A New Nitrogenase Mechanism Using a CFe8S9 ... - ACS Publications

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A New Nitrogenase Mechanism Using a CFe8S9 Model: Does H2 Elimination Activate the Complex to N2 Addition to the Central Carbon Atom? Michael L. McKee* Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States S Supporting Information *

ABSTRACT: A truncated model of the FeMo cofactor is used to explore a new mechanism for the conversion of N2 to NH3 by the nitrogenase enzyme. After four initial protonation/ reduction steps, the H4CFe8S9 cluster has two hydrogen atoms attached to sulfur, one hydrogen bridging two iron centers and one hydrogen bonded to carbon. The loss of the CH and FeHFe hydrogens as molecular hydrogen activates the cluster to addition of N2 to the carbon center. This unique step takes place at a nearly planar four-coordinate carbon center and leads to an intermediate with a significantly weakened N−N bond. A hydrogen attached to a sulfur atom is then transferred to the distal nitrogen atom. Additional prontonation/reduction steps are modeled by adding a hydrogen atom to sulfur and locating the transition states for transfer to nitrogen. The first NH3 is lost in a thermal neutral step, while the second step is endothermic. The loss of H2 activates the complex by reducing the barrier for N2 addition by 3.5 kcal/mol. Since this is the most difficult step in the mechanism, reducing the barrier for this step justifies the “extra expense” of H2 production.

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INTRODUCTION Some microorganisms are able to use the nitrogenase enzyme to convert N2 to ammonia at 1 atm and room temperature.1−6 By contrast, humans use the Haber−Bosch process, which requires high temperatures and pressures. Much effort has been spent to understand the nitrogenase mechanism in order to develop a bioinspired catalyst.7−36 Dance has been a major contributor to the exploration of the nitrogenase mechanism.37−49 The most widely studied FeMo cofactor is a MoFe7XS9 metal cluster, where X has recently been identified as a carbon atom.50,51 In addition to reducing N2 to NH3, this enzyme can reduce a variety of substrates such as C2H2 to C2H4, N2H2 to N2H4 and CO to CO2.17 In addition, the production of two ammonia molecules is accompanied by one H2 molecule (eq 1).

easier to calculate. It was felt that the energetics were similar enough between the high-spin and low-spin models that the broad features of a mechanism could be explored by a high-spin model. In the present study, the broken-symmetry, low-spin solution was computed. While the distribution of spins was similar in the low-spin (LS) and high-spin (HS) solutions, there are important energetic differences. Specifically, differences in LS and HS surfaces are dependent on the strength of sulfur bridging and capping interactions.56,57 As the strength decreases, the HS solution will be stabilized relative to the LS version. The current model (Figure 1) contains a unique carbon atom in the center of the cluster since the identity of that atom was determined by recent work.50,51 The exact function of the carbon atom is not known.58,59 In this model, a Fe atom is used in place of the Mo atom, and the overall charge is neutral. There are three bridging sulfides and six capping sulfides. The sulfide that is thought to be the source of protons49 (SB3) is capping the Fe6Fe7Fe8 irons (i.e., S678), where the adopted numbering system of iron atoms is that used by Dance37−49 and others. The formal oxidation states of the models in the resting cluster and the cluster with two and four PR steps are given in eqs 2−4

N2 + 8H+ + 8e− + 16ATP → 2NH3 + H 2 + 16ADP + 16Pi (1)

The oxidation states of the Fe/Mo atoms in the cluster have been the subject of much debate.7,42 The situation has become even more uncertain with the recent discovery that the Mo oxidation state is +3 rather than +4 as previously assumed.52,53 The spin state of the resting cofactor is S = 3/2, and it is known that at least three protonation/reduction (PR) steps are required before turnover begins.1−6 In a previous study of the nitrogenase mechanism,54,55 a high-spin model NFe8S9 with a plus one charge was used. While a broken-symmetry solution was computed to be lower in energy, the high-spin solution was © XXXX American Chemical Society

Fe8(C)S9

2Fe2 +6Fe3 +C4 −9S2 − neutral

(2)

Received: October 22, 2015 Revised: December 19, 2015

A

DOI: 10.1021/acs.jpca.5b10384 J. Phys. Chem. A XXXX, XXX, XXX−XXX

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The Journal of Physical Chemistry A

While intrinsic reaction coordinates were not used to connect reactants and products, transition vectors of all transition states were visualized. In all cases, the motion was appropriate for connecting the assumed reactant and product. The protonation-reduction step was modeled by adding a hydrogen atom to the sulfur capping Fe6Fe7Fe8, which becomes a bridge between Fe6Fe8 (i.e., S678 → SH68). It has been estimated that the nitrogenase environment is sufficiently reducing and acidic that a free energy of H-addition of greater than about 50 kcal/mol would be sponanteous.54,55 Transition states were located for the transfer of a hydrogen atom from sulfur to nitrogen. The present calculations provide hydrogen as 1/2H2, which is more endothermic than H atoms available in the protein environment. The D3BJ correction is in some cases quite large (over 10 kcal/mol). The cluster model has a number of interactions where separations are slightly larger than normal covalent distances and the D3BJ contribution is maximum. In several cases, the D3BJ correction caused the product to be less stable than the transition state. In light of the large corrections for structures that are not weakly bound, the discussion below will not include the D3BJ correction unless explicitly stated. However, relative enthalpies of all structures including the D3BJ correction are available in Supporting Information.

Figure 1. Simple drawing of the CFe8S9 model (1a). The numbering system is the one commonly used. The iron atoms involved in the bridging and capping interactions are given with subscripts. The sulfide S678 is the sulfide identified as the one that accepts the proton from the protein environment (i.e., SB3).

