Effect of Sr2+ association on the tautomerization processes of uracil and its dithio- and diseleno-derivatives

The structures and relative stabilities of the complexes formed by uracil and its thio- and seleno-derivatives with the Sr(2+) cation, in the gas phase, have been analyzed by means of G96LYP density functional theory (DFT) calculations. The attachment of the Sr(2+) cation to the heteroatom at position 4 is preferred systematically. Although the enolic forms of uracil and its derivatives should not be observed in the gas phase, the corresponding Sr(2+) complexes are the most stable. The enhanced stability of these tautomers is two-fold, on the one hand Sr(2+) interacts with two basic sites simultaneously, and on the other hand an aromatization of the six-membered ring takes place upon Sr(2+) association. Sr(2+) attachment also has a clear catalytic effect in the tautomerization processes involving uracil and its derivatives. This catalytic effect increases when oxygen is replaced by sulfur or selenium. The Sr(2+) binding energy with uracil and its derivatives is bigger than the tautomerization barriers connecting the dioxo forms with the corresponding enolic tautomers. Consequently, when associated with Sr(2+), all tautomers are energetically accessible and should all be observed in the gas phase.     

Theoretical Studies on the Binding of Cd~（2＋） to Uracil and Its Thio-derivatives

The interaction of Cd2+ with uracil,2-thiouracil,4-thiouracil and 2,4-dithiouracil have been investigated by the density functional theory(DFT) calculations.For uracil and 2,4-dithiouracil,where the two basic sites are the same,Cd2+ attachment to the heteroatom at position 4 is preferred.However,for the systems where both types of basic centers,a carbonyl and a thiocarbonyl groups,are present,Cd2+ association with sulfur is favorable.The enhanced stability of these enolic and thiol forms comes from Cd2+ interaction with two basic sites simultaneously,which thereby triggers a significant aromatization of the ring.More significantly,the Cd2+ binding energy with uracil and its thio-derivatives is larger than the tautomerization barriers connecting the diketo-like forms with the corresponding enolic-like tautomers.Consequently,when associated with Cd2+,all tautomers are energetically accessible and should be observed in the gas phase.     

Why Are Selenouracils as Basic as but Stronger Acids than Uracil in the Gas Phase?

The gas‐phase basicity and acidity of 2‐selenouracil ( 2SU ), 4‐selenouracil ( 4SU ), and 2,4‐diselenouracil ( 24SU ) have been calculated at the B3LYP/6‐311+G(3df,2p) level of theory. Our results showed that all these compounds behave as bases of moderate strength in the gas phase. As was found for uracil and for the thiouracil analogues, the most basic site is the heteroatom at position 4, and only for 2SU is there a certain ambiguity in assigning the basic site. More importantly, with the only exception of 2SU , selenouracils are as basic as or slightly less basic than uracil, because the replacement of the oxygen atom at position 2 by a selenium atom leads to an increase of the electron delocalization inside the six‐membered ring, which decreases the intrinsic basicity of the heteroatom at position 4. As already reported for uracil and thiouracils, for selenouracils N1 is the most acidic site. However, selenouracils are predicted to be stronger acids than uracil. This acidity enhancement is essentially due to a specific stabilization of the anion when O is replaced by Se. Two factors are responsible for this stabilization: a significant aromatization of the ring upon deprotonation and a better dispersion of the excess electron density when the system contains third‐row atoms.     

A theoretical study of hydration effects on the prototropic tautomerism of selenouracils

The prototropic tautomerism of 2-, 4-selenouracil and 2,4-diselenouracil has been studied using density functional theory (DFT) methods, at the B3LYP/6-311 + G(3df,2p)//B3LYP/6-31G(d,p) level. The relative stability order of selenouracil tautomers does not resemble that of uracil tautomers, but it is similar to that of thiouracils, even though the energy gaps between the different tautomers of selenouracils are smaller than for thiouracils. The tautomerism activation barriers are high enough as to conclude that only the oxo-selenone or the diselenone structures should be found in the gas phase. The specific interaction with one water molecule reduces these barriers by a half, but still the oxo-selenone form is always the most stable tautomer. The addition of a second water molecule has a relatively small effect, as well as bulk effects, evaluated by means of a continuum-polarized model. For isolated 2- and 4-selenouracils, the more favorable tautomerization process corresponds to a hydrogen transfer towards the selenium atom, the activation barriers for transfer towards the oxygen atom being much higher. This situation changes when specific and bulk effects are included, and the latter process becomes the more favorable one. For 2,4-diselenouracil the more favorable tautomerization, in the gas phase, corresponds to the H shift from N1 to the Se atom at C2, while solvation effects favor the transfer from N3 to the Se atom at C4.     

