Oxidation of Acid, Base, and Amide Side-Chain Amino Acid

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B: Biophysical Chemistry and Biomolecules

Oxidation of Acid, Base and Amide Side Chain Amino Acid Derivatives via Hydroxyl Radical Jon Uranga, Jon I. Mujika, Rafael Grande-Aztatzi, and Jon M. Matxain J. Phys. Chem. B, Just Accepted Manuscript • Publication Date (Web): 20 Apr 2018 Downloaded from http://pubs.acs.org on April 20, 2018

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The Journal of Physical Chemistry

Oxidation of Acid, Base and Amide Side Chain Amino Acid Derivatives Via Hydroxyl Radical Jon Uranga,∗,†,‡ Jon I. Mujika,‡ Rafael Grande-Aztatzi,‡ and Jon M. Matxain∗,†,‡ †Kimika Fakultatea - Chemistry Department, Euskal Herriko Unibertsitatea (UPV/EHU), P.K. 1072, 20080, Donostia, Euskadi, Spain ‡Donostia International Physics Center (DIPC), Manuel Lardizabal 4, 20018, Donostia, Euskadi, Spain E-mail: [email protected]; [email protected]

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Abstract Hydroxyl radical (• OH) is known to be highly reactive. Herein, we analyze the oxidation of acid (Asp and Glu), base (Arg and Lys) and amide (Asn and Gln) containing amino acid derivatives by the consecutive attack of two • OH. In this work we study the reaction pathway by means of density functional theory. The oxidation mechanism is divided into two steps: 1) the first • OH can abstract a H atom or an electron, leading to a radical amino acid derivative, which is the intermediate of the reaction 2) the second • OH can abstract another H atom or add itself to the formed radical, rendering the final oxidized products. The studied second attack of • OH is applicable to situations where high concentration of • OH is found, e.g. in vitro. Carbonyls are the best known oxidation products for these reactions. This work includes solvent dielectric and confirmation’s effects of the reaction, showing that both are negligible. Overall, the most favored intermediates of the oxidation process at the side chain correspond to the secondary radicals stabilized by hyper-conjugation. Intermediates show to be more stable in those cases where the spin density of the unpaired electron is lowered. Alcohols formed at the side chains are the most favored products followed by the double bond containing ones. Interestingly, Arg and Lys side chain scission lead to the most favored carbonyl containing oxidation products, in line with experimental results.

Introduction Reactive species are unstable chemical agents that display high capacity to react with other molecules. They could have a radical (e.g. • OH, • OOH, • NO) or non radical (e.g. H2 O2 , O2 , ONO2 − ) character, whose production can be exogenous or endogenous; the former may be due to radiation or pollutants, while the latter might occur under conditions of persistent oxidation production during mitochondrial processes. The mitochondria uses O2 in order to store energy and the most common product is H2 O, but in some cases, reactive species are produced. 1–4 Among all the possible reactive species, • OH is considered to be the most

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reactive one, with a life time of 1ns. 2 It is a radical species, which has an unpaired electron in the valence. These reactive species are usually assigned to be damaging for an organism. However, they play an important role and fulfill chores for the adequate function of the organism. They take part in several processes such as apoptosis, homeostasis or defense against pathogens and have interesting applications fighting against cancer. 5–13 Their high instability justifies the observed short life span, 14 as they are able to easily react with the neighboring molecules, therefore, their concentration requires from a careful balance. Whenever such balance is broken, there is an overproduction of the reactive species which uncontrollably react with the components of organisms, oxidizing the DNA, 10,11,15,16 lipids, 17 and proteins; 18,19 such stage is known as oxidative stress. The so called Free Radical theory states that the aging is a direct consequence of the oxidation processes, 20 however, antioxidant agents, such as vitamins, 21,22 are responsible to quench the excess of these species. Indeed, some organisms, as a last line of defense, have developed methods to recover damaged structures. 23,24 It is worth to note that, at the end of the day the oxidation is unavoidable and that it has been linked to many neurodegenerative diseases such as Alzheimer, Parkinson or Huntington. 15,25,26 The main driving factor for the oxidation to take place is the concentration of the components to be oxidized. Proteins are found to be at relatively high concentration in the organisms, 18 making them one of the main targets for these reactive species. The protein oxidation is known to cause a wide variety of processes such as protein aggregation, unfolding, miss-folding, dissociation, cross-linking, racemization or metal ion release from the active site, bringing dramatic consequences to the organism. 27–32 In this vein, all these events may lead to lowering enzymatic activity or complete inhibition. Carbonyl compounds are one of the most usual products after such oxidation process, and they are often employed as oxidation markers. 27,30,33,34 Different oxidation mechanisms caused by radicals have been studied, as H atom abstrac-

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tion, 3,28,29,32,35–40 addition to aromatic rings 41–43 or electron abstraction. 35,44,45 The attack of a single • OH yields a radical molecule, which is usually an intermediate in the oxidation reaction. The characterization of oxidized products by fast optical spectroscopy and/or electron paramagnetic resonance 14 may help to identify the most vulnerable protein sites, or the processes that give rise to them. The attack can occur at the backbone or at the side chains of proteins, depending on the relative stability of the formed intermediates and products. In this vein, it has been observed that proteins containing aliphatic side chains are prone to react at Cα position of the backbone, 39 this attack leads to the formation of relatively stable radical intermediate, due to the captodative effect. 3,46 Indeed, 90% of the formed radical in alanine are due to the H abstraction at Cα . 14 In previous studies, we have performed the consecutive attack of two • OH towards aromatic and -OH and -S containing amino acids. 35,41 Therefore, we employ the same strategy in this work (Figure 1a), in order to analyze the oxidation of the side chains of acid, base, and amide containing amino acid derivatives. The attack of • OH has been observed to have very low energy barriers. 18,32,35,41 In those cases, where the barriers are small, the kinetics control reaction rates. The transition states for the first attack of • OH are present in the Supporting Information (Tables S1, S4, S7, S11), and the discussion is focused on the relative stability of the intermediates. The reason for us to focus on intermediates relative stability relies on the fact that once an intermediate is formed it may interact with nearby residues in a protein, leading to thermodynamically favored radical, assuming that kinetic barriers are similar. The experimentally observed oxidation products of Asp, Glu, Lys and Arg are shown in Figure 1b. 27,30,47 However, little is known about the oxidation products of Asn and Gln, but it has been reported that the amide group is suitable to suffer from oxidation. 27 Moreover, theoretical studies showed that the H abstraction mechanism, of different amides, from the NH2 is the least favored process. 48 Therefore, the present study aims to shed light on the oxidation process and products for the already mentioned amino acids.

