Density Functional Theory Calculations of the Structure and the 15N and 13C Chemical Shifts of Methyl Bacteriopheophorbide a and Bacteriochlorophyll a

Unveiling the potential of superalkali cation Li3+ for capturing nitrogen

The potential of the superalkali cation Li3+ for capturing N2 and its behavior in gaseous nitrogen have been theoretically studied at the MP2/6-311+G(d) level. The evolution of structures and stability of the Li3+(N2)n (n = 1-7) complexes shows that the N2 molecules tend to bind to different vertices of the Li3+ core, and that Li3+ might have the capacity to capture up to twelve nitrogen molecules in the first coordination shell. Based on natural population and molecular orbital analyses, Li3+ keeps its superatom identity in the lowest-lying Li3+(N2)n (n = 1-4) complexes. The change in the Gibbs free energies of possible fragmentation channels also indicates the thermodynamic stability of Li3+ in the (N2)n clusters when n ≤ 4. Different from the case of Li3+(H2O)n, where the electrostatic interaction is dominant, the electrostatic and polarization components are found to make nearly equal contributions to Li3+(N2)n complex formation. In addition, it can be concluded that the superalkali cation Li3+ surpasses heavy alkali metal cations in capturing N2 molecules, since it has a larger binding energy with N2 than Na+ and K+ ions.

Conformational Analysis of 5,4'-Dihydroxy-7,5',3'-trimethoxyisoflavone in Solution Using 1H NMR: A Density Functional Theory Approach

Among 20 compounds isolated from the extracts of Ouratea ferruginea the 5,4'-dihydroxy-7,5',3'-trimethoxyisoflavone (9) showed the best inhibitory effect on glutathione S-transferase (GST) and so deserves our attention. In this work we investigated the preferred molecular structure of 9 in chloroform solution using the density functional theory (DFT) and molecular dynamics simulation. Comparison between experimental ¹H NMR data in CDCl₃ solution and calculated chemical shifts enabled us to precisely determine the conformation adopted by 9 in solution, which can be used in further theoretical studies involving interaction with biological targets. Moreover, the experimental NMR data were used as reference to assess the ability of DFT based methods to predict ¹H NMR spectrum in solution for organic compounds. Among various DFT functionals the hybrid B3LYP was the most adequate for the calculation of chemical shifts in what CH_n protons are concerned. Regarding the OH hydrogen, inclusion of explicit CHCl₃ solvent molecules adequately placed around the solute led to good agreement with the experimental chemical shifts (in CDCl₃). It is a well-known fact that theoretical prediction of chemical shifts for OH hydrogens poses as a challenge and also revealed that the way the solvent effects are included in the DFT calculations is crucial for the right prediction of the whole ¹H NMR spectrum. It was found in this work that a supermolecule solute-solvent calculation with a minimum of four CHCl₃ molecules is enough to correctly reproduce the ¹H NMR experimental profile observed in solution, revealing that the calculated solvated structure used to reproduce the NMR chemical shifts is not unique.

Investigation of two- and three-bond carbon-hydrogen coupling constants in cinnamic acid based compounds

Two- and three-bond coupling constants (² J_HC and ³ J_HC ) were determined for a series of 12 substituted cinnamic acids using a selective 2D inphase/antiphase (IPAP)-single quantum multiple bond correlation (HSQMBC) and 1D proton coupled ¹³ C NMR experiments. The coupling constants from two methods were compared and found to give very similar values. The results showed coupling constant values ranging from 1.7 to 9.7 Hz and 1.0 to 9.6 Hz for the IPAP-HSQMBC and the direct ¹³ C NMR experiments, respectively. The experimental values of the coupling constants were compared with discrete density functional theory (DFT) calculated values and were found to be in good agreement for the ³ J_HC . However, the DFT method under estimated the ² J_HC coupling constants. Knowing the limitations of the measurement and calculation of these multibond coupling constants will add confidence to the assignment of conformation or stereochemical aspects of complex molecules like natural products. Copyright © 2016 John Wiley & Sons, Ltd.

