Intramolecular Stabilization Research Articles

Mild/moderate haemophilia A: new insights into molecular mechanisms and inhibitor development

In mild/moderate haemophilia A (MHA) patients, many factor VIII (FVIII) gene defects, mainly missense mutations, have been identified and greatly improved the understanding of the structure and function of FVIII molecule. Characterization of the molecular mechanisms involved in MHA has helped to identify regions critical for proper FVIII biosynthesis, thrombin activation, intramolecular stability as well as binding regions for important intermolecular interactions with von Willebrand factor, factor IXa and the phospholipid surface. Some missense mutations were also recognized as contributing factors to inhibitor development in MHA, in parallel to acquired factors such as inflammatory state or intensity of treatment. Treatment of MHA with inhibitor patients raises questions on how best to stop or prevent bleeding episodes and eradicate the inhibitor. Longitudinal data collection is currently being conducted in France and Belgium to enhance our knowledge in this field and to further help make treatment decision. The description of mutations in MHA finally contributed to the identification of epitopes involved in the immune response to FVIII. In some patients, the epitope specificity of inhibitor antibodies recognizing normal exogenous FVIII alone and not patient ('self') FVIII was described. This distinguished epitope specificity could also be demonstrated at the T-cell clonal level. One might expect that these molecular studies will have a major impact on development of new FVIII products in the future.

Conformational Influence on the Type of Stabilization of Sulfur Radical Cations in Cyclic Peptides

The free-radical chemistry of two oxidized cyclic dipeptides is investigated using time-resolved optical and conductivity detection. Two cyclic dipeptides, cyclo-Gly-L-Met and cyclo-D-Met-L-Met, are synthesized and irradiated with nanosecond pulses of electrons, which initiate the oxidation of the methionine side chains with hydroxyl radicals from the radiolysis of water. The cyclic peptides are taken to be models for the interior of proteins where there are no terminal groups. This opens up the possibility that neighboring-group effects can be studied directly between the initially formed sulfur radical cations and the heteroatoms associated with the peptide bonds. Such complexation of the sulfur radical cations is observed with the amide nitrogen atoms. In addition, intermolecular stabilization with the unoxidized sulfur atoms on separate cyclic dipeptide molecules is observed. Little or no intramolecular stabilization by the unoxidized sulfur in the neighboring methionine occurs in cyclo-D-Met-L-Met, in contrast to the previously observed intramolecular sulfur stabilization of the sulfur radical cation in the isomer cyclo-L-Met-L-Met. This contrasting behavior is rationalized by conformational differences in the two isomers as seen through molecular-modeling simulations. The implications for the oxidation of the protein calmodulin, which contains multiple residues of methionine, are discussed as having analogous determining factors.

Conformational analysis of arginine in gas phase—A strategy for scanning the potential energy surface effectively

The determination of all possible low-lying energy conformers of flexible molecules is of fundamental interest for various applications. It necessitates a reliable conformational search that is able to detect all important minimum structures and calculates the energies on an adequate level of theory. This work presents a strategy to identify low-energy conformers using arginine as an example by means of a force-field based conformational search in combination with high-level geometry optimizations (RI-MP2/TZVPP+). The methods used for various stages in the conformational search strategy are shown and various pitfalls are discussed. We can show that electronic energies calculated on a DFT level of theory with standard exchange-correlation functionals strongly underestimate the intramolecular stabilization resulting from stacked orientations of the guanidine and carbonyl moiety of arginine due to the deficiency of DFT to describe dispersion effects. In this case by usage of electron correlation methods, low energy conformers comprising stacked arrangements that are counterintuitive become favorable.

