ARTICLE pubs.acs.org/JPCA
Comparison of Arsenic Acid with Phosphoric Acid in the Interaction with a Water Molecule and an Alkali/Alkaline-Earth Metal Cation Sung Woo Park, Chang Woo Kim, Ji Hyun Lee, Giwoong Shim, and Kwang S. Kim* Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea
bS Supporting Information ABSTRACT: Recently, Wolfe-Simon has discovered a bacterium which is able to survive using arsenic(V) rather than phosphorus(V) in its DNA. Thus it is important to investigate some important structural and chemical similarities and dissimilarities between phosphate and arsenate. We compared the monohydrated structures and the alkali/alkaline-earth metal (Na+, K+, Mg2+ and Ca2+) complexes of the arsenic acid/anions with those of the phosphoric acid/anions [i.e., HmPO4 (3 m) vs HmAsO4 (3 m) (m = 1 3)]. We carried out geometry optimization along with harmonic frequency calculations using ab initio calculations. Despite the increased van der Waals radius of As, the hydrated structures of both P and As systems show very close similarity (within 0.25 Å in the P/As 3 3 3 O(water) distance and within a few kJ/mol in binding energy) because of the increased induction energies by more polar arsenic acid/anons and slightly increased dispersion energy by a larger size of the As atom. In the metal complexes, the arsenic acid has a slightly larger binding distance (by 0.07 1.0 Å) and weaker binding energy because the As(V) ion has a slightly larger radius than the P(V) ion, and the electrostatic interaction is the dominating feature in these systems.
’ INTRODUCTION Phosphorus is one of the most important elements of all known forms of life on Earth along with carbon, hydrogen, nitrogen, oxygen and sulfur. In particular, it is an essential element for constructing a phosphate building block for the backbone of DNA and RNA, which carry genetic instructions for life. Phosphorus is a central component of the energy-carrying molecule in all life (by hydrolysis of adenosine triphosphate (ATP) and adenosine diphosphate (ADP)) and also of the phospholipids that form all cell membranes. Westheimer’s review article,1 “Why Nature Chose Phosphates”, is classic literature of bioorganic chemistry because it defines the chemical principles underlying a number of central biological process. Although arsenic has similar chemical properties to phosphorus, it is poisonous for most life by disrupting metabolic pathways. Recently, Wolfe-Simon has discovered a bacterium ‘GFAJ-1’2 in California’s Mono lake, which is able to survive using arsenic(V) rather than phosphorus(V) in its DNA, giving insight of arsenic ester linkages in the genetic material of the microorganism. The higher reactivity of arsenodiester, however, may not give DNA enough stability to support life (typical DNA with phosphate diester shows high stability in water, whereas the corresponding half-life of hypothetical arseno-DNA is approximately 1 min due to the redox instability of As(V) under physiological conditions).3 Thus, it is interesting to investigate the similarities and differences between arsenodiester and phosphodiester linkages. Some important structural and chemical similarities between phosphate and arsenate were cataloged in a recent article by Wolfe-Simon et al.4 entitled “Did Nature Also Choose Arsenic?”. r 2011 American Chemical Society
The sizes and electro-negativities of phosphate and arsenic are similar. Pauling electro-negativities for P and As in the trivalent states are 2.19 and 2.18, respectively.5 The atomic radii of P(V) and As(V) are 0.31 Å and 0.48 Å, respectively, while the van der Waals radii for P and As are 1.80 and 1.85 Å, respectively.6 Recently, Denning and Mackerell suggested that the arsenoDNA have similar conformations to phosphorus-based DNA on the basis of ab initio calculations.7 The backbone of the DNA strand is made from alternating phosphate and sugar residues. The sugars are joined together by phosphate groups that form phosphodiester bonds between the third and fifth carbon atoms of adjacent sugar rings. DNA exists in many possible conformations that include A-DNA, B-DNA and Z-DNA forms. The conformation that DNA adopts depends on the hydration level, DNA sequence, and the species and concentration of metal ions. When the hydration concentration is reduced by ∼70%, the conformation is changed from B-DNA to A-DNA, and the DNA replication commenses. As the alkali/ alkali-metal ion concentration increases, the A-DNA transforms to Z-DNA. Thus, in the arsenade-based backbone case, both the hydration phenomena and the cation effects are important. Herein, we study the DNA that uses arsenic backbone. It could be similar in nature to phosphate backbone to maintain the Special Issue: Pavel Hobza Festschrift Received: May 31, 2011 Revised: August 29, 2011 Published: September 16, 2011 11355
dx.doi.org/10.1021/jp2051245 | J. Phys. Chem. A 2011, 115, 11355–11361
The Journal of Physical Chemistry A
Figure 1. Structures of HmPO4 (Na+, K+; Mg2+, Ca2+).
