pKaValues of Guanine in Water: Density Functional Theory Calculations Combined with Poisson−Boltzmann Continuum−Solvation Model

Quantum chemical package Jaguar: A survey of recent developments and unique features

This paper is dedicated to the quantum chemical package Jaguar, which is commercial software developed and distributed by Schrödinger, Inc. We discuss Jaguar's scientific features that are relevant to chemical research as well as describe those aspects of the program that are pertinent to the user interface, the organization of the computer code, and its maintenance and testing. Among the scientific topics that feature prominently in this paper are the quantum chemical methods grounded in the pseudospectral approach. A number of multistep workflows dependent on Jaguar are covered: prediction of protonation equilibria in aqueous solutions (particularly calculations of tautomeric stability and pKa), reactivity predictions based on automated transition state search, assembly of Boltzmann-averaged spectra such as vibrational and electronic circular dichroism, as well as nuclear magnetic resonance. Discussed also are quantum chemical calculations that are oriented toward materials science applications, in particular, prediction of properties of optoelectronic materials and organic semiconductors, and molecular catalyst design. The topic of treatment of conformations inevitably comes up in real world research projects and is considered as part of all the workflows mentioned above. In addition, we examine the role of machine learning methods in quantum chemical calculations performed by Jaguar, from auxiliary functions that return the approximate calculation runtime in a user interface, to prediction of actual molecular properties. The current work is second in a series of reviews of Jaguar, the first having been published more than ten years ago. Thus, this paper serves as a rare milestone on the path that is being traversed by Jaguar's development in more than thirty years of its existence.

Snapshots of the Reaction Coordinate of a Thermophilic 2'-Deoxyribonucleoside/ribonucleoside Transferase

Nucleosides are ubiquitous to life and are required for the synthesis of DNA, RNA, and other molecules crucial for cell survival. Despite the notoriously difficult organic synthesis of nucleosides, 2'-deoxynucleoside analogues can interfere with natural DNA replication and repair and are successfully employed as anticancer, antiviral, and antimicrobial compounds. Nucleoside 2'-deoxyribosyltransferase (dNDT) enzymes catalyze transglycosylation via a covalent 2'-deoxyribosylated enzyme intermediate with retention of configuration, having applications in the biocatalytic synthesis of 2'-deoxynucleoside analogues in a single step. Here, we characterize the structure and function of a thermophilic dNDT, the protein from Chroococcidiopsis thermalis (CtNDT). We combined enzyme kinetics with structural and biophysical studies to dissect mechanistic features in the reaction coordinate, leading to product formation. Bell-shaped pH-rate profiles demonstrate activity in a broad pH range of 5.5-9.5, with two very distinct pKa values. A pronounced viscosity effect on the turnover rate indicates a diffusional step, likely product (nucleobase1) release, to be rate-limiting. Temperature studies revealed an extremely curved profile, suggesting a large negative activation heat capacity. We trapped a 2'-fluoro-2'-deoxyarabinosyl-enzyme intermediate by mass spectrometry and determined high-resolution structures of the protein in its unliganded, substrate-bound, ribosylated, 2'-difluoro-2'-deoxyribosylated, and in complex with probable transition-state analogues. We reveal key features underlying (2'-deoxy)ribonucleoside selection, as CtNDT can also use ribonucleosides as substrates, albeit with a lower efficiency. Ribonucleosides are the building blocks of RNA and other key intracellular metabolites participating in energy and metabolism, expanding the scope of use of CtNDT in biocatalysis.

Ultrafast Vibrational Wave Packet Dynamics of the Aqueous Guanine Radical Anion Induced by Photodetachment

Studying the ultrafast dynamics of ionized aqueous biomolecules is important for gaining an understanding of the interaction of ionizing radiation with biological matter. Guanine plays an essential role in biological systems as one of the four nucleobases that form the building blocks of deoxyribonucleic acid (DNA). Guanine radicals can induce oxidative damage to DNA, particularly due to the lower ionization potential of guanine compared to the other nucleobases, sugars, and phosphate groups that are constituents of DNA. This study utilizes femtosecond optical pump-probe spectroscopy to observe the ultrafast vibrational wave packet dynamics of the guanine radical anion launched by photodetachment of the aqueous guanine dianion. The vibrational wave packet motion is resolved into 11 vibrational modes along which structural reorganization occurs upon photodetachment. These vibrational modes are assigned with the aid of density functional theory (DFT) calculations. Our work sheds light on the ultrafast vibrational dynamics following the ionization of nucleobases in an aqueous medium.

