Intramolecular nonbonded S...N interaction in rabeprazole

Intramolecular nonbonded S...N interactions in the crystal structures of the derivatives (7a-d) of sodium rabeprazole (1) and an intermolecular nonbonded S...N interaction between ethylmethylsulfoxide and pyridine in a solution were recognized. These results made us estimate that the intramolecular nonbonded S...N interaction existed in 1 and its derivatives in a solution, and formed the 4-membered quasi-ring in 2 (Fig. 1) followed by the increase of the reactivity of 2 to give the putative spiro sulfoxide 3, which is the key intermediate in the reaction cascade of 1 (Chart 1).     

Activation of leinamycin by thiols: a theoretical study

Reaction of thiols with the 1,2-dithiolan-3-one 1-oxide heterocycle found in leinamycin (1) results in the conversion of this antitumor antibiotic to a DNA-alkylating episulfonium ion (5). While the products formed in this reaction have been rationalized by a mechanism involving initial attack of thiol on the central sulfenyl sulfur (S2') of the 1,2-dithiolan-3-one 1-oxide ring, the carbonyl carbon (C3') and the sulfinyl sulfur (S1') of this heterocycle are also expected to be electrophilic. Therefore, it is important to consider whether nucleophilic attack of thiol at these sites might contribute either to destruction of the antibiotic or conversion to its episulfonium ion form. To address this question, we have used computational methods to examine the attack of methyl thiolate on each of the three electrophilic centers in a simple analogue of the 1,2-dithiolan-3-one 1-oxide heterocycle found in leinamycin. Calculations were performed at the MP2/6-311+G(3df,p)//B3LYP/6-31G level of theory with inclusion of solvent effects. The results indicate that the most reasonable mechanism for thiol-mediated activation of leinamycin involves initial attack of thiolate at the S2'-position of the antibiotic's 1,2-dithiolan-3-one 1-oxide heterocycle, followed by conversion to the 1,2-oxathiolan-5-one intermediate (3).     

Noncovalent DNA binding drives DNA alkylation by leinamycin: evidence that the Z,E-5-(thiazol-4-yl)-penta-2,4-dienone moiety of the natural product serves as an atypical DNA intercalator

Molecular recognition and chemical modification of DNA are important in medicinal chemistry, toxicology, and biotechnology. Historically, natural products have revealed many interesting and unexpected mechanisms for noncovalent DNA binding and covalent DNA modification. The studies reported here characterize the molecular mechanisms underlying the efficient alkylation of duplex DNA by the Streptomyces-derived natural product leinamycin. Previous studies suggested that alkylation of duplex DNA by activated leinamycin (2) is driven by noncovalent association of the natural product with the double helix. This is striking because leinamycin does not contain a classical noncovalent DNA-binding motif, such as an intercalating unit, a groove binder, or a polycation. The experiments described here provide evidence that leinamycin is an atypical DNA-intercalating agent. A competition binding assay involving daunomycin-mediated inhibition of DNA alkylation by leinamycin provided evidence that activated leinamycin binds to duplex DNA with an apparent binding constant of approximately 4.3 ± 0.4 × 10(3) M(-1). Activated leinamycin caused duplex unwinding and hydrodynamic changes in DNA-containing solutions that are indicative of DNA intercalation. Characterization of the reaction of activated leinamycin with palindromic duplexes containing 5'-CG and 5'-GC target sites, bulge-containing duplexes, and 5-methylcytosine-containing duplexes provided evidence regarding the orientation of leinamycin with respect to target guanine residues. The data allow construction of a model for the leinamycin-DNA complex suggesting how a modest DNA-binding constant combines with proper positioning of the natural product to drive efficient alkylation of guanine residues in the major groove of duplex DNA.     

