The influence of electron donor and electron acceptor groups on the electronic structure of the anti‐inflammatory tripeptide Cys‐Asn‐Ser

It has been discussed in the literature that electron delocalization along the peptide backbone and side chain modulates the physical and chemical features of peptides and proteins. The structure and properties of peptides are determined by their charge‐density distribution, such that the modification of its side chain plays an important role on its electronic structure and physicochemical properties. Research on Entamoeba histolytica soluble factors led to the identification of the pentapeptide Met‐Gln‐Cys‐Asn‐Ser, with anti‐inflammatory in vivo and in vitro effects. A synthetic pentapeptide, Met‐Pro‐Cys‐Asn‐Ser, maintained the same anti‐inflammatory actions in experimental assays. A previous theoretical study allowed proposing the Cys‐Asn‐Ser tripeptide (CNS tripeptide) as the pharmacophore group of both molecules. This theoretical hypothesis was recently confirmed experimentally. The objective of this work was to study the influence of the electron donor and electron withdrawing substituent groups on the electronic structure and physicochemical properties of the CNS tripeptide derivatives through a theoretical study at the density functional theory level of theory. Our results in deprotonation energies showed that the relative acidity of hydrogen atom (H2) of the serine‐amide group increases with the electron withdrawing groups. This result was confirmed by means of a study of bond order. The proton affinities illustrated that the electron donor groups favored the basicity of the amino group of the cysteine amino acid. Atomic charges, Frontier molecular orbitals (HOMO–LUMO), and electrostatic potential isosurface and its geometric parameters permitted to analyze the effect that provoked the electron donor and electron attractor groups on its electronic structure and physicochemical features and to identify some reactive sites that could be associated with the anti‐inflammatory activity of tripeptide CNS derivatives. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2398–2410, 2010     

Metal‐stabilized rare tautomers: N4 metalated cytosine (M = Li+, Na+, K+, Rb+ and Cs+), theoretical views

Ab initio calculations indicate that metalation of the exocyclic amino group of cytosine by the elements of Group IA (Li, Na, K, Rb and Cs) induces protonation of a nucleobase ring nitrogen atom, and hence causes a proton shift from an exocyclic to an endocyclic nitrogen atom. Thus, this metal‐assisted process leads to the generation of rare nucleobase tautomers. The calculations suggest that this kind of metalation increases the protonation energies of the aromatic ring of the nucleobase. The present study reports the quantum chemistry analysis of the metal‐assisted tautomerization. The calculations clearly demonstrate that metalation of the exocyclic amino group of the nucleobase significantly increases the protonation energy of the aromatic rings of the nucleobase. Also, absolute anisotropy shift, molecular orbital and natural bond orbital calculations are compatible with these results. Copyright © 2003 John Wiley & Sons, Ltd.     

Quantum chemical investigation on the influence of amino substitution on proton affinity of oxazolidin-2-one

The scenarios of preferred protonation sites and the absolute gas-phase proton affinities of C5- and N4-amino derivatives of oxazolidinone (OXA) molecules possessing two oxygen and two nitrogen atoms, are studied to investigate the effect of substitution of amino group on geometry, electronic structure, and proton affinities of these molecules. The natural bond orbital analysis is invoked to obtain the second-order delocalization energies, occupations of lone pairs, charge distribution, and bond orders to rationalize the obtained results. Our findings reveal a strong nucleophilicity of O1 site in C5-amino and N4-amino-substituted OXA isomers just as in un-substituted OXA. The substituent nitrogen in N4-amino-substituted OXA has comparable electrophilicity to O1 site while lesser than acyl oxygen and higher than nitrogen of OXA ring in C5-amino-substituted OXA. The PA values of C5- and N4-amino-substituted OXA isomers span in the range 172.06–205.77 kcal mol^?1 (at CBS-Q). The PA values for the potential sites increase in the range 1.96–27.08 kcal mol^?1 as a result of the amino substitution at C5 and N4 in orientation (b) while exceptionally they decrease by 0.57–2.95 kcal mol^?1 as a result of the amino substitution at N4 in orientation (a). The results for the order of PA values of potential sites have been supported by molecular electrostatic potential maps. Our findings indicate that the factors such as geometrical rearrangements, variations in atomic charge densities and electron delocalization, effect of substituent, intramolecular hydrogen bonding, and electronic changes direct the relative stabilities and proton affinities of N, C5-substituted amino OXA isomers.     

