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Hydration of the cyanide ion: an ab initio quantum mechanical charge field molecular dynamics study Syed Tarique Moina and Thomas S. Hofer*b This paper presents an ab initio quantum mechanical charge field molecular dynamics simulation study of the cyanide anion (CN) in aqueous solution where hydrogen bond formation plays a dominant role in the hydration process. Preferential orientation of water hydrogens compared to oxygen atoms was quantified in terms of radial, angular as well as coordination number distributions. All structural results indicate that the water hydrogens are attracted towards CN atoms, thus contributing to the formation of the hydration layer. Moreover, a clear picture of the local arrangement of water molecules around the ellipsoidal CN ion is provided via angular-radial distribution and spatial distribution functions. Apart from the structural analysis, the evaluation of water dynamics in terms of ligand mean residence times and H-bond correlation functions indicates the weak structure making capacity of the CN ion. The
Received 18th August 2014, Accepted 17th October 2014 DOI: 10.1039/c4cp03697b
similar values of H-bond lifetimes obtained for the N Hwat and C Hwat bonds indicate an isokinetic behaviour of these H-bonds, since there is a very small difference in the magnitude of the lifetimes. On the other hand, the H-bond lifetimes between water molecules of the hydration shell, and between solute and solvent evidence the slightly stable hydration of the CN. Overall, the H-bonding dominates in the hydration process of the cyanide anion enabling it to become soluble in the aqueous environment
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associated to chemical and biological processes.
1 Introduction Anions are a prevalent class of molecules in the field of chemistry1,2 and have a great impact in biological3,4 as well as environmental5 processes. The awareness towards this species increased by the design and synthesis of abiotic receptors for anionic compounds.6–8 Among various anions the cyanide (CN) ion, the ionised product of hydrogen cyanide in water, is one of the most detrimental anions that has attracted considerable attention in the past.3,4 CN is abundantly found in natural sources such as in surface water from biological sources9 and is involved in a number of industrial processes10–12 such as gold mining, electroplating and metallurgy as well as in the production of organic chemicals and polymers. In biological systems cyanide acts toxic caused by absorption through lungs, the gastrointestinal tract and the skin.4 It is lethal to mammals making their cells unable to utilise oxygen, primarily upon binding to the heme unit of cytochrome c oxidase.13 Moreover, long-term exposure to lower levels of CN results in a variety of harmful effects leading to
a
H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan. E-mail: [email protected] b Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria. E-mail: [email protected]; Fax: +43-512-507-57199; Tel: +43-512-507-57102
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serious environmental damage.14 CN is also famed as ‘pseudohalogen’ having similar physical and chemical properties to halogens in many aspects15–20 but a distinctly different behaviour is displayed in its hydration mechanism.21 The structural attributes of the CN being an ellipsoidal22 instead of a spherical ion led to the formation of two nearly isoenergetic H-bonds with water molecules via either the carbon or nitrogen atom.21–23 Understanding the interaction between CN and water is desirable to investigate its physical properties and chemical processes in condensed environments, since little information is available so far about the molecular description of hydrated CN based on different cyanide–water clusters.24,25 A number of studies were reported on CN that provide information on its thermodynamic and spectroscopic properties.18,26 Furthermore, its molecular properties in crystals and dynamics of vibrational energy transfer in solutions were also investigated.16,27 High-pressure mass spectroscopic equilibrium methods and theoretical approaches were applied to understand its hydration and cluster forming properties with HCN.23 Details about the microscopic molecular interaction between the CN ion and water molecules were elucidated from the study of CN (H2O)n clusters.24 The H-bonding structure and dynamics of CN (H2O) monohydrate were evaluated by temperature-controlled photoelectron spectroscopy (PES) and high-level ab initio electronic structure calculations that were further extended to the larger CN (H2O)n, n = 2–5, clusters.25 Besides having H-bonding
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capacity,21–23 CN is also a strong coordinating ligand and a strong nucleophile.28–32 On the basis of these characteristic features, receptors are designed that are capable of sensing or binding cyanide selectively.33 The nucleophilic nature of cyanide is used to develop a simple, sensitive and highly selective sensor for the detection of very low concentrations of cyanide in an aqueous environment.34 Another study based on time-dependent density functional theory (TDDFT) focused on the investigation of the ground states and a number of singlet states of the cyanide sensors as well as their products, with a view to monitoring their geometries and photophysical properties.35 A similar study was also reported on a different cyanide sensor to probe the fluorescent sensing mechanism.36 Spectral profiles of the cyanide ion in aqueous solution were also analysed separating the vibrational and rotational components.37 Two dimensional infrared spectroscopy and relaxation of aqueous cyanide showed the combination mode from the 2D IR spectra of water and the cyanide ion having the same frequency range as that of water molecules, and the cyanide mode alone undergoes spectral diffusion on ultrafast time scales.38 A further study was also related to the measurement of the vibrational relaxation time of the CN ion in H2O and D2O.39 In addition to these studies, the H-bond energy of the CN–water complex and the hydration behaviour of the aqueous CN ion were evaluated via quantum chemical calculations and through force field based molecular dynamics (MD) simulation, respectively.40 Based on this background and in view of the importance of H-bonding not only for the evaluation of the solute–solvent interaction but also for designing and developing selective sensors for cyanide in an aqueous environment, the investigations of structural and dynamical properties of the hydrated CN ion and its hydrogen bonding capacity in a condensed phase were considered to be of great interest. For this reason, an ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) simulation of the aqueous CN ion was carried out to obtain detailed insight into its solvation properties in aqueous solution.
2 Methods Simulation method Like all hybrid quantum mechanical/molecular mechanical (QM/MM) methods, the ab initio quantum mechanical charge field molecular dynamics (QMCF-MD)41,42 formalism follows a similar partition scheme of dividing the system into a quantum mechanical (QM) and a molecular mechanical (MM) region. The main advantage of this technique is that it does not require non-Coulombic potential functions for solute–solvent interactions, but only for solvent–solvent contribution, i.e. no CN–water non-Coulombic interaction potentials were required in this study. This is achieved by employing an enlarged QM region, which is further divided into a core and a layer zone when considering the coupling between QM and MM regions. The large distance between particles located in the core region and MM atoms typically exceeds the cutoff distance of the nonCoulombic interactions and hence, these contributions are not
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required. Further details of the QMCF-MD formalism have been reported in a number of publications.42–44 The parallel version of the program ‘‘TURBOMOLE’’45 was used for the quantum chemical calculations whereas the MM region composed of water molecules was described by the BJH-CF2 water model.46,47 An adequate compromise between accuracy and computational effort was achieved by selecting Hartree–Fock (HF) level of theory with Dunning double zeta plus polarisation (DZP) basis sets48,49 for the QM region, which produced data in good agreement with experiments in a number of previous studies of hydrated anionic systems. The choice of the level of theory and basis sets was critical for the QMCF-MD simulation of the system and this was validated via binding energy calculations of different gas phase cyanide–water clusters at different levels of theory using DZP basis sets for atoms of the cyanide anion (CN) and water (H2O) molecules. Two possible configurations of cyanide monohydrate (CN H2O and OH2 CN) as well as cyanide dihydrate (OH2 CN H2O) along with their binding energies and geometrical features were obtained from optimisation calculations as given in Table 1. The binding energies calculated at the HF level are reasonably lower than obtained via the correlated MP2 and CCSD methods. On the other hand, the mostly widely employed DFT functional B3LYP produced higher values of the binding energies indicating a very rigid structure of the monohydrate whereas the dihydrate structure could not be reproduced – a deformed geometry was obtained after energy minimisation at this level of theory. The variation in the geometrical features of the hydrates also reflects the influence of different levels of theory. The optimised parameters obtained from the HF method represent a flexible description of the system, therefore, the method was considered more appropriate compared to DFT methods which also yield a too rigid description of aqueous solutions which in turn also affect the evaluation of dynamical properties.50–52 Simulation protocols The simulated system consists of one cyanide ion solvated in a cubic box of 1000 pre-equilibrated water molecules that corresponds to the density of pure water under ambient conditions (0.997 g cm3). The simulation box had a side length of 31.1 Å. The simulation was carried out in the canonical (NVT) ensemble and periodic boundary conditions were employed. The equations of motion were integrated using a second-order Adams–Bashforth predictor–corrector algorithm with a time step of 0.2 fs. The Nose–Hoover chain algorithm53 was employed to keep the temperature at 298.15 K. Long-range electrostatic interactions were treated by the reaction field method and the cutoff distance was set to 15.0 Å. As the starting configuration an equilibrated system obtained from the simulation of aqueous hydrogen peroxide54 has been employed due to the comparable size of the species. An extensive classical equilibration of more than one million MD steps (approx. 220 ps) employing the generalised AMBER force field parameters has been carried out, followed by an equilibration period of 50 000 MD steps (10 ps). Data collection was performed for 75 000 MD steps (15 ps).
