Guanidinium-Type resonance stabilization and its biological implications. 2. The doubly-extended-guanidine series

π-Electron delocalization in neutral and protonated “doubly-extended-guanidine,” (H₂N)₂C?N? CH?N—CH?NH, has been studied by ab initio methods at the self-consistent field (SCF) STO -3G and 3-21G levels for a large number of tautomeric, rotameric, pseudocyclic, and monocyclic (disubstituted triazine) forms. These π systems have been characterized in terms of a number of structural and energetic parameters: degree of single/bond character from bond lengths and π bond orders, electron distributions, and tautomer, rotamer, and protonation energies. The acyclic neutral forms exhibit largely alternant single–double bond patterns as predicted by classical bonding structures but with, however, significant deviations due to conjugation. The acyclic protonated forms exhibit bond patterns consistent with resonance delocalized structures extending over the whole molecule (“doubly-extended guanidinium”) or part of the molecule (“extended-guanidinium”) or guanidinium . All systems showed alternant charge distributions with electron-deficient carbons. The energy results have been analyzed in terms of possible contributions from steric interactions, lone-pair repulsions, purportive electrostatic interactions in pseudocyclic forms, overall π-system conformation (extended, kinked, or folded), and specific through-space π-overlap interactions in some pseudocyclic forms. It was found that these other interactions usually dominate the specifically π effects so that the general concept of preferential π delocalization in straight lines does not hold for the acyclic systems. Some interesting examples of pseudocyclic forms exhibiting strongly stabilizing intramolecular interactions attributed to π through-space coupling are identified. These systems with incipient-ring characteristics present intermediate bonding models between the acyclic and closed-ring π systems. The extent of stabilization of the guanidinium-type cations by resonance delocalization in cyclic systems depended on whether it reinforced or interfered with the overall ring delocalization.     

Analysis of inter-ring coupling effects in N-heterobicyclic π-systems using a structural definition of aromaticity

A purely structural definition of aromaticity based on the average ring bond length and -bond order is proposed. The definition is illustrated for N-heterocycles by reference to theoretical STO-3G and 3-21G geometries and charges for some pteridine derivatives. The treatment focuses on the gross structural changes (i.e., ring size, overall degree of π-electron delocalization, and net ring charges), accompanying chemical changes, such as substitution, tautomerization, ring reduction, and deazination, as well as the structural interdependence of the two rings in a bicyclic ring system.     

1,5-Diamino-1H-1,2,3,4-tetrazolium picrate: X-ray molecular and crystal structures and ab initio MO calculations

The crystal and molecular structures of 1,5-diamino-1H-1,2,3,4-tetrazolium picrate (DATP) were determined by X-ray diffraction analysis. The tetrazolium cation in DATP has a structure with protonated N4 atom of the ring. Two amino groups in the cation are found to be rather different. The 5-amino group lies in the plane of the tetrazole ring and valence angles around the N atom are close to 120°, which indicates sp² hybridization of atomic orbital of the nitrogen atom. In contrast, valence angles around the N atom of the 1-amino group are close to tetrahedral angle, which suggests sp³ hybridization. The exocyclic C-N bond in the cation is substantially shorter than that in 1,5-diaminotetrazole. The obtained results indicate a conjugation between the π-system of the tetrazole ring and the 5-amino group. The results of ab initio calculations of electronic structure and relative stability for various tautomeric forms of protonated 1,5-diaminotetrazole using MP2/6-31G* and B3LYP/6-31G* levels of theory are in a good agreement with X-ray data and show that there are differences in σ-electron overlap populations for the C-N bonds in the cation in DATP, while π-electrons are delocalized.     

Ab initio studies of structural features not easily amenable to experiment. 18. Conformational analysis and molecular structure of glycine methyl ester

The structures of four conformations of the methyl ester of glycine were determined by standard single-determinant molecular orbital (MO ) calculations using Pulay's force method and the 4-21G basis set. The most stable conformation of this compound has a symmetry plane which contains all the heavy atoms; it is stabilized by hydrogen bonds between the NH₂ group and the carbonyl oxygen; it corresponds to the most stable, stretched form of free glycine. The structural parameters in the different conformations can vary significantly (bond distance by more than 0.02 Å and bond angles by up to 15°). The structural changes which are caused in glycine by esterification are discussed and some of them are interpreted in terms of hyperconjugative π-electron delocalization.     