Comparative Analysis of pH and Target-Induced Conformational Changes of an Oxytetracycline Aptamer in Solution Phase and Surface-Immobilized Form

To date, numerous aptamer-based biosensing platforms have been developed for sensitive and selective monitoring of target analytes, relying on analyte-induced conformational changes in the aptamer for the quantification of the analyte and the conversion of the binding event into a measurable signal. Despite the impact of these conformational rearrangements on sensor performance, the influence of the environment on the structural conformations of aptamers has rarely been investigated, so the link between parameters directly influencing aptamer folding and the ability of the aptamer to bind to the target analyte remains elusive. Herein, the effect a number of variables have on an aptamer's 3D structure was examined, including the pH of the buffering medium, as well as the anchoring of the aptamer on a solid support, with the use of two label-free techniques. Circular dichroism spectroscopy was utilized to study the conformation of an aptamer in solution along with any changes induced to it by the environment (analyte binding, pH, composition and ionic strength of the buffer solution), while quartz crystal microbalance with dissipation monitoring was employed to investigate the surface-bound aptamer's behavior and performance. Analysis was performed on an aptamer against oxytetracycline, serving as a model system, representative of aptamers selected against small molecule analytes. The obtained results highlight the influence of the environment on the folding and thus analyte-binding capacity of an aptamer and emphasize the need to deploy appropriate surface functionalization protocols in sensor development as a means to minimize the steric obstructions and undesirable interactions of an aptamer with a surface onto which it is tethered.

Development of a New Route for the Immobilization of Unmodified Single-Stranded DNA on Chitosan Beads and Detection of Released Guanine after Hydrolysis

In this work, chitosan beads were used as a cost-effective platform for the covalent immobilization of unmodified single-stranded DNA, using glutaraldehyde as a cross-linking agent. The immobilized DNA capture probe was hybridized in the presence of miRNA-222 as a complementary sequence. The target was evaluated based on the electrochemical response of the released guanine, using hydrochloride acid as a hydrolysis agent. Differential pulse voltammetry technique and screen-printed electrodes modified with COOH-functionalized carbon black were used to monitor the released guanine response before and after hybridization. The functionalized carbon black provided an important signal amplification of guanine compared to the other studied nanomaterials. Under optimal conditions (6 M HCl at 65 °C for 90 min), an electrochemical-based label-free genosensor assay exhibited a linear range between 1 nM and 1 µM of miRNA-222, with a detection limit of 0.2 nM of miRNA-222. The developed sensor was successfully used to quantify miRNA-222 in a human serum sample.

Spectroscopic and Density Functional Studies on the Interaction of a Naphthalene Derivative with Anions

This article highlights the investigation of anion interactions and recognition abilities of naphthalene derivative, [(E)-1-(((4-nitrophenyl)imino)methyl)naphthalen-2-ol], (NIMO) by UV-visible spectroscopically and colorimetrically. NIMO shows selective recognition of F^- ions colorimetrically, and a visual color change from yellow to pink is observed by the naked eye. The F^- ions recognition is fully reversible in the presence of HSO₄^- ions. The limit of F^- ions detection by NIMO could be possible down to 0.033 ppm-level. A paper strips-based test kit has been demonstrated to detect F^- ions selectively by the naked eye, and a smartphone-based method for real sample analysis in the non-aqueous medium has also been demostrated. Spectroscopic behavior is well supported by pK_a value calculation and DFT analysis, to find a correlation with receptor analyte interaction. The optical response of NIMO towards the accumulation of F^- ions and, subsequently, HSO₄^- ions as chemical inputs provides an opportunity to construct INH and IMP molecular logic gates.

Acid-base and lipophilic properties of peptide nucleic acid derivatives

The first combined experimental and theoretical study on the ionization and lipophilic properties of peptide nucleic acid (PNA) derivatives, including eleven PNA monomers and two PNA decamers, is described. The acidity constants (pK_a) of individual acidic and basic centers of PNA monomers were measured by automated potentiometric pH titrations in water/methanol solution, and these values were found to be in agreement with those obtained by MoKa software. These results indicate that single nucleobases do not change their pK_a values when included in PNA monomers and oligomers. In addition, immobilized artificial membrane chromatography was employed to evaluate the lipophilic properties of PNA monomers and oligomers, which showed the PNA derivatives had poor affinity towards membrane phospholipids, and confirmed their scarce cell penetrating ability. Overall, our study not only is of potential relevance to evaluate the pharmacokinetic properties of PNA, but also constitutes a reliable basis to properly modify PNA to obtain mimics with enhanced cell penetration properties.

•

The first study on acid-base and lipophilic properties of peptide nucleic acids (PNA).

•

pK_a of acid-base centers of PNA evaluated by potentiometric method and MoKa prediction.

•

NMR experiments provide additional information on the protonation of PNA monomers.

•

Lipophilicity of PNA monomers and oligomers is investigated by IAM chromatography.

•

This study can lay the basis of evaluating the pharmacokinetic properties of PNA.

Investigation of tautomerism of 1,3,5-triazine derivative, stability, and acidity of its tautomers from density functional theory

Recent studies have identified N2,N4-bis(4-fluorophenethyl)-N6-(3-(dimethylamino)propyl)-1,3,5-triazine-2,4,6-triamine (1TZ(7,8,9)) as a potent, pure antagonist that inhibits thermosensory transient receptor potential vanilloid 1 channel (TRPV1) channel activity. This study provides theoretical data on the stability and acidity of the tautomers of this molecule. We show that this triazine can exist as three predominant tautomers (2TZ(5,7,8), 4TZ(3,7,9), 7TZ(1,8,9)). In the aqueous phase, equilibrium constants calculations show that only the tautomeric equilibria between 1TZ(7,8,9) and the three most stable triazines can be present which suggests that these three tautomeric equilibria would be the basis of 1TZ(7,8,9)'s biological activity.

