Gas-Phase Absolute Ca2+ and Mg2+ Affinity for Nucleic Acid Bases. A Theoretical Determination

Why Cellular Di/Triphosphates Preferably Bind Mg2+ and Not Ca2

Di/triphosphates perform a multitude of essential tasks, being important components of many vital organic cofactors such as adenosine/guanosine di/triphosphate (ADP/GDP, ATP/GTP), flavin adenine dinucleotide, and nicotinamide adenine dinucleotide and its phosphate derivative. They are generally bound to cations inside cells, in particular Mg²⁺ in the case of ATP/GTP. Yet how their metal-binding modes depend on the number, charge, and solvent exposure of the polyphosphate group and how Mg²⁺and Ca²⁺ dications that coexist in cellular fluids compete for di/triphosphates in biological systems remain elusive. Using density functional theory calculations combined with a polarizable continuum model, we have determined the relative free energies and stabilities of the different binding modes of di- and triphosphate groups to Mg²⁺ and Ca²⁺. We show that the thermodynamic outcome of the competition between Mg²⁺ and Ca²⁺ for cellular di/triphosphates depends mainly on the oligomericity/charge and metal-binding mode of the phosphate ligand as well as the solvent exposure of the binding site. Increasing the charge and thus denticity of the phosphate ligand from bi- to tridentate in a buried binding pocket enhances the affinity of the host system for the stronger charge acceptor, Mg²⁺. The cellular di/triphosphates's intrinsic properties and the protein matrix allowing them to bind a dication bi/tridentately, along with the higher cytosolic concentration of Mg²⁺ compared to Ca²⁺, enables Mg²⁺ to outcompete Ca²⁺ in binding to these highly charged anions. This suggests an explanation for why nature has chosen Mg²⁺ but not Ca²⁺ to perform most of the essential tasks associated with biological triphosphates.

Role of backbones on the interaction of metal ions with deoxyribonucleic acid and peptide nucleic acid: A DFT study

Metal ion interaction with deoxyribonucleic acid and peptide nucleic acid were studied using B3LYP-D3/6-311++g(d,p)//B3LYP/6-31 + G(d) level of theory in aqueous phase employing polarized continuum (PCM) model. This study reports the role of backbones on deoxyribonucleic acid and peptide nucleic acid for complexation with different metal ions. The systematic study performed with DFT calculations reveals that central binding (Type-4) shows the strongest binding compared to the other binding modes because of the involvement of the backbone as well as the nitrogenous bases. The charged backbone of DNA nucleotides contributes significantly towards binding with the metal ions. The deoxyguanosine monophosphate (dGMP) clearly indicates the strongest binding upon complexation with Mg²⁺ (-49.6 kcal/mol), Zn²⁺ (-45.3 kcal/mol) and Cu²⁺ (-148.4 kcal/mol), respectively. The neutral backbone of PNA also assists to complex the metal ions with PNA nucleotides. The Mg²⁺ and Cu²⁺ prefer to bind with the PNA-Cytosine (-32.9 kcal/mol & -132.9 kcal/mol) in central binding mode (type-4). PNA-Adenine-Zn²⁺ (-29.1 kcal/mol) is the preferred binding mode (type-4) compared to other modes of interaction for this metal ion with PNA-Adenine nucleotide. The Cu²⁺ ion showed the superior complexation ability with deoxyribonucleic acid and peptide nucleic acid compared to Mg²⁺ and Zn²⁺ ions. The cation-π complexation with the bases of nucleotides was also obtained with Cu²⁺ ion. The AIM (atoms in molecule) theory has been applied to examine the nature of the interaction of Mg²⁺, Zn²⁺, and Cu²⁺ ion to the deoxyribonucleic acid and peptide nucleic acid. The alkaline earth metal, Mg²⁺ ion shows electrostatic nature while interaction with deoxyribonucleic acid and peptide nucleic acid, however, the transition metal ions (Zn²⁺, Cu²⁺) showed partly covalent nature as well with deoxyribonucleic acid and peptide nucleic acid. The optical properties calculated for the binding of metal ions with deoxyribonucleic acid and peptide nucleic acid showed a diagnostic signature to ascertain the interaction of metal ions with such nucleotides. Cu²⁺ ion showed larger red shifts in the absorption spectrum values upon complexation with the DNAs and PNAs. The calculated results suggest that such metal ions would prefer to bind with the DNA compared to PNA in DNA-PNA duplexes. The preference for the binding of metal ions with DNA nucleotides is largely attributed to the contribution of charged backbones compared to the neutral PNA backbones.

