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A simple but efficient computational approach to calculate p

Diol dehydratase, dependent on coenzyme B12 (B12 -dDDH), displays a peculiar feature of being inactivated by its native substrate glycerol (GOL). Surprisingly, the isofunctional enzyme, B12 -independent glycerol dehydratase (B12 -iGDH), does not undergo suicide inactivation by GOL. Herein we present a series of QM/MM and MD calculations aimed at understanding the mechanisms of substrate-induced suicide inactivation in B12 -dDDH and that of resistance of B12 -iGDH to inactivation. We show that the first step in the enzymatic transformation of GOL, hydrogen abstraction, can occur from both ends of the substrate (either C1 or C3 of GOL). Whereas C1 abstraction in both enzymes leads to product formation, C3 abstraction in B12 -dDDH results in the formation of a low energy radical intermediate, which is effectively trapped within a deep well on the potential energy surface. The long lifetime of this radical intermediate likely enables its side reactions, leading to inactivation. In B12 -iGDH, by comparison, C3 abstraction is an endothermic step; consequently, the resultant radical intermediate is not of low energy, and the reverse process of reforming the reactant is possible.

n this study, using a computational approach, we are pursuing to find a proper answer about the possible application of fused TIs as superbases through the calculation and discussion of standard thermochemistry parameters, like gas-phase basicity (GB) and proton affinity (PA). In some studied cases, the role of aromaticity/antiaromaticity fluctuations supposed to be more important than mesomeric effects. In this sense, nucleus-independent chemical shift (NICS) and anisotropy of the induced current density (ACID) were utilized in this study to probe into the aromaticity-related parameters of the proposed molecules. Results revealed the highest GB/PA values for the molecules having cyclobutadiene in between two troponimines. Additional investigation was performed into the other candidates of cyclobutadiene-fused troponimines by substituting several electron donors along with the changing position of donors. Some novel superbases offered record-holding GB/PA values so that PA magnitudes higher than 300 kcal mol–1 are now feasible for nonphosphorous neutral organic superbases (NOS).

We present a convenient three-step synthesis of amino substituted phosphazenyl phosphines of the general formula (R2N)3P=N–P(NR2)2 [NR2 = N(CH2)4, N(CH2)5, N(CH2)6]. These easily accessible mixed valent compounds display a surprisingly high proton affinity and basicity in the same range as the corresponding Schwesinger diphosphazene (Me2N)3P=N–P=NEt(NMe2)2 (Et-P2) and Verkade’s proazaphosphatrane superbases. Within the central [PIII–N=PV] scaffold, the phosphine PIII and not the phosphazene NIII atom is the center of highest proton affinity, basicity and donor strength. As P-bases, the title compounds display calculated proton affinities between 265.8 (NR2 = NMe2) and 274.7 kcal·mol–1 [NR2 = N(CH2)4] and pKBH+ values between 26.4 (NR2 = NMe2) and 31.5 [NR2 = N(CH2)4] on the acetonitrile scale. As P- nucleophiles, they are key intermediates in the synthesis of hyperbasic bis(diphosphazene) proton sponges, chiral bis(diphosphazene) proton pincers, bisphosphazides, and superbasic P2- bisylides. Their Staudinger reactions as nucleophile towards 1, 8-diazidonaphthalene leading to 1, 8-naphthalene-bisphosphazides is described in detail. The donor strength of the title compounds towards fragments [Se] and [Ni(CO)3] is in the same range as that of N-heterocyclic carbenes.

ConspectusOne of the constant challenges of synthetic chemistry is the molecular design and synthesis of nonionic, metal-free superbases as chemically stable neutral organic compounds of moderate molecular weight, intrinsically high thermodynamic basicity, adaptable kinetic basicity, and weak or tunable nucleophilicity at their nitrogen, phosphorus, or carbon basicity centers. Such superbases can catalyze numerous reactions, ranging from C-C bond formation to cycloadditions and polymerization, to name just a few. Additional benefits of organic superbases, as opposed to their inorganic counterparts, are their solubility in organic reaction media, mild reaction conditions, and higher selectivity. Approaching such superbasic compounds remains a continuous challenge. However, recent advances in synthetic methodology and theoretical understanding have resulted in new design principles and synthetic strategies toward superbases. Our computational contributions have demonstrated that the gas-phase basicity region of 350 kcal mol-1 and even beyond is easily reachable by organosuperbases. However, despite record-high basicities, the physical limitations of many of these compounds become quickly evident. The typically large molecular weight of these molecules and their sensitivity to ordinary reaction conditions prevent them from being practical, even though their preparation is often not too difficult. Thus, obviously structural limitations with respect to molecular weight and structural complexity must be imposed on the design of new synthetically useful organic superbases, but strategies for increasing their basicity remain important.The contemporary design of novel organic superbases is illustrated by phosphazenyl phosphanes displaying gas-phase basicities (GB) above 300 kcal mol-1 but having molecular weights well below 1000 g·mol-1. This approach is based on a reconsideration of phosphorus(III) compounds, which goes along with increasing their stability in solution. Another example is the preparation of carbodiphosphoranes incorporating pyrrolidine, tetramethylguanidine, or hexamethylphosphazene as a substituent. With gas-phase proton affinities of up to 300 kcal mol-1, they are among the top nonionic carbon bases on the basicity scale. Remarkably, the high basicity of these compounds is achieved at molecular weights of around 600 g·mol-1. Another approach to achieving high basicity through the cooperative effect of multiple intramolecular hydrogen bonding, which increases the stabilization of conjugate acids, has recently been confirmed.This Account focuses on our efforts to produce superbasic molecules that embody many desirable traits, but other groups' approaches will also be discussed. We reveal the crucial structural features of superbases and place them on known basicity scales. We discuss the emerging potential and current limits of their application and give a general outlook into the future.

