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Journal of Molecular Structure: THEOCHEM 848 (2008) 119–127

Density functional theory study of water-assisted deprotonationof the C8 intermediate in the reaction of the 2-fluorenylnitrenium

ion with guanosine to form a C8 adduct

Zhen Guo a, Xufeng Lin a, Cunyuan Zhao b, David Lee Phillips a,*

a Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, PR Chinab School of Chemistry & Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, PR China

Received 16 July 2007; received in revised form 12 September 2007; accepted 25 September 2007Available online 1 October 2007

Abstract

A density functional theory study of the deprotonation reaction of the ‘‘C8 intermediate (8-(2-fluorenylamino)-guanosine cation)’’,which is the intermediate of reaction of 2-fluorenylnitrenium ion with guanosine, to produce the C8 adduct final product is described.The barrier to reaction is high in the gas phase and becomes substantially lower when explicit hydrogen bonding of water moleculesis considered. This is consistent with the experimentally observed decay of the ‘‘C8 intermediate’’ on the millisecond time scale. Bulksolvent effects caused only moderate changes in the barrier to reaction in the deprotonation reaction systems that include water mole-cules. Thus, the hydrogen bonding of the water molecules appears to account for most of the differences between the gas phase and aque-ous solution barriers for the deprotonation reaction of the C8 intermediate to form the C8 adduct product. These results suggest that awater-assisted deprotonation mechanism transforms the ‘‘C8 intermediate’’ into the C8 adduct final product in the reactions of arylni-trenium ions with guanine derivatives in aqueous environments.� 2007 Elsevier B.V. All rights reserved.

Keywords: Catalysis; Density functional theory; Deprotonation; Guanosine; Nitrenium ion; Water

1. Introduction

The properties and chemical reactions of arylnitreniumions have received attention since they are thought to bekey intermediates in the chemical carcinogenesis of aro-matic amines [1,2]. Aromatic amines like 2-acetylaminoflu-orene can be enzymatically transformed into the sulfate ofthe related N-hydroxylamines that in aqueous solutionswill dissociate to form an arylnitrenium ion [2a,d]. Arylni-trenium ions like the 2-fluorenylnitrenium ion (denotedhereafter as 2FN) can be selectively trapped by guaninebases in DNA causing modifications [1f,g,2b,3a] that maylead to carcinogenic mutations. Arylnitrenium ions arevery short-lived and reactive intermediates that have only

0166-1280/$ - see front matter � 2007 Elsevier B.V. All rights reserved.

doi:10.1016/j.theochem.2007.09.017

* Corresponding author. Tel.: +852 28592160; fax: +852 28571586.E-mail address: phillips@hkucc.hku.hk (D.L. Phillips).

recently been directly observed in room temperature solu-tions by several time-resolved spectroscopic methods liketransient absorption (TA) spectroscopy [3–5], time-resolved infrared (TRIR) spectroscopy [6], and time-resolved resonance Raman (TR [3]) spectroscopy [7].

McClelland and coworkers [2c,3] employed TA spec-troscopy to study the reaction of 2FN with 2 0-deoxyguano-sine and observed the production of a new intermediatethat was tentatively assigned to a 8-(2-fluorenylamino)-2 0-deoxyguanosine cation adduct or ‘‘C8 intermediate’’ based onseveral experimental observations. This ‘‘C8 intermediate’’was also observed to decay on the millisecond time scaleto produce the C8 adduct final product [3a]. We haverecently used TR [3] spectroscopy to investigate the reac-tion of 2FN with guanosine (denoted hereafter as G) andalso directly observed the formation of a new intermediate[8] similar to that observed by McClelland and coworkersin their TA experiments [3]. This first vibrational spectro-

120 Z. Guo et al. / Journal of Molecular Structure: THEOCHEM 848 (2008) 119–127

scopic characterization of an arylnitrenium ion reactionwith a guanine derivative [8] confirmed the assignment ofthe new intermediate to a ‘‘C8 intermediate’’ as proposedby McClelland and coworkers [3] and demonstrated thatthis species has two C@N conjugated bonds in ring 1 ofthe guanine moiety [8]. At this time, it is not clear howthe ‘‘C8 intermediate’’ proceeds to form the C8 adduct finalproduct observed after photolysis experiments since thisappears to involve breaking a fairly strong CAH bond [3].