Protonation of 5‐methylhydantoin and its thio derivatives in the gas phase: A theoretical study

The gas phase proton affinities of 5‐methylhydantoin and its thio derivatives were theoretically studied through the use of high‐level density functional theory calculations. The structure of all possible tautomers and their conformers were optimized at the B3LYP/6‐311+(d,p) level of theory. Final energies were obtained at the B3LYP/6‐311+(2df,2p) level. The imidazolidone derivatives 5‐methyl‐2,4‐dioxo imidazolidine, 5‐methyl‐2‐oxo‐4‐thio imidazolidine, 5‐methyl‐2‐thio‐4‐oxo imidazolidine, and 5‐methyl‐2,4‐dithio imidazolidine possess moderately strong proton affinities. Protonation at sulfur would be larger than protonation at oxygen. The most stable protonated forms of 2O4O and 2S4O have the proton attached to the heteroatom in position 2, whereas protonation of 2O4S and 2S4S preferentially takes place at position 4. The barriers for proton migration between the different tautomers are rather large. The energy decomposition analysis analysis of the O? H⁺ and S? H⁺ interactions suggests that the bonding interactions come mainly from the covalent bond formation. The contribution of the Coulomb attraction is rather small. © 2012 Wiley Periodicals, Inc.     

Protonation of thymine,cytosine, adenine,and guanine DNA nucleic acid bases: Theoretical investigation into the framework of density functional theory

Gradient-corrected density functional computations with triple-zeta-type basis sets were performed to determine the preferred protonation site and the absolute gas-phase proton affinities of the most stable tautomer of the DNA bases thymine (T), cytosine (C), adenine (A), and guanine (G). Charge distribution, bond orders, and molecular electrostatic potentials were considered to rationalize the obtained results. The vibrational frequencies and the contribution of the zero-point energies were also computed. Significant geometrical changes in bond lengths and angles near the protonation sites were found. At 298 K, proton affinities values of 208.8 (T), 229.1 (C), 225.8 (A), and 230.3 (G) kcal/mol were obtained in agreement with experimental results. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 989–1000, 1998     

Fluorine as a pi donor. Carbon 1s photoelectron spectroscopy and proton affinities of fluorobenzenes

The carbon 1s ionization energies for all of the carbon atoms in 10 fluorine-substituted benzene molecules have been measured by high-resolution photoelectron spectroscopy. A total of 30 ionization energies can be accurately described by an additivity model with four parameters that describe the effect of a fluorine that is ipso, ortho, meta, or para to the site of ionization. A similar additivity relationship describes the enthalpies of protonation. The additivity parameters reflect the role of fluorine as an electron-withdrawing group and as a pi-electron donating group. The ionization energies and proton affinities correlate linearly, but there are four different correlations depending on whether there are 0, 1, 2, or 3 fluorines ortho or para to the site of ionization or protonation. That there are four correlation lines can be understood in terms of the ability of the hydrogens at the site of protonation to act as a pi-electron acceptor. A comparison of the ionization energies and proton affinities, together with the results of electronic structure calculations, gives insight into the effects of fluorine as an electron-withdrawing group and as a pi donor, both in the neutral molecule and in response to an added positive charge.     