Consequences of Mg2+ binding on the geometry and stability of RNA base pairs

Quantum chemical calculations reveal the role of magnesium in stabilizing the geometries of intrinsically unstable RNA base pairs.

Exposing the G-quadruplex to electric fields: the role played by telomeres in the propagation of DNA errors

We use quantum calculations to assess the impact of external electric fields on the stability of G-quadruplex, a key structure in telomere functionality.

ESI-MS studies of the non-covalent interactions between biologically important metal ions and N-sulfonylcytosine derivatives

The aim of this report is to present the electrospray ionization mass spectrometry results of the non-covalent interaction of two biologically active ligands, N-1-(p-toluenesulfonyl)cytosine, 1-TsC, 1 and N-1-methanesulfonylcytosine, 1-MsC, 2 and their Cu(II) complexes Cu(1-TsC-N3)₂ Cl₂ , 3 and Cu(1-MsC-N3)₂ Cl₂ and 4 with biologically important cations: Na⁺ , K⁺ , Ca²⁺ , Mg²⁺ and Zn²⁺ . The formation of various complex metal ions was observed. The alkali metals Na⁺ and K⁺ formed clusters because of electrostatic interactions. Ca²⁺ and Mg²⁺ salts produced the tris ligand and mixed ligand complexes. The interaction of Zn²⁺ with 1-4 produced monometal and dimetal Zn²⁺ complexes as a result of the affinity of Zn²⁺ ions toward both O and N atoms. Copyright © 2016 John Wiley & Sons, Ltd.

An insight into the interaction of L-proline with the transition metal cations Fe(2+), Co(2+), Ni(2+): a gas phase theoretical study

The interaction of Fe(2+), Co(2+), and Ni(2+) with L-proline has been studied. Three modes of interaction have been considered: salt bridged (SB), involving binding in a bi-dentate manner through the carboxylate group of L-proline, charge solvated 1 (CS1) involving carbonyl and hydroxyl oxygen, and charge solvated 2 (CS2) involving carbonyl oxygen and the lone pair of the nitrogen atom. All calculations including geometry optimization, metal ion affinities (MIAs), and frequency calculations of the binding structures of Fe(2+), Co(2+), and Ni(2+) to L-proline were calculated using the hybrid density functional theory (DFT-B3LYP) method. All three cations were found to bind preferentially in a zwitterionic (SB) coordination pattern with the metal ion affinity in the order Ni(2+) ˃ Co(2+) ˃ Fe(2+) in all binding forms. The nature of the binding interaction between metal cations and L-proline was found to be mainly electrostatic. Comparison of the infrared vibrations of the C=O, the N-H and the O-H groups of free L-proline with L-proline-M(2+) in both CS1 and CS2 complex structures indicated a considerable shift to lower frequency during complexation. In order to gain more insight into the nature of the interaction of L-proline with group VIIIB metal ions, comparison of the interaction of L-proline with other cations such as (Li(+), Na(+), K(+), Be(2+), Mg(2+), and Ca(2+)) was made. Graphical Abstract L-proline with the transition metal cations Fe(2+), Co(2+), Ni(2.)