Gold Nanoparticles as Colorimetric Sensors for the Detection of DNA Bases and Related Compounds

Results regarding interaction of colloidal gold solutions with nucleobases, including uracil (U), as well as its sulfur derivatives, 2-thiouracil (2TU) and 4-thiouracil (4TU), cytosine (C), adenine (A), and guanine (G), as well as urea and thiourea (TU), are reported. Anionic stabilized citrate gold nanoparticles (AuNPs) were synthesized by reducing the tetrachloroaurate (III) trihydrate with trisodium citrate. The surface plasmon resonance (SPR) band was used in the characterization of synthesized AuNPs, as well as transmission electron microscope (TEM) imaging, which was used in the characterization of dispersed and aggregated gold nanoparticles. Interactions of nucleobases with the gold surface was analyzed by following the plasmon absorbance band red shift of the AuNPs. The sulfur-containing compounds adsorbed to the nanoparticle surfaces by chemisorption-type interactions; with TU and 4TU, the process is accompanied by a sudden change in color; in contrast, 2TU forms stable functionalized gold nanoparticles. Urea and U do not adsorb to nanoparticle surfaces, but the other heterocyclic bases containing nitrogen interact effectively with the gold surface, causing the assembly of nanoparticles, even though the interparticle self-aggregation process was slower than that mediated by either TU or 4TU. The method is efficient in the colorimetric detection of nucleobases and derivatives at concentration levels on the order of 1 µM.

Fluorescence Detection of Deoxyadenosine in Cordyceps spp. by Indicator Displacement Assay

A rapid, sensitive and reliable indicator displacement assay (IDA) for specific detection of 2′- and 3′-deoxyadenosine (2′-dAde and 3′-dAde), the latter is also known as cordycepin, was established. The formation of inclusion complex between protonated acridine orange (AOH⁺) and cucurbit[7]uril (CB7) resulted in the hypochromic shift of fluorescent emission from 530 nm to 512 nm. Addition of cordycepin to the highly fluorescent AOH⁺/CB7 complex resulted in a unique tripartite AOH⁺/CB7/dAde complex with diminished fluorescence, and such reduction in emission intensity serves as the basis for our novel sensing system. The detection limits were 11 and 82 μM for 2′- and 3′-deoxyadenosine, respectively. The proposed method also demonstrated high selectivity toward 2′- and 3′-deoxyadenosine, owing to the inability of other deoxynucleosides, nucleosides and nucleotides commonly found in Cordyceps spp. to displace the AOH⁺ from the AOH⁺/CB7 complex, which was confirmed by isothermal titration calorimetry (ITC), UV-Visible and proton nuclear magnetic resonance (¹H-NMR) spectroscopy. Our method was successfully implemented in the analysis of cordycepin in commercially available Ophiocordyceps and Cordyceps supplements, providing a novel and effective tool for quality assessment of these precious fungi with several health benefits.

Why Purine Nucleoside Phosphorylase Ribosylates 2,6-Diamino-8-azapurine in Noncanonical Positions? A Molecular Modeling Study

Protein nucleoside phosphorylase (PNP) is an enzyme that catalyzes a reversible conversion process (ribosylation and phosphorolysis) between nucleobases (purines) and their nucleosides. Experimental studies showed that calf PNP ribosylates purine analogues in specific positions: 2,6-diamino-8-azapurine in position 7 or 8 and 8-azaguanine in position 9 of the triazole ring. The reason for this phenomenon can be a result of different expositions of purine substrates to the channel leading to the binding site. This hypothesis was verified by the application of molecular modeling techniques to two complexes of purine analogues 2,6-diamino-azapurine, calf PNP (pdb-code: 1LVU), and 8-azaguanine, calf PNP (pdb-code: 2AI1). The results obtained with a combination of quantum chemistry, docking, and molecular dynamics methods showed qualitative validity of our hypothesis. Binding free energies of protein-ligand systems showed that most probable binding poses expose N8 nitrogen for 2,6-diamino-8-azapurine and N9 nitrogen for 8-azaguanine into the binding channel and ruled out the exposition of N9 for 2,6-diamino-8-azapurine and N7 for 8-azaguanine, partially in agreement with the experimental data. The other important result obtained in this study is a significantly higher population of the protonated form of crucial residue Glu-201 present in the binding pocket, compared to the standard protonation of free glutamic acid in solution. This result combined with populations of tautomeric forms of both investigated systems strongly suggests that 2,6-diamino-8-azapurine and 8-azaguanine are recognized by proteins with deprotonated and protonated Glu-201 residues, respectively. A comparison of computed binding poses of the investigated ligands to the inhibitors present in crystal structures suggests that the modification of the (S)-PMPDAP inhibitor, in which a 2-(phosphonomethoxy)propyl chain is attached at position 8 instead of position 9, might increase its binding affinity.

