Effects of hydrogen-bonding and stacking interactions with amino acids on the acidity of uracil

The effects of hydrogen-bonding interactions with amino acids on the (N1) acidity of uracil are evaluated using (B3LYP) density functional theory. Many different binding arrangements of each amino acid to three uracil binding sites are considered. The effects on the uracil acidity are found to significantly depend upon the nature of the amino acid and the binding orientation, but weakly depend on the binding site. Our results reveal that in some instances small models for the amino acids can be used, while for other amino acids larger models are required to properly describe the binding to uracil. The gas-phase acidity of uracil is found to increase by up to approximately 60 kJ mol(-1) due to discrete hydrogen-bonding interactions. Although (MP2) stacking interactions with aromatic amino acids decrease the acidity of uracil, unexpected increases in the acidity are found when any of the aromatic amino acids, or the backbone, hydrogen bond to uracil. Consideration of enzymatic and aqueous environments leads to decreases in the effects of the amino acids on the acidity of uracil. However, we find that the magnitude of the decrease varies with the nature of the molecule bound, as well as the (gas-phase) binding orientations and strengths, and therefore solvation effects should be considered on a case-by-case basis in future work. Nevertheless, the effects of amino acid interactions within enzymatic environments are as much as approximately 35 kJ mol(-1). The present study has general implications for understanding the nature of active site amino acids in enzymes, such as DNA repair enzymes, that catalyze reactions involving anionic nucleobase intermediates.     

Environmental effects on the enhancement in natural and damaged DNA nucleobase acidity because of discrete hydrogen-bonding interactions

The present study uses density functional theory to carefully consider the effects of the environment on the enhancement in (natural and damaged) DNA nucleobase acidities because of multiple hydrogen-bonding interactions. Although interactions with one small molecule can increase the acidity of the nucleobases by up to 60 kJ mol-1 in the gas phase, the maximum increase in enzymatic-like environments is expected to be approximately 40 kJ mol-1, which reduces to approximately 30 kJ mol-1 in water. Furthermore, the calculated (simultaneous) effects of two, three, or four molecules are increasingly less than the sum of the individual (additive) effects with an increase in the number and acidity of the small molecules bound or the dielectric constant of the solvent. Regardless of these trends, our calculations reveal that additional hydrogen-bonding interactions will have a significant effect on nucleobase acidity in a variety of environments, where the exact magnitude of the effect depends on the properties of the small molecule bound, the nucleobase binding site, and the solvent. The maximum increase in nucleobase acidity because of interactions with up to four small molecules is approximately 80 kJ mol-1 in enzymatic-like environments (or 65 kJ mol-1 in water). These results suggest that hydrogen-bonding interactions likely play an important role in many biological processes by changing the physical and chemical properties of the nucleobases.     

Design of neutral Lewis superacids of group 13 elements

A general approach toward superstrong neutral Lewis acids, featuring both the pyramidalization of acceptor molecules and the introduction of electron-withdrawing substituents, is proposed and examined theoretically. Complexes of group 13 element derivatives with ammonia at the B3LYP and MP2 levels of theory with def2-TZVPP basis set are considered as examples. Pyramidalization of the acceptor molecule significantly increases its Lewis acidity (by 50-60 kJ mol(-1) for aluminum and gallium compounds and by 120-130 kJ mol(-1) for boron compounds). An additional increase of the complex stability of 55-75 kJ mol(-1) may be achieved by fluorination. The combined increase of the bond dissociation energy amounts to 110-190 kJ mol(-1), which is equivalent to 19-33 orders of magnitude in Lewis acidity.     

How flexible are fleximer nucleobases? A computational study

Density functional theory was used to study the potential energy surface for rotation about the carbon-carbon bonds in a variety of guanosine, adenosine, and inosine fleximers, which are modified purines with the imidazole and pyrimidine rings separated by a single carbon-carbon bond. Various connectivities between C4 or C5 of the imidazole ring and C5' or C6' of the pyrimidine ring were considered. Calculations on fleximer nucleobases in the absence of the ribose moiety suggest that a planar relative arrangement of the imidazole and pyrimidine rings is favored, and that all fleximers are indeed very flexible with regards to rotation about the carbon-carbon bond, where calculated barriers are generally less than 40 kJ mol(-1). Furthermore, calculated binding energies of fleximer-pyrimidine pairs indicate that the hydrogen-bonding properties of these modified nucleobases mimic those of the corresponding natural purine. Inclusion of the sugar moiety often leads to a favored nonplanar orientation of the two rings, and either a reduction in the rotational barrier height or small changes in the rotational surface depending on the connectivity and nucleobase considered. It is concluded that several connectivities may have favorable properties for biochemical applications where flexible nucleobases would be beneficial.     