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Table 1 Geometrical features and binding energies obtained via structure optimisation of different cyanide–water clusters or complexes at different levels of theory
Level of theory
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Cyanide–water complexes
Optimised parameters
HF
MP2
CCSD
B3LYP
rC–N (Å) rN H (Å) rH–O (Å) rO–H (Å) +C–N H (1) +N H–O (1) +H–O–H (1) DE (kcal mol1)
1.16 1.88 0.97 0.94 175.5 167.4 103.3 16.98
1.21 1.76 0.99 0.96 176.7 170.2 101.4 20.32
1.19 1.79 0.99 0.96 176.8 169.5 101.6 19.29
1.19 1.72 1.01 0.97 177.0 170.6 101.8 21.93
rN–C (Å) rC H (Å) rH–O (Å) rO–H (Å) +N–C H (1) +C H–O (1) +H–O–H (1) DE (kcal mol1)
1.16 2.05 0.97 0.94 177.1 167.3 103.3 16.98
1.21 1.88 1.00 0.96 177.6 169.8 101.0 21.44
1.19 1.93 0.99 0.96 177.4 168.9 101.3 19.81
1.18 1.84 1.01 0.97 177.4 170.2 101.4 23.19
rH–O (Å) rO–H (Å) rH C (Å) rC–N (Å) rN H (Å) rH–O (Å) rO–H (Å) +H–O–H (1) +O–H C (1) +H C–N (1) +C–N H (1) +N H–O (1) +H–O–H (1) DE (kcal mol1)
0.94 0.96 2.08 1.16 1.93 0.96 0.94 103.6 167.1 176.9 176.0 166.9 103.6 32.07
0.96 1.00 1.92 1.20 1.82 0.99 0.96 101.4 169.4 177.1 176.6 169.5 101.7 38.72
0.96 0.99 1.97 1.19 1.85 0.98 0.96 101.7 168.7 176.9 176.7 168.8 101.9 36.50
Geometry not converged
The centre of the QM region was defined by the centre of mass of the CN ion. Based on the results obtained from the classical pre-equilibration the overall radius of the QM region was set to 5.5 Å divided into the inner core of 0.75 Å containing the solute and the layer zone up to 5.5 Å covering the entire first hydration shell. A smoothing region of 0.2 Å was chosen to ensure continuous transitions between the QM and MM regions. Thus, in the case of the CN simulation, the smoothing was applied between 5.3 and 5.5 Å. The average number of QM molecules including the solute and its immediate surrounding water molecules is 19.
3 Results and discussion Structure The results obtained from the QMCF-MD simulation of aqueous CN provide significant insight into the hydration and hydrogen bonding patterns of the solute. The hydration structure involves two kinds of H-bonds: N Hwat–Owat and C Hwat–Owat, with the nitrogen and carbon atoms of the solute acting as H-bond acceptors. The hydration seems to perturb the structure of the solute, as demonstrated by the varying bond distance of the CN ion, amounting to 1.18 0.015 Å in good agreement with crystal data.55,56 The minor deviation of the bond distance results from
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the interaction of the CN ion with solvent molecules. The hydration of CN was primarily analysed via radial distribution functions (RDFs) of atomic pairs of solute and solvent molecules. Fig. 1a illustrates CEN–Owat RDF plotted between the centre of mass (CEN) of CN and water oxygens evaluating the entire hydration shell. A well-defined first peak between 2.8 and 4.2 Å indicates a full hydration layer whereas the second peak at approx. 5.4 Å indicates the formation of a second hydration shell. In contrast to the CEN–Owat RDF, the first peak of the CEN–Hwat distribution is observed at 2.4 Å, which is a clear indication of H-bond formation between solute and water molecules. Integration of the CEN–Owat RDF up to the first peak corresponds to an average of 6.8 water molecules being accommodated in the first hydration layer of the CN ion. To further analyse the CN–water interaction, solute–solvent RDFs using nitrogen and carbon as reference atoms yielded N–Owat, N–Hwat, C–Owat and C–Hwat pair distributions. Fig. 1b displays the N–Owat RDF having its first peak maximum at C3.0 Å, whereas a second shell is barely visible. On the other hand, the first peak in the N–Hwat RDF was observed at a lower distance of 2.1 Å, again highlighting H-bond formation between solute and solvent. The corresponding integral yielded an average of two water molecules that interact with the nitrogen atom. The second peak in the N–Hwat occurs roughly at 3.2 Å which is B1.0 Å further than the first shell peak, indicating H-bonding
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Fig. 2 Hemispherically restricted radial distribution functions (proximal and distal) of (a) nitrogen and (b) carbon atoms of the CN ion with water oxygens in comparison to the spherical distribution functions.
Fig. 1 Radial distribution functions of (a) center of mass (CEN), (b) nitrogen and (c) carbon atoms of the CN ion with atoms of water molecules.
between water molecules in the first and second hydration layers. In the vicinity of carbon, water molecules were found at a mean distance of 3.3 Å which corresponds to the first peak in the C–Owat RDF (cf. Fig. 1c). On the other hand, the C–Hwat RDF reveals its first peak between 1.6 and 2.7 Å with a maximum at 2.4 Å which is longer compared to the N–Hwat case. Integration of the C–Hwat RDF up to the first peak also yielded an average of two water molecules involved in H-bond formation. In comparison to the N–Hwat RDF, no indication of a second shell peak was found in the C–Hwat RDF, signifying that water molecules are less influenced beyond the H-bond distance at the carbon site. Since in the full spherical RDFs contributions of N- as well as C-coordinated water molecules are superimposed, a segmentation
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of the simulation system via a plane located at the centre of mass calculated using the C–N bond as the normal vector was performed, to further elaborate the hydration behaviour at both CN terminals. This enables an independent analysis of the hydration at each terminal of the solute via the evaluation of hemi-spherical RDFs:57 the solvent exposed or the proximal hemisphere as well as distal hemisphere corresponding to the region pointing away from the solute. Fig. 2a and b illustrate the hemispherical N–Owat and C–Owat pair distributions referring to the proximal domain in comparison to the RDFs of the distal hemisphere as well as the fully spherical case. According to the intensities observed in the hemi-spherical pair correlations for particles located at the proximal hemispheres, the probability of water molecules near the nitrogen atom is higher compared to the carbon atom. Integration of the proximal RDFs up to the peak minima yields on average 4 and 3 water molecules that are interacting with the nitrogen and carbon atoms, respectively. Conversely, RDFs for the distal hemispheres exhibit peak maxima at larger distances overlapping with the peak minima for the proximal RDFs, which highlights the particular usefulness of hemi-spherical pair correlation functions. In the case of a fully spherical analysis the peak of the first shell ligands of one atom is located close to the minimum between the first hydration shell and the bulk of the other atom. This superposition implies a much weaker hydration than observed when using a hemi-spherical partitioning.
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Fig. 3 Normalized angular distribution functions of N H–O and C H–O angles in hydrated CN. Fig. 5 Snapshot representing the CN hydration shell showing different types of H-bonds.
The characteristic H-bond angles (N Hwat–Owat and C Hwat–Owat) formed at the carbon and nitrogen sites were analysed as normalised angular distribution functions (ADFnorm) displayed in Fig. 3. Nearly identical distribution functions were obtained for both angles showing the maximal probability at B1601, which demonstrates deviation from the linear characteristics of the H-bonds. Fig. 4 depicts the coordination number distributions (CNDs) of first shell water oxygens surrounding the entire CN ion and for the water hydrogens involved in H-bond formation within a cutoff limit of 2.5 Å. The CND of the water oxygens with respect to CEN of the CN ion shows that on average 7 water molecules form the full hydration layer, but indicates a different number of water molecules to be present at the termini of the solute (cf. Fig. 4a). A maximum of 2 water molecules form hydrogen bonds at carbon and nitrogen sites of the CN ion which was deduced from the CND ranging from 0 to 5 as shown in Fig. 4b. The snapshot displayed in Fig. 5 visualises the full hydration layer surrounding the entire solute as well as hydrogen bonds between the solute and solvent.