Spirocyclic and Fused Derivatives of Maleimide Based on Intra- and Intermolecular Reactions of Carbonyl Ylides from Diazocarbonyl Compounds

The reaction of maleimide with Rh(II)-ketocarbenoids, derived from acyclic diazocarbonyl compounds, proceeds chemoselectively at the oxygen atom of the imidic C=O group to give carbonyl ylides as reactive intermediates. The carbonyl ylide generated from maleimide and ethyl diazoacetate reacts intermolecularly with the double bond of another molecule of maleimide to yield tricyclic spiroadducts via [3+2]-cycloaddition. Intramolecular stabilization is characteristic for carbonyl ylides with two bulky electron-withdrawing groups at the carbanionic center and occurs in two different ways, depending on the structure of the substituents: carbonyl ylides from diazomalonate, which possess two alkoxycarbonyl groups at the carbanionic C-atom, experience a 1,3-dipolar electrocyclization with formation of an oxirane, while carbonyl ylides with at least one α-acyl group, derived from diazoacetoacetate or diazoacetylacetone, undergo an intramolecular 1,5-dipolar electrocyclization to produce 1,3-dioxole derivatives of maleimide.

RhII‐Catalyzed Reactions of Diazocarbonyl Compounds with Dicarboximides

AbstractThe reaction of RhII–oxocarbenoids derived from acyclic diazocarbonyl compounds with phthalimide and succinimide proceeds chemoselectively at the oxygen atom of the imidic carbonyl group, giving rise to the intermediate formation of carbonyl ylides. Intramolecular stabilization of these highly reactive species occurs in three different ways, and is controlled by the structure of the 2‐oxocarbenoids. Carbonyl ylides from diazo esters mainly experience a [1,4]‐hydrogen shift, and in this case, the corresponding O‐alkylimidates are formed as the final products. These ylides may also be stabilized by 1,3‐dipolar electrocyclization with intermediate formation of an oxirane. Carbonyl ylides with an acyl group in the carbene moiety undergo an intramolecular 1,5‐dipolar electrocyclization to produce 1,3‐dioxole derivatives. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)

Effect of pH on One-Electron Oxidation Chemistry of Organoselenium Compounds in Aqueous Solutions

Pulse radiolysis coupled with absorption detection has been employed to study one-electron oxidation of selenomethionine (SeM), selenocystine (SeCys), methyl selenocysteine (MeSeCys), and selenourea (SeU) in aqueous solutions. Hydroxyl radicals (*OH) in the pH range from 1 to 7 and specific one-electron oxidants Cl2*- (pH 1) and Br2*- (pH 7) have been used to carry out the oxidation reactions. The bimolecular rate constants for these reactions were reported to be in the range of 2 x 10(9) to 10 x 10(9) M(-1) s(-1). Reactions of oxidizing radicals with all these compounds produced selenium-centered radical cations. The structure and stability of the radical cation were found to depend mainly on the substituent and pH. SeM, at pH 7, produced a monomer radical cation (lambdamax approximately 380 nm), while at pH 1, a dimer radical cation was formed by the interaction between oxidized and parent SeM (lambdamax approximately 480 nm). Similarly, SeCys, at pH 7, on one-electron oxidation, produced a monomer radical cation (lambdamax approximately 460 nm), while at pH 1, the reaction produced a transient species with (lambdamax approximately 560 nm), which is also a monomer radical cation. MeSeCys on one-electron oxidation in the pH range from 1 to 7 produced monomer radical cations (lambdamax approximately 350 nm), while at pH < 0, the reaction produced dimer radical cations (lambdamax approximately 460 nm). SeU at all the pH ranges produced dimer radical cations (lambdamax approximately 410 nm). The association constants of the dimer radical cations of SeM, MeSeCys, and SeU were determined by following absorption changes at lambdamax as a function of concentration. From these studies it is concluded that formation of monomer and dimer radical cations mainly depends on the substitution, pH, and the heteroatoms like N and O. The availability of a lone pair on an N or O atom at the beta or gamma position results in monomer radical cations having intramolecular stabilization. When such a lone pair is not available, the monomer radical cation is converted into a dimer radical cation which acquires intermolecular stabilization by the other selenium atom. The pH dependency confirms the role of protonation on stabilization. The oxidation chemistry of these selenium compounds is compared with that of their sulfur analogues.