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For non aliphatic amino acids, a more complex reaction mechanism is expected in which the side chains are the primary sites for the attack of • OH radicals. For instance, Anglada investigated the • OH attack towards formic acid, observing that the H abstraction from formyl is the preferred mechanism, exhibiting lowest TS values. 49 Lys and Arg are known to oxidize leading to aldehydes and ketones (e.g. Citrulline), 27,30 although they remain unstable and can get further oxidized. In particular, the oxidation of aldehydes leads to the formation of carboxylic acids, 50 while ketones can react with amino groups present in the proteins and form Schiff bases. 27,50

Methods Gaussian09 package 51 was used in order to perform geometry optimizations and frequency calculations within density functional theory, 52,53 more specifically we used the meta-GGA functional MPWB1K. 54–57 The geometry optimizations and frequency calculations were done in gas-phase with the 6-31+G(d,p) basis set. Harmonic vibrational frequencies were obtained by analytical differentiation of gradients to identify whether a minima or a transition state was encountered. Such frequencies were then used to evaluate the zero-point vibrational energy (ZPVE) and the thermal (T = 298 K) vibrational corrections to the enthalpy. Single point calculations were done with 6-311++G(2df,2p) basis set and the integral equation formalism of the polarized continuum model (IEFPCM) 58,59 with the purpose of estimating the effect of the environment. Two dielectric constants were employed in order to fulfill the mentioned goal: ε = 4 to represent a low dielectric environment in a buried region of a protein, and ε = 80 to represent a high solvent accessible region of a protein. The discussion is done with the ∆H 298 due to the fact that infinitely separated reactants and products were considered, which renders unbalanced entropic effects. Notice that negative values for computed transition states (TS) relative enthalpies are obtained due to this procedure. The

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determination of these values is done by adding the enthalpic contributions in the gas-phase 298 to the electronic energy in solution to give the final enthalpies, ∆H4298 and ∆Haq . It has

been demonstrated elsewhere that this methodology is appropriate to study these type of reactions. 17,21,41,60 The model structure under study includes one entire amino acid flanked by two peptide bonds that are truncated at the neighbor Cα atom. Two conformers, α-helix-like or β-sheet were considered, which are typically found in proteins, by a proper orientation of the ϕ and φ dihedral angles. The model employed herein has its pros and cons. The main advantage is that the analyzed reaction mechanisms are general and therefore apply to a wide range of scenarios. However, due to the fact that proteins are macro-molecules the neighboring residues could play a role in such reactions which was not considered in this study as the goal was to supply with a general view, as it was already mentioned. Moreover, the obtained results apply for the presented conformations and were selected in order to explore the oxidation mechanism in a protein. Such model was previously employed for different amino acid derivatives, 32,35,41 so that enabling us to compare the oxidation processes. In order to quantify the degree of localization/delocalization of the unpaired electron formed once the hydrogen or electron abstraction, the APOST-3D program 61 was employed to compute atomic spin densities for all the species. We have made use of the topological fuzzy Voronoi cells (TFVC) 62 to define the atomic boundaries within the molecule. TFVC is a three-dimensional atomic partition based on the fuzzy atomic Voronoi cells introduced by Becke. 63,64 Results obtained with TFVC have been proved to be very similar to those obtained by using the more computationally demanding Quantum Theory of Atoms in Molecules partitioning of the three-dimensional space. 65

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Results and Discussion The oxidation of the peptides containing acid (Glu, Asp), base (Lys, Arg) or amide (Gln, Asn) groups at the side chains are analyzed. It must be said that during the protein oxidation not only they are exposed to the • OH, but to many other reactive species and a myriad of possibilities exist for such process. 32,35,41 Herein, we have studied the simplified oxidation reaction pathway which results by the consecutive attack of two • OH (see Figure 2). We remark that this is not the only possible oxidation mechanism, but it is the simplest one to reach the known experimental products. Such procedure is an approximation to analyze the oxidation products and may be applicable to cases where high concentration of • OH is found, e.g. in vitro occurring oxidation reactions. The discussion is focused on the relative stability of intermediates and products and some of the key transition states (TS) are shown in the Supporting Information (Tables S1, S4, S7, S11). The TS values for the H abstraction were observed to be very small and therefore, they are assumed to be barrierless. Analyzing the oxidation caused by the hydroxyl radical we have only considered this radical species. Moreover, alternative reaction mechanisms were considered for each step: the attack of the first • OH can 1) abstract a H atom, converting the initial • OH into H2 O and forming a radical intermediate (Figure 2a), 2) abstract an electron from the carboxylate group present in Asp and Glu, transforming the • OH to

−

OH (Figure 2b) or 3) addition of a • OH to

the unsaturated moiety of Arg. In every case an amino acid derivative radical is created, herein named as intermediate. The second • OH can 1) add itself to the radical, forming an alcohol, hydroxylamine or peroxide, depending on the intermediate group at the side chain, or 2) abstract another H atom from the neighboring atoms, leading to the formation of a double bond. Both steps are considered to be driven by thermodynamics, as similar reactions previously studied in other AA models. 35,41 A schematic representation of the overall reaction mechanism is shown in Figure 2. All the amino acid derivatives herein studied are the reactants (React) in the reactions together with the • OH. The radical intermediates formed by the first • OH attack is named as Int, whereas the final products obtained by the second 8


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significant difference is found when changing the conformation and the discussion is done with the α − helix − like conformation. The calculated values for both conformations can be found in the Supporting Information.