With the synthesis of N, N′, N″, N‴-tetrakis(3- (dimethylamino)propyl)triaminophosphazene (TDMPP, 1), we present the first phosphazene superbase with enhanced basicity through the effect of multiple intramolecular hydrogen bonding (IHB). Due to intramolecular solvation of four NH protons, the proton affinity is even higher than that of second-order phosphazene (dma)P2-tBu. X-ray structural proof, NMR titration experiments, and computational investigations provide a more detailed quantitative description of the IHB influence on the superbasicity of 1 in solid-state, solution, and the gas-phase.

The edge-cutting design, synthesis and characterization of the so far strongest non-ionic carbon superbases is presented., A new generation of carbodiphosphoranes (CDPs), incorporating pyrrolidine, tetramethylguanidine, or tris(dimethylamino)phosphazene as substituents is introduced as the most powerful class of non-ionic carbon superbases on the basicity scale to date. The synthetic approach as well as NMR spectroscopic and structural characteristics in the free and protonated form are described. Investigation of basicity in solution and in the gas phase by experimental and theoretical means provides the to our knowledge first reported pKBH+ values for CDPs in the literature and suggest them as upper tier superbases.

A simple but efficient computational approach to calculate pKa in acetonitrile for a set of phosphorus, nitrogen, and carbon bases was established. A linear function that describes relations between the calculated ΔG’a.sol(BH+) and pKa values was determined for each group of bases. The best model was obtained through the variations in the basis set, in the level of theory (density functionals or MP2), and in the continuum solvation model (IPCM, CPCM, or SMD). The combination of the IPCM/B3LYP/6-311+G(d,p) solvation approach with MP2/6-311+G(2df,p)//B3LYP/6-31G(d) gas-phase energies provided very good results for all three groups of bases with R2 values close to or above 0.99. Interestingly, the slopes and the intercepts of the obtained linear functions showed significant deviations from the theoretical values. We made a linear plot utilizing all the conducted calculations and all the structural variations and employed methods to prove the systematic nature of the intercept/slope dependence. The interpolation of the intercept to the ideal slope value enabled us to determine the Gibbs energy of the proton in acetonitrile, which amounted to −258.8 kcal mol−1. The obtained value was in excellent agreement with previously published results.

The metabolism of vitamin D

Diol dehydratase, dependent on coenzyme B

The metabolism of vitamin D3 includes a parallel C-3 epimerization pathway-in addition to the standard metabolic processes for vitamin D3-reversing the stereochemical configuration of the -OH group at carbon-3 (s→α). While the biological function of the 3α epimer has not been elucidated yet, the additional species cannot be neglected in the analytical determination of vitamin D3, as it has the potential to introduce analytical errors if not properly accounted for. Recently, some inconsistent mass spectral behavior was seen for the 25-hydroxyvitamin D3 (25(OH)D3) epimers during quantification using electrospray LC-MS/MS. The present work extends that of Flynn et al. ( Ann. Clin. Biochem. 2014, 51, 352-559) and van den Ouweland et al. ( J. Chromatogr. B 2014, 967, 195-202), who reported larger electrospray ionization response factors for the 3α epimer of 25(OH)D3 in human serum samples as compared to the regular 3s variant. The present work was concerned with the mechanistic reasons for these differences. We used a combination of electrospray ionization, atmospheric pressure chemical ionization, and density functional theory calculations to uncover structural dissimilarities between the epimers. A plausible mechanism is described based on intramolecular hydrogen bonding in the gas phase, which creates a small difference of proton affinities between the epimers. More importantly, this mechanism allows the explanation of the different ionization efficiencies of the epimers based on kinetic control of the ionization process, where ionization initially takes place at the hydroxyl group with subsequent proton transfer to a basic carbon atom. The barrier for this transfer differs between the epimers and is in direct competition with H2O elimination from the protonated hydroxyl group. The hidden" site of high gas phase basicity was revealed through computational calculations and appears to be inaccessible via direct protonation."

We present a series of QM/MM calculations aimed at understanding the mechanism of the biological dehydration of glycerol. Strikingly and unusually, this process is catalyzed by two different radical enzymes, one of which is a coenzyme-B12-dependent enzyme and the other which is a coenzyme-B12-independent enzyme. We show that glycerol dehydration in the presence of the coenzyme-B12-dependent enzyme proceeds via a 1, 2-OH shift, which benefits from a significant catalytic reduction in the barrier. In contrast, the same reaction in the presence of the coenzyme-B12-independent enzyme is unlikely to involve the 1, 2-OH shift ; instead, a strong preference for direct loss of water from a radical intermediate is indicated. We show that this preference, and ultimately the evolution of such enzymes, is strongly linked with the reactivities of the species responsible for abstracting a hydrogen atom from the substrate. It appears that the hydrogen-reabstraction step involving the product-related radical is fundamental to the mechanistic preference. The unconventional 1, 2-OH shift seems to be required to generate a product-related radical of sufficient reactivity to cleave the relatively inactive C–H bond arising from the B12 cofactor. In the absence of B12, it is the relatively weak S–H bond of a cysteine residue that must be homolyzed. Such a transformation is much less demanding, and its inclusion apparently enables a simpler overall dehydration mechanism.

In the present study, N-methyl-2, 4, 6- cycloheptatriene-1-imine (Troponimine) with (Me)2N- and MeO- substituents have been investigated theoretically to evaluate their suitability as a new neutral organic superbase. To introduce the aforementioned system, thermochemical parameters such as gas basicity and proton affinity have been calculated along with their pKBH+ values in acetonitrile. Results revealed that all studied troponimine derivatives are more basic than 1, 8- bis(dimethylamino)-naphthalene whose gas phase basicity of 237 kcal mol-1 is considered to be the borderline between ordinary bases and superbases. However, the most important finding is that some of the proposed troponeimines are much stronger bases than the well-established cyclopropenimine superbases. Origin of troponimine basicity is elucidated through NICS calculations which reveal that troponimines become aromatic upon protonation. AIM analyses revealed that the hydrogen bond could also contribute to the basicity if a suitable substituent is located on the adjacent of the imine group of the troponimine.