Here, we present a density functional theory study of thedeprotonation reaction of the ‘‘C8 intermediate’’ to pro-duce the C8 adduct final product. The calculations weredone for the ‘‘C8 intermediate’’ directly characterized byTR [3] spectroscopy [8] and formed from the reaction of2FN with G. The computational study here explores theeffects of bulk solvent properties and the effects of explicithydrogen bonding of one to three water molecules on thedeprotonation reaction.

2. Computational methods

Density functional theory methods have been used forreliably describing hydrogen-bonded systems [9] and suchcalculations have proved quite useful for studying hydro-gen-bonded complexes as well [10]. The B3LYP functionalin particular has been shown to be highly effective, at leastas long as an appropriate basis set is used [11]. Basis setextensions with polarization functions included for hydro-gen are also useful to properly describe hydrogen-bondinginteractions. In this paper, the B3LYP/6-31G(d) methodhas been employed to optimize the geometry of the station-ary points. Much higher basis set (6-31+G(d,p)) was alsoemployed to investigate the deprotonation reaction of C8intermediate with two water molecules. The computedresult shows that the inclusion of diffuse functions andpolarization functions on the system results in very smallerchanges in geometries (<0.01 A) (Supporting informationTable S1). This result supports our use of B3LYP/6-31G(d) geometries to analyze of structural changes andNBO calculation. Further calculation of single pointenergy at B3LYP/6-311++G(d,p) with the B3LYP/6-

HO

HO

HOO

NC

N

O

NH

NH2N

N

H

H

+ nH2O

C8 intermediate 1

Scheme

31G(d) geometries were carried out to evaluate the accu-racy of reaction barrier associated with the deprotonationreaction of the C8 intermediate 1 to form the C8 adduct 2

as shown below in Scheme 1.Initial calculations were done for a gas phase reaction.

Further calculations were done for one, two and threewater molecules explicitly hydrogen bonded to the reactionsystem (e.g. for the C8 intermediate 1 + n(H2O) fi C8

adduct 2 + (n � 1)H2O + H3O+ (n = 1, 2, 3) reactions).The bulk solvent effect for water using a polarizable contin-uum model described later in this section. All of the calcu-lations were carried out using the Gaussian 98 and 03program suites [12]. To confirm the nature of the stationarypoints and to obtain the zero-point energies and free ener-gies, a frequency analysis was performed for all of the opti-mized structures.

For the larger reaction systems, there are usually severallocal minima or saddle points corresponding to each inter-mediate. First, we carried out a conformational analysis atthe AM1 level of theory systematically searching for all ofthe rotatable bonds using an automatic search algorithm inorder to determine the relative low energy structures corre-sponding to the stationary points and then reoptimizedthese conformations at B3LYP/6-31G(d) level of theory.The lowest energy structure determined from theB3LYP/6-31G(d) level of theory was chosen for subse-quent use.

The contributions of the bulk solvent effects to the acti-vation free energy of the reactions and the thermodynamicstabilities of the stationary points involved in the abovereactions were calculated via the self-consistent field(SCRF) method, using the HF conductor version ofPCM(C-PCM) [13] employing the HF parameterizationof Barone’s united atom topological model (UAHF) [14],as implemented in the latest version of Gaussians. Such amodel includes the nonelectrostatic terms (cativation, dis-persion, and repulsion energy) in addition to the classicalelectrostatic contribution. The activation free energy inthe presence of the water solvent, noted as DG 6¼solv, was eval-uated as: DG 6¼solv ¼ DG 6¼gas þ dDG 6¼solv, where DG 6¼gas is the acti-vation free energy at the B3LYP/6-31G(d) level of theory;

HO

HO

HOO

NC

N

O

NH

NH2N

N

H

+ (n-1)H2O

C8 adduct 2

H3O++

1.

Z. Guo et al. / Journal of Molecular Structure: THEOCHEM 848 (2008) 119–127 121

and dDG6¼solv is defined as the difference between the solva-tion energy of reactant complexes and transition statesfrom the B3LYP/6-31G(d) calculations.

Fig. 1. The B3LYP/6-31G(d) optimized structure of the C8 intermediate 1

species and the C8 adduct 2 with selected atoms numbered and selectedbond lengths indicated for the structures.

