Molecular dynamics study of taxadiene synthase catalysis

Molecular dynamics (MD) simulations have been performed to study the dynamic behavior of noncovalent enzyme carbocation complexes involved in the cyclization of geranylgeranyl diphosphate to taxadiene catalyzed by taxadiene synthase (TXS). Taxadiene and the observed four side products originate from the deprotonation of carbocation intermediates. The MD simulations of the TXS carbocation complexes provide insights into potential deprotonation mechanisms of such carbocations. The MD results do not support a previous hypothesis that carbocation tumbling is a key factor in the deprotonation of the carbocations by pyrophosphate. Instead water bridges are identified which may allow the formation of side products via multiple proton transfer reactions. A novel reaction path for taxadiene formation is proposed on the basis of the simulations. © 2018 Wiley Periodicals, Inc.     

Structural and Catalytic Insight into the Unique Pentacyclic Triterpene Synthase TwOSC

The oxidosqualene cyclase (OSC) catalyzed cyclization of the linear substrate (3S)-2,3-oxidosqualene to form diverse pentacyclic triterpenoid (PT) skeletons is one of the most complex reactions in nature. Friedelin has a unique PT skeleton involving a fascinating nine-step cation shuttle run (CSR) cascade rearrangement reaction, in which the carbocation formed at C2 moves to the other side of the skeleton, runs back to C3 to yield a friedelin cation, which is finally deprotonated. However, as crystal structure data of plant OSCs are lacking, it remains unknown why the CSR cascade reactions occur in friedelin biosynthesis, as does the exact catalytic mechanism of the CSR. In this study, we determined the first cryogenic electron microscopy structure of a plant OSC, friedelin synthase, from Tripterygium wilfordii Hook. f (TwOSC). We also performed quantum mechanics/molecular mechanics simulations to reveal the energy profile for the CSR cascade reaction and identify key residues crucial for PT skeleton formation. Furthermore, we semirationally designed two TwOSC mutants, which significantly improved the yields of friedelin and β-amyrin, respectively.     

Cytochrome P450 Mediated Cyclization in Eunicellane Derived Diterpenoid Biosynthesis**

Terpene cyclization, one of the most complex chemical reactions in nature, is generally catalyzed by two classes of terpene cyclases (TCs). Cytochrome P450s that act as unexpected TC-like enzymes are known but are very rare. In this study, we genome-mined a cryptic bacterial terpenoid gene cluster, named ari, from the thermophilic actinomycete strain Amycolatopsis arida. By employing a heterologous production system, we isolated and characterized three highly oxidized eunicellane derived diterpenoids, aridacins A−C ( 1 – 3 ), that possess a 6/7/5-fused tricyclic scaffold. In vivo and in vitro experiments systematically established a noncanonical two-step biosynthetic pathway for diterpene skeleton formation. First, a class I TC (AriE) cyclizes geranylgeranyl diphosphate (GGPP) into a 6/10-fused bicyclic cis-eunicellane skeleton. Next, a cytochrome P450 (AriF) catalyzes cyclization of the eunicellane skeleton into the 6/7/5-fused tricyclic scaffold through C2−C6 bond formation. Based on the results of quantum chemical computations, hydrogen abstraction followed by electron transfer coupled to barrierless carbocation ring closure is shown to be a viable mechanism for AriF-mediated cyclization. The biosynthetic logic of skeleton construction in the aridacins is unprecedented, expanding the catalytic capacity and diversity of P450s and setting the stage to investigate the inherent principles of carbocation generation by P450s in the biosynthesis of terpenoids.     

Free energy landscape for glucose condensation reactions

Ab initio molecular dynamics and metadynamics simulations were used to determine the free energy surfaces (FES) for the acid catalyzed β-D-glucose condensation reaction. Protonation of C1-OH on the β-D-glucose, breakage of the C1-O1 bond, and the formation of C1 carbocation is the rate-limiting step. The effects of solvent on the reaction were investigated by determining the FES both in the absence and presence of solvent water. It was found that water played a critical role in these reactions. The reaction barrier for the proton-catalyzed glucose condensation reaction is solvent induced because of proton's high affinity for water. During these simulations, β-D-glucose conversion to α-d-glucose process via the C1 carbocation was also observed. The associated free energy change and activation barrier for this reaction were determined.     