The trans-configured square-planar complex of dichloropalladium and chiral monodentate phosphine ligands forms self-complementary dimers through 16 hydrogen bonded amides and π-π stacking in chlorinated solvents. The self-assembly is controlled by cis-trans isomerisation of the metal center, where the trans-configuration governs the dimer formation.

With the synthesis of

t was discovered that phosphazenyl phosphines (PAPs) can be stronger P‐superbases than the corresponding Schwesinger type phosphazene N‐superbases. A simple synthetic access to this class of PR3 derivatives including their homologization is described. XRD structures, proton affinities (PA), and gas‐phase basicities (GB) as well as calculated and experimental pKurn:x-wiley:14337851:media:anie201903342:anie201903342-math-0001 values in THF are presented. In contrast to their N‐basic counterparts, PAPs are also privileged ligands in transition metal chemistry. In fact, they are currently the strongest uncharged P‐donors known, exceeding classical and more recently discovered ligands such as PtBu3 and imidazolin‐2‐ylidenaminophosphines (IAPs) with respect to their low Tolman electronic parameters (TEPs) and large cone angles.

Molecular dynamics (MD) simulations have been employed for the first time to gain insight into the geometry of glycerol (GOL) bound within the active site of B12 -dependent diol dehydratase (B 12 -dDDH). A peculiar feature of the B 12 -dDDH enzyme is that it undergoes suicidal inactivation by the substrate glycerol. To fully understand the inactivation mechanism, it is crucial to identify all possible interactions between GOL and the surrounding amino acid residues in the enzyme−substrate complex. Particularly important is the orientation of the C3-OH group in GOL since the presence of this OH group is the only difference between GOL and propanediol (PDO), a substrate for B12 - dDDH that does not induce suicidal inactivation. The MD simulations indicate that glycerol can adopt two conformations that differ with respect to the orientation of the C3-OH group ; in one conformer, the C3-OH group is oriented toward Ser301 (C3-OH···Ser301), and in the other toward Asp335 (C3-OH··· Asp335). Although the former configuration is consistent with the crystal structure of B 12 -dDDH crystallized with cyanocobalamin (CNCbl) as the cofactor, MD simulations of this system suggest a substantial predominance of the latter conformer. A similar result with an even higher preference for the latter conformer is obtained for B 12 -dDDH with 5′-deoxyadenosylcobalamin (AdoCbl) as a cofactor. Employing QM/MM calculations it is found that the energy difference between the two conformers of GOL is very small in CNCbl B 12 -dDDH, where the slightly preferred conformer is C3-OH···Ser301. However, in AdoCbl B 12 -dDDH, this energy difference is higher, implying that GOL exists predominantly as the C3-OH···Asp335 conformer. These findings offer a new perspective for investigations of substrate-induced inactivation of the B 12 - dDDH enzyme.

New proton sponges with cyclopropeniminophospazenes as pincer ligands have been designed. It was shown that cyclopropeniminophosphazenes possess a gas phase basicity higher than the corresponding phosphazenes. Due to their lower steric demand in comparison to phosphazenes, cyclopropeniminophoshpazenes can be utilized in the design of synthetically accessible proton sponges with exceptionally high gas phase and solution phase basicity, with calculated PA values up to 330 kcal mol −1 and p K a in acetonitrile of 48.5 units.

We present a series of QM/MM calculations aimed at understanding the mechanism of the biological dehydration of glycerol. Strikingly and unusually, this process is catalyzed by two different radical enzymes, one of which is a coenzyme-B

Tissue-specific ion suppression is an unavoidable matrix effect in MALDI mass spectrometry imaging (MALDI-MSI), the negative impact of which on precision and accuracy in quantitative MALDI-MSI can be reduced to some extent by applying isotope internal standards for normalization and matrix-matched calibration routines. The detection sensitivity still suffers, however, often resulting in significant loss of signal for the investigated analytes. An MSI application considerably affected by this phenomenon is the quantitative spatial analysis of central nervous system (CNS) drugs. Most of these drugs are low molecular weight, lipophilic compounds, which exhibit inefficient desorption and ionization during MALDI using conventional polar acidic matrices (CHCA, DHB). Here, we present the application of the (2-[(2E)-3-(4-tert-butylphenyl)-2-methylprop-2-enylidene]malononitrile) matrix for high sensitivity imaging of CNS drugs in mouse brain sections. Since DCTB is usually described as an electron-transfer matrix, we provide a rationale (i.e., computational calculations of gas-phase proton affinity and ionization energy) for an additional proton-transfer ionization mechanism with this matrix. Furthermore, we compare the extent of signal suppression for five different CNS drugs when employing DCTB versus CHCA matrices. The results showed that the signal suppression was not only several times lower with DCTB than with CHCA but also depended on the specific tissue investigated. Finally, we present the application of DCTB and ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry to quantitative MALDI imaging of the anesthetic drug xylazine in mouse brain sections based on a linear matrix-matched calibration curve. DCTB afforded up to 100-fold signal intensity improvement over CHCA when comparing representative single MSI pixels and >440-fold improvement for the averaged mass spectrum of the adjacent tissue sections.