H 2Fe8(C)S9

2H+4Fe 2 +4Fe3 +C4 −9S2 − neutral

(3)

H4Fe8(C)S9

4H+6Fe2 +2Fe3 +C4 −9S2 − neutral

(4)

The calculations described below show that the unpaired electron spins on the iron centers are delocalized with values between 3 and 4 on each center. Calculations with different choices of total spin are compared to two broken-symmetry solutions for CFe8S9 in Table 1. The highest total spin for 2Fe2+6Fe3+C4−9S2− is S = 38/2 (2 × 4 + 6 × 5). The cluster energy decreases for S = 38/2−32/2 before increasing again for 30/2 and 28/2.

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RESULTS AND DISCUSSION The resting state of the CFe8S9 model is a singlet rather than the experimentally observed quartet. The iron centers are locally high-spin and antiferromagnetically coupled. The precise coupling is still not known. Based on previous studies of the FeMo cofactor, two couplings were considered, U(DUD)(UUD)D and U(DDD)(UUU)D, where “U” is an iron atom with majority spin up and “D” is an iron atom with majority spin down proceeding from right to left in the cluster model (Figure 1). The U(DDD)(UUU)D coupling in CFe8S9, which was 3.9 kcal/mol less stable than the U(DUD)(UUD)D coupling, was, nevertheless, chosen for other calculations because the ambiguity of the spin assignment of the six central iron atoms was removed. In the U(DUD)(UUD)D coupling scheme, it is not clear which of the three irons on either side of the carbon atom should have an opposite spin from the other two. The U(DUD)C(UUD)D coupling scheme was adopted by Dance42 in his recent study of a more realistic model of the FeMo cofactor [(O3C2H2)(N2C3H4)Mo(Fe)3(C) (Fe)3FeSCH3]4−, which leads to a [MoFe7CS9]− core cluster and the assumption of 4Fe2+ and 3Fe3+ [Mo4+4Fe2+3Fe3+C4−9S2−]−. The CFe8S9 model has more average spin density on iron atoms compared to the Dance model (Table 2). The magnitude of the computed spin densities for the U(DDD)(UUU)D model (1a) are very similar to 1x (the “x” indicates the U(DUD)(UUD)D coupling scheme). The potential energy surface (enthalpies at 298 K) of the initial stages of the mechanism is shown in Figure 2 with molecular drawings in Figure 3. The arrows in the diagram indicate PR steps where hydrogen atoms (as 1/2H2) are added. The first two PR steps produced 2a, and two more PR steps produced 3 with an overall endothermicity of 3.6 kcal/mol. In exploring structures with four PR steps, the “Janus” structure (3J) was considered (Figure 3), with hydrogens on two sulfides (SH62 and SH86) and two hydrogens bridging two irons (H62 and H67). The “Janus” intermediate (3J) is the term coined by Hoffmann and co-workers23 for the intermediate that lies

Table 1. Comparison of Electronic Properties for the CFe8S9 Model CFe8S9

ΔH (298 K)a

total spin

spin density on Fe

NPA (carbon)b

Ave Fe−C

1a 1x HS1 HS2 HS3 HS4 HS5 HS6

0.0 −3.9 62.2 54.4 48.2 56.7 76.0 100.0

0 0 28/2 30/2 32/2 34/2 36/2 38/2

3.49−3.73 3.68−3.72 3.11−3.76 3.28−3.78 3.58−3.80 3.68−3.81 3.77−3.97 3.77−3.96

−0.73 −0.72 −0.39 −0.43 −0.52 −0.73 −0.98 −1.27

2.164 2.115 2.117 2.134 2.124 2.164 2.191 2.219

a

B3LYP/6-311G(d,p)/Fe(SDD) plus zero-point and thermal corrections to 298 K. Enthalpies in kcal/mol relative to 1a. bNatural population analysis (NPA) charge66,67 on the carbon atom.

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COMPUTATIONAL METHOD The B3LYP/6-311G(d,p)/Fe(SDD) density functional method60,61 is used to compute geometries and vibrational frequencies with the Gaussian09 program package.62 Dispersion effects are included with Grimme’s D3 method63 with the BJ correction (D3BJ). The 10-electron core of iron is replaced by the Stuttgart ECP64 with a 6s5p3d1f basis set for Fe (Fe = SDD) and a 6-311G(d,p) basis set for H/C/N/S. All low-spin species are broken-symmetry singlets or doublets. Solvation effects, which are expected to be small for the neutral model, have not been included. Vibrational frequencies are computed to make zero-point and thermal corrections. The nitrogenase mechanism is complicated due to the number of possible coordination sites and different possible sequence of protonation and reduction steps. In the present study, a particular mechanism was explored with a tight coupling of protonation and reduction (PR steps). B


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The unique transition state for adding N2 to the carbon atom (ts2c/4a) resembles a planar four-coordinate carbon center surrounded by iron atoms. To explore the nature of this critical step, another model was chosen (Figure 4), planar Fe4S4 with a central carbon atom (11). With a C4− choice of oxidation state for carbon, the model has four Fe3+ (i.e., C4−4Fe3+4S2−). The same level of theory was employed with antiferromagneticcoupling of high-spin iron centers (i.e., UDUD). The N2 can coordinate end-on to either iron (12a) or carbon (12b), which are more stable by −8.6 and −8.2 kcal/mol, respectively. The barrier to adding N2 is 25.5 kcal/mol with respect to 11+N2. The product 13 is 21.4 kcal/mol less stable than 11+N2. Addition of H (as 1/2H2) is exothermic by 8.3 kcal/mol. In the H2CFe8S9 model, the activated cluster (2c) adds N2 with an activation barrier of 39.8 (23.9 with D3BJ correction) kcal/mol (via ts2c/4a). The product (4a) is 13.1 kcal/mol endothermic with respect to the activated complex plus N2. In this case, the carbon atom becomes four-coordinate, and the iron atoms have adjusted their interactions with neighboring bridging sulfur atoms. The bonding environment in 11 was probed by Natural Bonding Analysis (NBO).67,68 Two alpha electrons are in spx hybridized orbitals and form polar bonds with alpha electrons on iron in dx2−y2 orbitals (see Figure 5). These two 1-electron bonds each have 0.72 e− on carbon. In addition, there is 0.45 e− in a py orbital and 0.35 e− in a pz orbital perpendicular to the molecular plane. The bonding scenario is the same with the other two iron atoms, except, in this case, beta electrons are used. The total electron density in the pz orbital is 0.70 e− (0.35 alpha and beta e−), which means this orbital can accept additional electron density from a donor (Figure 5). The strong 9.9 kcal/mol binding of N2 to 11 is due to the donor(N2)− acceptor(CFe4S4) interaction. In the transition state (ts12b/ 13), the N2 interacts with the partially occupied orbital on carbon. A total of 0.27 e− is transferred from N2 to CFe4S4. The N−N bond increases slightly from 1.095 Å in 12b to 1.103 Å in ts12b/13 and the N−N stretching frequency decreases from 2448 to 2302 cm−1. The lowest unoccupied molecular orbital (LUMO) (sum of α and β MOs) of the transition state ts12b/13 (Figure 6a) shows significant interaction between the π* orbital of the N2 and CFe4S4. The occupied orbital (sum of α and β MOs) in ts12b/13, which shows σ-donation from N2 into the partial occupied pz orbital of carbon is depicted in Figure 6b. Although not completely analogous, the addition of N2 to CFe4S4 bears some similarities to the addition of N2 to a carbene.70−72 In both cases, the added N2 approaches the