On the structure and desorption dynamics of DNA bases adsorbed on gold: a temperature-programmed study

The structure and desorption dynamics of mono- and multilayer samples of adenine, cytosine, guanine, and thymine on polycrystalline gold thin films are studied using temperature-programmed desorption-infrared reflection absorption spectroscopy (TPD-IRAS) and temperature-programmed desorption-mass spectroscopy (TPD-MS). It is shown that the pyrimidines, adenine and guanine, adsorb to gold in a complex manner and that both adhesive (adenine) and cohesive (guanine) interactions contribute the apparent binding energies to the substrate surface. Adenine displays at least two adsorption sites, including a high-energy site (210 degrees C, approximately 136 kJ/mol), wherein the molecule coordinates to the gold substrate via the NH2 group in an sp3-like, strongly perturbed, nonplanar configuration. The purines, cytosine and thymine, display a less complicated adsorption/desorption behavior. The desorption energy for cytosine (160 degrees C, approximately 122 kJ/mol) is similar to those obtained for adenine and guanine, but desorption occurs from a single site of dispersed, nonaggregated cytosine. Thymine desorbs also from a single site but at a significantly lower energy (100 degrees C, approximately 104 kJ/mol). Infrared data reveal that the monolayer architectures discussed herein are structurally very different from those observed for the bases in the bulk crystalline state. It is also evident that both pyrimidines and purines adsorb on gold with the plane of the molecule in a nonparallel orientation with respect to the substrate surface. The results of this work are discussed in the context of improving the understanding of the design of capturing oligonucleotides or DNA strands for bioanalytical applications, in particular, for gold nanoparticle-based assays.     

Cooperativity, partially bound states, and enthalpy-entropy compensation

Efforts to develop a quantitative understanding of molecular recognition rely on the additivity of individual intermolecular interactions, and cooperativity represents one of the major potential stumbling blocks. A chemical double-mutant cycle has been used to experimentally measure cooperativity between functional group interactions within a complex framework. The interaction between two aromatic groups varies by 0.2 +/- 0.4 kJ mol(-1) in synthetic H-bonded complexes that differ by 8-13 kJ mol(-1) in overall stability. In these systems, the free energies associated with individual intermolecular interactions can therefore be reliably treated in an additive fashion. The results suggest that alternative explanations should be considered for cooperative phenomena observed in other systems, and a rationale based on the population of partially bound states in flexible molecules is proposed to account for the enthalpic chelate effect and enthalpy-entropy compensation.     

Molecular recognition in cyclodextrin complexes of amino acid derivatives. 1. Crystallographic studies of beta-cyclodextrin complexes with N-acetyl-L-phenylalanine methyl ester and N-acetyl-L-phenylalanine amide pseudopeptides

Cyclodextrins (CDs) are widely utilized in studies of chiral and molecular recognition. By changing the functionality of the guest molecule, the effect of such changes on recognition by the host CD molecule can be examined. We report crystal structure determinations for two nearly isomorphous complexes of phenylalanine derivatives: beta-CD/N-acetyl-L-phenylalanine methyl ester and beta-CD/N-acetyl-L-phenylalanine amide. The complexes crystallize as hydrated head-to-head host dimers with two included guest molecules in space group P1. The crystal packing is such that it presents a nonconstraining hydrophobic pocket adjacent to a hydrophilic region, where potential hydrogen-bonding interactions with hydroxyl groups of neighboring cyclodextrin molecules and waters of hydration can occur. The two host molecules display very similar conformations; only a few of the primary hydroxyl groups are conformationally disordered. There are a number of changes in the location of water of hydration molecules, some of which are the result of different hydrogen-bonding interactions. For the different guest molecules, similar modes of penetration are observed in the CD torus; however, there is a 0.985-A shift in the position of the guest molecules in the host torus, which takes place without changing the hydrophobic interactions displayed by the phenyl side chains. This observation and the thermal motion of the guest molecules in the ester complex are taken as evidence that complex binding forces are weak. The pseudopeptides experience a significant degree of flexibility in the crystalline environment provided by CD dimers. Conformational differences of the pseudopeptide backbones and the presence of disordered water molecules in the host-guest interface provide examples of different hydrogen-bonding schemes of similar potential energy. The crystal system presents an opportunity to establish a database of molecular interactions for small peptides and peptide analogues with waters of hydration and functional groups in nonconstraining binding environments.     