Combining radial and angular information into a 2D-density plot57 provides detailed information on the local hydration of the CN ion depicted as contour plots in Fig. 6. The density maps of Owat and Hwat atoms showing intense peaks at both termini of CN indicate the localised distributions of water molecules. In the case of the Hwat distribution, the peaks are closer than those obtained for the Owat distribution thus indicating the role that the solute atoms play as H-bond acceptors. It is also worthwhile to mention that the H-bonds are formed simultaneously, since the density patterns in the distribution functions are quite similar at both termini of the solute. In the region perpendicular to the C–N axis the water density approaches zero thus indicating the geometrical influence of the solute being an ellipsoidal ion,22 not a spherical one. Though the peak observed next to the first had a lower density at each terminus, H-bonding between water molecules of the first and second hydration layers is highlighted. Furthermore, the arrangement of water molecules around the CN atoms was probed by the spatial distribution function (SDF) computed for water atoms displayed in Fig. 7. The SDF plots provide a clear picture of the association of solute atoms and the water molecules via H-bonding. The density distributions of the Hwat atoms (represented in blue colour) covered by the Owat density (red in colour) further reflect the H-bonding between solute and solvent atoms. The distribution plot at the nitrogen atom is more diffused compared to the carbon atom where the density of the water atoms exhibits a more localised behaviour. This could be due to the atomic size of the two atoms, thus demonstrating the anisotropic behaviour of the CN in aqueous solution which is in contrast to an earlier study that reported the anion as nearly spherical.15 Dynamics
Fig. 4 Coordination number distributions of (a) water molecules surrounding the entire CN ion and (b) water hydrogens involved in H-bonding with the CN atoms.
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The Mulliken charges derived for the solute atoms were monitored throughout the simulation as presented in Fig. 8. The charge on the nitrogen atom varies between 0.64 and 0.36, with an average value of 0.49 0.14, whereas the partial
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Fig. 6
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Angular-radial distributions of the (a) water oxygen and (b) water hydrogens found at the termini of the CN ion.
Fig. 8 Fluctuation of the Mulliken partial charges on the carbon and nitrogen atoms of the CN ion.
Fig. 7 Spatial distribution functions of water atoms with respect to center of mass of the CN ion (colour: carbon in grey, nitrogen in green, spatial density of water oxygen and hydrogen atoms in red and blue).
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charge of the carbon atom fluctuates about a mean value of 0.39 0.16. The magnitude of partial charges on the solute atoms is approximately similar and indicates that both atoms
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can act as H-bond acceptors. Due to the substantially lower partial charges compared to other anionic species, weak H-bonding can be expected which is also confirmed via H-bonding analysis described below. The sum of partial charges of the carbon and nitrogen atoms amounts to 0.89 0.02. The standard deviation is much smaller compared to that of the individual atoms indicating smaller fluctuation of the total charge compared to the individual partial charges. On average a charge of 0.11 is transferred to the surrounding solvent molecules, highlighting the importance of a quantum chemical treatment of the solute– solvent interaction to adequately account for such charge transfer effects. Mean residence times (MRTs, t) were determined for the water ligands of the first hydration layer around the entire cyanide ion. The MRT t is determined according to a direct measurement58 considering all exchange events persisting for periods longer than the predefined threshold t* set to 0.5 and 0.0 ps.58 The coefficient Rex corresponds to the number of attempts required to obtain one lasting (40.5) exchange event and it is given as the ratio between the number of all transitions occurring through a shell boundary (t* = 0.0 ps) and the number of changes persisting longer than 0.5 ps given as Rex ¼
0:0 Nex 0:5 Nex
(1)
where h. . .i indicates an average over all donor–acceptor pairs. SHB(t) corresponds to the probability of an initially H-bonded donor acceptor pair that remains bonded from the time 0 to t. The intermittent correlation function CHB(t) is calculated using the following expression CHB ðtÞ ¼
hhð0ÞhðtÞi hhð0Þhð0Þi
(3)
CHB(t) denotes the probability that H-bonds remain intact at time t, given that they were bonded at time t = 0 as well, irrespective of possible breaking of the bonds in the interim period. The associated relaxation time tHB estimates the average lifetimes of H-bonds between CN and the water molecule, and between water molecules in the respective hydration layers by fitting time correlation functions to a double-exponential expression defined as y = a et/tl + (1 a) et/ts
(4)
where tl and ts correspond to the long and short contribution of the H-bond relaxation, and to the H-bond lifetime. The results of SHB(t) and CHB(t) for the cyanide–water H-bonds are displayed in Fig. 9, and the corresponding lifetimes are listed in Table 3. The decay of SHB(t) and CHB(t) correlation functions occurs at a very similar rate for the N Hwat and C Hwat bonds. Only a small difference in the magnitude of
0.5 where N0.0 ex and Nex correspond to the number of exchange events occurring for t* 0.0 and 0.5 ps, respectively. The MRT value obtained for water ligands with respect to the CEN of the CN is slightly higher than the MRT for pure water (1.30 ps) obtained from a similar simulation study58 (cf. Table 2). The dynamical data also predict an analogous behaviour regarding the stability of the hydration shell and pure water. Very close Rex values for the water ligands of the CN and of pure water further support the analogy between the two systems. In addition H-bonds between the CN ion and water molecules are a further significant factor to characterise the stability of the hydration shell. The evaluation of H-bond dynamics at each terminus of the solute will also be helpful for the interpretation of relative strength of these bonds. Dynamics of hydrogen bonds between specific donor–acceptor pairs were investigated using time correlation functions (TCFs). In this approach two H-bond population variables are defined: h(t) corresponds to unity when a particular H-bonding takes place between the solute and solvent at time t and is zero otherwise whereas H(t) = 1 if only the donor–acceptor pair remains continuously hydrogen-bonded in the time interval [0, t]. The continuous H-bond correlation function SHB(t) is defined as
SHB ðtÞ ¼
hHð0ÞHðtÞi hHð0ÞHð0Þi
(2)
Table 2 Dynamical data for water molecules of the hydrated CN in comparison to pure water from QMCF-MD simulation
CN –water system Pure water
N0.5 ex
N0.0 ex
t0.5 (ps)
t0.0 (ps)
Rex
75 20
358 131
1.37 1.30
0.04 0.19
4.8 6.6
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Fig. 9 Mean S(t) and C(t) of hydrogen bonds formed between the CN and water molecules. The respective double-exponential fitting is depicted in red.
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Table 3 C(t) and S(t) hydrogen bond correlation functions computed for H-bonds between the cyanide anion and water molecules, and between water molecules of the hydration shell
C(t)/ps tl
ts
tl
ts
N Hwat C Hwat H2Oa
0.68 0.91 0.99
0.06 0.04 0.11
0.18 0.07 0.48
0.05 0.003 0.13
a
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S(t)/ps
Type of H-bonds
H-bonds between water molecules in the hydration shell.
decay constants is observed, indicating that these two bonds are of comparable strength. Furthermore, the average lifetimes for the N Hwat and C Hwat bonds were obtained as 0.6 and 0.9 ps, respectively, demonstrating similar kinetics of the H-bonds (isoenergetic H-bonds).21–23 The isokinetic behaviour of H-bonds can be attributed to the similar partial charges and sizes of the solute atoms which share the same period and are groupneighbours in the periodic table. The higher H-bond lifetimes for the N Hwat and C Hwat bonds than that of the pure water (0.5 ps)50,59,60 indicate a slight structure making property of the solute. On the other hand, the small difference between the H-bond lifetimes for the two bonds was also found to possibly be due to the varying partial charges of the solute and the immediate solvent environment, since charge transfer takes place in the polar system leading to different polar interactions. The H-bond lifetime of the water molecules in the hydration shell was also computed using the same time correlation functions showing similar decay patterns as depicted in Fig. 10. The corresponding HB lifetimes of water molecules in the hydration shell were calculated as 0.99 ps, being slightly larger than those of the pure solvent (0.5 ps),50,59,60 which also indicates the occurrence of charge transfer from the solute to the solvent. In comparison to the H-bond lifetime of pure water, the dynamics of the N Hwat and C Hwat bonds and of the hydration shell demonstrate an intermediate stability of the hydration shell of the CN ion.
Fig. 10 Mean S(t) and C(t) of hydrogen bonds between water molecules of the CN hydration shell. The respective double-exponential fitting is depicted in red.
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4 Conclusion Detailed information on the solvation properties of the aqueous cyanide ion highlights the capabilities of the ab initio QMCFMD formalism, treating the solute and its immediate hydration environment at a quantum mechanical level. Structural and dynamical data obtained from the simulation demonstrate the specific localisation of water molecules at each atom of the cyanide ion due to its distinct geometrical feature. The simultaneous H-bond formation plays a key role in the solubility of the cyanide ion in aqueous solution as revealed by the H-bond lifetime calculations reflecting isokinetic behaviour of the H-bonds. The increased value of the H-bond lifetime and MRTs of the water molecules point towards a slight structure making ability of the ion. The characterisation of hydrated cyanide emphasises that H-bonding is responsible for the solubility of the cyanide ion in aqueous solution, implying its detrimental effects in the environment. Therefore, the description of the hydration behaviour based on the structural and dynamical analysis has a significant impact on the characterisation of such H-bonded systems associated chemically and biologically.
