The molecular electrostatic potentials for the nucleic acid bases: Adenine, thymine, and cytosine

Nature of Luminescence and Pharmacological Activity of Sulfaguanidine

Sulfonamides are one of the oldest groups of veterinary chemotherapeutic agents. Physico-chemical properties, the concentration and the nature of the environment are the factors responsible for the distribution of sulfonamides in the living organism. Although these drug compounds have been in use for more than half a century, knowledge about their behavior is still limited. Physiological activity is currently attributed to the sulfanyl radical. Our study is devoted to the spectral properties of aqueous solutions of sulfaguanidine, in which the formation of complexes with an H-bond and a protonated form takes place. The nature of the fluorescent state of sulfaguanidine was interpreted using computational chemistry, the electronic absorption method and the luminescence method. The structure of sulfaguanidine includes several active fragments: aniline, sulfonic and guanidine. To reveal the role of fragments in the physiological activity of the studied antibiotic, we calculated and compared the effective charges of the fragments of aniline and sulfaguanidine molecules. Chromophore groups were identified in molecules, which determine the intermolecular interaction between a molecule and a proton-donor solvent. The study also revealed the impact of sulfone and guanidine groups, as well as complexation, on the effective charge of the antibiotic fragment responsible for physiological activity and luminescent ability.

A Theoretical Study on the Medicinal Properties and Eletronic Structures of Platinum(IV) Anticancer Agents With Cl Substituents

In this paper, we selected Pt(en)Cl4, Pt(dach)Cl4, and Pt(bipy)Cl4 with gradually increasing ligands to explore the ligand effect on the properties of platinum(IV) anticancer drugs. The electronic structures and multiple drug properties of these three complexes were studied at the LSDA/SDD level using the density functional theory (DFT) method. By comparing the gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), electron affinity, atomic charge population, and natural bond orbital (NBO), we found that the order of reducibility is Pt(bipy)Cl4 > Pt(en)Cl4 > Pt(dach)Cl4. Our research can provide the theoretical basis for the development of anticancer drugs.

Electrostatic Potential Topology for Probing Molecular Structure, Bonding and Reactivity

Following the pioneering investigations of Bader on the topology of molecular electron density, the topology analysis of its sister field viz. molecular electrostatic potential (MESP) was taken up by the authors’ groups. Through these studies, MESP topology emerged as a powerful tool for exploring molecular bonding and reactivity patterns. The MESP topology features are mapped in terms of its critical points (CPs), such as bond critical points (BCPs), while the minima identify electron-rich locations, such as lone pairs and π-bonds. The gradient paths of MESP vividly bring out the atoms-in-molecule picture of neutral molecules and anions. The MESP-based characterization of a molecule in terms of electron-rich and -deficient regions provides a robust prediction about its interaction with other molecules. This leads to a clear picture of molecular aggregation, hydrogen bonding, lone pair–π interactions, π-conjugation, aromaticity and reaction mechanisms. This review summarizes the contributions of the authors’ groups over the last three decades and those of the other active groups towards understanding chemical bonding, molecular recognition, and reactivity through topology analysis of MESP.

The electrostatic potential as a descriptor for the protonation propensity in automated exploration of reaction mechanisms

We discuss the possibility of exploiting local minima of the molecular electrostatic potential for locating protonation sites in molecules in a fully automated manner. We implement and apply this concept to exploring the mechanism of proton reduction catalyzed by a hydrogenase model complex [Orthaber et al., Dalton Trans., 2014, 43, 4537]. A large number of distinct structures arising already in the early stages of the hydrogen evolution mechanism demonstrates the need for reliable, automated algorithms for the thorough analysis of catalytic processes.