Structural aspects of 4-aminoquinolines as reversible inhibitors of human acetylcholinesterase and butyrylcholinesterase

Eight derivatives of 4-aminoquinolines differing in the substituents attached to the C(4)-amino group and C(7) were synthesised and tested as inhibitors of human acetylcholinesterase (AChE) and butyrylcholinesterase (BChE). Both enzymes were inhibited by all of the compounds with inhibition constants (K_i) ranging from 0.50 to 50 μM exhibiting slight selectivity toward AChE over BChE. The most potent inhibitors of AChE were compounds with an n-octylamino chain or adamantyl group. The shortening of the chain length resulted in a decrease in AChE inhibition by 5-20 times. Docking studies revealed that the quinoline group within the AChE active site was positioned in the choline binding site, while the C(4)-amino group substituents, depending on their lipophilicity, could establish hydrogen bonds or π-interactions with residues of the peripheral anionic site. The most potent inhibitors of BChE were compounds with the most voluminous substituent on C(4)-amino group (adamantyl) or those with a stronger electron withdrawing substituent on C(7) (trifluormethyl group). Based on AChE inhibition, compounds with an n-octylamino chain or adamantyl substituent were shown to possess the capacity for further development as potential drugs for treatment of neurodegenerative diseases.

Predicting Mole-Fraction-Dependent Dissociation for Weak Acids

We demonstrate for formic and acetic acid dissolved in water as examples that the binary quantum cluster equilibrium (bQCE) approach can predict acid strengths over the whole range of acid concentrations. The acid strength increases in a complex rather than a simple way with increasing mole fraction of the acid from 0 to 0.7, reflecting the complex interplay between the dissociated ions or conjugate bases available as compared to the acid and water molecules. Furthermore, our calculated ion concentrations meet the experimental maximum of the conductivity with excellent agreement for acetic acid and satisfactorily for the formic acid/water mixture. As only a limited number of simple quantum-chemical calculations are required for the prediction, bQCE is clearly a valuable approach to access these quantities also in non-aqueous solutions. It is a highly valuable asset for predicting ionization processes in highly concentrated solutions, which are relevant for biological and chemical systems, as well as technological processes.

Direct observation of the oxidation of DNA bases by phosphate radicals formed under radiation: a model of the backbone-to-base hole transfer

In irradiated DNA, by the base-to-base and backbone-to-base hole transfer processes, the hole (i.e., the unpaired spin) localizes on the most electropositive base, guanine. Phosphate radicals formed via ionization events in the DNA-backbone must play an important role in the backbone-to-base hole transfer process. However, earlier studies on irradiated hydrated DNA, on irradiated DNA-models in frozen aqueous solution and in neat dimethyl phosphate showed the formation of carbon-centered radicals and not phosphate radicals. Therefore, to model the backbone-to-base hole transfer process, we report picosecond pulse radiolysis studies of the reactions between H2PO4˙ with the DNA bases - G, A, T, and C in 6 M H3PO4 at 22 °C. The time-resolved observations show that in 6 M H3PO4, H2PO4˙ causes the one-electron oxidation of adenine, guanine and thymine, by forming the cation radicals via a single electron transfer (SET) process; however, the rate constant of the reaction of H2PO4˙ with cytosine is too low (<107 L mol-1 s-1) to be measured. The rates of these reactions are influenced by the protonation states and the reorganization energies of the base radicals and of the phosphate radical in 6 M H3PO4.

Ganciclovir

Ganciclovir is synthetic nucleoside analog of guanine closely related to acyclovir but has greater activity against cytomegalovirus. This comprehensive profile on ganciclovir starts with a description of the drug: nomenclature, formulae, chemical structure, elemental composition, and appearance. The uses and application of the drug are explained. The methods that were used for the preparation of ganciclovir are described and their respective schemes are outlined. The methods which were used for the physical characterization of the dug are: ionization constant, solubility, X-ray powder diffraction pattern, crystal structure, melting point, and differential scanning calorimetry. The chapter contains the spectra of the drug: ultraviolet spectrum, vibrational spectrum, nuclear magnetic resonance spectra, and the mass spectrum. The compendial methods of analysis of ganciclovir include the United States Pharmacopeia methods. Other methods of analysis that were reported in the literature include: high-performance liquid chromatography alone or with mass spectrometry, electrophoresis, spectrophotometry, voltammetry, chemiluminescence, and radioimmunoassay. Biological investigation on the drug includes: pharmacokinetics, metabolism, bioavailability, and biological analysis. Reviews on the methods used for preparation or for analysis of the drug are provided. The stability of the drug in various media and storage conditions is reported. More than 240 references are listed at the end of the chapter.

Theoretical study of gas and solvent phase stability and molecular adsorption of noncanonical guanine bases on graphene

The gas and solvent phase stability of noncanonical (Gua)_n nucleobases is investigated in the framework of dispersion-corrected density functional theory (DFT). The calculated results strongly support the high tendency for the dimerization of (Gua)_n bases in both gas and solvent phases. An interplay between intermolecular and bifurcated H-bonds is suggested to govern the stability of (Gua)_n bases which bears a correlation with the description of dispersion correction terms employed in the DFT calculations. For example, a higher polarity is predicted for (Gua)_n bases by the dispersion-corrected DFT in contrast to the non-polar nature of (Gua)₃ and (Gua)₄ predicted by the hybrid meta-GGA calculations. This distinct variation becomes significant under physiological conditions as polar (Gua)_n is likely to exhibit greater stabilization in the gas phase compared to solvated (Gua)_n. Graphene acting as a substrate induces modification in base configurations via maximization of π-orbital overlap between the base and substrate. In solvent, the substrate-induced effects are further heightened with lowering of the dipole moments of (Gua)_n as also displayed by the corresponding isosurface of the electrostatic potential. The graphene-induced stability in both gas and solvent phases appears to fulfill one of the prerequisite criteria for molecular self-assembly. The DFT results therefore provide atomistic insights into the stability and molecular assembly of free-standing noncanonical (Gua)_n nucleobases which can be extended to understanding the self-assembly process of functional biomolecules on 2D materials for potential biosensing applications.