Acknowledgements Financial support for this work by the ATC-AIC-APC project from BMWF ASEA-UNINET Austria for Syed Tarique Moin is gratefully acknowledged. This work was supported by the Austrian Ministry of Science BMWF UniInfrastrukturprogramm as part of the Research Focal Point Scientific Computing at the University of Innsbruck.
References 1 F. A. Cotton, G. Wilkinson, C. A. Murillo and M. Bochmann, Advanced Inorganic Chemistry, Wiley, New York, 6th edn, 1999. ˜a, Supra2 A. Bianchi, K. Bowman-James and E. Garcı´a-Espan molecular Chemistry of Anions, Wiley-VCH, New York, 1997. 3 K. W. Kulig, Cyanide Toxicity, U.S. Department of Health and Human Services, Atlanta, GA, 1991. 4 S. I. Baskin and T. G. Brewer, Medical Aspects of Chemical and Biological Warfare, TMM Publications, 1997. 5 C. Baird and M. Cann, Environmental Chemistry, Freeman, 2012. 6 E. A. Katayev, Y. A. Ustynyuk and J. L. Sessler, Coord. Chem. Rev., 2006, 250, 3004–3037. 7 P. Anzenbacher Jr, R. Nishiyabu and M. A. Palacios, Coord. Chem. Rev., 2006, 250, 2929–2938. 8 P. A. Gale, Acc. Chem. Res., 2006, 39, 465–475. 9 Z. Xu, X. Chen, H. N. Kim and Y. Yoon, Chem. Soc. Rev., 2010, 39, 127–137. 10 G. C. Miller and C. A. Pritsos, Medical aspects of chemical and biological warfare, 2001. 11 C. Young, L. Tidwell and C. Anderson, Cyanide: Social, Industrial and Economic Aspects, Metals, and Materials Society, Warrendale, 2001.
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¨sch, A. Rubo, M. Sauer, 12 E. Gail, S. Gos, R. Kulzer, J. Loro R. Kellens, J. Reddy, N. Steier and W. Hasenpusch, Cyano Compounds, Inorganic, Ullmann’s Encyclopedia of Industrial Chemistry, Electronic Release, Wiley-VCH, Weinheim, October 2011. 13 B. Vennesland, E. E. Conn, C. J. Knownles, J. Westly and F. Wissing, Cyanide in Biology, Academic Press, London, 1981. 14 D. Nhassico, H. Muquingue, J. Cliff, A. Cumbana and J. H. Bradbury, J. Sci. Food Agric., 2008, 88, 2043–2049. 15 M. Meot-Ner, S. M. Cybulski, S. Scheinere and J. F. Liebman, J. Phys. Chem., 1988, 92, 2738–2745. 16 P. W. Fowler and M. L. Klein, J. Chem. Phys., 1986, 85, 3913–3916. 17 L. X. Dang, J. Phys. Chem. B, 2002, 106, 10388–10394. 18 S. E. Bradforth, E. H. Kim, D. W. Arnold and D. M. Neumark, J. Chem. Phys., 1993, 98, 800–810. 19 T. R. Miller, CRC Handbook of Chemistry and Physics, CRC, Cleveland, 72nd edn, 1991. 20 J. D. Payzant, R. Yamdagni and P. Kebarle, Can. J. Chem., 1971, 49, 3308–3314. 21 T. J. Lee, J. Am. Chem. Soc., 1989, 111, 7362–7371. 22 T. Ikeda, K. Nishimoto and T. Asada, Chem. Phys. Lett., 1996, 248, 329–335. 23 J. W. Larson and T. B. McMahon, J. Am. Chem. Soc., 1987, 109, 6230–6236. 24 X. Wang, J. C. Werhahn, L. Wang, K. Kowalski, A. Laubereau and S. S. Xantheas, J. Phys. Chem. A, 2009, 113, 9579–9584. 25 X. Wang, K. Kowalski, L. Wang and S. S. Xantheas, J. Chem. Phys., 2010, 132, 124306. 26 R. Klein, R. P. McGinnis and S. R. Leone, Chem. Phys. Lett., 1983, 100, 475–478. 27 M. Ferreira, I. R. Mcdonald and M. L. Klein, J. Chem. Phys., 1986, 84, 3975–3985. 28 Q. Zeng, P. Cai, Z. Li, J. Qin and B. Tang, Chem. Commun., 2008, 1094–1096. 29 Y. Kim and J. Hong, Chem. Commun., 2002, 512–513. 30 H. Miyaji, D. Kim, B. Chang, E. Park, S. Park and K. Ahn, Chem. Commun., 2008, 753–755. 31 Y. M. Chung, H. Lee and K. H. Ahn, J. Org. Chem., 2006, 71, 9470–9474. 32 Y. M. Chung, B. Raman, D. S. Kim and K. H. Ahn, Chem. Commun., 2006, 2186–2188. 33 K. C. Song, K. M. Lee, N. V. Nghia, W. Y. Sung, Y. Do and M. H. Lee, Organometallics, 2013, 32, 817–823. 34 H. Niu, D. Su, X. Jiang, W. Yang, Z. Yin, J. He and J. Cheng, Org. Biomol. Chem., 2008, 6, 3038–3040. 35 G. Li, P. Song and G. He, Chin. J. Chem. Phys., 2011, 24, 305–310.
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Paper
36 G. Li, G. Zhao, K. Han and G. He, J. Comput. Chem., 2011, 32, 668–674. 37 J. Lascombe and M. Perrot, Faraday Discuss. Chem. Soc., 1978, 66, 216–230. 38 C. Kuo and R. M. Hochstrasser, Chem. Phys., 2007, 341, 21–28. 39 P. Hamm, M. Lim and R. M. Hochstrasser, J. Chem. Phys., 1997, 107(24), 10523–10531. 40 R. Sansone, C. Ebner and M. Probst, J. Mol. Liq., 2000, 88, 129–150. 41 B. M. Rode, T. S. Hofer, B. R. Randolf, C. F. Schwenk, D. Xenides and V. Vchirawongkwin, Theor. Chem. Acc., 2006, 115, 77–85. 42 T. S. Hofer, A. B. Pribil, B. Randolf and B. Rode, Adv. Quantum Chem., 2010, 213–246. 43 T. S. Hofer, B. M. Rode, A. B. Pribil and B. R. Randolf, Adv. Inorg. Chem., 2010, 62, 143–175. 44 T. S. Hofer, Pure Appl. Chem., 2014, 86, 1–13. ¨r, M. Ha ¨ser, H. Horn and C. Ko ¨lmel, 45 R. Ahlrichs, M. Ba Chem. Phys. Lett., 1989, 162, 165–169. 46 F. H. Stillinger and A. Rahman, J. Chem. Phys., 1978, 68(2), 666–670. 47 P. Bopp, G. Jancso and K. Heinzinger, Chem. Phys. Lett., 1983, 98, 129–133. 48 T. H. Dunning, J. Chem. Phys., 1970, 53, 2823–2833. 49 E. Magnusson and H. F. Schaefer, J. Chem. Phys., 1985, 83, 5721–5726. 50 D. Xenides, B. R. Randolf and B. M. Rode, J. Chem. Phys., 2005, 122, 4506–4515. 51 S. Yoo, X. C. Zeng and S. S. Xantheas, J. Chem. Phys., 2009, 130, 221102–221105. 52 J. Schmidt, J. VandeVondele, I. F. W. Kuo, D. Sebastiani, J. I. Siepmann, J. Hutter and C. J. Mundy, J. Phys. Chem. B, 2009, 113(35), 11959–11964. 53 G. J. Martyna, M. L. Klein and M. Tuckerman, J. Chem. Phys., 1992, 97, 2635–2643. 54 S. T. Moin, T. S. Hofer, B. R. Randolf and B. M. Rode, Comput. Theor. Chem., 2012, 980, 15–22. 55 R. M. Bozorth, J. Am. Chem. Soc., 1922, 44, 317–323. 56 D. L. Price, J. M. Rowe, J. J. Rush, E. Prince, D. G. Hinks and S. Susman, J. Chem. Phys., 1972, 56, 3697–3702. 57 A. K. H. Weiss and T. S. Hofer, RSC Adv., 2014, 3, 1606–1635. 58 T. S. Hofer, H. T. Tran, C. F. Schwenk and B. M. Rode, J. Comput. Chem., 2004, 25(2), 211. 59 A. J. Lock, S. Woutersen and H. J. Bakker, J. Phys. Chem. A, 2001, 105(8), 1238. 60 A. J. Lock, S. Woutersen and H. J. Bakker, Femtochemistry and Femtobiology, Word Scientific, Singapore, 2001.