Atomic-scale investigation on the facilitation and inhibition of guanine tautomerization at Au(111) surface

Nucleobase tautomerization might induce mismatch of base pairing. Metals, involved in many important biophysical processes, have been theoretically proven to be capable of affecting tautomeric equilibria and stabilities of different nucleobase tautomers. However, direct real-space evidence on demonstrating different nucleobase tautomers and further revealing the effect of metals on their tautomerization at surfaces has not been reported to date. From the interplay of high-resolution STM imaging and DFT calculations, we show for the first time that tautomerization of guanine from G/9H to G/7H is facilitated on Au(111) by heating, whereas such tautomerization process is effectively inhibited by introducing Ni atoms due to its preferential coordination at the N7 site of G/9H. These findings may help to elucidate possible influence of metals on nucleobase tautomerization and provide from a molecular level some theoretical basis on metal-based drug design.

Large mixed complexes involving uracil, cytosine, thymine and/or 1-methyl uracil around Ca2+ ions: an electrospray ionization/MS study

We investigated the possible formation of mixed B(n)B'(n')Ca(2+) complexes where B and B' are two different nucleobases. Electrospray ionization (ESI) mass spectrometric experiments from solutions containing two different kinds of nucleobases and calcium ions were carried out to investigate the formation of magic number clusters that may be relevant in a biological point of view. The results presented here clearly show that mixed complexes can be formed and are stable in the gas phase. This represents an important step toward more complex solutions in which several nucleobases are present simultaneously and may compete in the formation of cationized clusters. We believe that thorough investigations on such systems may help understanding biological processes that may effect the tridimensional structure of the DNA macromolecule. The formation of mixed hexamers, decamers, dodecamers and tetradecamers are clearly favored from solution containing uracil (Ura), thymine (Thy) and Ca(2+), whereas mixed octamers are preferred from 1-methyl uracil (MeU), uracil and Ca(2+) mixtures. Cytosine (Cyto) can form mixed complexes with either uracil or 1-methyl uracil or thymine. On the other hand, the main species formed in these latter cases are mixed tetramers.

Modelling peptide-metal dication interactions: formamide-Ca2+ reactions in the gas phase

The collision induced dissociation of formamide-Ca(2+) complexes produced in the gas phase through nanoelectrospray ionization yields as main products ions [CaOH](+), [HCNH](+), [Ca(NH(2))](+), HCO(+) and [Ca(NH(3))](2+) and possibly [Ca(H(2)O)](2+) and [C,O,Ca](2+), the latter being rather minor. The mechanisms behind these fragmentation processes have been established by analyzing the topology of the potential energy surface by means of B3LYP calculations carried out with a core-correlated cc-pWCVTZ basis set. The Ca(2+) complexes formed by formamide itself and formimidic acid play a fundamental role. The former undergoes a charge separation reaction yielding [Ca(NH(2))](+) + HCO(+), and the latter undergoes the most favorable Coulomb explosion yielding [Ca-OH](+) + [HCNH](+) and is the origin of a multistep mechanism which accounts for the observed loss of water and HCN. Conversely, the other isomer of formamide, amino(hydroxyl)carbene, does not play any significant role in the unimolecular reactivity of the doubly charged molecular cation.

INTERACTIONS OF THE NUCLEOTIDES WITH THE METAL IONS Mg2+, Ca2+, Mn2+, Na+, AND K+

The interactions of the four typical nucleotides with the metal ions Mg 2+, Ca 2+, Mn 2+, Na +, and K + were studied by using the B3LYP/6-311++G(d,p)//B3LYP/6-31G(d,p) calculations in the PCM model. A lot of initial binding sites of the metal ions were designed and optimized to determine the most stable structures of the metal ion nucleotide compounds. It has been shown that the metal ions tend to attach at the center of the negatively charged atoms of the nucleotides. Furthermore, the vertical excitation energies of the metal ion nucleotide compounds were calculated at the same level with the TDDFT method, and also NBO charges were analyzed to understand the bonding characteristics between the metal ions and the nucleotides. That was also compared with the conclusion in the gas phase.