Dipeptidyl peptidase III (DPP III) is a zinc-dependent peptidase that cleaves dipeptides off of N-termini of its substrates. Previous studies on human DPP III reveal a reaction mechanism similar to that of thermolysin. Since the active site is conserved within the DPP III family, it is not surprising that the mechanism determined for Bacteroides thetaiotaomicron DPP III (BtDPP III) closely resembles that of hDPP III. However, the hydrogen bond network within the model differs slightly from that in the human ortholog, which results in two proposed pathways. The calculated Gibbs activation energy of 90.1 kJ mol–1 is larger than the one calculated from kinetic data for the preferred substrate Arg2-2-naphthylamide at room temperature (69 kJ mol–1), suggesting the importance of treating the whole DPP III enzyme in the calculations. This work is licensed under a Creative Commons Attribution 4.0 International License.

Model studies of prebiotic chemistry have re- vealed compelling routes for the formation of the building blocks of proteins and RNA, but not DNA. Today, deoxynu- cleotides required for the construction of DNA are produced by reduction of nucleotides catalysed by ribonucleotide re- ductases, which are radical enzymes. This study considers potential non-enzymatic routes via intermediate radicals for the ancient formation of deoxynucleotides. In this context, several mechanisms for ribonucleotide reduction, in a puta- tive H2S/HSC environment, are characterized using computa- tional chemistry. A bio-inspired mechanistic cycle involving a keto intermediate and HSSH production is found to be po- tentially viable. An alternative pathway, proceeding through an enol intermediate is found to exhibit similar energetic re- quirements. Non-cyclical pathways, in which HSSC is generat- ed in the final step instead of HSC, show a markedly in- creased thermodynamic driving force (ca. 70 kJ mol � 1 ) and thus warrant serious consideration in the context of the pre- biotic ribonucleotide reduction.

3-Hydroxyanthranilate 3,4-dioxygenase (3HAO) is a non-heme iron dependent enzyme. It catalyses the cleavage of the benzene ring of 3-hydroxyanthranilic acid (3-Ohaa), an intermediate in the kynurenine pathway, and therefore represents a potential target in treating numerous disorders related to the concentration of quinolinic acid (QUIN), the kynurenine pathway product, in tissues. The stability and behaviour of the enzyme in nearly physiological conditions, studied by the empirical molecular modelling methods enabled us to determine the influence of several, for the enzyme activity relevant, point mutations (Arg43Ala, Arg95Ala and Glu105Ala) on the protein structure, particularly on the active site architecture and the metal ion environment, as well as on the substrate, 3-Ohaa, binding. Besides, the water population of the active site, and the protein flexibility as well as the amino acid residues interaction networks relevant for the enzyme activity were determined for the 3-Ohaa complexes with the native and mutated enzyme variants. Finally, using the hybrid quantum-mechanics/molecular-mechanics (QM/MM) calculations the 3HAO catalysed 3-Ohaa oxidation into 2-amino-3-carboxymuconic acid semialdehyde was elucidated.

Utilizing dialkylamino cyclopropenimines as hydrogen bond acceptors in tri-substituted guanidines and cyclopropenimines, we computationally designed the most basic superbases possessing intramolecular hydrogen bonds (IHB-superbases) so far. The values of proton affinity in the gas phase range between 296.6 and 306 kcal mol−1, with estimated pKa values in acetonitrile between 35.5 and 39.7. The obtained PAs of five new IHB-superbases surpass the basicity of the paradigmatic P4-tBu Schwesinger phosphazene, whereas pKa values come close to that of P4-tBu. None of the designed superbases contain phosphorus, which puts them among few most basic non-phosphorus superbases desiged so far.

This study presents a detailed experimental investigation of charge isomers of protonated 4-quinolone antibiotics molecules formed during electrospray ionization (ESI) with proposed dissociation mechanisms after collisional activation. Piperazinyl quinolones have been previously shown to exhibit erratic behavior during tandem MS analyses of biological samples, which originated from varying ratios of two isomeric variants formed during ESI. Here, a combination of ESI-collision-induced dissociation (CID), differential ion mobility spectrometry (DMS), high resolution MS, and density functional theory (DFT) was used to investigate the underlying mechanisms of isomer formation and their individual dissociation behaviors. The study focused on ciprofloxacin; major findings were confirmed using structurally related 4-quinolones. DFT calculations showed a reversal of basicity for piperazinyl quinolones between liquid and gas phase. We provide an experimental comparison and theoretical treatment of factors influencing the formation ratio of the charge isomers during ESI, including solvent pH, protic/aprotic nature of solvent, and structural effects such as pK a and proton affinity. The actual dissociation mechanisms of the isomers of the protonated molecules were studied by separating the individual isomers via DMS-MS, which allowed type-specific CID spectra to be recorded. Both primary CID reactions of the two charge isomers originated from the same carboxyl group by charge-remote (CO(2) loss) and charge-mediated (H(2)O loss) fragmentation of the piperazinyl quinolones, depending on whether the proton resides on the more basic keto or the piperazinyl group, followed by a number of secondary dissociation reactions. The proposed mechanisms were supported by calculated energies of precursors, transition states, and products for competing pathways.

Herein we describe an easily accessible class of superbasic proton sponges based on the 1,8-bisphosphazenylnaphthalene (PN) proton pincer motif and P-alkyl substituents ranging from methyl (TMPN) to n-butyl (TBPN), isopropyl (TiPrPN) and cyclopentyl (TcyPPN). These neutral bases with a pK(BH)(+) value (MeCN) of ~30 were accessible via a Kirsanov condensation using commercially available 1,8-diaminonaphthalene, and in case of TMPN and TBPN, simple one-pot procedures starting from trisalkylphosphanes can be performed. Furthermore, the known pyrrolidinyl-substituted superbase TPPN previously synthesized via a Staudinger reaction could also be prepared by the Kirsanov strategy allowing its preparation in a larger scale. The four alkyl-substituted proton sponges were structurally characterized in their protonated form; molecular XRD structures were also obtained for unprotonated TiPrPN and TcyPPN. Moreover, we present a detailed description of spectroscopic features of chelating bisphosphazenes including TPPN and its hyperbasic homologue P2-TPPN on which we reported recently. The four alkyl-substituted superbases were investigated with respect to their basic features by computational means and by NMR titration experiments revealing unexpectedly high experimental pK(BH)(+) values in acetonitrile between 29.3 for TMPN and 30.9 for TBPN. Besides their thermodynamic basicity, we exemplarily studied the kinetic basicity of TMPN and TPPN by means of NMR-spectroscopic methods. Furthermore, the competing nucleophilic versus basic properties were examined by reacting the proton sponges with ethyl iodide. Insight into the coordination chemistry of chelating superbases was provided by reacting TMPN with trimethylaluminum and trimethylgallium to give cationic complexes of Group XIII metal alkyls that were structurally characterized.

