Light Activation and Photophysics of a Structurally Constrained Nickel(II)-Bipyridine Aryl Halide Complex.

Transition-metal photoredox catalysis has transformed organic synthesis by harnessing light to construct complex molecules. Nickel(II)-bipyridine (bpy) aryl halide complexes are a significant class of cross-coupling catalysts that can be activated via direct light excitation. This study investigates the effects of molecular structure on the photophysics of these catalysts by considering an underexplored, structurally constrained Ni(II)-bpy aryl halide complex in which the aryl and bpy ligands are covalently tethered alongside traditional unconstrained complexes. Intriguingly, the tethered complex is photochemically stable but features a reversible Ni(II)-C(aryl) ⇄ [Ni(I)···C(aryl)•] equilibrium upon direct photoexcitation. When an electrophile is introduced during photoirradiation, we demonstrate a preference for photodissociation over recombination, rendering the parent Ni(II) complex a stable source of a reactive Ni(I) intermediate. Here, we characterize the reversible photochemical behavior of the tethered complex by kinetic analyses, quantum chemical calculations, and ultrafast transient absorption spectroscopy. Comparison to the previously characterized Ni(II)-bpy aryl halide complex indicates that the structural constraints considered here dramatically influence the excited state relaxation pathway and provide insight into the characteristics of excited-state Ni(II)-C bond homolysis and aryl radical reassociation dynamics. This study enriches the understanding of molecular structure effects in photoredox catalysis and offers new possibilities for designing customized photoactive catalysts for precise organic synthesis.

From random to rational: improving enzyme design through electric fields, second coordination sphere interactions, and conformational dynamics.

Enzymes are versatile and efficient biological catalysts that drive numerous cellular processes, motivating the development of enzyme design approaches to tailor catalysts for diverse applications. In this perspective, we investigate the unique properties of natural, evolved, and designed enzymes, recognizing their strengths and shortcomings. We highlight the challenges and limitations of current enzyme design protocols, with a particular focus on their limited consideration of long-range electrostatic and dynamic effects. We then delve deeper into the impact of the protein environment on enzyme catalysis and explore the roles of preorganized electric fields, second coordination sphere interactions, and protein dynamics for enzyme function. Furthermore, we present several case studies illustrating successful enzyme-design efforts incorporating enzyme strategies mentioned above to achieve improved catalytic properties. Finally, we envision the future of enzyme design research, spotlighting the challenges yet to be overcome and the synergy of intrinsic electric fields, second coordination sphere interactions, and conformational dynamics to push the state-of-the-art boundaries.

Electronic Structures of Nickel(II)-Bis(indanyloxazoline)-dihalide Catalysts: Understanding Ligand Field Contributions That Promote C(sp2)-C(sp3) Cross-Coupling.

NiII(IB) dihalide [IB = (3aR,3a'R,8aS,8a'S)-2,2'-(cyclopropane-1,1-diyl)bis(3a,8a-dihydro-8H-indeno[1,2-d]-oxazole)] complexes are representative of a growing class of first-row transition-metal catalysts for the enantioselective reductive cross-coupling of C(sp2) and C(sp3) electrophiles. Recent mechanistic studies highlight the complexity of these ground-state cross-couplings but also illuminate new reactivity pathways stemming from one-electron redox and their significant sensitivities to reaction conditions. For the first time, a diverse array of spectroscopic methods coupled to electrochemistry have been applied to NiII-based precatalysts to evaluate specific ligand field effects governing key Ni-based redox potentials. We also experimentally demonstrate DMA solvent coordination to catalytically relevant Ni complexes. Coordination is shown to favorably influence key redox-based reaction steps and prevent other deleterious Ni-based equilibria. Combined with electronic structure calculations, we further provide a direct correlation between reaction intermediate frontier molecular orbital energies and cross-coupling yields. Considerations developed herein demonstrate the use of synergic spectroscopic and electrochemical methods to provide concepts for catalyst ligand design and rationalization of reaction condition optimization.

