Some practical aspects of free energy calculations from molecular dynamics simulation

In this work, we address two critical aspects of calculation of the free energy differences in molecular systems from molecular simulations. The first aspect involves checking whether the calculated free energy difference depends significantly on the extent of perturbation used for accomplishment of a given transformation. The second aspect of interest is to verify if the sampling errors in calculating the free energy differences between the wild-type molecule and a mutated one in its free state and in a complex are similar, or not, for a finite-length dynamic simulation. The reliability of the free energy estimates obtained from molecular simulations using thermodynamic cycles depends in part on this fact. For investigating these aspects, we use a self-transformation scheme in which a transformation of a part of a molecular system into itself is considered. We perform MD simulations of DNA fragments in which a part of a specific base is subjected to such a self-transformation. Results indicate that the estimated free energy differences do not depend significantly on the extent of perturbation used to achieve the transformation. Interestingly, the variation in the cumulative free energy difference, ΔA, with the coupling parameter, λ, depends significantly on the extent of perturbation. We examine the physical basis of the observed nature of the variation of the accumulated free energy difference, ΔA, against the λ value in the case of a self-transformation. In a thermodynamic cycle, the sampling errors due to the finite-length simulation for the molecular system are found to be similar to each other for the two perturbations (free and in a complex) justifying the use of such approach in calculating ΔΔA in molecular complexes. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 877–885, 1999     

Novel Vinylpyridine Based Cationic MIP Monoliths for Enantiomer Separation in CEC

Cationic vinylpyridine based molecularly imprinted polymer monoliths were, for the first time, applied to enantiomer separation using capillary electrochromatography. In order to map the synthesis conditions under which superporous monoliths are obtained, capillary columns were prepared by an in situ polymerization technique using varying monomer and porogen compositions. Both electrolyte pH and percentage of the organic modifier acetonitrile were found to affect the electrochromatographic behaviour on such columns. An interesting observation is that the electroosmotic flow changed direction from cathodic at high pH to anodic at low pH of the electrolyte, opening up the opportunity to manipulate the flow. This is attributed to the vinylpyridine based MIP becomes protonated and positively charged at low pH, whereas it is uncharged at high pH where instead negatively charged silanol groups drive the electroosmotic flow. Improved enantiomer resolution, as well as increased retention, was observed when the concentration of acetonitrile in the electrolyte decreased, indicating a significant element of hydrophobic effects in the molecular recognition of the imprinted enantiomer. Enantiomer separation of the non-steroidal anti-inflammatory drug ibuprofen was studied and efficiencies as high as 30,000 plates per meter with an asymmetry factor below 4 were obtained for the last eluting imprinted enantiomer. These values are better than that obtained generally using MIP based chromatography.     

Are recent water models obtained by fitting diffraction data consistent with infrared/Raman and x-ray absorption spectra?

X-ray absorption (XA) spectra have been computed based on water structures obtained from a recent fit to x-ray and neutron diffraction data using models ranging from symmetrical to asymmetrical local coordination of the water molecules [A. K. Soper, J. Phys.: Condens. Matter 17, S3273 (2005)]. It is found that both the obtained symmetric and asymmetric structural models of water give similar looking XA spectra, which do not match the experiment. The fitted models both contain unphysical structures that are allowed by the diffraction data, where, e.g., hydrogen-hydrogen interactions may occur. A modification to the asymmetric model, in which the non-hydrogen-bonded OH intramolecular distance is allowed to become shorter while the bonded OH distance becomes longer, improves the situation somewhat, but the overall agreement is still unsatisfactory. The electric field (E-field) distributions and infrared (IR) spectra are also calculated using two established theoretical approaches, which, however, show significant discrepancies in their predictions for the asymmetric structural models. Both approaches predict the Raman spectrum of the symmetric model fitted to the diffraction data to be significantly blueshifted compared to experiment. At the moment no water model exists that can equally well describe IR/Raman, x-ray absorption spectroscopy, and diffraction data.     

ESI-MS detection of proposed reaction intermediates in the air-promoted and ligand-modulated oxidative Heck reaction

Electrospray ionization mass spectrometry (ESI-MS) and subsequent MS/MS analyses were used to directly detect palladium-containing cationic reaction intermediates in a ligand controlled palladium(II)-catalyzed oxidative Heck arylation. All potential intermediates were observed as dmphen-ligated palladium(II) species, suggesting that the dmphen bidentate ligand is attached to the metal center during the entire catalytic cycle. The study supports previous mechanistic propositions and provides new information regarding the composition of aryl-containing Pd(II) complexes in an ongoing oxidative Heck reaction. In addition, sodium acetate was found to be a useful base alternative to previously used tertiary amines.     

