Electronic structures and spectra of halogenated purines and pyrimidines II.π-Electronic structure of 2-chloropurine and its related derivatives

Electronic structures and spectra of “non-alternant” heterocyclic 2-chloropurine and its analogs have been computed with different MO techniques, namely, HMO, ω-SCF -HMO (ω = 1.4 and 0.5), and PPP semiempirical SCF -ASMO -CI . Triplet-state energies have been calculated by the last method. In general, it is found that at least semiquantitatively consistent results on the ground-state properties of the molecules are obtained from the different MO methods. As expected, excited states of the molecules are not satisfactorily treated by the HMO and σ techniques. However, an excellent agreement between the observed and calculated π-π* transition energies has been obtained with the PPP method. In view of the semiquantitative consistency of the ground-state properties, the use of simple methods such as HMO and ω(=0.5)-SCF techniques is justifiable for limited application to molecular biology. Results on the molecular geometry, dipole moments, ionization potentials, xanthine oxidase reactivity and spectra have been discussed with regard to the halogen substitutions in the purine base. The significance of these results with reference to the biological uses of substituted purines is briefly described.     

Detection of milk oligosaccharides in plasma of infants

Human milk oligosaccharides (HMO) are one of the major components of human milk. HMO are non-digestible by the human gut, where they are known to play important functions as prebiotics and decoys for binding pathogens. Moreover, it has been proposed that HMO may provide sialic acids to the infant that are important in brain development, however this would require absorption of HMO into the bloodstream. HMO have consistently been found in the urine of humans and other mammals, suggesting systemic absorption. Here, we present a procedure for the profiling of milk oligosaccharides (MO) in plasma samples obtained from 13 term infants hospitalized for surgery for congenital heart disease. The method comprises protein denaturation, oligosaccharide reduction, and porous graphitized carbon solid phase extraction for purification followed by analysis using nHPLC-PGC-chip-TOF-MS. Approximately 15 free MO were typically observed in the plasma of human infants, including LNT, LDFP, LNFT, 3′SL, 6′SL, 3′SLN, and 6′SLN, of which the presence was confirmed using fragmentation studies. A novel third isomer of SLN, not found in human or bovine milk was also consistently detected. Differences in the free MO profiles were observed between infants that were totally formula-fed and infants that received at least some part breast milk. Our results indicate that free MO similar in structure to those found in human milk and urine are present in the blood of infants. The method and results presented here will facilitate further research toward the possible roles of free MO in the development of the infant.     

A comparison of various MO methods for predicting regioselectivity in Diels-Alder reactions

Various semiempirical MO methods for predicting regioselectivity in Diels-Alder reactions are compared in order to examine their reliability. They are the frontier molecular orbital method using CNDO/2, HMO and MNDO molecular orbitals and the HMO approach on pericyclic reactions presented by Tang.     

Mechanisms of the reactions of W AND W+ with H2O: computational studies

The mechanism of the reactions of W and W(+) with the water molecule have been studied for several lower-lying electronic states of tungsten centers at the CCSD(T)/6-311G(d,p)+SDD and B3LYP/6-31G(d,p)+SDD levels of theory. It is shown that these reactions are essentially multistate processes, during which lower-lying electronic states of the systems cross several times. They start with the formation of initial prereaction M(H(2)O) complexes with M-H(2)O bonding energies of 9.6 and 48.2 kcal/mol for M = W and W(+), followed by insertion of the metal center into an O-H bond with 20.0 and 53.3 kcal/mol barriers for neutral and cationic systems, respectively. The overall process of M + H(2)O --> t-HM(OH) is calculated to be highly exothermic, 48.4 and 48.8 kcal/mol for M = W and W(+). From the HM(OH) intermediate the reaction may proceed via several different channels, among which the stepwise HM(OH) --> HMO + H --> (H)(2)MO and concerted HM(OH) --> (H)(2)MO pathways are more favorable and can compete (energetically) with each other. For the neutral system (M = W), the concerted process is the most favorable, whereas for the charged system (M = W(+)), the stepwise pathway is slightly more favorable. From the energetically most favorable intermediate (H)(2)MO the reactions proceed via H(2)-molecule formation with a 53.1 kcal/mol activation barrier for the neutral system. For the cationic system, H-H formation and dissociation is an almost barrierless process. The overall reaction of W and W(+) with the water molecule leading to H(2) + MO formation is found to be exothermic by 48.2 and 39.8 kcal/mol, respectively. In the gas phase with the collision-less conditions the reactions W((7)S) + H(2)O --> H(2) + WO((3)Sigma(+)), and W(+)((6)D) + H(2)O --> H(2) + WO(+)((4)Sigma(+)) are expected to proceed via a 10.4 and 5.1 kcal/mol overall energy barrier corresponding to the first O-H dissociation at the TS1. On the basis of these PESs, we predict kinetic rate constants for the reactions of W and W(+) with H(2)O.     

