Protonation of the pyrimidine ring at the C(5) position: formation of a stable cationic sigma-complex

NMR studies showed that, in addition to the expected N(1) protonation, 2,4,6-pyrimidinetriamine, N,N,N',N',N",N"-hexamethyl- (1) could also be protonated at the C(5) position in water, leading to an equilibrium between the C(5) and N(1) protonated forms. Analysis of the NMR titration data gives 6.87 and 6.89 for the pK(a) of the C(5) and N(1) protonation equilibria. Moreover, the reaction of 1 with chloroacetyl chloride leads to a novel 1,1-bis(pyrimidin-5-yl)-2-chloroethene type derivative (4) that is, peculiarly, fully monoprotonated at the C(5) position in either of the pyrimidine rings, forming a stable cationic sigma-complex.     

Pyrimidine N-oxides. Oxidation of 5-nitroso-2,4,6-triaminopyrimidine

The peroxytrifluoroacetic acid oxidation of 5-nitroso-2,4,6-triaminopyrimidine ( 1b ) led to the formation of two products: 5-nitro-2,4,6-triaminopyrimidine 1-N-oxide ( 2 ) and 5-nitro-2,4,6-triaminopyrimidine 1-3-di-N-oxide ( 3 ). On the basis of previous experience 2 was the sole expected oxidation product. However, 3 represents a rather unexpected development in that di-N-oxides in the pyrimidine series are uncommon. The yields are good for both products and structures are assigned on the basis of elemental analysis, mass spectral data, and chemical reactions. The reaction sequence is also discussed.     

A new and efficient synthesis of pyrrolo[2,3-d]pyrimidine anticancer agents: Alimta (LY231514, MTA), homo-Alimta, TNP-351, and some aryl 5-substituted pyrrolo[2,3-d]pyrimidines

Alimta, as well as homo-Alimta, a nonbridged analogue of Alimta, and TNP-351 have been prepared by a new method that involves Michael addition of the appropriate 1-nitroalkene with 2,6-diamino-3H-pyrimidin-4-one or 2,4,6-triaminopyrimidine, followed by a Nef reaction of the resulting primary nitro Michael adduct. Spontaneous intramolecular cyclization of the resulting aldehyde with the pyrimidine 6-amino group yields the corresponding pyrrolo[2,3-d]pyrimidine. A series of previously unknown 5-arylpyrrolo[2,3-d]pyrimidines was prepared by the same methodology from the above pyrimidines and nitrostyrenes. It has been found that the intermediate primary nitro Michael adduct can be prepared in a single step by sonication of a mixture of an arylaldehyde, nitromethane, and the 6-aminopyrimidine in acetic acid containing ammonium acetate.     

Near ultraviolet spectroscopic studies of 2,4-diamino-6-piperidinopyrimidine-3-oxide (minoxidil) and 2,4-diamino-6-piperidinopyrimidine (desoxyminoxidil)

The near u.v. spectra of 2,4-diamino-6-piperidinopyrimidine (desoxyminoxidil) and 2,4-diamino-6-piperidinopyrimidine-3-oxide (minoxidil) can be viewed as perturbed pyrimidine spectra. The u.v. properties of pyrimidine and a series of aminopyrimidines, specifically 2,4,6-triaminopyrimidine, are examined to obtain u.v. spectral assignments for desoxyminoxidil and minoxidil. Minoxidil and its desoxy counterpart have C_s symmetry, and all π → π* absorptions are allowed ¹A′ ← ¹A′ transitions. The two lowest energy π →- π* absorptions observed in minoxidil (262 nm, 292 nm) are tentatively assigned as very mild oxygen → pyrimidine ring charge-transfer transitions. Intensity decreases in protic solvents, and the results of simple Hückel molecular orbital calculations indicate that the 292 nm transition has more charge-transfer character than the 262 nm absorption. The protonated species of desoxyminoxidil and minoxidil have very similar u.v. spectra. This is due to the lack of oxygen-related charge transfer in protonated minoxidil, and the high probability that the positive charge resides in similar environments in the minoxidil and desoxyminoxidil molecular frameworks.     