Fluorescence modulation in anion sensing by introducing intramolecular H-bonding interactions in host–guest adducts

Fluorescence signaling in anion binding is modulated from quenching to enhancement by intramolecular H-bonding stabilization of anion-ionophore adducts; the intramolecular H-bonding is suggested to suppress the quenching processes otherwise possible and increase the conformational rigidity of the anionic adducts, leading to fluorescence enhancement in a selective fashion towards cyanide ion, among the various anions examined.

Conformational Composition of Cyclopentadienylphosphine Investigated by Microwave Spectroscopy and Quantum Chemical Calculations

The properties of cyclopentadienylphosphine have been investigated by means of Stark-modulation microwave spectroscopy and quantum chemical calculations at the MP2/aug-cc-pVTZ, B3LYP/6-311++G(d,p), and G3 levels of theory. Spectra attributable to two rotamers denoted conformers I and II have been assigned. Conformer I has a symmetry plane (Cs symmetry) consisting of the bisectors of the cyclopentadiene ring and of the phosphino group with the lone electron pair of phosphorus pointing toward the carbon ring. In conformer II, the phosphino group is rotated approximately 120 degrees out of this plane. Relative intensity measurements have been made, and it was found that conformer II is more stable than I by 1.3(4) kJ/mol. The preferred conformer represents a borderline case of intramolecular hydrogen bond stabilization. The experimental and MP2/ aug-cc-pVTZ rotational constants differ by several percent, which indicates that the aug-cc-pVTZ basis set is not large enough to be able to predict an accurate structure for the two conformers that are close to the equilibrium geometries. 5-Substituted 1,3-cyclopentadienyl derivatives may undergo circumambulatory rearrangements. However, there is no manifestation of this effect in the microwave spectrum of cyclopentadienylphosphine.

Stabilization of Excess Charge in Isolated Adenosine 5‘-Triphosphate and Adenosine 5‘-Diphosphate Multiply and Singly Charged Anions

Multiply charged anions (MCAs) represent highly energetic species in the gas phase but can be stabilized through formation of molecular clusters with solvent molecules or counterions. We explore the intramolecular stabilization of excess negative charge in gas-phase MCAs by probing the intrinsic stability of the [adenosine 5'-triphosphate-2H](2-) ([ATP-2H](2-)), [adenosine 5'-diphosphate-2H](2-) ([ADP-2H](2-)), and H(3)P(3)O(10)(2-) dianions and their protonated monoanionic analogues. The relative activation barriers for decay of the dianions via electron detachment or ionic fragmentation are investigated using resonance excitation of ions isolated within a quadrupole trap. All of the dianions decayed via ionic fragmentation demonstrating that the repulsive Coulomb barriers (RCB) for ionic fragmentation lie below the RCBs for electron detachment. Both the electrospray ionization mass spectra (ESI-MS) and total fragmentation energies for [ATP-2H](2-), [ADP-2H](2-), and H(3)P(3)O(10)(2-) indicate that the multiply charged H(3)P(3)O(10)(2-) phosphate moiety is stabilized by the presence of the adenosine group and the stability of the dianions increases in the order H(3)P(3)O(10)(2-) < [ADP-2H](2-) < [ATP-2H](2-). Fully optimized, B3LYP/6-31+G* minimum energy structures illustrate that the excess charges in all of the phosphate anions are stabilized by intramolecular hydrogen bonding either within the phosphate chain or between the phosphate and the adenosine. We develop a model to illustrate that the relative magnitudes of the RCBs and hence the stability of these ions is dominated by the extent of intramolecular hydrogen bonding.