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.     

Effects of the ionization in the tautomerism of uracil: A reaction electronic flux perspective

The one‐step tautomerization processes of uracil and its radical cation and radical anion have been investigated in the light of the reaction force and reaction electronic flux (REF) formalisms. The relative energies of the different tautomers as well as the corresponding tautomerization barriers have been obtained through the use of the G4 high‐level ab initio method and by means of B3LYP/6‐311+G(3df,2p)//B3LYP/6‐311+G(d, p) calculations. Systematically, the enol radical cations are more stable in relative terms than the neutral, due to the higher ionization energy of the diketo forms with respect to the enolic ones. Conversely, the enol radical anions, with the only exception of the 2‐keto‐N1 anion, are found to be less stable than the neutral. The effects of the ionization are also sizable on the tautomerization barriers although this effect also depends on the particular tautomerization process. The reaction force analysis shows that all reactions are mainly activated through structural rearrangements that initiate the electronic activity. This electronic activity is monitored along the reaction coordinate through the REF that obeys a delicate balance between the acid and basic character of the atoms involved in the hydrogen transfer. © 2015 Wiley Periodicals, Inc.     

2,4-Ditellurouracil and its 5-fluoro derivative: Theoretical investigations of structural,energetics and ADME parameters

2,4-Ditellurouracil exhibits keto-enol tautomerism via different pathways resulting in seven tautomers. These pathways were studied in the gas phase using density functional theory method. The functionals used were BLYP, B3LYP and BHLYP and the basis sets were 6–311++G(d,p) for all atoms except that LanL2DZ ECP was used for tellurium atom only. The results indicate that the diketo form is more stable as observed for uracil and its sulfur and selenium analogues. The effect of introducing fluorine at position 5 was also investigated and the energy difference between the diketo and dienol forms is reduced. 2,4-Ditellurouracil and its 5-fluoro analogue are expected to exist exclusively as the diketo form due to the high interconversion energy barrier. We extended the investigation to predict ADME parameters of the most stable diketo and dienol tautomers in view of understanding their biological properties. This research enlightens keto-enol tautomerism of 2,4-ditellurouracil and its 5-fluoro derivative with additional insights to biological functions.     

A DFT study of uracil and 5-bromouracil in nanodroplets

The canonical (keto) and rare (enol) tautomers of uracil and 5-bromouracil in clusters comprising 50 and 100 water molecules (nanodroplets) were studied using density functional theory. The geometries of the various complexes were optimized at two different levels of theory, BLYP/6-31G(d,p) and B3LYP/6-31G(d,p). Tautomerization energies were computed using the BLYP, B3LYP and M05-2X density functionals. The gas-phase tautomerization energies of uracil and 5-bromouracil are very similar, favoring the keto tautomer. However, in the hydrated phase, the tautomeric preference of 5-bromouracil is reversed. This result is obtained for all four sets of clusters (BLYP or B3LYP optimized, containing 50 or 100 water clusters) and at all levels of theory employed, and indicates that a bromine atom in the 5-position considerably increases the proportion of the hydroxyl group present in uracil.     

2-酰基-1,3-环二酮类化合物互变异构的理论计算

采用MP2/6-31+G**//B3LYP/6-31+G**方法,系统地研究了2-酰基-1,3-环二酮类化合物的互变异构性质,探讨了环的饱和性、环的大小、环上杂原子以及溶剂效应对各互变异构体相对稳定性的影响。结果表明:(1)未烯醇化的异构体由于无法形成分子内氢键而具有较高的能量;(2)环上杂原子的推电子效应提高了邻位羰基氧上的负电荷,从而有利于相应环外烯醇式异构体的稳定;(3)对化合物3-酰基-1H-吡啶-2,4-二酮,3-酰基吡喃-2,4-二酮,2-酰基环戊-4-烯-1,3-二酮和3-酰基吡咯-2,4-二酮,由互变异构形成的环的芳香性在各异构体的相对稳定性中扮演着决定性的作用。     

Association of Cu2+ with uracil and its thio derivatives: a theoretical study.