Synthesis and antitumor evaluation of some 1,3-disubstituted tetrahydropyrimido[4,5-c]isoquinolines

Cyclocondensation of 6-amino-2,4-dioxopyrimidine or 2,4,6-triaminopyrimidine with 1-cyclohexenecarbox-aldehyde 13 afforded regiospecifically, tricyclic, angular 1,3-disubstituted tetrahydropyrimido[4,5-c]isoquin-olines 5 and 6 respectively. In addition, 2,4,6-triaminopyrimidine when condensed with 2-chloro-1-cyclohex-enecarboxaldehyde 14 , regiospecifically afforded the angular isomer 6 . However, the cyclocondensation of 2,6-diamino-4-oxopyrimidine with 13 was regioselective and afforded a mixture of the linear and angular tetrahydropyrimidoisoquinolines 2 and 4 . The growth of leukemia L-1210 cells in culture were inhibited 50% by 6 at 9 × 10^?8 M. Compounds 4 and 5 were not significantly active.     

2,4,6-triaminopyrimidine and its associates with bis(hydroxymethyl)phosphinic acid. State in solution, protolytic, and complexing properties

Protolytic and complexing properties of 2,4,6-triaminopyrimidine and its associates with bis (hydroxymethyl)phosphinic acid in aqueous solution were studied using pH measurements, spectrophotometry (298 K), and mathematical simulation of equilibria (CPESSP software). The stability constants of the associates formed in solution were calculated. It was found that the said associates and the nitrogen base in their composition did not form innner-sphere complexes with typical complexing agents like doubly charged cations of d-elements and lanthanum(III). 2,4,6-Triaminopyrimidine forms an outer-sphere complex with copper(II) ions to affording tetrachlorocuprate(II) with diprotonated 2,4,6-triaminopyrimidine.     

Structure and protonation of some indolizine derivatives studied by ab initio MO calculations

Some gauge invariant atomic orbitals-coupled-perturbed Hartree-Fock (GIAO-CPHF) calculations were performed for seven indolizine derivatives and their monoprotonated forms. Chemical shift, molecular geometry, and charge distribution data are reported for each molecule. The calculations support the results of nuclear magnetic resonance (NMR) spectroscopy measurements showing that protonation occurs preferentially at N1. The good agreement between the calculated and observed ¹³C and ¹⁵N chemical shifts show that such calculations can be used for chemical shift assignment purposes. Cation structures and probable sites for electrophilic reaction or second protonation are also discussed.     

Divalent carbon(0) chemistry, part 2: Protonation and complexes with main group and transition metal Lewis acids.

Quantum-chemical calculations with DFT (BP86) and ab initio methods (MP2, SCS-MP2) were carried out for protonated and diprotonated compounds N-H(+) and N-(H(+))(2) and for the complexes N-BH(3), N-(BH(3))(2), N-CO(2), N-(CO(2))(2), N-W(CO)(5), N-Ni(CO)(3) and N-Ni(CO)(2) where N=C(PH(3))(2) (1), C(PMe(3))(2) (2), C(PPh(3))(2) (3), C(PPh(3))(CO) (4), C(CO)(2) (5), C(NHC(H))(2) (6), C(NHC(Me))(2) (7) (Me(2)N)(2)C==C==C(NMe(2))(2) (8) and NHC (9) (NHC(H)=N-heterocyclic carbene, NHC(Me)=N-substituted N-heterocyclic carbene). Compounds 1-4 and 6-9 are very strong electron donors, and this is manifested in calculated protonation energies that reach values of up to 300 kcal mol(-1) for 7 and in very high bond strengths of the donor-acceptor complexes. The electronic structure of the compounds was analyzed with charge- and energy-partitioning methods. The calculations show that the experimentally known compounds 2-5 and 8 chemically behave like molecules L(2)C which have two L-->C donor-acceptor bonds and a carbon atom with two electron lone pairs. The behavior is not directly obvious when the linear structures of carbon suboxide and tetraaminoallenes are considered. They only come to the fore on reaction with strong electron-pair acceptors. The calculations predict that single and double protonation of 5 and 8 take place at the central carbon atom, where the negative charge increases upon subsequent protonation. The hitherto experimentally unknown carbodicarbenes 6 and 7 are predicted to be even stronger Lewis bases than the carbodiphosphoranes 1-3.     