Crystal Structures of the Mnk2 Kinase Domain Reveal an Inhibitory Conformation and a Zinc Binding Site

Human mitogen-activated protein kinases (MAPK)-interacting kinases 1 and 2 (Mnk1 and Mnk2) target the translational machinery by phosphorylation of the eukaryotic initiation factor 4E (eIF4E). Here, we present the 2.1 A crystal structure of a nonphosphorylated Mnk2 fragment that encompasses the kinase domain. The results show Mnk-specific features such as a zinc binding motif and an atypical open conformation of the activation segment. In addition, the ATP binding pocket contains an Asp-Phe-Asp (DFD) in place of the canonical magnesium binding Asp-Phe-Gly (DFG) motif. The phenylalanine of this motif sticks into the ATP binding pocket and blocks ATP binding as observed with inhibitor bound and, thus, inactive p38 kinase. Replacement of the DFD by the canonical DFG motif affects the conformation of Mnk2, but not ATP binding and kinase activity. The results suggest that the ATP binding pocket and the activation segment of Mnk2 require conformational switches to provide kinase activity.

Structural Determinants of the Agonist-independent Association of Human Peroxisome Proliferator-activated Receptors with Coactivators

Lipid homeostasis is controlled by various nuclear receptors (NRs), including the peroxisome proliferator-activated receptors (PPARalpha, delta, and gamma), which sense lipid levels and regulate their metabolism. Here we demonstrate that human PPARs have a high basal activity and show ligand-independent coactivator (CoA) association comparable with the NR constitutive androstane receptor. Using PPARgamma as an example, we found that four different amino acid groups contribute to the ligand-independent stabilization of helix 12 of the PPAR ligand-binding domain. These are: (i) Lys329 and Glu499, mediating a charge clamp-type stabilization of helix 12 via a CoA bridge; (ii) Glu352, Arg425, and Tyr505, directly stabilizing the helix via salt bridges and hydrogen bonds; (iii) Lys347 and Asp503, interacting with each other as well as contacting the CoA; and (iv) His351, Tyr(355), His477, and Tyr501, forming a hydrogen bond network. These amino acids are highly conserved within the PPAR subfamily, suggesting that the same mechanism may apply for all three PPARs. Phylogenetic trees of helix 12 amino acid and nucleotide sequences of all crystallized NRs and all human NRs, respectively, indicated a close relationship of PPARs with constitutive androstane receptor and other constitutive active members of the NR superfamily. Taking together, the ligand-independent tight control of the position of the PPAR helix 12 provides an effective alternative for establishing an interaction with CoA proteins. This leads to high basal activity of PPARs and provides an additional view on PPAR signaling.

A single intermolecular contact mediates intramolecular stabilization of both RNA and protein

An arginine-rich peptide from the Jembrana disease virus (JDV) Tat protein is a structural "chameleon" that binds bovine immunodeficiency virus (BIV) or HIV TAR RNAs in two different binding modes, with an affinity for BIV TAR even higher than the cognate BIV peptide. We determined the NMR structure of the JDV Tat-BIV TAR high-affinity complex and found that the C-terminal tyrosine in JDV Tat forms a network of inter- and intramolecular hydrogen bonding and stacking interactions that simultaneously stabilize the beta-hairpin conformation of the peptide and a base triple in the RNA. A neighboring histidine also appears to help stabilize the peptide conformation. Induced fit binding is recurrent in protein-protein and protein-nucleic acid interactions, and the JDV Tat complex demonstrates how high affinity can be achieved not only by optimization of the binding interface but also by inducing new intramolecular contacts that stabilize each binding partner. Comparison to the cognate BIV Tat peptide-TAR complex shows how such a costabilization mechanism can evolve with only small changes to the peptide sequence. In addition, the bound structure of BIV TAR in the chameleon peptide complex is strikingly similar to the bound conformation of HIV TAR, suggesting new strategies for the development of HIV TAR binding molecules.

1‐Aminoindan‐2‐ol, a Suitable Ligand for the Synthesis of Chiral, Intramolecularly Stabilized Compounds of Aluminum, Gallium, and Indium