Sigma-holes from iso-molecular electrostatic potential surfaces

Visualization of the halobenzene σ-hole region of molecules (PhX, X = Cl, Br, I) was conducted to investigate the nature of the σ-hole present between covalently bonded elements of groups IVB-VIIB (known as halogen bonding for group VIIB) and corresponding negative sites, such as Lewis base lone electron pairs, π-electrons, or anions. The σ-hole consists of a region of poor electron density and often relatively positive electrostatic potential surrounding the outermost portion of the halogen atom along the A-X bond axis. In this work, molecular electrostatic potential (MEP) isosurfaces for PhX obtained from ab initio calculations are examined to determine the σ-hole in 3D, showing the surfaces of corresponding positive and negative regions. Surfaces were mapped for isopotentials of PhX molecules as low as 0.003 V and scaled up by factors of 10 up to 3 V. The σ-hole is revealed as a positive region exposed underneath a predominantly negative MEP isosurface. As isopotential values move away from zero, this hole grows in radius; conversely, its presence completely fades as potential approaches zero with increasing distance from the molecule. This technique can also be used to compare behaviors of neutral molecules and their ionic counterparts like the case of neutral PF₆ (not observed experimentally) and the hexafluorophosphate anion, PF₆^-, a typical counter-ion in commercial Li-ion batteries. The pnictogen halide PF₅ features similar MEP trends as the neutral PF₆, which features reactive sites, shown as negative potential caps, at specific points in the molecule, similar to those of PF₅. The portrayal of MEP behavior in iso-surfaces at specific and practical values of chemical interest is crucial when defining lump parameter sets for Coulombic force fields for molecular dynamics simulations to be used in systems that go from biological macromolecules to crystal engineering to devices to final products. Active chemical sites can be described by the MEP function, V(r), more proficiently than just wavefunctions or electron densities that intrinsically contain the same information, and this is fully enhanced when color-coding electron densities on isopotential surfaces are shown. Graphical abstract The hidden features of orbital holes depicted by iso-potentials.

Mechanism Underlying the Nucleobase-Distinguishing Ability of Benzopyridopyrimidine (BPP)

Benzopyridopyrimidine (BPP) is a fluorescent nucleobase analogue capable of forming base pairs with adenine (A) and guanine (G) at different sites. When incorporated into oligodeoxynucleotides, it is capable of differentiating between the two purine nucleobases by virtue of the fact that its fluorescence is largely quenched when it is base-paired to guanine, whereas base-pairing to adenine causes only a slight reduction of the fluorescence quantum yield. In the present article, the photophysics of BPP is investigated through computer simulations. BPP is found to be a good charge acceptor, as demonstrated by its positive and appreciably large electron affinity. The selective quenching process is attributed to charge transfer (CT) from the purine nucleobase, which is predicted to be efficient in the BPP-G base pair, but essentially inoperative in the BPP-A base pair. The CT process owes its high selectivity to a combination of two factors: the ionization potential of guanine is lower than that of adenine, and less obviously, the site occupied by guanine enables a greater stabilization of the CT state through electrostatic interactions than the one occupied by adenine. The case of BPP illustrates that molecular recognition via hydrogen bonding can enhance the selectivity of photoinduced CT processes.

Metal Ion Modeling Using Classical Mechanics

Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems.

Sequence-Specific Recognition of DNA by Proteins: Binding Motifs Discovered Using a Novel Statistical/Computational Analysis

Decades of intensive experimental studies of the recognition of DNA sequences by proteins have provided us with a view of a diverse and complicated world in which few to no features are shared between individual DNA-binding protein families. The originally conceived direct readout of DNA residue sequences by amino acid side chains offers very limited capacity for sequence recognition, while the effects of the dynamic properties of the interacting partners remain difficult to quantify and almost impossible to generalise. In this work we investigated the energetic characteristics of all DNA residue—amino acid side chain combinations in the conformations found at the interaction interface in a very large set of protein—DNA complexes by the means of empirical potential-based calculations. General specificity-defining criteria were derived and utilised to look beyond the binding motifs considered in previous studies. Linking energetic favourability to the observed geometrical preferences, our approach reveals several additional amino acid motifs which can distinguish between individual DNA bases. Our results remained valid in environments with various dielectric properties.