A kinetic and thermodynamic study of the glycosidic bond cleavage in deoxyuridine

Density functional theory was used to study the thermodynamics and kinetics for the glycosidic bond cleavage in deoxyuridine. Two reaction pathways were characterized for the unimolecular decomposition in vacuo. However, these processes are associated with large reaction barriers and highly endothermic reaction energies, which is in agreement with experiments that suggest a (water) nucleophile is required for the nonenzymatic glycosidic bond cleavage. Two (S(N)1 and S(N)2) reaction pathways were characterized for direct hydrolysis of the glycosidic bond by a single water molecule; however, both pathways also involve very large barriers. Activation of the water nucleophile via partial proton abstraction steadily decreases the barrier and leads to a more exothermic reaction energy as the proton affinity of the molecule interacting with water increases. Indeed, our data suggests that the barrier heights and reaction energies range from that for hydrolysis by water to that for hydrolysis by the hydroxyl anion, which represents the extreme of (full) water activation (deprotonation). Hydrogen bonds between small molecules (hydrogen fluoride, water, or ammonia) and the nucleobase were found to further decrease the barrier and overall reaction energy but not to the extent that the same hydrogen-bonding interactions increase the acidity of the nucleobase. Our results suggest that the nature of the nucleophile plays a more important role in reducing the barrier to glycosidic bond cleavage than the nature of the small molecule bound, and models with more than one hydrogen fluoride molecule interacting with the nucleobase provide further support for this conclusion. Our results lead to a greater fundamental understanding of the effects of the nucleophile, activation of the nucleophile, and interactions with the nucleobase for this important biological reaction.     

A prototype calix[4]arene-based receptor for carbohydrate recognition containing peptide and phosphate binding groups

A novel class of macrobicyclic receptors for carbohydrate recognition based on upper rim, peptide-bridged calix[4]arenes has been designed and synthesized. Receptor 12, in which a charged phosphate group cooperates with peptide hydrogen-bonding donor and acceptor groups in the binding process, is the most efficient and selective in the complexation of simple carbohydrate derivatives. The selectivity observed is toward beta-glucoside 13a, which is better bound (DeltaG degrees = 19.6 kJ mol(-)(1)) compared to the corresponding alpha anomer 13b (DeltaG degrees = 17.0 kJ mol(-)(1)) and to the beta-galactoside 13c (DeltaG degrees = 17.7 kJ mol(-)(1)) in CDCl(3). A substantial drop in the stability constant is observed by esterification of the phosphate group in the host 12 or by alkylation of the OH groups in the 2 and 3 positions in the beta-glucoside and beta-galactoside derivatives. On the basis of a careful analysis of the (1)H NMR data available, a binding mode of the beta-octylglucoside 13a to receptor 12 is proposed.     

Insights into DNA binding of ruthenium arene complexes: role of hydrogen bonding and pi stacking

Density functional theory (DFT) methods are used to investigate the binding of ruthenium arene complexes, proposed as promising anticancer drugs, to isolated nucleobases. This shows a clear preference for binding at guanine over any other base and an approximately 100 kJ mol (-1) difference in binding between guanine and adenine in the gas phase, while binding to cytosine and inosine are intermediate in energy between these extremes. Solvation reduces binding energies and the discrimination between bases but maintains the overall pattern of binding. DFT and ab initio data on arene-base interactions in the absence of ruthenium show that stacking and hydrogen-bonding interactions play a significant role but cannot account for all of the energy difference between bases observed. Atoms-in-molecules analysis allows further decomposition of binding energies into contributions from covalent-binding, hydrogen-bonding, and pi-stacking interactions. Larger arenes undergo stabilizing stacking interactions, whereas N-H...X hydrogen bonding is independent of arene. Pairing of guanine to cytosine is affected by ruthenium complexation, with individual hydrogen-bonding energies being altered but the overall pairing energy remaining almost constant.     