Photogenerated Ni(I)-Bipyridine Halide Complexes: Structure-Function Relationships for Competitive C(sp2)-Cl Oxidative Addition and Dimerization Reactivity Pathways.

We report the facile photochemical generation of a library of Ni(I)-bpy halide complexes (Ni(I)(Rbpy)X (R = t-Bu, H, MeOOC; X = Cl, Br, I) and benchmark their relative reactivity toward competitive oxidative addition and off-cycle dimerization pathways. Structure-function relationships between the ligand set and reactivity are developed, with particular emphasis on rationalizing previously uncharacterized ligand-controlled reactivity toward high energy and challenging C(sp2)-Cl bonds. Through a dual Hammett and computational analysis, the mechanism of the formal oxidative addition is found to proceed through an SNAr-type pathway, consisting of a nucleophilic two-electron transfer between the Ni(I) 3d(z2) orbital and the Caryl-Cl σ* orbital, which contrasts the mechanism previously observed for activation of weaker C(sp2)-Br/I bonds. The bpy substituent provides a strong influence on reactivity, ultimately determining whether oxidative addition or dimerization even occurs. Here, we elucidate the origin of this substituent influence as arising from perturbations to the effective nuclear charge (Zeff) of the Ni(I) center. Electron donation to the metal decreases Zeff, which leads to a significant destabilization of the entire 3d orbital manifold. Decreasing the 3d(z2) electron binding energies leads to a powerful two-electron donor to activate strong C(sp2)-Cl bonds. These changes also prove to have an analogous effect on dimerization, with decreases in Zeff leading to more rapid dimerization. Ligand-induced modulation of Zeff and the 3d(z2) orbital energy is thus a tunable target by which the reactivity of Ni(I) complexes can be altered, providing a direct route to stimulate reactivity with even stronger C-X bonds and potentially unveiling new ways to accomplish Ni-mediated photocatalytic cycles.

Electrochemical Carbon Dioxide Capture and Concentration.

Electrochemical carbon capture and concentration (eCCC) offers a promising alternative to thermochemical processes as it circumvents the limitations of temperature-driven capture and release. This review will discuss a wide range of eCCC approaches, starting with the first examples reported in the 1960s and 1970s, then transitioning into more recent approaches and future outlooks. For each approach, the achievements in the field, current challenges, and opportunities for improvement will be described. This review is a comprehensive survey of the eCCC field and evaluates the chemical, theoretical, and electrochemical engineering aspects of different methods to aid in the development of modern economical eCCC technologies that can be utilized in large-scale carbon capture and sequestration (CCS) processes.

Molecular design of redox carriers for electrochemical CO2 capture and concentration.

Developing improved methods for CO2 capture and concentration (CCC) is essential to mitigating the impact of our current emissions and can lead to carbon net negative technologies. Electrochemical approaches for CCC can achieve much higher theoretical efficiencies compared to the thermal methods that have been more commonly pursued. The use of redox carriers, or molecular species that can bind and release CO2 depending on their oxidation state, is an increasingly popular approach as carrier properties can be tailored for different applications. The key requirements for stable and efficient redox carriers are discussed in the context of chemical scaling relationships and operational conditions. Computational and experimental approaches towards developing redox carriers with optimal properties are also described.

Understanding desaturation/hydroxylation activity of castor stearoyl Δ9-Desaturase through rational mutagenesis.

