鸟嘌呤红外光谱的密度泛函理论研究──标度量子力学(SQM)力场处理

用密度泛函理论DFT(B3LYP)/6-31G^*方法对鸟嘌呤分子的酮-胺式和醇-胺式异构体的几何结构、振动谐性力场和红外光谱进行了研究.理论力场由迁移自相关分子异胞嘧啶和咪唑的力常数标度因子进行标度.算得振动频率与鸟嘌呤的实验基质隔离IR光谱比较平均偏差对酮-胺式和醇-胺式分别为6.6和6.0cm^-1.根据振动频率的势能分布和DFT计算的光谱强度值对鸟嘌呤分子的实验振动基频进行了理论归属.     

Convenient Synthesis of Piperazine Substituted Quinolones

A series of 1‐[(4‐hydroxy‐2‐oxo‐1‐phenyl‐1,2‐dihydroquinolin‐3‐yl)carbonyl]‐4‐(substituted) piperazines 3a–c and methyl 2‐[(4‐hydroxy‐2‐oxo‐1‐phenyl‐1,2‐dihydroquinolin‐3‐yl)carbonylamino] alkanoates 5a–d has been developed by the direct condensation of ethyl [4‐hydroxy‐2‐oxo‐1‐phenyl‐1,2‐dihydro‐3‐quinoline] carboxylate 2 with N ¹‐monosubstituted piperazine hydrochlorides or amino acid ester hydrochloride in the presence of triethyl amine. The quinolone amino acid esters 5a–d were the key intermediate for the preparation of a series of 1‐[2‐((4‐hydroxy‐2‐oxo‐1‐phenyl‐1,2‐dihydroquinolin‐3‐yl)carbonylamino)alkylcarbony]‐4‐substituted piperazine derivatives 8–11 (a‐d) via azide coupling method with amino acid ester hydrochloride.     

Self‐aggregation of Synthetic Zinc Chlorophyll Derivatives Possessing 31‐Hydroxy or Methoxy Group and 131‐Mono‐ or Dicyanomethylene Moiety in Nonpolar Organic Solvents as Models of Chlorosomal Bacteriochlorophyll‐d Aggregates

Methyl 13¹‐(di)cyanomethylene‐pyropheophorbides were synthesized by Knoevenagel reactions of the corresponding 13¹‐oxo‐chlorins prepared from modifying chlorophyll‐a with malononitrile or cyanoacetic acid. Alternatively, methyl 13¹‐cyanomethylene‐pyropheophorbides were produced by Wittig reactions of 13¹‐oxo‐chlorins with Ph₃P=CHCN. Self‐aggregation of zinc complexes of the semi‐synthetic chlorophyll derivatives possessing a hydroxy or methoxy group at the 3¹‐position was examined in 1%(v/v) tetrahydrofuran or dichloromethane and hexane by electronic absorption and circular dichroism spectroscopy. Although intermolecular hydrogen‐bonding between the 3¹‐hydroxy and 13¹‐oxo groups of bacteriochlorophylls‐c/d/e/f was essential for their self‐aggregation in natural light‐harvesting antenna systems (=chlorosomes), zinc 3¹‐hydroxy‐13¹‐di/monocyanomethylene‐chlorins self‐aggregated in the less/lesser polar organic solvents to form chlorosome‐like large oligomers in spite of lacking the 13¹‐oxo moiety as the hydrogen‐bonding acceptor. Zinc 3¹‐methoxy‐13¹‐dicyanomethylene‐chlorin gave similar self‐aggregates regardless of lack of both the 3¹‐hydroxy and 13¹‐oxo groups. The present self‐aggregation was ascribable to stronger coordination of the 3¹‐oxygen atom to the central zinc than the conventional systems, where the electron‐withdrawing cyano group(s) increased the coordinative ability of the central zinc through the chlorin π‐system.     

The computed force constants and vibrational spectra of toluene

The complete harmonic force field and dipole moment derivatives have been computed for toluene at the Hartree-Fock level using a 4-21G basis set. The six scale factors optimized for benzene were used to scale the computed harmonic force constants of toluene. The vibrational frequencies of toluene computed from this scaled quantum mechanical force field are quite good. After a correction was made to two previously proposed spectral assignments, the mean deviation from the experimental frequencies is only 7.8 cm^?1 except for the frequencies related to the methyl group. Five more scale factors for the vibrational modes of the methyl group were reoptimized. The final comparison showed an overall mean deviation of 7.5 cm^?1 between the theoretical spectrum and the experimental spectrum. Computed intensities are qualitatively in agreement with experiments. They are highly useful in the investigation of questionable assignments.     