3. Results and discussion

3.1. The optimized geometry of the C8 intermediate 1 and its

deprotonation reaction in the gas phase

The C8 intermediate 1 species is computed to be lower inenergy than the separated reactants (2FN and G). It isinteresting to note that the C8 intermediate 1 species per-mits the possibility for anomeric stabilization of its chargeby delocalization of a lone pair density on the former nitre-nium nitrogen into an accepting r�CAN orbital (see top partof Fig. 1) and geometric analysis of the minimum energystructure suggests this is an important effect. The exocyclicCAN bond (N12AC8), at 1.43 A, is very short for a singlebond while the accepting endocyclic bond (N9AC8), at1.50 A, is quite long. The other endocyclic C8AN7 bondin the five-membered ring has a bond length of 1.46 A.These bond lengths are consistent with a large contributionof a formal double-bond/no-bond resonance structure tothe molecular character. In addition, the sum of the valencebond angles of about 344.2� provides another strong indi-cation for anomeric stabilization. While there is no simpleway to quantify the magnitude of the anomeric stabiliza-tion contribution to the overall stability of this isomer, itslarge effects on the geometry suggests it also has an impor-tant effect on the energetics. We note that these calculatedresults are similar to those for a previous study on the reac-tions of guanine with the phenylnitrenium ion [15].

Next, the B3LYP/6-31G(d) optimized structure of theC8 adduct 2 was determined and Fig. 1(bottom) shows asimple schematic diagram of this structure. Table 1 alsolists selected bond lengths for the optimized structures forthe C8 intermediate 1 and the C8 adduct 2. Comparisonof the optimized structures for the C8 intermediate 1 speciesand the C8 adduct 2 shows that they do not differ fromeach other very much for the phenyl rings but do exhibitsignificant changes in the nitrenium and guanosine

Table 1The selected bond lengths (in A) for all reactant complexes, transition states anC8 intermediate 1 + n(H2O) fi C8 adduct 2 + (n � 1)H2O + H3O+ where n = 1

N12AC8 C8AN7 C8AH13 N7AC11 C11AC10

C8 intermediate 1 1.43 1.46 1.09 1.29 1.47C8 adduct 2 1.38 1.31 – 1.38 1.39RC(H2O) 1.43 1.46 1.10 1.29 1.47RC(H2O)2 1.42 1.47 1.10 1.28 1.48RC(H2O)3 1.41 1.46 1.11 1.28 1.47TS(H2O) 1.41 1.37 1.44 1.33 1.43TS(H2O)2 1.42 1.38 1.38 1.32 1.43TS(H2O)3 1.45 1.39 1.33 1.31 1.43PC(H2O) 1.35 1.34 – 1.39 1.37PC(H2O)2 1.35 1.34 – 1.40 1.38PC(H2O)3 1.39 1.31 – 1.39 1.38

moieties. For example, the N12AC8, C8AN7, N7AC11,C11AC10, C10AN9 and N9AC8 bonds lengths are about1.43 A, 1.46 A, 1.29 A, 1.47 A, 1.32 A and 1.50 A, respec-tively, in the C8 intermediate 1 species and then become1.38 A, 1.31 A, 1.38 A, 1.39 A, 1.38 A and 1.40 A, respec-tively, in the C8 adduct 2. These changes indicate thatthe N12AC8, C8AN7, C11AC10 and N9AC8 bondsstrengthen while the N7AC11 and C10AN9 weaken whenthe C8 intermediate 1 deprotonates to form the C8 adduct

2 in the gas phase.We next examined the deprotonation of the C8 interme-

diate 1 species and found that this was an endothermicreaction. The potential energy surface along the C8AH13

d product complexes from the B3LYP/6-31G(d) calculations are shown for, 2, 3

C10AN9 N9AC8 H13AO15 H17AO14 H20AO14 N12AH22

1.32 1.50 – – – –1.38 1.40 – – – –1.32 1.51 1.98 1.87 – –1.32 1.51 – – 1.84 –1.32 1.52 1.87 – 2.08 –1.35 1.46 1.21 1.64 – –1.34 1.47 1.27 – 1.77 –1.33 1.46 1.31 – 1.88 1.961.40 1.37 – 1.94 – –1.40 1.37 1.74 – 1.98 –1.39 1.40 1.03 – 2.04 2.10

= C8= H13

1.0 1.5 2.0 2.5 3.0

-20

0

20

40

60

80

100

ΔE in

kca

l/mol

Distance of C8-H13 bond in angstrom

Fig. 2. The potential energy surface along the C8AH13 bond of the C8

intermediate 1 species (see text for more details).

