suggested.     

Analysis of Significance of Unite Examination of AFP and DNA Polymorphism of P3 Promoter of IGF- Ⅱ Gene

IntroductionTheinnatecharacterofthesolidcarcinomaistheresultthatcellgrowthgetsoutofcontrol.Itsbasicreasonconsistsintheabnormalityofthetumorgene .SomeonethinksthatthegeneofIGF Ⅱisoneofthecancergenesofthe primaryhepatocellularcarcino ma[1] ,andalsothinkstheoverexpressionofthegeneofIGF Ⅱtakesplaceintheearlierperiodofthepri maryhepatocellularcarcinoma ,whichmaybetheear lierdiagnosticnormofprimaryhepatocellularcarcino ma .ThefurtherresearcheshavedemonstratedthattheactivationofIGF Ⅱ genepromo…     

Analysis of Significance of Unite Examination of AFP and DNA Polymorphism of P3 Promoter of IGF-ⅡGene

The DNA of P3 promoter region of IGF-Ⅱ gene was obtained by means of PCR technique. The examination of DNA polymorphism by restriction endonuclease BstE Ⅱ and the examination of AFP by bioluminescence immunoassay technique were carried out. The results have a significant difference(P<0.005). But the positive rate of AFP is higher than that of DNA polymorphism. The experimental result shows that the change of the DNA polymorphism of IGF-Ⅱis not the only carcinogenic factor. The suggested unite examination is the best method for the diagnosis of the primary hepatocellular carcinoma.     

2D NMR Investigation of Dynamic Equilibrium of Tautomers of Gossypol

Gossypol was obtained as an yellow platelike crystal with m.p. 210-214o . In CDCl3 there were three tautomers of gossypol: I aldehyde, II lactol,III ketal , in equilibrium .Their total H 1 NMR spectra were assigned by means of 1D and 2D NMR techniques including 1H-1H cosy , DEPT , HMQC (1H Detected Heteronuclear Multiple Quantum Coherence) and HMBC (1H Detected Heteronuclear Multiple Bond Connectivity) experiments . This paper first reported that we took use of the 2D NMR t…     

Peculiarities of dissociative ionization of alkylcyclopentadienyl nitrosyl π-complexes of nickel

The decomposition of alkylcyclopentadienyl nitrosyl -complexes of nickel, (C₅H₄R)(NO)Ni (R=H, Et,i-Pr, CH₂Ph), under the action of electron impact has been studied. The nature of the nitrosyl ligand has been shown to be the factor determining the main fragmentation pathway which involves the abstraction of an NO molecule. The effect of the nature of the ligand on the ability of the molecular ion (C₅H₄R)LNi⁺ (L=C₅H₄R, C₅H₅, C₃H₅, NO) to rearrange with hydrogen atom migration from one ligand to another has been considered. The structure of the alkyl group R determines a competing fragmentation pathway involving cleavage of the -C-C bond with respect to the cyclopentadienyl ring in the substituent.Translated fromIzyestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 1985–1988, November, 1993.     

Synthesis of Related Compounds of Carotenoid

类胡萝卜素是一类奇特的色素，由高等植物和微生物光化学合成，作为防止单线氧通过光敏反应产生危害的必要基团，类胡萝卜素最近受到了关注。类胡萝卜素联于富勒烯上，既可大大增加在可见光区域光诱导电子转移的有效吸收断面，又可抑制富勒烯敏化单线氧的危害能力。合成了类胡萝卜素的相关化合物，报道的某些反应条件先进且简洁。     

Dependence of the basic properties of meso-nitro-substituted derivatives of β-octaethylporphyrin on the nature of substituents

Spectrophotometric titration is used to study the basic properties of a series of porphyrins with a continuously increasing degree of macrocycle deformation resulting from the introduction of strong electron-withdrawing substituents: 2,3,7,8,12,13,17,18-octaethylporphyrin (I), 5-nitro-2,3,7,8,12,13,17,18-octaethylporphyrin (II), 5,15-dinitro-2,3,7,8,12,13,17,18-octaethylporphyrin (III), 5,10,15-trinitro-2,3,7,8,12,13,17,18-octaethylporphyrin (IV), and 5,10,15,20-tetranitro-2,3,7,8,12,13,17,18-octaethylporphyrin (V). It is found that the values of logK _b (total basicity constants) obtained for the investigated compounds consistently diminish with an increase in the number of meso-substituents: 11.85 (I) > 10.45 (II) > 10.31 (III) > 10.23 (IV) > 9.56 (V). It is shown that two opposing factors, the steric and electronic effects of the substituents, change the basic properties of the above series of compounds.     

