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We used a range of computational techniques to assess the effect of selective C-H deuteration on the antagonist istradefylline affinity for the adenosine A 2A receptor, which was discussed relative to its structural analogue caffeine, a well-known and likely the most widely used stimulant. The obtained results revealed that smaller caffeine shows high receptor flexibility and exchanges between two distinct poses, which agrees with crystallographic data. In contrast, the additional C8- trans -styryl fragment in istradefylline locks the ligand within a uniform binding pose, while contributing to the affinity through the C-H···π and π···π contacts with surface residues, which, together with its much lower hydration prior to binding, enhances the affinity over caffeine. In addition, the aromatic C8-unit shows a higher deuteration sensitivity over the xanthine part, so when both of its methoxy groups are d 6 -deuterated, the affinity improvement is -0.4 kcal mol -1 , which surpasses the overall affinity gain of -0.3 kcal mol -1 in the perdeuterated d 9 -caffeine. Yet, the latter predicts around 1.7-fold potency increase, being relevant for its pharmaceutical implementations, and also those within the coffee and energy drink production industries. Still, the full potential of our strategy is achieved in polydeuterated d 19 -istradefylline, whose A 2A affinity improves by -0.6 kcal mol -1 , signifying a 2.8-fold potency increase that strongly promotes it as a potential synthetic target. This knowledge supports deuterium application in drug design, and while the literature already reports about over 20 deuterated drugs currently in the clinical development, it is easily foreseen that more examples will hit the market in the years to come. With this in mind, we propose that the devised computational methodology, involving the ONIOM division of the QM region for the ligand and the MM region for its environment, with an implicit quantization of nuclear motions relevant for the H/D exchange, allows fast and efficient estimates of the binding isotope effects in any biological system.

The enzyme-catalyzed degradation of the biogenic amine serotonin is an essential regulatory mechanism of its level in the human organism. In particular, monoamine oxidase A (MAO A) is an important flavoenzyme involved in the metabolism of monoamine neurotransmitters. Despite extensive research efforts, neither the catalytic nor the inhibition mechanisms of MAO enzymes are currently fully understood. In this article, we present the quantum mechanics/molecular mechanics simulation of the rate-limiting step for the serotonin decomposition, which consists of hydride transfer from the serotonin methylene group to the N5 atom of the flavin moiety. Free-energy profiles of the reaction were computed by the empirical valence bond method. Apart from the enzymatic environment, the reference reaction in the gas phase was also simulated, facilitating the estimation of the catalytic effect of the enzyme. The calculated barrier for the enzyme-catalyzed reaction of 14.82 ± 0.81 kcal mol -1 is in good agreement with the experimental value of 16.0 kcal mol -1 , which provides strong evidence for the validity of the proposed hydride-transfer mechanism. Together with additional experimental and computational work, the results presented herein contribute to a deeper understanding of the catalytic mechanism of MAO A and flavoenzymes in general, and in the long run, they should pave the way toward applications in neuropsychiatry.

Quinolino[7,8- h ]quinoline is a superbasic compound, with a p K aH in acetonitrile greater than that of 1,8-bis(dimethylaminonaphthalene) (DMAN), although its synthesis and the synthesis of its derivatives can be problematic. The use of halogen derivatives 4,9-dichloroquinolino[7,8- h ]quinoline ( 16 ) and 4,9-dibromoquinolino[7,8- h ]quinoline ( 17 ) as precursors has granted the formation of a range of substituted quinolinoquinolines. The basicity and other properties of quinolinoquinolines can be modified by the inclusion of suitable functionalities. The experimentally obtained p K aH values of quinolino[7,8- h ]quinoline derivatives show that N 4 , N 4 , N 9 , N 9 -tetraethylquinolino[7,8- h ]quinoline-4,9-diamine ( 26 ) is more superbasic than quinolino[7,8- h ]quinoline. Computationally derived p K aH values of quinolinoquinolines functionalized with dimethylamino (NMe 2 ), 1,1,3,3-tetramethylguanidino (N═C(NMe 2 ) 2 ) or N , N , N ', N ', N ″, N ″-hexamethylphosphorimidic triamido (N═P(NMe 2 ) 3 ) groups are significantly greater than those of quinolino[7,8- h ]quinoline. Overall, electron-donating functionalities are observed to increase the basicity of the quinolinoquinoline moiety, while the substitution of electron-withdrawing groups lowers the basicity.