Insights into the effect of minor groove interactions and metal cofactors on mutagenic replication by human DNA polymerase β

DNA polymerases accommodate various base-pair conformations in the event of incorrect insertions. In particular, Watson-Crick-like dG:dTTP base pair has been observed at the insertion site of human DNA polymerase β (pol β). A potential factor contributing to the diverse conformations of base-pair mismatches is minor groove interactions. To gain insights into the effect of minor groove interactions on base-pair conformations, we generated an Asn279Ala polβ mutant that cannot make minor groove contacts with an incoming nucleotide. We conducted structural and kinetic studies of Asn279Ala polβ in complex with incoming dTTP and templating dG or O6-methyl-dG. The crystal structure of the Asn279Ala polβ-G:T complex showed a wobble dG:dTTP base pair, indicating that the previously observed Watson-Crick-like dG:dTTP conformation was induced by the minor groove contact. In contrast, O6-methyl-dG, an analog of the enol tautomer of guanine, formed a Watson-Crick-like base pair with dTTP in the absence of the minor groove contact. These results suggest that the Watson-Crick-like G:T base pair at the insertion site is formed by the rare enol tautomers of G or T, whose population is increased by the minor groove hydrogen bond with Asn279. Kinetic studies showed that Asn279Ala mutation decreased dG:dTTP misincorporation rate six-fold in the presence of Mg²⁺ but increased the rate three-fold in the presence of Mn²⁺, highlighting the effect of minor groove interactions and metal ions on promutagenic replication by polβ.

Weighted Averaging Scheme and Local Atomic Descriptor for pKa Prediction Based on Density Functional Theory

As a continuation of our work on developing a density functional theory-based pK_a predictor, we present conceptual improvements to our previously published shell model, which is a hierarchical organization of pK_a training sets and which, in principle, covers all chemical space. The improvements concern the way the studied chemical compound is associated with the data points from the training sets. By introducing a new descriptor of the local atomic environment which foregoes dependence on chemical bonding and connectivity, we are able to automatically locate molecules from the training set that are most relevant to the proton dissociation equilibrium under study. This new scheme leads to the prediction of a single pK_a value weighted across multiple training sets and thus patches a defect disclosed in the formulation of our previous model. Using the new parametrization approach, the pK_a prediction gets rid of outliers reported in previous applications of our approach, eliminates ambiguity in interpreting the results, and improves the overall accuracy. Our new treatment accounts for multiple conformations both on the level of energetics and parametrization. Illustrative results are shown for several types of chemical structures containing guanidine, amidine, amine, and phenol functional groups, and which are representative of practically important large and flexible drug-like molecules. Our method's performance is compared to the performance of other previously published pK_a prediction methods. Further possible improvements to the organization of the training sets and the potential application of our new local atomic descriptor to other kinds of parametrizations are discussed.

Deprotonated guanine·cytosine and 9-methylguanine·cytosine base pairs and their "non-statistical" kinetics: a combined guided-ion beam and computational study

We report a guided-ion beam mass spectrometric study on collision-induced dissociation (CID) of deprotonated guanine(G)·cytosine(C) base pairs and their 9-methylguanine (9MG) analogue with Xe, including measurements of product cross sections as a function of collision energy and determination of dissociation thresholds. DFT, RI-MP2 and DLPNO-CCSD(T) calculations and Rice-Ramsperger-Kassel-Marcus (RRKM) modeling were performed to elucidate structures and kinetics. The experiment and theoretical study have provided considerable insight into tautomerization, intra-base-pair proton transfer and dissociation of deprotonated G·C and 9MG·C. In contrast to the previously reported lowest-energy deprotonated base pair structure G·[C-H1]^- that consists of H-bonded neutral guanine and N1-deprotonated cytosine, we found that proton transfer from guanine N1 to cytosine N3 within G·[C-H1]^- (or 9MG·[C-H1]^-) leads to another slightly more stable conformer denoted as G·[C-H1]^-_PT1 (or 9MG·[C-H1]^-_PT1). The conventional (non-proton-transferred) and the proton-transferred conformers are close in energy and interconvert quickly, but they can be distinguished by dissociation products. The conventional structure dissociates into deprotonated cytosine and neutral guanine, while the other dissociates into deprotonated guanine and neutral cytosine. The two dissociation asymptotes have similar threshold energies, but surprisingly the CID product mass spectra of deprotonated G·C and 9MG·C are both overwhelmingly dominated by deprotonated G or 9MG, with their branching ratios greater than RRKM predictions by one to two orders of magnitude. The proton-transferred structures of deprotonated base pairs and the "unexpected" non-statistical kinetics provide new leads for understanding purine-pyrimidine interactions, forming rare nucleobase tautomers, and base pair opening.