New organic superbases have been designed using the concept of multiple intramolecular hydrogen bonds. Substituents capable of forming strong intramolecular H-bonds were selected on the basis of the energy of stabilization that occurs upon the formation of a complex between N,N',N"-trimethylguanidine and small model molecules. The proton affinities and the corresponding pK(a) values in acetonitrile of the new superbases are examined by Density Functional Theory (DFT). It is shown that N,N',N"-substitution of guanidine with appropriate substituents results in new organic superbases with gas phase proton affinities between 286 and 293 kcal mol(-1), thus being 15 to 20 kcal mol(-1) more basic than parental superbase N,N',N"-tris[(3-dimethylamino)propyl]-guanidine (tris-DMPG), whereas estimated pK(a) values in acetonitrile range between 29.5 and 33.2.

Human dipeptidyl-peptidase III (h.DPP III) is a zinc-exopeptidase that hydrolyses dipeptides from the N-terminus of its substrates. Its mechanism of action was assumed to be similar to that of thermolysin, but was never thoroughly investigated. This study presents the first insight into the reaction mechanism of h.DPP III, determined on the model and real (hydrated enzyme with Leu-enkephalin bound in the active site) systems. The Glu451-assisted water addition on amide carbon atoms and nitrogen inversion (i.e. change of pyramidalization on the leaving nitrogen) are shown to be the rate-determining steps with the activation energies in a good agreement with the experimental results for the Leu-enkephalin hydrolysis. The energy barrier for nucleophilic attack is about 28 kJ mol-1, while barriers for the N-inversion differ as a consequence of the number of hydrogen bonds that have to be changed, which is smaller in the model active site than in the solvated enzyme. Although precisely defined geometry of the enzyme binding site puts an additional restraint on the hydrogen bonding interactions, at the same time it stimulates the forward reaction towards the final hydrolytic product. Namely, different from the model, the N-inversion is in a concerted fashion followed by favourable hydrogen bonding with Glu451 that immediately "locks" the system into the configuration where reversion to the enzyme-substrate complex is hardly achievable. Therefore we propose that the functional significance of DPP III is dual: to lower the energy barrier of the peptide hydrolysis and to suppress the reverse reaction.

The linkage of two P2 -phosphazenyl groups through a C2 -symmetric (R,R)-1,2-diaminocyclohexane (DACH) backbone yielded the new chiral superbases DACH-P2 NMe2 and DACH-P2 Pyr (Pyr=pyrrolidinyl). These bases were prepared by a Kirsanov reaction and studied with respect to their spectroscopic and structural characteristics. Theoretical calculations concerning their basicity properties revealed remarkable pKBH+ values of 38.1 and 39.9 on the acetonitrile scale; this makes them the strongest nonionic chiral superbases known to date.

A magnificent edifice called acid/base chemistry is rooted in a single proton, small in size but of enormous importance. The upper floors of this building are reserved for biochemistry, while the penthouse belongs to life science. The edifice will grow into a sky scraper-like in the 21st century. Evidence provided by this Review shows that the coalescence of experimental and theoretical/computational work is not only highly desirable for that purpose, but, in fact, greatly needed.

Intriguing inactivation: Calculations suggest that the ability of relatively high-energy radical intermediates to inactivate glycerol dehydratase (GDH) may reflect a general and hitherto unidentified inactivation mechanism in the reaction of coenzyme B12-dependent enzymes and 3-unsaturated 1,2-diols (see scheme; AdoCbl: adenosylcobalamin or coenzyme B12). High-level conventional ab initio and density functional theory (DFT) calculations have been performed to examine the fate of the native substrate glycerol (1) and its analogue but-3-ene-1,2-diol (7) in the coenzyme B12-dependent enzyme glycerol dehydratase (GDH). Experimental studies find that 7 irreversibly inactivates GDH, though the mechanism for the inactivation remains unknown. Interestingly, the EPR data suggest that the spin density for an observed radical is located in the vicinity of the C1 atom, which has been interpreted to indicate termination of the pathway at the substrate-derived radical 8. Our calculations show that if analogue 7 were to follow a similar mechanistic pathway to that followed by 1, then the reaction would be unlikely to stop at 8 but would rather proceed to the highly stabilized product-related radical 9. However, the EPR characteristics of 9 would not be consistent with the observed EPR data. Calculations involving an initial H-atom abstraction from the C2 position of 7 identify alternative radicals that might account for the EPR data, though they are of relatively high energy. A proposal that could explain the experimental observations is that the enzyme binds 7 in such a manner as to prevent the efficient transformation of 8. Recent work with the related enzyme diol dehydratase suggests that a common, but as yet unexplained, inactivation mechanism may be operative for both enzymes. Finally, we note the good overall performance of the MPWB1K, BMK, M05-2X, and B2-PLYP DFT procedures for these reactions, with the BMK method producing the best results.

It is shown by a reliable DFT method that supramolecular structures 1 and 2, constructed using pyridine as an essential building block, act as powerful neutral organic superbases in the gas phase and in acetonitrile due to cationic resonance and hydrogen bonding in the conjugate acids amplified by the NMe2 groups placed at strategic positions on the molecular backbone.