Structural determination of complex natural products by quantum mechanical calculations of (13)C NMR chemical shifts: development of a parameterized protocol for terpenes

Nuclear magnetic resonance (NMR) spectroscopy is one of the most important tools for determining the structures of organic molecules. Despite the advances made in this technique, revisions of erroneously established structures for natural products are still commonly published in the literature. In this context, the prediction of chemical shifts through ab initio and density functional theory (DFT) calculations has become a very powerful tool for assisting with the structural determination of complex organic molecules. In this work, we present the development of a protocol for (13)C chemical shift calculations of terpenes, a class of natural products that are widely distributed among plant species and are very important due to their biological and pharmacological activities. This protocol consists of GIAO-DFT calculations of chemical shifts and the application of a parameterized scaling factor in order to ensure accurate structural determination of this class of natural products. The application of this protocol to a set of five terpenes yielded accurate calculated chemical shifts, showing that this is a very attractive tool for the calculation of complex organic structures such as terpenes.

Structural studies of malonaldehyde–glyoxal and malonaldehyde–methylglyoxal etheno adducts of adenine nucleosides based on spectroscopic methods and DFT-GIAO calculations

The substitution position in the etheno rings of M₁Gx-A and M₁MGx-dA was determined based on the comparison of data derived from NMR spectra with results obtained from computational calculations.

Factors affecting the computation of the 13C shielding in disaccharides

Knowledge of the three-dimensional structures of glycans and glycoproteins is useful for a full understanding of molecular processes in which glycans are involved, such as antigen-recognition and virus infection, to name a few. Among the ubiquitous nuclei in glycan molecules, the (13)C nucleus is an attractive candidate for computation of theoretical chemical shifts at the quantum chemical level of theory to validate and determine glycan structures. For this purpose, it is important to determine, first, which carbons can be used as probes to sense conformational changes and, second, all factors that affect the computation of the shielding, at the density functional theory (DFT) level of theory, of those carbons. To answer such questions, we performed a series of analyses on low-energy conformations, obtained by sampling the glycosidic torsional angles (ϕ, ψ) every 10°, of 12 disaccharides. Our results provide evidence that: (i) the carbons that participate in the glycosidic linkage are the most sensitive probes with which to sense conformational changes of disaccharides; (ii) the rotation of the hydroxyl groups closest to the glycosidic linkage significantly affects the computation of the shieldings of the carbons that participate in the glycosidic linkage; (iii) it is not possible to obtain the shieldings of one disaccharide from the computed values of a different disaccharide or from those disaccharides that differ in the anomeric state; and (iv) a proper basis set distribution, a functional, and a step size, with which to sample the conformational space, are necessary to compute shieldings accurately and rapidly.

1H and 13C NMR scaling factors for the calculation of chemical shifts in commonly used solvents using density functional theory

Calculation of NMR chemical shifts and coupling constants using quantum mechanical calculations [density functional theory (DFT)], has become a very popular tool for the determination of conformation and the assignment of stereochemistry within a molecule. We present the scaling factors (linear regression parameters) from 10 DFT methods for 10 commonly used NMR solvents using the same set of reference compounds. The results were compared with the corresponding gas-phase calculations to assess the inclusion of the polarizable continuum model for solvent effects.

Insights into the photoprotective switch of the major light-harvesting complex II (LHCII): a preserved core of arginine-glutamate interlocked helices complemented by adjustable loops