The value of the π-bond order–bond length relationship in geometry prediction and chemical bonding interpretation

The π-bond order–bond length relationship is reintroduced to the literature and extended to heteronuclear bonds by presenting graphs derived solely by theoretical methods. π-bond order and overlap population results for carbon–carbon, carbon–nitrogen, and carbon–oxygen bonds obtained from ab initio STO -3G calculations using theoretically-optimized geometries are reported for a series of pteridines and for a wide range of small organic molecules. The order–length correlation graphs are used in predicting the “intrinsic” single bond lengths for sp² – sp² and sp – sp hybridized C? C, C? N, and C? O bonds, and in evaluating the relative importance of hybridization, π-electron delocalization and bond polarization effects in causing bond shortening in conjugated and hyperconjugated molecules. The calculated value of the π-bond order for a given bond in a molecule is shown to be relatively insensitive to moderate geometry changes: Hence, a use for the correlation graphs in geometry prediction is suggested. Some results for the extended 4-21G basis set are also presented.     

Electronic structure of guanidine and its derivatives from X-ray photoelectron spectroscopy and density functional theory studies

Electronic structure of guanidine, diphenylguanidine, their protonated forms, and guanidinium chloride have been studied by X-ray photoelectron spectroscopy and quantum-chemical modeling. From the derived geometry parameters and electronic structure, the effect of protonation on localization of the electron density has been revealed. The lines in the valence region of the X-ray photoelectron spectra have been assigned.     

Influence of calculation level and effect of methylation on axial/equatorial equilibria in piperidines

A detailed conformational analysis was performed on the chair forms of piperidine, N-methylpiperidine, and some methylated derivatives using Hartree–Fock (HF) and MP2 ab initio methods with several basis sets (from 3–21G to 6–311++G**), and the most widely used semiempirical approaches (MNDO, AM1, and PM3). It was found that the use of polarized basis sets at the HF level is adequate enough for the prediction of conformational preferences in the axial/equatorial equilibrium of the N-R group in piperidines. On the other hand, the inclusion of electron correlation becomes necessary for predicting the axial/equatorial energy differences of the equilibria of the methyl group. Semiempirical methods are not recommended, because AM1 and PM3 predict opposite stabilities to those obtained experimentally and MNDO ring geometries are systematically too flat. The origin of the conformational stabilities was interpreted in terms of the natural bond orbital analysis of the HF/6–31G** wave functions. The equatorial preferences in the N-H equilibria is mainly due to lower Lewis energies, although delocalization of the nitrogen lone pair is favored in N-H axial forms. N-Methylation increases the equatorial M-Me preferences, because the Lewis energy of axial N-Me forms increases due to larger 1,3-diaxial interactions. Geometrical trends associated with the delocalization of the nitrogen lone pair and with interactions between the introduced N-R and C-Me groups were discussed and related to the degree of planarity of the six-membered ring by means of the puckering coordinates defined by Pople and Cremer. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 961–976, 1998     

Triaziridines. Part III. Triaziridine,azimine, and triazene: A SCF study of the energy and structure of N3H3-isomers