An Efficient Method for the Synthesis of Laquinimod

Laquinimod, 5‐chloro‐1,2‐dihydro‐N‐ethyl‐4‐hydroxy‐1‐methyl‐2‐oxo‐N‐ phenyl‐3‐quinoline carboxamide, is an oral drug in clinical trials for the treatment of multiple sclerosis. An efficient synthetic method for laquinimod from 2‐amino‐6‐chlorobenzoic acid via four steps was established. The overall yield of laquinimod is up to 82% as compared with 70% reported in literature. It has also been demonstrated that green reagent dimethyl carbonate is not suitable for the N‐methylation of 5‐chloroisatoic anhydride owing to the ring‐cleavage reaction induced by the generated methanol. The ring‐cleavage by‐products were isolated and characterized by ¹H‐NMR and ¹³C‐NMR. In addition, in the study of laquinimod derivatives, we found that 5‐chloro‐1,2‐dihydro‐N‐ethyl‐4‐hydroxy‐1‐methyl‐2‐oxo‐N‐phenyl‐3‐quinoline carboxamide (laquinimod) was obtained in much higher yield than 7‐chloro‐1,2‐dihydro‐N‐ethyl‐4‐hydroxy‐1‐methyl‐2‐oxo‐N‐phenyl‐3‐quinoline carboxamide under the same reaction conditions, and it is possibly attributed to a neighboring group effect.     

A new Sequiterpenoid from Eupatorium adenophorum Spreng

A new sequiterpenoid compound 8aα-hydroxy-1-isopropyl-4,7-dimethyl-1,2,3,4,6,8a-hexahydro-naphthalene-2,6-dione(1),together with seven known compounds anti-HH-dimer-coumarin(2),(-)-5-exo-hydroxy-bomeol(3),O-hydroxyl cinnamic acid(4),9β-hydroxy-ageraphorone(5),10Hα-9-oxo-ageraphorone(6),10Hβ-9-oxo-ageraphorone(7)and 9-oxo-10,11-dehydroageraphorone 8,was isolated from the leaves of Eupatorium adenopho-rum Spreng.The structures were elucidated by IR,~1H and ~(13)C NMR,EIMS,HMBC and single-crystal X-ray spec-tral data.     

Vibrational analysis of 2-nitrophenol. A joint FT-IR,FT-Raman and scaled quantum mechanical study

FT-IR (gas, solution, solid) and FT-Raman (solution, solid) spectra of 2-nitrophenol have been recorded in the range of 4000–30 cm⁻¹. The spectra were interpreted with the aid of normal coordinate analysis based on a scaled Becke3–Lee–Yang–Parr/6-31G^* density functional force field utilising a set of scale factors introduced recently by Rauhut and Pulay (G. Rauhut, P. Pulay, J. Phys. Chem. 99 (1995) 3093). These scale factors, developed on a small training set of organic molecules containing no hydrogen bonding moieties, were found to be well transferable to 2-nitrophenol including the strong intramolecular (O)H⋯O(N) hydrogen bonding moiety as well. The scaled force field reproduced the experimental frequencies of the molecule by a weighted mean deviation of 10.5 cm⁻¹. Based on the calculated results, 38 fundamentals from a total of 39 were identified and assigned, revising the assignments of earlier experimental studies for several fundamentals.     

Studies on nitramide and its methyl derivatives with ab initio calculations. IV. The harmonic force field and vibrational spectra of dimethylnitramine and its isotopic derivatives

The complete harmonic vibrational force field of dimethylnitramine has been calculated at the Hartree-Fock level using 4–21G basis set. The harmonic force field was then scaled with scale factors previously derived from N-methylnitramine, and the vibrational spectrum of dimethylnitramine was computed. This a priori prediction, made with no reference to observations on dimethylnitramine, agrees with the experimental IR spectrum in gas phase with a mean deviation of 8.4 cm^?1. Some of the scale factors were reoptimized by fitting of the computed force field to experimental data. The new set of scale factors reduced the mean deviation to 4.5 cm^?1, and was used to predict the vibrational spectrum of deuterated form of dimethylnitramine(-6D). Dipole moment derivatives were also calculated and used to predict infrared intensities which are comparable with experimental values.     