N-Fluoro functionalization of heterocyclic azoles: a new strategy towards insensitive high energy density materials

The finding of this study shows the introduction of a highly dense –F group instead of hydrogen atoms by N-functionalization, which is a very effective method for increasing the densities and detonation properties and decreasing the sensitivities of energetic molecules.

Reactivity of prehydrated electrons toward nucleobases and nucleotides in aqueous solution

DNA damage induced via dissociative attachment by low-energy electrons (0 to 20 eV) is well studied in both gas and condensed phases. However, the reactivity of ultrashort-lived prehydrated electrons ([Formula: see text]) with DNA components in a biologically relevant environment has not been fully explored to date. The electron transfer processes of [Formula: see text] to the DNA nucleobases G, A, C, and T and to nucleosides/nucleotides were investigated by using 7-ps electron pulse radiolysis coupled with pump-probe transient absorption spectroscopy in aqueous solutions. In contrast to previous results, obtained by using femtosecond laser pump-probe spectroscopy, we show that G and A cannot scavenge [Formula: see text] at concentrations of ≤50 mM. Observation of a substantial decrease of the initial yield of hydrated electrons ([Formula: see text]) and formation of nucleobase/nucleotide anion radicals at increasing nucleobase/nucleotide concentrations present direct evidence for the earliest step in reductive DNA damage by ionizing radiation. Our results show that [Formula: see text] is more reactive with pyrimidine than purine nucleobases/nucleotides with a reactivity order of T > C > A > G. In addition, analyses of transient signals show that the signal due to formation of the resulting anion radical directly correlates with the loss of the initial [Formula: see text] signal. Therefore, our results do not agree with the previously proposed dissociation of transient negative ions in nucleobase/nucleotide solutions within the timescale of these experiments. Moreover, in a molecularly crowded medium (for example, in the presence of 6 M phosphate), the scavenging efficiency of [Formula: see text] by G is significantly enhanced. This finding implies that reductive DNA damage by ionizing radiation depends on the microenvironment around [Formula: see text].

DNA Polymerase λ Active Site Favors a Mutagenic Mispair between the Enol Form of Deoxyguanosine Triphosphate Substrate and the Keto Form of Thymidine Template: A Free Energy Perturbation Study

Human DNA polymerase λ is an intermediate fidelity member of the X family, which plays a role in DNA repair. Recent X-ray diffraction structures of a ternary complex of a loop-deletion mutant of polymerase λ, a deoxyguanosine triphosphate analogue, and a gapped DNA show that guanine and thymine form a mutagenic mispair with an unexpected Watson-Crick-like geometry rather than a wobble geometry. Hence, there is an intriguing possibility that either thymine in the DNA or guanine in the deoxyguanosine triphosphate analogue may spend a substantial fraction of time in a deprotonated or enol form (both are minor species in aqueous solution) in the active site of the polymerase λ mutant. The experiments do not determine particular forms of the nucleobases that contribute to this mutagenic mispair. Thus, we investigate the thermodynamics of formation of various mispairs between guanine and thymine in the ternary complex at a neutral pH using classical molecular dynamics simulations and the free energy perturbation method. Our free energy calculations, as well as a comparison of the experimental and computed structures of mispairs, indicate that the Watson-Crick-like mispair between the enol tautomer of guanine and the keto tautomer of thymine is dominant. The wobble mispair between the keto forms of guanine and thymine and the Watson-Crick-like mispair between the keto tautomer of guanine and the enol tautomer of thymine are less prevalent, and mispairs that involve deprotonated guanine or thymine are thermodynamically unlikely. These findings are consistent with the experiment and relevant for understanding mechanisms of spontaneous mutagenesis.

Tautomeric equilibria of isoguanine and related purine analogs

Nucleobase pairs in DNA match hydrogen-bond donor and acceptor groups on the nucleobases. However, these can adopt more than one tautomeric form, and can consequently pair with nucleobases other than their canonical complements, possibly a source of natural mutation. These issues are now being re-visited by synthetic biologists increasing the number of replicable pairs in DNA by exploiting unnatural hydrogen bonding patterns, where tautomerism can also create mutation. Here, we combine spectroscopic measurements on methylated analogs of isoguanine tautomers and tautomeric mixtures with statistical analyses to a set of isoguanine analogs, the complement of isocytosine, the 5th and 6th "letters" in DNA.

Formation mechanism of glyoxal-DNA adduct, a DNA cross-link precursor

DNA nucleobases undergo non-enzymatic glycation to nucleobase adducts which can play important roles in vivo. In this work, we conducted a comprehensive experimental and theoretical kinetic study of the mechanisms of formation of glyoxal-guanine adducts over a wide pH range in order to elucidate the molecular basis for the glycation process. Also, we performed molecular dynamics simulations to investigate how open or cyclic glyoxal-guanine adducts can cause structural changes in an oligonucleotide model. A thermodynamic study of other glycating agents including methylglyoxal, acrolein, crotonaldehyde, 4-hydroxynonenal and 3-deoxyglucosone revealed that, at neutral pH, cyclic adducts were more stable than open adducts; at basic pH, however, the open adducts of 3-deoxyglucosone, methylglyoxal and glyoxal were more stable than their cyclic counterparts. This result can be ascribed to the ability of the adducts to cross-link DNA. The new insights may contribute to improve our understanding of the connection between glycation and DNA cross-linking.