The portions of the N₃H₃ singlet potential energy surface corresponding to triaziridines ( 1 ), azimines ( 2 ) and triazenes ( 3 ) have been calculated by ab initio SCF using 3-21G, 6-31G, and 6-31G** basis sets. Minima and transition states were located by force gradient geometry optimization. The most important computation results are: (1) Triaziridines ( 1 ): The configuration at the 3 N-atoms is pyramidal. There are 2 stereoisomers, 1a and 1b . The c,t-isomer 1a has less energy than the c,c-isomer 1b . The 2 stereoisomerizations by N-inversion hve rather high activation energies. The N,N bonds in 1 are longer and weaker (STO-3G estimation) than in hydrazine. The N-homocycle 1 exhibits less ring strain than the C-homocycle cyclopropane or three-membered heterocycles. (2) Azimine ( 2 ): All 6 Atoms are in the same plane. There are 3 stereoisomers, 2a, 2b , and 2c . The order of ground state energies is (Z,Z) < (E,Z) ? (E,E). The 2 N,N bond lengths correspond to multiplicity 1½. The electronic structure of 2 corresponds to a 1,3-dipole with almost equal delocalization of the 4 π-electrons over all 3 N-atoms. The negative net charge at the central N-atom is much less than that at the terminal N-atoms. Azimines should behave as π-donors in complexation with transition metals (3) Triazene ( 3 ): All 6 atoms are in the same plane. There are 2 stereoisomers, 3a and 3b . The order of ground-state energies is (E) < (Z). The stereoisomerization proceeds as pure N-inversion. N-Inversion has a high energy barrier inversion at N(1) is faster than at N(2). One of the N,N bond lengths is typical for a double, the other for a single bond. The electronic structure of triazene 3 entails rather localized π- and p-electron pairs at N(1),N(2) and at N(3). Triazenes should behave as p-donors in complexation with transition metals. (4) -N₃H₃-Isomers: The order of ground-state energies is 3 < 2 < 1 . The energy differences between these constitutional isomers are much larger than between the stereoisomers of each. The [1,2]-H shifts for conversions of 2 to 3 and the [1,3]-H shift for tautomerization of 3 have relatively high activation energies; both shifts can be excluded as modes of thermal, unimolecular transformations.     

Theoretical analysis of pyridine protonation in water clusters of increasing size.

The protonation of pyridine in water clusters as a function of the number of water molecules was theoretically analyzed as a prototypical case for the protonation of organic bases. We determined the variation of structural, bonding, and energetic properties on protonation, as well as the stabilization of the ionic species formed. Thus, we used supermolecular models in which pyridine interacts with clusters of up to five water molecules. For each complex, we determined the most stable unprotonated and protonated structures from a simulated annealing at the semi ab initio level. The structures were optimized at the B3LYP/cc-pVDZ level. We found that the hydroxyl group formed on protonation of pyridine abstracts a proton from the ortho-carbon atom of the pyridine ring. The "atoms in molecules" theory showed that this C-H group loses its covalent character. However, starting with clusters of four water molecules, the C-H bond recovers its covalent nature. This effect is associated with the presence of more than one ring between the water molecules and pyridine. These rings stabilize, by delocalization, the negative charge on the hydroxyl oxygen atom. Considering the protonation energy, we find that the protonated forms are increasingly stabilized with increasing size of the water cluster. When zero-point energy is included, the variation follows closely an exponential decrease with increasing number of water molecules. Analysis of the vibrational modes for the strongest bands in the IR spectra of the complexes suggests that the protonation of pyridine occurs by concerted proton transfers among the different water rings in the structure. Symmetric water stretching was found to be responsible for hydrogen transfer from the water molecule to the pyridine nitrogen atom.     

Theoretical study of some heterocyclic amines with applications to the chemistry of 9-amino-1,2,3,4-tetrahydroacridine

9-Amino-1,2,3,4-tetrahydroacridine (THA ), a potent cholinesterase inhibitor, was recently used in the treatment of Alzheimer's disease. On attempting to prepare a dihydropyridine ? pyridinium salt-based redox chemical delivery system (CDS ) to enhance brain delivery of THA , several of the practical synthetic challenges were examined by using a theoretical MO approach. The structures, reactivities and stability of THA , derivatives of THA and a model compound, 4-aminopyridine, a simple dibasic heterocyclic amine, were studied in the framework of the AM -1 approximation. The study included the possible protonated forms of THA and 4-aminopyridine. The calculated heats of formation showed that ring nitrogen protonated forms are more stable for both THA and 4-aminopyridine. The calculated heats of formation showed that ring nitrogen protonated forms are more stable for both THA and 4-aminopyridine, consistent with experimental results. Electron delocalization is responsible for the remarkable stability of these molecules and for the observed lack of reactivity of the amino group, both in the basic and protonated forms. The site of N-alkylation of the 9-nicotinamide derivative of THA (an intermediate in the synthesis of THA -CDS ) is controlled by electronic, thermodynamic, and steric factors.     