Light-harvesting antennae of the LHC family form transmembrane three-helix bundles of which two helices are interlocked by conserved arginine-glutamate (Arg-Glu) ion pairs that form ligation sites for chlorophylls. The antenna proteins of photosystem II have an intriguing dual function. In excess light, they can switch their conformation from a light-harvesting into a photoprotective state, in which the excess and harmful excitation energies are safely dissipated as heat. Here we applied magic angle spinning NMR and selective Arg isotope enrichment as a noninvasive method to analyze the Arg structures of the major light-harvesting complex II (LHCII). The conformations of the Arg residues that interlock helix A and B appear to be preserved in the light-harvesting and photoprotective state. Several Arg residues have very downfield-shifted proton NMR responses, indicating that they stabilize the complex by strong hydrogen bonds. For the Arg Cα chemical shifts, differences are observed between LHCII in the active, light-harvesting and in the photoprotective, quenched state. These differences are attributed to a conformational change of the Arg residue in the stromal loop region. We conclude that the interlocked helices of LHCII form a rigid core. Consequently, the LHCII conformational switch does not involve changes in A/B helix tilting but likely involves rearrangements of the loops and helical segments close to the stromal and lumenal ends.

Structural variability in wild-type and bchQ bchR mutant chlorosomes of the green sulfur bacterium Chlorobaculum tepidum

The self-aggregated state of bacteriochlorophyll (BChl) c molecules in chlorosomes belonging to a bchQ bchR mutant of the green sulfur bacteria Chlorobaculum tepidum, which mostly produces a single 17(2)-farnesyl-(R)-[8-ethyl,12-methyl]BChl c homologue, was characterized by solid-state nuclear magnetic resonance (NMR) spectroscopy and high-resolution electron microscopy. A nearly complete (1)H and (13)C chemical shift assignment was obtained from well-resolved homonuclear (13)C-(13)C and heteronuclear (1)H-(13)C NMR data sets collected from (13)C-enriched chlorosome preparations. Pronounced doubling (1:1) of specific (13)C and (1)H resonances revealed the presence of two distinct and nonequivalent BChl c components, attributed to all syn- and all anti-coordinated parallel stacks, depending on the rotation of the macrocycle with respect to the 3(1)-methyl group. Steric hindrance from the 20-methyl functionality induces structural differences between the syn and anti forms. A weak but significant and reproducible reflection at 1/0.69 nm(-1) in the direction perpendicular to the curvature of cylindrical segments observed with electron microscopy also suggests parallel stacking of BChl c molecules, though the observed lamellar spacing of 2.4 nm suggests weaker packing than for wild-type chlorosomes. We propose that relaxation of the pseudosymmetry observed for the wild type and a related BChl d mutant leads to extended domains of alternating syn and anti stacks in the bchQ bchR chlorosomes. Domains can be joined to form cylinders by helical syn-anti transition trajectories. The phase separation in domains on the cylindrical surface represents a basic mechanism for establishing suprastructural heterogeneity in an otherwise uniform supramolecular scaffolding framework that is well-ordered at the molecular level.

Equilibrium, photophysical, photochemical and quantum chemical examination of anionic mercury(I) porphyrins

Hg22+ ion and 5,10,15,20-tetrakis(parasulphonato-phenyl)porphyrin anion can form 2:1 (2 clusters:1 porphyrin) and 2:2 complexes, while the formation of the 1:1 species is not observable: it is only an intermediate, similarly to the cases of other large metal ions of small charge-density. The differences between mercury(I) and mercury(II) porphyrins in the composition of monoporphyrins (2:1 vs. 1:1), in the stability and the Soret absorption based on the arrangement of 2:2 complexes (asymmetric vs. probably symmetric sandwich-structure), in the kinetic behavior (molecularities and the special dimerization of HgIIP4-), in the product of the photoinduced dissociations of 2:2 bisporphyrins (free-base ligand vs. 1:1 complex) can prove that no mercury(II) porphyrins can form due to the possible disproportion of dimercury(I) ions. However, the similarities in the absorption, photophysical and photochemical features (also to other out-of-plane metalloporphyrins) suggest that the out-of-plane position of metal center and the distorted structure of complexes may be responsible for these common properties, the so-called sitting-atop characteristics. Moreover, the calculated structural data of the theoretically studied 1:1 mercury(I) porphyrin are very similar to those of Hg II P as a consequence of the charge separation in the cluster based on the strength of metal-nitrogen bonds. In the case of the 2:2 species, neither the increased distance (because of the Hg-Hg bond), nor the absence of 45° rotation of the two ligands can significantly modify the π-π interaction because its both measured and calculated absorption spectra are similar to those of Hg II2 P 2.

