Effects of protonation on proton-transfer processes in guanine–cytosine Watson–Crick base pairs

Intermolecular proton-transfer processes in guanine–cytosine Watson–Crick base pairs have been studied using the B3LYP density functional method. Protonation of the base pair was carried out both at the N7 and at the O6 atoms of guanine. It is found that protonation induces a strengthening of the base pair and facilitates the N1–N3 single-proton-transfer reaction. The double-proton-transfer reaction, however, turns out to be unfeasible when the system is protonated at these sites. Mutagenic implications of these proton-transfer processes are discussed.Proceedings of the 11th International Congress of Quantum Chemistry satellite meeting in honor of Jean-Louis Rivail     

Effects of Hydrogen Bonding on the Transition Properties of Ethanol–Water Clusters: A TD-DFT Study

In this work, time-dependent density functional theory method was used to study the electronic transitions of hydrogen-bonded ethanol–water complexes Dimer-I, Dimer-II and Trimer. The intermolecular hydrogen bonds H₁···O₁ and O···H₂ were demonstrated by the optimized geometric structures of the three hydrogen-bonded ethanol–water complexes. It is demonstrated that the S₁-state electronic transitions for ethanol monomer and the hydrogen-bonded complex Dimer-I (through HB-I) should be of LE nature on the ethanol molecule, while those of complexes Dimer-II and Trimer should be of CT character from the hydrogen-bonded water molecule (through HB-II) to the ethanol moiety. The different electronic transition types should be the reasons for the tiny redshift of the S₁-state electronic energy for Dimer-I and the large blueshifts for Dimer-II and the Trimer compared with that of the ethanol monomer.     

Theoretical Study on the Structures and Properties of Hydrogen Bonding Complexes between Diazines and Water

Density functional theory B3LYP method and second-order Moller-Plesset perturbation theory MP2 method were employed to obtain the optimized geometries of the ground state and interaction energy for diazines and water complexes. The results show that the ground state complexes have strong hydrogen bonding interaction with -20.99, -16.73 and -15.31 kJ/mol after basis set superposition error and zero-point vibration energy correction for pyridazine-water, pyrimidine-water and pyrazine-water, respectively, and large red-shift for the symmetric H-O stretching vibration frequencies due to the formation of N…H-O hydrogen bond in the diazine-water complexes. The NBO analysis indicates that intermolecular charge transfer are 0.0316, 0.0255 and 0.0265 e respectively. In addition, the first singlet （n,n＊） vertical excitation energy of the monomer and the hydrogen bonding complexes between diazines and water was investigated by time-dependent density functional theory.     

Silver(I) Coordination in Silver(I)-Mediated Homo Base Pairs of 6-Pyrazolylpurine in DNA Duplexes Involves the Watson–Crick Edge

DNA duplexes comprising 6-(1H-pyrazol-1-yl)-9H-purine (6PP), 1-deaza-6PP (^1D6PP), 7-deaza-6PP (^7D6PP) and 1,7-dideaza-6PP (^1,7D6PP) 2′-deoxyribonucleosides, respectively, were investigated towards their ability to form metal-mediated base pairs in the presence of Ag^I. In 6PP and ^7D6PP, the Ag^I ion can coordinate to the nucleobase via the endocyclic N1 nitrogen atom, that is, via the Watson–Crick edge. In contrast, this nitrogen atom is not available in ^1D6PP and ^1,7D6PP, so that in ^1D6PP an Ag^I coordination is only possible via the Hoogsteen edge (N7). Reference duplexes with either adenine:adenine mispairs or canonical adenine:thymine base pairs were used to investigate the impact of the pyrazolyl moiety on the Ag^I-binding properties. To determine the thermal and structural duplex stabilities in the absence or presence of Ag^I, all duplexes were examined by UV and circular dichroism spectroscopic studies. These investigations shed light on the question of whether N1- or N7-coordination is preferred in purine-based metal-mediated base pairs.     

A Theoretical Study on the Hydrogen—bonded Dimers of HNCO Molecules

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Theoretical ab Initio Study on Cooperativity Effects between Nitro π-hole and Halogen Bonding Interactions