Electronic structures and spectra of halogenated purines and pyrimidines III.σ-Electronic structure and some comments on the mechanism of the xanthine oxidase reaction of 2-halopurines and related analogs

The extended HMO (EHMO) and Pople-Segal SCF-MO-CNDO /2 calculations on purine, 8-oxopurine, 2-oxopurine, 2-fluoropurine, and 2-chloropurine indicate significant polarizations of the σ cores. It is shown that the polarizations of both σ and π frameworks are mutually opposing in some cases. The results from the two methods are compared for these complex biomolecules. It is found that the EHMO calculations tend to over-polarize the σ and π frameworks. However, the CNDO shows anomalous π-electron densities on N₍₇₎ and C₍₈₎ of the purine rings, and the reason for this anomaly is not certain. The application of the results to the xanthine oxidase system indicates that the substrate molecules are subject to a specific orientation on the enzyme surface to counteract the electronic reactivity, in support of the previous prediction based on the π-electron calculations. The CNDO results appear to be more satisfactory than the EHMO in this respect.     

Matrix isolation spectroscopic and theoretical study of water adsorption and hydrolysis on molecular tantalum and niobium oxides

The reactions of molecular tantalum and niobium monoxides and dioxides with water were investigated by matrix isolation infrared spectroscopy. In solid neon, the metal monoxide and dioxide molecules reacted with water to form the MO(H(2)O) and MO(2)(H(2)O) (M = Ta, Nb) complexes spontaneously on annealing. The MO(H(2)O) complexes photochemically rearranged to the more stable HMO(OH) isomers via one hydrogen atom transfer from water to the metal center under visible light excitation. In contrast, the MO(2)(H(2)O) complexes isomerized to the more stable MO(OH)(2) molecules via a hydrogen atom transfer from water to one of the oxygen atoms of metal dioxide upon visible light irradiation. The aforementioned species were identified by isotopic-substituted experiments as well as density functional calculations.     

pi Molecular Orbital Crossing a(2)(chi)/b(1)(psi) in 1,10-Phenanthroline Derivatives. Ab Initio Calculations and EPR/ENDOR Studies of the 4,7-Diaza-1,10-phenanthroline Radical Anion and Its M(CO)(4) Complexes (M = Cr, Mo, W)

Ab initio, semiempirical, and HMO perturbation calculations were employed to assess the relative positioning of the closely situated low-lying unoccupied pi MOs a(2)(chi) and b(1)(psi) in 1,10-phenanthroline (phen) and its 3,4,7,8-tetramethyl (tmphen) and four symmetrical diaza derivatives (n,m-dap). Compared to a(2)(chi), the b(1)(psi) pi MO is distinguished by markedly higher MO coefficients at the chelating nitrogen pi centers in 1,10-positions; eventually, a higher Coulomb integral value at those positions will thus always favor the lowering of b(1) beyond a(2). Using the Coulomb integral parameter at the chelating 1,10-nitrogen pi centers as the HMO perturbation variable, the crossing of both energy levels in terms of decreasing preference for the a(2)(chi) over the b(1)(psi) orbital as the lowest unoccupied MO follows the sequence 5,6-dap > 2,9-dap > 4,7-dap > phen > 3,8-dap. The calculations reveal a(2)(chi) as the LUMO in 5,6-dap for all reasonable perturbation parameters, in agreement with previous observations for ruthenium(II) complexes which reveal a discrepancy between the lowest-lying "redox pi orbital" (a(2)) and the "optical pi MO" (b(1)) to which the most intense low-energy MLCT transition occurs. According to the HMO calculations, the situation is more ambiguous for the 4,7-dap analogue, yet EPR/ENDOR studies clearly show that the one-electron-reduced ligand and its tetracarbonylmetal(0) complexes (Cr, Mo, W) have the b(1)(psi) orbital singly occupied. Only ab initio calculations with double-zeta basis and inclusion of d polarization functions reproduced correctly the experimentally observed orbital ordering for tmphen (a(2) < b(1)) and for phen and 4,7-dap (b(1) < a(2)).     