Fig. 3. Simple schematic diagrams of the optimized structures obtainedfor the RC(H2O), TS(H2O) and PC(H2O) stationary points for thedeprotonation reaction that involves one water molecule. Selected bondlengths (in A) are displayed (see text for more details).

122 Z. Guo et al. / Journal of Molecular Structure: THEOCHEM 848 (2008) 119–127

bond of the C8 intermediate 1 species was scanned as afunctional of the distance of the C8AH13 bond to roughlyestimate its cleavage energy or deprotonation. Inspectionof Fig. 2 shows that the bond breaking energy is probably80–90 kcal/mol. This indicates that the deprotonation ofthe C8 intermediate 1 species takes a lot of energy and isnot likely to occur. However, the C8 intermediate 1 specieswas observed to have a lifetime on the millisecond timescale in an aqueous solution as deduced from a transientabsorption study [3a]. This suggests that the solvent playsan important role in facilitating the deprotonation reactionof the C8 intermediate 1 species to produce the C8 adductfinal product in an aqueous solution. In the next section,we explore the effects of explicitly hydrogen-bonding watermolecules to the deprotonation reaction system. We alsoexamine bulk solvent effects on the deprotonation reaction.

3.2. Water-assisted deprotonation of the C8 intermediate 1to produce the C8 adduct

A DFT investigation of the water-assisted deprotona-tion of the C8 intermediate 1 species as a function of thenumber of water molecules (up to 3) is presented here.To better mimic the environment of the deprotonationreaction of the C8 intermediate 1 the effect of water solventon the reaction was considered by explicitly adding watermolecules one by one into the reactant complexes (orwater-solvated clusters). The reactant complexes of theC8 intermediate 1 species and the product complexes ofthe C8 adduct 2 species with one, two and three water mol-ecules are denoted hereafter by RC(H2O), RC(H2O)2 andRC(H2O)3, respectively, and by PC(H2O), PC(H2O)2 andPC(H2O)3, respectively. The deprotonation reactions forthe reactant complexes (RC(H2O)n where n is the numberof water molecules) to form their corresponding productcomplex (PC(H2O)n where n is the number of water

molecules) proceed through transition states TS(H2O),TS(H2O)2 and TS(H2O)3, respectively. The stationarystructures for all of these reactant complexes, transitionstates and product complexes were fully optimized withoutsymmetry constraints (C1 symmetry). The standard 6-31G(d) basis set was employed in both optimization andfrequency calculations. Analytical frequency calculationswere performed in order to confirm the optimized struc-tures to be either a minimum or a first order saddle pointas well as to obtain the zero-point energy correction forthe reactions.

Fig. 3 depicts simple schematic diagrams of the opti-mized structures obtained for the RC(H2O), TS(H2O)and PC(H2O) stationary points for the deprotonation reac-tion that involves one water molecule and Fig. 4 presentsthe optimized structures found for the RC(H2O)3,

Fig. 4. Simple schematic diagrams of the optimized structures obtainedfor the RC(H2O)3, TS(H2O)3 and PC(H2O)3 stationary points for thedeprotonation reaction that involves three water molecule. Selected bondlengths (in A) are displayed (see text for more details).

Z. Guo et al. / Journal of Molecular Structure: THEOCHEM 848 (2008) 119–127 123

TS(H2O)3 and PC(H2O)3 stationary points for the deproto-nation reaction that involves three water molecules. A sim-ple schematic diagram of the optimized structurescalculated for the RC(H2O)2, TS(H2O)2 and PC(H2O)2 sta-tionary points for the deprotonation reaction that involvestwo water molecules is displayed in the Supporting Infor-mation as Figure S1. The atom numbering for all of thestationary structures are also shown in the supportinginformation as Figures S2 to S4 and selected bond lengthsare displayed in Figs. 3 and 4 as well as tabulated in Table1. We also carried out a natural bond order analysis to esti-mate the charges on the atoms of the stationary structures

reported here and selected results from this analysis aregiven in Table 2. Fig. 5 displays the activation free energyprofiles (in kcal/mol) obtained from B3LYP/6-31G(d)DFT calculations for the RC(H2O)n fi TS(H2O)n fiPC(H2O)n (where n = 1, 2, 3) deprotonation reactions.

