Singlet Nitric Oxide Dimer Revisited: An Unexpected High Stability Isomer

A new form of the asymmetric cis isomer of the nitric oxide dimer, a cyclic parallelogram, has been found and characterized as the second most stable conformation by ab initio computational methods. Optimum equilibrium geometries, energetics, and harmonic frequencies are computed for the cyclic structure and the more common symmetric cis and trans isomers at the levels of second-order perturbation theory (MP2) and coupled-cluster theory limited to double excitations (CCD) using the 6-311G(2d) and 6-311+G(2d) basis sets. Single-point, more highly correlated calculations are then performed at these CCD optimum geometries. In addition, second-order geometries and frequencies are computed using the larger 6-311G(3df) basis, and single-point MP2 calculations are performed at these geometries using the Aug-cc-pVTZ and Aug-cc-pVQZ basis sets. At the highest levels of theory considered, the cyclic isomer lies within 17 kJ/mol of the symmetric cis global minimum and is more stable than the often-studied symmetric trans conformation.     

Synthesis and Characterization of Some Ru( tmeda ) Complexes Containing Chloride, Hydride, and Vinylidene Ligands

 The polymeric compound [Ru(cod)Cl₂] _x (cod = cyclooctadiene) reacts with 2 equivalents of tmeda (N,N,N′,N′-tetramethylethylenediamine) in refluxing MeOH to afford trans-[Ru(cod)(tmeda)(Cl)(H)] (1), which upon treatment with CHCl₃ is readily converted to the dichloro complex trans-[Ru(cod)(tmeda)Cl₂] (2). When [Ru(cod)Cl₂] _x is reacted with tmeda under an atmosphere of H₂ (3 bar), the bis-tmeda complex trans-[Ru(tmeda)₂Cl₂] (3) is obtained in 80% yield. DFT calculations revealed that 3 is by 52 kJ/mol more stable than the corresponding cis isomer. Attempts to prepare the coordinatively unsaturated complex [Ru(tmeda)₂Cl]⁺ by reacting 1 with TICF₃SO₃ were unsuccessful. According to DFT calculations, however, such a complex should be stable and, interestingly, should adopt a square pyramidal rather than a trigonal bipyramidal structure. If halide abstraction of 3 is performed in the presence of terminal alkynes HC*CR (R*t-Bu, n-Bu), the cationic vinylidene complexes [Ru(tmeda)₂(Cl)(*C*CHR)]⁺ (4a,b) are obtained.     

Synthesis,characterization and in vitro cytotoxicity of platinum(II) complexes of selenones [Pt(selenone)2Cl2]

Platinum(II) complexes with various selenones (L) having the general formula [PtL₂Cl₂] were prepared and characterized by elemental analysis and, IR and NMR (¹H, ¹³C, and ⁷⁷Se) spectroscopies. A decrease in the IR frequency of the >C=Se mode and an upfield shift in ¹³C NMR for the >C=Se resonance of selenones are consistent with their selenium coordination to platinum(II). The NMR data show that the complexes are stable in solution and do not undergo equilibration at 297 K. The geometrical structures of the complexes were predicted theoretically (with DFT method) using Gaussian09 program. DFT calculations predicted that the trans configurations were up to 1.7 kcal/mol more stable than the cis forms in gas phase, while in solution form the cis isomers were predicted to be more stable. The UV–vis spectra of the two complexes, 6 and 7 were also recorded at room temperature for 24 h and it was observed that the complexes were stable and did not undergo decomposition. The in vitro antitumor properties of the complexes as well as of cisplatin were evaluated on two human cancer cell lines, HeLa (cervical cancer cells) and MCF7 (breast cancer cells) using MTT assay. The results indicated that the prepared complexes exerted significant inhibition on the selected cancer cells.     

Separation and characterization of oxaliplatin dinucleotides from DNA using HPLC-ESI ion trap mass spectrometry