(3 m)
and HmAsO4
ARTICLE
(3 m)
acids/anions interacting with a water molecule and alkali or alkali-earth metal cations
biological activity. Especially, surrounding materials such as water, Mg2+, and Mn2+, would have no side effects when interacting with the DNA backbone of arsenade basis. We focus our attention on comparing the interactions between HmPO4 (3 m) and HmAsO4 (3 m) (m = 1 3) acids and anions, since these are model molecules of the DNA backbone interacting with water molecules or metal ions. We investigate these interactions using ab initio calculations. The phosphoric acid (H3PO4) is used as the electrolyte in fuel cells, and the phosphorous acid (H3PO3; HP(OH)2O] is commonly used as oxoacids of phosphorus.8 12 The hydration phenomena of diverse molecular systems13,14 including cations,15 19 anions,20 26 simple acids27 29/bases,30 32 and salts33 37 have been reported. However, the structures, spectra, and thermochemical data for hydration of the inorganic acids containing phosphorus and arsenic atoms are still scarce.38 40 Thus, we are interested in studying the hydration of H3PO4 and H3AsO4. In these cases, we note some differences in noncovalent van der Waals interactions between the P and As inorganic acid systems interacting with the O atom in a water molecule as well as some differences between the P+ 3 3 3 O and As+ 3 3 3 O electrostatic interactions. Both arsenic and phosphorus are in the same Va group elements in the periodic table of the elements, and arsenic in period 4 is just in the next period with respect to phosphorus in period 3. Thus, we expect that
the size is similar, but arsenic of a slightly larger radius should have slightly larger bond distances with other interacting molecules and ions. To find the similarity and dissimilarity between arsenic and phosphoric acids/anions interacting with water and metal cations, as a mimic for DNA hydration and metal complexation, we compare their interaction energies, H-bond lengths (rOH), natural bond orbital (NBO) charges (q), and OH IR (infrared) stretching vibrational frequencies (νs) using ab initio calculations.
’ COMPUTATIONAL DETAILS We carried out geometry optimization along with harmonic frequency analysis, and calculated the interaction energies. Geometry optimization and harmonic frequency calculations were done at the Møller Plesset second order perturbation theory (MP2) with the aug-cc-pVDZ basis set (which will be denoted as aVDZ) and the effective core potential (CRENBL) for K+ and Ca+ by using the Gaussian 09 suite of programs.41 All the reported structures are at the local or global minima without imaginary frequencies. We also carried out MP2/aug-cc-pVTZ(aVTZ) and CCSD(T)/aVDZ calculations on the MP2/aVDZ optimized geometries. Then, we estimated the complete basis set (CBS) limit interaction energies using the extrapolation scheme 11356
dx.doi.org/10.1021/jp2051245 |J. Phys. Chem. A 2011, 115, 11355–11361
The Journal of Physical Chemistry A
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Table 1. Structures (Interacting Distances r in Å) of HmPO4 (3 m) and HmAsO4 Molecule or an Alkali/Alkaline-Earth Metal Cation (Na+, K+, Mg2+, or Ca2+)a
(3 m)
Acids/Anions Interacting with a Water
r(O Hw) r(P Y)
r(O Y)
r(H Ow)
H3PO4 3 3 3 H2O
3.235
2.702
1.939 1.759
H2PO4 3 3 3 H2O
3.348
2.659
1.672
r(O Hw) r(As Y)
r(O Y)
r(H Ow)
H3AsO4 3 3 3 H2O
3.258
2.726
1.925 1.783
H2AsO4 3 3 3 H2O
3.463
2.996
2.122 MeHPO4 3 3 3 H2O
3.242
3.050
1.742
MeHAsO4 3 3 3 H2O
3.360
2.968
1.667
Me2AsO4 3 H2AsO4 3 3 H2AsO4 3 3 HAsO42 3 3
3.333
2.941
2.042
2.787 (3.098)
2.319 (2.653)
3.184 (3.487) 2.373 (2.706)
2.696 (3.025) 1.994 (2.049)
2.711 (3.15)
2.311 (2.488)
2.216 Me2PO4 3 3 3 H2O H2PO4 3 3 3 Na+ H2PO4 3 3 3 K+ HPO42 3 3 3 Mg2+ a
HPO42 3 3 3 Ca2+
3.311
2.910
2.714 (2.969)
2.301 (2.563)
3.088 (3.438) 2.308 (2.437)
2.834 (2.895) 2.004 (2.069)
2.644 (3.071)
2.313 (2.477)
2.027
1.646 2.079 2.046
3 3 H2O + 3 Na + 3K 2+ 3 Mg
HAsO42 3 3 3 Ca2+
Y: Ow in a water molecule or a metal cation; Hw: H of a water molecule. Values in parentheses are optimized structures by PCM calculation.