It is shown by reliable DFT B3LYP/6-311+G(2df, p)//B3LYP/6-31G* method that pyridine and s-triazine can serve as useful building blocks in tailoring neutral superbases. The former compound is used in constructing the four-fragment macrocycles substituted by a number of NMe2 substituents placed at strategic positions on the suprastructures backbone. The calculated proton affinities are within the range of 270-290 kcal mol-1, thus belonging to the upper part of the superbasicity ladder. It is shown that proton affinities of polysubstituted derivatives follow a simple additivity rule, which facilitates prediction and interpretation of the results in multiply substituted systems. The s-triazine motif is employed in forming manxane-like systems by using guanidine fragments or 1, 1-dimethylaminoethylenes, which exhibit proton affinities spread over the lower part of the superbasicity scale (256-272 kcal mol-1). The amplified basicity in both families of compounds is a consequence of the strong cationic resonance in conjugate acids supported by stabilization provided by intramolecular hydrogen bonds (IMHB). The nature of the IMHBs is examined. It is found that IMHBs in large macrocycles constructed by pyridine moieties is of a bicentric type. They are not cationic resonance supported IMHBs in the first approximation. In contrast, protonation in one of the manxane-like systems yields the IMH bonds that are stabilized by substantial cationic resonance through the hydrogen H+ bridge. Consequently, the cationic resonance supported hydrogen bonds (CRSHBs) do exist in some protonated species. The basicity of pyridine macrocycles is examined in acetonitrile. It is found that their pKa values span a range between 26-30 units meaning that they are also strong superbases in MeCN solutions compared to the threshold given by pKa(MeCN) of DMAN (18.2 units).

The reactivity of new biologically active thymine derivatives substituted with 2-(arylsulfonamidino)ethyl group at N1 and N3 position was investigated in the gas phase using CID experiments (ESI-MS/MS) and by density functional theory (DFT) calculations. Both derivatives show similar chemistry in the negative mode with a retro-Michael addition (Path A(-)) being the most abundant reaction channel, which correlate well with the fluoride induced retro-Michael addition observed in solution. The difference in the fragmentation of N-3 substituted thymine 5 and N-1 substituted thymine 1 in the positive mode relates to the preferred cleavage of the sulfonyl group (m/z 155, Path B) in N-3 isomer and the formation of the acryl sulfonamidine 3 (m/z 309) via Path A in N-1 isomer. Mechanistic studies of the cleavage reaction conducted by DFT calculations give the trend of the calculated activation energies that agree well with the experimental observations. A mechanism of the retro-Michael reaction was interpreted as a McLafferty type of fragmentation, which includes Hβ proton shift to one of the neighboring oxygen atoms in a 1,5-fashion inducing N1(N3)-Cα bond scission. This mechanism was found to be kinetically favorable over other tested mechanisms. Significant difference in the observed fragmentation pattern of N-1 and N-3 isomers proves the ESI-MS/MS technique as an excellent method for tracking the fate of similar sulfonamidine drugs. Also, the observed N-1 and/or N-3 thymine alkylation with in situ formed reactive acryl sulfonamidine 3 as a Michael acceptor may open interesting possibilities for the preparation of other N-3 substituted pyrimidines.

The MP2(fc)/6-311+G**//HF/6-31G* and B3LYP/6-311+G**//HF/6-31G* calculations show that N-[3-(dimethylamino)propyl] and N-[4-(dimethylamino)butyl] derivatives of 2,3-diamino-cycloprop-2-ene-1-imine (CPI) possess high gas phase proton affinities (PA) and pronounced basicities in acetonitrile (MeCN). Tris[N-dimethylaminopropyl(-butyl)]-CPI derivatives achieve superbasic PA and pKa values. The reason behind these remarkable features is the stability of the resulting conjugate acids. They are stabilized by aromatization of the three-membered ring accompanied by the cationic resonance between the cyclopropyl ring and amino nitrogen atoms of the side chains, and, last but not least, by the cooperative multiple intramolecular hydrogen bonding effect. The latter is particularly enhanced in tris-substituted CPIs. It was found that the N-[4-(dimethylamino)butyl] side chains contribute more to the stability of the conjugate acids than those of the corresponding compound with a propyl chain, because they undergo a somewhat larger relaxation upon protonation. The studied compounds might be helpful in building up a dense ladder of strong bases and superbases, which could contribute to the development of the chemistry of superacids and superbases. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)

The extrinsic antiaromaticity of archetypal cyclobutadiene (CBD) is addressed with particular emphasis on the sigma-pi separability problem. The destabilization energy E(d)(CBD) of CBD is obtained by appropriate homodesmotic reactions involving the open chain zigzag, polyene(s). It is shown that E(d)(CBD) does not depend on the electron correlation and the zero-point vibrational energy contributions, since they are small and of the opposite sign. Consequently, they cancel in the first approximation. Further, it turns out that E(d)(CBD) can be estimated accurately enough with a very modest cc-pVDZ basis set at the Hartree-Fock (HF) level. The extrinsic antiaromatic destabilization E(ean)(CBD) of CBD is deduced after extracting the angular strain energy estimated to be 32 kcal/mol. The resulting E(ean)(CBD) value of 52 kcal/mol is in excellent agreement with the experimental thermodynamic data. If the E(ean)(CBD) is estimated relative to two isolated C=C double bonds, then it assumes 38 kcal/mol, which is roughly 10 kcal/mol per one pi electron. It is, therefore, safe to state that extrinsic antiaromaticity of CBD is larger than its angular strain. Although the sigma and pi electrons are coupled by a mutual Coulomb interaction V-ee(sigmapi), several attempts of their decoupling is made by using three partitioning schemes: stockholder, equipartition, and standard pi-electron theory recipe. The latter allocates the V-nn and V-ee(sigmapi) terms to the sigma- and pi-electron frameworks, respectively. The nuclear repulsion term V-nn is dissected into sigma and pi components in the former two partitioning schemes by using stockholder criterion. It appears that the extrinsic antiaromatic destabilization E(ean)(CBD) is determined by the pi-electron framework according to all three partitioning models.