Coordination chemistry of the solvated AgI and AuI ions in liquid and aqueous ammonia, trialkyl and triphenyl phosphite, and tri-n-butylphosphine solutions

The coordination chemistry of solvated Ag(I) and Au(I) ions has been studied in some of the most strong electron-pair donor solvents, liquid and aqueous ammonia, and the P donor solvents triethyl, tri-n-butyl, and triphenyl phosphite and tri-n-butylphosphine. The solvated Ag(I) ions have been characterized in solution by means of extended X-ray absorption fine structure (EXAFS), Raman, and (107)Ag NMR spectroscopy and the solid solvates by means of thermogravimetry and EXAFS and Raman spectroscopy. The Ag(I) ion is two- and three-coordinated in aqueous and liquid ammonia solutions with mean Ag-N bond distances of 2.15(1) and 2.26(1) A, respectively. The crystal structure of [Ag(NH3)3]ClO4.0.47 NH3 (1) reveals a regular trigonal-coplanar coordination around the Ag(I) ion with Ag-N bond distances of 2.263(6) A and a Ag...Ag distance of 3.278(2) A separating the complexes. The decomposition products of 1 have been analyzed, and one of them, [Ag(NH3)2]ClO4, has been structurally characterized by means of EXAFS, showing [Ag(NH3)2] units connected into chains by double O bridges from perchlorate ions; the Ag...Ag distance is 3.01(1) A. The linear bisamminegold(I) complex, [Au(NH3)2]+, is predominant in both liquid and aqueous ammonia solutions, as well as in solid [Au(NH3)2]BF4, with Au-N bond distances of 2.022(5), 2.025(5), and 2.026(7) A, respectively. The solvated Ag(I) ions are three-coordinated, most probably in triangular fashion, in the P donor solvents with mean Ag-P bond distances of 2.48-2.53 A. The Au(I) ions are three-coordinated in triethyl phosphite and tri-n-butylphosphine solutions with mean Au-P bond distances of 2.37(1) and 2.40(1) A, respectively.     

Broadband measurement of true transverse relaxation rates in systems with coupled protons: application to the study of conformational exchange

Accurate measurement of transverse relaxation rates in coupled spin systems is important in the study of molecular dynamics, but is severely complicated by the signal modulations caused by scalar couplings in spin echo experiments. The most widely used experiments for measuring transverse relaxation in coupled systems, CPMG and PROJECT, can suppress such modulations, but they also both suppress some relaxation contributions, and average relaxation rates between coupled spins. Here we introduce a new experiment which for the first time allows accurate broadband measurement of transverse relaxation rates of coupled protons, and hence the determination of exchange rate constants in slow exchange from relaxation measurements. The problems encountered with existing methods are illustrated, and the use of the new method is demonstrated for the classic case of hindered amide rotation and for the more challenging problem of exchange between helical enantiomers of a gold(i) complex.

Existing methods for measuring transverse relaxation give incorrect results in coupled spin systems. Measuring true relaxation rates extends their utility.     

A General Method for Extracting Individual Coupling Constants from Crowded 1H NMR Spectra

Couplings between protons, whether scalar or dipolar, provide a wealth of structural information. Unfortunately, the high number of ¹H‐¹H couplings gives rise to complex multiplets and severe overlap in crowded spectra, greatly complicating their measurement. Many different methods exist for disentangling couplings, but none approaches optimum resolution. Here, we present a general new 2D J‐resolved method, PSYCHEDELIC, in which all homonuclear couplings are suppressed in F₂, and only the couplings to chosen spins appear, as simple doublets, in F₁. This approaches the theoretical limit for resolving ¹H‐¹H couplings, with close to natural linewidths and with only chemical shifts in F₂. With the same high sensitivity and spectral purity as the parent PSYCHE pure shift experiment, PSYCHEDELIC offers a robust method for chemists seeking to exploit couplings for structural, conformational, or stereochemical analyses.     

Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium

The B-form of DNA can populate two different backbone conformations: BI and BII, defined by the difference between the torsion angles ε and ζ (BI = ε-ζ < 0 and BII = ε-ζ > 0). BI is the most populated state, but the population of the BII state, which is sequence dependent, is significant and accumulating evidence shows that BII affects the overall structure of DNA, and thus influences protein-DNA recognition. This work presents a reparametrization of the CHARMM27 additive nucleic acid force field to increase the sampling of the BII form in MD simulations of DNA. In addition, minor modifications of sugar puckering were introduced to facilitate sampling of the A form of DNA under the appropriate environmental conditions. Parameter optimization was guided by quantum mechanical data on model compounds, followed by calculations on several DNA duplexes in the condensed phase. The selected optimized parameters were then validated against a number of DNA duplexes, with the most extensive tests performed on the EcoRI dodecamer, including comparative calculations using the Amber Parm99bsc0 force field. The new CHARMM model better reproduces experimentally observed sampling of the BII conformation, including sampling as a function of sequence. In addition, the model reproduces the A form of the 1ZF1 duplex in 75 % ethanol, and yields a stable Z-DNA conformation of duplex (GTACGTAC) in its crystal environment. The resulting model, in combination with a recent reoptimization of the CHARMM27 force field for RNA, will be referred to as CHARMM36.