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Hydration of the cyanide ion: an ab initio quantum mechanical charge field molecular dynamics study Syed Tarique Moina and Thomas S. Hofer*b This paper presents an ab initio quantum mechanical charge field molecular dynamics simulation study of the cyanide anion (CN) in aqueous solution where hydrogen bond formation plays a dominant role in the hydration process. Preferential orientation of water hydrogens compared to oxygen atoms was quantified in terms of radial, angular as well as coordination number distributions. All structural results indicate that the water hydrogens are attracted towards CN atoms, thus contributing to the formation of the hydration layer. Moreover, a clear picture of the local arrangement of water molecules around the ellipsoidal CN ion is provided via angular-radial distribution and spatial distribution functions. Apart from the structural analysis, the evaluation of water dynamics in terms of ligand mean residence times and H-bond correlation functions indicates the weak structure making capacity of the CN ion. The
Received 18th August 2014, Accepted 17th October 2014 DOI: 10.1039/c4cp03697b
similar values of H-bond lifetimes obtained for the N Hwat and C Hwat bonds indicate an isokinetic behaviour of these H-bonds, since there is a very small difference in the magnitude of the lifetimes. On the other hand, the H-bond lifetimes between water molecules of the hydration shell, and between solute and solvent evidence the slightly stable hydration of the CN. Overall, the H-bonding dominates in the hydration process of the cyanide anion enabling it to become soluble in the aqueous environment
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associated to chemical and biological processes.
1 Introduction Anions are a prevalent class of molecules in the field of chemistry1,2 and have a great impact in biological3,4 as well as environmental5 processes. The awareness towards this species increased by the design and synthesis of abiotic receptors for anionic compounds.6–8 Among various anions the cyanide (CN) ion, the ionised product of hydrogen cyanide in water, is one of the most detrimental anions that has attracted considerable attention in the past.3,4 CN is abundantly found in natural sources such as in surface water from biological sources9 and is involved in a number of industrial processes10–12 such as gold mining, electroplating and metallurgy as well as in the production of organic chemicals and polymers. In biological systems cyanide acts toxic caused by absorption through lungs, the gastrointestinal tract and the skin.4 It is lethal to mammals making their cells unable to utilise oxygen, primarily upon binding to the heme unit of cytochrome c oxidase.13 Moreover, long-term exposure to lower levels of CN results in a variety of harmful effects leading to
a
H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan. E-mail: [email protected] b Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria. E-mail: [email protected]; Fax: +43-512-507-57199; Tel: +43-512-507-57102
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serious environmental damage.14 CN is also famed as ‘pseudohalogen’ having similar physical and chemical properties to halogens in many aspects15–20 but a distinctly different behaviour is displayed in its hydration mechanism.21 The structural attributes of the CN being an ellipsoidal22 instead of a spherical ion led to the formation of two nearly isoenergetic H-bonds with water molecules via either the carbon or nitrogen atom.21–23 Understanding the interaction between CN and water is desirable to investigate its physical properties and chemical processes in condensed environments, since little information is available so far about the molecular description of hydrated CN based on different cyanide–water clusters.24,25 A number of studies were reported on CN that provide information on its thermodynamic and spectroscopic properties.18,26 Furthermore, its molecular properties in crystals and dynamics of vibrational energy transfer in solutions were also investigated.16,27 High-pressure mass spectroscopic equilibrium methods and theoretical approaches were applied to understand its hydration and cluster forming properties with HCN.23 Details about the microscopic molecular interaction between the CN ion and water molecules were elucidated from the study of CN (H2O)n clusters.24 The H-bonding structure and dynamics of CN (H2O) monohydrate were evaluated by temperature-controlled photoelectron spectroscopy (PES) and high-level ab initio electronic structure calculations that were further extended to the larger CN (H2O)n, n = 2–5, clusters.25 Besides having H-bonding
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capacity,21–23 CN is also a strong coordinating ligand and a strong nucleophile.28–32 On the basis of these characteristic features, receptors are designed that are capable of sensing or binding cyanide selectively.33 The nucleophilic nature of cyanide is used to develop a simple, sensitive and highly selective sensor for the detection of very low concentrations of cyanide in an aqueous environment.34 Another study based on time-dependent density functional theory (TDDFT) focused on the investigation of the ground states and a number of singlet states of the cyanide sensors as well as their products, with a view to monitoring their geometries and photophysical properties.35 A similar study was also reported on a different cyanide sensor to probe the fluorescent sensing mechanism.36 Spectral profiles of the cyanide ion in aqueous solution were also analysed separating the vibrational and rotational components.37 Two dimensional infrared spectroscopy and relaxation of aqueous cyanide showed the combination mode from the 2D IR spectra of water and the cyanide ion having the same frequency range as that of water molecules, and the cyanide mode alone undergoes spectral diffusion on ultrafast time scales.38 A further study was also related to the measurement of the vibrational relaxation time of the CN ion in H2O and D2O.39 In addition to these studies, the H-bond energy of the CN–water complex and the hydration behaviour of the aqueous CN ion were evaluated via quantum chemical calculations and through force field based molecular dynamics (MD) simulation, respectively.40 Based on this background and in view of the importance of H-bonding not only for the evaluation of the solute–solvent interaction but also for designing and developing selective sensors for cyanide in an aqueous environment, the investigations of structural and dynamical properties of the hydrated CN ion and its hydrogen bonding capacity in a condensed phase were considered to be of great interest. For this reason, an ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) simulation of the aqueous CN ion was carried out to obtain detailed insight into its solvation properties in aqueous solution.
2 Methods Simulation method Like all hybrid quantum mechanical/molecular mechanical (QM/MM) methods, the ab initio quantum mechanical charge field molecular dynamics (QMCF-MD)41,42 formalism follows a similar partition scheme of dividing the system into a quantum mechanical (QM) and a molecular mechanical (MM) region. The main advantage of this technique is that it does not require non-Coulombic potential functions for solute–solvent interactions, but only for solvent–solvent contribution, i.e. no CN–water non-Coulombic interaction potentials were required in this study. This is achieved by employing an enlarged QM region, which is further divided into a core and a layer zone when considering the coupling between QM and MM regions. The large distance between particles located in the core region and MM atoms typically exceeds the cutoff distance of the nonCoulombic interactions and hence, these contributions are not
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required. Further details of the QMCF-MD formalism have been reported in a number of publications.42–44 The parallel version of the program ‘‘TURBOMOLE’’45 was used for the quantum chemical calculations whereas the MM region composed of water molecules was described by the BJH-CF2 water model.46,47 An adequate compromise between accuracy and computational effort was achieved by selecting Hartree–Fock (HF) level of theory with Dunning double zeta plus polarisation (DZP) basis sets48,49 for the QM region, which produced data in good agreement with experiments in a number of previous studies of hydrated anionic systems. The choice of the level of theory and basis sets was critical for the QMCF-MD simulation of the system and this was validated via binding energy calculations of different gas phase cyanide–water clusters at different levels of theory using DZP basis sets for atoms of the cyanide anion (CN) and water (H2O) molecules. Two possible configurations of cyanide monohydrate (CN H2O and OH2 CN) as well as cyanide dihydrate (OH2 CN H2O) along with their binding energies and geometrical features were obtained from optimisation calculations as given in Table 1. The binding energies calculated at the HF level are reasonably lower than obtained via the correlated MP2 and CCSD methods. On the other hand, the mostly widely employed DFT functional B3LYP produced higher values of the binding energies indicating a very rigid structure of the monohydrate whereas the dihydrate structure could not be reproduced – a deformed geometry was obtained after energy minimisation at this level of theory. The variation in the geometrical features of the hydrates also reflects the influence of different levels of theory. The optimised parameters obtained from the HF method represent a flexible description of the system, therefore, the method was considered more appropriate compared to DFT methods which also yield a too rigid description of aqueous solutions which in turn also affect the evaluation of dynamical properties.50–52 Simulation protocols The simulated system consists of one cyanide ion solvated in a cubic box of 1000 pre-equilibrated water molecules that corresponds to the density of pure water under ambient conditions (0.997 g cm3). The simulation box had a side length of 31.1 Å. The simulation was carried out in the canonical (NVT) ensemble and periodic boundary conditions were employed. The equations of motion were integrated using a second-order Adams–Bashforth predictor–corrector algorithm with a time step of 0.2 fs. The Nose–Hoover chain algorithm53 was employed to keep the temperature at 298.15 K. Long-range electrostatic interactions were treated by the reaction field method and the cutoff distance was set to 15.0 Å. As the starting configuration an equilibrated system obtained from the simulation of aqueous hydrogen peroxide54 has been employed due to the comparable size of the species. An extensive classical equilibration of more than one million MD steps (approx. 220 ps) employing the generalised AMBER force field parameters has been carried out, followed by an equilibration period of 50 000 MD steps (10 ps). Data collection was performed for 75 000 MD steps (15 ps).