Photodissociation dynamics of pyrimidine

Photodissociation of pyrimidine at 193 and 248 nm was investigated separately using vacuum ultraviolet photoionization at 118.4 and 88.6 nm and multimass ion imaging techniques. Six dissociation channels were observed at 193 nm, including C4N2H4 --> C4N2H3 + H and five ring opening dissociation channels, C4N2H4 --> C3NH3 + HCN, C4N2H4 --> 2C2NH2, C4N2H4 --> CH3N + C3NH, C4N2H4 --> C4NH2 + NH2, and C4N2H4 --> CH2N + C3NH2. Only the first four channels were observed at 248 nm. Photofragment translational energy distributions and dissociation rates indicate that dissociation occurs in the ground electronic state after internal conversion at both wavelengths. The dissociation rates were found to be >5 x 10(7) and 1 x 10(6) s(-1) at 193 and 248 nm, respectively. Comparison with the potential energies from ab initio calculations have been made.     

Flexible N,N,N-chelates as supports for iron and cobalt chloride complexes; synthesis, structures, DFT calculations and ethylene oligomerisation studies

The aryl-substituted N-picolylethylenediamine and diethylenetriamine ligands, (ArNHCH(2)CH(2))[(2-C(5)H(4)N)CH(2)]NH and (ArNHCH(2)CH(2))(2)NH (Ar = 2,6-Me(2)C(6)H(3), 2,4,6-Me(3)C(6)H(2)), have been prepared by employing palladium-catalysed N-C(aryl) coupling reactions of the corresponding primary amines with aryl bromide. Treatment of MCl(2) with (ArNHCH(2)CH(2))[(2-C(5)H(4)N)CH(2)]NH affords [[(ArNHCH(2)CH(2))((2-C(5)H(4)N)CH(2))NH]CoCl(2)](Ar = 2,6-Me(2)C(6)H(3) 1a; 2,4,6-Me(3)C(6)H(2)) 1b and [[(ArNHCH(2)CH(2))((2-C(5)H(4)N)CH(2))NH]FeCl(2)](n)(n= 1, Ar = 2,6-Me(2)C(6)H(3) 2a; n= 2, 2,4,6-Me(3)C(6)H(2) 2b) in high yield. The X-ray structures of 1a and 1b are isostructural and reveal the metal centres to adopt distorted trigonal bipyramidal geometries with the N,N,N-chelates adopting fac-structures. A facial coordination mode of the ligand is also observed in bimetallic 2b, however, in 2a the N,N,N-chelate adopts a mer-configuration with the metal centre adopting a geometry best described as square pyramidal. Solution studies indicate that mer-fac isomerisation is a facile process for these systems at room temperature. Quantum mechanical calculations (DFT) have been performed on 1a and 2a, in which the ligands employed are identical, and show the fac- to be marginally more stable than the mer-configuration for cobalt (1a) while for iron (2a) the converse is evident. Reaction of (ArNHCH(2)CH(2))(2)NH with CoCl(2) gave the five-coordinate complexes [[(ArNHCH(2)CH(2))(2)NH]CoCl(2)](Ar = 2,6-Me(2)C(6)H(3) 3a, 2,4,6-Me(3)C(6)H(2) 3b), in which the ligand adopts a mer-configuration; no reaction occurred with FeCl(2). All complexes 1-3 act as modest ethylene oligomerisation catalysts on activation with excess methylaluminoxane (MAO); the iron systems giving linear alpha-olefins while the cobalt systems give mixtures of linear and branched products.     

Synthesis of phosphorus ylides bearing a P-H bond from a kinetically stabilized 1,3,6-triphosphafulvene

In mixing 2,4,6-tris(2,4,6-tri-tert-butylphenyl)-1,3,6-triphosphafulvene with alkyllithium compounds and acetic acid, both of nucleophilic alkylation and electrophilic protonation occurred at the exo sp2-phosphorus atoms to afford [2,4-bis(2,4,6-tri-tert-butylphenyl)-1,3-diphosphacyclopentadienylidene](alkyl)(2,4,6-tri-tert-butylphenyl)phosphoranes which are phosphorus ylides that bear a P-H bond. A phosphorus ylide bearing both P-H and P-F bonds was obtained by reaction of 2,4,6-tris(2,4,6-tri-tert-butylphenyl)-1,3,6-triphosphafulvene with hydrogen tetrafluoroborate, and the structure was determined by X-ray crystallography. Both P=C double bond and P(+)-C(-) zwitterionic character was indicated by the metric parameters. The isolated phosphorus ylide bearing a P-H bond, [2,4-bis(2,4,6-tri-tert-butylphenyl)-1,3-diphosphacyclopentadienylidene](2,4,6-tri-tert-butylphenyl)phosphorane, showed no isomerization by H-migration to the corresponding phosphinodiphospholes, probably due to the pi-accepting ability of the unsaturated PC bonds and aromaticity of the C3P2 ring. The ylide structure and aromaticity of 2,4-diphosphacyclopenta-2,4-dienylidenephosphorane was characterized by theoretical calculations. In addition, the regioselective protonation of the lithiated phosphinodiphospholes generated from the 1,3,6-triphosphafulvene is discussed.     