A recently proposed reaction mechanism of soluble Δ9 desaturase (Δ9D) allowed us to identify auxiliary residues His203, Asp101, Thr206 and Cys222 localized near the di-iron active site that are supposedly involved in the proton transfer (PT) to and from the active site. The PT, along with the electron transfer (ET), seems to be crucial for efficient desaturation. Thus, perturbing the major PT chains is expected to impair the native reaction and (potentially) amplify minor reaction channels, such as the substrate hydroxylation. To verify this hypothesis, we mutated the four residues mentioned above into their counterparts present in a soluble methane monooxygenase (sMMO), and determined the reaction products of mutants. We found that the mutations significantly promote residual monohydroxylation activities on stearoyl-CoA, often at the expense of native desaturation activity. The favored hydroxylation positions are C9, followed by C10 and C11. Reactions with unsaturated substrate, oleoyl-CoA, yield erythro-9,10-diol, cis-9,10-epoxide and a mixture of allylic alcohols. Additionally, using 9- and 11-hydroxystearoyl-CoA, we showed that the desaturation reaction can proceed only with the hydroxyl group at position C11, whereas the hydroxylation reaction is possible in both cases, i.e. with hydroxyl at position C9 or C11. Despite the fact that the overall outcome of hydroxylation is rather modest and that it is mostly the desaturation/hydroxylation ratio that is affected, our results broaden understanding of the origin of chemo- and stereoselectivity of the Δ9D and provide further insight into the catalytic action of the NHFe2 enzymes.

Elucidating the Mechanism of Excited-State Bond Homolysis in Nickel-Bipyridine Photoredox Catalysts.

Ni 2,2'-bipyridine (bpy) complexes are commonly employed photoredox catalysts of bond-forming reactions in organic chemistry. However, the mechanisms by which they operate are still under investigation. One potential mode of catalysis is via entry into Ni(I)/Ni(III) cycles, which can be made possible by light-induced, excited-state Ni(II)-C bond homolysis. Here, we report experimental and computational analyses of a library of Ni(II)-bpy aryl halide complexes, Ni(Rbpy)(R'Ph)Cl (R = MeO, t-Bu, H, MeOOC; R' = CH3, H, OMe, F, CF3), to illuminate the mechanism of excited-state bond homolysis. At given excitation wavelengths, photochemical homolysis rate constants span 2 orders of magnitude across these structures and correlate linearly with Hammett parameters of both bpy and aryl ligands, reflecting structural control over key metal-to-ligand charge-transfer (MLCT) and ligand-to-metal charge-transfer (LMCT) excited-state potential energy surfaces (PESs). Temperature- and wavelength-dependent investigations reveal moderate excited-state barriers (ΔH‡ ∼ 4 kcal mol-1) and a minimum energy excitation threshold (∼55 kcal mol-1, 525 nm), respectively. Correlations to electronic structure calculations further support a mechanism in which repulsive triplet excited-state PESs featuring a critical aryl-to-Ni LMCT lead to bond rupture. Structural control over excited-state PESs provides a rational approach to utilize photonic energy and leverage excited-state bond homolysis processes in synthetic chemistry.

Predicting Effects of Site-Directed Mutagenesis on Enzyme Kinetics by QM/MM and QM Calculations: A Case of Glutamate Carboxypeptidase II.

Quantum and molecular mechanics (QM/MM) and QM-only (cluster model) modeling techniques represent the two workhorses in mechanistic understanding of enzyme catalysis. One of the stringent tests for QM/MM and/or QM approaches is to provide quantitative answers to real-world biochemical questions, such as the effect of single-point mutations on enzyme kinetics. This translates into predicting the relative activation energies to 1-2 kcal·mol-1 accuracy; such predictions can be used for the rational design of novel enzyme variants with desired/improved characteristics. Herein, we employ glutamate carboxypeptidase II (GCPII), a dizinc metallopeptidase, also known as the prostate specific membrane antigen, as a model system. The structure and activity of this major cancer antigen have been thoroughly studied, both experimentally and computationally, which makes it an ideal model system for method development. Its reaction mechanism is quite well understood: the reaction coordinate comprises a "tetrahedral intermediate" and two transition states and experimental activation Gibbs free energy of ∼17.5 kcal·mol-1 can be inferred for the known kcat ≈ 1 s-1. We correlate experimental kinetic data (including the E424H variant, newly characterized in this work) for various GCPII mutants (kcat = 8.6 × 10-5 s-1 to 2.7 s-1) with the energy profiles calculated by QM/MM and QM-only (cluster model) approaches. We show that the near-quantitative agreement between the experimental values and the calculated activation energies (ΔH⧧) can be obtained and recommend the combination of the two protocols: QM/MM optimized structures and cluster model (QM) energetics. The trend in relative activation energies is mostly independent of the QM method (DFT functional) used. Last but not least, a satisfactory correlation between experimental and theoretical data allows us to provide qualitative and fairly simple explanations of the observed kinetic effects which are thus based on a rigorous footing.