Theoretical investigation on DNA/RNA base pairs mediated by copper, silver, and gold cations

B3LYP density functional based computations were performed in order to characterize the interactions present in some Cu(+), Ag(+), and Au(+) metal ion-mediated DNA and RNA base pairs from both structural and electronic points of view. Examined systems involve as ligands canonical Watson-Crick, Hoogsteen and Wobble base pairs. Two artificial Hoogsteen base pairs were also taken into account. Binding energy values indicate that complexes involving silver cations are less stable than those in which copper or gold are present, and propose a similar behaviour for these two latter ions. The nature of the bond linking metal ions and bases was described by the NBO analysis that suggests metal coordinative interactions to be covalent. An evaluation of the dispersion contributions for the investigated systems was performed with the B3LYP-D3 functional.

DFT STUDY ON METAL CATIONIZATION AND O6-PROTONATION ON 2′-DEOXYGUANOSINE CONFIGURATION: CHANGES ON SUGAR PUCKERING AND STRENGTH OF THE N-GLYCOSIDIC BOND

Density functional theory (DFT) calculations were performed at the B3LYP/6-311++G (d, p) level to determine coordination geometries, absolute metal ion affinities, and free energies for all possible complexation stable products formed by monovalent metal cations including Li+ , Na+ , K+ with the nucleoside 2′-Deoxyguanosine. All computations indicate that the metal ion affinity (MIA) decreases on going from Li+ to Na+ and K+ for 2′-Deoxyguanosine. For example, the affinities for the metal ions described above are 75.2, 57.3, 43.4 kcal/mol, respectively.

Furthermore, the influence of metal cationization and O6 protonation on the strength of the N-glycosidic bond, torsion angles and angle of pseudorotation (P) have been studied. With respect to the results, it has been found that metal binding significantly change the values of the phase angle of pseudorotation (P) in the sugar unit of these nucleosides but, O6 -protonation do not significantly change the values of the torsion angles and angle of pseudorotation (P). In all modified forms, the length of the C1'–N9 bond increases. The Mulliken population analysis and natural bond orbital (NBO) analysis on atomic charges have been carried out on the optimized geometries.

Understanding selectivity of hard and soft metal cations within biological systems using the subvalence concept. I. Application to blood coagulation: direct cation-protein electronic effects vs. indirect interactions through water networks

Following a previous study by de Courcy et al. ((2009) Interdiscip. Sci. Comput. Life Sci. 1, 55-60), we demonstrate in this contribution, using quantum chemistry, that metal cations exhibit a specific topological signature in the electron localization of their density interacting with ligands according to its "soft" or "hard" character. Introducing the concept of metal cation subvalence, we show that a metal cation can split its outer-shell density (the so-called subvalent domains or basins) according to it capability to form a partly covalent bond involving charge transfer. Such behaviour is investigated by means of several quantum chemical interpretative methods encompasing the topological analysis of the Electron Localization Function (ELF) and Bader's Quantum Theory of Atoms in Molecules (QTAIM) and two energy decomposition analyses (EDA), namely the Restricted Variational Space (RVS) and Constrained Space Orbital Variations (CSOV) approaches. Further rationalization is performed by computing ELF and QTAIM local properties such as electrostatic distributed moments and local chemical descriptors such as condensed Fukui Functions and dual descriptors. These reactivity indexes are computed within the ELF topological analysis in addition to QTAIM offering access to non atomic reactivity local index, for example on lone pairs. We apply this "subvalence" concept to study the cation selectivity in enzymes involved in blood coagulation (GLA domains of three coagulation factors). We show that the calcium ions are clearly able to form partially covalent charge transfer networks between the subdomain of the metal ion and the carboxylate oxygen lone pairs whereas magnesium does not have such ability. Our analysis also explains the different role of two groups (high affinity and low affinity cation binding sites) present in GLA domains. If the presence of Ca(II) is mandatory in the central "high affinity" region to conserve a proper folding and a charge transfer network, external sites are better stabilised by Mg(II), rather than Ca(II), in agreement with experiment. The central role of discrete water molecules is also discussed in order to understand the stabilities of the observed X-rays structures of the Gla domain. Indeed, the presence of explicit water molecules generating indirect cation-protein interactions through water networks is shown to be able to reverse the observed electronic selectivity occuring when cations directly interact with the Gla domain without the need of water.