The structures and relative stabilities of the complexes between Cu2+ and uracil, 2-thiouracil, 4-thiouracil, and 2,4-dithiouracil were investigated by B3LYP/6-311+G(2df,2p)//B3LYP/6-31G* DFT calculations. In those systems in which both types of basic centers, that is, a carbonyl and a thiocarbonyl group, are present, association of Cu2+ with the oxygen atom is systematically favored, in contrast to what was found for the corresponding Cu+ complexes. This can be understood by considering that association of Cu2+ is immediately followed by oxidation of the base, which accumulates the negative charge at the oxygen atoms. Similarly, for 2,4-dithiouracil the most basic site for Cu+ attachment is the sulfur atom at the 4-position, while for association of Cu2+ it is sulfur at the 2-position. In contrast, differences between uracil-Cu+ and uracil-Cu2+ complexes are very small, and in both cases the oxygen atom at the 4-position is the most basic. Cu2+ binding energies are about 4 and 1.2 times larger than Cu+ binding energies and proton affinities, respectively. Uracil- and thiouracil-Cu2+ complexes are thermodynamically unstable but kinetically stable with respect to their dissociation into uracil*+ + Cu+ or thiouracil*+ + Cu+. The Cu2+ binding energies vary with the difference between the second ionization potential of the metal and the first ionization potential of the base. regardless of the reference acid (H+, Cu+, Cu2+) the basicity trend is 2,4-dithiouracil > 4-thiouracil > 2-thiouracil > uracil.     

Specific hydration effects on oxo-thio triazepine derivatives

The specific hydration of 2,7-dimethyl-1,2,4-triazepine oxo-thio derivatives by one water molecule has been investigated at the B3LYP/6-311++G(3df,2p)//B3LYP/6-311+G(d,p) level of theory. The existence of different hydrogen bond (HB) donor and acceptor centers in these molecules led to different kinds of hydrogen bonds (CH-O, OH-S, NH-O, OH-N, and OH-O) and different kinds of complexes. Among them, the most stable structures correspond to complexes where the heteroatom X or Y at positions 3 and 5 behaves as HB acceptor and the hydrogen atom associated with the nitrogen atom at position 4 as HB donor. In accordance with previous studies, it has been shown that the thiocarbonyl group forms stronger HBs than the carbonyl group because the sulfur atom is a better HB acceptor than the oxygen one. With the help of the AIM (atoms in molecules) theory and ELF (electron localization function) analysis, it has been shown that, in the case of 3O5O, 3S5O, and 3S5S, the most basic site is the heteroatom at position 3, while in 3O5S species the most basic center is the sulfur atom.     

Interaction with glycine increases stability of a mutagenic tautomer of uracil. A density functional theory study

The most stable structures for the gas-phase complexes of minor tautomers of uracil (U) with glycine (G) were characterized at the density functional B3LYP/6-31++G level of theory. These are cyclic structures stabilized by two hydrogen bonds. The relative stability of isolated tautomers of uracil was rationalized by using thermodynamic and structural arguments. The stabilization energies for complexes between the tautomers of U and G result from interplay between the stabilizing two-body interaction energies and destabilizing one-body terms. The latter are related to the energies of (i) tautomerization of the unperturbed moieties and (ii) distortions of the resulting rare tautomers in the complex. The two-body term describes the interaction energy between distorted tautomers. The two-body interaction energy term correlates with perturbations of length of the proton-donor bonds as well as with deprotonation enthalpies and proton affinities of the appropriate monomer sites. It was demonstrated that the relative instability of rare tautomers of uracil is diminished due to their interactions with glycine. In particular, the instability of the third most stable tautomer (U(III)) is decreased from 11.9 kcal/mol for non-interacting uracil to 6.7 kcal/mol for uracil in a complex with the zwitterionic tautomer of glycine. A decrease of instability by 5.2 kcal/mol could result in an increase of concentration of U(III) by almost 5 orders of magnitude. This is the tautomer with proton donor and acceptor sites matching guanine rather than adenine. Moreover, kinetic characteristics obtained for the glycine-assisted conversion of the most stable tautomer of uracil (U(I)) to U(III) indicate that the U(I)<-->U(III) thermodynamic equilibrium could be easily attained at room temperature. The resulting concentration of this tautomer falls in a mutationally significant range.     