Multifunctional Tricarbazolo Triazolophane Macrocycles: One-Pot Preparation, Anion Binding, and Hierarchical Self-Organization of Multilayers

Programming the synthesis and self-assembly of molecules is a compelling strategy for the bottom-up fabrication of ordered materials. To this end, shape-persistent macrocycles were designed with alternating carbazoles and triazoles to program a one-pot synthesis and to bind large anions. The macrocycles bind anions that were once considered too weak to be coordinated, such as PF6 (-) , with surprisingly high affinities (β2 =10(11)  M(-2) in 80:20 chloroform/methanol) and positive cooperativity, α=(4 K2 /K1 )=1200. We also discovered that the macrocycles assemble into ultrathin films of hierarchically ordered tubes on graphite surfaces. The remarkable surface-templated self-assembly properties, as was observed by using scanning tunneling microscopy, are attributed to the complementary pairing of alternating triazoles and carbazoles inscribed into both the co-facial and edge-sharing seams that exist between shape-persistent macrocycles. The multilayer assembly is also consistent with the high degree of molecular self-association observed in solution, with self-association constants of K=300 000 M(-1) (chloroform/methanol 80:20). Scanning tunneling microscopy data also showed that surface assemblies readily sequester iodide anions from solution, modulating their assembly. This multifunctional macrocycle provides a foundation for materials composed of hierarchically organized and nanotubular self-assemblies.

An amplified electrochemical aptasensor based on hybridization chain reactions and catalysis of silver nanoclusters

In the present study, based on the mimic oxidase catalytic character of nucleic-acid-stabilized silver nanoclusters (DNA/AgNCs) and hybridization chain reactions for signal amplification, the fabrication of a label-free sensitive "turn-on" electrochemical aptasensor for the amplified determination of lysozyme was demonstrated. First, the designed DNA duplex was modified on the electrode. With the specific binding of the target, lysozyme and its aptamer, the lysozyme-binding DNA sequence was liberated, exposing the induced DNA sequence, which in turn triggered the formation of the supersandwich DNA structure. Because the cytosine-rich sequence was designed ingeniously on the DNA sequence, DNA/AgNCs were formed on the supersandwich DNA structure. The peroxidase-like character of DNA/AgNCs produced detectable electrochemical signals for the lysozyme aptasensor, which showed a satisfying sensitive detection of lysozyme with a low detection limit of 42 pM and a wide linear range of 10(-10) M to 10(-5) M.

Nucleic acid bases in anionic 2'-deoxyribonucleotides: a DFT/B3LYP study of structures, relative stability, and proton affinities

Protonation of nucleobases in anions of canonical 2'-deoxyribonucleotides has been investigated by the DFT computational study at the B3LYP/aug-cc-pvdz level of theory. It is demonstrated that the protonation leads to a significant decrease of conformational space of purine nucleotides while almost all conformers found for non-protonated molecules correspond to minima of the potential energy surface for protonated mdTMP and mdCMP. However, in all nucleotides, only one conformer is populated. This applies to all tautomers of protonated molecules except the mdTMP and mdCMP with the proton attached to the carbonyl group where a minor population of second conformer is observed. Protonation of nucleobase leads to significant elongation of the N-glycosidic bond. These findings agree well with suggestions that protonation of nucleobase is a first step in cleavage of the glycosidic bond. The oxygen atoms of both carbonyl groups of thymine and the N3 atom of the pyrimidine ring of cytosine, guanine, and adenine represent the most preferable sites for protonation of anions of 2'-deoxyrobonucleotides. The highest proton affinity is observed for the base in mdGMP and the lowest for the thymine moiety in mdTMP. It should be noted that calculated values of the proton affinities in anionic nucleotides are significantly higher (by 2-3 eV) than for nucleosides and neutral nucleotides. This allows assuming that the proton affinity of the base in DNA macromolecule may be tuned by changing the extent of shielding or neutralization of negative charge of the phosphate group.