Metal complexes of iminodiacetamide ( imda ) ligands and metal ions Zn(II), Cu(II), Ni(II), and Co(II) were prepared using eight imda ligands ( L1 - L8 ) substituted with groups of different steric and electronic properties on the central amine N atom (H atom, methyl, isopropyl, and benzyl) and the para position of the phenyl rings (nitro and dimethylamino). The effect of these substituents on the stoichiometry ( ML and ML 2 ), geometry, and stereochemistry ( mer , trans - fac , cis - fac ) of the complexes was studied in the solid state, in solution, and by density functional theory calculations. Single-crystal and powder X-ray diffraction, thermogravimetry, and IR spectroscopy showed that in the solid state imda ligands preferentially form trans - fac ML 2 complexes, with the exception of the cis - fac complex 7 Zn . NMR spectroscopy of diamagnetic Zn(II) and paramagnetic Co(II) complexes revealed the formation of both ML and ML 2 complexes in solution, which was also confirmed by UV-vis titrations. Variable-temperature NMR was used to study the effect of the substituent on the central amine N atom on the Zn-N bond strength and nitrogen inversion. The relative stabilities of the isomers were rationalized by computations and the optimized structures used for geometry analysis.

In the reaction of purines with ferrocenoyl chloride in dimethylformamide (DMF), a regioselective acylation occurred. The two products have been isolated and, according to detailed NMR analysis, identified as N7 - and N9 -ferrocenoylated isomers. In a more polar solvent, for example, in dimethylsulfoxide (DMSO), the two isomers interconvert to each other. The N7 / N9 isomerization was followed by 1 H NMR spectroscopy, until dynamic equilibrium was reached. Both kinetics and thermodynamics of the transacylation process are governed by a C6-substituent on the purine ring (R = NH 2 , Me, NHBz, OBz). The observed rate constant for the N7 / N9 -isomerization in the adenine system (R = NH 2 ) is k obs = 0.3668 h -1 , whereas the corresponding process in the C6-benzyloxypurine is 56 times slower. By use of density functional theory calculations and molecular dynamics simulations, several reaction pathways were considered and explored. Only the reaction mechanism involving DMSO as a nucleophilic reactant is in harmony with the experimental kinetic data. The calculated barrier (Δ G ⧧ = 107.9 kJ/mol; at the M06L/6-311+G(d,p)/SDD level of theory) for this S N 2-like reaction in the adenine system agrees well with the experimental value of 102.7 kJ/mol. No isomerization was detected in other organic solvents, for example, acetonitrile, N , N -dimethylformamide, or acetone, which indicated the exceptional nucleophilicity of DMSO. Our results raise a warning when treating or dissolving acylated purines in DMSO as they are prone to isomerization. We observed that the N7 / N9 -group transfer was specific not only for the organometallic moiety only, but for other acyl groups in purines as well. The relevance of this isomerization may be expected for a series of nucleobases and heterocyclic systems in general.

Monoamine oxidases (MAOs) are flavin adenine dinucleotide containing flavoenzymes that catalyze the degradation of a range of brain neurotransmitters, whose imbalance is extensively linked with the pathology of various neurological disorders. This is why MAOs have been the central pharmacological targets in treating neurodegeneration for more than 60 years. Still, despite this practical importance, the precise chemical mechanisms underlying the irreversible inhibition of the MAO B isoform with clinical drugs rasagiline (RAS) and selegiline (SEL) remained unknown. Here we employed a combination of MD simulations, MM-GBSA binding free energy evaluations, and QM cluster calculations to show the MAO inactivation proceeds in three steps, where, in the rate-limiting first step, FAD utilizes its N5 atom to abstracts a hydride anion from the inhibitor α-CH 2 group to ultimately give the final inhibitor-FAD adduct matching crystallographic data. The obtained free energy profiles reveal a lower activation energy for SEL by 1.2 kcal mol -1 and a higher reaction exergonicity by 0.8 kcal mol -1 , with the former being in excellent agreement with experimental ΔΔ G ‡ EXP = 1.7 kcal mol -1 , thus rationalizing its higher in vivo reactivity over RAS. The calculated Δ G BIND energies confirm SEL binds better due to its bigger size and flexibility allowing it to optimize hydrophobic C-H···π and π···π interactions with residues throughout both of enzyme's cavities, particularly with FAD, Gln206 and four active site tyrosines, thus overcoming a larger ability of RAS to form hydrogen bonds that only position it in less reactive orientations for the hydride abstraction. Offered results elucidate structural determinants affecting the affinity and rates of the inhibition reaction that should be considered to cooperate when designing more effective compounds devoid of untoward effects, which are of utmost significance and urgency with the growing prevalence of brain diseases.