Application of second-order Møller-Plesset perturbation theory with resolution-of-identity approximation to periodic systems

Efficient periodic boundary condition (PBC) calculations by the second-order M?ller-Plesset perturbation (MP2) method based on crystal orbital formalism are developed by introducing the resolution-of-identity (RI) approximation of four-center two-electron repulsion integrals (ERIs). The formulation and implementation of the PBC RI-MP2 method are presented. In this method, the mixed auxiliary basis functions of the combination of Poisson and Gaussian type functions are used to circumvent the slow convergence of the lattice sum of the long-range ERIs. Test calculations of one-dimensional periodic trans-polyacetylene show that the PBC RI-MP2 method greatly reduces the computational times as well as memory and disk sizes, without the loss of accuracy, compared to the conventional PBC MP2 method.     

Distributed memory parallel implementation of energies and gradients for second-order Møller-Plesset perturbation theory with the resolution-of-the-identity approximation

We present a parallel implementation of second-order M?ller-Plesset perturbation theory with the resolution-of-the-identity approximation (RI-MP2). The implementation is based on a recent improved sequential implementation of RI-MP2 within the Turbomole program package and employs the message passing interface (MPI) standard for communication between distributed memory nodes. The parallel implementation extends the applicability of canonical MP2 to considerably larger systems. Examples are presented for full geometry optimizations with up to 60 atoms and 3300 basis functions and MP2 energy calculations with more than 200 atoms and 7000 basis functions.     

Analytic gradient for second order Møller-Plesset perturbation theory with the polarizable continuum model based on the fragment molecular orbital method

A new energy expression is proposed for the fragment molecular orbital method interfaced with the polarizable continuum model (FMO/PCM). The solvation free energy is shown to be more accurate on a set of representative polypeptides with neutral and charged residues, in comparison to the original formulation at the same level of the many-body expansion of the electrostatic potential determining the apparent surface charges. The analytic first derivative of the energy with respect to nuclear coordinates is formulated at the second-order M?ller-Plesset (MP2) perturbation theory level combined with PCM, for which we derived coupled perturbed Hartree-Fock equations. The accuracy of the analytic gradient is demonstrated on test calculations in comparison to numeric gradient. Geometry optimization of the small Trp-cage protein (PDB: 1L2Y) is performed with FMO/PCM/6-31(+)G(d) at the MP2 and restricted Hartree-Fock with empirical dispersion (RHF/D). The root mean square deviations between the FMO optimized and NMR experimental structure are found to be 0.414 and 0.426 A? for RHF/D and MP2, respectively. The details of the hydrogen bond network in the Trp-cage protein are revealed.     

Large-scale correlated electronic structure calculations: the RI-MP2 method on parallel computers

The approximate ‘resolution of the identity’ second-order many-body perturbation theory method (RI-MP2) recently introduced by Feyereisen, Fitzgerald and Komornicki utilizes a combination of two- and three-center integrals to approximate the usual four-center two-electron repulsion integrals. Like the exact MP2, the overall cost of the RI-MP2 method scales with the fifth power of the number of basis functions, however the balance of the work shifts in such a way as to make the RI-MP2 method particularly well suited for implementation on massively parallel computers. We describe such an implementation and examine its parallel performance for several chemical systems. We are able to accurately reproduce the exact MP2 binding energy of K⁺ to 12-crown-4 ether in roughly 5% of the time.     

Dual-basis second-order Moller-Plesset perturbation theory: A reduced-cost reference for correlation calculations

The resolution-of-the-identity (RI) approximation has placed the onus of the cost of a second-order Moller-Plesset (MP2) calculation on the underlying self-consistent field (SCF) calculation for many moderately sized molecules. A dual-basis approach to the SCF calculation, based on previous methods demonstrated for density functional theory, is combined with RI-MP2 calculations, and small basis subsets for cc-pVTZ, cc-pVQZ, and 6-311++G(3df,3pd) are presented. These subsets provide time savings of greater than 90%, with negligible errors in absolute and relative energies, compared to the associated full-basis counterpart. The method is tested with a series of rotational barriers, relative conformational energies of alanine tetrapeptides, as well as the full G3/99 molecular set. RI-MP2 calculations on alanine octapeptides (40 heavy atoms, 3460 basis functions), using cc-pVQZ, are presented. Results improve upon previous methods that diagonalize the virtual space separately.     