Effects of alkylation upon the proton affinities of nitrogen and oxygen bases

The protonation energies of alkylated derivatives of NH₃ and OH₂ are calculated at the Hartree–Fock level with the split-valence 4-31G basis set. The methyl, dimethyl, and ethyl amines are studied; oxygen bases include methanol, dimethylether, and ethanol. The geometries of each molecule and its protonated analog are fully optimized. It is found that protonation leads to significant changes in the molecular structures. In particular, the bonds to the N and O atoms are substantially elongated, especially when the other atom involved is C rather than H. The calculated absolute proton affinities are somewhat larger than the experimental values. However, the differences in protonation energies of the various molecules relative to one another agree quantitatively with experiment. Replacement of one H atom of the base by a methyl group induces an increase in proton affinity of some 10 kcal/mol. If a second methyl group is added to the N or O atom, a further increment of about 70% this amount is noted. On the other hand, placement of the second C atom on the first methyl group (to form an ethyl substituent) leads to a smaller increase (～30%). The magnitudes of these alkyl substituent effects are somewhat larger for the oxygen bases than for the amines.     

Electron Attachment to Hydrated Oligonucleotide Dimers: Guanylyl‐3′,5′‐Cytidine and Cytidylyl‐3′,5′‐Guanosine

The dinucleoside phosphate deoxycytidylyl‐3′,5′‐deoxyguanosine (dCpdG) and deoxyguanylyl‐3′,5′‐deoxycytidine (dGpdC) systems are among the largest to be studied by reliable theoretical methods. Exploring electron attachment to these subunits of DNA single strands provides significant progress toward definitive predictions of the electron affinities of DNA single strands. The adiabatic electron affinities of the oligonucleotides are found to be sequence dependent. Deoxycytidine (dC) on the 5′ end, dCpdG, has larger adiabatic electron affinity (AEA, 0.90 eV) than dC on the 3′ end of the oligomer (dGpdC, 0.66 eV). The geometric features, molecular orbital analyses, and charge distribution studies for the radical anions of the cytidine‐containing oligonucleotides demonstrate that the excess electron in these anionic systems is dominantly located on the cytosine nucleobase moiety. The π‐stacking interaction between nucleobases G and C seems unlikely to improve the electron‐capturing ability of the oligonucleotide dimers. The influence of the neighboring base on the electron‐capturing ability of cytosine should be attributed to the intensified proton accepting–donating interaction between the bases. The present investigation demonstrates that the vertical detachment energies (VDEs) of the radical anions of the oligonucleotides dGpdC and dCpdG are significantly larger than those of the corresponding nucleotides. Consequently, reactions with low activation barriers, such as those for O? C σ bond and N‐glycosidic bond breakage, might be expected for the radical anions of the guanosine–cytosine mixed oligonucleotides.     

Ab initio structural study of some substituted ibuprofen derivatives as possible anti‐inflammatory agents

The formation energies of a series of substituted derivatives in α‐position of ibuprofen (2‐p‐isobutyl‐phenyl‐propionic acid) are determined, at the ab initio level RHF/6‐311G** with full geometry optimization, in their neutral and anionic forms and in the gas phase and water solution to correlate their physical–chemical properties with their anti‐inflammatory activity. Conformational calculations on the acidic moiety were also performed on five of them. The ab initio methods foresee that all these molecules present two preferred conformations in which the substituting atom in α‐position is lying approximately in the aromatic ring plane, in contrast with the results obtained with semiempirical methods. In this article, the protonation energy in solution, the solvation energy, the HOMO energy of the neutral form, and the lipophilicity will be considered as possible factors of anti‐inflammatory activity. The protonation energy in solution, together with the lipophilicity, are verified to be good activity factors: The smaller the protonation energy and the lipophilicity, the larger the anti‐inflammatory activity. In contrast, the larger the solvation energy, the smaller the activity. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

The correlation of proton affinities with atomic charges and electronegativities for the group 14 to 17 hydrides