The Driving Force for the Acylation of β-Lactam Antibiotics by L,D-Transpeptidase 2: Quantum Mechanics/Molecular Mechanics (QM/MM) Study

β-lactam antibiotics, which are used to treat infectious diseases, are currently the most widely used class of antibiotics. This study focused on the chemical reactivity of five- and six-membered ring systems attached to the β-lactam ring. The ring strain energy (RSE), force constant (FC) of amide (C−N), acylation transition states and second-order perturbation stabilization energies of 13 basic structural units of β-lactam derivatives were computed using the M06-2X and G3/B3LYP multistep method. In the ring strain calculations, an isodesmic reaction scheme was used to obtain the total energies. RSE is relatively greater in the five-(1a–2c) compared to the six-membered ring systems except for 4b, which gives a RSE that is comparable to five-membered ring lactams. These variations were also observed in the calculated inter-atomic amide bond distances (C−N), which is why the six-membered ring lactams C−N bond are more rigid than those with five-membered ring lactams. The calculated ΔG^# values from the acylation reaction of the lactams (involving the S−H group of the cysteine active residue from L,D transpeptidase 2) revealed a faster rate of C−N cleavage in the five-membered ring lactams especially in the 1–2 derivatives (17.58 kcal mol⁻¹). This observation is also reflected in the calculated amide bond force constant (1.26 mDyn/A) indicating a weaker bond strength, suggesting that electronic factors (electron delocalization) play more of a role on reactivity of the β-lactam ring, than ring strain.     

Theoretical studies on pteridines. 2. Geometries,tautomer, ionization and reduction energies of substrates and inhibitors of dihydrofolate reductase

Ab initio SCF calculations with STO-3G and 3-21G basis sets are reported for approximately 85 pteridines of interest to the study of the reaction and inhibition mechanisms of dihydrofolate reductase. These include tautomeric, protonated, deprotonated, reduced and 6-substituted forms of the 2-amino-4-oxo- and 2,4-diamino-pteridines, many of which are not easily amenable to experimental investigation. Full geometry optimizations at the SCF/STO-3G level for 30 such pteridines have been performed. A step-wise computational protocol designed to identify the minimum level of theory necessary for reliable prediction of relative tautomer, reduction and ionization energies has been developed in an effort to minimize the cost of calculations for this reasonably large N-heterobicylic system. In general, SCF/STO-3G results were found to be inadequate while SCF/3-21G results obtained with STO-3G optimized geometries agreed with all available experimental evidence with the exception of the relative acidity of 6-methyl-7,8-dihydropterin. Correlation graphs relating experimental pK_a's to the calculated ionization energies are presented: these are of potential predictive value. An analysis is given of the importance of resonance substructures, such as the guanidinium and extended-guanidinium groups, in stabilizing some preferred tautomeric and ionized forms, and in explaining the observed geometry changes.     

Generalized anomeric interpretation of the "high-energy" N-P bond in N-methyl-N'-phosphorylguanidine: importance of reinforcing stereoelectronic effects in "high-energy" phosphoester bonds

Electronic structure calculations have been performed on a model N-phosphorylguanidine, or phosphagen, to understand the stereoelectronic factors contributing to the lability of the "high-energy" N-P bond. The lability of the N-P bond is central to the physiological role of phosphagens involving phosphoryl transfer reactions important in cellular energy buffering and metabolism. Eight protonated forms of N-methyl-N'-phosphorylguanidine have been energy minimized at levels of theory ranging up to B3LYP/6-311++G(d,p) and MP2/6-311++G(d,p) to investigate the correlation between protonation state and N-P bond length. Selected forms have also been minimized using the CCSD/6-311++G(d,p) and QCISD/6-311++G(d,p) levels of theory. Bulk solvation energies using the polarized continuum model (PCM) with B3LYP/6-311++G(d,p) test the influence of the surroundings on computed structures and energies. The N-P bond length depends on the overall protonation state where increased protonation at the phosphoryl group or deprotonation at the unsubstituted N' nitrogen results in shorter, stronger N-P bonds. Natural bond orbital analysis shows that the protonation state affects the N-P bond length by altering the magnitude of stabilizing n(O) --> sigma*(N-P) stereoelectronic interactions and to a lesser extent the sigma(N-P) --> sigma*(C-N') and sigma(N-P) --> sigma*(C-N) interactions. The computations do not provide evidence of a competition between the phosphoryl and guanidinium groups for the same lone pair on the bridging nitrogen, as previously suggested by opposing resonance theory. The computed n(O) --> sigma*(N-P) anomeric effect provides a novel explanation of "high-energy" N-P bond lability. This offers new mechanistic insight into phosphoryl transfer reactions involving both phosphagens and other biochemically important "high-energy" phosphoester bonds.     

