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A simple but efficient computational approach to calculate p

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.

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.

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.

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.

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.

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 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.

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.

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...

It is shown that st simple scaled Hartree-Fock (ScHF) model describes very well the ring proton affinity (PA) of a vast variety of polysubstituted benzenes, naphthalenes, and biphenylenes. Its utility in predicting PAs of large alternant aromatics is illustrated on pyrene and monofluoropyrenes. The calculated PAs are in accordance with the available experimental evidence providing at the same time useful complementary information. Finally, it is found that PAs in polyfluoropyrenes follow the same simple additivity rule, based on the independent substituent approximation (ISA), which was observed earlier in smaller alternant aromatic systems. The origin of the additivity property of the proton affinity is briefly discussed.

The influence of fluorine substitutions on the stability of benzene is examined by using the Hartree-Fock (HF) and MP2 models. It is conclusively demonstrated that homodesmotic reactions based on the open-chain zigzag polyenes are unsatisfactory. A comparison of the intramolecular interactions of educts and products shows that they are not well balanced. Hence, these reactions should be abandoned in discussing aromaticity. A much better vehicle for exploring aromaticity is provided by homostructural reactions, which employ cyclic monoene and diene as reference model compounds. Their heavy atoms are enforced to assume planar geometries to enable sigma/pi separation. The HF/cc-pVTZ calculations show that extrinsic aromaticity of benzene B DeltaE(ease)(B)() arises both from the sigma- and pi-contributions. They are -14.8 and -23.1 in kcal/mol, respectively, if the stockholder energy partitioning scheme is employed. This result implies that both the sigma- and pi-frameworks contribute to the aromatic stabilization of B, the latter being more important. The total aromatic stabilization DeltaE(ease)(B)() is -37.9 kcal/mol. Schleyer's indene-isoindene isomerization approach also strongly indicates that the decisive factor in determining the aromatic stability of the benzene moiety is the pi-electron framework. The origin of extrinsic aromaticity is identified as the increased nuclear-electron attraction of both sigma- and pi-electrons, if 1,3-cyclohexadiene is used as a gauge compound. Further, by using a system of isostructural reactions, it is conclusively demonstrated that fluorobenzenes exhibit a remarkable additivity of the substituent effects, as far as the stability of multiply substituted benzenes is concerned. This additivity rule is so accurate that it enables delineation of the fluorine repulsions and the aromaticity defect DeltaE(AD). It appears that the DeltaE(AD) values increase upon sequential fluorine substitution at the next nearest (vicinal) position thus making multiply fluorinated benzenes less stable.

Gas-phase H/D exchange experiments with CD3OD and D2O and quantum chemical ab initio G3(MP2) calculations were carried out on protonated histidine and protonated histidine methyl ester in order to elucidate their bonding and structure. The H/D exchange experiments show that both ions have three equivalent fast hydrogens and one appreciably slower exchangeable hydrogen assigned to the protonated amino group participating in a strong intramolecular hydrogen bond (IHB) with the nearest N(sp2) nitrogen of the imidazole fragment and to the distal ring NH-group, respectively. It is taken for granted that the proton exchange in the IHB is much faster than the H/D exchange. Unlike in other protonated amino acids (glycine, proline, phenylalanine, tyrosine, and tryptophan) studied earlier, the exchange rate of the carboxyl group in protonated histidine is slower than that of the amino group. The most stable conformers and the enthalpies of neutral and protonated histidine and its methyl ester are calculated at the G3(MP2) level of theory. It is shown that strong intramolecular hydrogen bonding between the amino group and the imidazole ring nitrogen sites is responsible for the stability and specific properties of the protonated histidine. It is found that the proton fluctuates between the amino and imidazole groups in the protonated form across an almost vanishing barrier. Proton affinity (PA) of histidine calculated by the G3(MP2) method is 233.2 and 232.4 kcal mol(-1) for protonation at the imidazole ring and at the amino group nitrogens, respectively, which is about 3-5 kcal mol(-1) lower than the reported experimental value.

The aim of this study was to investigate the behavior of the protonated paralytic shellfish poisons saxitoxin (STX) and neosaxitoxin (NEO) in the gas-phase after ion activation using different tandem mass spectrometry techniques. STX and NEO belong to a group of neurotoxins produced by several strains of marine dinoflagellates. Their chemical structures are based on a tetrahydropurine skeleton to which a 5-membered ring is fused. STX and NEO only vary in their substituent at N-1, with STX carrying hydrogen and NEO having a hydroxyl group at this position. The collision-induced dissociation (CID) spectra exhibited an unusually rich variety and abundance of species due to the large number of functional groups within the small skeletal structures. Starting with triple-quadrupole CID spectra as templates, linked ion-trap MSn data were added to provide tentative dissociation schemes. Subsequent high-resolution FTICR experiments gave exact mass data for product ions formed via infrared multiphoton dissociation (IRMPD) from which elemental formulas were derived. Calculations of proton affinities of STX and NEO suggested that protonation took place at the guanidinium group in the pyrimidine ring for both molecules. Most of the observed parallel and consecutive fragmentations could be rationalized through neutral losses of H2O, NH3, CO, CO2, CH2O and different isocyanate, ketenimine and diimine species, many of which were similar for STX and NEO. Several exceptions, however, were noted and differences could be readily correlated with reactions involving NEO's additional hydroxyl group. A few interesting variations between CID and IRMPD spectra are also highlighted in this paper.

1,8-Bis(dimethylethyleneguanidino)naphthalene (DMEGN), the second example of a peralkyl guanidine “proton sponge” based on the 1,8-naphthalene backbone, was prepared and fully characterized. The crystal structure analysis of monoprotonated DMEGN reveals an unsymmetrical intramolecular hydrogen bridge. A decrease in the basicity with respect to the noncyclic parent 1,8-bis(tetramethylguanidino)naphthalene was found. Nevertheless, a new proton sponge provides a new crossbar in the ladder of highly basic neutral organic compounds. A detailed theoretical study of DMEGN and related cyclic guanidines explains this surprising experimental result. Homodesmotic reactions reveal that the intramolecular hydrogen bond contributes effectively 10 kcal/mol to proton affinity of DMEGN.

The problem of the absolute proton affinity (APA) of some polyguanides is addressed by the MP2(fc)/6-311+G//HF/6-31G theoretical model. It is shown that the linear chain polyguanides exhibit increased basicity as a function of the number of guanide subunits. However, the saturation effect yields an asymptotic APA value of 254 kcal/mol. Branched polyguanides on the other hand have higher APAs than their linear counterparts. The largest proton affinity is found in a doubly bifurcated heptaguanide, being as high as 285 kcal/mol, thus potentially representing one of the strongest organic bases. Finally, it is found that all polyguanides protonate at imino nitrogen atoms, since they are apparently susceptible the most to the proton attack. The origin of their very high intrinsic basicity is traced down to a dramatic increase in the resonance interaction of the corresponding conjugate bases. For instance, the increase in the resonance energy in the protonated guanidine is estimated to be in a range of 24-27 kcal/mol, which is higher than the aromatic stabilization in benzene. The proton affinity of some polycyclic guanides including Schwesinger proton sponge and porphine is briefly discussed.