Proton affinities for hydrides of formula $\mathrm{AH}^{-}_{n-1}$ containing the elements A from the second to the fifth period of the periodic table and groups 14 to 17 are predicted at the Hartree–Fock, MP2 and B3LYP levels of theory employing both core potential basis sets and the 3‐21G basis set. The core potential methods perform well when compared with all electron calculations using the 3‐21++G** basis set. The proton affinities of the hydrides containing elements from groups 15 and 16 of the periodic table are more accurate than those with elements from groups 14 and 17. A cancellation of errors appears to occur more completely if the protonated and nonprotonated molecules contain both bond and lone pairs before and after the protonation reaction. Proton affinities correlate nearly linearly with the atomic charges on the hydrogen atoms when these charges are determined by the generalized atomic polar tensor (GAPT) method. This tendency can be associated, in principle, with the group electronegativities as introduced by Iczkowski and Margrave. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1119–1131, 2000     

Proton Transfer Influence on Geometry and Electron Density in Benzoic Acid–Pyridine Complexes

The influence of the proton transfer on the geometry of donor and acceptor molecule in benzoic acid–pyridine complexes is investigated by theoretical calculations at the B3LYP/6‐311++G** level of theory. Systematic shifts of the H‐atom in the H‐bond are reflected in the geometry of the COOH group and the lengths of aromatic ring bond lengths of the proton acceptor. Changes in electron densities have been studied by atoms in molecules analysis. A systematic natural bond orbital analysis has been performed to study the proton transfer mechanism. Two donor orbitals are engaged in the proton transfer process which is accompanied by a change in orbital delocalization of H‐atom that can switch between two donor orbitals so the path of proton transfer in intermolecular H‐bond is not determined by the orbital shape. Theoretical results have been confirmed by experimental results published previously.     

Control of stereoselective protonation of enols1,2

A decalyl framework with a siloxy enolic moiety and proximate proton transferring groups was synthesized. On enolate generation with fluoride two competitive reaction modes were possible: (a) intermolecular protonation, and (b) intramolecular proton transfer by the proximate group. Control of the protonation stereochemistry proved possible by varying the proximate group and by changing the acidity of the medium. With the groups -CH2OH, -CH=O, and -CH2OCH2OCH3 as the proximate groups, only intermolecular proton transfer was observed with no dependence on acidity. In contrast, with -COO- and COOH, only intramolecular protonation resulted but again with no dependence on acidity of the medium. In contrast, with -CH2NH2 as the proximate group, intramolecular proton transfer predominated with a dependence on the effective pH of the medium. A kinetic analysis provided a linear-log relationship of the ratio of the two stereoisomers with the medium acidity. The analysis revealed that two acetic acid molecules are involved in providing the proton to the enolate moiety. A theoretical analysis was developed paralleling the experimental results. In the ketonization transition state, the hybridization was shown to be close to sp2 hybridized at the alpha-enolate carbon.     

Quantum chemical studies on some potentially tautomeric oxazolidin-4-one derivatives and their thio and azo anologs

The basicities and nucleophilicities along with prototautomerism of biologically active oxazolidin-4-one and its thio and azo analogs were investigated by semi-empirical methods. The oxo and thion protonation were found to be easier than that of azo protonation for 4-oxo and 4-thion derivatives whereas amino protonation was found to be easier than imino and azo protonation in 4-imino derivative. The preferred tautomeric form for 4-oxo and 4-thion derivatives were found to be the keto and thion forms, respectively, whereas the amino form was found to be preferred in 4-imino derivatives. An acceptable correlation between gas phase proton affinities and aqueous phase acidity constants as well as the correlation between nucleophilicity and acidity constants was observed.     