Table 2. Comparison of Spin Densities of the U(DUD)(UUD)D (1x) and U(DDD)(UUU)D (1a) Couplings of [2Fe2+6Fe3+C4−9S2−]a

a

center

Danceb

1x

1a

C Fe1 Fe2 Fe3 Fe4 Fe5 Fe6 Fe7 Mo/Fe

0.00 3.15 −2.75 2.94 −2.73 2.49 2.47 −2.62 −0.29

0.00 3.60 −3.72 3.68 −3.72 3.72 3.72 −3.68 −3.60

0.00 3.49 −3.73 −3.73 −3.73 3.73 3.73 3.73 −3.49

For numbering system, see Figure 1. bReference 42.

midway between reactants N2+H2 and product NH3. Sitting at the crossroad, it is the key intermediate for understanding the nitrogenase mechanism. A structure (3J) with small gradients (but not meeting the full stopping criterion) was found, but the optimization continued to 3, where the H62 hydrogen moved to the carbon (HC), which was 47.3 kcal/mol more stable than 3J “Janus”. In comparing 3 with “Janus” (Figure 3), the special hydrogen (H62) moves from bridging (H−Fe6, 1.548; H−Fe2, 2.346 Å) in “Janus” to 1.099 Å from carbon in 3. In 3, the H−Fe6 and H− Fe2 distances are 2.172 and 2.494 Å, respectively.65 The NPA charges66,67 on H67 and HC in 3 show significant negative and positive charge, respectively (−0.25 and +0.23 e−), which will facilitate the H2 elimination step (ts3/2b, Figure 3). In the transition state ts3/2b, the H−Fe6 and H−C distances are 2.260 and 1.462 Å, respectively, while the forming H−H distance is 1.021 Å. The NPA charges on hydrogens in the transition state ts3/2b are −0.10 and +0.19 e−. In the product cluster 2b, the coordination number around carbon has decreased from six to five (2a → 2b). A very small barrier was located (ts2b/2c) that leads to cluster 2c where the coordinate environment around carbon has changed. A bridging sulfide becomes capping (S54 → S457), and the carbon is nearly planar four-coordinate.68,69 The cluster 2c can add N2 with a 39.8 kcal/mol (23.9 kcal/mol with D3BJ correction) activation barrier (ts2c/4a) to form the C−N2 intermediate 4a where the carbon center is approximately four-coordinate. In the transition state ts2c/4a, the N2 unit has acquired a + 0.21 e− charge (NPA), which suggests that σ donation exceeds π back-donation.

Figure 2. Potential energy profile (enthalpies at 298 K) for the initial steps in production of NH3 from N2 with the CFe8S9 model for the FeMo cofactor in nitrogenase. The larger barriers are for loss of H2 from H4CFe8S9 (3) via ts3/2b and the addition of N2 to 2c via ts2c/4a. All structures are neutral with S0 with broken-symmetry solutions. All values are enthalpies in kcal/mol at 298 K relative to 1a (plus the appropriate number of N2 and H2). C


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Figure 3. Structures of 1a, 2a, 3, 3J(“Janus”), 2b, 2c, 4a, and corresponding transition states. For 1a, 2a, 3, 3J, and ts3/2b, selected distances are given in units of angstroms.

is initiated with electron donation from the N2 HOMO into a partially occupied orbital on the carbon center. Starting from 4a, the nitrogenase mechanism is fairly straightforward (PES in Figure 7; structures in Figures 8 and 9). A hydrogen atom can migrate from the “SB3” sulfide (i.e., S86) to the distal nitrogen with an activation barrier of 15.7 kcal/mol (ts4a/4b). The low barrier is due to the fact that the N−N bond is significantly lengthened (1.096(N2) → 1.132(4a) Å) and weakened (2447(N2) → 2124(4a) cm−1) compared to

carbon center perpendicular to the molecular plane (Figure 5). In the case of the carbene, the product is formed when the N2 moves into the molecular plane. In the case of N2−CFe4S4, this migration is prevented by the ring of iron atoms. Kim and co-workers73 recently considered the activation of N2 by a carbene center as an organocatalyst model for nitrogenase. However, in their model they suggested that the reaction was initiated with electron donation from the carbene HOMO into the N2 LUMO. In the present model, the reaction D


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Figure 4. Potential energy diagram for the addition of N2 to CFe4S4 (11). The boldface numbers are NPA charges on carbon, the numbers followed by “cm−1” are N2 stretching frequencies, and the other numbers are distances in angstroms.