Acid containing amino acid derivatives The carboxylic group has a pKa of 3.9 and in some proteins even higher. Asp and Glu show deprotonated state at both high and physiological pH values (carboxylate), while at low pH values the protonated state of the functional group can be found (carboxylic acid). Hence we have considered both protonation states for each case. The employed nomenclature involves Asp and Glu for the carboxylate containing amino acids. On the other hand, an "h" letter is added in the cases where the carboxylic acid is present, i.e. Asph and Gluh. Aspartic acid In this subsection, the aspartate (Asp) and the aspartic acid (Asph) are studied. Figure 3 and Tables S1, S2 and S3 displays the stages of the Asp reaction pathway. The attack of the first • OH produces the intermediates (Int) in Figure 3, whereas the second • OH attack renders the products (Prod). In the same line, Figure 4 shows the reaction mechanism for Asph.

1st • OH

can abstract a H atom from Cα , Cβ or an electron from the O atom of the

carboxylate group (Oδ ), leading to the formation of a radical intermediate. The relative α enthalpies and TFVC spin densities are presented in Figure 3 and Table S2. IntC Asp is the

298 most stable radical intermediate △Haq = −33.7 kcal/mol and lies about 10 kcal/mol lower C

β . As reported previously, 32 any radical at Cα position is more favored than at than IntAsp

Cβ due to the captodative effect occurring at the former.

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δ IntO Asp represents the radical intermediate formed after the electron abstraction, which

C

β . The former is a primary radical, while is about 13 kcal/mol higher in energy than IntAsp

C

β is a secondary radical, which is further stabilized by the hyper-conjugation effect. IntAsp

The spin densities, at the atom where the radical sits, indicate the localization of the unpaired electron, the more delocalized it is, the more stable the intermediate would be. C

β 3,32,46 α , a secIntAsp IntC Asp has the lowest value (0.51 at Cα ) due to the captodative effect.

ondary radical that is stabilized due to hyper-conjugation effects, Cβ presents a spin density δ value of 0.76. Finally, the radical remains localized at the O atom of IntO Asp (0.91).

In the case of the carboxylic acid (Asph), energetically the same trend is obtained (Figure 4). That is, the most stable intermediate is the one corresponding to the H abstraction at Cα C

β 298 α (IntC Asph ) △Haq = −28.6 kcal/mol, which is about 5 kcal/mol more favored than IntAsph ,

while the H abstraction of the carboxylic group (Oδ ) leads to an intermediate about 21 α kcal/mol less stable than IntC Asph .

Looking at the spin densities at which the radical sits, the lowest value is obtained for C

β α IntC Asph , a tertiary radical stabilized by the captodative effect. IntAsph is a secondary radical

stabilized by the hyper-conjugation effect as mentioned, while the highest spin density is δ obtained for Oδ atom of IntO Asph .

α Side chain splitting Alternatively, IntC Asp could drive to a side chain splitting through

an heterolytic mechanism, where a CO2 molecule is released and the radical remains on the 298 amino acid. However, such intermediate, Intαβ Asp (△Haq = −7.7 kcal/mol), is about 27 −

α kcal/mol higher than IntC Asp , and this reaction mechanism is energetically unfavorable.

The spin density of the side chain scission intermediate (Intαβ Asp ), is distributed along the −

backbone with a little preference by the Cα atom, and because of the heterolytic splitting the intermediate has a negative charge. αβ α The side chain splitting could also take place with the IntC Asph , leading to (IntAsph ). Con−

298 trary to the deprotonated system, the reaction is now endothermic (△Haq = 7.3 kcal/mol)

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αβ (Table S2). Note that Intαβ Asph and IntAsp are the same chemical entities with different −

−

reactants as reference, so their spin density values are the same. 2nd • OH

can abstract another H atom from Asp, add itself to the already formed radical

intermediate, or abstract an electron from either the carboxylate group or the formed negαβ . Note that the addition of the • OH toward the formed atively charged amino acid IntAsp −

α IntC Asph is not considered as the purpose is to investigate the side chain oxidation mechanisms.

This second attack yields the final products and herein we analyze their thermodynamic stability (Table S3). C

β , leading The most favored products correspond to the • OH addition to the formed IntAsp

s−βoh r−βoh 298 298 (△Haq = -115.7 kcal/mol). Finally, (△Haq = -111.6 kcal/mol) and P rodAsp to P rodAsp

the addition of the • OH to the formed Oδ radical to produce the peroxide group yields the s−βoh least stable product, P rodooh Asp , which lies 100 kcal/mol higher than P rodAsp .

The same trend of products is observed for Asph (Table S3). Interestingly, even though 298 it is still the most unstable product, P rodooh Asph (△Haq = -46.9 kcal/mol) is greatly stabilized s−βoh r−βoh (by about 30 kcal/mol) when comparing to P rodooh Asp . Once again, P rodAsph and P rodAsph

are the most stable ones. Side chain splitting can take place after the attack of two • OH. In this sense, departing • α from IntC Asp if the OH abstracts an electron from the carboxylate, CO2 is released by an Oδ 298 homolytic splitting forming P rodαβ Asp (△Haq = -108.0 kcal/mol). In the same way, IntAsp

leads to the same product if the • OH abstracts a H atom from Cα . The same mechanism is 298 observed for Asph and P rodαβ Asph displays a △Haq = −103.4 kcal/mol.

Glutamic acid As in the previous case, the H atom or e− abstraction stages of the oxidation pathway of Glutamate (Glu) and Glutamic acid (Gluh) are analyzed in two attacks of • OH.