On the Bonding of First-Row Transition Metal Cations to Guanine and Adenine Nucleobases

The binding of first-row transition metal monocations (Sc+-Cu+) to N7 of guanine and N7 or N3 of adenine nucleobases has been analyzed using the hybrid B3LYP density functional theory (DFT) method. The nature of the bonding is mainly electrostatic, the electronic ground state being mainly determined by metal-ligand repulsion. M+-guanine binding energies are 18-27 kcal/mol larger than those of M+-adenine, the difference decreasing along the row. Decomposition analysis shows that differences between guanine and adenine mainly arise from Pauli repulsion and the deformation terms, which are larger for adenine. Metal cation affinity values at this level of calculation are in very good agreement with experimental data obtained by Rodgers et al. (J. Am. Chem. Soc. 2002, 124, 2678) for adenine nucleobases.

On the interaction of bare and hydrated aluminum ion with nucleic acid bases (U, T, C, A, G) and monophosphate nucleotides (UMP, dTMP, dCMP, dAMP, dGMP)

The B3LYP/6-311+G(2df,2p) density functional approach was used to study the interaction that aluminum trication, in the bare and hydrated forms, establishes with the nucleic acid bases and the corresponding monophosphate nucleotides. In this investigation, we determine equilibrium geometry of all possible complexes resulting from the attachment of the ion on the different binding sites selected on each ligand. The relative energies of complexes and metal ion affinities are also given. The most meaningful aspect was found to lie in the energetics of this interaction that underlines a very high affinity of aluminum ion for the examined biological systems.

Tautomerism of Uracil and 5-Bromouracil in a Microcosmic Environment with Water and Metal Ions. What Roles Do Metal Ions Play?

The base tautomerization processes of uracil/5-bromouracil were investigated in a microcosmic environment with both H2O and Na+ (W-M environment). It was found that uracil was more stable in the W-M environment than in the microcosmic environment with only water, which suggested that the metal ions and water work cooperated to maintain the classical nucleic acid bases. However, 5-bromouracil, a chemical mutagen, was found to be less stable than uracil in the W-M environment. Why the 5-bromouracil is easier to tautomerize and therefore induce gene mutation was explained to some extent. Further research revealed that the water molecule would assist the tautomerization in the W-M environment. However, the metal ions in different regions play absolutely opposite roles: in one region, the metal ions can prevent the base from tautomerizing, whereas in another region, the metal ion can assist the tautomerization process. Furthermore, from the viewpoint of ionization of the base, it seems BrU has a stronger tendency to lose the proton at N3, which is an intrinsic consequence of the bromine atom and is not affected by the metal cation.

Gas-Phase Reactions Between Thiourea and Ca2+: New Evidence for the Formation of [Ca(NH3)]2+ and Other Doubly Charged Species