Design of density functionals that are broadly accurate for thermochemistry, thermochemical kinetics, and nonbonded interactions

This paper develops two new hybrid meta exchange-correlation functionals for thermochemistry, thermochemical kinetics, and nonbonded interactions. The new functionals are called PW6B95 (6-parameter functional based on Perdew-Wang-91 exchange and Becke-95 correlation) and PWB6K (6-parameter functional for kinetics based on Perdew-Wang-91 exchange and Becke-95 correlation). The resulting methods were comparatively assessed against the MGAE109/3 main group atomization energy database, against the IP13/3 ionization potential database, against the EA13/3 electron affinity database, against the HTBH38/4 and NHTBH38/04 hydrogen-transfer and non-hydrogen-transfer barrier height databases, against the HB6/04 hydrogen bonding database, against the CT7/04 charge-transfer complex database, against the DI6/04 dipole interaction database, against the WI7/05 weak interaction database, and against the new PPS5/05 pi-pi stacking interaction database. From the assessment and comparison of methods, we draw the following conclusions, based on an analysis of mean unsigned errors: (i) The PW6B95, MPW1B95, B98, B97-1, and TPSS1KCIS methods give the best results for a combination of thermochemistry and nonbonded interactions. (ii) PWB6K, MPWB1K, BB1K, MPW1K, and MPW1B95 give the best results for a combination of thermochemical kinetics and nonbonded interactions. (iii) PWB6K outperforms the MP2 method for nonbonded interactions. (iv) PW6B95 gives errors for main group covalent bond energies that are only 0.41 kcal (as measured by mean unsigned error per bond (MUEPB) for the MGAE109 database), as compared to 0.56 kcal/mol for the second best method and 0.92 kcal/mol for B3LYP.     

Entering the leinamycin rearrangement via 2-(trimethylsilyl)ethyl sulfoxides

Attack of cellular thiols on the antitumor natural product leinamycin is believed to generate a sulfenate intermediate that undergoes subsequent rearrangement to a DNA-alkylating episulfonium ion. Here, 2-(trimethylsilyl)ethyl sulfoxides were employed in a fluoride-triggered generation of sulfenate anions related to the putative leinamycin-sulfenate. The resulting sulfenates enter smoothly into a leinamycin-type rearrangement reaction to afford an episulfonium ion alkylating agent. The results provide evidence that the sulfenate ion is, indeed, a competent intermediate in the leinamycin rearrangement. Further, the molecules examined here may provide a foundation for the design of functional leinamycin analogues that bypass the unstable and synthetically challenging 1,2-dithiolan-3-one 1-oxide moiety found in the natural product.     

Theoretical investigations on the weak nonbonded CS···CH2 interactions: Chalcogen‐bonded complexes with singlet carbene as an electron donor

In this article, we explored the noncovalent bonding interactions between O?C?S, S?C?S, F₂C?S, Cl₂C?S, and singlet carbene. Six chalcogen‐bonded complexes were obtained. It is found that all the vibrational frequencies of C?S bond presented a red shift character. Interaction energy, topology property of the electron density and its Laplacian, and the donor–acceptor interaction have been investigated. All these results show that there exists a weak nonbonded interaction between the chalcogen bond donor and CH₂. An energy decomposition analysis was performed to disclose that the electrostatic interaction is the main stabilized factor in these nonbonded complexes. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Intramolecular nonbonded S?O interaction in acetazolamide and thiadiazolinethione molecules in their dimeric crystalline structures and complex crystalline structures with enzymes

The dimeric crystalline structure of acetazolamide 1 and thiadiazolinethione 2 bearing intramolecular nonbonded S?O interactions, in each different hydrogen-bonding manner was clarified by their X-ray crystallographic analysis. Existence of the dimeric structure of 1 and 2 in a MeOH solution could be suggested on the basis of their cold-spray ionization mass spectrometry. The intramolecular nonbonded S?O interaction was precisely recognized in the complex crystalline structures of carbonic anhydrase I inhibitor 1 and stromelysin inhibitors 2-4 with each specific enzyme. The computational evaluation of the possible monomeric seven conformers of 1 and two model compounds 5 and 6 of 2-4 based on DFT calculations defined that the conformer bearing the intramolecular nonbonded S?O interaction is most stable.     