Zinc chlorins for artificial light-harvesting self-assemble into antiparallel stacks forming a microcrystalline solid-state material

We introduce a concept to solve the structure of a microcrystalline material in the solid-state at natural abundance without access to distance constraints, using magic angle spinning (MAS) NMR spectroscopy in conjunction with X-ray powder diffraction and DFT calculations. The method is applied to a novel class of materials that form (semi)conductive 1D wires for supramolecular electronics and artificial light-harvesting. The zinc chlorins 3-devinyl-3(1)-hydroxymethyl-13(2)-demethoxycarbonylpheophorbide a (3',5'-bis-dodecyloxy)benzyl ester zinc complex 1 and 3-devinyl-3(1)-methoxymethyl-13(2)-demethoxycarbonylpheophorbide a (3',5'-bis-dodecyloxy)benzyl ester zinc complex 2, self-assemble into extended excitonically coupled chromophore stacks. (1)H-(13)C heteronuclear dipolar correlation MAS NMR experiments provided the (1)H resonance assignment of the chlorin rings that allowed accurate probing of ring currents related to the stacking of macrocycles. DFT ring-current shift calculations revealed that both chlorins self-assemble in antiparallel pi-stacks in planar layers in the solid-state. Concomitantly, X-ray powder diffraction measurements for chlorin 2 at 80 degrees C revealed a 3D lattice for the mesoscale packing that matches molecular mechanics optimized aggregate models. For chlorin 2 the stacks alternate with a periodicity of 0.68 nm and a 3D unit cell with an approximate volume of 6.28 nm(3) containing 4 molecules, which is consistent with space group P2(1)22(1).

Alternating syn-anti bacteriochlorophylls form concentric helical nanotubes in chlorosomes

Chlorosomes are the largest and most efficient light-harvesting antennae found in nature, and they are constructed from hundreds of thousands of self-assembled bacteriochlorophyll (BChl) c, d, or e pigments. Because they form very large and compositionally heterogeneous organelles, they had been the only photosynthetic antenna system for which no detailed structural information was available. In our approach, the structure of a member of the chlorosome class was determined and compared with the wild type (WT) to resolve how the biological light-harvesting function of the chlorosome is established. By constructing a triple mutant, the heterogeneous BChl c pigment composition of chlorosomes of the green sulfur bacteria Chlorobaculum tepidum was simplified to nearly homogeneous BChl d. Computational integration of two different bioimaging techniques, solid-state NMR and cryoEM, revealed an undescribed syn-anti stacking mode and showed how ligated BChl c and d self-assemble into coaxial cylinders to form tubular-shaped elements. A close packing of BChls via pi-pi stacking and helical H-bonding networks present in both the mutant and in the WT forms the basis for ultrafast, long-distance transmission of excitation energy. The structural framework is robust and can accommodate extensive chemical heterogeneity in the BChl side chains for adaptive optimization of the light-harvesting functionality in low-light environments. In addition, syn-anti BChl stacks form sheets that allow for strong exciton overlap in two dimensions enabling triplet exciton formation for efficient photoprotection.

Characterisation of uniformly 13C, 15N labelled bacteriochlorophyll a and bacteriopheophytin a in solution and in solid state: complete assignment of the 13C, 1H and 15N chemical shifts