utilizing the election correlation error proportional to N 3 for the aug-cc-pVNZ basis set (to be abbreviated as aVNZ).42,43 The CCSD(T)/CBS energies are estimated by using ΔE[CCSD(T)/ CBS] = ΔE(MP2/CBS) + [ΔE(CCSD(T)/aVDZ ΔE(MP2/ aVDZ)].43,44 Then, with the MP2/aVDZ zero-point energies (ZPEs) and thermal energies, the interaction energies (ΔEe) are used to evaluate the ZPE corrected interaction energies (ΔE0) at 0 K, and the enthalpy (ΔHr) and Gibbs free energies (ΔGr) at room temperature (298.15K) and 1 bar. It is generally known that the formation of monohydrated inorganic acids is determined mainly by hydrogen bonding, which is governed by electrostatic interaction between the positively/negatively charged O/H atom of an acid molecule and the negatively/positively charged O/H atom of a water molecule, while the dispersion-driven van der Waals interaction would not be insignificant. However, the As atom is larger than the P atom, and so the dispersion energy could not be neglected. Thus, we study the rXO distances related to the van der Waals interaction as well as the NBO charges localized on the X of the central atom of an acid molecule (X = P/As) and the O in a water molecule, which are related to the electrostatic energy. The NBO charges (q in a.u.) of the X/Y/H atom will be denoted as qX/Y/H, where Y denotes the O in the water molecule (or Ow where “w” denotes the water molecule) or a metal cation (Na+, K+, Mg2+ and Ca2+). To provide a more indepth analysis, we carried out a series of symmetry-adapted perturbation theory (SAPT) calculations45 52 based on dispersion-corrected density functional theory (DFT-D) using the SAPT-DFT implemented in the Molpro package.53 It provides a detailed description of molecular interactions in clusters, which are decomposed into electrostatic (Ees), induction (Eind), dispersion (Edisp), and exchange repulsion (Eexch) terms. However, the exchange-induction term (Eind-exch) and exchange-dispersion term (Edisp-exch) can often been added to Eind and Edisp, respectively, to form the effective induction (Eind*= Eind + Eind-exch) and the effective dispersion (Edisp*= Edisp + Edisp-exch), respectively, while the two terms are extracted from Eexch to form the effective exchange term (E ind-exch +E disp-exch )) as described pre(E exch *= E exch viously. 52,53
’ RESULTS AND DISCUSSION Figure 1 presents the most stable structures of HmPO4 (3 m) and HmAsO4 (3 m) acids/anions interacting with a water molecule and alkali or alkaline-earth metal cations (Na+, K+, Mg2+, and Ca2+) at the MP2/aVDZ level of theory. Tables 1 and 2 list structural parameters and binding energies, respectively. The structural parameters include the H-bond distances [r(O Y), r(H Y)] from a water molecule or a cation (Y: O in a water molecule, Na+, K+, Mg2+, or Ca2+) to the nearest O or H atom in an acid, and the van der Waals interaction distances [r(P/ As Y)] between the P/As atom of an acid and a Y atom. The binding energies include ZPE-corrected energies, binding enthalpies, and free binding energies at room temperature (298.15K) and 1 bar. As to the most stable structures, we calculated the NBO charges at the MP2/aVDZ level of theory. Table 3 shows the atomic charges via NBO analysis. The charge of P/As is 2.78/2.86 au, and the negative charges of the O atoms in the arsenic acid ( 1.09 au) are slightly larger than those in the phosphoric acid ( 1.06 au). Thus, the arsenic acid is more polar, which can give a larger contribution to the induction energy than the phosphoric acid. Table 4 shows the decomposed binding energies based on SAPT-DFT-D calculations with the aVDZ basis set using the PBE0 functional. Figure 1(1) depicts the most stable complexes of H3PO4 and H3AsO4 with a water molecule. The structures are topologically very similar. These global minimum energy structures have effective strong hydrogen bonds. The hydrogen bonds between the one OH group in H3XO4 (X = P, As) and the O atom in the water molecule and those between the H atom in the water molecule and the Od group in H3XO4, are on the same plane. The P 3 3 3 O and As 3 3 3 O distances are 3.235 and 3.258 Å, respectively. The binding energy of [H 3 AsO 4 3 3 3 H 2 O] is ∼3.2 kJ/mol lower than that of [H3PO4 3 3 3 H2O]. Although the van der Waals radius of the arsenic atom is slightly larger than the phosphorus atom by ∼0.05 Å, the difference of the rXO distances is reduced to only ∼0.025 Å, while the distances of [OH 3 3 3 O] in the hydrogen bonds of complexes of H3PO4 and H3AsO4 with a water are 1.814 and 1.839 Å, respectively. The angles (