The carbon-skeleton rearrangement in tropane alkaloid biosynthesis

High-level quantum chemistry calculations have been performed to examine the carbon-skeleton rearrangement of the tropane alkaloid littorine to hyoscyamine. Two pathways involving radical and carbocation intermediates have been investigated in this regard, namely, stepwise (or fragmentation-recombination) and concerted. The fragmentation products are calculated to be of high energy for both the radical- and carbocation-based mechanisms (136.3 and 170.9 kJ mol(-1), respectively). Similarly, the rearrangement barrier for the radical-based concerted pathway is calculated to be quite high (135.6 kJ mol(-1)). In contrast, the carbocation-based concerted pathway is found to be associated with a relatively low barrier (47.4 kJ mol(-1)). The ionization energy of the substrate-derived radical 3a is calculated to be 7.01 eV, suggesting that its oxidation to generate the substrate-derived carbocation 3b ought to be facile. In an attempt to investigate how an enzyme might modulate the rearrangement barriers, the separate and combined influences of partially protonating the migrating group and partially deprotonating the spectator OH group of the substrate were investigated. Such interactions can lead to significant reductions in the rearrangement barrier for both the radical- and carbocation-based concerted pathways, although the carbocation pathway continues to have significantly lower energy requirements. Also, the relatively high (gas-phase) acidity of the OH group of the product-related carbocation 4b indicates that the direct formation of hyoscyamine aldehyde (6) is a highly exothermic process. Although we would not wish to rule out alternative possibilities, our calculations suggest that a concerted rearrangement mechanism involving carbocations constitutes a viable low-energy pathway for the carbon-skeleton rearrangement in tropane alkaloid biosynthesis.     

HZSM-5催化甲苯和甲醇烷基化反应机理的密度泛函理论研究

对二甲苯(PX)是重要的有机化工原料,主要用于生产对苯二甲酸(PTA)和对苯二甲酸二甲酯(DMT), PTA和 DMT可经缩聚生产化纤、合成树脂和塑料等聚酯产品. PX主要通过甲苯歧化、二甲苯异构化或甲苯与 C9芳烃烷基转移等方式生产.由于三种二甲苯和乙苯的沸点接近,需要经过吸附分离或深冷分离才能得到高纯度的 PX,传统工艺物料循环量大,设备庞大,操作费用高.而通过甲苯和甲醇烷基化反应直接高选择性生成 PX,可大大降低成本,具有非常高的经济效益和研究价值.自1970年代以来,国内外众多科研院所对甲苯和甲醇烷基化催化剂进行了广泛研究,但催化剂选择性和稳定性仍需进一步提高.为了加深对甲苯和甲醇烷基化反应的认识,指导催化剂开发,有必要对甲苯和甲醇烷基化生成二甲苯的反应机理进行深入研究.当前甲苯和甲醇烷基化机理研究主要存在以下问题：(1)计算得到的能量多为电子能,而非自由能;(2)所采用的模型多为团簇模型,使用 ONIOM方法,对长程作用力描述不充分;(3)认为甲苯只有一种吸附状态;(4)没有考虑偕烷基化反应.本文采用周期性模型,通过密度泛函理论研究了 HZSM-5分子筛上甲苯和甲醇烷基化反应机理,通过计算熵得到了反应自由能,并考虑了偕烷基化反应.由于甲基的存在,在甲苯的吸附态中,甲基会伸向孔道的不同方向,因此我们认为甲苯有多种吸附态,而不同的吸附态会生成不同的二甲苯.结果表明,甲苯可以在对位、间位、邻位和偕位上通过协同机理或分步机理发生烷基化反应.在协同机理中,甲苯在对位、间位、邻位和偕位发生烷基化反应的自由能垒分别为167,138,139和183 kJ/mol.在分步机理中,甲醇脱水生成甲氧基的自由能垒为145 kJ/mol,是决速步骤;而甲苯和甲氧基对位、间位、邻位和偕位烷基化的自由能垒分别为127,105,106和114 kJ/mol.两种机理中 PX的生成能垒均比 MX和 OX高,与文献报道的结果不同.文献均认为, PX的生成能垒最低.一方面这可能是由于所采用模型的不同,本文采用周期性模型,能更充分考虑长程作用力的影响;另一方面可能是由于对甲苯吸附态的不同处理,我们认为甲苯有多种吸附态,不同的吸附态会生成不同的二甲苯,而文献均只考虑了一种甲苯吸附态.但是,在实验中, PX选择性最高.这可能是由于：(1) PX在 HZSM-5孔道的扩散速率比 MX和 OX高2–3个数量级;(2)甲苯和甲醇烷基化生成的 MX和OX迅速发生异构化反应生成 PX,异构化反应速率高于甲苯烷基化速率.两种机理中, C8H11+都是重要的中间物种,它可以反馈一个质子给分子筛骨架,生成二甲苯;也可以脱烷基生成甲烷和乙烯等气相产物.研究发现,甲烷的生成是由于 C8H11+物种中的一个 H质子从苯环上的碳原子转移到甲基上的碳原子造成的,计算得到的对位、间位和邻位 C8H11+生成甲烷的能垒分别为136,132和134 kJ/mol.由于十元环孔道的限制, HZSM-5孔道中很难通过甲苯歧化反应生成苯;偕烷基化生成的碳正离子有可能脱烷基生成乙烯和乙烷等产物,进而生成苯.碳正离子脱烷基反应生成了大量气相产物,造成反应液收降低.碳正离子脱烷基反应与甲醇制烯烃过程的烃池机理相一致,因此甲苯和甲醇烷基化反应也遵循烃池机理.     