Study on reactivity of five‐coordinate bicycloazastannoxides III. New method for preparing β‐hydroxy‐α‐amino acids

Five‐coordinate bicycloazastannoxides containing a β‐hydroxy‐α‐amino acid moiety were synthesized. By hydrolysis under the action of 10% HCl, five β‐hydroxy‐α‐amino acids were prepared, and their structures were characterized by ¹H NMR spectroscopy, MS, and elemental analyses. The mechanism of the hydrolysis of the organotin (IV) complexes is discussed, and the yields of diastereomers are investigated by the HPLC method. This represents a new method for preparing β‐hydroxyl‐α‐amino acids. © 1999 John Wiley & Sons, Inc. Heteroatom Chem 10: 183–186, 1999     

Reaction of olefins using cerium(IV) sulfate tetrahydrate in carbonyl compounds–H2O

The reaction of olefins with cerium(IV) sulfate tetrahydrate [Ce(SO₄)₂·4H₂O, CS] in acetone–H₂O under reflux for 5 h gave 2‐oxo‐ and 2‐oxo‐5‐hydroxy derivatives. In this reaction, the yields of 2‐oxo‐5‐hydroxy derivatives were dependent on the quantity of H₂O. Moreover, the reaction of α, β‐unsaturated ketones with CS in acetone–H₂O yielded 2,7‐dioxo‐3‐hydroxy or 3,8‐dioxo‐4‐hydroxy derivatives. The reaction mechanism is also discussed. Copyright © 2005 John Wiley & Sons, Ltd.     

Synthesis and CD Spectra in MeCN,MeOH, and H2O of γ‐Oligopeptides with Hydroxy Groups on the Backbone,Preliminary Communication

γ⁴‐Tripeptides and γ⁴‐hexapeptides, 1 – 4 , with OH groups in the 2‐ or 3‐position on each residue have been prepared. The corresponding 2‐hydroxy amino acids were obtained by Si‐nitronate (3+2) cycloadditions to the acryloyl derivative of Oppolzer's sultam and Raney‐Ni reduction of the resulting 1,2‐oxazolidines (Scheme 1). The 3‐hydroxy amino acid derivatives were prepared by chain elongation via Claisen condensation of Boc‐Ala‐OH, Boc‐Val‐OH, and Boc‐Leu‐OH, and NaBH₄ reduction of the methyl 4‐amino 3‐oxo carboxylates formed (Scheme 2). The N‐Boc hydroxy amino acids were coupled in solution to give the γ‐peptides. CD Spectra of the new types of γ‐peptides were recorded and compared with those of simple γ²‐, γ³‐, γ⁴‐, and γ^2,3,4‐peptides (Figs. 3, 4, and 5). An intense Cotton effect at ca. 200 nm ([Θ]=−2⋅10⁵ deg⋅cm²⋅dmol⁻¹) indicates that the hexapeptide built of (3R,4S)‐4‐amino‐3‐hydroxy acids (with the side chains of Val, Ala, Leu) folds to a secondary structure so far unknown. The stability of peptides from β‐ and γ‐amino acids, which carry heteroatoms on their backbones is discussed (Fig. 1). Positions on the γ‐peptidic 2.6₁₄ helix are identified at which non‐H‐atoms are `allowed' (Fig. 2).     

Solid‐state tautomeric structure and invariom refinement of a novel and potent HIV integrase inhibitor

The conformation and tautomeric structure of (Z)‐4‐[5‐(2,6‐difluorobenzyl)‐1‐(2‐fluorobenzyl)‐2‐oxo‐1,2‐dihydropyridin‐3‐yl]‐4‐hydroxy‐2‐oxo‐N‐(2‐oxopyrrolidin‐1‐yl)but‐3‐enamide, C₂₇H₂₂F₃N₃O₅, in the solid state has been resolved by single‐crystal X‐ray crystallography. The electron distribution in the molecule was evaluated by refinements with invarioms, aspherical scattering factors by the method of Dittrich et al. [Acta Cryst. (2005), A 61 , 314–320] that are based on the Hansen–Coppens multipole model [Hansen & Coppens (1978). Acta Cryst. A 34 , 909–921]. The β‐diketo portion of the molecule exists in the enol form. The enol –OH hydrogen forms a strong asymmetric hydrogen bond with the carbonyl O atom on the β‐C atom of the chain. Weak intramolecular hydrogen bonds exist between the weakly acidic α‐CH hydrogen of the keto–enol group and the pyridinone carbonyl O atom, and also between the hydrazine N—H group and the carbonyl group in the β‐position from the hydrazine N—H group. The electrostatic properties of the molecule were derived from the molecular charge density. The molecule is in a lengthened conformation and the rings of the two benzyl groups are nearly orthogonal. Results from a high‐field ¹H and ¹³C NMR correlation spectroscopy study confirm that the same tautomer exists in solution as in the solid state.     