We prepared a range of N-arylbenzamides with a variable number of methoxy and hydroxy groups, bearing either amino or amino-protonated moieties, and used DPPH and FRAP assays to evaluate their antioxidant capacity. Most of the systems exhibit improved antioxidative properties relative to the reference BHT molecule in both assays. Combining results from both sets of experiments, the most promising antioxidative potential was displayed by the trihydroxy derivative 26, which we propose as a lead compound for a further optimization of the benzamide scaffold. Computational analysis helped in interpreting the observed trends and demonstrated that protonated systems are better antioxidants than their neutral counterparts, while underlying the positive influence of the electron-donating methoxy group on the antioxidant properties, thus confirming the experiments. It also revealed that the introduction of the hydroxy groups shifts the reactivity from both amide and amine groups toward this moiety and additionally enhances antioxidative features. This is particularly evident in 26H •+ , which owes its pronounced reactivity to the stabilizing [O • ···H-O] hydrogen bonding between the created phenoxyl radical and the two neighboring hydroxy groups. We demonstrated that its antioxidative activities are more favorable than those for analogous trihydroxy derivatives without the N-phenyl group or without the amide moiety, which strongly justifies the employed strategy in utilizing bisphenylamides in designing potent antioxidants.

Diamine oxidase (DAO) is an enzyme involved in the regulation of cell proliferation and the immune response. This enzyme performs oxidative deamination in the catabolism of biogenic amines, including, among others, histamine, putrescine, spermidine, and spermine. The mechanistic details underlying the reductive half-reaction of the DAO-catalyzed oxidative deamination which leads to the reduced enzyme cofactor and the aldehyde product are, however, still under debate. The catalytic mechanism was proposed to involve a prototropic shift from the substrate-Schiff base to the product-Schiff base, which includes the rate-limiting cleavage of the Cα-H bond by the conserved catalytic aspartate. Our detailed mechanistic study, performed using a combined quantum chemical cluster approach with empirical valence bond simulations, suggests that the rate-limiting cleavage of the Cα-H bond involves direct hydride transfer to the topaquinone cofactor-a mechanism that does not involve the formation of a Schiff base. Additional investigation of the D373E and D373N variants supported the hypothesis that the conserved catalytic aspartate is indeed essential for the reaction; however, it does not appear to serve as the catalytic base, as previously suggested. Rather, the electrostatic contributions of the most significant residues (including D373), together with the proximity of the Cu 2+ cation to the reaction site, lower the activation barrier to drive the chemical reaction., Competing Interests: The authors declare no competing financial interest.

DFT B3LYP calculations convincingly showed that aromatic pnictogen oxides offer scaffolds suitable for tailoring powerful organic superbases exhibiting exceptional oxygen basicity in both the gas phase and polar aprotic acetonitrile solution. With their protonation enthalpies and pK a values, they surpass the basicity of classical proton sponges and related nitrogen bases. The most potent system is provided with two arsenic oxide moieties on the phenanthrene framework assisted by the two phosphazeno groups in the para-position to both basic centers. With its proton affinity PA = 300.5 kcal mol -1 , the latter system breaks the gas-phase hyperbasicity threshold of 300 kcal mol -1 , while its pK a = 54.8 promotes it as an unprecedented superbase in acetonitrile. The origin of such a dramatic basicity enhancement is traced to a fine interplay between (a) steric repulsions of the two negatively charged oxygens destabilizing a neutral base, (b) favorable intramolecular [O-H···O] - hydrogen bonding in conjugate acids, and (c) efficient cationic resonance upon protonation supported by the electron-donating substituents. Given the growing interest in highly basic compounds together with related basic catalysts and metal complexing agents, we hope that the results presented here will open a new avenue of research in these fields and direct attention toward utilizing aromatic pnictogen oxides in designing improved organic materials.