Different Enzyme Conformations Induce Different Mechanistic Traits in HIV-1 Protease

The influence of the dynamical flexibility of enzymes on reaction mechanisms is a cornerstone in biological sciences. In this study, we aim to 1) study the convergence of the activation free energy by using the first step of the reaction catalysed by HIV-1 protease as a case study, and 2) provide further evidence for a mechanistic divergence in this enzyme, as two different reaction pathways were seen to contribute to this step. We used quantum mechanics/molecular mechanics molecular dynamics simulations, on four different initial conformations that led to different barriers in a previous study. Despite the sampling, the four activation free energies still spanned a range of 5.0 kcal ⋅ mol⁻¹. Furthermore, the new simulations did confirm the occurrence of an unusual mechanistic divergence, with two different mechanistic pathways displaying equivalent barriers. An active-site water molecule is proposed to influence the mechanistic pathway.     

木质素模化物紫丁香酚热解机理的量子化学研究

采用密度泛函理论方法B3LYP/6-31G++(d,p),对木质素模化物紫丁香酚的热解反应机理进行了量子化学理论研究。提出了三种可能的热解反应途径,对各种反应的反应物、产物、中间体和过渡态的结构进行了能量梯度全优化。计算了各热解反应途径的标准动力学参数,分析了各种主要热解产物的形成演化机理。键离解能计算结果表明,紫丁香酚中CH₃-O键的键离解能最小,各种键离解能的大小顺序为CH₃-O < O-H < CH₃O-C_aromatic < CH₂-H < HO-C_aromatic < C_aromatic-H。在反应路径(1)中,主要热解产物是3-甲氧基邻苯二酚,其形成反应的总能垒为366.6 kJ/mol;在反应路径(2)中主要热解产物是2-甲氧基-6-甲基苯酚,其形成反应的总能垒为474.8 kJ/mol;在反应路径(3)中形成邻甲氧基苯酚的总能垒很低,为21.4 kJ/mol,这表明,在连接甲氧基的碳原子上加氢后能够有效地降低木质素芳环模化物紫丁香酚去甲氧基反应的反应能垒。     

Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis: the case of histone lysine methyltransferase SET7/9

To elucidate enzyme catalysis through computer simulation, a prerequisite is to reliably compute free energy barriers for both enzyme and solution reactions. By employing on-the-fly Born-Oppenheimer molecular dynamics simulations with the ab initio quantum mechanical/molecular mechanical approach and the umbrella sampling method, we have determined free energy profiles for the methyl-transfer reaction catalyzed by the histone lysine methyltransferase SET7/9 and its corresponding uncatalyzed reaction in aqueous solution, respectively. Our calculated activation free energy barrier for the enzyme catalyzed reaction is 22.5 kcal/mol, which agrees very well with the experimental value of 20.9 kcal/mol. The difference in potential of mean force between a corresponding prereaction state and the transition state for the solution reaction is computed to be 30.9 kcal/mol. Thus, our simulations indicate that the enzyme SET7/9 plays an essential catalytic role in significantly lowering the barrier for the methyl-transfer reaction step. For the reaction in solution, it is found that the hydrogen bond network near the reaction center undergoes a significant change, and there is a strong shift in electrostatic field from the prereaction state to the transition state, whereas for the enzyme reaction, such an effect is much smaller and the enzyme SET7/9 is found to provide a preorganized electrostatic environment to facilitate the methyl-transfer reaction. Meanwhile, we find that the transition state in the enzyme reaction is a little more dissociative than that in solution.     