Figure 5. Orbitals used in the interaction of N2 with the low-spin CFe4S4 model 11. Below is a scheme showing the approach of N2 to 11 and N2 to a carbene center. Figure 6. (a) Plot of the LUMO in the transition state ts12b/13 (with summed α and β MOs). (b) Plot of the bonding molecular orbital in transition state ts12b/13 (with summed α and β MOs) showing σ donation from N2 into the pz orbital of carbon.

free N2. In the transition state (ts4a/4b), the migrating H atom is 1.710 and 1.239 Å from sulfur and nitrogen, respectively. Addition of another hydrogen atom, is quite exothermic (with respect to 1/2H2) which indicates that the 4b complex should be readily protonated and reduced (i.e., one PR step). The 5a complex can migrate a H atom with a small barrier (2.7 kcal/ mol) in a much earlier TS (1.538 Å to S; 1.421 Å to N). In the

5b complex, the C−N bond is short (1.172 Å) with double bond character, and the carbon atom is bonded to only two other iron atoms (2.275 and 2.371 Å). Another PR step gives 6a, which is exothermic by 22.9 kcal/mol with respect to added E


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The elimination of the second NH3 and formation of the HCFe8S9 cluster (10b) is endothermic by 7.0 kcal/mol. The most stable H2CFe8S9 cluster 2a is formed by the sixth PR step (PR#6), which is endothermic by 0.6 kcal/mol (with respect to 1/2H2). In the acidic/reducing protein environment, the “cost” of adding H (less than 50 kcal/mol) is less than breaking a H− H bond, and the sixth PR step should be spontaneous. The cycle is completed by two more PR steps and loss of H2 to form the “open” intermediate (2b) and then the “4-coord” intermediate (2c), which can add N2.

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GENERAL REMARKS The current mechanism explains why H2 production is required. The H4CFe8S9 (4 PR steps) forms 3, which leads first to the “open” intermediate (2b) and then to the “4-coord” intermediate (2c). The H2CFe8S9 intermediate 2c is 3.5 kcal/ mol less stable than 2a, which reduces the barrier for N2 addition by this amount. The N2 addition barrier is the highest barrier in the entire cycle (except for the second NH3 elimination step) so lowering it justifies the extra energy associated with H2 production. A problem with this mechanism is that a low energy transition state (ts2c/2a) was located between the “4-coord” and “closed” intermediates (Figure 2). In order for the present mechanism to be viable, the N2 molecule must be “captured” by the “4-coord” intermediate faster than 2c can rearrange back to 2a. One attractive scenario is an SN2 reaction where the N2 binds as the H2 is lost. Despite considerable effort, a reasonable SN2 transition state could not be located for this process. Another possibility is the rapid binding of N2 to the “4-coord” form (2c), which would prevent rearrangement to the “closed” form (2a). The N2−CFe4S4 complex (12b), bound by 8.2 kcal/mol, gave hope for such a complex. A search for a complex between N2 and the “4-coord” form 2c was made at the normal level of theory and the level of theory where dispersion corrections were included in the geometry optimization. In both cases, the only complex that could be located was a complex with very long distances to N2, which was dispersion-bound by about 3 kcal/mol.74 One concern regarding the present mechanism is that there is evidence that the cluster is rather stiff as judged by Fe−S distances.19 George et al.10 were able to establish that no Fe−S bonds were broken during turnover. In this mechanism, the Fe−C distances change, and the capping sulfide becomes bridging in the intermediate. However, at no point is there a terminal Fe−S or terminal Fe−SH group. The most stable intermediate is CNFe8S9 7a, where a nitrogen atom forms an interaction with two iron atoms. The incorporation of the N atom into the cluster makes loss of NH3 5.7 kcal/mol endothermic with respect to 6a. In order to support the results using the CFe8S9 (S = 0, 1/2) model, calculations were made with the Dance model42 ([(O3C2H2)(N2C3H4)Mo(Fe)3(C)(Fe)3FeSCH3]4−; 43-atom CMoFe7S9-core, S = 3/2) at the same level of theory. Eight structures were optimized, D3, D3x, D3Jx, Dts3x/2bx, D2bx, D2cx, Dts2cx/4ax, and D4ax, where “D” represents the Dance model and “x” represents the U(UDD)(UDU)D spin coupling. The D3 and D3x structures (Figure 10) correspond to two different spin couplings. Because the U(UDD)(UDU)D spin coupling (D3x) is 8.5 kcal/mol more stable than the U(DDD)(UUU)D coupling (D3), the former spin-coupling is applied to D3Jx, Dts3x/2bx, D2bx, D2cx, Dts2cx/4ax, and D4ax. Unlike the H4CFe8S9 model, the Janus structure D3Jx was a minimum (zero imaginary frequencies) but still 25.7

Figure 7. Potential energy diagram for the six PR steps that convert 4a to 10b and two molecules of ammonia.

1/2H2. The 6a intermediate can migrate a H atom to the distal nitrogen (ts6a/6b, Ea = 24.9 kcal/mol) or to the proximal nitrogen (ts6a/6c, Ea = 33.1 kcal/mol). Thus, the present mechanism predicts a more favorable pathway through a N− NH3 intermediate. In fact, the N−NH3 bond lengthens after a H atom is migrated (ts6a/6b) and a “N−NH3” structure could not be located. When NH3 is lost, the structure rearranges to 6b where the N atom is coordinated to the carbon and two iron atoms. The next PR step gives 7a and has a higher barrier (20.4 kcal/mol) for migrating a H atom to the tricoordinate nitrogen with long N−Fe distances of 2.221 and 2.293 Å. The higher barrier (ts7a/7b) is due to loss of the N−Fe interactions in the transition state, which have lengthened to 3.231 and 3.597 Å. The product 7b, a C-NH intermediate, is slightly less stable than the transition state due to corrections to the electronic energy (zero-point and thermal corrections). The next PR step (PR#4) is exothermic by 14.9 kcal/mol (with respect to added 1/2H2). The migrating H atom has a barrier of 26.3 kcal/mol to form the C−NH intermediate (8b). The fifth PR step (PR#5) is exothermic by 18.3 kcal/mol and has a 16.3 kcal/mol barrier to form the C−NH3 intermediate (9b). The second NH3 has a 1.520 Å bond to a four-coordinate carbon (9b). The barrier for loss of NH3 is 24.8 kcal/mol. The geometry around the carbon atom in the transition state is very similar to that for adding N2 (ts2c/4a) in that the carbon is nearly planar and surrounded by four iron centers. The product (10a + NH3) is 3.2 kcal/mol higher than the transition state (ts9b/10a) due to zero-point and thermal corrections. The intermediate 10a has a very small barrier to form 10b where the carbon atom moves to the center of the cluster and becomes six-coordinate. The loss of NH3 from 9b is assisted by the formation of additional Fe−C interactions as the carbon center is drawn back into the center of the cluster. Another possible pathway for losing NH3, which was not explored in this study, is protonation of 9b and the loss of NH4+. F