Inspection of Fig. 5 shows that the reaction barriers(the relative energy at B3LYP/6-311++G(d,p)//B3LYP/6-31G(d)) for the RC(H2O)n fi TS(H2O)n fi PC(H2O)n

(where n = 1, 2, 3) deprotonation reactions are about 10.8kcal/mol for n = 1, 9.9 kcal/mol for n = 2 and 8.5 kcal/molfor n = 3. These values are all much lower than the gasphase deprotonation of the C8 intermediate 1 species toform the C8 adduct 2 which was estimated to take 80–90 kcal/mol of energy to break the C8AH13 bond. Thissuggests that the hydrogen bonding of the water moleculesto the C8 intermediate 1 species greatly assists the deproto-nation process.

In order to better understand this effect, it is useful tocompare some structural and charge changes that occurupon going from the isolated molecule to the case of awater molecule explicitly hydrogen bonded to the reactionsystem. When one water molecule interacts with the C8intermediate 1 species to form RC(H2O) there are only afew minor changes in the structure in the C8 intermediate

1 part of the complex when the H13AO15 hydrogen bondis formed. For instance, the C8AH13 bond becomesslightly weaker and changes its bond length a little bit fromabout 1.09 A in the gas phase to 1.10 A in RC(H2O). Theperturbation of the hydrogen-bonded water molecule is alittle more noticeable in the atom charge changes deducedfrom the NBO analysis. For example, the charges on theC8 and the H13 atoms go from 0.277 and 0.303, respec-tively, in the gas phase to 0.268 and 0.328, respectively,in RC(H2O). This suggests that the hydrogen bonding ofwater only very slightly weakens the C8AH13 bond whichis consistent with the long H13AO15 bond length of1.98 A. As the deprotonation reaction proceeds to reachthe transition state, TS(H2O), much larger changes in boththe structures and atom charges can be observed. Forexample, the C8AH13 bond becomes much weaker andgoes from 1.10 A in RC(H2O) to 1.44 A in TS(H2O) andthe H13AO15 bond becomes much stronger and goes from1.98 A in RC(H2O) to 1.21 A in TS(H2O). These structuralchanges are accompanied by noticeable changes in theatom charges. For instance the charge on the H13 atomincreases significantly from 0.328 in RC(H2O) to 0.457 inTS(H2O) as the C8AH13 bond lengthens substantiallyand begins to break. The preceding changes in the struc-tures and charges as one goes from RC(H2O) to TS(H2O)suggests that as the C8AH13 bond begins to break in thedeprotonation reaction, the structures and charges alsochange noticeably in the nitrenium and guanine ring 1 moi-eties and thus provide an alternative reaction pathway notavailable for the isolated C8 intermediate 1.

It is interesting to note that as the RC(H2O)n go to theirrespective TS(H2O)n the changes in their structure andcharges can be significantly less than the changes that occur

Table 2NBO charges on the selected atoms for the reaction of C8 intermediate 1 + n(H2O) fi C8 adduct 2 + (n � 1)H2O + H3O+ where n = 1, 2, 3

C6 N7 C8 N9 C10 C11 N12 H13

C8 intermediate 1 0.147 �0.303 0.277 �0.376 0.470 0.077 �0.647 0.303C8 adduct 2 0.170 �0.502 0.598 �0.440 0.396 �0.028 �0.636 –RC(H2O) 0.159 �0.289 0.268 �0.377 0.478 0.069 �0.643 0.328RC(H2O)2 0.150 �0.304 0.273 �0.382 0.494 0.113 �0.661 0.313RC(H2O)3 0.168 �0.278 0.259 �0.364 0.476 0.083 �0.649 0.341TS(H2O) 0.120 �0.330 0.279 �0.381 0.428 0.007 �0.702 0.457TS(H2O)2 0.140 �0.313 0.264 �0.381 0.440 0.013 �0.670 0.439TS(H2O)3 0.117 �0.312 0.265 �0.379 0.449 0.025 �0.722 0.424PC(H2O) 0.074 �0.536 0.708 �0.408 0.409 �0.026 �0.620 0.481PC(H2O)2 0.110 �0.550 0.679 �0.411 0.400 �0.023 �0.616 0.492PC(H2O)3 0.118 �0.581 0.646 �0.429 0.401 �0.039 �0.687 0.540

-30

-20

-10

0

10

-30.5-29.5

-25.2

8.19.2

11.3

PC(H2O)n

TS(H2O)n

RC(H2O)n

0.0

Rel

ativ

e fr

ee e

nerg

y in

gas

pha

se (k

cal m

ol-1)

Reaction coordinate

n=1 n=2 n=3

Fig. 5. The activation free energy profiles (in kcal/mol) obtained fromB3LYP/6-31G(d) DFT calculations for the RC(H2O)n fi TS(H2O)n fi P-C(H2O)n (where n = 1, 2, 3) deprotonation reactions (see text for moredetails).