Structures and energetics of electrosprayed uracil(n)Ca2+ clusters (n = 14-4) in the gas phase

Clusters of uracil (U) about a calcium dication, U(n)Ca(2+) (n = 14-4), have been studied in the gas phase by both experimental and theoretical methods. Temperature dependent blackbody infrared radiative dissociation (BIRD) experiments were performed on U(n)Ca(2+) clusters with n = 14-5 and the observed Arrhenius parameters are reported here. Master equation modeling of the BIRD kinetics data was carried out to determine threshold dissociation energies. Initial geometry calculations were performed using the B3LYP density functional and 3-21G(d) basis set. A sample of ten conformations per cluster was obtained through a simulated annealing study. These structures were optimized using B3LYP/6-31G(d) level of theory. Fragment-based hybrid many body interaction (HMBI) MP2/6-311++G(2df,2p)/Amoeba calculations were performed on representative conformations to determine theoretical binding energies. Results were examined in relation to cluster size (n). A significant increase in the energy required to remove uracil from U(6)Ca(2+) when compared to larger clusters supports previous reports that the calcium ion is coordinated by six uracil molecules in the formation of an inner shell. For clusters larger than n = 6, an odd-even alternation in threshold dissociation energies was observed, suggesting that the outer shell uracil molecules bind as dimers to the inner core. Proposed binding schemes are presented. Multiple structures of U(5)Ca(2+) are suggested as being present in the gas phase where the fifth uracil may be either part of the first or second solvation shell.     

Gas-phase reactivity of 2,7-dimethyl-[1,2,4]-triazepine thio derivatives toward Cu+ cation: a DFT study

The gas-phase interactions of 2,7-dimethyl-[1,2,4]-triazepine and its thio derivatives with Cu+ were studied through the use of high-level density functional theory (DFT) calculations. The structure of all possible tautomers and their conformers was optimized at the B3LYP/6-31G(d) level of theory. Final energies were obtained at the B3LYP/6-311+G(2df,2p) level. It has been found that the direct association of Cu+ occurs at the oxygen atom attached to position 3 in the case of the dioxo derivative and at the sulfur atom in all other cases. For the dithio derivatives, the global minimum of the PES corresponds to the structure in which the metal ion bridges between the heteroatom at position 3 and the nitrogen atom at position 4 of the corresponding enolic tautomer, forming a four-membered ring structure; for the dioxo derivative, this conformer competes with the ketone tautomer. Moreover, the isomerization processes leading from the most stable adduct to the other stable conformers were investigated. Among all the considered compounds, the 3,5-dithiotriazepines-Cu+ is found to be the one that associates Cu+ more tightly in the gas phase. The calculated Cu+ binding energies show a good correlation with the experimental proton affinities.     

尿嘧啶水助质子转移反应机理的研究

用密度泛函理论,在B3LYP/6-311++G**计算水平下分别对尿嘧啶所有的气相、液相、过渡态和质子转移异构体的结构进行全优化,获得它们在气相和水相中的几何结构和电子结构,PGM反应场溶剂模型用于水相计算.结果显示:在气相和水相中,水参与反应降低了互变异构质子迁移的反应活化能,对互变异构质子迁移的反应起到催化作用,但...     

An investigation of keto–enol tautomerism in N-vinyl-2-, and 3-pyrrolidinones using ab initio and density functional theory calculations

We investigated the protomeric tautomerism of N-vinyl-2-pyrrolidinone (NV2P) and N-vinyl-3-pyrrolidinone (NV3P) molecules, and considered the three neutral tautomers for NV2P (1a, 1b, 1c) and the five for NV3P (2a, 2b, 2c, 2d, 2e). Full geometry optimizations were carried out at the HF/6-31G**, HF/6-31+G** and B3LYP/6-31+G** levels in the gas phase and in water. Additionally, single-point MP2/6-31+G** calculations were performed on the HF/6-31+G** optimized geometries. The tautomerization processes in water (=78.54) were studied using the self-consistent reaction field theory. According to our estimations, the tautomerization of NV2P and NV3P molecules are not strongly influenced by the polar solvents, the improvement of the basis set quality and the electron correlation effects in the gas phase and in water. The calculated relative free energies (ΔG) predict that 1a and 2a are the energetically preferred tautomers in the gas phase and in water.     