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Figure 8. Molecular structure of species (4a to 7a) from Figure 7.

kcal/mol less stable than D3x. Using the H4CFe8S9 model, the difference in energy between the two structures (3J and 3) was 43.7 kcal/mol. The transition state for elimination of H2 from D3x is 19.3 kcal/mol higher than D3x, and the products D2bx +H2 are exothermic by −10.1 kcal/mol. These values can be compared to 19.0 and 3.0 kcal/mol for the CFe8S9 model (ts3/ 2b and 2b+H2). The transition state for addition of N2 (Dts2cx/4ax) is 43.7 kcal/mol higher than D2cx+N2 (30.8 kcal/mol with D3BJ). These values can be compared to 39.8

kcal/mol (23.3 kcal/mol with D3BJ) for the CFe8S9 model (2c +N2 → ts2c/4a). Geometric parameters among different spin coupling and different size models are compared in Supporting Information (Tables S2a−S2c). It can be seen that adding ligands to the two ends of the larger model (“D”) increases the Fe−Fe separations from Fe1 and Fe8/Mo to the neighboring iron atoms. The biggest difference that occurs as a result of using the “standard” and “alternative” spin coupling is the geometry of the “Janus” G


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Figure 9. Molecular structure of species (ts7a/7b to 10b) from Figure 7.

intermediate (“J”). The “alternative” spin coupling (i.e. “x”) gives a much more symmetrical Fe6HFe2 bridge than the “standard” spin coupling. Overall, the limited results with the larger Dance cluster model (using U(DUD)(UUD)D spin coupling) for the FeMo cofactor support the idea of an intermediate with a C−H bond with a low barrier for elimination of H2.

However, a more detailed model will be required to confirm the viability of this model. These details include computing the entire potential energy surface replacing one iron center with a molybdenum atom at one end of the cluster, adding the appropriate charge, adding the correct substituent and ligands and solvation effects. The new features of this new mechanism are the FeMo cofactor is activated by loss of H2; formation of a four-coordinate carbon center is important; and addition of N2 takes place at the carbon center. Calculation of several structures using a larger model of the FeMo cofactor support the results obtained with the smaller CFe8S9 cluster model.

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CONCLUSION The present low-spin, broken-symmetry CFe8S9 model allows the investigation of broad features of a new mechanism. H