In this investigation we report a complete assignment of (13)C, (1)H and (15)N solution and solid state chemical shifts of two bacterial photosynthetic pigments, bacteriochlorophyll (BChl) a and bacteriopheophytin (BPheo) a. Uniform stable-isotope labelling strategies were developed and applied to biosynthetic preparation of photosynthetic pigments, namely uniformly (13)C, (15)N labelled BChl a and BPheo a. Uniform stable-isotope labelling with (13)C, (15)N allowed performing the assignment of the (13)C, (15)N and (1)H resonances. The photosynthetic pigments were isolated from the biomass of photosynthetic bacteria Rhodopseudomonas palustris 17001 grown in uniformly (13)C (99%) and (15)N (98%) enriched medium. Both pigments were characterised by NMR in solution (acetone-d(6)) and by MAS NMR in solid state and their NMR resonances were recorded and assigned through standard liquid 2D (13)C-(13)C COSY, (1)H-(13)C HMQC, (1)H-(15)N HMBC and solid 2D (13)C-(13)C RFDR, (1)H-(13)C FSLG HETCOR and (1)H-(15)N HETCOR correlation techniques at 600 MHz and 750 MHz. The characterisation of pigments is of interest from biochemical to pharmaceutical industries, photosynthesis and food research.

Equilibrium, photophysical, photochemical, and quantum chemical examination of anionic mercury(II) mono- and bisporphyrins

Mercury(II) ion and 5,10,15,20-tetrakis(parasulfonato-phenyl)porphyrin anion can form 1:1, 2:2, and 3:2 (metal ion/porphyrin) out-of-plane (OOP) complexes, from which Hg2P2(8-) has not been identified until now. Identification of this species significantly promoted the confirmation of the composition and the precise elucidation of the equilibrium of Hg3P2(6-). Since the formation of each complex is too fast, their kinetic behavior was studied from the side of dissociation. The rate-determining step in dissociations, as well as in the formation of the 2:2 complex, that is, the dimerization of 1:1 complex, proved to be virtually first-order under these conditions, while the consecutive formations of HgP(4-) and Hg3P2(6-) are second-order reactions. The equilibria can be spectrophotometrically investigated because the Soret- as well as the Q-absorption bands of the free-base ligand are more and more red-shifted in the series of 1:1, 2:2, and 3:2 complexes, and the split of Q-bands disappears as the singlet-1 excited states become degenerate; in the case of bisporphyrins, the bands broaden, especially in the longer-wavelength region of the spectra. The quantum yield and the lifetime of S1-fluorescence from the macrocycle is decreased by the insertion of a mercury(II) ion due to distortion, and in bisporphyrins the luminescence totally ceases because their more complicated structure promotes other ways of energy dissipation. The lifetime of the triplet excited-state is also reduced by metalation. The transient absorption measured upon excitation of Hg3P2(6-) probably originates from Hg2P2(8-) formed by efficient photodissocation during the laser pulse. This photoinduced dissociation is characteristic to out-of-plane complexes, but in metallo-monoporphyrins it needs the energetically higher Soret-excitation; in bisporphyrins, it can take place during irradiation at the longer Q-wavelengths. Investigation of the intramolecular photoredox reactions has proved that for the increased efficiency of the indirect photoinduced LMCT, not the redox potential, but the position of the metal center is responsible. The two orders of magnitude higher photoredux quantum yield for the 3:2 complex, compared to that of the 2:2 species, can be explained by the repulsive effect of the inner mercury(II) ion pushing the other two farther out of the ligand cavity. In bisporphyrins the second excited states are photochemically more reactive than the first ones, while most of the photochemical processes of HgP(4-) originate from the first excited state. According to our quantum chemical calculations, the mercury(II) ion causes the expansion of the porphyrin-cavity; therefore its out-of-plane position is smaller than the value expected based on its ionic radius. In the hitherto unknown 2:2 dimer two 1:1 saucer-shaped monomers are kept together by secondary forces, mostly by pi-pi interaction, but their relative arrangement was not unequivocally determined by the two DFT functionals used. The arrangements with a symmetry axis or plane perpendicular to both rings are not favored; instead, the two monomers are shifted along the porphyrin planes, either in a Hg-P-Hg-P or a Hg-P-P-Hg order. Our time-dependent density functional theory (TD-DFT) calculations indicate that the electronic spectra are not very sensitive to the structure of the dimer, even though the environment of the porphyrin rings is quite different if one of the metal ions is between or outside of both macrocycles. The calculated spectral shifts agree only partially with the experimental data. The TD-DFT calculations suggest that the chromophores are not fully independent in the bisporphyrins and that the observed spectral shift cannot be uniquely assigned to the geometrical distortion of the porphyrin macrocyle.