This article analyzes the interplay between nitro's π-hole and halogen–bonding (XB) interactions in nitroarenes. Remarkable cooperativity effects are observed when π–hole and XB interactions coexist in the same complex. The nitroarene presents two π-holes, one approximately over the N atom of the nitro group and the other over the aromatic ring, being the former more positive. The interplay between both interactions has been analyzed in terms of energetic and geometric features of the complexes, which are computed at the RI-MP2/def2-TZVPD level of theory. Molecular electrostatic potential (MEP) surface calculations have been used to explore the variation of the MEP values at the π-hole upon the formation of halogen bonding interactions between the nitroarene and CF₃X (X=Cl, Br and I) molecules. In addition, the Bader's theory of atoms in molecules” (AIM) is used to characterize the interactions by means of the distribution of bond critical points and bond paths and to analyze their strengthening or weakening depending upon the variation of charge density at critical points. The aforementioned computational methods are adequate to examine how these interactions mutually influence each other. Natural bond orbital (NBO) and noncovalent interaction plot (NCIPlot) computational tools have been also used in some representative complexes to further analyze cooperativity effects. Finally, the Cambridge Structural Database (CSD) is used to provide some experimental evidence.     

Substituent Effects on the Hydrogen Bonding between 4-Substituted Phenols and HF, H2O, NH3

Density function theory UB3LYP/6-31 g(d) calculations were performed to study the hydrogen bonds between para-substituted phenols and HF, H2O, or NH3. It revealed that many properties of the non-covalent complexes, such as the interaction energies, donor-acceptor distances, bond lengths and vibration frequencies, showed well-defined substituent effects. Therefore, from the substituent effects not only the mechanism of a certain non-covalent interaction can be better understood, but also the interaction energies and structures of a certain non-covalent complex, which otherwise might be very hard or resource-consuming to estimate, can be easily predicted.     

5-Aza-7-deazaguanine–Isoguanine and Guanine–Isoguanine Base Pairs in Watson–Crick DNA: The Impact of Purine Tracts,Clickable Dendritic Side Chains,and Pyrene Adducts

The Watson–Crick coding system depends on the molecular recognition of complementary purine and pyrimidine bases. Now, the construction of hybrid DNAs with Watson–Crick and purine–purine base pairs decorated with dendritic side chains was performed. Oligonucleotides with single and multiple incorporations of 5-aza-7-deaza-2′-deoxyguanosine, its tripropargylamine derivative, and 2′-deoxyisoguanosine were synthesized. Duplex stability decreased if single modified purine–purine base pairs were inserted, but increased if pyrene residues were introduced by click chemistry. A growing number of consecutive 5-aza-7-deazaguanine–isoguanine base pairs led to strong stepwise duplex stabilization, a phenomenon not observed for the guanine–isoguanine base pair. Spacious residues are well accommodated in the large groove of purine–purine DNA tracts. Changes to the global helical structure monitored by circular dichroism spectroscopy show the impact of functionalization to the global double-helix structure. This study explores new areas of molecular recognition realized by purine base pairs that are complementary in hydrogen bonding, but not in size, relative to canonical pairs.     

Time-Dependent Density Functional Theory Study on Hydrogen and Dihydrogen Bonding in Electronically Excited State of 2-Pyridone–Borane–Trimethylamine Cluster

In this work, the intermolecular dihydrogen and hydrogen bonding interactions in electronically excited states of a 2-pyridone (2PY)–borane–trimethylamine (BTMA) cluster have been theoretically studied using time-dependent density functional theory method. Our computational results show that the S₁ state of 2PY–BTMA cluster is a locally excited state, in which only 2PY moiety is electronically excited. The theoretical infrared (IR) spectra of the 2PY–BTMA cluster demonstrate that the N–H stretching vibrational mode is slightly blue-shifted upon the electronic excitation. Moreover, the computed IR spectrum of the 2PY–BTMA cluster exhibits no carbonyl character due to the extension of the C=O bond length in the S₁ state. However, the N–H bond is shortened slightly upon photoexcitation. At the same time, the H···H and H···O distances are obviously lengthened in the S₁ sate by comparison with those in ground state. In addition, the electron density of the carbonyl oxygen is diminished due to the electronic excitation. Consequently, the proton acceptor ability of carbonyl oxygen is decreased in the electronic excited state. As a result, it is demonstrated that the intermolecular dihydrogen and hydrogen bonds are significantly weakened in the electronically excited state.     