5-氟胞嘧啶气相及水助质子转移异构化的理论研究

采用密度泛函B3LYP/6-311G**方法,对6种5-氟胞嘧啶异构体孤立分子的稳定性及质子转移引起的酮式-烯醇式、氨基式-亚胺式互变异构反应机理进行了计算研究,获得了零点能、吉布斯自由能及质子转移过程的反应焓、活化能、活化吉布斯自由能和速率常数等参数.计算结果表明,气相中烯醇-氨基式FC4是最稳定的异构体.分子内质子转移设计了FC1→FC2和FC1→FC6两条通道,分别标记为P(1)和P(2),各通道速控步骤的活化能和速率常数分别为155.9 kJ·mol-1,4.70×10-15 s-1和173.1 kJ·mol-1,1.41×10-18 s-1.水助催化时,相应通道P(3) 和P(4) 速控步骤的活化能和速率常数分别为51.0 kJ·mol-1,1.41×103 s-1和88.2 kJ·mol-1,4.53×10-3 s-1.可见,水分子的加入极大地降低了质子转移的活化能垒.另外发现,水分子参与形成协同的双质子转移机理比水助单质子转移机理更利于降低活化能垒.     

金属离子与腺嘌呤异构体复合物的稳定性

在B3LYP/6-311++G**//6-31+G*基组水平上结合PCM模型系统的优化了气相和液相环境中14种腺嘌呤异构体与四种金属离子(Na+,K+,Mg2+,Ca2+)形成的132个稳定复合物。通过能量对比,得到了所有复合物异构体在气液两相中的稳定性顺序及不同金属离子与同一异构体形成的复合物的能量排序,首次给出了液相中这些不同金属离子复合物的最稳定结构。结果发现溶剂效应导致了液相中的复合物稳定性顺序与气相中的相比发生了很大变化;同一异构体与不同金属离子形成的复合物其稳定性在排序中也变化很大。对于这些变化,本文分别从金属离子与腺嘌呤的复合物在气相中的结合能(EBE)及在液相中的溶质溶剂相互作用能(Epol)能等方面进行了系统的阐述     

DFT,AIM, and NBO analyses of 1-methyl-2-thioxoimidazolidin-4-one tautomers and their complexes with iodine

Thioimidazoline derivatives can be used to treat hyperthyroidism due to their ability to make complexes with iodine. In this research designed to find new structures with the same ability, 1-methyl-2-thioxoimidazolidin-4-one (MTIO) and the structures of MTIO tautomers (5 tautomers), their isomers (total 9 isomers) and their complexes with iodine are optimized using the B3LYP method with two different basis sets to obtain their molecular parameters, relative energies, and vibrational frequencies. The relative energies show that in all tautomers and complexes, ketone and thione forms are more stable than enol and thienol forms, and also Z isomers are more stable than E isomers. Moreover, the NBO calculation is carried out for tautomers and complexes to obtain atomic charges and acceptor-donor interactions. These results confirm the ability of MTIO tautomers to form complexes and show that the planar complexes have more effective interaction than the perpendicular complexes. The essence and important complexation properties are also calculated and confirmed using the AIM analysis.     

Proton affinity of uracil. A computational study of protonation sites

Relative stabilities of uracil tautomers and cations formed by gas-phase protonation were studied computationally with the B3LYP, MP2, QCISD, and QCISD(T) methods and with basis sets expanding from 6-31G(d,p) to 6-311+G(3df,2p). In accordance with a previous density functional theory study, the dioxo tautomer 1a was the most stable uracil isomer in the gas phase. Gibbs free energy calculations using effective QCISD(T)/6-311+G(3df,2p) energies suggested >99.9% of 1a at equilibrium at 523 K. The most stable ion isomer corresponded to N-1 protonated 2,4-dihydroxypyrimidine, which however is not formed by direct protonation of 1a. The topical proton affinities in 1a followed the order O-8 > O-7 > C-5 > N-3 > N-1. The thermodynamic proton affinity of 1a was calculated as 858 kJ mol⁻¹ at 298 K. A revision is suggested for the current estimate included in the ion thermochemistry database.