The analysis of structural and electronic properties for assessment of intramolecular hydrogen bond (IMHB) interaction: a comprehensive study into the effect of substitution on intramolecular hydrogen bond of 4-nitropyridine-3-thiol in ground and electronic excited state

The hydrogen bond strength, molecular geometry, π-electron delocalization, and physical properties such as dipole moment, chemical potential, and chemical hardness of 4-nitropyridine-3-thiol and its 29 derivatives have been studied by means of density functional method with 6-311++G** basis set in gas phase and water solution. Also, the excited-state properties of intramolecular hydrogen bonding in these systems have been investigated theoretically using the time-dependent density functional theory method. The HOMA, NICS, PDI, ATI, FLU, and FLU_π indices as well-established aromaticity indicators have been examined. Natural bond orbital analysis is also performed for better understanding the nature of intramolecular interactions. The electron density and Laplacian (?² ρ) properties, estimated by AIM calculations, indicate that H···O bond possesses low ρ and positive ?² ρ values, which are in agreement with electrostatic character of the HBs, whereas S–H bond has covalent character. Numerous correlations between topological, geometrical, and energetic parameters are also found.     

Ab initioSCF MO calculations on the reactions of hydroxyl radical with imidazole and monoprotonated imidazole

The addition reactions of hydroxyl radical with imidazole and its protonated form to yield radical adducts have been investigated by ab initio SCF MO methods using STO -3G and 4-31G basis sets. Analogous radical species are of importance in radiation damage to biological systems. Of the possible radical products, the calculations indicate that the allylic species are generally favored energetically over the nonallylic forms. On an energetic basis, the results show that the allylic adducts formed by addition at the C2 and C5 positions are about equally favorable. Although the C5 species is generally identified as the experimentally observed product in aqueous media for both protonated and unprotonated imidazole, some experimental evidence exists indicating the presence of other forms. Our results suggest that this other form is the C2 adduct. The calculations also point to the protonated form of imidazole being less reactive than imidazole, which is in accord with experimental observations.     

Influence of DFT-calculated electron correlation on energies and geometries of retinals and of retinal derivatives related to the bacteriorhodopsin and rhodopsin chromophores

DFT-calculations were performed on retinal in the all-trans, 1, 11-cis-12-s-cis, 2, and 11-cis-12-s-trans configuration, 3, and on the corresponding N-methyl Schiff base and protonated N-methyl Schiff base derivatives; for the latter, the corresponding 6-s-trans conformations and the 6-s-trans-13-cis-14-s-trans isomer which play a role in the bacteriorhodopsin photocycle were also studied. All geometries were fully optimized using the Becke- three-parameter Lee-Yang-Parr method in conjunction with the 6-31G^** basis set (B3LYP/6-31G^**). The stabilities in order of increasing energy are 1, 3 and 2 regardless of the type of substitution of the end group. While the energy of 3 relative to 1 is almost constant (5 ± 0.2 kcal mol⁻¹), the relative energy of 2 depends somewhat on the nature of the functional group: it is highest in the protonated Schiff base derivative 2-SBH + with its steric congestion along the C12-C13 bond. Comparison with results previously obtained on the basis of RHF/6-31G^** ab initio calculations reveals that the B3LYP method is more biased towards π-electron delocalization. This is indicated by the reduced degree of double bond fixation along the chromophore and also in the increased tendency towards planarization as manifest, e.g. by the change of the C5-C6-C7-C8 dihedral angle between the cyclohexene ring and the open chain double bond system.