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1st • OH

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The results for Glu (Table S5) point out that the most stable intermediate correC

C

β γ 298 298 (△Haq = -20.3 kcal/mol) and IntGlu (△Haq = sponds to the H abstraction at Cγ . IntGlu

-24.2 kcal/mol) are secondary radicals but the latter is about 4 kcal/mol more stable than the former owing to the neighboring carboxylate group, which further stabilizes the radical. ε IntO Glu , is a primary radical formed after the electron transfer from the Oε of the carboxylate

to the • OH, forming the

−

C

γ OH and therefore it is about 14 kcal/mol higher than IntGlu

Figure 5. For the intermediates of the H abstraction from Gluh, the same stability trend is observed, C

C

γ β the IntGluh is more stable than the secondary radical IntGluh due to the neighboring carε boxylic group that contributes to the radical delocalization, and the primary radical IntO Gluh

is the least stable one Figure 6. Regarding the spin densities of the Glu and Gluh intermediates, as in the previous cases, the highest the value at the centered atom, the less stable the radical would be. 2nd • OH

The final products are shown in Figure 5 . The most stable products correspond C

C

β γ to the • OH additions to IntGlu and IntGlu below 110 kcal/mol (Table S6). The P rodcis−βγ Glu

that contain a double bond in the side chain are about 8 kcal/mol less stable and P rodtrans−βγ Glu than P rods−γoh Glu . Such products are formed after two H atom abstractions. The second H C

C

γ β abstraction occurs at the neighboring position of the IntGlu or IntGlu radicals generating the

respective isomers. Finally, the formation of the peroxide is the least favored mechanism, since the P rodooh Glu is about 100 kcal/mol above the most stable product. The products for Gluh follow the same trend as already discussed for Glu, Figure 6. The addition of • OH to the formed C radical intermediate yield the most favored products. r−βoh 298 P rodGluh is the most stable one (△Haq = -110.7 kcal/mol). Once again, the peroxide βγ product, P rodooh Gluh , is the least favored one, being about 55 kcal/mol higher than P rodGluh

(Table S6). 16


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Figure 6: Schematic representation of Glutamic acid oxidation reaction mechanism. Reactants (React), intermediates (Int) and products (Prod) are labeled depending on the attack site. Relative enthalpy values are given in kcal/mol. TFVC spin densities are shown for all Int. 17



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C

β Side chain splitting IntGlu can lead to the side chain dissociation when the second • OH

abstracts an electron from Oε rendering P rodβγ Glu (Table S6), which contains a double bond 298 ε between Cβ -Cγ and a CO2 molecule (△Haq = -104.6 kcal/mol). IntO Glu leads to the same

product if a H atom is abstracted from Cβ . The same mechanism is true for Gluh and 298 P rodβγ Gluh shows △Haq = -100.7 kcal/mol.

Base containing amino acids Arg and Lys side chains are formed by N atom containing groups. These groups are known to act as bases and are often protonated. Indeed, the estimated pKa values are relatively high so herein we have just considered the protonated states of the amino acids. Arginine(Arg) The Arg oxidation mechanism occurs by a first H abstraction or • OH addition to the side chain atoms, and in the second step by a H abstraction or addition of the • OH to the formed radical amino acid derivative. 1st • OH

The intermediates that can be created from H abstractions are shown in Figure

298 δ = -23.9 7 (Tables S7 and S8). The most stable intermediate corresponds to IntC Arg (△H4

kcal/mol), which is a secondary radical, where the lone pair of the neighboring Nε atom C

C

β γ and IntArg , are very helps to stabilize the radical. The other two secondary radicals, IntArg δ close in energy and show to be about 5 kcal/mol higher than IntC Arg . Finally the abstraction ε of H at N atoms have been investigated, such abstractions yield IntN Arg (secondary radical)

N

η ε (primary radical). Both of them are the most unstable ones, but IntN and IntArg Arg is about

N

η (Table S7). 6 kcal/mol more favored than IntArg δ The TFVC spin densities, at the position of the attack, show the lowest values for IntC Arg

due to the delocalization to the neighboring Nε atom. The rest of the secondary radicals, C

C

β γ ε , IntArg and IntN IntArg Arg display higher spin densities, due to the lack of a neighbor N atom.

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another H atom from the neighboring atom of the radical intermediate. 1st • OH

Once again, the secondary radicals are the most stable intermediates and the

values spread between -14.7/-19.1 kcal/mol range (Figure 10 and Table S8). A primary N

ζ radical is formed after the abstraction from the Nζ atom at the end of the side chain. IntLys

C

γ lies about 10 kcal/mol higher than the most stable secondary radical intermediate, IntLys

(Table S8). The spin densities are very similar for all these intermediates. The lowest values are Cε δ estimated for IntC Lys and IntLys with a value of 0.77, at Cδ and Cε respectively. Meanwhile,

the highest value is obtained for the primary radical, 0.80, at the N atom. Side chain splitting As in the Asp case, a homolytic dissociation mechanism may occur generating an ammonia radical (• N H3+ ), however, its capacity to abstract H atom from water 298 is an endothermic process, △Haq = 5.5 kcal/mol according to the reaction (2). Meaning that

the ammonia radical is stabler than the • OH. •

N H3+ + H2 O → N H4+ + • OH

(2)

δ Departing from the IntC Lys the side chain can be splitted. The product from this side

298 chain scission, P rodδε Lys , is slightly favored (△Haq = -0.1 kcal/mol). Then, the formation of + • IntCε OLys occurs by the H abstraction from Cε by the ammonia radical ( N H3 ). This process 298 is endothermic (△Haq ≈ 2 kcal/mol).

2nd • OH

The products where an alcohol group is formed are the most stable ones and are

spread between -110 to -114 kcal/mol (Figure 10 and Table S10). On the other hand, the double bond containing products are about 15 to 20 kcal/mol less favored. The formation of hydroxylamine by the addition of a • OH to the Nζ radical is the least favored product, 298 being △Haq of -66 kcal/mol. ε The products obtained by another • OH attack to the formed IntC OLys can lead to alcohols

εo (P rodεoh OLys ) or an aldehyde (P rodOLys ). The aldehyde lies about 10 kcal/mol lower than the

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corresponding alcohols; it is indeed the most stable product, and very close to the previously mentioned alcohols.

Amide containing amino acid derivatives Asn and Gln have an amide group in the side chain. Little documentation about their oxidation is found, but are known to be a suitable site for the H atom abstraction. 27,48 Asparagine(Asn) Herein the possible oxidation mechanism for Asn by two • OH is analyzed. The first • OH abstracts a H atom, while the second • OH generates the respective alcohols or the unsaturated products, as it was already described. 1st • OH

can abstract a H atom from Cα , Cβ or Nδ . The H abstraction from the backbone

Cα has been considered as it could lead to the side chain dissociation. As shown in Figure α 11 and Table S12 the intermediate formed after the abstraction at Cα , IntC Asn , is the most

C

β , a secondary radical, is about 7 kcal/mol less favored, and the abstraction favored one. IntAsn δ of a H atom from Nδ , which leads to a primary radical (IntN Asn ), is about 30 kcal/mol higher α than IntC Asn .