Protonation of glycine and alanine: proton affinities, intrinsic basicities and proton transfer path

Proton affinities and intrinsic basicities for nitrogen and oxygen protonation in the gas phase of the amino acids glycine and alanine were calculated using density functional theory (DFT) and ab initio methods at different levels of theory from Hartree-Fock (HF) to G2 approximations. All methods gave good agreement for proton affinities for nitrogen protonation for both amino acids. However, dramatic differences were found between DFT, MP4//MP2, and G2 results on one hand, and MP4//HF results on the other to the calculation of structural and energetic characteristics of oxygen protonation in glycine and alanine. An investigation into the source of these differences revealed that electron correlation effects are chiefly responsible for the differences in calculated oxygen proton affinities between the various methods. It has been found that proton transfer between nitrogen and oxygen protonation sites in both amino acids occurs without a transfer path barrier when correlated methods were used to calculate the path energetics.     

Proton character of the peptide unit in the Ca2+-binding sites of calcium pump

The effect of forming calcium pump structures in biological systems on the proton character of the peptide unit has been studied theoretically using the density-functional theory calculations with a large basis set. One acetic acid, one acetate, and three acetamide molecules as well as the modeling peptide unit (MPU) have been employed to mimic the amino acid residues forming the Ca2+-binding sites. To highlight the limiting case of the Ca2+-binding effect on the proton property and the proton countertransport possibility in the direction opposite to the ion, the MPU bounded by the bare or the hydrated Ca2+ has also been investigated. The natural bond orbital (NBO) analysis indicates that the increase of the p-character of the (N-H) sigma orbital results in weakening of the N-H bond which is lengthened when a Ca2+ ion is introduced to the MPU. Calculated NMR shielding sigma(H1) of the MPU shifts upfield upon the Ca2+ ion combination, which reveals the donating of the electron from the amide H as represented by the increase of the calculated positive natural charge for amide H of the MPU. Moreover, the proton affinities (PA) and gas-phase basicities (GB) for the amide nitrogen active site of the MPU are reduced; that is, the acidity of the amide hydrogen gets stronger because of the influence of the Ca2+ ion. To prove the transport possibility of the N-H proton in the direction opposite to the Ca2+ ion along the N-H...O=C hydrogen bond in the helical peptide linkage, NH3 and H2O are used here to assist the dissociation of the amide H of the MPU, and the calculated results show the notable decrease of the deprotonation energies compared to that of the case without this assistance. Moreover, calculated results also reveal that the variation of the quantities discussed here for amide H of the MPU gets smaller when the acidity of Ca2+ ion decreases. Ionization states of the acidic residues forming the Ca2+-binding sites may influence the activity of the amide H of the MPU and further affect the transport tendency of the peptide unit proton in the direction opposite to Ca2+.     

Methyl formate and its mono and difluoro derivatives: conformational manifolds, basicity, and interaction with HF theoretical investigation

The conformational manifolds, scenarios of protonation, and hydrogen bond propensity of methyl formate and its mono and difluoro derivatives, which possess two oxygen atoms with different basicities, are studied at the B3LYP/6-311++G(3df,3pd) computational level. The optimized geometries of the title molecules, their energetics, and relevant harmonic vibrational frequencies, mainly of the ν(CH) mode of the H-C═O group, are of a primary focus. The Natural Bond Orbital analysis is invoked to obtain the second-order intra- or intermolecular hyperconjugation energies, occupations of antibonding orbitals, and hybridization of the carbon atoms. It is demonstrated that the Z conformers (and their rotamers) of the three title molecules are characterized by a higher stability compared to the E ones. The stabilities depend on the intramolecular hyperconjugative interaction and on the attraction or repulsion nonbonded interaction. The proton affinity of the carbonyl oxygen exceeds, by 15-20 kcal·mol(-1), that of the methoxy oxygen. Fluorine substitution causes a moderate lowering of the proton affinity of the oxygens. Protonation on the oxygen atoms yields a contraction of the C-H bond and large concomitant blue shift of the ν(CH) vibration. These changes are mainly determined by a lowering of the occupation of the corresponding σ*(CH) orbitals. The esters under consideration are probed on the interaction with the HF molecule. The complexes that are formed under this interaction on the oxygen of the H-C═O group are stronger than those formed on the oxygen belonging to the methoxy one. It is deduced that the hydrogen bond energies show a linear dependence on the proton affinities of the corresponding oxygen atoms. Hydrogen-bonded complexes of moderate strength are also formed, while HF interacts with the fluorine atoms of the fluorinated esters.     