A method for predicting individual residue contributions to enzyme specificity and binding-site energies, and its application to MTH1

A new method for predicting the energy contributions to substrate binding and to specificity has been developed. Conventional global optimization methods do not permit the subtle effects responsible for these properties to be modeled with sufficient precision to allow confidence to be placed in the results, but by making simple alterations to the model, the precisions of the various energies involved can be improved from about ±2 kcal mol⁻¹ to ±0.1 kcal mol⁻¹. This technique was applied to the oxidized nucleotide pyrophosphohydrolase enzyme MTH1. MTH1 is unusual in that the binding and reaction sites are well separated—an advantage from a computational chemistry perspective, as it allows the energetics involved in docking to be modeled without the need to consider any issues relating to reaction mechanisms. In this study, two types of energy terms were investigated: the noncovalent interactions between the binding site and the substrate, and those responsible for discriminating between the oxidized nucleotide 8-oxo-dGTP and the normal dGTP. Both of these were investigated using the semiempirical method PM7 in the program MOPAC. The contributions of the individual residues to both the binding energy and the specificity of MTH1 were calculated by simulating the effect of mutations. Where comparisons were possible, all calculated results were in agreement with experimental observations. This technique provides fresh insight into the binding mechanism that enzymes use for discriminating between possible substrates.

A comparison of X-ray and calculated structures of the enzyme MTH1

Modern computational chemistry methods provide a powerful tool for use in refining the geometry of proteins determined by X-ray crystallography. Specifically, computational methods can be used to correctly place hydrogen atoms unresolved by this experimental method and improve bond geometry accuracy. Using the semiempirical method PM7, the structure of the nucleotide-sanitizing enzyme MTH1, complete with hydrolyzed substrate 8-oxo-dGMP, was optimized and the resulting geometry compared with the original X-ray structure of MTH1. After determining hydrogen atom placement and the identification of ionized sites, the charge distribution in the binding site was explored. Where comparison was possible, all the theoretical predictions were in good agreement with experimental observations. However, when these were combined with additional predictions for which experimental observations were not available, the result was a new and alternative description of the substrate-binding site interaction. An estimate was made of the strengths and weaknesses of the PM7 method for modeling proteins on varying scales, ranging from overall structure to individual interatomic distances. An attempt to correct a known fault in PM7, the under-estimation of steric repulsion, is also described. This work sheds light on the specificity of the enzyme MTH1 toward the substrate 8-oxo-dGTP; information that would facilitate drug development involving MTH1. Graphical Abstract Overlay of the backbone traces of the two MTH1 protein chains (green and orange respectively) in PDB 3ZR0 and the equivalent PM7 structures (magenta and cyan respectively) each optimized separately.

Modeling of Toxicity-Relevant Electrophilic Reactivity for Guanine with Epoxides: Estimating the Hard and Soft Acids and Bases (HSAB) Parameter as a Predictor

According to the electrophilic theory in toxicology, many chemical carcinogens in the environment and/or their active metabolites are electrophiles that exert their effects by forming covalent bonds with nucleophilic DNA centers. The theory of hard and soft acids and bases (HSAB), which states that a toxic electrophile reacts preferentially with a biological macromolecule that has a similar hardness or softness, clarifies the underlying chemistry involved in this critical event. Epoxides are hard electrophiles that are produced endogenously by the enzymatic oxidation of parent chemicals (e.g., alkenes and PAHs). Epoxide ring opening proceeds through a SN2-type mechanism with hard nucleophile DNA sites as the major facilitators of toxic effects. Thus, the quantitative prediction of chemical reactivity would enable a predictive assessment of the molecular potential to exert electrophile-mediated toxicity. In this study, we calculated the activation energies for reactions between epoxides and the guanine N7 site for a diverse set of epoxides, including aliphatic epoxides, substituted styrene oxides, and PAH epoxides, using a state-of-the-art density functional theory (DFT) method. It is worth noting that these activation energies for diverse epoxides can be further predicted by quantum chemically calculated nucleophilic indices from HSAB theory, which is a less computationally demanding method than the exacting procedure for locating the transition state. More importantly, the good qualitative/quantitative correlations between the chemical reactivity of epoxides and their bioactivity suggest that the developed model based on HSAB theory may aid in the predictive hazard evaluation of epoxides, enabling the early identification of mutagenicity/carcinogenicity-relevant SN2 reactivity.