Oxaliplatin is a third-generation platinum complex, and has a broad spectrum of antitumor activity. Such platinum complexes with the DACH carrier ligand have recently received increasing attention since they show efficacy against cisplatin-resistant cell lines. As the foremost indication of antitumor activity of platinum drugs is the formation of adducts with genomic DNA, calf thymus DNA-oxaliplatin adducts were the major target in this study. Calf thymus DNA was incubated with oxaliplatin, resulting in the formation of a large number of platinum-DNA adducts. Treated DNA was digested into the dinucleotides with a combination of enzymes, namely, benzonase, alkaline phosphatase, and nuclease S1. Using a high-performance liquid chromatography, we carried out the separation of individual platinum-DNA adducts which were concurrently identified using electrospray ionization ion trap mass spectrometry (MS). Both 1,2-intrastrand and 1,2-interstrand cross-linked adducts were found; however, those of the intrastrand nature have a considerably higher abundance than those of the interstrand cross-links. Among them, d(GpG)-oxaliplatin was the most abundant bifuctional adduct. To a lesser extent, a few monofunctional adducts were detected as well. MS ⁿ experiments served to ascertain the detailed structures of oxaliplatin adducts of dinucleoside monophosphates and of dinucleotides. Figure Three-dimensional view of the d(GpG)-Pt(DACH) adduct of m/z 902 (a) and of the d(ApG)-Pt(DACH) adduct of m/z 886 (b). DACH 1,2-diaminocyclohexane, green phosphorus, red oxygen, light blue carbon, dark blue nitrogen, gray platinum Abbreviations  They are shown in Fig. 1     

Ab initio study on the mechanism of reaction HNCO+NH2

Ab initio UMP2 and UQCISD(T) calculations, with 6-311G** basis sets, were performed for the titled reactions. The results show that the reactions have two product channels: NH₂+ HNCO?NH₃+NCO (1) and NH₂+HNCO?N₂H₃+CO (2), where reaction (1) is a hydrogen abstraction reaction via an H-bonded complex (HBC), lowering the energy by 32.48 kJ/mol relative to reactants. The calculated QCISD(T)//MP2(full) energy barrier is 29.04 kJ/mol, which is in excellent accordance with the experimental value of 29.09 kJ/mol. In the range of reaction temperature 2300–2700 K, transition theory rate constant for reaction (1) is 1.68×10¹¹–3.29×10¹¹ mL·mol^-1·s^-1, which is close to the experimental one of 5.0×10¹¹mL·mol^-1·s^-1or less. However, reaction (2) is a stepwise reaction proceeding via two orientation modes,cis andtrans, and the energy barriers for the rate-control step at our best calculations are 92.79 kJ/mol (forcis-mode) and 147.43 kJ/mol (fortrans-mode), respectively, which is much higher than reaction (1). So reaction (1) is the main channel for the titled reaction.     

A PROTON NMR STUDY OF THE STEREOCHEMISTRY AND KINETICS OF THE REACTIONS OF DIMETHYL SULFOXIDE WITH POTASSIUM DICLOROGLYCINATOPLATINATE(II) AND ITS METHYL DERIVATIVES

Abstract

Amino acid complexes of general formula K[Pt(NO)Cl₂], where NO denotes the metal bonded atoms of the amino acid, react completely with solvent DMSO to yield two products, cis- and trans-Pt(NO) (DMSO)Cl, where cis and trans refer to positions of DMSO relative to coordinated nitrogen. The products were identified and kinetic data were obtained from changes in the proton nmr spectra of the amino acid, when DMSO-d₆ was the solvent, or of both amino acid and coordinated DMSO, when ordinary DMSO was the solvent. For glycine and π-aminoisobutyric acid complexes, the rate of displacement of trans chloride exceeds that of cis chloride by a factor of 3. However, subsequent equilibration favors the cis isomer over the trans isomer by a factor of 10. By contrast, for the corresponding N, N-dimethyl derivatives, the rates of formation of the two isomers are more nearly the same and the equilibrium ratio does not differ from the kinetic ratio. In addition to providing a sensitive technique for evaluating small differences in kinetic trans-effects, these observations strongly suggest that the stereochemistry of Pt(NO) (DMSO)Cl for the corresponding alanine complex described by Kukushkin and Guryamava should be denoted cis, rather than the trans reported.     

A DFT study of a novel oxime anticancer trans platinum complex: Monofunctional and bifunctional binding to purine bases