AbstractThe reactions of enantiomerically pure (1R, 2S)‐(+)‐cis‐1‐aminoindan‐2‐ol, (1S, 2R)‐(‐)‐cis‐1‐aminoindan‐2‐ol, and racemic trans‐1‐aminoindan‐2‐ol with trimethylaluminum, ‐gallium, and ‐indium produce the intramolecularly stabilized, enantiomerically pure dimethylmetal‐1‐amino‐2‐indanolates (1R, 2S)‐(+)‐cis‐Me2AlO‐2‐C*HC7H6‐1‐C*HNH2 (1), (1S, 2R)‐(‐)‐cis‐Me2AlO‐2C*HC7H6‐1‐C*HNH2 (2), (1R, 2S)‐(+)‐cis‐Me2GaO‐2‐C*HC7H6‐1‐C*HNH2 (3), (1R, 2S)‐(+)‐cis‐Me2InO‐2‐C*HC7H6‐1‐C*HNH2 (4), (1S, 2R)‐(‐)‐cis‐Me2InO‐2‐C*HC7H6‐1‐C*HNH2 (5), and racemic (+/‐)‐trans‐Me2InO‐2‐C*HC7H6‐1‐C*HNH2 (6). The compounds were characterized by 1H NMR, 13C NMR, 27Al NMR and mass spectra as well as 1 and 3 to 6 by determination of their crystal and molecular structures. The dynamic dissociation/association behavior of the coordinative metal‐nitrogen bond was studied by low temperature 1H NMR spectroscopy.

Role of oxidative metabolites of cocaine in toxicity and addiction: oxidative stress and electron transfer

Cocaine is one of the principal drugs of abuse. Although impressive advances have been made, unanswered questions remain concerning mechanism of toxicity and addiction. Discussion of action mode usually centers on receptor binding and enzyme inhibition, with limited attention to events at the molecular level. This review provides extensive evidence in support of the hypothesis that oxidative metabolites play important roles comprising oxidative stress (OS), reactive oxygen species (ROS), and electron transfer (ET). The metabolites include norcocaine and norcocaine derivatives: nitroxide radical, N-hydroxy, nitrosonium, plus cocaine iminium and formaldehyde. Observed formation of ROS is rationalized by redox cycling involving several possible ET agents. Three potential ones are present in the form of oxidative metabolites, namely, nitroxide, nitrosonium, and iminium. Most attention has been devoted to the nitroxide-hydroxylamine couple which has been designated by various investigators as the principal source of ROS. The proximate ester substituent is deemed important for intramolecular stabilization of reactive intermediates. Reduction potential of nitroxide is in accord with plausibility of ET in the biological milieu. Toxicity by cocaine, with evidence for participation of OS, is demonstrated for many body components, including liver, central nervous system, cardiovascular system, reproductive system, kidney, mitochondria, urine, and immune system. Other adverse effects associated with ROS comprise teratogenesis and apoptosis. Examples of ROS generated are lipid peroxides and hydroxyl radical. Often observed were depletion of antioxidant defenses, and protection by added antioxidants, such as, thiol, salicylate, and deferoxamine. Considerable evidence supports the contention that oxidative ET metabolites of cocaine are responsible for much of the observed OS. Quite significantly, the pro-oxidant, toxic effects, including generation of superoxide and lipid peroxyl radicals, plus depletion of glutathione, elicited by nitroxide or the hydroxylamine derivative, were greater than for the parent drug. The formaldehyde metabolite also appears to play a role. Mechanistic similarity to the action of neurotoxin 3,3'-iminodipropionitrile is pointed out. A number of literature strategies for treatment of addiction are addressed. However, no effective interventions are currently available. An hypothesis for addiction is offered based on ET and ROS at low concentrations. Radicals may aid in cell signaling entailing redox processes which influence ion transport, neuromodulation, and transcription. Ideas are suggested for future work dealing with health promotion. These include use of AOs, both dietary and supplemental, trapping of the norcocaine metabolite by non-toxic complexing agents, and use of nitrones for capturing harmful radical species.