Among the spin densities of the intermediates, the lowest value corresponds to Cα of C

β α IntC Asn (0.57) due to the captodative effect. IntAsn displays a higher value (0.80 at Cβ ), δ whereas the highest value is obtained for IntN Asn (0.81 at Nδ ), the primary radical.

αβ α Side chain splitting The homolytic dissociation of IntC Asn yields P rodAsn , which contains

a double bond between atoms Cα and Cβ , and a radical species (• CONH2 ). However, this 298 reaction is endothermic, with a enthalpy value of △Haq = 3.9 kcal/mol. At the same time,

the formed radical species (• CONH2 ) can abstract H atoms (in the same way as the • OH) and to quantify its reactivity, relative to the • OH, reaction (3) was computed:

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However, we have considered the possibility by which P rodαβ Asn gets oxidized by the radical obtained from the scission of the side chain, i.e. • CON H2 . In this case, the H abstraction C

β . The relative enthalpies indicate from Cβ position leads to the radical intermediate IntOAsn

that the reaction is endothermic and therefore, such oxidation is not prone to take place. • Notice, that if the P rodαβ Asn is oxidized by the OH, the reaction is still endothermic with an 298 estimated △Haq of about 1.5 kcal/mol.

2nd • OH

can add itself to the already formed radical intermediate, in this case at Cβ or

Nδ . The addition to the former leads to two possible enantiomer products which show to s−βoh r−βoh 298 298 (△Haq (△Haq = -111.7 kcal/mol) and P rodAsn be the most favorable ones, P rodAsn

= -110.3 kcal/mol). On the other hand, the addition to Nδ is again the least favorable one, lying about 40 kcal/mol higher than the previous products (Figure 11 and Table S13). C

β ) formed after the scission The second • OH can also be added to the radical (IntOAsn

298 (△Haq = -90.2 of the side chain. It renders two possible alcohol conformers (P rodcis−βoh OAsn 298 298 (△Haq = -86.4 kcal/mol)) and an aldehyde (P rodβo kcal/mol) and P rodtrans−βoh OAsn (△Haq OAsn

= -90.9 kcal/mol) ), obtained by the keto-enol tautomerization of any of the isomers, which shows to be slightly more favored than the enol tautomers. Glutamine(Gln) As in the Asn case, the Gln oxidation mechanism proceeds through the H abstraction from Cβ , Cγ or Nε side chain atoms, and then a second • OH is added to form alcohols or abstract another H atom. 1st • OH

C

γ 298 In this case, the formation of IntGln (△Haq = -26.7 kcal/mol) is the most

C

β favorable one, IntGln lying about 6 kcal/mol higher. Meanwhile, the H abstraction from Nε

C

γ ε leads to the formation of IntN Gln , which is about 23 kcal/mol higher than IntGln . ε Regarding the spin densities at the site of attack, the primary radical IntN Gln has the

largest value (0.86), indicating the localization of the unpaired electron, while the secondary 26


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radicals have lower values (0.80 and 0.72). On the other hand, the values close to 1 for the isomers reflect once again high reactivity of them (Table S12). C

β could proceed through the side chain splitting via homolytic Side chain splitting IntGln

dissociation. In this case, the product, P rodβγ Gln , has a double bond between Cβ and Cγ , 298 but once again the process is endothermic, △Haq = 5.1 kcal/mol. Subsequent oxidation by C

γ the • CONH2 to form the intermediates cis- and trans- IntOGln , are endothermic processes

as well, around 20 kcal/mol, as it was the case for Asn. On the other hand, using the • OH to abstract the H atom from P rodβγ Gln makes the process slightly exothermic, around -0.5 kcal/mol. 2nd • OH

The most favored products are obtained in the case where the • OH is added to

the radical containing C atom, leading to the formation of alcohol groups, Figure 12 (Table S13). Observe that different enantiomers could be obtained with no significant energetic differences. The formation of a double bond occurs after a H atom abstraction from Cγ or C

C

β γ Cβ of the IntGln and IntGln , respectively; generating the cis and trans isomers, being the

the most favorable one, roughly by 3.6 kcal/mol. The addition of a • OH to the P rodtrans−βγ Gln r−βoh ε Nε atom of IntN Gln is the least favored one, lying about 40 kcal/mol higher than P rodGln . C

γ Finally, the addition of • OH to IntOGln , produces the respective cis- and trans- alcohols

γOH (P rodγOH OGln ) and the keto tautomer (P rodOGln ) products.

Radical intermediates’ stability The results presented in this article allow us to provide a general picture of the H atom abstraction by the attack of the first • OH to the amino acid side chains. In Figure 13, Mulliken spin density with respect to the relative enthalpy is shown for the C atom centered radicals, herein and previously studied cases. 32,35,41 Interestingly, a trend can be observed, indicating that the more delocalized the spin density, the more stable the radical would be.

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In the left corner Cα centered radicals can be found. The spin densities of these species are the lowest ones due to the already known captodative effect, which makes them to be the stablest ones (spin densities at Cα are spread between 0.62-0.69). At the same time, Cβ centered radicals at the aromatic amino acids display quite low spin density values (0.690.76). 41 In fact, in this case the spin density is delocalized through the aromatic moiety and therefore such radicals are pretty much stabilized. The next ones correspond to secondary radicals, which have an electron donor group as neighbor. Following the same nomenclature C

C

C

β β γ δ herein described, we can find IntC Arg (0.93), IntSer (0.89), IntT hr (0.82), IntM et (0.76),

C

β ε IntC M et (0.85), IntCys (0.78). Radicals stabilized by a neighboring unsaturated system display

C

C

C

γ γ β slightly higher spin densities than the previous cases, IntGluh (0.80), IntGlu (0.90), IntAsph

C

C

C

γ β β (0.88) and IntGln (0.81). On the other hand, the secondary (0.89), IntAsn (0.78), IntAsp

radicals merely stabilized by the hyper-conjugation show even higher spin density values and close to primary radicals, around 1.