The physical nature of aromaticity is addressed at a high ab initio level. It is conclusively shown that the extrinsic aromatic stabilization energy of benzene E(ease)B, estimated relative to its linear polyene counterpart(s), is very well-reproduced at the Hartree-Fock (HF) level. This is a consequence of the fact that the contributions arising from the zero-point vibrational energy (ZPVE) and electron correlation are rather small. More specifically, they yield together 2.0 kcalmol(-1) to the destabilization of benzene. A careful scrutiny of the HF energies by virial theorem shows further that the kinetic energies of the sigma and pi electrons E(T)HF(sigma) and E(T)HF(pi) are strictly additive in the gauge linear zig-zag polyenes, which also holds for their sum Et(T)HF This finding has the important corollary that E(ease)B is little dependent on the choice of the homodesmic reactions involving zig-zag polyenes. A detailed physical analysis of the sigma- and pi-electron contributions to extrinsic aromaticity requires explicit introduction of the potential energy terms Vne, Vee, and Vnn, which signify Coulomb interactions between the electrons and the nuclei. The Vee term involves repulsive interaction Vee(sigmapi) between the sigma and pi electrons, which cannot be unequivocally resolved into sigma and pi contributions. The same holds for the Vnn energy, which implicitly depends on the electron density distribution via the Born-Oppenheimer (BO) potential energy surface. Several possibilities for partitioning Vee(sigmapi) and Vnn terms into sigma and pi components are examined. It is argued that the stockholder principle is the most realistic, which strongly indicates that E(ease)B is a result of favorable sigma-framework interactions. In contrast, the pi-electron framework prefers the open-chain linear polyenes.

The acidities of mono- and polysubstituted benzenes incorporating one, two, or three OCH3, OCF3, or CF3 groups were investigated by use of reliable ab initio theoretical models. The calculated deprotonation energies are in very good agreement with available experimental data, although these are unfortunately sparse. A recently developed novel trichotomy formula proved useful for interpretation of predicted variation in acidity in the monosubstituted compounds. In particular, the long-range final state effect in OCF3 and CF3 derivatives is confirmed. It is reflected in the stabilization of the lone-pair electrons formed upon deprotonation at the meta and para positions. The theoretically established long-range influence of OCF3 and CF3 substituents is in accordance with empirical knowledge obtained by experimental chemical reactivity studies. The acidities of multiply substituted benzenes exhibit additivity properties based on the ISA (independent substituent approximation) model established earlier. It is conclusively shown that the combination of the additivity rule and the trichotomy formula offers a powerful tool for interpretation of the acidity of polysubstituted benzenes and of other multiply substituted aromatics, thus shedding new light on this very old and important problem. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003)

The spatial and electronic structure of the very strong neutral organic bases bis(tetramethylguanidino)naphthalene (TMGN), 4,5-bis(tetramethylguanidino)fluorene (TMGF) and some related compounds are explored by ab initio computational methods. Their affinity towards the proton is scrutinized both in the gas phase and in solution in acetonitrile. The protonation at the most basic center (the imine nitrogen) yields asymmetric and relatively strong intramolecular hydrogen bonds (IHB). It is found that the angular strain effect and steric repulsion practically vanish in TMGN which implies that its high absolute proton affinity (APA) has its origin in the inherent basicity of the guanidine fragment and a relatively strong IHB in [TMGN]H(+). The nonbonded repulsions in TMGF are higher than in TMGN, which in conjunction with a slightly stronger IHB in the corresponding conjugate acid makes it more basic: APA(TMGF)>APA(TMGN). An interesting new phenomenon is observed in both TMGN and TMGF: the proton triggers the resonance stabilization not only in the directly bonded guanidine moiety, but also in the other guanidine fragment which is more distant from the proton, albeit in a less pronounced manner. The latter feature is termed a partial protonation. This supports the hydrogen bonding and contributes to the IHB stabilization. Convincing evidence is presented that the solvent effect in acetonitrile is determined by two antagonistic factors: 1) the intrinsic (gas phase) proton affinity and 2) the size effect which is given by the ratio between the positive charge in molecular cation (conjugate acid) and the magnitude of the molecular surface. The resulting pK(a) values are given by an interplay of these factors.

The intrinsic proton affinities of iminopolyenes and their amino derivatives are considered. It is shown that substitution of amino groups at strategic positions increases proton affinity (PA) to superbasic values particularly in branched polyenes. It follows that the number of double bonds, selection of the conformations and a judicious choice of substituents offer a closely spaced ladder of highly basic compounds spanning the range of values of PAs between 206.5 and 271.9 kcal mol−1, which might be of some importance in acid–base chemistry. This conclusion is strengthened by the fact that several of the studied amino derivatives of iminopolyenes exhibit very high pKa values between 30.0–33.5 in acetonitrile. Hence, they qualify as candidates for powerful neutral organic superbases.