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(5) Barrière, F. Model Complexes of the Active Site of Nitrogenases: Recent Advances. In Bioinspired Catalysis Metal-Sulfur Complexes; Weigand, W., Schollhammer, P., Eds.; Wiley-VCH: Weinheim, Germany, 2015; pp 225−248. (6) Henderson, R. A. Binding Substrates to Synthetic Fe−S-Based Clusters and the Possible Relevance to Nitrogenases. In Bioinspired Catalysis Metal-Sulfur Complexes; Weigand, W., Schollhammer, P., Eds.; Wiley-VCH: Weinheim, Germany, 2015; pp 289−323. (7) Lukoyanov, D.; Pelmenschikov, V.; Maeser, N.; Laryukhin, M.; Yang, T. C.; Noodleman, L.; Dean, D. R.; Case, D. A.; Seefeldt, L. C.; Hoffman, B. M. Testing if the Interstitial Atom, X, of the Nitrogenase Molybdenum-Iron Cofactor Is N or C: ENDOR, ESEEM, and DFT Studies of the S = 3/2 Resting State in Multiple Environments. Inorg. Chem. 2007, 46, 11437−11449. (8) Xie, H.; Wu, R.; Zhou, Z.; Cao, Z. Exploring the Interstitial Atom in the FeMo Cofactor of Nitrogenase: Insights from QM and QM/ MM Calculations. J. Phys. Chem. B 2008, 112, 11435−11439. (9) Hazari, N. Homogeneous Iron Complexes for the Conversion of Dinitrogen into Ammonia and Hydrazine. Chem. Soc. Rev. 2010, 39, 4044−4056. (10) George, S. J.; Barney, B. M.; Mitra, D.; Igarashi, R. Y.; Guo, Y.; Dean, D. R.; Cramer, S. P.; Seefeldt, L. C. EXAFS and NRVS Reveal a Conformational Distortion of the FeMo-Cofactor in the MoFe Nitrogenase Propargyl Alcohol Complex. J. Inorg. Biochem. 2012, 112, 85−92. (11) Seefeldt, L. C.; Hoffman, B. M.; Dean, D. R. Electron Transfer in Nitrogenase Catalysis. Curr. Opin. Chem. Biol. 2012, 16, 19−25. (12) Asatryan, R.; Bozzelli, J. W.; Ruckenstein, E. Dihydrogen Catalysis: A Degradation Mechanism for N2-Fixation Intermediates. J. Phys. Chem. A 2012, 116, 11618−11642. (13) Lukoyanov, D.; Yang, Z.-Y.; Barney, B. M.; Dean, D. D.; Seefeldt, L. C.; Hoffman, B. M. Unification of Reaction Pathway and Kinetic Scheme for N2 Reduction Catalyzed by Nitrogenase. Proc. Natl. Acad. Sci. U. S. A. 2012, 109, 5583−5587. (14) Yang, Z.-Y.; Khadka, N.; Lukoyanov, D.; Hoffman, B. M.; Dean, D. R.; Seefeldt, L. C. On reversible H2 Loss upon N2 Binding to FeMo-cofactor of Nitrogenase. Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 16327−16332. (15) Rittle, J.; Peters, J. C. Fe-N2/CO Complexes that Model a Possible Role for the Interstitial C Atom of FeMo-cofactor (FeMoco). Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 15898−15903. (16) MacLeod, K. C.; Holland, P. L. Recent Developments in the Homogeneous Reduction of Dinitrogen by Molybdenum and Iron. Nat. Chem. 2013, 5, 559−565. (17) Seefeldt, L. C.; Yang, Z.-Y.; Duval, S.; Dean, D. R. Nitrogenase reduction of carbon-containing compounds. Biochim. Biophys. Acta, Bioenerg. 2013, 1827, 1102−1111. (18) Hoffman, B. M.; Lukoyanov, D.; Dean, D. R.; Seefeldt, L. C. Nitrogenase: A Draft Mechanism. Acc. Chem. Res. 2013, 46, 587−595. (19) Jia, H. P.; Quadrelli, E. A. Mechanistic Aspects of Dinitrogen Cleavage and Hydrogenation to Produce Ammonia in Catalysis and Organometallic Chemistry: Relevance of Metal Hydride Bonds and Dihydrogen. Chem. Soc. Rev. 2014, 43, 547−64. (20) Einsle, O. Nitrogenase FeMo Cofactor: an Atomic Structure in Three Simple Steps. JBIC, J. Biol. Inorg. Chem. 2014, 19, 737−745. (21) Hu, Y.; Ribbe, M. W. A Journey into the Active Center of Nitrogenase. JBIC, J. Biol. Inorg. Chem. 2014, 19, 731−736. (22) Lukoyanov, D.; Yang, Z.-Y.; Duval, S.; Danyal, K.; Dean, D. R.; Seefeldt, L. C.; Hoffman, B. M. A Confirmation of the QuenchCryoannealing Relaxation Protocol for Identifying Reduction States of Freeze-Trapped Nitrogenase Intermediates. Inorg. Chem. 2014, 53, 3688−3693. (23) Hoffman, B. M.; Lukoyanov, D.; Yang, Z.-Y.; Dean, D. R.; Seefeldt, L. C. Mechanism of Nitrogen Fixation by Nitrogenase: The Next Stage. Chem. Rev. 2014, 114, 4041−4062. (24) Shaw, S.; Lukoyanov, D.; Danyal, K.; Dean, D. R.; Hoffman, B. M.; Seefeldt, L. C. Nitrite and Hydroxylamine as Nitrogenase Substrates: Mechanistic Implications for the Pathway of N2 Reduction. J. Am. Chem. Soc. 2014, 136, 12776−12783.

Figure 10. Molecular structures (and relative enthalpies in kcal/mol) of D3x and D3Jx, where “D” refers to model adopted by Dance (see ref 42) in his recent study of a more realistic model of the FeMo cofactor [(O3C2H2)(N2C3H4)Mo(Fe)3(C)(Fe)3FeSCH3]4−.

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ASSOCIATED CONTENT

S Supporting Information *

The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.jpca.5b10384. Total energies, zero-point energies, thermal corrections to 298 K, entropies, and NPA charge on the central carbon atom are presented in Table S1. Comparisons of geometric parameters for 3 with 3x and with D3x, 3J with 3Jx and with D3Jx, and ts3/2b with Dts3x/2bx are made in Table S2a−c. Cartesian coordinates of relevant species are tabulated in Table S3. (PDF)

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AUTHOR INFORMATION

Corresponding Author

*E-mail: [email protected]. Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS The author is grateful for computer time provided by the Alabama Supercomputer Center. REFERENCES

(1) Hu, Y.; Ribbe, M. The Interstitial Carbide of the Nitrogenase Mcluster: Insertion Pathway and Possibe Function. In Iron-Sulfur Clusters in Chemistry and Biology; Rouault, T., Ed.; deGruyter: Berlin, 2014; pp 77−88. (2) Spatzal, T.; Andrade, S. L. A.; Einsle, O. The Iron-Molybdenum Cofactor of Nitrogenase. In Iron-Sulfur Clusters in Chemistry and Biology; Rouault, T., Ed.; deGruyter: Berlin, 2014; pp 89−105. (3) Dance, I. A Unified Chemical Mechanism for Hydrogenation Reactions Catalyzed by Nitrogenase In Bioinspired Catalysis MetalSulfur Complexes; Weigand, W., Schollhammer, P., Eds.; Wiley-VCH: Weinheim, Germany, 2015; pp 249−288. (4) Lee, C. C.; Wiig, J. A.; Hu, Y.; Ribbe, M. W. Structures and Functions of the Active Sites of Nitrogenases. In Bioinspired Catalysis Metal-Sulfur Complexes; Weigand, W., Schollhammer, P., Eds.; WileyVCH: Weinheim, Germany, 2015; pp 201−224. I