Understanding the fate of the oxyallyl cation following Nazarov electrocyclization: sequential Wagner-Meerwein migrations and the synthesis of spirocyclic cyclopentenones

A general reaction sequence is described that involves Nazarov cyclization followed by two sequential Wagner-Meerwein migrations, to afford spirocyclic compounds from divinyl ketones in the presence of 1 equiv of copper(II) complexes. A detailed investigation of this sequence is described including a study of substrate scope and limitations. It was found that after 4π electrocyclization, two different pathways are available to the oxyallyl cation intermediate: elimination of a proton can give the usual Nazarov cycloadduct, or ring contraction can give an alternative tertiary carbocation. After ring contraction, either [1,2]-hydride or carbon migration can occur, depending upon the substitution pattern of the substrate, to furnish spirocyclic products. The rearrangement pathway is favored over the elimination pathway when catalyst loading is high and the copper(II) counterion is noncoordinating. Several ligands were found to be effective for the reaction. Thus, the reaction sequence can be controlled by judicious choice of reaction conditions to allow selective generation of richly functionalized spirocycles. The three steps of the sequence are stereospecific: electrocyclization followed by two [1,2]-suprafacial Wagner-Meerwein shifts, the ring contraction and then a hydride, alkenyl, or aryl shift. The method allows stereospecific installation of adjacent stereocenters or adjacent quaternary centers arrayed around a cyclopentenone ring.     

Hydrogen bonding pathways in human dihydroorotate dehydrogenase

Dihydroorotate dehydrogenase (DHOD) catalyzes the only redox reaction in the pathway for pyrimidine biosynthesis. In this reaction, a proton is transferred from a carbon atom of the substrate to a serine residue, and a hydride is transferred from another carbon atom of the substrate to a cofactor. The deprotonation of the substrate is postulated to involve a proton relay mechanism along a hydrogen bonding pathway in the active site. In this paper, molecular dynamics simulations are used to identify and characterize potential hydrogen bonding pathways that could facilitate the redox reaction catalyzed by human DHOD. The observed pathways involve hydrogen bonding of the active base serine to a water molecule, which is hydrogen bonded to the substrate carboxylate group or a threonine residue. The threonine residue is positioned to enable proton transfer to another water molecule leading to the bulk solvent. The impact of mutating the active base serine to cysteine is also investigated. This mutation is found to increase the average donor-acceptor distances for proton and hydride transfer and to disrupt the hydrogen bonding pathways observed for the wild-type enzyme. These effects could lead to a significant decrease in enzyme activity, as observed experimentally for the analogous mutant in Escherichia coli DHOD.     

QM/MM study of the taxadiene synthase mechanism

Combined quantum mechanics/molecular mechanics (QM/MM) calculations were used to investigate the reaction mechanism of taxadiene synthase (TXS). TXS catalyzes the cyclization of geranylgeranyl diphosphate (GGPP) to taxadiene (T) and four minor cyclic products. All these products originate from the deprotonation of carbocation intermediates. The reaction profiles for the conversion of GGPP to T as well as to minor products were calculated for different configurations of relevant TXS carbocation complexes. The QM region was treated at the M06-2X/TZVP level, while the CHARMM27 force field was used to describe the MM region. The QM/MM calculations suggest a reaction pathway for the conversion of GGPP to T, which slightly differs from previous proposals regarding the number of reaction steps and the conformation of the carbocations. The QM/MM results also indicate that the formation of minor products via water-assisted deprotonation of the carbocations is highly exothermic, by about −7 to −23 kcal/mol. Curiously, however, the computed barriers and reaction energies indicate that the formation of some of the minor products is more facile than the formation of T. Thus, the present QM/MM calculations provide detailed insights into possible reaction pathways and into the origin of the promiscuity of TXS, but they do not reproduce the product distribution observed experimentally. © 2019 Wiley Periodicals, Inc.     