Spectroscopic, computational, and kinetic studies of the mu4-sulfide-bridged tetranuclear CuZ cluster in N2O reductase: pH effect on the edge ligand and its contribution to reactivity

A combination of spectroscopy and density functional theory (DFT) calculations has been used to evaluate the pH effect at the CuZ site in Pseudomonas nautica (Pn) nitrous oxide reductase (N2OR) and Achromobacter cycloclastes (Ac) N2OR and its relevance to catalysis. Absorption, magnetic circular dichroism, and electron paramagnetic resonance with sulfur K-edge X-ray absorption spectra of the enzymes at high and low pH show minor changes. However, resonance Raman (rR) spectroscopy of PnN2OR at high pH shows that the 415 cm-1 Cu-S vibration (observed at low pH) shifts to higher frequency, loses intensity, and obtains a 9 cm-1 18O shift, implying significant Cu-O character, demonstrating the presence of a OH- ligand at the CuICuIV edge. From DFT calculations, protonation of either the OH- to H2O or the mu4-S2- to mu4-SH- would produce large spectral changes which are not observed. Alternatively, DFT calculations including a lysine residue at an H-bonding distance from the CuICuIV edge ligand show that the position of the OH- ligand depends on the protonation state of the lysine. This would change the coupling of the Cu-(OH) stretch with the Cu-S stretch, as observed in the rR spectrum. Thus, the observed pH effect (pKa approximately 9.2) likely reflects protonation equilibrium of the lysine residue, which would both raise E degrees and provide a proton for lowering the barrier for the N-O cleavage and for reduction of the [Cu4S(im)7OH]2+ to the fully reduced 4CuI active form for turnover.     

Study of the protonation (methylation) position and tautomeric structure of thiopyrimidine derivatives by 2D <Superscript>1</Superscript>H—<Superscript>15</Superscript>H NMR HSQC/HMBC. Experimental approach and theoretical modeling

Two-dimensional ₁H—₁₅N NMR HSQC/HMBC experiments enable the unambiguous determination of the protonation (methylation) position and tautomeric structure of nitrogen-containing heterocycles. In investigated thiopyrimidines protonation (or methylation) occurs at the N(1) atom of the pyrimidine ring. The tautomeric structures of these compounds were established based on the analysis of ₁H—₁₅N NMR spectra. Ab initio calculations of chemical shifts (GIAO B3LYP/6-31G(d)//HF/6-31G) are in full agreement with experimental values. The stability of various protonated (methylated) and tautomeric species is explained in terms of a thermodynamic approach.     

Gas-phase protonation thermochemistry of adenosine

The goal of this work was to obtain a detailed insight on the gas-phase protonation energetic of adenosine using both mass spectrometric experiments and quantum chemical calculations. The experimental approach used the extended kinetic method with nanoelectrospray ionization and collision-induced dissociation tandem mass spectrometry. This method provides experimental values for proton affinity, PA(adenosine) = 979 +/- 1 kJ.mol (-1), and for the "protonation entropy", Delta p S degrees (adenosine) = S degrees (adenosineH (+)) - S degrees (adenosine) = -5 +/- 5 J.mol (-1).K (-1). The corresponding gas-phase basicity is consequently equal to: GB(adenosine) = 945 +/- 2 kJ.mol (-1) at 298K. Theoretical calculations conducted at the B3LYP/6-311+G(3df,2p)//B3LYP/6-31+G(d,p) level, including 298 K enthalpy correction, predict a proton affinity value of 974 kJ.mol (-1) after consideration of isodesmic proton transfer reactions with pyridine as the reference base. Moreover, computations clearly showed that N3 is the most favorable protonation site for adenosine, due to a strong internal hydrogen bond involving the hydroxyl group at the 2' position of the ribose sugar moiety, unlike observations for adenine and 2'-deoxyadenosine, where protonation occurs on N1. The existence of negligible protonation entropy is confirmed by calculations (theoretical Delta p S degrees (adenosine) approximately -2/-3 J.mol (-1).K (-1)) including conformational analysis and entropy of hindered rotations. Thus, the calculated protonation thermochemical properties are in good agreement with our experimental measurements. It may be noted that the new PA value is approximately 10 kJ.mol (-1) lower than the one reported in the National Institute of Standards and Technology (NIST) database, thus pointing to a correction of the tabulated protonation thermochemistry of adenosine.     