S-Adenosylmethionine-dependent alkylation reactions: when are radical reactions used?

S-Adenosylmethionine (SAM) is a versatile small molecule used in many biological reactions. This review focuses on the mechanistic consideration of SAM-dependent methylation and 3-amino-3-carboxypropylation reactions. Special emphasis is given to methylation and 3-amino-3-carboxypropylation of carbon atoms, for which both nucleophilic mechanisms and radical mechanisms are used, depending on the specific enzymatic reactions. What is the logic behind Nature's choice of different reaction mechanisms? Here I aim to rationalize the choice of different reaction mechanisms in SAM-dependent alkylation reaction by analyzing a few enzymatic reactions in depth. These reactions include SAM-dependent cyclopropane fatty acid synthesis, DNA cytosine methylation, RNA adenosine C2 and C8 methylation, and 3-amino-3-carboxypropylation involved in diphthamide biosynthesis and wybutosine biosynthesis.

Structures of alkali metal ion-adenine complexes and hydrated complexes by IRMPD spectroscopy and electronic structure calculations

Complexes between adenine and the alkali metal ions Li(+), Na(+), K(+), and Cs(+) have been investigated by infrared multiple photon dissociation (IRMPD) spectroscopy between 2800 and 3900 cm(-1), as have some singly hydrated complexes. The IRMPD spectra clearly show the N-H stretching and the NH(2) symmetric and asymmetric stretching vibrations of adenine; and for the solvated ions, the O-H stretching vibrations are observed. These experimental spectra were compared with those for a variety of possible structures, including both A9 (A9 refers to the tautomer where hydrogen is on the nitrogen in position 9 of adenine, see Scheme 1) and A7 adenine tautomers, computed using B3-LYP/6-31+G(d,p). By comparing the experimental and the simulated spectra it is possible to rule out various structures and to further assign structures to the species probed in these experiments. Single-point calculations on the B3-LYP/6-31+G(d,p) geometries have been performed at MP2/6-311++G(2d, p) to obtain good estimates of the relative thermochemistries for the different structures. In all cases the computed IR spectrum for the lowest energy structure is consistent with the experimental IRMPD spectrum, but in some cases structural assignment cannot be confirmed based solely upon comparison with the experimental spectra so computed thermochemistries can be used to rule out high-energy structures. On the basis of the IRMPD spectra and the energy calculations, all adenine-M(+) and adenine-M(+)-H(2)O are concluded to be composed of the A7 tautomer of adenine, which is bound to the cations in a bidentate fashion through N3 and N9 (see Scheme 1 for numbering convention). For the hydrated ions water binds directly to the metal ion through oxygen, as would be expected since the metal contains most positive charge density. For the hydrated lithium cation-bound adenine dimer, the water molecule is concluded to be hydrogen bonded to a free basic site of one of the adenine monomers, which is also bound to the lithium cation. Experimental and theoretical results on adenine-Li(+)-H(2)O suggest that the electrosprayed adenine-Li(+) resembles the lowest-energy solution phase ion rather than the lowest-energy gas-phase ion, which is the imine form.

Through-Space Effects of Substituents Dominate Molecular Electrostatic Potentials of Substituted Arenes