SrLip is an extracellular enzyme from Streptomyces rimosus (Q93MW7) exhibiting lipase, phospholipase, esterase, thioesterase, and tweenase activities. The structure of SrLip is one of a very few lipases, among the 3D-structures of the SGNH superfamily of hydrolases, structurally characterized by synchrotron diffraction data at 1.75 Å resolution (PDB: 5MAL ). Its crystal structure was determined by molecular replacement using a homology model based on the crystal structure of phospholipase A 1 from Streptomyces albidoflavus (PDB: 4HYQ ). The structure reveals the Rossmann-like 3-layer αβα sandwich fold typical of the SGNH superfamily stabilized by three disulfide bonds. The active site shows a catalytic dyad involving Ser10 and His216 with Ser10-OγH···NεHis216, His216-NδH···O═C-Ser214, and Gly54-NH···Oγ-Ser10 hydrogen bonds essential for the catalysis; the carbonyl oxygen of the Ser214 main chain acts as a hydrogen bond acceptor ensuring the orientation of the His216 imidazole ring suitable for a proton transfer. Molecular dynamics simulations of the apoenzyme and its complex with p-nitrophenyl caprylate were used to probe the positioning of the substrate ester group within the active site and its aliphatic chain within the binding site. Quantum-mechanical calculations at the DFT level revealed the precise molecular mechanism of the SrLip catalytic activity, demonstrating that the overall hydrolysis is a two-step process with acylation as the rate-limiting step associated with the activation free energy of ΔG ⧧ ENZ = 17.9 kcal mol -1 , being in reasonable agreement with the experimental value of 14.5 kcal mol -1 , thus providing strong support in favor of the proposed catalytic mechanism based on a dyad.

Monoamine oxidases (MAOs) A and B are flavoenzymes responsible for the metabolism of biogenic amines, such as dopamine, serotonin, and noradrenaline (NA), which is why they have been extensively implicated in the etiology and course of various neurodegenerative disorders and, accordingly, used as primary pharmacological targets to treat these debilitating cognitive diseases. The precise chemical mechanism through which MAOs regulate the amine concentration, which is vital for the development of novel inhibitors, is still not unambiguously determined in the literature. In this work, we present atomistic empirical valence bond simulations of the rate-limiting step of the MAO-A-catalyzed NA (norepinephrine) degradation, involving hydride transfer from the substrate α-methylene group to the flavin moiety of the flavin adenine dinucleotide prosthetic group, employing the full dimensionality and thermal fluctuations of the hydrated enzyme, with extensive configurational sampling. We show that MAO-A lowers the free energy of activation by 14.3 kcal mol -1 relative to that of the same reaction in aqueous solution, whereas the calculated activation free energy of ΔG ‡ = 20.3 ± 1.6 kcal mol -1 is found to be in reasonable agreement with the correlated experimental value of 16.5 kcal mol -1 . The results presented here strongly support the fact that both MAO-A and MAO-B isoforms function by the same hydride-transfer mechanism. We also considered a few point mutations of the "aromatic cage" tyrosine residue (Tyr444Phe, Tyr444Leu, Tyr444Trp, Tyr444His, and Tyr444Glu), and the calculated changes in the reaction barriers are in agreement with the experimental values, thus providing further support to the proposed mechanism.