DFT calculations on the protonation of two 1,3-butadiyne units fixed in medium-sized rings

The N-bis-protonated forms of 1-azacyclotetradeca-3,5,10,12-tetrayne (19) and 1,8-diazacyclotetradeca-3,5,10,12-tetrayne (20) were used as model systems to study the HCl addition to two 1,3-butadiyne units in close proximity using quantum chemical means. The model calculations were carried out mainly at the B3LYP/3-21G or 6-31G level. The basis set 6-311G was used for single-point calculations. The calculations reveal that 19 and 20 are preferably protonated at the C4 center accompanied by a transannular ring closure between C3 and C13 yielding the bicyclic systems 23 and 24, respectively. Further stabilization of these vinyl cations is achieved by a second transannular ring closure between C6 and C10 leading to the 5-8-5 tricyclic systems 27 and 28, which are further stabilized by the addition of a chloride anion. The different regiochemistry experimentally observed for 13b and 16b was rationalized by calculating local softness parameters. The observed product selectivities for the formation of 14b and 15b were traced back to the relative stabilities of the primary protonation products 23 and 24, respectively. Model calculations on 1-azacyclopentadeca-3,5,11,13-tetrayne (65) and 1-azacyclohexa-deca-3,5,12,14-tetrayne (66) as examples for medium-sized rings with nonparallel 1,3-butadiyne units revealed a concerted process of protonation and C3-C15 (65) or C3-C16 (66) ring closure. The second step is the formation of an aromatic central ring as a result of a ring closure between C6-C13 and C6-C14, respectively.     

Theoretical studies of mechanisms and kinetic isotope effects on the decarboxylation of orotic acid and derivatives.

The mechanism of orotidine 5'-monophosphate decarboxylase was studied computationally by using the decarboxylation of orotic acid analogues as model systems. These calculations indicate that mechanisms involving proton transfer to the 2-oxygen or the 4-oxygen are energetically favorable, as compared to direct decarboxylation without proton transfer, for a series of model compounds where N1 is substituted with respectively H, CH(3), and a tetrahydrofuran moiety. Proton transfer to the 4-oxygen during decarboxylation is found to be energetically more favorable than 2-protonation, which is attributable to both the 4-oxygen site being more basic and an apparent intrinsic preference for the 4-protonation pathway. (15)N isotope effect calculations were also conducted, and compared to experimental (15)N isotope effects previously measured at N1 by Rishavy and Cleland (Biochemistry 2000, 39, 4569-4574). The theoretical isotope effects establish, for the first time, that the experimental (15)N isotope effect is consistent with decarboxylation without protonation, as well as with decarboxylation with protonation, at either O2 or at O4. Furthermore, we propose herein an isotope measurement that could potentially distinguish among mechanisms involving protonation from those that do not involve proton transfer.     

Gas-phase tautomers of protonated 1-methylcytosine. Preparation, energetics, and dissociation mechanisms

Tautomers of 1-methylcytosine that are protonated at N-3 (1+) and C-5 (2+) have been specifically synthesized in the gas phase and characterized by tandem mass spectrometry and quantum chemical calculations. Ion 1+ is the most stable tautomer in aqueous and methanol solution and is likely to be formed by electrospray ionization of 1-methylcytosine and transferred in the gas phase. Gas-phase protonation of 1-methylcytosine produces a mixture of 1+ and the O-2-protonated tautomer (3+), which are nearly isoenergetic. Dissociative ionization of 6-ethyl-5,6-dihydro-1-methylcytosine selectively forms isomer 2+. Upon collisional activation, ions 1+ and 3+ dissociate by loss of ammonia and [C,H,N,O], whose mechanisms have been established by deuterium labeling and ab initio calculations. The main dissociations of 2+ following collisional activation are losses of CH2=C=NH and HN=C=O. The mechanisms of these dissociations have been elucidated by deuterium labeling and theoretical calculations.     