Article

The Journal of Physical Chemistry A (25) Kowalska, J.; DeBeer, S. The Role of X-ray Spectroscopy in Understanding the Geometric and Electronic Structure of Nitrogenase. Biochim. Biophys. Acta, Mol. Cell Res. 2015, 1853, 1406−1415. (26) Burger, E.-M.; Andrade, S. L. A.; Einsle, O. Active Sites without Restraints: High-Resolution Analysis of Metal Cofactors. Curr. Opin. Struct. Biol. 2015, 35, 32−40. (27) Spatzal, T. The Center of Biological Nitrogen Fixation: FeMoCofactor. Z. Anorg. Allg. Chem. 2015, 641, 10−17. (28) Hallmen, P. P.; Kästner, J. N2 Binding to the FeMo-Cofactor of Nitrogenase. Z. Anorg. Allg. Chem. 2015, 641, 118−122. (29) Hu, Y.; Ribbe, M. W. Nitrogenase and Homologs. JBIC, J. Biol. Inorg. Chem. 2015, 20, 435−445. (30) McWilliams, S. F.; Holland, P. L. Dinitrogen Binding and Cleavage by Multinuclear Iron Complexes. Acc. Chem. Res. 2015, 48, 2059−2065. (31) Nishibayashi, Y. Recent Progress in Transition-Metal-Catalyzed Reduction of Molecular Dinitrogen under Ambient Reaction Conditions. Inorg. Chem. 2015, 54, 9234−9247. (32) Anderson, J. S.; Cutsail, G. E.; Rittle, J.; Connor, B. A.; Gunderson, W. A.; Zhang, L.; Hoffman, B. M.; Peters, J. C. Characterization of an Fe≡N-NH2 Intermediate Relevant to Catalytic N2 Reduction to NH3. J. Am. Chem. Soc. 2015, 137, 7803−7809. (33) Lukoyanov, D.; Yang, Z.-Y.; Khadka, N.; Dean, D. R.; Seefeldt, L. C.; Hoffman, B. M. Identification of a Key Catalytic Intermediate Demonstrates That Nitrogenase Is Activated by the Reversible Exchange of N2 for H2. J. Am. Chem. Soc. 2015, 137, 3610−3615. (34) Nishibayashi, Y. Recent Progress in Transition-Metal-Catalyzed Reduction of Molecular Dinitrogen under Ambient Reaction Conditions. Inorg. Chem. 2015, 54, 9234−9247. (35) Č orić, I.; Mercado, B. Q.; Bill, E.; Vinyard, D. J.; Holland, P. L. Binding of Dinitrogen to an Iron−Sulfur−Carbon Site. Nature 2015, 526, 96−99. (36) Varley, J. B.; Wang, Y.; Chan, K.; Studt, F.; Nørskov, J. K. Mechanistic Insights into Nitrogen Fixation by Nitrogenase Enzymes. Phys. Chem. Chem. Phys. 2015, 17, 29541−29547. (37) Dance, I. Mechanistic Significance of the Preparatory Migration of Hydrogen Atoms around the FeMo-co Active Site of Nitrogenase. Biochemistry 2006, 45, 6328−6340. (38) Dance, I. The Mechanistically Significant Coordination Chemistry of Dinitrogen at FeMo-co, the Catalytic Site of Nitrogenase. J. Am. Chem. Soc. 2007, 129, 1076−1088. (39) Dance, I. The Chemical Mechanism of Nitrogenase: Calculated Details of the Intramolecular Mechanism for Hydrogenation of η2-N2 on FeMo-co to NH3. Dalton Trans. 2008, 5977−5991. (40) Dance, I. Mimicking Nitrogenase. Dalton Trans. 2010, 39, 2972−2983. (41) Dance, I. Electronic Dimensions of FeMo-co, the Active Site of Nitrogenase, and Its Catalytic Intermediates. Inorg. Chem. 2011, 50, 178−192. (42) Dance, I. Ramifications of C-centering Rather than N-centering of the Active Site FeMo-co of the Enzyme Nitrogenase. Dalton Trans. 2012, 41, 4859−4865. (43) Dance, I. The Controlled Relay of Multiple Protons Required at the Active Site of Nitrogenase. Dalton Trans. 2012, 41, 7647−59. (44) Arnet, N. A.; Dugan, T. R.; Menges, F. S.; Mercado, B. Q.; Brennessel, W. W.; Bill, E.; Johnson, M. A.; Holland, P. L. Synthesis, Characterization, and Nitrogenase-Relevant Reactions of an Iron Sulfide Complex with a Bridging Hydride. J. Am. Chem. Soc. 2015, 137, 13220−13223. (45) Dance, I. Nitrogenase: a General Hydrogenator of Small Molecules. Chem. Commun. 2013, 49, 10893−10907. (46) Dance, I. The Stereochemistry and Dynamics of the Introduction of Hydrogen Atoms onto FeMo-co, the Active Site of Nitrogenase. Inorg. Chem. 2013, 52, 13068−13077. (47) Dance, I. Activation of N2, the Enzymatic Way. Z. Anorg. Allg. Chem. 2015, 641, 91−99. (48) Dance, I. Misconception of Reductive Elimination of H2, in the Context of the Mechanism of Nitrogenase. Dalton Trans. 2015, 44, 9027−9037.