Capturing Transient Endoperoxide in the Singlet Oxygen Oxidation of Guanine

The chemistry of singlet O2 toward the guanine base of DNA is highly relevant to DNA lesion, mutation, cell death, and pathological conditions. This oxidative damage is initiated by the formation of a transient endoperoxide through the Diels-Alder cycloaddition of singlet O2 to the guanine imidazole ring. However, no endoperoxide formation was directly detected in native guanine or guanosine, even at -100 °C. Herein, gas-phase ion-molecule scattering mass spectrometry was utilized to capture unstable endoperoxides in the collisions of hydrated guanine ions (protonated or deprotonated) with singlet O2 at ambient temperature. Corroborated by results from potential energy surface exploration, kinetic modeling, and dynamics simulations, various aspects of endoperoxide formation and transformation (including its dependence on guanine ionization and hydration states, as well as on collision energy) were determined. This work has pieced together reaction mechanisms, kinetics, and dynamics data concerning the early stage of singlet O2 induced guanine oxidation, which is missing from conventional condensed-phase studies.

Solvent effects on the properties of hyperbranched polythiophenes

QM/MM-MD simulations of dendrimers using explicit solvent molecules capture the conformational flexibility and microfluctuations induced by different types of solvents.

How protonation and deprotonation of 9-methylguanine alter its singlet O2 addition path: about the initial stage of guanine nucleoside oxidation

Protonated and deprotonated 9-methylguanine follow completely different oxidation routes.

N7 methylation alters hydrogen-bonding patterns of guanine in duplex DNA

N7-Alkyl-2'-deoxyguanosines are major adducts in DNA that are generated by various alkylating mutagens and drugs. However, the effect of the N7 alkylation on the hydrogen-bonding patterns of the guanine remains poorly understood. We prepared N7-methyl-2'-deoxyguanosine (N7mdG)-containing DNA using a transition-state destabilization strategy, developed a novel polβ-host-guest complex system, and determined eight crystal structures of N7mdG or dG paired with dC, dT, dG, and dA. The structures of N7mdG:dC and N7mdG:dG are very similar to those of dG:dC and dG:dG, respectively, indicating the involvement of the keto tautomeric form of N7mdG in the base pairings with dC and dG. On the other hand, the structure of N7mdG:dT shows that the mispair forms three hydrogen bonds and adopts a Watson-Crick-like geometry rather than a wobble geometry, suggesting that the enol tautomeric form of N7mdG involves in its base pairing with dT. In addition, N7mdG:dA adopts a novel shifted anti:syn base pair presumably via the enol tautomeric form of N7mdG. The polβ-host-guest complex structures reveal that guanine-N7 methylation changes the hydrogen-bonding patterns of the guanine when paired with dT or dA and suggest that N7 alkylation may alter the base pairing patterns of guanine by promoting the formation of the rare enol tautomeric form of guanine.

The Degradation of dG Phosphoramidites in Solution

The reaction of 2'-deoxynucleoside phosphoramidites with water is an important degradation reaction that limits the lifetimes of reagents used for chemical deoxyoligonucleotide synthesis. The hydrolysis of nucleoside phosphoramidites in solution has therefore been investigated. The degree of degradation depends not only on the presence of water but also on the specific nucleoside, 2'-deoxyguanosine (dG) being especially susceptible. Additionally, the nature of the group protecting the exocyclic amine on the nucleoside base strongly influences the rate of hydrolysis. For dG, the degradation is second order in phosphoramidite concentration, indicating autocatalysis of the hydrolysis reaction. Comparison of the degradation rates of dG phosphoramidites with different protecting groups as well as with phosphoramidites containing bases that are structurally similar to dG affords clues to the nature of how dG catalyzes its own destruction and indicates a direct correlation between ease of protecting group removal and propensity to undergo autocatalytic degradation.

Photoaddition of two guanine bases to single Ru-TAP complexes. Computational studies and ultrafast spectroscopies to elucidate the pH dependence of primary processes

The covalent photoadduct (PA) between [Ru(TAP)3](2+) (TAP = 1,4,5,8-tetraazaphenanthrene) and guanosine monophosphate (GMP) opened the way to interesting photobiological applications. In this context, the PA's capability upon illumination to give rise to the addition of a second guanine base is especially interesting. The origins of these intriguing properties are for the first time thoroughly investigated by an experimental and theoretical approach. The PA's spectroscopic and redox data combined with TDDFT results corroborated with resonance Raman data show that the properties of this PA (pKa around 7) depend on the solution pH. Theoretical results indicate that the acid form PA.H(+) when excited should relax to MLCT (metal-to-ligand charge transfer) excited states, in contrast to the basic form PA whose excited state should have LLCT/ILCT (ligand-to-ligand charge transfer/intra ligand charge transfer) characteristics. Ultrafast excitation of PA.H(+) at pH 5.9 produces continuous dynamic processes in a few hundred picoseconds involving coupled proton-electron transfers responsible for luminescence quenching. Long-lived species of a few microseconds capable of reacting with GMP are produced at that pH, in agreement with the formation of covalent addition of a second GMP to PA, as shown by mass spectrometry results. In contrast, at pH 8 (mainly nonprotonated PA), other ultrafast transient species are detected and no GMP biadduct is formed in the presence of GMP. This pH dependence of photoreaction can be rationalized with the different nature of the excited states, thus at pH 8, unreactive LLCT/ILCT states and at pH 5.9 reactive MLCT states.