Watson–Crick versus imidazopyridopyrimidine base pairs: theoretical study on differences in stability and hydrogen bonding strength

Matsuda and coworkers demonstrated that imidazopyridopyrimidine nucelobases (N ^N , O ^O , N ^O , tO ^O , and O ^N ) can mimic Watson–Crick nucleobase in forming H-bonds in DNA double helix. In the present study, we address the question about the strengths of the H-bonds in imidazopyridopyrimidine base pairs compared to those in Watson–Crick ones by focusing particularly on the nature of these interactions. Optimized structures of imidazopyridopyrimidine, imidazopyridopyrimidine–Watson–Crick, and Watson–Crick base pairs are obtained at the DFTB3LYP/6-311++G (d,p). The nature and strength of the intramolecular H-bonds in these base pairs have been investigated based on natural bond orbital (NBO method) to consider the effect of charge transfer, “atoms-in-molecules” (AIM) topological parameters, and decomposition of the interaction energies using the energy decomposition analysis (EDA). These investigations imply that N ^N –O ^O and N ^O –O ^N can form base pairs with four H-bonds (most stable than those of Watson–Crick base pairs) when they incorporated into DNA double helix. Furthermore, it can be deduced that O ^N and N ^N nucleobases form energetically more favorable pairs with adenine and guanine than the normal Watson–Crick counter parts. These results can be helpful for the stabilization and regulation of a variety of new base-pairing motif of DNA structures.     

A Theoretical Study on the Mechanism of Iodine-Photocatalyzed cis–transIsomerization of Stilbene

Based on nonempirical quantum-chemical calculations, the mechanism of iodine-photocatalyzed cis–transisomerization of stilbene was detailed. The formation of the complex of atomic iodine with a stilbene molecule was found to be an essential intermediate step that had been ignored in the earlier considerations. According to the calculation results, the rate-limiting step of the process is the transition from the complex to the 1,2-diphenyl-2-iodoethyl radical.     

Hydrogen Bonding Interaction of Formic Acid-, Formaldehyde-, Formylfluoride-Nitrosyl Hydride： Theoretical Study on the Geometries, Interaction Energies and Blue- or Red-Shifted Hydrogen Bonds

The hydrogen bonding interaction of formic acid-, formaldehyde-, formylfluoride-nitrosyl hydride complexes was investigated by the density functional theory （DFT） and ab inito method in conjunction with 6-311＋＋G（2d,2p） basis set. The geometries, vibrational frequencies and interaction energies of the complexes were calculated by both standard and CP-corrected methods respectively. Moreover, G3B3 method was employed to estimate the interaction energies. There are C--H…O, N--H…O, N--H…F blue-shifted H-bonds and red-shifted O----H…O H-bond in the complexes. Electron density redistribution and rehybridization contribute to the N--H and C--H blue shifts. All geometric reorganizations contribute to the N--H blue shifts and partial geometric reorganizations contribute to the C--H blue shifts. The geometric reorganizations of the complex C except ZH（5）-O（4）-C（1） contribute to the O----H red shift. For the N--H blue shifts, the effect of r（N--O） variation on the N--H blue shifts is larger than that of ZH-N-O variation. Rehybridization plays a dominant role in the degree of N--H blue shifts, whereas the electron density redistribution contributes more to the degree of C--H blue shifts than the other effects do.     

Extended Peptide Nucleic Acid Nucleobases Based on Isoorotic Acid for the Recognition of A–U Base Pairs in Double-Stranded RNA

Peptide nucleic acids (PNA) with extended isoorotamide containing nucleobases ( I _o ) were designed for binding A–U base pairs in double-stranded RNA. Isothermal titration calorimetry and UV thermal melting experiments revealed improved affinity for A–U using the Io scaffold in PNA. PNAs having four sequential Io extended nucleobases maintained high binding affinity.     

A DFT Study on Intramolecular Hydrogen Bond in Substituted Catechols and Their Radicals

Density functional theory(DFT)at B3LYP/6-31G(d,p) level was employed to calculate intramolecular hydrogen bond enthalpies (H1HB),O-H charge differencces,O-H bond lengths and bond orders for various substituted catechols and their radicals generated after H-abstraction.It was found that although the charge difference between hydrogen-bonded H and O played a role in determining H1HB,H1HB was mainly governed by the hydrogen bond length.As the oxygen-centedred radiocal has great tendency to form a chemical bond with the H atom,hydrogen bond lengths in catechloic radicals are systematically shorter than those in catechlos,hence,the H1HB for the former are higher than those for the latter.     

Theoretical Study of Interaction between Hydrogen and Small Pt–Sn Intermetallic Clusters

Small clusters, which simulate the active sites of Pt–Sn intermetallics exhibiting a high level of activity and selectivity in the deoxygenation reaction of esters without the loss of carbon mass to form C₁, C₂, and carbon oxides, are constructed and studied with the density functional theory. Molecular adsorption of hydrogen, dissociation of hydrogen molecules at Pt sites, and transition of adsorbed hydrogen atoms from Pt to Sn are considered. The introduction of Sn significantly decreases the affinity of platinum to hydrogen, so that the transition of H atoms to Sn atoms is facilitated with the increase in the amount of Sn. A comparison of the activation energies for such a transition with those of the possible association of hydrogen atoms on tin and the molecular desorption of H₂ showed that the hydrogen spillover in the Pt–Sn intermetallics should not lead to a significant accumulation of hydrogen on tin. In other words, in contrast to Pt atoms, Sn atoms probably cannot serve as active sites of hydrogen adsorption in the deoxygenation reaction.     