Binding energies of hydrogen molecules to isoreticular metal-organic framework materials

Recently, several novel isoreticular metal-organic framework (IRMOF) structures have been fabricated and tested for hydrogen storage applications. To improve our understanding of these materials, and to promote quantitative calculations and simulations, the binding energies of hydrogen molecules to the MOF have been studied. High-quality second-order Moller-Plesset (MP2) calculations using the resolution of the identity approximation and the quadruple zeta QZVPP basis set were used. These calculations use terminated molecular fragments from the MOF materials. For H2 on the zinc oxide corners, the MP2 binding energy using Zn4O(HCO2)6 molecule is 6.28 kJ/mol. For H2 on the linkers, the binding energy is calculated using lithium-terminated molecular fragments. The MP2 results with coupled-cluster singles and doubles and noniterative triples method corrections and charge-transfer corrections are 4.16 kJ/mol for IRMOF-1, 4.72 kJ/mol for IRMOF-3, 4.86 kJ/mol for IRMOF-6, 4.54 kJ/mol for IRMOF-8, 5.50 and 4.90 kJ/mol for IRMOF-12, 4.87 and 4.84 kJ/mol for IRMOF-14, 5.42 kJ/mol for IRMOF-18, and 4.97 and 4.66 kJ/mol for IRMOF-993. The larger linkers are all able to bind multiple hydrogen molecules per side. The linkers of IRMOF-12, IRMOF-993, and IRMOF-14 can bind two to three, three, and four hydrogen molecules per side, respectively. In general, the larger linkers have the largest binding energies, and, together with the enhanced surface area available for binding, will provide increased hydrogen storage. We also find that adding up NH2 or CH3 groups to each linker can provide up to a 33% increase in the binding energy.     

A computational characterization of the hydrogen-bonding and stacking interactions of hypoxanthine

The hydrogen-bonding and stacking interactions of hypoxanthine, a potential universal nucleobase, were calculated using a variety of methodologies (CCSD(T), MP2, B3LYP, PWB6K, AMBER). All methods predict that the hydrogen-bonding interaction in the hypoxanthine-cytosine pair is approximately 25 kJ mol(-1) stronger than that in the other dimers. Although the calculations support suggestions from experiments that hypoxanthine preferentially binds with cytosine, the trend in the calculated hydrogen-bond strengths for the remaining natural nucleobases do not show a strong correlation with the experimentally predicted binding preferences. However, our calculations suggest that the stacking interactions of hypoxanthine are similar in magnitude to the hydrogen-bonding interactions at all levels of theory (with the exception of B3LYP, which incorrectly predicts stacked dimers to be unstable). Therefore, stacking interactions should also be considered when analyzing the stability of DNA helices containing hypoxanthine and the use of larger models that account for both hydrogen-bonding and stacking within DNA duplexes will likely result in better agreement with experimental observations. For the majority of the dimers, PWB6K and AMBER provide reasonable binding strengths at reduced computational costs, and therefore will be useful techniques for considering larger models.     

A systematic investigation of hydrogen-bonding effects on the 17O, 14N, and 2H nuclear quadrupole resonance parameters of anhydrous and monohydrated cytosine crystalline structures: a density functional theory study

A systematic computational study was carried out to characterize the 17O, 14N, and 2H nuclear quadrupole resonance (NQR) parameters in the anhydrous and monohydrated cytosine crystalline structures. To include the hydrogen-bonding effects in the calculations, the most probable interacting molecules with the central molecule in the crystalline phase were considered in the pentameric clusters of both structures. To calculate the parameters, couples of the methods B3LYP and B3PW91 and the basis sets 6-311++G** and CC-pVTZ were employed. The mentioned methods calculated reliable values of 17O, 14N, and 2H NQR tensors in the pentameric clusters, which are in good agreements with the experiment. The different influences of various hydrogen-bonding interactions types, N-H...N, N-H...O, and O-H...O, were observed on the 17O, 14N, and 2H NQR tensors. Lower values of quadrupole coupling constants and higher values of asymmetry parameters in the crystalline monohydrated cytosine indicate the presence of stronger hydrogen-bonding interactions in the monohydrated form rather than that of crystalline anhydrous cytosine.     