Electrostatic regulation of blue copper sites.

In the last 50 years, the blue copper proteins became central targets of investigation. Extensive experiments focused on the Cu coordination to probe the effect of local perturbations on its properties. We found that local electric fields, generated by charged residues evolutionarily placed throughout the protein edifice, mainly second sphere, but also more remotely, constitute an additional significant factor regulating blue copper proteins. These fields are not random, but exhibit a highly specific directionality, negative with respect to the and vectors in the Cu first shell. The field magnitude contributes to fine-tuning of the geometric and electronic properties of Cu sites in individual blue copper proteins. Specifically, the local electric fields evidently control the Cu-SMet bond distance, Cu(ii)-SCys bond covalency, and the energies of the frontier molecular orbitals, which, in turn, govern the Cu(ii/i) reduction potential and the relative absorption intensities at 450 nm and 600 nm.

Local Electric Fields as a Natural Switch of Heme-Iron Protein Reactivity.

Heme-iron oxidoreductases operating through the high-valent FeIVO intermediates perform crucial and complicated transformations, such as oxidations of unreactive saturated hydrocarbons. These enzymes share the same Fe coordination, only differing by the axial ligation, e.g., Cys in P450 oxygenases, Tyr in catalases, and His in peroxidases. By examining ~200 heme-iron proteins, we show that the protein hosts exert highly specific intramolecular electric fields on the active sites, and there is a strong correlation between the direction and magnitude of this field and the protein function. In all heme proteins, the field is preferentially aligned with the Fe-O bond ( Fz ). The Cys-ligated P450 oxygenases have the highest average Fz of 28.5 MV cm-1, i.e., most enhancing the oxyl-radical character of the oxo group, and consistent with the ability of these proteins to activate strong C-H bonds. In contrast, in Tyr-ligated proteins, the average Fz is only 3.0 MV cm-1, apparently suppressing single-electron off-pathway oxidations, and in His-ligated proteins, Fz is -8.7 MV cm-1. The operational field range is given by the trade-off between the low reactivity of the FeIVO Compound I at the more negative Fz , and the low selectivity at the more positive Fz . Consequently, a heme-iron site placed in the field characteristic of another heme-iron protein class loses its canonical function, and gains an adverse one. Thus, electric fields produced by the protein scaffolds, together with the nature of the axial ligand, control all heme-iron chemistry.

From Synthetic to Biological Fe4 S4 Complexes: Redox Properties Correlated to Function of Radical S-Adenosylmethionine Enzymes.

By employing the computational protocol for calculation of reduction potentials of the Fe4 S4 -containing species validated using a representative series of well-defined synthetic complexes, we focused on redox properties of two prototypical radical SAM enzymes to reveal how they transform SAM into the reactive 5'-deoxyadenosyl radical, and how they tune this radical for its proper biological function. We found the reduction potential of SAM is indeed elevated by 0.3-0.4 V upon coordination to Fe4 S4 , which was previously speculated in the literature. This makes a generation of 5'-deoxyadenosyl radical from SAM less endergonic (by ca. 7-9 kcal mol-1 ) and hence more feasible in both enzymes as compared to the identical process in water. Furthermore, our calculations indicate that the enzyme-bound 5'-deoxyadenosyl radical has a significantly lower reduction potential than in referential aqueous solution, which may help the enzymes to suppress potential side redox reactions and simultaneously elevate its proton-philic character, which may, in turn, promote the radical hydrogen-atom abstraction ability.