Can Flory-Stockmayer theory be applied to predict conventional free radical polymerization of multivinyl monomers? A study via Monte Carlo simulations

The conventional free radical polymerization (FRP) of multivinyl monomers (MVMs) inevitably leads to gelation even at low monomer conversion resulting in difficulties to control and monitor the reaction process. Flory and Stockmayer (F-S theory) studied it based on two fundamental assumptions: (1) independent and equivalent vinyl groups; (2) no intramolecular cyclization. However, until now its applicability to FRP of MVMs (especially regarding the extent of intramolecular cyclization) is still controversial. In this paper, Monte Carlo simulations are used to study FRP of divinyl monomers by two kinetic models: with/without cyclization models. The results of the simulations are compared with the calculated gel points based on F-S theory and the experimental data. It is found that the intramolecular cyclization has a negligible impact on the polymerization process and the gel point before gelation, which are in agreement with the prediction by F-S theory, but the effect becomes significant above the gel points.     

Physical constraints on sesquiterpene diversity arising from cyclization of the eudesm-5-yl carbocation

The biogenic origins of complex cyclic terpenes derive from the interplay of enzymes and the intrinsic reactivity of carbocation species at major branch-points along intramolecular cyclization pathways to ultimately determine the distribution of terpene skeletal types in nature. Solanaceous plants biosynthesize chemical defense compounds, largely derived from the eremophilane and spirovetivane-type sesquiterpenes. These hydrocarbon skeletons share a common biogenic origin, stemming from alternative Wagner-Meerwein rearrangements of the eudesm-5-yl carbocation during the cyclization of farnesyl pyrophosphate (FPP) catalyzed by sesquiterpene synthases. While the spirojatamane skeleton shares the same carbocation intermediate, this class of sesquiterpenes has not been reported in the Solanaceae and is exceedingly rare in nature. To investigate the physical basis for alternative rearrangements of the eudesm-5-yl carbocation, we carried out quantum mechanics (QM) analyses to calculate the allowable conformations, energies, and transition states linking conformers of the eudesm-5-yl carbocation to the eremophilene, spirovetivane, and spirojatamane skeletons. Additionally, we conducted parallel investigations on simplified decalin carbocation systems to examine the contribution of ring substituents to allowable conformations and rearrangement pathways. Our study reveals that ring substituents expand the conformational space accessible to the eudesm-5-yl carbocation while sterically blocking rearrangements in certain contexts. From our analysis, we define a conformational threshold for each possible rearrangement based on dihedral angles describing transition state geometry. Further, our calculations indicate that methylene migration rearrangements leading to spiro compounds are thermodynamically dominant in the eudesm-5-yl and simpler decalin carabocation systems. Interestingly, the theoretical abundance of sesquiterpene skeletal types arising from the intrinsic reactivity of the eudesm-5-yl carbocation stands in sharp contrast to their currently known natural abundance. The implications of these results for the catalytic tragectories catalyzed by sesquiterpene synthases are discussed.     

Synthetic efficiency in enzyme mechanisms involving carbocations: aristolochene synthase

An intramolecular proton-transfer mechanism has been proposed for the carbocationic cyclization of farnesyl pyrophosphate (FPP) to (+)-aristolochene catalyzed by aristolochene synthase. This novel mechanism, which is based on results obtained by high-level ab initio molecular orbital and density functional theory calculations, differs from the previous proposal in the key step of carbocation propagation prior to the formation of the bicyclic carbon skeleton. Previously, germacrene A was proposed to be generated as an intermediate by deprotonation of germacryl cation followed by reprotonation of the C6-C7 double bond to yield eudesmane cation. In the mechanism proposed here the direct intramolecular proton transfer has a computed barrier of about 22 kcal/mol, which is further lowered to 16-20 kcal/mol by aristolochene synthase. An alternative pathway is also possible through a proton shuttle via a pyrophosphate-bound water molecule. The mechanism proposed here is consistent with the observation that germacrene A is not a substrate of aristolochene synthase. Furthermore, the modeled substrate-enzyme complex suggests that Trp 334 and Phe 178 play key roles in positioning the substrate in the reactive orientation in the binding pocket. This is consistent with experimental findings that mutations of either residue lead to pronounced generation of aborted cyclization products.     

A DFT study on a mutipathways,one product reaction: Initially divergent radical reactions reconverge to form a single product

The mechanism for initially divergent radical reactions reconverging to form a single product is studied using density functional theory calculations. The calculation results suggest that there are six possible pathways from reactants to products. The free energy barriers of the rate‐determining steps of each pathway are almost equal. Thus, different from usual reaction, the selectivity of this reaction is determined by the relative value of free energy barriers of the two competitive reactions, that is, cyclization and bimolecular trapping, rather than that of rate‐determining steps. In all reaction pathways, cyclization reaction is more competitive than bimolecular trapping reaction due to its low free energy barrier. In addition, the free energy barriers of bimolecular trapping reaction between Bu₃SnH and reactants are all lower than that of NC? C₆H₁₁. However, Bu₃SnH is not always suitable due to its large steric repulsion. © 2014 Wiley Periodicals, Inc.     