Intramolecular dimer radical cations of α,ω-di(2-naphthyl)alkanes in solutions studied by near-IR transient absorption spectroscopy

Formation of intramolecular dimer radical cations in a series of α,ω-di(2-naphthyl)alkanes (DNp n, where n is the number of carbon atoms in the methylene chain) in solutions was investigated by near-IR transient absorption spectroscopy, which enables one to quantitatively evaluate the equilibrium constant ( K) for the formation of the intramolecular dimer radical cations and stabilization energy ( E CR) due to charge delocalization. The dependence of K on n corresponds to the probability of ring closure in a syn fashion where the chain attaches at the same side of the two naphthalene (Np) moieties. The dependence of E CR on n is similar to that of K except at n=3. For DNp n with a shorter chain, the mutual configuration of the two Np moieties cannot be optimal because the ring closure itself is difficult owing to the restriction by the short chain. For DNp n with a longer chain, the two Np moieties are in a more stable configuration because of the loose restriction of the long chain. The small value of E CR at n=3 indicates that the optimal configuration for the dimer radical cation of Np is not a sandwich-like one, but a distorted one.

Molecular Design of Bis-Chelate N-Donor-Stabilized Silaethenes: Theoretical Study of 1,1-Bis[N-(dimethylamino)acetimidato]silene

RHF/6-31G* and B3LYP/6-31G* computations were performed on the silene [Me2NNC(Me)O]2SiCH2 (6) and analyzed through the use of properties of atoms in molecules. Three stationary states of 6 belong to its non-chelate (6a) and two intramolecularly N-donor-stabilized forms, five-membered mono-chelate (6b) and previously unknown (for the silenes) bis-chelate (6c), with three-, four-, and five-coordinate doubly bonded silicon, respectively. On going from 6a to 6b and 6c, initially planar silicon attains distorted tetrahedral and square pyramidal structures, whereas the SiC double bond becomes more polar and changes its distance from 1.674 Å to 1.693 and 1.704 Å and from 1.691 Å to 1.701 and 1.713 Å at the RHF and B3LYP levels, respectively. The RHF and B3LYP N−Si distances in 6b (1.988 and 2.031 Å) are shorter than in 6c (2.187 and 2.140 Å). The N→Si bond in chelates 6b,c is described as highly polar, but of sufficiently covalent character. The four-center six-electron (4c-6e) model is proposed for the silicon bonding in the N2SiC moiety of 6c. High energetic advantages of the chelate 6b and 6c forms over 6a (26.8 and 31.4 kcal/mol at the B3LYP/6-31G* level including the ZPE correction and 32.4 and 36.3 kcal/mol at the RHF/6-31G* level, respectively) suggest that intramolecular N-donor stabilization may be sufficient to observe silene 6 under relatively mild conditions.

Effects of common buffer systems on drug activity: the case of clerocidin.

Two widely used biological buffers [tris(hydroxymethyl)aminomethane (TRIS) and phosphate] covalently react with the topoisomerase II inhibitor clerocidin, affecting the drug's reactivity profile. Comprehensive analytical and structural analysis obtained by LC/MS, MS/MS, NMR, and IR techniques shows that these buffers form reversible and irreversible adducts through reactions with chemical groups, such as carbonyls, aldehydes, and epoxide. Analysis of the kinetic data on adducts formation suggests two parallel mechanisms for the inhibition of drug activity. The first involves modulation of the reactivity of the epoxide group obtained by elimination of the spiro system and relief of ring strain. This effect does not abolish epoxide reactivity and is more evident for the TRIS adduct, which can count on intramolecular stabilization of the form devoid of the spiro system. The second mechanism involves the slow nucleophilic attack to the epoxide ring, which results in permanent deactivation of the functional group responsible for topoisomerase II inhibition. This effect is predominant in phosphate buffer and is more evident for longer reaction times. These results provide a compelling reminder that the activity of chemically complex drugs in biological systems can be severely altered by buffer interactions, which may not be immediately predictable from the identity of the active group(s) and may require a more detailed knowledge of the subtle effects induced by vicinal groups.

Palladium Catalyzed Cross‐Methylation of Bromoheterocycles with Intramolecularly Stabilized Dimethyl Indium Reagents.

AbstractFor Abstract see ChemInform Abstract in Full Text.