The first and second substitution reactions binding of the anticancer drug trans‐[Pt((CH₃)₂C?NOH)((CH₃)₂CHNH₂)Cl₂] to purine bases were studied computationally using a combination of density functional theory and isoelectric focusing polarized continuum model approach. Our calculations demonstrate that the trans monoaqua and diaqua reactant complexes (RCs) can generate either trans‐ or cis‐monoadducts via identical or very similar trans trigonal‐bipyramidal transition‐state structures. Furthermore, these monoadducts can subsequently close by coordination to the adjacent purine bases to form 1,2‐intrastrand Pt‐DNA adducts and eventually distort DNA in the same way as cisplatin. Thus, it is likely that the transplatin analogues have the same mechanism of anticancer activity as cisplatin. For the first substitutions, the activation free energies of monoaqua complexes are always lower than that of diaqua complexes. The lowest activation energy for monoaqua substitutions is 16.2 kcal/mol for guanine and 16.5 kcal/mol for adenine, whereas the lowest activation energy for diaqua substitutions is 17.1 kcal/mol for guanine and 25.9 kcal/mol for adenine. For the second substitutions, the lowest activation energy from trans‐monoadduct to trans‐diadduct is 19.1 kcal/mol for GG adduct and 20.7 kcal/mol for GA adduct, whereas the lowest activation energy from cis‐monoadduct to cis‐diadduct is 18.9 kcal/mol for GG adduct and 18.5 kcal/mol for GA adduct. In addition, the first and second substitutions prefer guanine over adenine, which is explained by the remarkable larger complexation energy for the initial RC in combination with lower activation energy for the guanine substitution. Overall, the hydrogen‐bonds play an important role in stabilizing these species of the first and second substitutions. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Synthesis and Characterization of Some Ru(tmeda) Complexes Containing Chloride, Hydride, and Vinylidene Ligands

Summary.  The polymeric compound [Ru(cod)Cl₂] _x (cod = cyclooctadiene) reacts with 2 equivalents of tmeda (N,N,N′,N′-tetramethylethylenediamine) in refluxing MeOH to afford trans-[Ru(cod)(tmeda)(Cl)(H)] (1), which upon treatment with CHCl₃ is readily converted to the dichloro complex trans-[Ru(cod)(tmeda)Cl₂] (2). When [Ru(cod)Cl₂] _x is reacted with tmeda under an atmosphere of H₂ (3 bar), the bis-tmeda complex trans-[Ru(tmeda)₂Cl₂] (3) is obtained in 80% yield. DFT calculations revealed that 3 is by 52 kJ/mol more stable than the corresponding cis isomer. Attempts to prepare the coordinatively unsaturated complex [Ru(tmeda)₂Cl]⁺ by reacting 1 with TICF₃SO₃ were unsuccessful. According to DFT calculations, however, such a complex should be stable and, interestingly, should adopt a square pyramidal rather than a trigonal bipyramidal structure. If halide abstraction of 3 is performed in the presence of terminal alkynes HC*CR (R*t-Bu, n-Bu), the cationic vinylidene complexes [Ru(tmeda)₂(Cl)(*C*CHR)]⁺ (4a,b) are obtained. Received March 26, 2001. Accepted April 26, 2001     

Electron-Transfer-Catalyzed cis → trans Isomerization of 1,1′-Azonorborane. Prototype of a reversible two-stage storage system

ESR and cyclic voltammetry investigations show that isomerization of the radical cation of cis-1,1′-azonorbornane (cis- 1 ) to the trans-radical ion proceeds too fast in solution for direct investigation of the cis-radical ion even at ?78°. The facile isomerization of the radical cation is in agreement with PM 3 calculations proposing an activation barrier of only 17 kJ/mol. As a consequence, quantitative cis → trans isomerization of 1,1′-azonorbornane can effectively be accomplished by addition of catalytic amounts of one-electron oxidants. This is the first evidence for a radical-cation-catalyzed cis → trans isomerization of azo compounds.     

Structural aspects of the anti-cancer drug oxaliplatin: A combined theoretical and experimental study

The conformational behavior of the third generation antitumor drug, oxaliplatin, has been explored by GGA-PW91 density functional calculations and FT-IR spectra. The difference in the biological activities of cisplatin and oxaliplatin are attributed to the presence of the DACH ligand in the latter. The trans forms of the ligand are found to be more stable than the cis form, but, of the two equally stable enantiomers, the trans-l (1R,2R) one is found to be more potent biologically. Since very minor differences are observed in the electronic structures of the two enantiomers, their difference in activity is attributed to the chiral recognition of the ligand by DNA. The calculated vibrational frequencies are in good agreement with our experimental FT-IR spectrum. Calculations have also been performed on the cis isomer and its monohydrate. Comparison between the theoretically predicted geometries and the experimental ones yielded good correspondence, validating our methodology.     

Selective formation of thecis isomer of the nitridotechnetium(V) complex with 2,2′:6′,2″-terpyridine

The reaction of [TcNCl₂(PPh₃)₂] with 2,2′:6′,2″-terpyridine producedcis-[TcNCl₂(terpy)] selectively. The resulting complexes were characterized by¹H NMR and IR spectroscopy. The geometries of thecis andtrans isomers were estimated by theoretical calculations following a density functional method. Thecis isomer is likely more stable than thetrans one with respect to thetrans influence of the nitrido ligand. Furthermore, the behavior of nitridotechnetium complexes in polar solvents was compared to Os-analogues.     