Pyridine substituted with one and two bicyclic guanidine groups has been studied as a potential source of superbases. 2-{hpp}C5H4N (I) and 2,6-{hpp}2C5H3N (II) (hppH = 1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-a]pyrimidine) were protonated using [HNEt3][BPh4] to afford [I-H][BPh4] (1a), [II-H][BPh4] (2), and [II-H2][BPh4]2 (3). Solution-state (1)H and (15)N NMR spectroscopy shows a symmetrical cation in 2, indicating a facile proton-exchange process in solution. Solid-state (15)N NMR data differentiates between the two groups, indicating a mixed guanidine/guanidinium. X-ray diffraction data are consistent with protonation at the imine nitrogen, confirmed for 1a by single-crystal neutron diffraction. The crystal structure of 1a shows association of two [I-H](+) cations within a cage of [BPh4](-) anions. Computational analysis performed in the gas phase and in MeCN solution shows that the free energy barrier to transfer a proton between imino centers in [II-H](+) is 1 order of magnitude lower in MeCN than in the gas phase. The results provide evidence that linking hpp groups with the pyridyl group stabilizes the protonation center, thereby increasing the intrinsic basicity in the gas phase, while the bulk prevents efficient cation solvation, resulting in diminished pKa(MeCN) values. Spectrophotometrically measured pKa values are in excellent agreement with calculated values and confirm that I and II are superbases in solution.

Brain monoamines regulate many centrally mediated body functions, and can cause adverse symptoms when they are out of balance. A starting point to address challenges raised by the increasing burden of brain diseases is to understand, at atomistic level, the catalytic mechanism of an essential amine metabolic enzyme-monoamine oxidase B (MAO B). Recently, we demonstrated that the rate-limiting step of MAO B catalyzed conversion of amines into imines represents the hydride anion transfer from the substrate α-CH2 group to the N5 atom of the flavin cofactor moiety. In this article we simulated for MAO B catalyzed dopamine decomposition the effects of nuclear tunneling by the calculation of the H/D kinetic isotope effect. We applied path integral quantization of the nuclear motion for the methylene group and the N5 atom of the flavin moiety in conjunction with the QM/MM treatment on the empirical valence bond (EVB) level for the rest of the enzyme. The calculated H/D kinetic isotope effect of 12.8 ± 0.3 is in a reasonable agreement with the available experimental data for closely related biogenic amines, which gives strong support for the proposed hydride mechanism. The results are discussed in the context of tunneling in enzyme centers and advent of deuterated drugs into clinical practice.

The ionization state of drugs influences many pharmaceutical properties such as their solubility, permeability, and biological activity. It is therefore important to understand the structure property relationship for the acid-base dissociation constant pKa during the lead optimization process to make better-informed design decisions. Computational approaches, such as implemented in MoKa, can help with this; however, they often predict with too large error especially for proprietary compounds. In this contribution, we look at how retraining helps to greatly improve prediction error. Using a longitudinal study with data measured over 15 years in a drug discovery environment, we assess the impact of model training on prediction accuracy and look at model degradation over time. Using the MoKa software, we will demonstrate that regular retraining is required to address changes in chemical space leading to model degradation over six to nine months.

A novel OH(-)-promoted tandem reaction involving C(β)-N(+)(pyridinium) cleavage and ether C(β)-O(oxime) bond formation in aqueous media has been presented. The study fully elucidates the fascinating reaction behavior of N-benzoylethylpyridinium-4-oxime chloride in aqueous media under mild reaction conditions. The reaction journey begins with the exclusive β-elimination and formation of pyridine-4-oxime and phenyl vinyl ketone and ends with the formation of O-alkylated pyridine oxime ether. A combination of experimental and computational studies enabled the introduction of a new type of rearrangement process that involves a unique tandem reaction sequence. We showed that (E)-O-benzoylethylpyridine-4-oxime is formed in aqueous solution by a base-induced tandem β-elimination/hetero-Michael addition rearrangement of (E)-N-benzoylethylpyridinium-4-oximate, the novel synthetic route to this engaging target class of compounds. The complete mechanistic picture of this rearrangement process was presented and discussed in terms of the E1cb reaction scheme within the rate-limiting β-elimination step.

Monoamine oxidases (MAO) A and B are important flavoenzymes involved in the metabolism of amine neurotransmitters. Orru et al. ( J. Neural Transm. 2013 , 120 , 847 - 851 ) recently presented experimental results that have challenged the prevailing assumption that MAO A and MAO B employ an identical catalytic mechanism. We compared the spatial configuration of ionizable groups in both isozymes and estimated the time-averaged electrostatic potential by calculating the pKa values of five active site residues. Superimposition of both experimental structures shows very close overlap and the RMSD in placements of ionizable groups within 16 Å of the reaction center is only 0.847 Å. This similarity is also reflected in the calculated pKa values, where the largest difference between the MAO A and MAO B pKa values was found for residues Tyr188 in MAO B and the corresponding Tyr197 in MAO A assuming 1.23 units. The pKa values for the other four studied residues differ by less than 0.75 units. The results show that the electrostatic preorganizations in both active sites are very similar, supporting the idea that both enzymes work by the same mechanism.