Small molecules that mimic the thiol-triggered alkylating properties seen in the natural product leinamycin

Reaction of the antitumor agent leinamycin with cellular thiols results in conversion of the natural product to a DNA-alkylating episulfonium alkylating agent via an intriguing sequence of chemical reactions. To establish whether the chemistry first seen in leinamycin represents a general motif that can function in various molecular frameworks, construction of greatly simplified analogues containing only the "core" funcional groups anticipated to be necessary for thiol-triggered generation of an alkylating agent was undertaken. For this purpose, the "stripped-down" leinamycin analogue 7-(3-methyl-but-2-enyl)-1-oxo-1H-lambda4-benzo[1,2]dithiol-3-one (4) was synthesized. Treatment of 4 with thiol under several different conditions results in efficient conversion of the compound to cyclized 2,3-dihydro-benzo[b]thiophene-7-carboxylic acid products (13) that are envisioned to arise from Markovnikov addition of solvent to an intermediate episulfonium ion (14). Thus, the relatively simple molecule 4 is able to mimic the thiol-triggered alkylating properties displayed by the natural product leinamycin. This work helps define why the core functional groups required thiol-accelerated generation of an alkylating intermediate from leinamycin and indicates that substantially altered analogues of the natural product may retain alkylating properties. In a broader context, the results provide evidence that the unique cascade of chemical reactions first seen in the context of leinamycin represents a general motif that can operate in a variety of molecular frameworks.     

Highly stereoselective asymmetric Pummerer reactions that incorporate intermolecular and intramolecular nonbonded S...O interactions

New chiral sulfoxides (R(S),S)-3, (S(S),S)-3, (R(S),S)-4, and (S(S),S)-4 and known chiral sulfoxides (R(S))-5, (R(S))-6, and (R(S))-7 were synthesized, and the stereochemistry of the new sulfoxides (R(S),S)-3 and (R(S),S)-4 was determined by X-ray crystallographic analysis. In their crystallographic structures, the intramolecular nonbonded S...O close contacts were recognized. Analyses of several sulfoxide complexes including rac-11 with N,N-dimethylacetamide (DMAC) or N-methyl-2-pyrrolidone (NMP) in a MeOH solution utilizing cold-spray ionization mass spectrometry provided, for the first time, direct information for intermolecular nonbonded S...O interactions between sulfoxides and amide (or lactam) in a solution. Highly diastereoselective and enantioselective Pummerer reactions based on the concept of intermolecular and intramolecular nonbonded S...O interactions were performed by treatment of several chiral sulfoxides (R(S), S)-3, (S(S), S)-3, (R(S), S)-4, (S(S), S)-4, (R(S))-5, (R(S))-6, and (R(S))-7 with acetic anhydride and trimethylsilyl triflate (TMSOTf) in DMAC, NMP, N,N-dimethylformamide, and N-formylpiperidine. Mechanistic studies on these facile stereoselective Pummerer reactions revealed the necessity for the amide/TMSOTf complex, such as 26 or 27, to be an efficient activation reagent for Ac(2)O and a trapping reagent for the released acetate ion, and that DMAC and NMP had a positive effect on this highly stereoselective chiral transfer reaction.     

Synthesis of 5-(7-Hydroxyheptyl)-1,2-dithiolan-3-one 1-Oxide,a Core Functionality of Antibiotic Leinamycin

5-(7-Hydroxyheptyl)-1,2-dithiolan-3-one 1-oxide was designed and synthesized in our laboratories that contain the heterocycle of 1,2-dithiolan-3-one 1-oxide, a reactive core of antibiotic leinamycin. In addition, the activated ester of 5-(7-hydroxyheptyl)-1,2-dithiolan-3-one 1-oxide was prepared, which presumably is useful for coupling this DNA-cleaving functionality to certain DNA-binding agents.     