Structure–activity relationship and the mechanism of analgesia of the analgesic drug 3-methyl-fentanyl and its analogs

The semiempirical self-consistent field MO (CNDO /2) calculations have been undertaken for 13 compounds involving 3-methyl-fentanyl and its analogs. Various quantum chemical indices were obtained. The relationships between the biological activity and quantum chemical indices of molecules of these compounds were investigated and it was found that there are remarkable relationships between the activity and some important quantum chemical indices such as the α-electron density of β substituent and the electron density of piperidyl nitrogen. The nature of interaction between the analgesics' molecule and the receptor was discussed on the basis of the relationships between the activity and quantum chemical indices and it was proposed that the β-substituent functions not only as a hydrophobic group, but also its electronic property has important effect on the activity. It may act as an electron acceptor and form acceptor–donor complex with receptor through the charge transfer process. The piperidyl nitrogen interacts with receptor forming quaternary ammonium ion and acting as positive charge center, and its electron density also has an important effect on the activity. The amide oxygen and nitrogen may be other active centers which function as donors when they interact with the receptor. The influence on activity through introduction of the hydroxyl group to the β-position of the 1-substituent of the piperdyl ring has also been discussed.     

LUMINESCENCE SPECTRA AND PHOTOCYCLOADDITION OF THE EXCITED COUMARINS TO DNA BASES

Abstract— The lowest excited singlet and triplet states of coumarin, psoralen, and 4-hydroxy-coumarin have been assigned to the (π,π * ) type on the basis of the luminescence spectroscopy and MO calculations. The mechanism of photocycloaddition of courmarin and psoralen to thymine has been described in terms of the perturbational MO model and MO reactivity indices. All possible cycloaddition patterns have been examined. Results suggest that the 3,4-bond of coumarin in the excited state is somewhat more reactive than the same bond of psoralen in the excited state. It is also predicted that the 3,4-bond of psoralen in the triplet state is more reactive than the 4', 5'-bond. The results have been favorably correlated with the electronic characteristics of excited coumarin molecules and with available experimental data on the relative yields of photoadducts.     

Selective removal of enzymes from substrate and products. An alternative to immobilization for enzymes acting on macromolecular or solid substrates

A new approach for the control and interruption of enzymatic reactions via selective enzyme immobilization has been developed. The technique was exemplified by the use of three model enzymes with the corresponding macromolecular substrates: α-amylase/starch, trypsin/ insoluble collagen, and alkaline phosphatase/plasmid DNA. Prior to incubation with its substrate, each enzyme was provided withde novo thiol-groups by a two-step reaction involvingN-succinimidyl-3-(2-pyridyldithio) propionate (SPDP) and DTT. The chemical modification was achieved such that at least 80% of the native enzyme activity was preserved in all cases. In order to interrupt rapidly the reactions in which the enzymes were used, the modified enzyme was immobilized by reaction via its thiol groups on a thiolsulfinate-agarose derivative. The gel-bound enzyme could then be easily removed from unreacted substrate and product by filtration or centrifugation. Comparative studies showed that the immobilized enzymes had much lower activities in the reactions studied than the corresponding soluble ones. The potential for enzyme reuse was also demonstrated with the a-amylase derivatives, which were quantitatively released and eluted in fully active form from the agarose. We have shown that it is possible to achieve practically complete enzyme immobilization in short times and thus to control the progress of the reactions. Because of its simplicity and high efficiency, this approach may represent an interesting alternative for biotechnological processes involving macromolecular or solid substrates.     

Prediction of the mechanisms of enzyme-catalysed reactions using hybrid quantum mechanical/molecular mechanical methods

The use of hybrid methods, involving both quantum mechanics and molecular mechanics, to model the mechanism of enzyme-catalysed reactions, is discussed. Two alternative approaches to treating the electrostatic interactions between the quantum mechanical and molecular mechanical regions are studied, involving either the inclusion of this term in the electronic Hamiltonian (QM/MM), or evaluating it purely classically (MO + MM). In the latter scheme, possible problems of using force fields that are standard for macromolecular modelling are identified. The use of QM/MM schemes to investigate the mechanism of the enzymes thymidine phosphorylase (ThdPase) and protein tyrosine phosphatase (PTP) is described. For both systems, transition states have been identified using a PM3 Hamiltonian. For ThdPase, concerted motion of the enzyme during the course of the reaction is suggested and, for PTP, a two-step dephosphorylation reaction is indicated, both with quite low barriers.     