Monoamine oxidase (MAO), which exists in two isozymic forms, MAO A and MAO B, is an important flavoenzyme responsible for the metabolism of amine neurotransmitters such as dopamine, serotonin, and norepinephrine. Despite extensive research effort, neither the catalytic nor the inhibition mechanisms of MAO have been completely understood. There has also been dispute with regard to the protonation state of the substrate upon entering the active site, as well as the identity of residues that are important for the initial deprotonation of irreversible acetylenic inhibitors, in accordance with the recently proposed mechanism. Therefore, in order to investigate features essential for the modes of action of MAO, we have calculated pKa values of three relevant tyrosine residues in the MAO B active site, with and without dopamine bound as the substrate (as well as the pKa of the dopamine itself in the active site). The calculated pKa values for Tyr188, Tyr398, and Tyr435 in the complex are found to be shifted upward to 13.0, 13.7, and 14.7, respectively, relative to 10.1 in aqueous solution, ruling out the likelihood that they are viable proton acceptors. The altered tyrosine pKa values could be rationalized as an interplay of two opposing effects: insertion of positively charged bulky dopamine that lowers tyrosine pKa values, and subsequent removal of water molecules from the active site that elevates tyrosine pKa values, in which the latter prevails. Additionally, the pKa value of the bound dopamine (8.8) is practically unchanged compared to the corresponding value in aqueous solution (8.9), as would be expected from a charged amine placed in a hydrophobic active site consisting of aromatic moieties. We also observed potentially favorable cation-π interactions between the -NH3(+) group on dopamine and aromatic moieties, which provide a stabilizing effect to the charged fragment. Thus, we offer here theoretical evidence that the amine is most likely to be present in the active site in its protonated form, which is similar to the conclusion from experimental studies of MAO A (Jones et al. J. Neural Trans.2007, 114, 707-712). However, the free energy cost of transferring the proton from the substrate to the bulk solvent is only 1.9 kcal mol(-1), leaving open the possibility that the amine enters the chemical step in its neutral form. In conjunction with additional experimental and computational work, the data presented here should lead toward a deeper understanding of mechanisms of the catalytic activity and irreversible inhibition of MAO B, which can allow for the design of novel and improved MAO B inhibitors.

Hydration of histamine was examined by infrared spectroscopy and Car-Parrinello molecular dynamics simulation. Histamine is a neurotransmitter and inflammation mediator, which at physiological pH conditions is present mainly in monocationic form. Our focus was on the part of vibrational spectra that corresponds to histamine N-H stretching, since these degrees of freedom are essential for its interactions with either water molecules or transporters and receptors. Assignment of the experimental spectra revealed a broad feature between 3350 and 2300 cm(-1), being centered at 2950 cm(-1), which includes a mixed contribution from the ring N-H and the aminoethyl N-H stretching vibrations. Computational analysis was performed in two ways: first, by making Fourier transformation on the autocorrelation function of all four N-H bond distances recorded during CPMD run, and second, and most importantly, by incorporating quantum effects through applying an a posteriori quantization of all N-H stretching motions utilizing our snapshot analysis of the fluctuating proton potential. The one-dimensional vibrational Schrödinger equation was solved numerically for each snapshot, and the N-H stretching envelopes were calculated as a superposition of the 0→1 transitions. The agreement with the experiment was much better in the case of the second approach. Our calculations clearly demonstrated that the ring amino group absorbs at higher frequencies than the remaining three amino N-H protons of the protonated aminoethyl group, implying that the chemical bonding in the former group is stronger than in the three amino N-H bonds, thus forming weaker hydrogen bonding with the surrounding solvent molecules. In this way the results of the simulation complemented the experimental spectrum that cannot distinguish between the two sets of protons. The effects of deuteration were also considered. The resulting N-D absorption is narrower and red-shifted. The presented methodology is of general applicability to strongly correlated systems, and it is particularly tuned to provide computational support to vibrational spectroscopy. Perspectives are given for its future applications in computational studies of tunneling in enzyme reactive centers and for receptor activation., (© 2011 American Chemical Society)