Structural determination of dihydro- and tetrahydrogeranylgeranyl groups at the 17-propionate of bacteriochlorophylls-a

In the final stage of bacteriochlorophyll (BChl) biosynthesis, the presence of BChl-a molecules possessing dihydrogeranylgeranyl and tetrahydrogeranylgeranyl groups at the 17-propionate has been reported. However, the molecular structures of such BChls-a have not yet been determined in terms of the positions of CC double bonds in the 17(2)-ester. In this study, we isolated significant amounts of such pure BChls-a from Rhodopseudomonas palustris and determined their structures by both mass spectrometry and (1)H and (13)C NMR spectroscopy. The determined structures enable us to discuss a stepwise reduction from a geranylgeranyl to phytyl substituent.

Photo-CIDNP MAS NMR in Intact Cells ofRhodobactersphaeroidesR26: Molecular and Atomic Resolution at Nanomolar Concentration

Photochemically induced dynamic nuclear polarization (photo-CIDNP) is observed in photosynthetic reaction centers of the carotenoid-less strain R26 of the purple bacterium Rhodobacter sphaeroides by (13)C solid-state NMR at three different magnetic fields (4.7, 9.4, and 17.6 T). The signals of the donor appear enhanced absorptive (positive) and of the acceptor emissive (negative). This spectral feature is in contrast to photo-CIDNP data of reactions centers of Rhodobacter sphaeroides wildtype reported previously (Prakash, S.; Alia; Gast, P.; de Groot, H. J. M.; Jeschke, G.; Matysik, J. J. Am. Chem. Soc. 2005, 127, 14290-14298) in which all signals appear emissive. The difference is due to an additional mechanism occurring in RCs of R26 in the long-living triplet state of the donor, allowing for spectral editing by different enhancement mechanisms. The overall shape of the spectra remains independent of the magnetic field. The strongest enhancement is observed at 4.7 T, enabling the observation of photo-CIDNP enhanced NMR signals from reaction center cofactors in entire bacterial cells allowing for detection of subtle changes in the electronic structure at nanomolar concentration of the donor cofactor. Therefore, we establish in this paper photo-CIDNP MAS NMR as a method to study the electronic structure of photosynthetic cofactors at the molecular and atomic resolution as well as at cellular concentrations.

Quantum chemical simulation of excited states of chlorophylls, bacteriochlorophylls and their complexes

The present review describes the use of quantum chemical methods in estimation of structures and electronic transition energies of photosynthetic pigments in vacuum, in solution and imbedded in proteins. Monomeric Mg-porphyrins, chlorophylls and bacteriochlorophylls and their solvent 1:1 and 1:2 complexes were studied. Calculations were performed for Mg-porphyrin, Mg-chlorin, Mg-bacteriochlorin, mesochlorophyll a, chlorophylls a, b, c(1), c(2), c(3), d and bacteriochlorophylls a, b, c, d, e, f, g, h, plus several homologues. Geometries were optimised with PM3, PM3/CISD, PM5, ab initio HF (6-31G*/6-311G**) and density functional B3LYP (6-31G*/6-311G**) methods. Spectroscopic transition energies were calculated with ZINDO/S CIS, PM3 CIS, PM3 CISD, ab initio CIS, time-dependent HF and time-dependent B3LYP methods. Estimates for experimental transition energies were obtained from linear correlations of the calculated transition energies of 1:1 solvent complexes against experimentally recorded solution energies (scaling). According to the calculations in five-coordinated solvent complexes the magnesium atom lies out of the porphyrin plane, while in six-coordinated complexes the porphyrin is nearly planar. Charge densities on magnesium and nitrogen atoms were strongly dependent on the computational method deployed. Several dark states of low oscillator strength below the main Soret band were predicted for solvent complexes and chlorophylls and bacteriochlorophylls in protein environment. Such states, though not yet identified experimentally, might serve as intermediate states for excitation energy transfer in photosynthetic complexes. Q(y), Q(x) and Soret transition energies were found to depend on the orientation of the acetyl group and external pressure. A method to estimate site energies and dimeric interaction energies and to simulate absorption and CD spectra of photosynthetic complexes is described. Simulations for the light harvesting complexes Rhodospirillum molischianum, chlorosomes of Chlorobium tepidum and Chloroflexus aurantiacus, and LHC-II of Spinacia oleracea are presented as examples.