Structure and synthesis of 6-(substituted-imidazol-1-yl)purines: versatile substrates for regiospecific alkylation and glycosylation at N9

X-ray crystal structures of several 6-(azolyl)purine base and nucleoside derivatives show essentially coplanar conformations of the purine and appended 6-(azolyl) rings. However, the planes of the purine and imidazole rings are twisted approximately 57 degrees in a 2-chloro-6-(4,5-diphenylimidazol-1-yl)purine nucleoside, and a twist angle of approximately 61 degrees was measured between the planes of the purine and pyrrole rings in the structure of a 6-(2,5-dimethylpyrrol-1-yl)purine nucleoside derivative. Shielding "above" N7 of the purine ring by a proximal C-H on the 6-azolyl moiety is apparent with the coplanar compounds, but this effect is diminished in those without coplanarity. Syntheses of 6-(azolyl)purines from both base and nucleoside starting materials are described. Treatment of 2,6-dichloropurine with imidazole gave 2-chloro-6-(imidazol-1-yl)purine. Modified Appel reactions at C6 of trityl-protected hypoxanthine and guanine derivatives followed by detritylation gave 6-(imidazol-1-yl)- and 2-amino-6-(imidazol-1-yl)purines. Imidazole was introduced at C6 of 2',3',5'-tri-O-acetylinosine by a modified Appel reaction, and solvolysis of the glycosyl linkage gave 6-(imidazol-1-yl)purine. Guanosine triacetate was transformed into the protected 2,6-dichloropurine nucleoside, which was subjected to S(N)Ar displacement with imidazoles at C6 followed by glycosyl solvolysis to provide 2-chloro-6-(substituted-imidazol-1-yl)purines. Potential applications of these purine derivatives are outlined.     

Pd(Cu)在MgO(100)表面吸附CO和O2的理论研究

采用固体镶嵌势能模型和DFT/B3LYP方法研究了在Pd/MgO和Cu/MgO表面吸附CO和O₂分子的电子性质. 计算结果表明, 在完美MgO(100)表面Pd原子对CO和O₂的吸附能分别为206.5和84.8 kJ/mol, 因此可知Pd原子更容易吸附CO分子; 而当Pd原子附着于有氧缺陷的MgO表面时, 它对两种分子的吸附都非常弱. 相反, 附着于MgO表面的Cu原子对O₂分子的吸附更为有利, 其吸附能在140～155 kJ/mol之间. 研究结果还表明, 对于双分子吸附体系, 即CO＋CO, CO＋O₂, O₂＋O₂体系, 双分子之间的结合力可减小完美MgO表面上Pd原子与被吸附分子的相互作用, 使吸附能减少了46～96 kJ/mol. 而对于在MgO表面上的Cu原子, 只有O₂＋O₂ 体系使吸附能减少了大约50～71 kJ/mol.     

Molecule dynamics and combined QM/MM study on one-carbon unit transfer reaction catalyzed by GAR transformylase

Both a molecule dynamic study and a combined quantum mechanics and molecule mechanics (QM/MM) study on Glycinamide ribonucleotide transformylase (GAR Tfase) catalytic mechanism are presented. The results indicate a direct one-carbon unit transfer process but not a stepwise mechanism in this reaction. The residues near the active center can fix the cofactor (N10-formyltetrahydrofolate) and GAR in proper relative positions by a H-bond network. The transition state and the minimum energy pathway are located on the potential energy surface. After all the residues (including H₂O molecules) are removed from the system the activation energy has increased from 145.1 kJ/mol to 243.3 kJ/mol, and the formly transfer reaction is very hard to achieve. The interactions between coenzyme, GAR and residues near the reactive center are discussed as well.     