B3LYP/6-311+G(2df,p)//B3LYP/6-31+G(d) calculations convincingly show that tricyclic organic compounds 1 and 2 offer scaffolds suitable for tailoring powerful neutral organic acids. Their cyanation at all C(sp(2))-H positions provide superacids as evidenced by their enthalpies of deprotonation ΔHacid(1bCN) = 257.2 and ΔHacid(2bCN) = 250.9 kcal mol(-1), which are close to the threshold of hyperacidity of 245 kcal mol(-1). On the other hand hexacyclic system 3 cyanated at all possible substitution sites along the perimeter except the acidic C(sp(3))-H position provides a true hyperacid with ΔHacid(3aCN) = 242.8 kcal mol(-1). The reason behind the dramatic acidifying effect is a vigorous anionic resonance effect in the corresponding conjugate bases assisted by a cooperative substituent effect of the CN groups. It is convincingly shown that compounds 1 and 2 represent rigid antiaromatic quasi-[12]annulene and aromatic quasi-[14]annulene par excellence, respectively, conforming to Hückel's (4n + 2)π electron count rule in the bridged polycyclic systems. Calculations of the pKa values in DMSO show that the polycyano derivatives are powerful superacids in solutions too.

The bis-guanidino compound H(2)C{hpp}(2) (I; hppH = 1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-a]pyrimidine) has been converted to the monocation [I-H](+) and isolated as the chloride and tetraphenylborate salts. Solution-state spectroscopic data do not differentiate the protonated guanidinium from the neutral guanidino group but suggest intramolecular "-N-H...N=" hydrogen bonding to form an eight-membered C(3)N(4)H heterocycle. Solid-state CPMAS (15)N NMR spectroscopy confirms protonation at one of the imine nitrogens, although line broadening is consistent with solid-state proton transfer between guanidine functionalities. X-ray diffraction data have been recorded over the temperature range 50-273 K. Examination of the carbon-nitrogen bond lengths suggests a degree of "partial protonation" of the neutral guanidino group at higher temperatures, with greater localization of the proton at one nitrogen position as the temperature is lowered. Difference electron density maps generated from high-resolution X-ray diffraction studies at 110 K give the first direct experimental evidence for proton transfer in a poly(guanidino) system. Computational analysis of I and its conjugate acid [I-H](+) indicate strong cationic resonance stabilization of the guanidinium group, with the nonprotonated group also stabilized, albeit to a lesser extent. The maximum barrier to proton transfer calculated using the Boese-Martin for kinetics method was 2.8 kcal mol(-1), with hydrogen-bond compression evident in the transition state; addition of zero-point vibrational energy values leads to the conclusion that the proton transfer is barrierless, implying that the proton shuttles freely between the two nitrogen atoms. Calculations determining the gas-phase proton affinity and the pK(a) in acetonitrile both indicate that compound I should behave as a superbase. This has been confirmed by spectrophotometric titrations in MeCN using polyphosphazene references, which give an average pK(a) of 28.98 +/- 0.05. Triadic analysis indicates that the dominant term causing the high basicity is the relaxation energy.