Magnetic Field Dependence of Photo-CIDNP MAS NMR on Photosynthetic Reaction Centers ofRhodobacter sphaeroidesWT

Photochemically induced dynamic nuclear polarization (photo-CIDNP) is observed in frozen and quinone depleted photosynthetic reaction centers of the purple bacteria Rhodobacter sphaeroides wild type (WT) by (13)C solid-state NMR at three different magnetic fields. All light-induced signals appear to be emissive at all three fields. At 4.7 T (200 MHz proton frequency), the strongest enhancement of NMR signals is observed, which is more than 10 000 above the Boltzmann polarization. At higher fields, the enhancement factor decreases. At 17.6 T, the enhancement factor is about 60. The field dependence of the enhancement appears to be the same for all nuclei. The observed field dependence is in line with simulations that assume two competing mechanisms of polarization transfer from electrons to nuclei, three-spin mixing (TSM) and differential decay (DD). These simulations indicate a ratio of the electron spin density on the special pair cofactors is 3:2 in favor of the L-BChl during the radical cation state. The good agreement of simulations with the experiments raises expectations that artificial solid reaction centers can be tuned to show photo-CIDNP in the near future.

Direct Experimental Evaluation of Charge Scheme Performance by a Molecular Charge-Meter

The remarkable advances accomplished in the past two decades in theoretical and computational capabilities have made the in silico study of complex chemical systems feasible. However, this progress is in strong contrast to the lag in experimental capabilities relating to the measurement of fundamental chemical quantities within convoluted environments such as solvents or protein milieu. As a result, many works rely extensively on predictions provided by ab initio methodologies without having independent experimental support. Such a proliferation of theory and computational approaches without being substantiated by appropriate experimental data is undesirable. The feasibility of using nickel-bacteriochlorophyll as a molecular potentiometer was recently demonstrated for the systematic evaluation of fragmental charge density transfer for metal complexes in solution, thus providing an experimental assay with high accuracy and sensitivity (better than +/-0.005 e(-); Yerushalmi, R.; Baldridge, K. K.; Scherz, A. J. Am. Chem. Soc. 2003, 125, 12706-12707). Here the experimentally determined fragmental charge density transfer values measured by the molecular potentiometer for metal complexes in solvent are used to provide, for the first time, an independent and critical experimental evaluation of theoretical approaches commonly used in determining atomic charges and fragmental charge density transfer among interacting molecular systems. Importantly, these findings indicate that the natural population analysis (NPA) charge analysis is highly robust and well-suited for determining charge transfer processes involving donor-acceptor coordination interactions. The majority of computational charge schemes fail to provide an accurate chemical picture for the whole range of systems considered here. In cases where the role of electronic correlation varies significantly among chemically related structures, as with mono- and biligated complexes, the widely used electrostatic potential fit-based methods for evaluating atomic charges may prove to be problematic for predictive studies. In such cases, alternative methods that do not rely on the net dipole moment or other higher multipoles of the system for determining charges should be employed.