Probing Protonation Sites of Isolated Flavins Using IR Spectroscopy: From Lumichrome to the Cofactor Flavin Mononucleotide

Infrared spectra of the isolated protonated flavin molecules lumichrome, lumiflavin, riboflavin (vitamin B₂), and the biologically important cofactor flavin mononucleotide are measured in the fingerprint region (600–1850 cm^?1) by means of IR multiple‐photon dissociation (IRMPD) spectroscopy. Using density functional theory calculations, the geometries, relative energies, and linear IR absorption spectra of several low‐energy isomers are calculated. Comparison of the calculated IR spectra with the measured IRMPD spectra reveals that the N10 substituent on the isoalloxazine ring influences the protonation site of the flavin. Lumichrome, with a hydrogen substituent, is only stable as the N1‐protonated tautomer and protonates at N5 of the pyrazine ring. The presence of the ribityl unit in riboflavin leads to protonation at N1 of the pyrimidinedione moiety, and methyl substitution in lumiflavin stabilizes the tautomer that is protonated at O2. In contrast, flavin mononucleotide exists as both the O2‐ and N1‐protonated tautomers. The frequencies and relative intensities of the two C?O stretch vibrations in protonated flavins serve as reliable indicators for their protonation site.     

Spectroscopic identification of carbenium and ammonium isomers of protonated aniline (AnH+): IR spectra of weakly bound AnH+ -Ln clusters (L = Ar, N2)

Infrared photodissociation (IRPD) spectra of mass-selected clusters composed of protonated aniline (C6H8N+ = AnH+) and a variable number of neutral ligands (L = Ar, N2) are obtained in the N-H stretch range. The AnH+ -Ln complexes (n < or = 3) are produced by chemical ionization in a supersonic expansion of An, H2, and L. The IRPD spectra of AnH+-Ln feature the unambiguous fingerprints of at least two different AnH+ nucleation centers, namely, the ammonium isomer (5) and the carbenium ions (1 and/or 3) corresponding to protonation at the N atom and at the C atoms in the para and/or ortho positions, respectively. Protonation at the meta and ipso positions is not observed. Both classes of observed AnH+-Ln isomers exhibit very different photofragmentation behavior upon vibrational excitation arising from the different interaction strengths of the AnH+ cores with the surrounding neutral ligands. Analysis of the incremental N-H stretch frequency shifts as a function of cluster size shows that microsolvation of both 5 and 1/3 in Ar and N2 starts with the formation of intermolecular H bonds of the ligands to the acidic NH protons and proceeds by intermolecular pi bonding to the aromatic ring. The analysis of both the photofragmentation branching ratios and the N-H stretch frequencies demonstrates that the N-H bonds in 5 are weaker and more acidic than those in 1/3, leading to stronger intermolecular H bonds with L. The interpretation of the spectroscopic data is supported by density functional calculations conducted at the B3LYP level using the 6-31G* and 6-311G(2df,2pd) basis sets. Comparison with clusters of neutral aniline and the aniline radical cation demonstrates the drastic effect of protonation and ionization on the acidity of the N-H bonds and the topology of the intermolecular potential, in particular on the preferred aromatic substrate-nonpolar ligand recognition motif.     

DFT studies on key intermediates in thiamin catalysis

The diphosphate ester (ThDP) of thiamin (vitamin B₁) is an important cofactor of enzymes within the carbohydrate metabolism. From experiments of site‐specific variants and nuclear magnetic resonance (NMR) studies, it is known that the protonation of the N1′ atom is a significant step in the coenzyme activation by the enzymatic environment. Therefore, we have performed density functional theory (DFT) calculations on the B3LYP/6‐31G* level of N1′H and N1′CH₃ thiamin as model systems to study the protonation and methylation effect on the structure and the electronic properties of the 4′‐amino group. The relaxed rotational barriers related to the C4′‐4′N bond are correlated with findings of ¹H NMR studies and proton/deuterium exchange experiments. Moreover, the effect of N1′ protonation was studied in more detail on the hydroxyethyl‐thiamin carbanion (HETh^?), a key intermediate during catalysis of some ThDP‐dependent enzymes. The relaxed rotational barriers related to the C2? C2α bond and the reaction coordinates of the proton transfer 4′N? H→C2α of HETh^? and N1′H‐HETh^? show that they are significantly determined by the protonation at N1′ of HETh^?. The influence of the apoenzyme environment on the active coenzyme conformation is modeled in a very simple way. The characteristic torsion angles Φ_T and Φ_P are considered to be restricted in terms of their values in the corresponding enzyme as well as free optimization parameters. Frequency calculations were performed to characterize the minima and transition state structures, respectively. The applicability of the DFT method was checked by comparing calculations on the MP2‐HF‐SCF/6‐31G* level. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004