On the OCS2 Singlet potential energy surface

The reaction between atomic oxygen and carbon disulfide is predicted to lead to at least two primary products, which are the dithiiranone ( 1 ) and the oxathiirane-thione ( 2 ) and/or the carbon disulfide S-oxide ( 4 ). The possible intramolecular equilibria 1 ? 2, 1 ? 3, 2 ? 4 , and 2 ? 5 as well as the fragmentations of the possible intermediates 1 – 5 have been studied theoretically within the semiempirical CNDO /B framework as conceivable ground-state reactions. On the basis of MO correlations and potential energy changes along the reaction paths, supplementary with previously reported experimental data, the single molecular transformations and the eventual product formations are discussed.     

SNAr iodination of 6-chloropurine nucleosides: aromatic Finkelstein reactions at temperatures below -40 degrees C

Mesitoyl or toluoyl esters of inosine and 2'-deoxyinosine were deoxychlorinated at C6 to give the crystalline 6-chloropurine nucleoside derivatives, which underwent quantitative conversion to the 6-iodo analogues with NaI/TFA/butanone at -50 to -40 degrees C. The 6-iodo compounds were efficient substrates for SNAr, Sonogashira, and Suzuki-Miyaura reactions, in contrast with the 6-chloro analogues, and gave good to high yields of C-N and C-C coupled products.     

Nucleic acid related compounds. 116. Nonaqueous diazotization of aminopurine nucleosides. Mechanistic considerations and efficient procedures with tert-butyl nitrite or sodium nitrite

Nonaqueous diazotization-dediazoniation of two types of aminopurine nucleoside derivatives has been investigated. Treatment of 9-(2,3,5-tri-O-acetyl-beta-D-ribofuranosyl)-2-amino-6-chloropurine (1) with SbCl(3)/CH(2)Cl(2) was examined with benzyltriethylammonium (BTEA) chloride as a soluble halide source and tert-butyl nitrite (TBN) or sodium nitrite as the diazotization reagent. Optimized yields (>80%) of the 2,6-dichloropurine derivative were obtained with SbCl(3). Combinations with SbBr(3)/CH(2)Br(2) gave the 2-bromo-6-chloropurine product (>60%), and SbI(3)/CH(2)I(2)/THF gave the 2-iodo-6-chloropurine derivative (>45%). Antimony trihalide catalysis was highly beneficial. Mixed combinations (SbX(3)/CH(2)X'(2); X/X' = Br/Cl) gave mixtures of 2-(bromo, chloro, and hydro)-6-chloropurine derivatives that were dependent on reaction conditions. Addition of iodoacetic acid (IAA) resulted in diversion of purine radical species into a 2-iodo-6-chloropurine derivative with commensurate loss of other radical-derived products. This allowed evaluation of the efficiency of SbX(3)-promoted cation-derived dediazoniations relative to radical-derived reactions. Efficient conversions of adenosine, 2'-deoxyadenosine, and related adenine nucleosides into 6-halopurine derivatives of current interest were developed with analogous combinations.     

Orbital symmetry,orbital stability,and orbital pairing rules for organic reactions in the ground state

A generalization of the Hartree–Fock molecular orbital (MO) theory for treating diradical intermediates was explained pictorially by drawing molecular orbitals of diradical species such as ring-opened trimethylene. The generalized MO theory applied to elucidate electronic mechanisms of concerted, ionic, radical, and ion-radical reactions of organic reactants in the ground state. Generalized MO computations revealed the most essential characteristics of these reactions and mutal relationships between the worlds of Woodward–Hoffmann and Hughes–Ingold. Generalized MO studies supported our orbital symmetry, stability and pairing rules for concerted, ionic and radical reactions in the ground state, respectively. An extension of MO treatments to excited states reactions was briefly pointed out in relation to the density and spin correlation functions by the multireference CI wave functions.     