Proton-Electron Transfer to the Active Site Is Essential for the Reaction Mechanism of Soluble Δ9-Desaturase.

A full understanding of the catalytic action of non-heme iron (NHFe) and non-heme diiron (NHFe2) enzymes is still beyond the grasp of contemporary computational and experimental techniques. Many of these enzymes exhibit fascinating chemo-, regio-, and stereoselectivity, in spite of employing highly reactive intermediates which are necessary for activations of most stable chemical bonds. Herein, we study in detail one intriguing representative of the NHFe2 family of enzymes: soluble Δ9 desaturase (Δ9D), which desaturates rather than performing the thermodynamically favorable hydroxylation of substrate. Its catalytic mechanism has been explored in great detail by using QM(DFT)/MM and multireference wave function methods. Starting from the spectroscopically observed 1,2-µ-peroxo diferric P intermediate, the proton-electron uptake by P is the favored mechanism for catalytic activation, since it allows a significant reduction of the barrier of the initial (and rate-determining) H-atom abstraction from the stearoyl substrate as compared to the "proton-only activated" pathway. Also, we ruled out that a Q-like intermediate (high-valent diamond-core bis-µ-oxo-[FeIV]2 unit) is involved in the reaction mechanism. Our mechanistic picture is consistent with the experimental data available for Δ9D and satisfies fairly stringent conditions required by Nature: the chemo-, stereo-, and regioselectivity of the desaturation of stearic acid. Finally, the mechanisms evaluated are placed into a broader context of NHFe2 chemistry, provided by an amino acid sequence analysis through the families of the NHFe2 enzymes. Our study thus represents an important contribution toward understanding the catalytic action of the NHFe2 enzymes and may inspire further work in NHFe(2) biomimetic chemistry.

Reactive mode composition factor analysis of transition states: the case of coupled electron-proton transfers.

A simple method for the evaluation of the kinetic energy distribution within the reactive mode of a transition state (TS), denoted as the Reactive Mode Composition Factor (RMCF), is presented. It allows one to directly map the barrier properties onto the atomic-motion components of the reaction coordinate at the TS, which has potential to shed light onto some mechanistic features of a chemical process. To demonstrate the applicability of RMCF to reactivity, we link the kinetic energy distribution within a reactive mode with the asynchronicity (η) in C-H bond activation, as they both evolve in a series of coupled proton-electron transfer (CPET) reactions between FeIVO oxidants and 1,4-cyclohexadiene. RMCF shows how the earliness or lateness of a process manifests as a redistribution of kinetic energy in the reactive mode as a function of the free energy of reaction (ΔG0) and η. Finally, the title analysis can be applied to predict H-atom tunneling contributions and kinetic isotope effects in a set of reactions, yielding a transparent rationalization based on the kinetic energy distributions in the reactive mode.

Preparation of (Pentafluorosulfanyl)benzenes by Direct Fluorination of Diaryldisulfides: Synthetic Approach and Mechanistic Aspects.

Direct fluorination of ortho-, meta- and para-substituted aromatic thiols and disulfides using elemental fluorine afforded substituted (pentafluorosulfanyl)benzenes. This work thus represents the first study of the scope and limitation of direct fluorination for the synthesis of new SF5 -containing building blocks. Fluorinations in batch and flow modes were compared. A comprehensive computational study was carried out employing density functional and wave function methods to elucidate the reaction mechanism of the transformation of ArSF3 into ArSF5 . Eliminating various nonradical pathways, it has been shown that the reaction proceeds by a radical mechanism, initiated by the attack of the F. on the ArSF3 moiety, propagated via an almost barrierless F2 +ArSF4 . →ArSF5 +F. step and terminated by the ArSF4 . +F. →ArSF5 . Most of the calculated data are in very good agreement with experimental observations concerning the ortho-substituent effect on the reaction rates and yields.

Structural and computational basis for potent inhibition of glutamate carboxypeptidase II by carbamate-based inhibitors.