Conclusions In the present work we have studied the oxidation mechanism for acid, base and amide containing amino acid side chains. The simplified oxidation protocol is performed by the consecutive attack of two • OH to the amino acid side chains, which is divided and discussed into two stages. The attack of the first • OH produces the radical amino acids whose relative thermodynamic stabilization is analyzed in order to establish the most favorable reaction pathway. Then, the second attack of the • OH quenches the previously formed radical, leading to final oxidized products. This procedure allows us not only to rationale experimentally observed oxidized products but also to analyze some other alternative reaction pathways not considered before. Two dielectric constants were employed in order to simulate the reaction in water and a low dielectric environment in order to represent buried regions of the protein. The confor-

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mation’s effect was taken into account performing the reaction in α-helix-like and β-sheet conformations. The obtained results do not vary in a significant way and so we conclude that the conformation and dielectric do not affect the reaction mechanisms herein discussed. Notice that this conclusion is applicable only for the general scheme herein proposed and that may change in case that neighboring residues were considered. In all cases the H abstraction mechanism leads to the most favored intermediates. Overall possibilities, it is observed that Cα is the most favored position in terms of energetic stability. Radicals formed close to a carbonyl (Asp, Glu, Asn and Gln) are also stabilized but not as much as the ones centered at Cα . Concerning the side chain splitting mechanism, the carboxylate or carboxylic acid containing groups showed that this mechanism is a possibility in the oxidation process. Interestingly, for Arg and Lys the most favored product is the aldehyde formed after the side chain splitting, which is experimentally observed. However, together with Asn, Gln, Arg and Lys displayed energetic penalties in order to lead to such process. At this point, it has to be outlined that side chain splitting is a possibility by a single attack of a • OH for Arg, Lys, Asn and Gln and that it may take place. Overall, the most favored products correspond to the alcohol group formations at the side chains. This should be highlighted herein, as it could be the preceding for the formation of ketones at the side chains if it is further oxidized. Therefore, we could say that the obtained results are in line with the experimental observations. The formation of hydroxylamines is observed to be little probable as the intermediates from where they are formed and the products itself are not that probable if alternatives are possible. In the same way, the formation of hydroperoxide in Asp, Asph, Glu and Gluh are shown to be very little favored products. Moreover, the formed intermediate (primary radical) is also the least favored one, remarking the little propensity for this pathway to take place. Finally, the formation of unsaturated bonds at the side chains is pretty much probable but their hydrated states (alcohols) show to be more stable. Thus, the formation of an alcohol group in the side chain

31



is observed to be the most favored product obtained from stable intermediates.

Supporting Information In the Supporting Information relative enthalpies of all intermediates and products at both conformations and with both dielectric used can be found. In the case of the intermediates the spin density values are also shown (Table S2, S5, S8, S12). Besides, computed relative enthalpies of TS for the first hydroxyl radical attack are shown (Table S1, S4, S7, S11) whose values are small thus considering them a barrier less event. Finally, the energies for the products are shown (Table S3, S6, S9, S10, S13).

Acknowledgements The authors are thankful for technical and human support provided by IZO-SGI SGIker of UPV/EHU and European funding (ERDF and ESF). Financial support came from Eusko Jaurlaritza (Basque Government) through Project No. IT588-13. JU would like to thank the Basque Government for funding through a predoctoral fellowship (PRE 2013 1 1156). R.G.-A. gratefully acknowledges to Consejo Nacional de Ciencia y Tecnología (CONACYT) for the postdoctoral fellowship.

References (1) Thomas, C.; Mackey, M. M.; Diaz, A.; Cox, D. P. Hydroxyl Radical is Produced via the Fenton Reaction in Submitochondrial Particles Under Oxidative Stress: Implications for Diseases Associated with Iron Accumulation. Redox Rep 2009, 14, 102–108. (2) Valdez, L. B.; Lores Arnaiz, S.; Bustamante, J.; Alvarez, S.; Costa, L. E.; Boveris, A. Free Radical Chemistry in Biological Systems. Biol Res 2000, 33, 65–70.

32


Page 32 of 50

Page 33 of 50 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


(3) Rauk, A.; Yu, D.; Taylor, J.; Shustov, G. V.; Block, D. A.; Armstrong, D. A. Effects of Structure on α C-H Bond Enthalpies of Amino Acid Residues: Relevance to H Transfers in Enzyme Mechanisms and in Protein Oxidation. Biochemistry-US 1999, 38, 9089–9096. (4) Knuuti, J.; Belevich, G.; Sharma, V.; Bloch, D. A.; Verkhovskaya, M. A Single Amino Acid Residue Controls ROS Production in the Respiratory Complex I from Escherichia Coli. Mol Microbiol 2013, 90, 1190–1200. (5) Agostinis, P.; Berg, K.; Cengel, K. A.; Foster, T. H.; Girotti, A. W.; Gollnick, S. O.; Hahn, S. M.; Hamblin, M. R.; Juzeniene, A.; Kessel, D. et al., Photodynamic Therapy of Cancer: an Update. Ca-Cancer J Clin 2011, 61, 250–281. (6) Dabrowski, J. M.; Arnaut, L. G. Photodynamic Therapy (PDT) of Cancer: from Local to Systemic Treatment. Photochem Photobiol Sci 2015, 14, 1765–1780. (7) Antoni, P. M.; Naik, A.; Albert, I.; Rubbiani, R.; Gupta, S.; Ruiz-Sanchez, P., Munikorn, P., Mateos, J. M.; Luginbuehl, V.; Thamyongkit, P. et al. (Metallo) Porphyrins as Potent Phototoxic Anti-Cancer Agents after Irradiation with Red Light. Chem-Eur J 2015, 21, 1179–1183. (8) Uranga, J.; Matxain, J. M.; Lopez, X.; Ugalde, J. M.; Casanova, D. Photosensitization Mechanism of Cu(ii) Porphyrins. Phys Chem Chem Phys 2017, 19, 20533–20540. (9) Jacobson, M. D. Reactive Oxygen Species and Programmed Cell Death. Trends Biochem. Sci. 1996, 21, 83–86. (10) Dröge, W. Free Radicals in the Physiological Control of Cell Function. Physiol Rev 2002, 82, 47–95. (11) Curtin, J. F.; Donovan, M.; Cotter, T. G. Regulation and Measurement of Oxidative Stress in Apoptosis. J Immunol Methods 2002, 265, 49–72. 33