The first 3′:5′‐cyclic nucleotide–amino acid complex: l‐His–cIMP

In the crystal structure of the l ‐His–cIMP complex, i.e.l ‐histidinium inosine 3′:5′‐cyclic phosphate [systematic name: 5‐(2‐amino‐2‐carboxyethyl)‐1H‐imidazol‐3‐ium 7‐hydroxy‐2‐oxo‐6‐(6‐oxo‐6,9‐dihydro‐1H‐purin‐9‐yl)‐4a,6,7,7a‐tetrahydro‐4H‐1,3,5,2λ⁵‐furo[3,2‐d][1,3,2λ⁵]dioxaphosphinin‐2‐olate], C₆H₁₀N₃O₂⁺·C₁₀H₁₀N₄O₇P⁻, the Hoogsteen edge of the hypoxanthine (Hyp) base of cIMP and the Hyp face are engaged in specific amino acid–nucleotide (His...cIMP) recognition, i.e. by abutting edge‐to‐edge and by π–π stacking, respectively. The Watson–Crick edge of Hyp and the cIMP phosphate group play a role in nonspecific His...cIMP contacts. The interactions between the cIMP anions (anti/C3′–endo/trans–gauche/chair conformers) are realized mainly between riboses and phosphate groups. The results for this l ‐His–cIMP complex, compared with those for the previously reported solvated l ‐His–IMP crystal structure, indicate a different nature of amino acid–nucleotide recognition and interactions upon the 3′:5′‐cyclization of the nucleotide phosphate group.     

Scaled quantum mechanical force fields and vibrational spectra of solid state nucleic acid constituents V: thymine and uracil

The scale factors of the ab initio SCF STO-3G and MINI-1, and semiempirical PM3 harmonic force fields were determined by fitting to the Raman and IR spectra of polycrystalline uracil and thymine. Both in-plane and out-of-plane vibrational modes have been interpreted. The transferability of the scale factors between uracil and thymine and the performance of different computational methods were discussed. The Fermi resonance of the overtones of the out-of-plane deformation vibrations of oxygens with their stretching modes have been proposed as an explanation for the band splitting observed in the 1600–1800 cm⁻¹ region of uracil.     

Building a database of force constants based on scaled ab initio (SQM) results. I. Chlorobenzenes

As part of a project for developing a database of harmonic force constants for organic molecules, the complete force fields for chlorobenzene, ortho-, meta-, para-dichlorobenzene and sym-trichlorobenzene have been determined, on the basis of ab initio Hartree—Fock calculations combined with empirical adjustments. The latter serve to correct for systematic errors in the theory, and are applied at two stages: the geometry is corrected by using empirical offset forces during the optimization; force constants are corrected by a few scale factors according to the SQM (scaled quantum mechanical) force field procedure. With scale factors taken over fixed from benzene and only two new scale factors introduced for the chlorobenzenes, experimental frequencies are reproduced with mean deviations of about 10 cm⁻¹. Some controversial assignments, still present in the deuterated derivatives, are discussed. Theoretical IR and Raman intensities have also been calcuated and used as semiquantitative information to assist assignments.     

Wolves in Sheep's Clothing: μ‐Oxo‐Diiron Corroles Revisited

For well over 20 years, μ‐oxo‐diiron corroles, first reported by Vogel and co‐workers in the form of μ‐oxo‐bis[(octaethylcorrolato)iron] (Mössbauer δ 0.02 mm s^?1, ΔE_Q 2.35 mm s^?1), have been thought of as comprising a pair antiferromagnetically coupled low‐spin Fe^IV centers. The remarkable stability of these complexes, which can be handled at room temperature and crystallographically analyzed, present a sharp contrast to the fleeting nature of enzymatic, iron(IV)‐oxo intermediates. An array of experimental and theoretical methods have now shown that the iron centers in these complexes are not Fe^IV but intermediate‐spin Fe^III coupled to a corrole^.2?. The intramolecular spin couplings in {Fe[TPC]}₂(μ‐O) were analyzed via DFT(B3LYP) calculations in terms of the Heisenberg–Dirac–van Vleck spin Hamiltonian H=J_Fe–corrole(S_Fe?S_corrole)+J_Fe–Fe′(S_Fe?S_Fe′)+J_{Fe′–corrole}(S_Fe′?S_corrole′), which yielded J_Fe–corrole=J_{Fe′–corrole′}=0.355 eV (2860 cm^?1) and J_Fe–Fe′=0.068 eV (548 cm^?1). The unexpected stability of μ‐oxo‐diiron corroles thus appears to be attributable to charge delocalization via ligand noninnocence.     