Regioselectivity prediction of CYP1A2-mediated phase I metabolism

A kinetic, reactivity-binding model has been proposed to predict the regioselectivity of substrates meditated by the CYP1A2 enzyme, which is responsible for the metabolism of planar-conjugated compounds such as caffeine. This model consists of a docking simulation for binding energy and a semiempirical molecular orbital calculation for activation energy. Possible binding modes of CYP1A2 substrates were first examined using automated docking based on the crystal structure of CYP1A2, and binding energy was calculated. Then, activation energies for CYP1A2-mediated metabolism reactions were calculated using the semiempirical molecular orbital calculation, AM1. Finally, the metabolic probability obtained from two energy terms, binding and activation energies, was used for predicting the most probable metabolic site. This model predicted 8 out of 12 substrates accurately as the primary preferred site among all possible metabolic sites, and the other four substrates were predicted into the secondary preferred site. This method can be applied for qualitative prediction of drug metabolism mediated by CYP1A2 and other CYP450 family enzymes, helping to develop drugs efficiently.     

Reactions of late lanthanide metal atoms with water molecules: a matrix isolation infrared spectroscopic and theoretical study

The reactions of late lanthanide metal atoms (Gd-Lu) with water molecules have been investigated using matrix isolation infrared spectroscopy. The reaction intermediates and products were identified on the basis of isotopic substitution experiments and density functional theory calculations. All of the metal atoms except Lu react with water to form the M(H2O) complexes spontaneously upon annealing (M = Gd, Tb, Dy, Ho, Er, Tm, and Yb). The Dy(H2O) and Ho(H2O) complexes are able to coordinate a second water molecule to form the Dy(H2O)2 and Ho(H2O)2 complexes. The M(H2O) complexes isomerize to the inserted HMOH isomers under visible light irradiation, which further decompose to give the MO and/or HMO molecules upon UV light irradiation. The M(OH)2 molecules (M = Gd-Lu) were also produced. The results have been compared with our earlier work covering the early lanthanide metal atoms (Nd, Sm, Eu) to observe the existent trends for the lanthanide metal atom reactions.     

Single-molecule Förster resonance energy transfer reveals an innate fidelity checkpoint in DNA polymerase I

Enzymatic reactions typically involve complex dynamics during substrate binding, conformational rearrangement, chemistry, and product release. The noncovalent steps provide kinetic checkpoints that contribute to the overall specificity of enzymatic reactions. DNA polymerases perform DNA replication with outstanding fidelity by actively rejecting noncognate nucleotide substrates early in the reaction pathway. Substrates are delivered to the active site by a flexible fingers subdomain of the enzyme, as it converts from an open to a closed conformation. The conformational dynamics of the fingers subdomain might also play a role in nucleotide selection, although the precise role is currently unknown. Using single-molecule F?rster resonance energy transfer, we observed individual Escherichia coli DNA polymerase I (Klenow fragment) molecules performing substrate selection. We discovered that the fingers subdomain actually samples through three distinct conformations--open, closed, and a previously unrecognized intermediate conformation. We measured the overall dissociation rate of the polymerase-DNA complex and the distribution among the various conformational states in the absence and presence of nucleotide substrates, which were either correct or incorrect. Correct substrates promote rapid progression of the polymerase to the catalytically competent closed conformation, whereas incorrect nucleotides block the enzyme in the intermediate conformation and induce rapid dissociation from DNA. Remarkably, incorrect nucleotide substrates also promote partitioning of DNA to the spatially separated 3'-5' exonuclease domain, providing an additional mechanism to prevent misincorporation at the polymerase active site. These results reveal the existence of an early innate fidelity checkpoint, rejecting incorrect nucleotide substrates before the enzyme encloses the nascent base pair.     

Properties and construction of azo-dye reagents for inorganic photometric analysis

An approach to constructing new organic reagents (based on azo dyes) for photometric analysis is described. Its essence is the detailed consideration of the electronic structure of the chromophore nuclei of the dyes in the ground and excited states. Knowing the nature of the electron transition, it is possible to construct the organic reagents with optimal properties. The electronic structure of the azo dyes has been analysed in a pi-approximation by an MO LCAO SCF method.     

2,5-二取代(口恶)唑的研究(Ⅱ)——HMO计算及光谱的取代基效应

本文对2-苯基上邻、间、对取代的三个系列2-苯基-5-联苯基噁唑的衍生物进行了HMO计算,并结合所得到的分子轨道能量和分子图,对取代基效应与光谱性质以及MO有关指数的影响做了量子化学说明;同时,考虑到基团的邻位效应对2-苯基邻位取代系列中的HMO参数进行了适当调整,所得计算结果与实验数据有较好的相关性。