124 Z. Guo et al. / Journal of Molecular Structure: THEOCHEM 848 (2008) 119–127

when the C8 intermediate 1 species deprotonates to formthe C8 adduct 2 in the gas phase. For example, the chargeon the C8 atom goes from 0.277 in the C8 intermediate 1 to0.598 in the C8 adduct 2 but only goes from 0.268 inRC(H2O) to 0.279 in TS(H2O). Similarly, the charges onthe N7, N9, C10 and C11 atoms of the guanine moietygo from �0.303, �0.376, 0.470 and 0.077, respectively, inthe C8 intermediate 1 to �0.502, �0.440, 0.396 and�0.028, respectively, in the C8 adduct 2 but only go from�0.289, �0.377, 0.470 and 0.069, respectively, in RC(H2O)to �0.330, �0.381, 0.428 and 0.007, respectively, inTS(H2O). This suggests smaller changes in the structureand charge redistribution are needed to reach the reactionbarriers in a hydrogen-bonded complex in an aqueous envi-ronment for the C8 intermediate 1 deprotonation reactionthan in the gas phase deprotonation reaction to producea C8 adduct 2. This is consistent with the deprotonationreaction barrier heights of 10.8 kcal/mol for n = 1,9.9 kcal/mol for n = 2 and 8.5 kcal/mol for n = 3 for theRC(H2O)n fi TS(H2O)n fi PC(H2O)n (where n = 1, 2, 3)deprotonation reactions being much smaller than the esti-mated 80–90 kcal/mol of energy to break the C8AH13

bond in the deprotonation of the C8 intermediate 1 to formthe C8 adduct 2 in the gas phase.

As the number of water molecules increase from one tothree in the deprotonation reaction system, the barrier toreaction decreases from 10.8 kcal/mol for n = 1, 9.9 kcal/mol for n = 2 and 8.5 kcal/mol for n = 3 and this suggestthe additional water molecules further assist the deproto-nation reaction. Inspection of the structures and chargesfor the RC(H2O)n fi TS(H2O)n fi PC(H2O)n (wheren = 1, 2, 3) deprotonation reactions reveals some trendsthat appear to correlate with a decrease in the reaction bar-rier height. For example, the C8AH13 bond lengths in thetransition states go from 1.44 A in TS(H2O) to 1.38 A inTS(H2O)2 to 1.33 A in TS(H2O)3 and the H13AO15 bondlengths go from 1.21 A in TS(H2O) to 1.27 A in TS(H2O)2

to 1.31 A in TS(H2O)3. It is interesting to note that thetrends in the C8AH13 and H13AO15 bond lengths suggestthat as the H13 atom becomes more a shared protonbetween the C8 atom of the C8 intermediate 1 moiety ofthe transition state and the hydrogen-bonded water mole-cule, the lower the barrier for the deprotonation reaction.This also correlates with a smaller change in the C8AH13bond lengths as one goes from RC(H2O)n fi TS(H2O)n

where the differences are about 0.34 A for RC(H2O) toTS(H2O), 0.28 A for RC(H2O)2 to TS(H2O)2 and 0.22 Afor RC(H2O)3 to TS(H2O)3 in the deprotonation reactions.Similar trends are also seen in the differences of the chargesfor the C8 and the H13 atoms as one goes from theRC(H2O)n to the TS(H2O)n. For example, the differencesin the charges for the C8 atom are about 0.011 fromRC(H2O) to TS(H2O), 0.009 from RC(H2O)2 to TS(H2O)2

and 0.006 from RC(H2O)3 to TS(H2O)3 and in the H13atom they are about 0.129 for RC(H2O) to TS(H2O),0.126 for RC(H2O)2 to TS(H2O)2 and 0.083 for RC(H2O)3

to TS(H2O)3 in the deprotonation reactions. The precedingtrends in the structures of the C8AH13 and H13AO15bonds and the charges of the C8 and H13 atoms associatedwith going from the RC(H2O)n to their respectiveTS(H2O)n suggest less energy is needed to change the struc-ture and charge distribution of the main deprotonationcoordinate to approach the transition state as the numberof water molecules increase from one to three in the reac-