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Table 1 Geometrical features and binding energies obtained via structure optimisation of different cyanide–water clusters or complexes at different levels of theory
Level of theory
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Cyanide–water complexes
Optimised parameters
HF
MP2
CCSD
B3LYP
rC–N (Å) rN H (Å) rH–O (Å) rO–H (Å) +C–N H (1) +N H–O (1) +H–O–H (1) DE (kcal mol1)
1.16 1.88 0.97 0.94 175.5 167.4 103.3 16.98
1.21 1.76 0.99 0.96 176.7 170.2 101.4 20.32
1.19 1.79 0.99 0.96 176.8 169.5 101.6 19.29
1.19 1.72 1.01 0.97 177.0 170.6 101.8 21.93
rN–C (Å) rC H (Å) rH–O (Å) rO–H (Å) +N–C H (1) +C H–O (1) +H–O–H (1) DE (kcal mol1)
1.16 2.05 0.97 0.94 177.1 167.3 103.3 16.98
1.21 1.88 1.00 0.96 177.6 169.8 101.0 21.44
1.19 1.93 0.99 0.96 177.4 168.9 101.3 19.81
1.18 1.84 1.01 0.97 177.4 170.2 101.4 23.19
rH–O (Å) rO–H (Å) rH C (Å) rC–N (Å) rN H (Å) rH–O (Å) rO–H (Å) +H–O–H (1) +O–H C (1) +H C–N (1) +C–N H (1) +N H–O (1) +H–O–H (1) DE (kcal mol1)
0.94 0.96 2.08 1.16 1.93 0.96 0.94 103.6 167.1 176.9 176.0 166.9 103.6 32.07
0.96 1.00 1.92 1.20 1.82 0.99 0.96 101.4 169.4 177.1 176.6 169.5 101.7 38.72
0.96 0.99 1.97 1.19 1.85 0.98 0.96 101.7 168.7 176.9 176.7 168.8 101.9 36.50
Geometry not converged
The centre of the QM region was defined by the centre of mass of the CN ion. Based on the results obtained from the classical pre-equilibration the overall radius of the QM region was set to 5.5 Å divided into the inner core of 0.75 Å containing the solute and the layer zone up to 5.5 Å covering the entire first hydration shell. A smoothing region of 0.2 Å was chosen to ensure continuous transitions between the QM and MM regions. Thus, in the case of the CN simulation, the smoothing was applied between 5.3 and 5.5 Å. The average number of QM molecules including the solute and its immediate surrounding water molecules is 19.
3 Results and discussion Structure The results obtained from the QMCF-MD simulation of aqueous CN provide significant insight into the hydration and hydrogen bonding patterns of the solute. The hydration structure involves two kinds of H-bonds: N Hwat–Owat and C Hwat–Owat, with the nitrogen and carbon atoms of the solute acting as H-bond acceptors. The hydration seems to perturb the structure of the solute, as demonstrated by the varying bond distance of the CN ion, amounting to 1.18 0.015 Å in good agreement with crystal data.55,56 The minor deviation of the bond distance results from
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the interaction of the CN ion with solvent molecules. The hydration of CN was primarily analysed via radial distribution functions (RDFs) of atomic pairs of solute and solvent molecules. Fig. 1a illustrates CEN–Owat RDF plotted between the centre of mass (CEN) of CN and water oxygens evaluating the entire hydration shell. A well-defined first peak between 2.8 and 4.2 Å indicates a full hydration layer whereas the second peak at approx. 5.4 Å indicates the formation of a second hydration shell. In contrast to the CEN–Owat RDF, the first peak of the CEN–Hwat distribution is observed at 2.4 Å, which is a clear indication of H-bond formation between solute and water molecules. Integration of the CEN–Owat RDF up to the first peak corresponds to an average of 6.8 water molecules being accommodated in the first hydration layer of the CN ion. To further analyse the CN–water interaction, solute–solvent RDFs using nitrogen and carbon as reference atoms yielded N–Owat, N–Hwat, C–Owat and C–Hwat pair distributions. Fig. 1b displays the N–Owat RDF having its first peak maximum at C3.0 Å, whereas a second shell is barely visible. On the other hand, the first peak in the N–Hwat RDF was observed at a lower distance of 2.1 Å, again highlighting H-bond formation between solute and solvent. The corresponding integral yielded an average of two water molecules that interact with the nitrogen atom. The second peak in the N–Hwat occurs roughly at 3.2 Å which is B1.0 Å further than the first shell peak, indicating H-bonding
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Fig. 2 Hemispherically restricted radial distribution functions (proximal and distal) of (a) nitrogen and (b) carbon atoms of the CN ion with water oxygens in comparison to the spherical distribution functions.
Fig. 1 Radial distribution functions of (a) center of mass (CEN), (b) nitrogen and (c) carbon atoms of the CN ion with atoms of water molecules.
between water molecules in the first and second hydration layers. In the vicinity of carbon, water molecules were found at a mean distance of 3.3 Å which corresponds to the first peak in the C–Owat RDF (cf. Fig. 1c). On the other hand, the C–Hwat RDF reveals its first peak between 1.6 and 2.7 Å with a maximum at 2.4 Å which is longer compared to the N–Hwat case. Integration of the C–Hwat RDF up to the first peak also yielded an average of two water molecules involved in H-bond formation. In comparison to the N–Hwat RDF, no indication of a second shell peak was found in the C–Hwat RDF, signifying that water molecules are less influenced beyond the H-bond distance at the carbon site. Since in the full spherical RDFs contributions of N- as well as C-coordinated water molecules are superimposed, a segmentation
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of the simulation system via a plane located at the centre of mass calculated using the C–N bond as the normal vector was performed, to further elaborate the hydration behaviour at both CN terminals. This enables an independent analysis of the hydration at each terminal of the solute via the evaluation of hemi-spherical RDFs:57 the solvent exposed or the proximal hemisphere as well as distal hemisphere corresponding to the region pointing away from the solute. Fig. 2a and b illustrate the hemispherical N–Owat and C–Owat pair distributions referring to the proximal domain in comparison to the RDFs of the distal hemisphere as well as the fully spherical case. According to the intensities observed in the hemi-spherical pair correlations for particles located at the proximal hemispheres, the probability of water molecules near the nitrogen atom is higher compared to the carbon atom. Integration of the proximal RDFs up to the peak minima yields on average 4 and 3 water molecules that are interacting with the nitrogen and carbon atoms, respectively. Conversely, RDFs for the distal hemispheres exhibit peak maxima at larger distances overlapping with the peak minima for the proximal RDFs, which highlights the particular usefulness of hemi-spherical pair correlation functions. In the case of a fully spherical analysis the peak of the first shell ligands of one atom is located close to the minimum between the first hydration shell and the bulk of the other atom. This superposition implies a much weaker hydration than observed when using a hemi-spherical partitioning.
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Fig. 3 Normalized angular distribution functions of N H–O and C H–O angles in hydrated CN. Fig. 5 Snapshot representing the CN hydration shell showing different types of H-bonds.
The characteristic H-bond angles (N Hwat–Owat and C Hwat–Owat) formed at the carbon and nitrogen sites were analysed as normalised angular distribution functions (ADFnorm) displayed in Fig. 3. Nearly identical distribution functions were obtained for both angles showing the maximal probability at B1601, which demonstrates deviation from the linear characteristics of the H-bonds. Fig. 4 depicts the coordination number distributions (CNDs) of first shell water oxygens surrounding the entire CN ion and for the water hydrogens involved in H-bond formation within a cutoff limit of 2.5 Å. The CND of the water oxygens with respect to CEN of the CN ion shows that on average 7 water molecules form the full hydration layer, but indicates a different number of water molecules to be present at the termini of the solute (cf. Fig. 4a). A maximum of 2 water molecules form hydrogen bonds at carbon and nitrogen sites of the CN ion which was deduced from the CND ranging from 0 to 5 as shown in Fig. 4b. The snapshot displayed in Fig. 5 visualises the full hydration layer surrounding the entire solute as well as hydrogen bonds between the solute and solvent.