Model systems have been studied using density functional theory to assess the contributions of π-resonance and through-space effects on electrostatic potentials of substituted arenes. The results contradict the widespread assumption that changes in molecular ESPs reflect only local changes in the electron density. Substituent effects on the ESP above the molecular plane are commonly attributed to changes in the aryl π-system. We show that ESP changes for a collection of substituted benzenes and more complex aromatic systems can be accounted for mostly by through-space effects, with no change in the aryl π-electron density. Only when π-resonance effects are substantial do they influence changes in the ESP above the aromatic ring to any extent. Examples of substituted arenes studied here are taken from the fields of drug design, host-guest chemistry, and crystal engineering. These findings emphasize the potential pitfalls of assuming ESP changes reflect changes in the local electron density. Since ESP changes are frequently used to rationalize and predict intermolecular interactions, these findings have profound implications for our understanding of substituent effects in countless areas of chemistry and molecular biology. Specifically, in many non-covalent interactions there are significant, often neglected, through-space interactions with the substituents. Finally, the present results explain the perhaps unexpectedly good performance of many molecular mechanics force-fields applied to supramolecular assembly phenomena and π-π interactions in biological systems despite the neglect of the polarization of the aryl π-system by substituents.

Interaction of adenosine, guanosine and inosine with ruthenium hydride complexes

Complexes of adenosine, guanosine and inosine with some ruthenium hydride complexes have been prepared and studied by UV, visible, IR, 1H NMR and 13C NMR spectroscopies. The ligands have been found to coordinate through their exocyclic groups and the N(7) atom to the RuHCl(PPh3)3 unit and through only exocyclic groups to the RuHCl(CO)(PPh3)3 unit.

Investigation of proton transport tautomerism in clusters of protonated nucleic acid bases (cytosine, uracil, thymine, and adenine) and ammonia by high-pressure mass spectrometry and ab initio calculations

The energetics of the ion-molecule interactions and structures of the clusters formed between protonated nucleic acid bases (cytosine, uracil, thymine, and adenine) and ammonia have been studied by pulsed ionization high-pressure mass spectrometry (HPMS) and ab initio calculations. For protonated cytosine, uracil, thymine, and adenine with ammonia, the measured enthalpies of association with ammonia are -21.7, -27.9, -22.1, and -17.5 kcal mol-1, respectively. Different isomers of the neutral and protonated nucleic acid bases as well as their clusters with ammonia have been investigated at the B3LYP/6-31+G(d,p) level of theory, and the corresponding binding energetics have also been obtained. The potential energy surfaces for proton transfer and interconversion of the clusters of protonated thymine and uracil with ammonia have been constructed. For cytosine, the experimental binding energy is in agreement with the computed binding energy for the most stable isomer, CN01-01, which is derived from the enol form of protonated cytosine, CH01, and ammonia. Although adenine has a proton affinity similar to that of cytosine, the binding energy of protonated adenine to ammonia is much lower than that for protonated cytosine. This is shown to be due to the differing types of hydrogen bonds being formed. Similarly, although uracil and thymine have similar structures and proton affinities, the binding energies between the protonated species and ammonia are different. Strikingly, the addition of a single methyl group, in going from uracil to thymine, results in a significant structural change for the most stable isomers, UN01-01 and TN03-01, respectively. This then leads to the difference in their measured binding energies with ammonia. Because thymine is found only in DNA while uracil is found in RNA, this provides some potential insight into the difference between uracil and thymine, especially their interactions with other molecules.

Activation barriers for DNA alkylation by carcinogenic methane diazonium ions

Methylation reactions of the DNA bases with the methane diazonium ion, which is the reactive intermediate formed from several carcinogenic methylating agents, were examined. The SN2 transition states of the methylation reactions at N7, N3, and O6 of guanine; N7, N3, and N1 of adenine; N3 and O2 of cytosine; and O2 and O4 of thymine were calculated using the B3LYP density functional method. Solvation effects were examined using the conductor-like polarizable continuum method and the combined discrete/SCRF method. The transition states for reactions at guanine N3, adenine N7, and adenine N1 are influenced by steric interactions between the methane diazonium ion and exocyclic amino groups. Both in the gas phase and in aqueous solution, the methylation reactions at N atoms have transition states that are looser, and generally occur earlier along the reaction pathways than reactions at O atoms. The forming bonds in the transition states in water are 0.03 to 0.13 A shorter than those observed in the gas phase, and the activation energies are 13 to 35 kcal/mol higher. The combined discrete/SCRF solvation energy calculations using base-water complexes with three water molecules yield base solvation energies that are larger than those obtained from the CPCM continuum method, especially for cytosine. Reactivities calculated using barriers obtained with the discrete/SCRF method are consistent with the experimentally observed high reactivity at N7 of guanine.