(49) Dance, I. The Pathway for Serial Proton Supply to the Active Site of Nitrogenase: Enhanced Density Functional Modeling of the Grotthuss Mechanism. Dalton Trans. 2015, 44, 18167−18186. (50) Spatzal, T.; Aksoyoglu, M.; Zhang, L.; Andrade, S. L. A.; Schleicher, E.; Weber, S.; Rees, D. C.; Einsle, O. Evidence for Interstitial Carbon in Nitrogenase FeMo Cofactor. Science 2011, 334, 940−940. (51) Lancaster, K. M.; Roemelt, M.; Ettenhuber, P.; Hu, Y. L.; Ribbe, M. W.; Neese, F.; Bergmann, U.; DeBeer, S. X-ray Emission Spectroscopy Evidences a Central Carbon in the Nitrogenase IronMolybdenum Cofactor. Science 2011, 334, 974−977. (52) Bjornsson, R.; Lima, F. A.; Spatzal, T.; Weyhermüller, T.; Glatzel, P.; Bill, E.; Einsle, O.; Neese, F.; DeBeer, S. Identification of a Spin-coupled Mo(III) in the Nitrogenase Iron-Molybdenum Cofactor. Chem. Sci. 2014, 5, 3096−3103. (53) Bjornsson, R.; Neese, F.; Schrock, R. R.; Einsle, O.; DeBeer, S. The discovery of Mo(III) in FeMoco: Reuniting Enzyme and Model Chemistry. JBIC, J. Biol. Inorg. Chem. 2015, 20, 447−460. (54) McKee, M. L. Modeling the Nitrogenase FeMo Cofactor with High-Spin Fe8S9X+ (X = N,C) Clusters. Is the First Step for N2 Reduction to NH3 a Concerted Dihydrogen Transfer? J. Comput. Chem. 2007, 28, 1342−1356. (55) McKee, M. L. Modeling Hydrogen Evolution from the Fe4S4 and Fe8S9X (X = N,C) Clusters. Can a Fe-S High-Spin Cluster Serve as a Surrogate for the FeMo Cofactor? J. Comput. Chem. 2007, 28, 1796−1808. (56) Solomon, E. I.; Xie, X.; Dey, A. Mixed Valent Sites in Biological Electron Transfer. Chem. Soc. Rev. 2008, 37, 623−638. (57) Harris, T. V.; Szilagyi, R. K. Iron-Sulfur Bond Covalency from Electronic Structure Calculations for Classical Iron-Sulfur Clusters. J. Comput. Chem. 2014, 35, 540−52. (58) Scott, A. D.; Pelmenschikov, V.; Guo, Y.; Yan, L.; Wang, H.; George, S. J.; Dapper, C. H.; Newton, W. E.; Yoda, Y.; Tanaka, Y.; Cramer, S. P. Structural Characterization of CO-Inhibited MoNitrogenase by Combined Application of Nuclear Resonance Vibrational Spectroscopy, Extended X-ray Absorption Fine Structure, and Density Functional Theory: New Insights into the Effects of CO Binding and the Role of the Interstitial Atom. J. Am. Chem. Soc. 2014, 136, 15942−15954. (59) Gee, L. B.; Leontyev, I.; Stuchebrukhov, A.; Scott, A. D.; Pelmenschikov, V.; Cramer, S. P. Docking and Migration of Carbon Monoxide in Nitrogenase: The Case for Gated Pockets from Infrared Spectroscopy and Molecular Dynamics. Biochemistry 2015, 54, 3314− 3319. (60) Cramer, C. J. Essentials of Computational Chemistry: Theories and Models; Wiley: Hoboken, NJ, 2004. (61) Glukhovtsev, M. N.; Bach, R. D.; Nagel, C. J. Performance of the B3LYP/ECP DFT Calculations of Iron-Containing Compounds. J. Phys. Chem. A 1997, 101, 316−323. (62) Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A. et al. Gaussian 09, revision D.01; Gaussian, Inc.: Wallingford, CT, 2009. (63) Grimme, S.; Ehrlich, S.; Goerigk, L. Effect of the Damping Function in Dispersion Corrected Density Functional Theory. J. Comput. Chem. 2011, 32, 1456−1465. (64) Dolg, M.; Wedig, U.; Stoll, H.; Preuss, H. Energy-Adjusted Ab Initio Pseudopotentials for the First Row Transition Elements. J. Chem. Phys. 1987, 86, 866−872. (65) Two spin-couplings, U(DDD)(UUU)D (3 and 3J) and U(UDD)(UDU)D (3x and 3Jx), were applied to H4CFe8S9 structures. The Dance coupling (U(UDD)(UDU)D; denoted with “x”) reduces the difference between the two structures from 43.9 to 34.2 kcal/mol. In addition, the Janus structure with the U(UDD)(UDU)D) coupling (3Jx) is a local minimum (no imaginary frequencies). (66) Weinhold, F.; Landis, C. R. In Discovering Chemistry with Natural Bond Orbitals; Wiley: Hoboken, NJ, 2012. J


Article

The Journal of Physical Chemistry A (67) Weinhold, F. Valency and Bonding: A Natural Bond Orbital Donor−Acceptor Perspective; Landis, C. R., Ed.; Cambridge University Press: Cambridge, U.K., 2005. (68) Yang, L.-M.; Ganz, E.; Chen, Z.; Wang, Z.-X.; Schleyer, P. v. R. Four Decades of the Chemistry of Planar Hypercoordinate Compounds. Angew. Chem., Int. Ed. 2015, 54, 9468−9501. (69) Nandula, A.; Trinh, Q. T.; Saeys, M.; Alexandrova, A. N. Origin of Extraordinary Stability of Square-Planar Carbon Atoms in Surface Carbides of Cobalt and Nickel. Angew. Chem., Int. Ed. 2015, 54, 5312− 5316. (70) Shilov, A. E.; Shteinman, A. A.; Tjabin, M. B. Reaction of Carbenes with Molecular Nitrogen. Tetrahedron Lett. 1968, 9, 4177− 4180. (71) Baron, W. J.; DeCamp, M. R.; Hendrick, M. E.; Jones, M., Jr.; Levin, R. H.; Sohn, M. M. Carbenes from Diazo Compounds. In Carbenes; Jones, M., Moss, R. A., Eds.; Wiley-Interscience: New York, 1973; Vol. 1. (72) Miller, D. M.; Schreiner, P. R.; Schaefer, H. F. Singlet Methylcarbene: An Elusive Intermediate of the Thermal Decomposition of Diazoethane and Methyldiazirine. J. Am. Chem. Soc. 1995, 117, 4137−4143. (73) Park, S.-W.; Chun, Y.; Cho, S. J.; Lee, S.; Kim, K. S. Design of Carbene-Based Organocatalysts for Nitrogen Fixation: Theoretical Study. J. Chem. Theory Comput. 2012, 8, 1983−1988. (74) A structure (2c-N2) was optimized (low-spin broken-symmetry) with the Fe6−N2 distance fixed at 2.20 Å. At the standard level of theory with dispersion included, the complex was 5.1 kcal/mol lower in enthalpy than 2c+N2 (including D3BJ correction). During optimization, the S86 bridging sulfide became a S87 bridging sulfide. Such a complex could not easily rearrange to the 2a complex (plus N2).

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