Mechanism of OMP decarboxylation in orotidine 5'-monophosphate decarboxylase

Despite extensive experimental and theoretical studies, the detailed catalytic mechanism of orotidine 5'-monophosphate decarboxylase (ODCase) remains controversial. In particular simulation studies using high level quantum mechanics have failed to reproduce experimental activation free energy. One common feature of many previous simulations is that there is a water molecule in the vicinity of the leaving CO2 group whose presence was only observed in the inhibitor bound complex of ODCase/BMP. Various roles have even been proposed for this water molecule from the perspective of stabilizing the transition state and/or intermediate state. We hypothesize that this water molecule is not present in the active ODCase/OMP complex. Based on QM/MM minimum free energy path simulations with accurate density functional methods, we show here that in the absence of this water molecule the enzyme functions through a simple direct decarboxylation mechanism. Analysis of the interactions in the active site indicates multiple factors contributing to the catalysis, including the fine-tuned electrostatic environment of the active site and multiple hydrogen-bonding interactions. To understand better the interactions between the enzyme and the inhibitor BMP molecule, simulations were also carried out to determine the binding free energy of this special water molecule in the ODCase/BMP complex. The results indicate that the water molecule in the active site plays a significant role in the binding of BMP by contributing approximately -3 kcal/mol to the binding free energy of the complex. Therefore, the complex of BMP plus a water molecule, instead of the BMP molecule alone, better represents the tight binding transition state analogue of ODCase. Our simulation results support the direct decarboxylation mechanism and highlight the importance of proper recognition of protein bound water molecules in the protein-ligand binding and the enzyme catalysis.     

The acidity of uracil and uracil analogs in the gas phase: four surprisingly acidic sites and biological implications

The gas phase acidities of a series of uracil derivatives (1-methyluracil, 3-methyluracil, 6-methyluracil, 5,6-dimethyluracil, and 1,3-dimethyluracil) have been bracketed to provide an understanding of the intrinsic reactivity of uracil. The experiments indicate that in the gas phase, uracil has four sites more acidic than water. Among the uracil analogs, the N1-H sites have deltaH(acid) values of 331-333 kcal mol(-1); the acidity of the N3 sites fall between 347-352 kcal mol(-1). The vinylic C6 in 1-methyluracil and 3-methyluracil brackets to 363 kcal mol(-1), and 369 kcal mol(-1) in 1,3-dimethyluracil; the C5 of 1,3-dimethyluracil brackets to 384 kcal mol(-1). Calculations conducted at B3LYP/6-31+G* are in agreement with the experimental values. The bracketing of several of these sites involved utilization of an FTMS protocol to measure the less acidic site in a molecule that has more than one acidic site, establishing the generality of this method. In molecules with multiple acidic sites, only the two most acidic sites were bracketable, which is attributable to a kinetic effect. The measured acidities are in direct contrast to in solution, where the two most acidic sites of uracil (N1 and N3) are indifferentiable. The vinylic C6 site is also particularly acidic, compared to acrolein and pyridine. The biological implications of these results, particularly with respect to enzymes for which uracil is a substrate, are discussed.     

Effect of microhydration on the electronic structure of the chromophores of the photoactive yellow and green fluorescent proteins

Electronic structure calculations of microhydrated model chromophores (in their deprotonated anionic forms) of the photoactive yellow and green fluorescent proteins (PYP and GFP) are reported. Electron-detachment and excitation energies as well as binding energies of mono- and dihydrated isomers are computed and analyzed. Microhydration has different effects on the excited and ionized states. In lower-energy planar isomers, the interaction with one water molecule blueshifts the excitation energies by 0.1-0.2 eV, whereas the detachment energies increase by 0.4-0.8 eV. The important consequence is that microhydration by just one water molecule converts the resonance (autoionizing) excited states of the bare chromophores into bound states. In the lower-energy microhydrated clusters, interactions with water have negligible effect on the chromophore geometry; however, we also identified higher-energy dihydrated clusters of PYP in which two water molecules form hydrogen-bonding network connecting the carboxylate and phenolate moieties and the chromophore is strongly distorted resulting in a significant shift of excitation energies (up to 0.6 eV).