Interaction of dihydrogen with small and light molecules

Second-order M?ller-Plesset (MP2) calculations (using the approximate resolution of the identity, RI-MP2), explicitly correlated MP2 (MP2-R12) calculations, and coupled-cluster calculations including all single and double excitations with a perturbative estimate of triple excitations [CCSD(T)] are performed to study the interaction of molecular hydrogen with the small molecules HF, H2O, NH3, and LiOH. Different adsorption positions are studied. In the cases of H2O and NH3, the most favorable configuration places H2 in an end-on fashion on the O or N atom, respectively. In the cases of HF and LiOH, the H2 molecule takes a side-on position on the H atom of HF or the Li atom. With respect to MP2 calculations in a triple-zeta basis, both the enlargement of the basis set and the extension of the correlation treatment (CCSD(T) vs MP2) increase the interaction energy. The basis set limit CCSD(T) estimates of the interaction energy of H2 with the HF, H2O, NH3, and LiOH molecules amount to 4.40, 2.67, 3.02, and 10.74 kJ mol-1, respectively. The interaction energy for the simultaneous interaction of H2 with two LiOH molecules does not significantly exceed the value obtained for the interaction with a single LiOH molecule. Furthermore, the interaction energies (by MP2) of H2 with glycine, the glycine dimer, and imidazolium chloride amount to 2.78, 5.00, and 6.30 kJ mol-1, respectively.     

Examination of numerical accuracy on fragment-DFT calculations with integral values of total electron density functions

Fragment molecular orbital (FMO) method gives a powerful tool to investigate electronic structures for biological substances, and ABINIT-MP program has been developed to implement ab initio FMO calculations effectively. We introduced DFT code into ABINIT-MP and applied fragment-DFT (F-DFT) calculations to model polypeptides. The total accuracy of numerical integrations employed in those calculations was examined by the total numbers of electrons in the molecules. It is shown that the numerical integral of the total density function under the fragment approximation works as an indicator for the numerically total accuracy on the F-DFT implementation.     

Application of fragment molecular orbital scheme to silicon-containing systems

The fragment molecular orbital (FMO) scheme has been successfully used for a variety of large-scale molecules such as proteins and nucleic acids so far. We have applied the FMO calculations to the silicon-containing systems like polysilanes. The error caused by the fragmentation was examined by the Hartree–Fock method and the second-order Møller-Plesset (MP2) perturbation method for the ground state energy. The dynamic polarizability as a linear response property was also evaluated with and without the fragmentation. A series of numerical comparisons showed that the FMO scheme is applicable to silicon-based molecules with reasonable accuracy. This implied a potential availability of FMO calculations for the issues relevant to nanoscience and nanotechnology.     

Accurate interaction energies of hydrogen-bonded nucleic acid base pairs

Hydrogen-bonded nucleic acids base pairs substantially contribute to the structure and stability of nucleic acids. The study presents reference ab initio structures and interaction energies of selected base pairs with binding energies ranging from -5 to -47 kcal/mol. The molecular structures are obtained using the RI-MP2 (resolution of identity MP2) method with extended cc-pVTZ basis set of atomic orbitals. The RI-MP2 method provides results essentially identical with the standard MP2 method. The interaction energies are calculated using the Complete Basis Set (CBS) extrapolation at the RI-MP2 level. For some base pairs, Coupled-Cluster corrections with inclusion of noniterative triple contributions (CCSD(T)) are given. The calculations are compared with selected medium quality methods. The PW91 DFT functional with the 6-31G basis set matches well the RI-MP2/CBS absolute interaction energies and reproduces the relative values of base pairing energies with a maximum relative error of 2.6 kcal/mol when applied with Becke3LYP-optimized geometries. The Becke3LYP DFT functional underestimates the interaction energies by few kcal/mol with relative error of 2.2 kcal/mol. Very good performance of nonpolarizable Cornell et al. force field is confirmed and this indirectly supports the view that H-bonded base pairs are primarily stabilized by electrostatic interactions.