(12) Winterbourn, C. C.; Hampton, M. B. Thiol Chemistry and Specificity in Redox Signaling. Free Radical Bio Med 2008, 45, 549–561. (13) Brieger, K.; Schiavone, S.; Miller, F. J.; Krause, K. H. Reactive Oxygen Species: from Health to Disease. Swiss Med Wkly 2012, 142, w13659. (14) Hawkins, C. L.; Davies, M. J. Generation and Propagation of Radical Reactions on Proteins. Biochim Biophys Acta 2001, 1504, 196–219. (15) Markesbery, W. R.; Carney, J. M. Oxidative Alterations in Alzheimer’s Disease. Brain Pathol 1999, 9, 133–146. (16) Levine, R. L.; Williams, J. A.; Stadtman, E. R. Carbonyl Assays for Determination of Oxidatively Modified Proteins. Method Enzymol 1991, 233, 346–357. (17) Tejero, I.; González-Lafont, A.; Lluch, J.; Eriksson, L. Theoretical Modeling of Hydroxyl-Radical-Induced Lipid Peroxidation Reactions. J Phys Chem B 2007, 111, 5684–5693. (18) Davies, M. J. The Oxidative Environment and Protein Damage. Biochim Biophys Acta 2005, 1703, 93–109. (19) Ugarte, N.; Petropoulos, I.; Friguet, B. Oxidized Mitochondrial Protein Degradation and Repair in Aging and Oxidative Stress. Antioxid Redox Sign 2010, 13, 539–49. (20) Harman, D. Aging: a Theory Based on Free Radical and Radiation Chemistry. J Gerontol 1956, 11, 298–300. (21) Matxain, J. M.; Ristilä, M.; Strid, A.; Eriksson, L. A. Theoretical Study of the Reaction of Vitamin B6 with 1O2. Chem-Eur J 2007, 13, 4636–4642. (22) Matxain, J. M.; Padro, D.; Ristilä, M.; Strid, A.; Eriksson, L. A. Evidence of High ·OH Radical Quenching Efficiency by Vitamin B6. J Phys Chem B 2009, 113, 9629–9632. 34


Page 34 of 50

Page 35 of 50 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


(23) Vogt, W. Oxidation of Methionyl Residues in Proteins: Tools, Targets, and Reversal. Free Radical Bio Med 1995, 18, 93–105. (24) Levine, R. L.; Mosoni, L.; Berlett, B. S.; Stadtman, E. R. Methionine Residues as Endogenous Antioxidants in Proteins. P Natl A Sci USA 1996, 93, 15036–40. (25) Bonda, D. J.; Wang, X.; Perry, G.; Nunomura, A.; Tabaton, M.; Zhu, X.; Smith, M. Oxidative Stress in Alzheimer Disease: a Possibility for Prevention. Neuropharmacology 2010, 59, 290–4. (26) Halliwell, B.; Gutteridge, J. Free Radicals in Biology and Medicine; Vol. 10. (27) Chondrogianni, N.; Petropoulos, I.; Grimm, S.; Georgila, K.; Catalgol, B.; Friguet, B.; Grune, T.; Gonos, E. S. Protein Damage, Repair and Proteolysis. Mol Aspects Med 2014, 35, 1–71. (28) Owen, M. C.; Viskolcz, B.; Csizmadia, I. G. Quantum Chemical Analysis of the Unfolding of a Penta-Alanyl 3 10-Helix Initiated by HO·, HO2· and O2-·. J Phys Chem B 2011, 115, 8014–8023. (29) Owen, M. C.; Szori, M.; Csizmadia, I. G.; Viskolcz, B. Conformation-Dependent ·OH/H2O2 Hydrogen Abstraction Reaction Cycles of Gly and Ala Residues: a Comparative Theoretical Study. J Phys Chem B 2012, 116, 1143–1154. (30) Lushchak, V. I. Free Radical Oxidation of Proteins and its Relationship with Functional State of Organisms. Biochemistry-Moscow+ 2007, 72, 809–827. (31) Thomas, D. A.; Sohn, C. H.; Gao, J.; Beauchamp, J. L. Hydrogen Bonding Constrains Free Radical Reaction Dynamics at Serine and Threonine Residues in Peptides. J Phys Chem A 2014, 118, 8380–8392.

35



(32) Uranga, J.; Lakuntza, O.; Ramos-Cordoba, E.; Matxain, J. M.; Mujika, J. I. A Computational Study of Radical Initiated Protein Backbone Homolytic Dissociation on All Natural Amino Acids. Phys Chem Chem Phys 2016, 18, 30972–81 (33) Stadtman, E. R.; Levine, R. L. Free Radical-Mediated Oxidation of Free Amino Acids and Amino Acid Residues in Proteins. Amino acids 2003, 25, 207–18. (34) Dalle-Donne, I.; Rossi, R.; Giustarini, D.; Milzani, A.; Colombo, R. Protein Carbonyl Groups as Biomarkers of Oxidative Stress. Clin Chim Acta 2003, 329, 23–38. (35) Uranga, J.; Mujika, J. I.; Matxain, J. M. ·OH Oxidation Toward S- and OH-Containing Amino Acids. J Phys Chem B 2015, 119, 15430–15442. (36) Enescu, M.; Cardey, B. Mechanism of Cysteine Oxidation by a Hydroxyl Radical: a Theoretical Study. Chemphyschem 2006, 7, 912–919. (37) Marino, T.; Soriano-Correa, C.; Russo, N. Oxidation Mechanism of Methionine by HO· Radical: A Theoretical Study. J Phys Chem B 2012, 116, 5349–5354. (38) Chen, H.-Y.; Jang, S.; Jinn, T.-R.; Chang, J.-Y.; Lu, H.-F.; Li, F.-Y. Oxygen RadicalMediated Oxidation Reactions of an Alanine Peptide Motif - Density Functional Theory and Transition State Theory Study. Chem Cent J 2012, 6, 33. (39) Galano, A.; Alvarez-Idaboy, J. R.; Cruz-Torres, A.; Ruiz-Santoyo, M. E. Rate Coefficients and Mechanism of the Gas Phase OH Hydrogen Abstraction Reaction from Serine: a Quantum Mechanical Approach. J Mol Struc-Theochem 2003, 629, 165–174. (40) Galano, A.; Alvarez-Idaboy, J. R.; Cruz-Torres, A.; Ruiz-Santoyo, M. E. Kinetics and Mechanism of the Gas-Phase OH Hydrogen Abstraction Reaction from Methionine: A Quantum Mechanical Approach. Int J Chem Kinet 2003, 35, 212–221. (41) Mujika, J. I.; Uranga, J.; Matxain, J. M. Computational Study on the Attack of ·OH Radicals on Aromatic Amino Acids. Chem-Eur J 2013, 19, 6862–73. 36