Combining radial and angular information into a 2D-density plot57 provides detailed information on the local hydration of the CN ion depicted as contour plots in Fig. 6. The density maps of Owat and Hwat atoms showing intense peaks at both termini of CN indicate the localised distributions of water molecules. In the case of the Hwat distribution, the peaks are closer than those obtained for the Owat distribution thus indicating the role that the solute atoms play as H-bond acceptors. It is also worthwhile to mention that the H-bonds are formed simultaneously, since the density patterns in the distribution functions are quite similar at both termini of the solute. In the region perpendicular to the C–N axis the water density approaches zero thus indicating the geometrical influence of the solute being an ellipsoidal ion,22 not a spherical one. Though the peak observed next to the first had a lower density at each terminus, H-bonding between water molecules of the first and second hydration layers is highlighted. Furthermore, the arrangement of water molecules around the CN atoms was probed by the spatial distribution function (SDF) computed for water atoms displayed in Fig. 7. The SDF plots provide a clear picture of the association of solute atoms and the water molecules via H-bonding. The density distributions of the Hwat atoms (represented in blue colour) covered by the Owat density (red in colour) further reflect the H-bonding between solute and solvent atoms. The distribution plot at the nitrogen atom is more diffused compared to the carbon atom where the density of the water atoms exhibits a more localised behaviour. This could be due to the atomic size of the two atoms, thus demonstrating the anisotropic behaviour of the CN in aqueous solution which is in contrast to an earlier study that reported the anion as nearly spherical.15 Dynamics
Fig. 4 Coordination number distributions of (a) water molecules surrounding the entire CN ion and (b) water hydrogens involved in H-bonding with the CN atoms.
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The Mulliken charges derived for the solute atoms were monitored throughout the simulation as presented in Fig. 8. The charge on the nitrogen atom varies between 0.64 and 0.36, with an average value of 0.49 0.14, whereas the partial
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Fig. 6
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Angular-radial distributions of the (a) water oxygen and (b) water hydrogens found at the termini of the CN ion.
Fig. 8 Fluctuation of the Mulliken partial charges on the carbon and nitrogen atoms of the CN ion.
Fig. 7 Spatial distribution functions of water atoms with respect to center of mass of the CN ion (colour: carbon in grey, nitrogen in green, spatial density of water oxygen and hydrogen atoms in red and blue).
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charge of the carbon atom fluctuates about a mean value of 0.39 0.16. The magnitude of partial charges on the solute atoms is approximately similar and indicates that both atoms
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can act as H-bond acceptors. Due to the substantially lower partial charges compared to other anionic species, weak H-bonding can be expected which is also confirmed via H-bonding analysis described below. The sum of partial charges of the carbon and nitrogen atoms amounts to 0.89 0.02. The standard deviation is much smaller compared to that of the individual atoms indicating smaller fluctuation of the total charge compared to the individual partial charges. On average a charge of 0.11 is transferred to the surrounding solvent molecules, highlighting the importance of a quantum chemical treatment of the solute– solvent interaction to adequately account for such charge transfer effects. Mean residence times (MRTs, t) were determined for the water ligands of the first hydration layer around the entire cyanide ion. The MRT t is determined according to a direct measurement58 considering all exchange events persisting for periods longer than the predefined threshold t* set to 0.5 and 0.0 ps.58 The coefficient Rex corresponds to the number of attempts required to obtain one lasting (40.5) exchange event and it is given as the ratio between the number of all transitions occurring through a shell boundary (t* = 0.0 ps) and the number of changes persisting longer than 0.5 ps given as Rex ¼
0:0 Nex 0:5 Nex
(1)
where h. . .i indicates an average over all donor–acceptor pairs. SHB(t) corresponds to the probability of an initially H-bonded donor acceptor pair that remains bonded from the time 0 to t. The intermittent correlation function CHB(t) is calculated using the following expression CHB ðtÞ ¼
hhð0ÞhðtÞi hhð0Þhð0Þi
(3)
CHB(t) denotes the probability that H-bonds remain intact at time t, given that they were bonded at time t = 0 as well, irrespective of possible breaking of the bonds in the interim period. The associated relaxation time tHB estimates the average lifetimes of H-bonds between CN and the water molecule, and between water molecules in the respective hydration layers by fitting time correlation functions to a double-exponential expression defined as y = a et/tl + (1 a) et/ts
(4)
where tl and ts correspond to the long and short contribution of the H-bond relaxation, and to the H-bond lifetime. The results of SHB(t) and CHB(t) for the cyanide–water H-bonds are displayed in Fig. 9, and the corresponding lifetimes are listed in Table 3. The decay of SHB(t) and CHB(t) correlation functions occurs at a very similar rate for the N Hwat and C Hwat bonds. Only a small difference in the magnitude of
0.5 where N0.0 ex and Nex correspond to the number of exchange events occurring for t* 0.0 and 0.5 ps, respectively. The MRT value obtained for water ligands with respect to the CEN of the CN is slightly higher than the MRT for pure water (1.30 ps) obtained from a similar simulation study58 (cf. Table 2). The dynamical data also predict an analogous behaviour regarding the stability of the hydration shell and pure water. Very close Rex values for the water ligands of the CN and of pure water further support the analogy between the two systems. In addition H-bonds between the CN ion and water molecules are a further significant factor to characterise the stability of the hydration shell. The evaluation of H-bond dynamics at each terminus of the solute will also be helpful for the interpretation of relative strength of these bonds. Dynamics of hydrogen bonds between specific donor–acceptor pairs were investigated using time correlation functions (TCFs). In this approach two H-bond population variables are defined: h(t) corresponds to unity when a particular H-bonding takes place between the solute and solvent at time t and is zero otherwise whereas H(t) = 1 if only the donor–acceptor pair remains continuously hydrogen-bonded in the time interval [0, t]. The continuous H-bond correlation function SHB(t) is defined as
SHB ðtÞ ¼
hHð0ÞHðtÞi hHð0ÞHð0Þi
(2)
Table 2 Dynamical data for water molecules of the hydrated CN in comparison to pure water from QMCF-MD simulation
CN –water system Pure water
N0.5 ex
N0.0 ex
t0.5 (ps)
t0.0 (ps)
Rex
75 20
358 131
1.37 1.30
0.04 0.19
4.8 6.6
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Fig. 9 Mean S(t) and C(t) of hydrogen bonds formed between the CN and water molecules. The respective double-exponential fitting is depicted in red.
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Table 3 C(t) and S(t) hydrogen bond correlation functions computed for H-bonds between the cyanide anion and water molecules, and between water molecules of the hydration shell
C(t)/ps tl
ts
tl
ts
N Hwat C Hwat H2Oa
0.68 0.91 0.99
0.06 0.04 0.11
0.18 0.07 0.48
0.05 0.003 0.13
a
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S(t)/ps
Type of H-bonds
H-bonds between water molecules in the hydration shell.
decay constants is observed, indicating that these two bonds are of comparable strength. Furthermore, the average lifetimes for the N Hwat and C Hwat bonds were obtained as 0.6 and 0.9 ps, respectively, demonstrating similar kinetics of the H-bonds (isoenergetic H-bonds).21–23 The isokinetic behaviour of H-bonds can be attributed to the similar partial charges and sizes of the solute atoms which share the same period and are groupneighbours in the periodic table. The higher H-bond lifetimes for the N Hwat and C Hwat bonds than that of the pure water (0.5 ps)50,59,60 indicate a slight structure making property of the solute. On the other hand, the small difference between the H-bond lifetimes for the two bonds was also found to possibly be due to the varying partial charges of the solute and the immediate solvent environment, since charge transfer takes place in the polar system leading to different polar interactions. The H-bond lifetime of the water molecules in the hydration shell was also computed using the same time correlation functions showing similar decay patterns as depicted in Fig. 10. The corresponding HB lifetimes of water molecules in the hydration shell were calculated as 0.99 ps, being slightly larger than those of the pure solvent (0.5 ps),50,59,60 which also indicates the occurrence of charge transfer from the solute to the solvent. In comparison to the H-bond lifetime of pure water, the dynamics of the N Hwat and C Hwat bonds and of the hydration shell demonstrate an intermediate stability of the hydration shell of the CN ion.
Fig. 10 Mean S(t) and C(t) of hydrogen bonds between water molecules of the CN hydration shell. The respective double-exponential fitting is depicted in red.
26082 | Phys. Chem. Chem. Phys., 2014, 16, 26075--26083
4 Conclusion Detailed information on the solvation properties of the aqueous cyanide ion highlights the capabilities of the ab initio QMCFMD formalism, treating the solute and its immediate hydration environment at a quantum mechanical level. Structural and dynamical data obtained from the simulation demonstrate the specific localisation of water molecules at each atom of the cyanide ion due to its distinct geometrical feature. The simultaneous H-bond formation plays a key role in the solubility of the cyanide ion in aqueous solution as revealed by the H-bond lifetime calculations reflecting isokinetic behaviour of the H-bonds. The increased value of the H-bond lifetime and MRTs of the water molecules point towards a slight structure making ability of the ion. The characterisation of hydrated cyanide emphasises that H-bonding is responsible for the solubility of the cyanide ion in aqueous solution, implying its detrimental effects in the environment. Therefore, the description of the hydration behaviour based on the structural and dynamical analysis has a significant impact on the characterisation of such H-bonded systems associated chemically and biologically.