Nature of nonbonded Se...O interactions characterized by 17O NMR spectroscopy and NBO and AIM analyses

To investigate the nature of nonbonded Se...O interactions, three series of 2-substituted benzeneselenenyl derivatives [2-(CHO)C6H4SeX (1), 2-(CH2OH)C6H4SeX, (2), 2-(CH2OiPr)C6H4SeX (3); X = Cl, Br, CN, SPh, SeAr, Me] were synthesized. The 17O NMR absorption observed for 17O-enriched aldehydes 1 appeared upfield relative to benzaldehyde (PhCHO), while the opposite downfield shifts relative to benzyl alcohol (PhCH2OH) were observed for 17O-enriched alcohols 2 and ethers 3. The magnitude of both the upfield and the downfield shifts became larger as the electron-withdrawing ability of a substituent X increased. Quantum chemical calculations at the B3LYP level revealed that for all model compounds the most stable conformer has an intramolecular nonbonded Se.O interaction. Thus, the relative 17O NMR chemical shifts (DeltadeltaO) for 1-3 would reflect the strengths of the Se...O interactions. The natural bond orbital (NBO) analysis demonstrated that the stabilization energy due to an nO --> sigma Se-X orbital interaction (ESe...O) correlates with the Se...O atomic distance on a single curve irrespective of the type of the O atom. On the other hand, the atoms in molecules (AIM) analysis showed that the nonbonded Se...O interactions can be characterized by the presence of a bond critical point, the total energy density (HSe...O) of which decreases with strengthening of the interaction. The results suggested that Se...O interactions have a dominant covalent character rather than an electrostatic one.     

Synthesis and antibacterial activity of new 1beta-methylcarbapenems having the potential for intramolecular nonbonded S...O interactions.

Mercaptoacetyliminothiadiazoline derivatives (19, 20) useful for the pendant moiety of 1beta-methylcarbapenem antibiotics were efficiently synthesized. Acetyl derivative (18) of 20 was submitted to X-ray analysis, and a significant nonbonded S...O close contact was recognized in the crystallographic structure. New 1beta-methylcarbapenems (5, 6) were synthesized by exploiting 19 and 20, and exhibited considerable antibacterial activities in vitro.     

Two (E,E)- and (Z,E)-thiazol-5-ylpenta-2,4-dienones

In order to characterize the structural elements that might play a role in non-covalent DNA binding by the antitumor antibiotic leinamycin, we have solved the crystal structures of the two leinamycin analogs, methyl (R)-5-{2-[1-(tert-butoxy­carbonyl­amino)­ethyl]­thia­zol-4-yl}penta-(E,E)-2,4-dienoate, C₁₆H₂₂N₂O₄S, (II), and 2-methyl-8-oxa-16-thia-3,17-di­aza­bicyclo­[12.2.1]­heptadeca-(Z,E)-1(17),10,12,14-tetraene-4,9-di­one, C₁₄H₁₆N₂O₃S, (III). The penta-2,4-dienone moiety in both of these analogs adopts a conformation close to planarity, with the thia­zole ring twisted out of the plane by 12.9 (2)° in (II) and by 21.4 (4)° in (III).     

Magnetic face-to-face interaction and electrocommunication in chromium sandwich compounds