Page 36 of 50

Page 37 of 50 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


(42) Wood, G. P. F.; Sreedhara, A.; Moore, J. M.; Wang, J.; Trout, B. L. Mechanistic Insights into Radical-Mediated Oxidation of Tryptophan from ab Initio Quantum Chemistry Calculations and QM/MM Molecular Dynamics Simulations. J Phys Chem A 2016, acs.jpca.6b02429. (43) Galano, A.; Cruz-Torres, A. OH Radical Reactions with Phenylalanine in Free and Peptide Forms. Org Biomol Chem 2008, 6, 732. (44) Bobrowski, K.; Hug, G. L.; Pogocki, D.; Marciniak, B.; Schöneich, C. Stabilization of Sulfide Radical Cations Through Complexation with the Peptide Bond: Mechanisms Relevant to Oxidation of Proteins Containing Multiple Methionine Residues. J Phys Chem B 2007, 111, 9608–20. (45) Fourré, I.; Bergès, J.; Houée-Levin, C. Structural and Topological Studies of Methionine Radical Cations in Dipeptides: Electron Sharing in Two-Center Three-Electron Bonds. J Phys Chem A 2010, 114, 7359–68. (46) Viehe, H. G.; Merényi, R.; Stella, L.; Janousek, Z. Capto-dative Substituent Effects in Syntheses with Radicals and Radicophiles. Angew Chem Int Ed 1979, 18, 917–932. (47) Stadtman, E. R. Protein Oxidation and Aging. Free Radical Res 2006, 40, 1250–8. (48) Doan, H. Q.; Davis, A. C.; Francisco, J. S. Primary Steps in the Reaction of OH Radicals with Peptide Systems: Perspective from a Study of Model Amides. J Phys Chem A 2010, 114, 5342–5357. (49) Anglada, J. M. Complex Mechanism of the Gas Phase Reaction Between Formic Acid and Hydroxyl Radical. Proton Coupled Electron Transfer Versus Radical Hydrogen Abstraction Mechanisms. J Am Chem Soc 2004, 126, 9809–9820. (50) Utrera, M.; Rodríguez-Carpena, J. G.; Morcuende, D.; Estévez, M. Formation of Lysine-

37



Derived Oxidation Products and Loss of Tryptophan During Processing of Porcine Patties with Added Avocado Byproducts. J Agr Food Chem 2012, 60, 3917–3926. (51) 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 A.1. Gaussian Inc. Wallingford CT 2009. (52) Hohenberg, P. Inhomogeneous Electron Gas. Phys Rev 1964, 136, B864–B871. (53) Kohn, W.; Sham, L. J. Self-Consistent Equations Including Exchange and Correlation Effects. Phys Rev 1965, 140, A1133–A1138. (54) Zhao, Y.; Lynch, B. J.; Truhlar, D. G. Development and Assessment of a New Hybrid Density Functional Model for Thermochemical Kinetics. J Phys Chem A 2004, 108, 2715–2719. (55) Zhao, Y.; Lynch, B. J.; Truhlar, D. G. Doubly Hybrid Meta DFT: New Multi-Coefficient Correlation and Density Functional Methods for Thermochemistry and Thermochemical Kinetics. J Phys Chem A 2004, 108, 4786–4791. (56) Zhao, Y.; Pu, J.; Lynch, B. J.; Truhlar, D. G. Tests of Second-Generation and ThirdGeneration Density Functionals for Thermochemical Kinetics. Phys Chem Chem Phys 2004, 6, 673. (57) Zhao, Y.; Truhlar, D. G. Hybrid Meta Density Functional Theory Methods for Thermochemistry, Thermochemical Kinetics, and Noncovalent Interactions: The MPW1B95 and MPWB1K Models and Comparative Assessments for Hydrogen Bonding and van der Waals Interactions. J Phys Chem A 2004, 108, 6908–6918. (58) Tomasi, J.; Mennucci, B.; Cancès, E. The IEF Version of the PCM Solvation Method: an Overview of a New Method Addressed to Study Molecular Solutes at the QM Ab Initio Level. J Mol Struc-Theochem 1999, 464, 211–226. 38


Page 38 of 50

Page 39 of 50 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


(59) Mennucci, B.; Tomasi, J. Continuum Solvation Models: A New Approach to the Problem of Solute’s Charge Distribution and Cavity Boundaries. J Chem Phys 1997, 106, 5151. (60) Matxain, J. M.; Ristilä, M.; Strid, A.; Eriksson, L. A. Theoretical Study of the Antioxidant Properties of Pyridoxine. J Phys Chem A 2006, 110, 13068–72. (61) Salvador, P.; Ramos-Cordoba, E. APOST-3D program. 2012; Universitat de Girona (Spain). (62) Salvador, P.; Ramos-Cordoba, E. Communication: An approximation to Bader’s topological atom. J Chem Phys 2013, 139, 071103. (63) Mayer, I. Atomic Orbitals from Molecular Wave Functions: The Effective Minimal Basis. J Phys Chem-US 1996, 100, 6249–6257. (64) Becke, A. A Multicenter Numerical Integration Scheme for Polyatomic Molecules. JCP 1988, 88, 2547–2553. (65) Bader, R. F. W. Atoms in Molecules: A Quantum Theory; Oxford Univ. Press: Oxford, 1990.

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Oxidation of Acid, Base, and Amide Side-Chain Amino Acid

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