An ab initio force field for the cofactors of bacterial photosynthesis

This article presents a new ab initio force field for the cofactors of bacterial photosynthesis, namely quinones and bacteriochlorophylls. The parameters has been designed to be suitable for molecular dynamics simulations of photosynthetic proteins by being compatible with the AMBER force field. To our knowledge, this is the first force field for photosynthetic cofactors based on a reliable set of ab initio density functional reference data for methyl bacteriochlorophyll a, methyl bacteriopheophytin a, and of a derivative of ubiquinone. Indeed, the new molecular mechanics force field is able to reproduce very well not only the experimental and ab initio structural properties and the vibrational spectra of the molecules, but also the eigenvectors of the molecular normal modes. For this reason it might also be helpful to understand vibrational spectroscopy results obtained on reaction center proteins.

Selective detection and assignment of the solution NMR signals of bacteriochlorophyll a in a reconstituted subunit of a light-harvesting complex

High-resolution solution NMR spectra have been obtained for bacteriochlorophyll (BChl) a molecules in a biologically functional subunit of a bacterial core light-harvesting complex based on a modified reconstitution method. The reconstituted subunit of pigment-integral membrane polypeptides is stable and homogeneous at high concentrations at room temperature and exhibits a Q(y) absorption peak at 818 nm. (1)H and (13)C chemical shifts have been specifically assigned for BChl a using the fully and selectively (13)C-labeled pigments incorporated with natural abundance polypeptides in deuterated detergent solution. Remarkable signal broadening has been observed upon reconstitution, where the bacteriochlorin macrocycle is shown in a highly restricted molecular motion while the phytol side chain remains relatively mobile. Two sets of resonances are revealed for 3(2), 8(1), 10, 12(1), and 13(4) protons, and 8(2) methyl protons exhibit four resonances with large upfield complexation shifts. The result indicates a nonequivalent state for the two BChl a molecules in the subunit and can be best interpreted in terms of a parallel face-to-face configuration with partial overlap over the pyrrolic rings II, III, and V. In comparison with BChl a in acetone, 8(2), 13(2), and 13(4) protons are largely perturbed, and the propionic and phytol side chain may adopt a different conformation in the reconstituted subunit. The (13)C chemical shift of 3(1) carbonyl carbon shows a large change downfield, indicating strong hydrogen bonding for all the acetyl carbonyls. Carbonyl carbons at 13(1) give rise to two (13)C resonances with equal intensities, suggesting that the keto carbonyl in one BChl a molecule within a subunit forms a stronger hydrogen bond than that in another BChl a molecule.

Orientation of amide-nitrogen-15 chemical shift tensors in peptides: a quantum chemical study

Knowledge of the orientation of the nitrogen-15 chemical shift anisotropy (CSA) tensor is critical for a variety of experiments that provide information on protein structure and dynamics in the solid and solution states. Unfortunately, the methods available for determining the orientation of the CSA tensor experimentally have inherent limitations. Rotation studies of a single crystal provide complete information but are tedious and limited in applicability. Solid-state NMR studies on powder samples can be applied to a greater range of samples but suffer from ambiguities in the results obtained. Density functional gauge-including-atomic-orbitals (GIAO) calculations of the orientations of (15)N CSA tensors in peptides are presented here as an independent source of confirmation for these studies. A comparison of the calculated (15)N CSA orientations with the available experimental values from single-crystal and powder studies shows excellent agreement after a partial, constrained optimization of some of the crystal structures used in the calculation. The results from this study suggest that the orientation as well as the magnitudes of (15)N CSA tensors may vary from molecule to molecule. The calculated alpha(N) angle varies from 0 degrees to 24 degrees with the majority in the 10 degrees to 20 degrees range and the beta(N) angle varies from 17 degrees to 24 degrees in good agreement with most of the solid-state NMR experimental results. Hydrogen bonding is shown to have negligible effect on the orientation of (15)N CSA tensor in accordance with recent theoretical predictions. Furthermore, it is demonstrated that the orientation of the (15)N CSA can be calculated accurately with much smaller basis sets than is needed to calculate the chemical shift, suggesting that the routine application of ab initio calculations to the determination of (15)N CSA tensor orientations in large biomolecules might be possible.