Batch tautomer generation with MolTPC

Besides all their conformational degrees of freedom, drug‐like molecules and natural products often also undergo tautomeric interconversions. Compared to the huge efforts made in experimental investigation of tautomerism, open and free algorithmic solutions for prototropic tautomer generation are surprisingly rare. The few freely available software packages limit their output to a subset of the possible configurational space by sometimes unwanted prior assumptions and complete neglection of ring‐chain tautomerism. Here, we describe an adjustable fully automatic tautomer enumeration approach, which is freely available and also incorporates the detection of ring‐chain variants. The algorithm is implemented in the MolTPC framework and accessible on SourceForge. © 2013 Wiley Periodicals, Inc.     

Integrated multidimensional and comprehensive 2D GC analysis of fatty acid methyl esters

Fatty acid methyl ester (FAME) profiling in complex fish oil and milk fat samples was studied using integrated comprehensive 2D GC (GC × GC) and multidimensional GC (MDGC). Using GC × GC, FAME compounds – cis‐ and trans‐isomers, and essential fatty acid isomers – ranging from C18 to C22 in fish oil and C18 in milk fat were clearly displayed in contour plot format according to structural properties and patterns, further identified based on authentic standards. Incompletely resolved regions were subjected to MDGC, with Cn (n = 18, 20) zones transferred to a ²D column. Elution behavior of C18 FAME on various ²D column phases (ionic liquids IL111, IL100, IL76, and modified PEG) was evaluated. Individual isolated Cn zones demonstrated about four‐fold increased peak capacities. The IL100 provided superior separation, good peak shape, and utilization of elution space. For milk fat‐derived FAME, the ²D chromatogram revealed at least three peaks corresponding to C18:1, more than six peaks for cis/trans‐C18:2 isomers, and two peaks for C18:3. More than 17 peaks were obtained for the C20 region of fish oil‐derived FAMEs using MDGC, compared with ten peaks using GC × GC. The MDGC strategy is useful for improved FAME isomer separation and confirmation.     

Stability and structure of mixed-ligand metal ion complexes that contain Ni2+, Cu2+, or Zn2+, and Histamine, as well as adenosine 5'-triphosphate (ATP4-) or uridine 5'-triphosphate (UTP(4-): an intricate network of equilibria

With a view on protein–nucleic acid interactions in the presence of metal ions we studied the “simple” mixed‐ligand model systems containing histamine (Ha), the metal ions Ni²⁺, Cu²⁺, or Zn²⁺ (M²⁺), and the nucleotides adenosine 5′‐triphosphate (ATP^4?) or uridine 5′‐triphosphate (UTP^4?), which will both be referred to as nucleoside 5′‐triphosphate (NTP^4?) . The stability constants of the ternary M(NTP)(Ha)^2? complexes were determined in aqueous solution by potentiometric pH titrations. We show for both ternary‐complex types, M(ATP)(Ha)^2? and M(UTP)(Ha)^2?, that intramolecular stacking between the nucleobase and the imidazole residue occurs and that the stacking intensity is approximately the same for a given M²⁺ in both types of complexes: The formation degree of the intramolecular stacks is estimated to be 20 to 50 %. Consequently, in protein–nucleic acid interactions imidazole–nucleobase stacks may well be of relevance. Furthermore, the well‐known formation of macrochelates in binary M²⁺ complexes of purine nucleotides, that is, the phosphate‐coordinated M²⁺ interacts with N7, is confirmed for the M(ATP)^2? complexes. It is concluded that upon formation of the mixed‐ligand complexes the M²⁺? N7 bond is broken and the energy needed for this process corresponds to the stability differences determined for the M(UTP)(Ha)^2? and M(ATP)(Ha)^2? complexes. It is, therefore, possible to calculate from these stability differences of the ternary complexes the formation degrees of the binary macrochelates: The closed forms amount to (65±10) %, (75±8) %, and (31±14) % for Ni(ATP)^2?, Cu(ATP)^2?, and Zn(ATP)^2?, respectively, and these percentages agree excellently with previous results obtained by different methods, confirming thus the internal validity of the data and the arguments used in the evaluation processes. Based on the overall results it is suggested that M(ATP)^2? species, when bound to an enzyme, may exist in a closed macrochelated form only, if no enzyme groups coordinate directly to the metal ion.     

Comparative nonempirical study and isodesmic calculations of heats of formation of HNCO and HPCO isomers

The structural, electronic, and energetic characteristics of CHNO and CHOP isomers, and also of several related compounds, were calculated by a nonempirical method. Enthalpies of these isomers, obtained using the method of isodesmic reactions, are given.V. I. Lenin Moscow Pedagogical State University, 117913 Moscow. Institute of Physiologically Active Compounds, Russian Academy of Sciences, 142432 Chernogolovka. Institute of New Chemical Problems, Russian Academy of Sciences, 142432 Chernogolovka. Translated from Izvestiya Akademii Nauk, Seriya Khimicheskaya, No. 7, pp. 1585–1590, July, 1992.     