Gold(I)-catalyzed intramolecular [4+2] cycloadditions of arylalkynes or 1,3-enynes with alkenes: scope and mechanism

The cyclizations of enynes substituted at the alkyne gives products of formal [4+2] cyclization with Au(I) catalysts. 1,8-Dien-3-ynes cyclize by a 5-exo-dig pathway to form hydrindanes. 1,6-Enynes with an aryl ring at the alkyne give 2,3,9,9a-tetrahydro-1H-cyclopenta[b]naphthalenes by a 5-exo-dig cyclization followed by a Friedel-Crafts-type ring expansion. A 6-endo-dig cyclization is also observed in some cases as a minor process, although in a few cases, this is the major cyclization pathway. In addition to cationic gold complexes bearing bulky biphenyl phosphines, a gold complex with tris(2,6-di-tert-butylphenyl)phosphite is exceptionally reactive as a catalyst for this reaction. This cyclization can also be carried out very efficiently with heating under microwave irradiation. DFT calculations support a stepwise mechanism for the cycloaddition by the initial formation of an anti-cyclopropyl gold(I)-carbene, followed by its opening to form a carbocation stabilized by a pi interaction with the aryl ring, which undergoes a Friedel-Crafts-type reaction.     

Chemical rescue of enzymes: proton transfer in mutants of human carbonic anhydrase II

In human carbonic anhydrase II (HCA II), the mutation of position 64 from histidine to alanine (H64A) disrupts the rate limiting proton transfer (PT) event, resulting in a reduction of the catalytic activity of the enzyme as compared to the wild-type. Potential of mean force (PMF) calculations utilizing the multistate empirical valence bond (MS-EVB) methodology for H64A HCA II yields a PT free energy barrier significantly higher than that found in the wild-type enzyme. This high barrier, determined in the absence of exogenous buffer and assuming no additional ionizable residues in the PT pathway, indicates the likelihood of alternate enzyme pathways that utilize either ionizable enzyme residues (self-rescue) and/or exogenous buffers (chemical rescue). It has been shown experimentally that the catalytic activity of H64A HCA II can be chemically rescued to near wild-type levels by the addition of the exogenous buffer 4-methylimidazole (4MI). Crystallographic studies have identified two 4MI binding sites, yet site-specific mutations intended to disrupt 4MI binding have demonstrated these sites to be nonproductive. In the present work, MS-EVB simulations show that binding of 4MI near Thr199 in the H64A HCA II mutant, a binding site determined by NMR spectroscopy, results in a viable chemical rescue pathway. Additional viable rescue pathways are also identified where 4MI acts as a proton transport intermediary from the active site to ionizable residues on the rim of the active site, revealing a probable mode of action for the chemical rescue pathway.     

Investigation of the catalytic mechanism of farnesyl pyrophosphate synthase by computer simulation

Farnesyl pyrophosphate synthase (FPPS) catalyses the formation of a key cellular intermediate in isoprenoid metabolic pathways, farnesyl pyrophosphate, by the sequential head-to-tail condensation of two molecules of isopentenyl diphosphate (IPP) with dimethylallyl diphosphate (DMAPP). Recently, FPPS has been shown to represent an important target for the treatment of parasitic diseases such as Chagas disease and African trypanosomiasis. Bisphosphonates, pyrophosphate analogues in which the oxygen bridge between the two phosphorus atoms has been replaced by a carbon substituted with different side chains, are able to inhibit the FPPS enzyme. Moreover, nitrogen-containing bisphosphonates have been proposed as carbocation transition state analogues of FPPS. On the basis of structural and kinetic data, different catalytic mechanisms have been proposed for FPPS. By analyzing different reaction coordinates we propose that the reaction occurs in one step through a carbocationic transition state and the subsequent transfer of a hydrogen atom from IPP to the pyrophosphate moiety of DMAPP. Moreover, we have analyzed the role of the active site amino acids on the activation barrier and the reaction mechanism. The structure of the active site is well conserved in the isoprenyl diphosphate synthase family; thus, our results are relevant for the understanding of this important class of enzymes and for the design of more potent and specific inhibitors for the treatment of parasitic diseases.