取代基对1-甲基尿嘧啶与N-甲基乙酰胺氢键复合物中氢键强度的影响

使用密度泛函理论B3LYP方法和二阶微扰理论MP2方法对由1-甲基尿嘧啶与N-甲基乙酰胺所形成的氢键复合物中的氢键强度进行了理论研究, 探讨了不同取代基取代氢键受体分子1-甲基尿嘧啶中的氢原子对氢键强度的影响和氢键的协同性. 研究表明: 供电子取代基使N－H…O＝C氢键键长r(H…O)缩短, 氢键强度增强; 吸电子取代基使N－H…O＝C氢键键长r(H…O)伸长, 氢键强度减弱. 自然键轨道(NBO)分析表明: 供电子基团使参与形成氢键的氢原子的正电荷增加, 使氧原子的负电荷增加, 使质子供体和受体分子间的电荷转移量增多; 吸电子基团则相反. 供电子基团使N－H…O＝C氢键中氧原子的孤对电子轨道n(O)对N－H的反键轨道σ^*(N－H)的二阶相互作用稳定化能增强, 吸电子基团使这种二阶相互作用稳定化能减弱. 取代基对与其相近的N－H…O＝C氢键影响更大.     

Computational Study of Proton Transfer in Tautomers of 3‐ and 5‐Hydroxypyrazole Assisted by Water

The tautomerism of 3‐ and 5‐hydroxypyrazole is studied at the B3LYP, CCSD and G3B3 computational levels, including the gas phase, PCM–water effects, and proton transfer assisted by water molecules. To understand the propensity of tautomerization, hydrogen‐bond acidity and basicity of neutral species is approached by means of correlations between donor/acceptor ability and H‐bond interaction energies. Tautomerism processes are highly dependent on the solvent environment, and a significant reduction of the transition barriers upon solvation is seen. In addition, the inclusion of a single water molecule to assist proton transfer decreases the barriers between tautomers. Although the second water molecule further reduces those barriers, its effect is less appreciable than the first one. Neutral species present more stable minima than anionic and cationic species, but relatively similar transition barriers to anionic tautomers.     

Carbodicarbenes and Related Divalent Carbon(0) Compounds

Quantum‐chemical calculations using DFT and ab initio methods have been carried out for fourteen divalent carbon(0) compounds (carbones), in which the bonding situation at the two‐coordinate carbon atom can be described in terms of donor–acceptor interactions L→C←L. The charge‐ and energy‐decomposition analysis of the electronic structure of compounds 1 – 10 reveals divalent carbon(0) character in different degrees for all molecules. Carbone‐type bonding L→C←L is particularly strong for the carbodicarbenes 1 and 2 , for the “bent allenes” 3 a , 3 b , 4 a , and 4 b , and for the carbocarbenephosphoranes 7 a , 7 b , and 7 c . The last‐named molecules have very large first and large second proton affinities. They also bind two BH₃ ligands with very high bond energies, which are large enough that the bis‐adducts should be isolable in a condensed phase. The second proton affinities of the complexes 5 , 6 , and 8 – 10 bearing CO or N₂ as ligand are significantly lower than those of the other molecules. However, they give stable complexes with two BH₃ ligands and thus are twofold Lewis bases. The calculated data thus identify 1 – 10 as carbones L→C←L in which the carbon atom has two electron pairs. The chemistry of carbones is different from that of carbenes because divalent carbon(0) compounds CL₂ are π donors and thus may serve as double Lewis bases, while divalent carbon(II) compounds are π acceptors. The theoretical results point toward new directions for experimental research in the field of low‐coordinate carbon compounds.