Z. Guo et al. / Journal of Molecular Structure: THEOCHEM 848 (2008) 119–127 125

tion system. This is consistent with the barrier heightdecreasing from 10.8 kcal/mol for n = 1 to 9.9 kcal/molfor n = 2 and then to 8.5 kcal/mol for n = 3 for theRC(H2O)n fi TS(H2O)n fi PC(H2O)n (where n = 1, 2, 3)deprotonation reactions. We note that similar trends inhaving smaller changes in the key structural features andatom charges as one goes from the reactant complexes totheir corresponding transition states when the number ofwater molecules increase in the water-solvated reaction sys-tem and correlate with lower reaction barriers as the num-ber of water molecules increases has also been observed fora number of water-assisted dehalogenation reactionsinvolving isopolyhalomethanes, halogenated methanolsand halogenated formaldehyde molecules [16–18].

We next explored bulk solvent effects on the deprotona-tion reactions and Table 3 shows the B3LYP/6-311++G(d,p)calculated energy (DEa, kcal/mol) and the B3LYP/6-31G(d) calculated energy (DEb, kcal/mol), activation freeenergy (DGgas, kcal/mol) and the difference between the sol-vation energy of the reactant complexes and the transitionstates from the B3LYP/6-31G(d) calculations (dDGc

solv,kcal/mol) and the Gibbs free energy in water solutioncalculated as DGsolv = DGgas + dDGsolv for the deprotona-tion reaction of the C8 intermediate 1 including the numberof water molecules from 1 to 3 in the gas phase and usingthe C-PCM solvation model.

As noted in previous discussion, the energy needed tobreak the C8AH13 bond is roughly more than 80 kcal/mol in the gas phase and this suggests that the deprotona-tion reaction is unlikely to proceed readily in the gas phase.However, the incorporation of one water molecule into thereaction appears to dramatically catalyze the reaction andthe activation Gibbs free energy (at the level of B3LYP/6-31G(d)) for the reaction of RC(H2O) fi TS(H2O) fiPC(H2O) is 11.3 kcal/mol. The significant water catalytic

Table 3Activation energy (DEa, DEb, in kcal/mol), free energy in the gas phase(DGgas, in kcal/mol), solvation effect on the free energy (dDGb

solv, in kcal/mol), and the activation free energy in water (DGc

solv, in kcal/mol) forthe reactions of C8 intermediate 1 + n(H2O) fi C8 adduct

2 + (n � 1)H2O + H3O+ where n = 1, 2, 3

n B3LYP/6-311++G(d,p)//B3LYP/6-31G(d)

B3LYP/6-31G(d)

DEa DEb DGgas dDGsolvc DGsolv

d

1 10.8 9.4 11.3 0.7 122 9.9 8.1 9.2 �0.9 8.13 8.5 6.2 8.1 2.6 10.7

n: The numbers of water molecules involved in the titled reactions.a Energies of activation at the level of B3LYP/6-311++G(d,p)//B3LYP/

6-31G(d) with ZPE correction obtained from the level of B3LYP/6-31G(d).

b Energies of activation at B3LYP/6-31G(d) Level for the reactions withZPE correction.

c The difference between the solvation energy of reactant complexes andtransition states from B3LYP/6-31G(d) calculations.

d Gibbs Free energy in water solution calculated as DGsolv =DGgas + dDGsolv for the reactions with different water molecules.

effect could be accounted for by the formation of stronghydrogen bond between the water molecule and the reac-tion system (see also the previous discussion of the struc-tures and charges on the atoms for the reactions studiedhere) and also by the strong stabilization of the leavingH atom by the water cluster for the transition state. As asecond water molecule (n = 2) is added to the reaction,DGgas are decreased by 2.1 kcal/mol. Addition of a thirdwater molecule (from n = 2 to 3) decreases DGgas by1.1 kcal/mol.