Synthesis and Spectroscopic Characterization of New Double‐Armed Benzo‐15‐Crown‐5 Derivatives and Their Sodium Complexes

Double‐armed crown ether aldehydes ( 1–3 ) were synthesized from the reaction of 2 equiv salicylaldehyde, 4‐hydroxy‐3‐methoxybenzaldehyde (vanillin), and 3‐hydroxy‐4‐methoxybenzaldehyde (iso‐vanillin) with 4′,5′‐bis(bromomethyl)benzo‐15‐crown‐5. New crown ethers imine compounds ( 4–9 ) were synthesized by the condensation of corresponding crown ether aldehydes ( 1–3 ) with 4‐amino‐1,2‐dihydro‐1,5‐dimethyl‐2‐phenyl‐3H‐pyrazole‐3‐one and 2‐furan‐2‐yl‐methylamine. Sodium complexes ( 1a–9a) of the crown compounds form crystalline 1:1 (Na⁺:ligand) stoichiometries and were also synthesized. The structures of the crown ether aldehydes ( 1–3 ), imine compounds ( 4–9 ), and complexes ( 1a–9a ) were confirmed on the basis of elemental analyses, IR, ¹H and ¹³C NMR, and mass spectrometry. © 2013 Wiley Periodicals, Inc. Heteroatom Chem 24:100–109, 2013; View this article online at wileyonlinelibrary.com . DOI 10.1002/hc.21070     

Solvent‐Specific C―N Bond Formation: Synthesis of Novel Ninhydrin–Creatinine Heterocyclic Condensation Products

Novel ninhydrin–creatinine heterocyclic condensation products ( 3–5 ) were synthesized under different solvent conditions. The compound 2‐(2‐amino‐1‐methyl‐4‐oxo‐4,5‐dihydro‐1H‐imidazol‐5‐yl)‐2‐hydroxy‐1H‐ind‐ene‐1,3(2H)‐dione ( 3 ) was formed by reacting ninhydrin ( 1 ) with creatinine ( 2 ) in the presence of sodium acetate in acetic acid. The same reactants afforded the zwitterionic compound 4 when the reaction was carried out in water, and a novel oxadiazine ring system (product 5 ) was generated when benzene was used as solvent.     

Synthesis anti‐fungal and anti‐bacterial screening of 3‐phenyl‐1,4,5‐trihydro‐pyrazol and 2, 4‐dihydro[ 1,2,4]‐triazol‐3‐one derivatives of 4‐hydroxy‐2‐oxo‐2H‐1‐benzopyran

4‐Hydroxy‐2‐oxo‐2H‐1‐benzopyran‐3‐carboxaldehydes 2a‐d are prepared from 4‐hydroxy‐2‐oxo‐2H‐1‐benzopyrans 1a‐d via the Vielsmeyer Haack reaction. The 4‐hydroxy‐2‐oxo‐3‐(3′oxo‐3′‐phenylprop‐1′‐enyl)‐2H‐1‐benzopyrans 3a‐d are obtained from 2a‐d via the Claisen reaction. Refluxing compounds 3a‐d with hydrazine hydrate gave the 3‐phenyl‐5‐(4‐hydroxy‐2‐oxo‐2H‐1‐benzopyran‐3‐yl)‐1,4,5‐trihydropyra‐zols 4a‐d . Stirring compounds 2a‐d with semicarbazide hydrochloride in acidic medium gave the 4‐hydroxy‐2‐oxo‐2H‐1‐benzopyran‐3‐aldehyde‐semicarbazone 5a‐d , which on cyclisation with ferric chloride hexahydrate gave the 5‐(4‐hydroxy‐2‐oxo‐2H‐1‐benzopyran‐3‐yl)‐2,4‐dihydro[1,2,4]triazol‐3‐ones 6a‐d . All these compounds show significant antibacterial activities.     

New 9,10‐Secosteroids from Biotransformations of Hyodeoxycholic Acid with Rhodococcus spp.

The biotransformations of hyodeoxycholic acid with various Rhodococcus spp. are reported. Some strains (i.e., Rhodococcus zopfii, Rhodococcus ruber, and Rhodococcus aetherivorans) are able to partially degrade the side chain at C(17) to afford 6α‐hydroxy‐3‐oxo‐23,24‐dinor‐5β‐cholan‐22‐oic acid ( 2 ; 23%) and 6α‐hydroxy‐3‐oxo‐23,24‐dinorchol‐1,4‐dien‐22‐oic acid ( 3 ; 23–30%), together with two new 9,10‐secosteroids 4 and 5 (10–45%), still bearing the partial side chain at C(17) and adopting an intramolecular hemiacetal form. In addition, the 9,10‐secosteroid 5 showed an unprecedented C(4)‐hydroxylation. The new secosteroids were fully characterized by MS, IR, NMR, and 2D‐NMR analyses.