Multiple aminopropyl substitutions of the initial N,N′,N″-trimethylguanidine lead to high intrinsic absolute proton affinities (APA) and basicities culminating in APA = 268.4 kcal mol−1 (1 kcal = 4.184 kJ) in N,N′,N″-tris(3-aminopropyl)guanidine (9). The reason behind a high proton affinity is identified as a strong cationic resonance in the central guanidine moiety and the strength of the intramolecular hydrogen bonding (IMHB), which is enhanced upon protonation. A cooperative IMHB effect in 9 and 9H+ realized by three N(sp3)H···N(sp3) H-bridges is estimated to be as high as 14.7 and 33.0 kcal mol−1, respectively. It follows that the IMHB effect contributes 18.3 kcal mol−1 to the absolute proton affinity of 9, which is a respectable amount. The basicity of 9 in acetonitrile is estimated to be very high, as evidenced by the corresponding pKa = 28.8. A derivative of 9, N,N′,N″-tris(3-dimethylaminopropyl)guani-dine (10), assumes an even higher superbasic proton affinity of 275 kcal mol−1 due to an additional relaxation effect caused by the methyl groups. The corresponding pKa(MeCN) = 29.4. Copyright © 2002 John Wiley & Sons, Ltd.

The role of intramolecular hydrogen bonding (IMHB) in determining the proton affinities and basicities of some bis(tetramethylguanidine)systems was examined. For this purpose a series of molecular backbone moieties serving as carriers of the bis(tetramethylguanidine)crowns were explored. It was found that the best backbones are provided by phenanthrene and 9,10-dihidrophenanthrene, giving rise to proton affinities as large as 268.2 and 266.8 kcal mol1−, respectively. The corresponding pKa values in acetonitrile are 29.0 and 28.8, implying that these two compounds [6(bs)and 5(bs)] are candidates for powerful superbases. Their intramolecular hydrogen bond strengths are ≈19 kcal mol1−, which result inter alia from the partial protonation of the vis-a-vis guanidine group.

Imines are an interesting but relatively poorly-characterized class of organic compounds: for example, is the gas phase ion-derived C7H7N species observed by Nibbering et al. benzaldimine or troponimine? Proton affinities are important quantities for the understanding of organic compounds. We have investigated the structure, energetics and proton affinities of benzaldimine, troponimine, and their carbonyl and olefinic analogs (benzaldehyde, tropone, styrene, heptafulvene) using G2(MP2) computational theory. We find the benzenoid species (benzaldimine, benzaldehyde, styrene) to be more stable by 20–25 kcal mol−1 than their nonbenzenoid isomers (troponimine, tropone, heptafulvene). From our calculations and analysis of literature data, we derive the enthalpy of formation and proton affinity of benzaldimine to be 39 ± 3 and 220 ± 3 kcal mol−1 respectively and conclude Nibbering's C7H7N is, in fact, this species.

Utilizing several different trialkylarsine oxides and substituted pyridine N-oxides as a hydrogen bond acceptors in tri-substituted guanidines we designed several very basic superbases possessing intramo-lecular hydrogen bonds (IHB-superbases), with proton affinity in the gas phase that comes very close to that of paradigmatic P4-tBu Schwesinger superbase and with pKa in acetonitrile up to 36 units.

Investigations on the Staudinger reaction between 1,8-diazidonaphthalene and phosphorous(III) building blocks, a key step in the synthesis of superbasic bisphospha- zene proton sponges, yielded a set of bisphosphazides with a constrained geometry 1,8-disubstituted naphthalene back- bone. This compound class has attracted our interest not only due to their surprisingly high stability, but in particular because of their theoretically predicted basicity in the range of their bisphosphazene analogues that can be referred to the constrained geometry interaction of two highly basic ni- trogen atoms. Eleven new bisphosphazides bearing simple P-amino groups as well as P-guanidino substituents, aza- phosphatrane moieties, P2 building blocks, or chiral P-amino substituents derived from l-proline are presented. They were studied concerning their spectroscopic properties and partly also their chromophoric and structural features. In the case of the pyrrolidino-substituted TPPN(2N2) (TPPN = 1,8- bis(trispyrrolidinophosphazenyl)naphthalene), the stepwise nitrogen elimination is investigated theoretically and experi- mentally, which led to the isolation and structural characteri- zation of TPPN(1N2) bearing a phosphazide and a phospha- zene functionality in one molecule. Attempts to protonate the obtained bisphosphazides and to prove the computa- tionally predicted pKBH + values through NMR titration reac- tions resulted in their decay, which again was rationalized by theoretical calculations. Altogether we present the so far most extensive spectroscopic, structural and theoretical in- vestigation of constrained geometry bisphosphazides and their Bronsted and Lewis basic properties.

It is shown, by utilizing a reliable model at the MP2 level of theory, that the imino group attached to the cyclopropene moiety exhibits a high proton affinity (PA). The reason behind the appreciable PA is identified as significant aromatization of the three-membered ring spurred by the protonation. Further amplification of the PA can be achieved by NH2 substitutions at the CC endo double bond, since amino groups stimulate aromatization of the cyclopropene fragment. Additionally, they release some of their lone pair electron density thus contributing to a uniform distribution of the positive charge over the entire molecular system. This effect is even more pronounced if the diaminoiminocyclopropene system is substituted by sizable alkyl groups. The aromatic stabilization in the protonated 2,3-diaminocyclopropeneimine, estimated by the corresponding homodesmic reaction, seems to be as high as 59.5 kcal/mol. Very potent organic bases can be obtained by designing polycyclic systems possessing two or more cyc...

The absolute proton affinities (APA) of 20 α-amino acids, as obtained by the MP2(fc)/6-311+G∗∗//HF/6-31G∗ + ZPVE(HF/6-31G∗) and the scaled Hartree–Fock (HFsc) models, are presented. It is shown that the α-NH2 group is protonated in all but four cases: lysine (K), proline (P), histidine (H), and arginine (R). There is a good overall agreement with experimental data measured by the kinetic method. However, there are some notable exceptions such as glutamine (Q) and lysine (K), where strong hydrogen bonds in the protonated forms occur. It is suggested that the present results and theoretical models employed could be useful for resolving such experimental ambiguities. Furthermore, it appears that the HFsc model provides an efficient tool for elucidating APAs of artificial α-AAs, derivatives of natural α-AAs and their oligomers.