To better mimic the real aqueous environment for thereactions, we also considered the bulk solvent effects (withinclusion of the C-PCM solvent model) on the water-assisted mechanism for the deprotonation reaction of theC8 intermediate 1. It is interesting to compare the activa-tion free energies in the gas phase and in the aqueous phaseversus the number of water molecules. Inspection of Table3 and Fig. 5 shows that the reaction barriers for the sol-vated reactions with the water clusters (n = 1 and 3) areincreased by 0.7 and 2.6 kcal/mol compared to those ofthe gas phase, respectively. This leads to TS(H2O) andTS(H2O)3 being a little less stable in the aqueous phasethan in gas phase. However, the activation free energy ofthe two water molecule assisted mechanism of the deproto-nation reaction is reduced by �0.9 kcal/mol as a conse-quence of the bulk solvent effects. Among all of theTS(H2O)n located by us for the deprotonaton reaction ofC8 intermediate 1, TS(H2O)3 is the most stable one in thegas phase, featuring the lowest activation free energy(8.1 kcal/mol). The bulk effect of water induces a moderatedestabilization (+2.6 kcal/mol) on TS(H2O)3, a minordestabilization (+0.7 kcal/mol) on TS(H2O) and a weakstabilization (�0.9 kcal/mol) on TS(H2O)2. This leads tothe TS(H2O)2 having the lowest activation free energyamong the three transition states for the water-assisteddeprotonation reactions in the aqueous phase. In boththe gas phase clusters and in the aqueous phase clusters,the two and the three water-solvated reactions have lowerreaction barriers than the one water molecule cluster andthis suggests that the actual deprotonation reaction inaqueous environments involve more than one water mole-cule. In addition, the bulk solvent effects are relativelysmall (on the order of <1–3 kcal/mol) and only moderatelyperturb the gas phase water cluster reaction systems. Wenote that it is mainly the explicit hydrogen bonding ofthe water molecules to the C8 intermediate 1 deprotonationreaction system that is responsible for the deprotonationreaction being able to occur with low enough barrierheights that can help explain how the experimentallyobserved C8 intermediate 1 can decay on the millisecondtime scale [3a] to likely produce the C8 adduct 2 finalproduct.

4. Conclusions

A density functional theory study of the deprotonationreaction of the ‘‘C8 intermediate’’ to produce the C8 adduct

126 Z. Guo et al. / Journal of Molecular Structure: THEOCHEM 848 (2008) 119–127

final product was presented. The calculations investigatedthe effects of explicit hydrogen bonding of one to threewater molecules on the deprotonation reaction. The effectsof bulk solvent properties were also examined for the watermolecule involved reactions. The barrier to reaction wasestimated to be high in the gas phase. In contrast, the bar-rier for the deprotonation reaction was found to becomesignificantly lower when explicit hydrogen bonding of sev-eral water molecules was taken into account and this isconsistent with the experimentally observed decay of the‘‘C8 intermediate’’ on the millisecond time scale to likelyform the C8 adduct final product [3a]. The deprotonationreaction barriers were only moderately affected when bulksolvent effects were added to the computations for thewater molecule involved reactions. This suggests that expli-cit hydrogen bonding of the water molecules is probablyresponsible for most of the differences between the gasphase and aqueous solution barriers for the deprotonationreaction of the C8 intermediate to form the C8 adduct prod-uct. The results presented here suggest that a water-assisteddeprotonation mechanism converts the ‘‘C8 intermediate’’into the C8 adduct final product in the reactions of arylni-trenium ions with guanine derivatives in aqueousenvironments.

Acknowledgements

This research has been supported by grants from theResearch Grants Council of Hong Kong (HKU7040/06P), the award of a Croucher Foundation SeniorResearch Fellowship (2006–07) from the Croucher Foun-dation and an Outstanding Researcher Award (2006) fromthe University of Hong Kong to D.L.P.

Appendix A. Supplementary material

The optimized geometry for all the reactants, reactantcomplexes, transition states and product complexesobtained from the B3LYP/6-31G(d) calculations areshown for the C8 intermediate 1 + n(H2O) fi C8 adduct

2 + (n � 1)H2O + H3O+ where n = 1, 2, 3 reactions. A sim-ple schematic diagram of the optimized structures calcu-lated for the RC(H2O)2, TS(H2O)2 and PC(H2O)2

stationary points for the deprotonation reaction thatinvolves two water molecules is displayed in Figure S1.The atom numbering for all of the stationary structuresare also shown in Figures S2 to S4. This material is avail-able free of charge via the Internet at http://pubs.acs.org.Supplementary data associated with this article can befound, in the online version, at doi:10.1016/j.theochem.2007.09.017.

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