Computational studies of 1,2-dithiete and dithioglyoxal

Ab initio calculations are reported on the energies, geometries, vibrational frequencies, and ionization potentials of the H₂C₂S₂ isomers: 1,2-dithiete, cis-dithioglyoxal, and trans-dithioglyoxal. In contrast to most earlier computations, the results of this work indicate that 1,2-dithiete and cis-dithioglyoxal lie close in energy (within 3 kcal/mol) with the dithial more stable. Trans-dithioglyoxal is found to be 4.1 kcal/mol more stable than the cis isomer and faces a barrier to internal rotation of 5.5 kcal/mol. The predicted rotational constants for 1,2-dithiete agree within ～0.05 GHz with the experimentally observed values thus lending credence to the predictions for cis-dithioglyoxal (A_e 14.30683, B_e 2.46324, C_e 2.10143 GHz). Vibrational frequencies are given as potential aids to the identification of these molecules. 6-31G* ΔSCF calculations predict that at low energies (8 to 13 eV) the photoelectron spectra of 1,2-dithiete, cis-dithioglyoxal and trans-dithioglyoxal should be similar.     

Theoretical study on coordination of methanol clusters to 3-methyl-4-pyrimidone

Density functional theory (DFT), MP2, and couple cluster ab initio methods were employed to investigate the microsolvation of 3-methyl-4-pyrimidone (3M4P) surrounded by methanol (MeOH) molecules. Structures are analyzed based on hydrogen bonds with a focus on relative energies, interaction energies, hydrogen bond cooperativity, hydrogen bonding geometries, and redshifts in the frequencies of O–H and C=O stretching modes. Our results show that there is no preferential orientation of MeOH attacks on the carbonyle site of 3M4P; both trans and cis 3M4P-MeOH complexes have same chance to be observed. cis 3M4P-MeOH and 3M4P-MeOH complex in which MeOH is located on N lie 0.56 and 3.11 kJ/mol at CCSD(T)/6-31+G(d,p) (0.63 and 1.67 kJ/mol at MP2/6-311++G(d,p)) above trans 3M4P-MeOH. MeOH dimers form more stable 3M4P-(MeOH)₂ complexes compare to 3M4P-(MeOH)₂ complexes in which individual MeOH molecules bind to carbonyl and N. Relative energies of 3M4P-(MeOH)₃ computed using various DFT methods point out the complex formed by linear MeOH trimer along methyl group of 3M4P (cis 3M4P-(MeOH)₃) as lowest. Carbonyl group is predicted as preferential site for hydrogen bond interaction. Besides O–H…O and O–H…N hydrogen bonds, 3M4P-(MeOH)₂ and 3M4P-(MeOH)₃ complexes are also stabilized by H–O…H–C weak interactions.     

Quantum-Chemical Study of Adducts of Silicon Halides with Nitrogen-containing Donors: IV. Adducts with Pyridine

The structural and thermodynamic characteristics of SiX₄·Py and SiX₄·2Py adducts (X = H, F, Cl, Br) were calculated by ab initio and DFT methods (RHF and B3LYP). The resulting data were used to estimate for the first time the enthalpies of sublimation of trans-SiX₄·2Py complexes. The distortion energies of the donor and acceptor fragments and the energies of the Si-N bonds in the 1:1 and 1:2 halide complexes were calculated. The high distortion energy makes thermodynamically unfavorable equatorial monopyridine adducts with Si-N bond energies of 150-200 kJ/mol. In trans 1:2 complexes, pyridine acts as a weaker donor than ammonia with respect to silicon tetrahalides.     

Ab initio study on the internal rotation of five π-conjugated hydrocarbons at MP2 level

The potential-energy curves of internal rotation were calculated for 1,3-butadiene at the MP2/6-311G** level, for isoprene and 1,3-pentadiene at the MP2/6-311G* level, and for 2,3-dimethyl-1,3-butadiene and styrene at the MP2/6-31G* level. The geometries of the energy minima (stable conformers) and maxima (transition states) on the curves are completely optimized. For butadiene and its methyl derivatives, two stable rotamers, s-trans and gauche conformers, are obtained. s-trans forms have the lowest energies and gauche conformers twisted by 39.9°–48.3° around the central bond of the butadiene skeleton are, on average, 9.8 kJ/mol above the trans forms. s-cis forms are rotational transition states. The computed gauche–cis barriers range from 4.30 to 11.70 kJ/mol. The regular effects of methyl substitutions at the end and central carbons are found. For styrene, the planar form is calculated to be a saddle point which is only about 1 kJ/mol higher in total energy than a twisted minimum, in which the torsional angle between the phenyl and vinyl planes is 27.4°. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 69: 659–667, 1998     