Deprotonation enthalpies and the gas-phase acidities of 24 inorganic acids are calculated by using composite G3 and G2 methodologies. The computed values are in very good accordance with available measured data. It is found that the experimental DeltaH(acid) values of the FSO(3)H and CF(3)SO(3)H are too high by some 6 and 7 kcal mol(-1), respectively. Furthermore, a new DeltaH(acid) value for HClO(4) of 300 kcal mol(-1) is recommended and suggested as a threshold of superacidicity in the gas phase. The calculated deprotonation enthalpies are interpreted by employing the trichotomy paradigm. Taking into account that the deprotonation enthalpy is a measure of acidity, it can be safely stated that the pronounced acidities of mineral acids are to a very large extent determined by Koopmans' term with very few exceptions, one of them being H(2)S. To put it in another way, acidities are predominantly a consequence of the ability of the conjugate bases to accommodate the excess electron charge, since Koopmans' term in trichotomy analysis is related to conjugate base anion. The final state is decisive in particular for superacids like ClSO(3)H, CF(3)SO(3)H, HClO(4), HBF(4), HPF(6), HAlCl(4), and HAlBr(4). However, in the latter two molecules the bond dissociation energy of the halogen-H bond substantially contributes to their high acidity too. Therefore, acidity of these two most powerful superacids studied here is determined by cooperative influence of both initial and final state effects. It should be emphasized that acidity of hydrogen halides HCl and HBr is a result of concerted action of all three terms included in triadic analysis. A byproduct of the triadic analysis are the first adiabatic ionization energies of the anionic conjugate bases. They are in fair to good agreement with the experimental data, which are unfortunately sparse. A fairly good qualitative correlation is found between the gas-phase deprotonation enthalpies of six mineral O-H acids and available Hammett-Taft sigma(p)- constants of the corresponding substituent groups.

Hydride affinities (HAs) of the ethynes substituted by a wide range of different substituents are considered by using the B3LYP methodology. The computed values are in fair agreement with available experimental data, which are unfortunately scarce. The trend of changes of the HAs is rationalized by trichotomy formula. One of the important results of this analysis is a finding that similar HA values might result from completely different effects. Alternative sites of the H- attack are examined and the difference in energies relative to the most susceptible positions is interpreted. Structural features of substituted ethyne hydrides are briefly discussed.

Identification of metabolic biotransformations can significantly affect the drug discovery process. Since bioavailability, activity, toxicity, distribution, and final elimination all depend on metabolic biotransformations, it would be extremely advantageous if this information could be produced early in the discovery phase. Once obtained, this information can help chemists to judge whether a potential candidate should be eliminated from the pipeline or modified to improve chemical stability or safety of new compounds. The use of in silico methods to predict the site of metabolism in phase I cytochrome-mediated reactions is a starting point in any metabolic pathway prediction. This paper presents a new method, specifically designed for chemists, that provides the cytochrome involved and the site of metabolism for any human cytochrome P450 (CYP) mediated reaction acting on new substrates. The methodology can be applied automatically to all the cytochromes for which 3D structure is known and can be used by chemists to detect positions that should be protected in order to avoid metabolic degradation or to check the suitability of a new scaffold or prodrug. The fully automated procedure is also a valuable new tool in early ADME-Tox assays (absorption, distribution, metabolism, and excretion toxicity assays), where drug safety and metabolic profile patterns must be evaluated as soon, and as early, as possible.

The problem of intrinsic Lewis acidities of simple boron compounds (BH3-mXm, m = 0-3, X = F, Cl, Br, CH3, and OH) is assessed by their gas-phase hydride affinities (HAs). A simple and intuitively appealing picture of the interaction process including detachment of an electron from the hydride ion H-, capture of the pruned electron to the investigated Lewis acid (LA), and subsequent formation of the homolytic chemical bond between two newly created radicals is proposed. It enables transparent and straightforward dissection of the initial and final state effects, which taken together with the intermediate relaxation stabilization determine the trend of changes in the hydride affinities. The former effect is reflected in the electron affinities of the neutral Lewis acids given within Koopmans' approximation, while the final state effect involves properties of the formed Lewis acid-base adducts mirrored in the bond dissociation energy of the formed [LA-H]- chemical bond. It is demonstrated that unexpectedly low Lewis acidity of fluoroboranes relative to the corresponding chlorine and bromine derivatives can be traced down to the unfavorable Koopmans' electron affinities. Hence, it is a consequence of the initial state effect. In contrast, chloroboranes are more potent Lewis acids than fluoroboranes, because the relaxation and final state effects decisively influence their Lewis acidity. Finally, bromine-substituted borane compounds provide the most powerful studied Lewis acids. Their hydride affinities are result of a synergic interplay of the initial state, intermediate stabilization via relaxation, and final state effects. It is shown that Pearson's global hardness indices defined within his hard and soft acid-base (HSAB) principle fail to adequately predict and interpret the calculated hydride affinities.