Acknowledgements Financial support for this work by the ATC-AIC-APC project from BMWF ASEA-UNINET Austria for Syed Tarique Moin is gratefully acknowledged. This work was supported by the Austrian Ministry of Science BMWF UniInfrastrukturprogramm as part of the Research Focal Point Scientific Computing at the University of Innsbruck.
References 1 F. A. Cotton, G. Wilkinson, C. A. Murillo and M. Bochmann, Advanced Inorganic Chemistry, Wiley, New York, 6th edn, 1999. ˜a, Supra2 A. Bianchi, K. Bowman-James and E. Garcı´a-Espan molecular Chemistry of Anions, Wiley-VCH, New York, 1997. 3 K. W. Kulig, Cyanide Toxicity, U.S. Department of Health and Human Services, Atlanta, GA, 1991. 4 S. I. Baskin and T. G. Brewer, Medical Aspects of Chemical and Biological Warfare, TMM Publications, 1997. 5 C. Baird and M. Cann, Environmental Chemistry, Freeman, 2012. 6 E. A. Katayev, Y. A. Ustynyuk and J. L. Sessler, Coord. Chem. Rev., 2006, 250, 3004–3037. 7 P. Anzenbacher Jr, R. Nishiyabu and M. A. Palacios, Coord. Chem. Rev., 2006, 250, 2929–2938. 8 P. A. Gale, Acc. Chem. Res., 2006, 39, 465–475. 9 Z. Xu, X. Chen, H. N. Kim and Y. Yoon, Chem. Soc. Rev., 2010, 39, 127–137. 10 G. C. Miller and C. A. Pritsos, Medical aspects of chemical and biological warfare, 2001. 11 C. Young, L. Tidwell and C. Anderson, Cyanide: Social, Industrial and Economic Aspects, Metals, and Materials Society, Warrendale, 2001.
This journal is © the Owner Societies 2014
View Article Online
Published on 17 October 2014. Downloaded by Boston College on 28/11/2014 22:14:32.
PCCP
¨sch, A. Rubo, M. Sauer, 12 E. Gail, S. Gos, R. Kulzer, J. Loro R. Kellens, J. Reddy, N. Steier and W. Hasenpusch, Cyano Compounds, Inorganic, Ullmann’s Encyclopedia of Industrial Chemistry, Electronic Release, Wiley-VCH, Weinheim, October 2011. 13 B. Vennesland, E. E. Conn, C. J. Knownles, J. Westly and F. Wissing, Cyanide in Biology, Academic Press, London, 1981. 14 D. Nhassico, H. Muquingue, J. Cliff, A. Cumbana and J. H. Bradbury, J. Sci. Food Agric., 2008, 88, 2043–2049. 15 M. Meot-Ner, S. M. Cybulski, S. Scheinere and J. F. Liebman, J. Phys. Chem., 1988, 92, 2738–2745. 16 P. W. Fowler and M. L. Klein, J. Chem. Phys., 1986, 85, 3913–3916. 17 L. X. Dang, J. Phys. Chem. B, 2002, 106, 10388–10394. 18 S. E. Bradforth, E. H. Kim, D. W. Arnold and D. M. Neumark, J. Chem. Phys., 1993, 98, 800–810. 19 T. R. Miller, CRC Handbook of Chemistry and Physics, CRC, Cleveland, 72nd edn, 1991. 20 J. D. Payzant, R. Yamdagni and P. Kebarle, Can. J. Chem., 1971, 49, 3308–3314. 21 T. J. Lee, J. Am. Chem. Soc., 1989, 111, 7362–7371. 22 T. Ikeda, K. Nishimoto and T. Asada, Chem. Phys. Lett., 1996, 248, 329–335. 23 J. W. Larson and T. B. McMahon, J. Am. Chem. Soc., 1987, 109, 6230–6236. 24 X. Wang, J. C. Werhahn, L. Wang, K. Kowalski, A. Laubereau and S. S. Xantheas, J. Phys. Chem. A, 2009, 113, 9579–9584. 25 X. Wang, K. Kowalski, L. Wang and S. S. Xantheas, J. Chem. Phys., 2010, 132, 124306. 26 R. Klein, R. P. McGinnis and S. R. Leone, Chem. Phys. Lett., 1983, 100, 475–478. 27 M. Ferreira, I. R. Mcdonald and M. L. Klein, J. Chem. Phys., 1986, 84, 3975–3985. 28 Q. Zeng, P. Cai, Z. Li, J. Qin and B. Tang, Chem. Commun., 2008, 1094–1096. 29 Y. Kim and J. Hong, Chem. Commun., 2002, 512–513. 30 H. Miyaji, D. Kim, B. Chang, E. Park, S. Park and K. Ahn, Chem. Commun., 2008, 753–755. 31 Y. M. Chung, H. Lee and K. H. Ahn, J. Org. Chem., 2006, 71, 9470–9474. 32 Y. M. Chung, B. Raman, D. S. Kim and K. H. Ahn, Chem. Commun., 2006, 2186–2188. 33 K. C. Song, K. M. Lee, N. V. Nghia, W. Y. Sung, Y. Do and M. H. Lee, Organometallics, 2013, 32, 817–823. 34 H. Niu, D. Su, X. Jiang, W. Yang, Z. Yin, J. He and J. Cheng, Org. Biomol. Chem., 2008, 6, 3038–3040. 35 G. Li, P. Song and G. He, Chin. J. Chem. Phys., 2011, 24, 305–310.
This journal is © the Owner Societies 2014
Paper
36 G. Li, G. Zhao, K. Han and G. He, J. Comput. Chem., 2011, 32, 668–674. 37 J. Lascombe and M. Perrot, Faraday Discuss. Chem. Soc., 1978, 66, 216–230. 38 C. Kuo and R. M. Hochstrasser, Chem. Phys., 2007, 341, 21–28. 39 P. Hamm, M. Lim and R. M. Hochstrasser, J. Chem. Phys., 1997, 107(24), 10523–10531. 40 R. Sansone, C. Ebner and M. Probst, J. Mol. Liq., 2000, 88, 129–150. 41 B. M. Rode, T. S. Hofer, B. R. Randolf, C. F. Schwenk, D. Xenides and V. Vchirawongkwin, Theor. Chem. Acc., 2006, 115, 77–85. 42 T. S. Hofer, A. B. Pribil, B. Randolf and B. Rode, Adv. Quantum Chem., 2010, 213–246. 43 T. S. Hofer, B. M. Rode, A. B. Pribil and B. R. Randolf, Adv. Inorg. Chem., 2010, 62, 143–175. 44 T. S. Hofer, Pure Appl. Chem., 2014, 86, 1–13. ¨r, M. Ha ¨ser, H. Horn and C. Ko ¨lmel, 45 R. Ahlrichs, M. Ba Chem. Phys. Lett., 1989, 162, 165–169. 46 F. H. Stillinger and A. Rahman, J. Chem. Phys., 1978, 68(2), 666–670. 47 P. Bopp, G. Jancso and K. Heinzinger, Chem. Phys. Lett., 1983, 98, 129–133. 48 T. H. Dunning, J. Chem. Phys., 1970, 53, 2823–2833. 49 E. Magnusson and H. F. Schaefer, J. Chem. Phys., 1985, 83, 5721–5726. 50 D. Xenides, B. R. Randolf and B. M. Rode, J. Chem. Phys., 2005, 122, 4506–4515. 51 S. Yoo, X. C. Zeng and S. S. Xantheas, J. Chem. Phys., 2009, 130, 221102–221105. 52 J. Schmidt, J. VandeVondele, I. F. W. Kuo, D. Sebastiani, J. I. Siepmann, J. Hutter and C. J. Mundy, J. Phys. Chem. B, 2009, 113(35), 11959–11964. 53 G. J. Martyna, M. L. Klein and M. Tuckerman, J. Chem. Phys., 1992, 97, 2635–2643. 54 S. T. Moin, T. S. Hofer, B. R. Randolf and B. M. Rode, Comput. Theor. Chem., 2012, 980, 15–22. 55 R. M. Bozorth, J. Am. Chem. Soc., 1922, 44, 317–323. 56 D. L. Price, J. M. Rowe, J. J. Rush, E. Prince, D. G. Hinks and S. Susman, J. Chem. Phys., 1972, 56, 3697–3702. 57 A. K. H. Weiss and T. S. Hofer, RSC Adv., 2014, 3, 1606–1635. 58 T. S. Hofer, H. T. Tran, C. F. Schwenk and B. M. Rode, J. Comput. Chem., 2004, 25(2), 211. 59 A. J. Lock, S. Woutersen and H. J. Bakker, J. Phys. Chem. A, 2001, 105(8), 1238. 60 A. J. Lock, S. Woutersen and H. J. Bakker, Femtochemistry and Femtobiology, Word Scientific, Singapore, 2001.
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