The gas-phase reactions between Ca(2+) and thiourea are investigated by means of electrospray ionization/mass spectrometry experiments. The MS/MS spectra of [Ca(thiourea)](2+) complexes show the appearance of new doubly charged species formed by the loss of NH(3) and HNCS. Other intense peaks at m/z 43, 56, 60, 73, 76 and 98 are also observed, and assigned to monocations produced in different coulomb-explosion processes. The structures and bonding characteristics of the different stationary points of the [Ca(thiourea)](2+) potential energy surface (PES) were theoretically studied by DFT calculations carried out at B3LYP/cc-pWCVTZ level. The analysis of the topology of this PES permits to propose different mechanisms for the loss of ammonia and HNCS, and to identify, the m/z 43, 56, 60, 73, 76 and 98 peaks as H(2)NCNH(+), CaNH(2) (+), H(2)NCS(+), CaSH(+), thiourea(+) and CaNCS(+) ions respectively. There are significant dissimilarities between the reactivity of urea and thiourea, which are related to the lower ionization energy of the latter, and to the fact that thioenols are intrinsically more stable than enols with respect to the corresponding keto forms.

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.

Effect of Ni(ii), Cu(ii) and Zn(ii) association on the keto-enol tautomerism of thymine in the gas phase

The effect of Ni(II), Cu(II) and Zn(II) association on the diketo/keto-enol tautomerism of thymine has been investigated through the use of B3LYP density functional theory calculations. Final energies were obtained at the B3LYP/6-311+G(2df,2p)//B3LYP/6-311+G(d,p) level of theory. Ni(II) and Cu(II) lead to an oxidation of thymine which for Zn(ii) is only partial and catalyze the tautomerization process, this catalytic effect being much larger for Ni(2+) and Zn(2+) than for Cu(2+). One of the most significant consequences of the oxidation of the base is that the calculated BDE's are primarily dictated by the value of the second ionization potential of the metal, and therefore follow the sequence Cu(2+) > Ni(2+) > Zn(2+). Also importantly, metal dication association leads to a stabilization of the keto-enol tautomer, which becomes the most stable form upon interaction with Ni(2+) and Zn(2+). This stabilization enhancement is the consequence of three concomitant factors, namely, (i) a stronger interaction of the metal cation with the carbonyl oxygen, (ii) the interaction of the metal with the dehydrogenated ring nitrogen, (iii) an aromatization of the six-membered ring.

Interactions of nucleobases with alkali earth metal cations--electrospray ionization mass spectrometric study

Interactions of nucleobases with alkali earth metal cations have been studied by electrospray ionization mass spectrometry (ESI-MS). Nucleobases containing at least one oxygen atom form stable complexes with alkali earth metal cations. This phenomenon can be explained on the grounds of the well known theory of hard and soft acids and bases. Uracil and thymine make complexes only when in their deprotonoted forms. The cations of great radii (Sr(2+), Ba(2+)) are more prone to form complexes of stoichiometry 1:1 with uracil and thymine than the cations of small radii (Mg(2+), Ca(2+)). On the other hand, Mg(2+) forms complexes of stoichiometry 2:1 and 3:2 with uracil and thymine. Gas-phase stabilities of the 1:1 complexes are higher for the cations of small radii, in contrast to the solution stabilities. For cytosine and 9- methylhypoxantine the 1:1 complexes of their deprotonated forms are observed at higher cone voltage as a result of HCl molecule loss from the complexes containing the counter ion (Cl(-)). In solution, more stable complexes are formed with metal cations of low radii. Gas-phase stability of the complexes formed by deprotonated 9- methyl-hypoxantine increases with increasing metal cation radius.

Reaction Force Analysis of the Effect of Mg(II) on the 1,3 Intramolecular Hydrogen Transfer in Thymine

The 1,3 intramolecular hydrogen transfer reaction in free thymine and in Mg(II)-thymine have been studied at the density functional theory level. The mechanism of intramolecular proton transfer in these systems emerges from the analysis of the reaction force profile along the reaction path; it is rationalized in terms of structural and electronic reorganizations that take place during the chemical transformation. Results show that the presence of Mg(II) monocoordinated to thymine activates the hydrogenic motion by inducing structural and electronic changes in the molecular backbone. In the metallic complex, it is found that the hydrogen transfer is followed by a relaxation process that facilitates the metal cation migration to form a bicoordinated complex.