Protonated adenine: tautomers, solvated clusters, and dissociation mechanisms

Ab initio and density functional theory calculations at the B3-MP2 and CCSD(T)/6-311 + G(3df,2p) levels of theory are reported that address the protonation of adenine in the gas phase, water clusters, and bulk aqueous solution. The calculations point to N-1-protonated adenine (1+) as the thermodynamically most stable cationic tautomer in the gas phase, water clusters, and bulk solution. This strongly indicates that electrospray ionization of adenine solutions produces tautomer 1+ with a specificity calculated as 97-90% in the 298-473 K temperature range. The mechanisms for elimination of hydrogen atoms and ammonia from 1+ have also been studied computationally. Ion 1+ is calculated to undergo fast migrations of protons among positions N-1, C-2, N-3, N-10, N-7, and C-8 that result in an exchange of five hydrogens before loss of a hydrogen atom forming adenine cation radical at 415 kJ mol(-1) dissociation threshold energy. The elimination of ammonia is found to be substantially endothermic requiring 376-380 kJ mol(-1) at the dissociation threshold and depending on the dissociation pathway. The overall dissociation is slowed by the involvement of ion-molecule complexes along the dissociation pathways. The competing isomerization of 1+ proceeds by a sequence of ring opening, internal rotations, imine flipping, ring closures, and proton migrations to effectively exchange the N-1 and N-10 atoms in 1+, so that either can be eliminated as ammonia. This mechanism explains the previous N-1/N-10 exchange upon collision-induced dissociation of protonated adenine.

Binding of the fluorescein derivative eosin Y to the mitochondrial ADP/ATP carrier: characterization of the adenine nucleotide binding site

As the SH-reactive fluorescein derivative eosin-5-maleimide (EMA) specifically labels Cys159 in the second loop facing the matrix space (loop M2) of the ADP/ATP carrier in bovine heart submitochondrial particles [Majima, E., Koike, H., Hong, Y.-M., Shinohara, Y., and Terada, H. (1993) J. Biol. Chem. 268, 22181-22187], we studied the interaction of non-SH-reactive eosin Y, an analog of EMA, with the carrier under various conditions to characterize its binding. Eosin Y was found to inhibit ADP transport by binding to loop M2 in submitochondrial particles, but not in mitochondria. Its Ki for transport (0.33 microM) was found to be very similar to its Kd (0.53 microM) for specific binding to the carrier. Bound eosin Y was displaced by the transport substrates ADP and ATP, but not by untransportable GTP, suggesting that eosin Y bound to the specific binding site of ADP and ATP. The three-dimensional structure and electrostatic features of eosin Y were very similar to those of ADP, and the hydrophobic property and divalent charge of eosin Y were very important for its binding to the carrier. Based on these results, the features of the binding site of the transport substrates are considered.

Structural requirements for inhibitors of poly(ADP-ribose) polymerase

The purpose of this study was to examine the structure/activity relationships of a series of substituted benzamides as poly(ADP-ribose) polymerase inhibitors. The experimental approach has involved the use of in vitro and in vivo assays in order to gather information either on the intrinsic activity of the benzamides or on the effect of various pharmacodynamic parameters on the activity in vivo. Although some discrepancies between the data obtained in vivo and in vitro were found in this study, results seem to indicate that most powerful inhibitors were characterized by acylation of the -NH2 function in the 3 position or by substitution in this same position with hydroxy or methoxy groups. The best inhibitors were not cytotoxic under these experimental conditions. Computed calculations of molecular electrostatic potential of these molecules were also performed and a good correlation was found between the similarity index and the experimental inhibitory activity.