水溶液中亚硝基甲烷与甲醛肟之间互变异构反应的理论研究

采用超分子-连续介质(PCM)模型,在密度泛函B3LYP/6-311++G^**水平上对水溶液中亚硝基甲烷异构化反应的机理进行了理论研究.结果表明,在水溶液中亚硝基甲烷可以通过两条反应途径(Ⅰ和Ⅱ)经质子迁移得到更稳定的重排产物--反式甲醛肟,但优势反应途径与在气相反应不同.在水溶液中亚硝基甲烷异构化反应最有可能的途径Ⅰ是通过氢迁移先生成顺式甲醛肟,然后绕N-O键旋转生成更稳定的反式甲醛肟.并且由于水分子的催化作用使得反应活化能从气相中240.6和196.2 kJ/mol分别降低至水溶液中的61.7和92.1 kJ/mol.     

Relative stability,potential barrier and intensity parameters of the trans and cis isomers of fluoroacetyl fluoride: An ab initio study

Ab initio calculations have been performed to determine molecular geometries, relative stabilities and the potential barrier of the fluoroacetyl fluoride molecule. The calculations indicate the existence of two stable conformations, trans and cis, in agreement with experimental studies. The potential barrier presents a maximum around 80° and an energy difference of ⋍ 17.5 kJ mol⁻¹ with respect to the most stable conformer (trans). These calculations also confirm that this conformer is more polar than the cis form, with the total dipole moment oriented along the carbonylic bond. The intensity parameters of the trans and cis isomers in terms of their atomic polar tensors have been analysed using the “charge-charge flux-overlap” model. The calculations predict similar atomic polar tensors for both forms, suggesting practically equivalent electronic structures in the ground state.     

Theoretical study of thermal decomposition of azomethane

Summary.  Thermal one- and two-bond dissociation processes of cis- and trans-azomethane were studied by ab initio computation with DZP and TZ2P basis sets, using the d(N–C) bond lengths as the reaction coordinates. The geometries were optimized at the MP2 level, and the dissociation energies obtained exploiting a single-point, fourth-order M?ller–Plesset calculations [MP4SDTQ/TZ2P]. At this level of theory including zero-point energies, the trans-isomer is by 9.3 kcal/mol more stable than the cis-isomer. The results show that the energetically more favourable one-bond cleavage proceeds without transition state with the predicted bond dissociation energy D ₀ of 47.8 kcal/mol for trans-azomethane and 38.5 kcal/mol for cis-azomethane. With calculated barrier heights the unimolecular dissociation rate constants have been determined by means of the RRKM theory. The second-order saddle points localized for synchronous decomposition pathways lie 13 (trans)-23(cis) kcal/mol above the one-bond dissociation energies [MP2/DZP]. Received May 28, 1996/Final version received November 1, 1996 / Accepted November 1, 1996     

Titanium cis‐1,2‐Diaminocyclohexane (cis‐DACH) Salalen Catalysts for the Asymmetric Epoxidation of Terminal Non‐Conjugated Olefins with Hydrogen Peroxide

Chiral Ti salalen complexes catalyze the asymmetric epoxidation of terminal non‐conjugated olefins with hydrogen peroxide. Modular ligands based on cis‐1,2‐diamino‐cyclohexane (cis‐DACH) were developed, giving high yields and enantiomeric excesses (ee, up to 96 %) at catalyst loadings as low as 0.1–0.5 mol %, and even under solvent‐free conditions.     

Tin(IV) Chloride Complexes of β-Chlorovinyl Aldehydes: A Multinuclear Nmr Characterization in Solution

Abstract

The reaction of SnCl₄ with β-chlorovinyl aldehydes in anhydrous dichloromethane gave a series of octahedral complexes of the general formula SnCl₄·2L (L = aldehyde). The adducts have been characterized in solution using multinuclear (¹H, ¹³C, and ¹¹⁹Sn) NMR and IR spectroscopy. Solution NMR studies show that the complexes undergo rapid ligand dissociation at ambient temperature. Ligand exchange is slowed significantly at low temperature, such that, in most of the complexes, it is possible to identify both the cis and trans isomers with predominance of the cis form. The magnitude of the metal-ligand interaction was estimated on the basis of ¹¹⁹Sn NMR chemical shifts and used to classify the aldehydes studied according to their Lewis basicity.