The effects of conformation on the acidity of ascorbic acid: a density functional study

Ascorbic acid (AsA; ascorbate; vitamin C; C 6H 8O 6) is a potent antioxidant in both the cytosolic and membrane components of the human body. AsA serves a protective function as a free radical scavenger and plays a non-direct antioxidant role by aiding in the reduction of the α-tocopheroxy radical back to α-tocopherol. Two hydroxyl moieties (defined as χ 1 and χ 2) are paramount to the conformational profile of AsA. One hydroxyl group, χ 1, is initially deprotonated in AsA's antioxidant mechanism. To explore AsA's acidic character, selected conformations were optimized at the B3LYP/6-31G(d) level of theory and their adiabatic energies of deprotonation calculated. The lowest and highest energies of deprotonation were found to occur in the conformers aa3h-p (χ 1= g +, χ 2= g +, χ 3= g −, χ 4= anti, χ 5= g −, χ 6= g −) at 320.92 kcal mol −1 and aa1l-p (χ 1= g −, χ 2= anti, χ 3= anti, χ 4= g +, χ 5= g −, χ 6= anti) at 343.84 kcal mol −1, respectively. Conformers with minimal intramolecular stabilization had the lowest energies of deprotonation while conformers exhibiting multiple hydrogen bonds had larger energies of deprotonation. In light of these findings, it is hypothesized that higher energy conformations will be favoured in the deprotonation of AsA antioxidant mechanism of action.

Conformational-dependent basicity of carvedilol Fragment C: an ab initio study on the primary amine, aminoethoxy-2-methoxy-benzene

Carvedilol produces various physiological effects via multiple modes of action. In mitochondria, it is purported that carvedilol is cardioprotective by acting as a mild uncoupler of oxidative phosphorylation; the mechanism is thought to involve the protonable amino group in its side-chain. This uncoupling subsequently leads to a decrease in production of reactive oxygen species and reduced mitochondrial oxidative stress. In the current work, the carvedilol fragment aminoethoxy-2-methoxy-benzene (Fragment C) has been investigated to illustrate the effects of molecular conformation on intrinsic basicity as related to such proton shuttling pathways. It has been previously been shown for carvedilol Fragment B that molecular conformation dictates the energetics of deprotonation. Fragment C is also studied in this context because, as a primary amine which may be deprotonated via three different protons, it provides an ideal structure to elucidate such conformational effects. By calculating the associated energies of deprotonation for each proton, the relative effects of conformation on intrinsic basicity can be determined. The ab initio Hartree–Fock, RHF/3-21G, level of theory was employed for structural analysis and the potential energy hypersurface of Fragment C was computed with geometry optimizations of the conformational minima. Energies of deprotonation were determined with vertical and adiabatic calculations for each proton in each converged minima. Multi-dimensional conformational analysis of the protonated potential energy hypersurface revealed a total of 24 converged minima out of a possible 81 (≈30% convergence). Conformers with the lowest relative energies possessed a motif consisting of bifurcated hydrogen-bonds forming an eight-membered ring. Hydrogen bond networks forming five-membered rings along with intramolecular dipole-type interactions were also evident. In contrast, protonated conformers with large relative energies were devoid of any significant structural features. Geometry optimization of the deprotonated potential energy hypersurface revealed similar structural features; further, optimization of conformational minima belonging to the deprotonated hypersurface revealed a novel amine–aromatic pi electronic interaction currently under study. In analyzing the derived energetics of deprotonation for the primary amine, it was found that conformers lacking significant stabilizing structural motifs were favored and possessed the lowest energies of deprotonation for Fragment C. The route with the lowest energy of deprotonation (optimized) was via the deprotonation of conformer ag + ag + which required 238.34 kcal mol −1. It can thus be concluded that, as previously shown for the secondary amine Fragment B, and now for the primary amine Fragment C, proton shuttling mechanisms involving carvedilol, and amines in general, will favor conformations with minimal intramolecular stabilization. As such, molecular conformation and associated structural features will determine, at least with regards to energetics, the intrinsic basicity of compounds and can be used to describe and predict favored substrate conformations for protonophoretic pathways as that postulated for carvedilol in mitochondria.