Quantum Study on the Hydrogen Bonding Interaction of Luteolin-（CH_3OH）_n

The optimized geometries and vibration frequencies of luteolin,methanol and luteolin-(CH3OH)n complexes have been investigated by density functional theory using B3LYP method.Four stable luteolin-CH3OH complexes,six stable luteolin-(CH3OH)2 complexes and four stable luteolin-(CH3OH)3 complexes have been obtained.The theories of atoms in molecules(AIM) and natural bond orbital(NBO) have been used to analyze the hydrogen bonds of these compounds,and their interaction energies corrected by basis set superposition error are between-8.046 and-76.124 kJ/mol.The calculation results indicate strong hydrogen bonding interactions in the luteolin-(CH3OH)n complexes.Then the nuclear magnetic resonance(NMR) and electronic absorption spectrum of luteolin have been calculated,and the results are in agreement with the experimental data.     

Substituent Effects in π-Hole Regium Bonding Interactions Between Au(p-X-Py)2 Complexes and Lewis Bases: An ab initio Study

Long range substituent effects in regium bonding interactions involving Au(I) linear complexes are investigated for the first time. The Au(I) atom is coordinated to two para-substituted pyridine ligands. The interaction energy (RI-MP2/def2-TZVP level of theory) of the π-hole regium bonding assemblies is affected by the pyridine substitution. The Hammett's plot representations for several sets of Lewis bases have been carried out and, in all cases, good regression plots have been obtained (interaction energies vs. Hammett's σ parameter). The Bader's theory of “atoms-in-molecules” has been used to evidence that the electron density computed at the bond critical point that connects the Au-atom to the electron donor can be used as a measure of bond order in regium bonding. Several X-ray structures retrieved from the Cambridge Structural Database (CSD) provide experimental support to the existence of π-hole regium bonding in [Au(Py)₂]⁺ derivatives.     

Theoretical Study of Remote Substituent Effects on X-H （X=CH2, NH,O） Bond Dissociation Energies of Azulene

In the study, the X-H （X=CH2, NH, O） bond dissociation energies （BDE） of para-substituted azulene （Y-C10H8X-H） were predicted theoretically for the first time using Density Functronal Theory （DFT） methods at UB3LYP/6-311 ＋ ＋g（2df,2p）//UB3LYP/6-31 ＋g（d） level. It was found that the substituents exerted similar effects on the X-H BDE of azulene as those on benzene, except for 6-substituted 2-methylazulene. Owing to the substituent-dipole interaction, the reaction constants （ρ^＋） of 2- and 6-Y-CIoHsX-H （X=NH and O only） varied violently. The origin of the substituent effects on the X-H BDE of azulene was found, by both GE/RE and SIE theory, to be directly associated with variation of the radical effects, although the ground effects also played a modest role in determining the net. substituent effects.     

The damage of the Watson–Crick base pairs by nickel nanoparticles: A first-principles molecular dynamics study

The nickel nanoparticles are harmful atmospheric pollutants, and the damage caused by them in humans has become a topic of great relevance. In this study we investigate the interaction of the Ni₂ and Ni₃ clusters with the AT and GC Watson–Crick base pairs in an aqueous medium. Molecular dynamics in combination with density functional theory are employed. A novel method is implemented to create realistic thermodynamic conditions (NVT) in the simulations. The energies, the charges of the interacting compounds, the temperature changes, and the geometric rearrangements are reported. The results show the formation of stable organometallic compounds of the nickel nanoparticles with the DNA nucleic acid bases. In this respect, the biological processes where the DNA is implicated may be altered by the formation of such super-structures.     

Substituent Effects on 31P NMR Chemical Shifts and 1JP–Se of triarylselenophosphates

The effect of electron-withdrawing (EW) and electron-releasing (ER) substituents on the ³¹P NMR chemical shifts and the structural parameters of a series of tris-(p-X-aryl)selenophosphates is reported in this article. Similarly to O-aryl phosphates and O-aryl thiophosphates, EW groups attached to aromatic rings induce a shielding effect on the ³¹P NMR signal. After a detailed experimental and theoretical analysis, we confirmed that the selenium atom is the main part responsible for the charge density transfer toward phosphorus through a back-bonding effect. The obtained ¹J_P-Se values for the complete series agree with this observation.

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