The reaction of [{(C5Me5)CrCl2}2] with [2.2](1,4)cyclophane gave [(C5Me5)Cr{[2.2](1,4)cyclophane}] (1) and [(C5Me5)Cr{[2.2](1,4)cyclophane}Cr(C5Me5)] (2), depending on the reaction conditions. X-ray structure analysis showed 2 to be a ministack which in turn is stacked in the lattice. The chromium atoms are 6.035 A apart, and the distortion of the benzene rings to boat-shaped moieties is less pronounced than in parent [2.2](1,4)cyclophane. The NMR and EPR spectra were consistent with a S=1/2 ground state for 1 and with two interacting S=1/2 centers in 2. Spin density was found in the ligand pi systems, where its sign was negative when the pi system was adjacent to chromium, while on the nonbonded benzene moiety of 1 it was positive. Cyclic voltammograms showed reductions to 1- and 2(2-), as well as oxidations to 1+, 2+, and 2(2+) which were quasireversible, whereas oxidations to 1(2+) and 2(3+) were irreversible. Interaction between the metal ions was revealed by a 260 mV separation of the redox waves belonging to 2+, and 2(2+). Both cations were isolated as [B(C6H5)4]- salts, which in solution decomposed to [2.2](1,4)cyclophane and [(C5Me5)Cr{(eta6-C6H5)B(C6H5)3}] (3). The 1H and 13C NMR spectra of 3 were in accordance with an S=1 ground state. Solid-state magnetic measurements of the dimetallic compounds showed antiferromagnetic interaction with J=-122 cm-1 for 2, J=-31 cm-1 for 2+ (ground state S=1/2), and J=-23.5 cm-1 for 2(2+) (with H=-JS1S2). The decrease of J in the series 2, 2+, and 2(2+) was traced to the number of unpaired electrons and, for the mixed-valent cation 2+, to additional double exchange.     

First linear alignment of five C-Se...O...Se-C atoms in anthraquinone and 9-(methoxy)anthracene bearing phenylselanyl groups at 1,8-positions

Five Ci-Se...O...Se-Ci atoms in anthraquinone and 9-(methoxy)anthracene bearing phenylselanyl groups at 1,8-positions align linearly, the origin of which is shown to be a nonbonded 5c-6e interaction of the five atoms.     

Statistical and theoretical investigations on the directionality of nonbonded S...O interactions. Implications for molecular design and protein engineering

Weak nonbonded interactions between a divalent sulfur (S) atom and a main-chain carbonyl oxygen (O) atom have recently been characterized in proteins. However, they have shown distinctly different directional propensities around the O atom from the S...O interactions in small organic compounds, although the linearity of the C-S...O or S-S...O atomic alignment was commonly observed. To elucidate the observed discrepancy, a comprehensive search for nonbonded S.O interactions in the Cambridge Structural Database (CSD) and MP2 calculations on the model complexes between dimethyl disulfide (CH(3)SSCH(3)) and various carbonyl compounds were performed. It was found that the O atom showed a strong intrinsic tendency to approach the S atom from the backside of the S-C or S-S bond (in the sigma(S) direction). On the other hand, the S atom had both possibilities of approach to the carbonyl O atom within the same plane (in the n(O) direction) and out of the plane (in the pi(O) direction). In the case of S...O(amide) interactions, the pi(O) direction was significantly preferred as observed in proteins. Thus, structural features of S...O interactions depend on the type of carbonyl groups involved. The results suggested that S.O interactions may control protein structures to some extent and that the unique directional properties of S...O interactions could be applied to molecular design.     

Nonbonded P···P and P···Se Interactions in Naphthalene 1,8-Positions: Role of Lone-Pair Orbitals

The lone pair-lone pair repulsion plays an important role in the nonbonded P;;;P interaction in naphthalene 1,8-positions. The conformations around P and Se in 8-(PhSe)-1-(Ph 2 P=O)C 10 H 6 are determined by the attractive O;;;Se--C 3c-4e type interaction. The P;;;Se interaction in the 1,8-positions is also discussed.     

Lewis vs. Brønsted-basicities of diiron dithiolates: spectroscopic detection of the "rotated structure" and remarkable effects of ethane- vs. propanedithiolate

The new complexes Fe2(S2CnH2n)(CO)2(dppv)2 (n = 2, 3; dppv = cis-1,2-C2H2(PPh2)2) form adducts with AlBr3 and B(C6F5)3, which adopt the "rotated structure" proposed for the active site of the Fe-only hydrogenases--the propanedithiolate is significantly more Lewis basic due to nonbonded interactions between the dithiolate strap and the ligands on Fe.     