A series of carbamate-based inhibitors of glutamate carboxypeptidase II (GCPII) were designed and synthesized using ZJ-43, N-[[[(1S)-1-carboxy-3-methylbutyl]amino]carbonyl]-l-glutamic acid, as a molecular template in order to better understand the impact of replacing one of the two nitrogen atoms in the urea-based GCPII inhibitor with an oxygen atom. Compound 7 containing a C-terminal 2-oxypentanedioic acid was more potent than compound 5 containing a C-terminal glutamic acid (2-aminopentanedioic acid) despite GCPII's preference for peptides containing an N-terminal glutamate as substrates. Subsequent crystallographic analysis revealed that ZJ-43 and its two carbamate analogs 5 and 7 with the same (S,S)-stereochemical configuration adopt a nearly identical binding mode while (R,S)-carbamate analog 8 containing a d-leucine forms a less extensive hydrogen bonding network. QM and QM/MM calculations have identified no specific interactions in the GCPII active site that would distinguish ZJ-43 from compounds 5 and 7 and attributed the higher potency of ZJ-43 and compound 7 to the free energy changes associated with the transfer of the ligand from bulk solvent to the protein active site as a result of the lower ligand strain energy and solvation/desolvation energy. Our findings underscore a broader range of factors that need to be taken into account in predicting ligand-protein binding affinity. These insights should be of particular importance in future efforts to design and develop GCPII inhibitors for optimal inhibitory potency.

Beyond the classical thermodynamic contributions to hydrogen atom abstraction reactivity.

Hydrogen atom abstraction (HAA) reactions are cornerstones of chemistry. Various (metallo)enzymes performing the HAA catalysis evolved in nature and inspired the rational development of multiple synthetic catalysts. Still, the factors determining their catalytic efficiency are not fully understood. Herein, we define the simple thermodynamic factor η by employing two thermodynamic cycles: one for an oxidant (catalyst), along with its reduced, protonated, and hydrogenated form; and one for the substrate, along with its oxidized, deprotonated, and dehydrogenated form. It is demonstrated that η reflects the propensity of the substrate and catalyst for (a)synchronicity in concerted H+/e- transfers. As such, it significantly contributes to the activation energies of the HAA reactions, in addition to a classical thermodynamic (Bell-Evans-Polanyi) effect. In an attempt to understand the physicochemical interpretation of η, we discovered an elegant link between η and reorganization energy λ from Marcus theory. We discovered computationally that for a homologous set of HAA reactions, λ reaches its maximum for the lowest |η|, which then corresponds to the most synchronous HAA mechanism. This immediately implies that among HAA processes with the same reaction free energy, ΔG0, the highest barrier (≡ΔG≠) is expected for the most synchronous proton-coupled electron (i.e., hydrogen) transfer. As proof of concept, redox and acidobasic properties of nonheme FeIVO complexes are correlated with activation free energies for HAA from C-H and O-H bonds. We believe that the reported findings may represent a powerful concept in designing new HAA catalysts.

Near-UV Water Splitting by Cu, Ni, and Co Complexes in the Gas Phase.

(2,2'-Bipyridine)M═O+ ions (M = Cu, Ni, Co) were generated by collision-induced dissociation and near-UV photodissociation of readily available [(2,2'-bipyridine)MII(NO3)]+ ions in the gas phase, and their structure was confirmed by ion-molecule reactions combined with isotope labeling. Upon storage in a quadrupole ion trap, the (2,2'-bipyridine)M═O+ ions spontaneously added water, and the formed [(2,2'-bipyridine)M═O + H2O]+ complexes eliminated OH upon further near-UV photodissociation. This reaction sequence can be accomplished at a single laser wavelength in the range of 260-340 nm to achieve stoichiometric homolytic cleavage of gaseous water. Structures, spin states, and electronic excitations of the metal complexes were characterized by ion-molecule reactions using 2H and 18O labeling, photodissociation action spectroscopy, and density functional theory calculations.