Novel supramolecular isomerism in coordination polymer synthesis from unsymmetrical bridging ligands: solvent influence on the ligand placement orientation and final network structure

The assembly of Co(NCS)(2) with 1-methyl-1'-(3-pyridyl)-2-(4-pyridyl)ethene (L(1)) exhibits a novel supramolecular isomerism of [Co(L(1))(2)(NCS)(2)](infinity) caused by different placement orientation of L(1) around metal centers. The reaction in MeOH/H(2)O and EtOH/H(2)O resulted in a double chain structure of 1, and that in EtOH/CH(3)NO(2) led to an open framework structure of 2. The reaction in MeOH/CH(3)NO(2) solvent system concomitantly afforded 1 and 2. The assemblies of 1-(3-pyridyl)-2-(4-pyrimidyl)ethene (L(2)) with Co(NCS)(2) created the water-coordinated complexes of Co(L(2))(2)(H(2)O)(2)(NCS)(2) (3 and 4), an MeOH coordinated complex of Co(L(2))(2)(H(2)O)(2)(NCS)(2) (5), and an open framework coordination polymer of [Co(L(1))(2)(NCS)(2)](infinity) (6) depending on the reaction solvent system. From these observations, it is suggested that in the formation of 1, the solvent-coordinated intermediate species would be generated first and its trans coordination configuration should define the placement orientation of L(1) in the resulting polymer of 1. On the other hand, it is presumed that the solvent-coordinated intermediate would not be produced during the formation of 2 due to the weaker coordination ability of EtOH and CH(3)NO(2) molecules. The open framework coordination polymers of 2 and 6 are converted in the solid state into the isomeric coordination polymer of 1 and hydrogen bonded network structure of 3, respectively.     

Organometallic alkane CH activation

The title topic is reviewed with emphasis on catalysis and on recent advances. Alkane σ complexes, Shilov chemistry and oxidative addition routes are covered. Attention is also given to σ bond metathesis, surface-bound organometallics and CH activation involving carbene complexes. Closely related reactions of non-alkane substrates such as the Murai reaction are also discussed.     

Isomers of C20: an energy profile III

Semiempirical calculations, at the PM3 level provided within the Winmopac v2.0 software package, are used to geometrically optimize and determine the absolute energies (heats of formation) of a variety of C(20) isomers that are predicted to exist in and around the ring and cage isomers. Using the optimized Cartesian coordinates for the ring and the cage isomers, a saddle-point calculation was performed. The resulting energy profile, consisting of a series of peaks and valleys, is used as a starting point for the identification and location of fifteen additional isomers of C(20) that are predicted to be energetically stable, both via geometry optimizations and force constant analysis. These additional isomers were subsequently determined to lie adjacent to one another on the potential surface and establish a step-wise transformation between the ring and the cage. Transition-state optimization of the Cartesian coordinates at the saddle point between adjacent isomers was performed to quantify the energy of the transition state. The step-wise process from one isomer to another, which extends out over the three-dimensional surface, is predicted to require approximately 15% less energy than that of the direct, two-dimensional transformation predicted in the bowl-cage profile. However, the net atomic rearrangement for the step-wise process is about four times greater than that of the direct process. Although less in energy, the amount of atomic rearrangement in the step-wise process would make the occurrence of such a route prohibitive. Utilizing the direct distance separating the three primary isomers (ring, bowl, cage), the method of triangulation is performed to quantitatively position other C(20) structures on the potential surface, relative to the ring, bowl, and cage isomers.     

含钴、锰杂原子分子筛上烷烃低温分子氧氧化

用水热法合成了MeAlPO-5,MeAPSO-35,MeAlPO-18(MeAPS-18(Me=Co,Mn)分子筛,并用XRD和TPD对其进行表征。考察了在氧气作氧化剂的情况下,辛烷在这些杂原子分子筛上的氧化反应行为。辛烷氧化反应产物中,除辛酮和辛醇外,还出现了辛烷裂解氧化产物和辛烷多氧代产物。不同结构的分子筛催化剂上,辛烷氧化反应产物的选择性差异不大。在含有较多酸中心的MeAPSO分子筛上,n(辛酮)/n(辛醇)比要高于相同结构的MeAlPO分子筛。催化剂转移实验显示,氧化反应在多相体系中进行。考察了反应时间和温度变化对辛烷氧化反应的转化率及产物选择性等的影响,根据实验结果对反应机理进行了讨论。