Structure of 1-(arylselanyl)naphthalenes. 2. G dependence in 8-G-1-(p-YC(6)H(4)Se)C(10)H(6).

The structures of 8-G-1-(p-YC(6)H(4)Se)C(10)H(6) (1 (G = Cl) and 2 (G = Br): Y = H (a), OMe (b), Me (c), Cl (d), Br (e), COOEt (f), and NO(2) (g)) were investigated by X-ray crystallographic analysis, NMR spectroscopy, and ab initio MO calculations. The structures of all members in 1 and 2 are concluded to be type B, which is in striking contrast to the type A structure for 4d-g (4 (g(n)), where G = H). The Se-C(i) bond of the p-YC(6)H(4)Se group in 8-G-1-(p-YC(6)H(4)Se)C(10)H(6) is almost perpendicular to the naphthyl plane in type A, and it is located on the plane in type B. The chlorine and bromine substitution at the 8-position in 1 and 2 dramatically changes the type A structure of 4 (g(n)) to type B. The nonbonded G- - -Se-C 3c-4e type interaction must contribute to stabilize the type B structure. The type B structure in 1 and 2 should also be more stabilized than the same structure in 4 by the 3c-4e type interaction: The structure of 4b is type B in the crystals and type B would be more stable for 4c and might be for 4a in solutions. Ab initio MO calculations are performed on 8-G-1-(p-YC(6)H(4)Se)C(10)H(6), 8-G-C(10)H(6)SeH-1, and models HG- - -SeH(2), where G = Cl, Br, and F, to clarify the reason for the dramatic change in the structures. The type B structure is optimized to be more stable than the type A for all species examined, which supports the observations. The energy differences between type B and type A are larger for the models than for the naphthalenes. While the superiority of the type B for the former is Br > Cl > F, that of the latter is Br approximately Cl >/= F. These results show that the main factor of the structural change from type A to type B is the nonbonded G- - -Se-C 3c-4e interaction. The electronic effect of halogens through the naphthalene pi-framework would also contribute to some extent, although the direct comparison of the evaluated values between the naphthalene systems and the models is not so easy. Factors to stabilize the two structures of 1, 2, 4, and 8-(MeSe)-1-(p-YC(6)H(4)Se)C(10)H(6) are reexamined from a viewpoint of the nonbonded G- - -Se-C 3c-4e interaction (G dependence), together with the electronic effect of Y (Y dependence).     

Effect of temperature and concentration on the structure of tert-butyl alcohol/water mixtures: near-infrared spectroscopic study

The effect of temperature and concentration on the structure of tert-butyl alcohol/water binary mixtures in the alcohol-rich region (X(H2O) < 0.3) has been studied by using Fourier transform near-infrared (FT-NIR) spectroscopy. The obtained results demonstrate that the addition of a small amount of water to tert-butyl alcohol (2-methyl-2-propanol, abbreviated as TBA) leads to minor changes in the structure of neat TBA and suggest that molecules of TBA in the mixture are in the same environment as those in pure TBA. The bands of water are red-shifted in the mixture relative to bulk water, implying that the molecules of water in TBA are involved in stronger hydrogen bonding. The present experimental data give no evidence for the existence of nonbonded water in the mixture. Even at a very low content of water, the main NIR bands of water (nu(2) + nu(3) and nu(1) + nu(3)) have two components showing markedly different behavior upon an increase in temperature. From the power spectra, it is seen that the extent of intensity changes due to the free OH groups of TBA is smaller in the mixture relative to pure TBA. All of these results support the model of chain-end bonding of water molecules to TBA associates. An increase in X(H2O) reduces the population of nonbonded OH groups of TBA, yet both processes do not appear at the same rate. The amount of bonded OH groups of water increases faster than that of the nonbonded ones. It seems that the water-water interaction becomes more important as X(H2O) increases. At high alcohol content, the position of the CH alkyl stretching bands is constant, evidencing a negligible role of the hydrophobic hydration in the mixture.