Toward Accurate Conformational Energies of Smaller Peptides and Medium-Sized Macrocycles: MPCONF196 Benchmark Energy Data Set.

A carefully selected set of acyclic and cyclic model peptides and several other macrocycles, comprising 13 compounds in total, has been used to calibrate the accuracy of the DFT(-D3) method for conformational energies, employing BP86, PBE0, PBE, B3LYP, BLYP, TPSS, TPSSh, M06-2X, B97-D, OLYP, revPBE, M06-L, SCAN, revTPSS, BH-LYP, and ωB97X-D3 functionals. Both high- and low-energy conformers, 15 or 16 for each compound adding to 196 in total, denoted as the MPCONF196 data set, were included, and the reference values were obtained by the composite protocol, yielding the CCSD(T)/CBS extrapolated energies or their DLPNO-CCSD(T)/CBS equivalents in the case of larger systems. The latter was shown to be in near-quantitative (∼0.10-0.15 kcal·mol-1) agreement with the canonical CCSD(T), provided the TightPNO setting is used, and, therefore, can be used as the reference for larger systems (likely up to 150-200 atoms) for the problem studied here. At the same time, it was found that many D3-corrected DFT functionals provide results of ∼1 kcal·mol-1 accuracy, which we consider as quite encouraging. This result implies that DFT-D3 methods can be, for example, safely used in efficient conformational sampling algorithms. Specifically, the DFT-D3/DZVP-DFT level of calculation seems to be the best trade-off between computational cost and accuracy. Based on the calculated data, we have not found any cheaper variant for the treatment of conformational energies, since the semiempirical methods (including DFTB) provide results of inferior accuracy (errors of 3-5 kcal·mol-1).

Macrocycle Conformational Sampling by DFT-D3/COSMO-RS Methodology.

To find and calibrate a robust and reliable computational protocol for mapping conformational space of medium-sized molecules, exhaustive conformational sampling has been carried out for a series of seven macrocyclic compounds of varying ring size and one acyclic analogue. While five of them were taken from the MD/LLMOD/force field study by Shelley and co-workers ( Watts , K. S. ; Dalal , P. ; Tebben , A. J. ; Cheney , D. L. ; Shelley , J. C. Macrocycle Conformational Sampling with MacroModel . J. Chem. Inf. MODEL: 2014 , 54 , 2680 - 2696 ), three represent potential macrocyclic inhibitors of human cyclophilin A. The free energy values (GDFT/COSMO-RS) for all of the conformers of each compound were obtained by a composite protocol based on in vacuo quantum mechanics (DFT-D3 method in a large basis set), standard gas-phase thermodynamics, and the COSMO-RS solvation model. The GDFT/COSMO-RS values were used as the reference for evaluating the performance of conformational sampling algorithms: standard and extended MD/LLMOD search (simulated-annealing molecular dynamics with low-lying eigenvector following algorithms, employing the OPLS2005 force field plus GBSA solvation) available in MacroModel and plain molecular dynamics (MD) sampling at high temperature (1000 K) using the semiempirical quantum mechanics (SQM) potential SQM(PM6-D3H4/COSMO) followed by energy minimization of the snapshots. It has been shown that the former protocol (MD/LLMOD) may provide a more complete set of initial structures that ultimately leads to the identification of a greater number of low-energy conformers (as assessed by GDFT/COSMO-RS) than the latter (i.e., plain SQM MD). The CPU time needed to fully evaluate one medium-sized compound (∼100 atoms, typically resulting in several hundred or a few thousand conformers generated and treated quantum-mechanically) is approximately 1,000-100,000 CPU hours on today's computers, which transforms to 1-7 days on a small-sized computer cluster with a few hundred CPUs. Finally, our data sets based on the rigorous quantum-chemical approach allow us to formulate a composite conformational sampling protocol with multiple checkpoints and truncation of redundant structural data that offers superior insights at affordable computational cost.