Inter- and intramolecular potential for the N-formylglycinamide-water system. A comparison between theoretical modeling and empirical force fields

An intramolecular NEMO potential is presented for the N-formylglycinamide molecule together with an intermolecular potential for the N-formylglycinamide-water system. The intramolecular N-formylglycinamide potential can be used as a building block for the backbone of polypeptides and proteins. Two intramolecular minima have been obtained. One, denoted as C5, is stabilized by a hydrogen bonded five member ring, and the other, denoted as C7, corresponds to a seven membered ring. The interaction between one water molecule and the N-formylglycinamide system is also studied and compared with Hartree-Fock SCF calculations and with the results obtained for some of the more commonly used force fields. The agreement between the NEMO and SCF energies for the complexes is in general superior to that of the other force fields. In the C7 region the surfaces obtained from the intramolecular part of the commonly used force fields are too flat compared to the NEMO potential and the ab initio calculations. We further analyze the possibility of using a charge distribution obtained from one conformation to describe the charge distribution of other conformations. We have found that the use of polarizabilities and generic dipoles can model most of the changes in charge density due to the different geometry of the new conformations, but that one can expect additional errors in the interaction energies that are of the order of 1 kcal/mol.     

Proton transfers in hydrogen bonded systems. Electron correlation effects in (H3NHOH2)+

The energetics of proton transfer between the N and O atoms of (H₃NHOH₂)⁺ are calculated via ab initio molecular orbital methods. A single-well potential is obtained at the equilibrium intermolecular separation Inclusion of electron correlation via the POL CI technique produces a less steep potential, reducing the energy barrier to proton transfer at greater NO distances.     

The tautomerism of Omeprazole in solution: a 1H and 13C NMR study

The tautomerism of 5(6)-methoxy-2-([(4-methoxy-3,5-dimethyl-2-pyridinyl)methyl] sulfinyl)-1H-benzimidazole (omeprazole) was determined in solution, K(T) = 0.59 in THF at 195 K, in favor of the 6-methoxy tautomer. The assignment of the signals was made by comparison with its two N-methyl derivatives in acetone-d6 and through theoretical calculations of the absolute shieldings (GIAO/DFT/6-311++G**).     

Strong solute-solute dispersive interactions in a protein-ligand complex

The contributions of solute-solute dispersion interactions to binding thermodynamics have generally been thought to be small, due to the surmised equality between solute-solvent dispersion interactions prior to the interaction versus solute-solute dispersion interactions following the interaction. The thermodynamics of binding of primary alcohols to the major urinary protein (MUP-I) indicate that this general assumption is not justified. The enthalpy of binding becomes more favorable with increasing chain length, whereas the entropy of binding becomes less favorable, both parameters showing a linear dependence. Despite the hydrophobicity of the interacting species, these data show that binding is not dominated by the classical hydrophobic effect, but can be attributed to favorable ligand-protein dispersion interactions.     

Photodissociation dynamics of the methyl radical at 212.5 nm: effect of parent internal excitation

Photodissociation dynamics of the CH3 radical at 212.5 nm has been investigated using the H atom Rydberg tagging time-of-flight method with a pure CH3 radical source generated by the photolysis of CH3I at 266 nm. Time-of-flight spectra of the H atom products from the photolysis of both cold and hot methyl radicals have been measured at different photolysis polarizations. Experimental results indicate that the photodissociation of the methyl radical in its ground vibrational state at 212.5 nm excitation occurs on a very fast time scale in comparison with its rotational period, indicating the CH3 dissociation at 212.5 nm occurs on the excited 3s Rydberg state surface. Experimental evidence also shows that the photodissociation of the methyl radical in the nu2 = 1 state of the umbrella mode at 212.5 nm excitation is characteristically different from that in the ground vibrational state.     

Automated linkage of proteins and payloads producing monodisperse conjugates

Controlled protein functionalization holds great promise for a wide variety of applications. However, despite intensive research, the stoichiometry of the functionalization reaction remains difficult to control due to the inherent stochasticity of the conjugation process. Classical approaches that exploit peculiar structural features of specific protein substrates, or introduce reactive handles via mutagenesis, are by essence limited in scope or require substantial protein reengineering. We herein present equimolar native chemical tagging (ENACT), which precisely controls the stoichiometry of inherently random conjugation reactions by combining iterative low-conversion chemical modification, process automation, and bioorthogonal trans-tagging. We discuss the broad applicability of this conjugation process to a variety of protein substrates and payloads.

Controlled protein functionalization holds great promise for a wide variety of applications.

Applications of protein conjugates are limitless, including imaging, diagnostics, drug delivery, and sensing.^1–4 In many of these applications, it is crucial that the conjugates are homogeneous.⁵ The site-selectivity of the conjugation process and the number of functional labels per biomolecule, known as the degree of conjugation (DoC), are crucial parameters that define the composition of the obtained products and are often the limiting factors to achieving adequate performance of the conjugates. For instance, immuno-PCR, an extremely sensitive detection technique, requires rigorous control of the average number of oligonucleotide labels per biomolecule (its DoC) in order to achieve high sensitivity.⁶ In optical imaging, the performance of many super-resolution microscopy techniques is directly defined by the DoC of fluorescent tags.⁷ For therapeutics, an even more striking example is provided by antibody–drug conjugates, which are prescribed for the treatment of an increasing range of cancer indications.⁸ A growing body of evidence from clinical trials indicates that bioconjugation parameters, DoC and DoC distribution, directly influence the therapeutic index of these targeted agents and hence must be tightly controlled.⁹Standard bioconjugation techniques, which rely on nucleophile–electrophile reactions, result in a broad distribution of different DoC species (Fig. 1a), which have different biophysical parameters, and consequently different functional properties.¹⁰Open in a separate windowFig. 1Schematic representation of the types of protein conjugates.To address this key issue and achieve better DoC selectivity, a number of site-specific conjugation approaches have been developed (Fig. 1b). These techniques rely on protein engineering for the introduction of specific motifs (e.g., free cysteines,¹¹ selenocysteines,¹² non-natural amino acids,^13,14 peptide tags recognized by specific enzymes^15,16) with distinct reactivity compared to the reactivity of the amino acids present in the native protein. These motifs are used to simultaneously control the DoC (via chemo-selective reactions) and the site of payload attachment. Both parameters are known to influence the biological and biophysical parameters of the conjugates,¹¹ but so far there has been no way of evaluating their impact separately.The influence of DoC is more straightforward, with a lower DoC allowing the minimization of the influence of payload conjugation on the properties of the protein substrate. The lowest DoC that can be achieved for an individual conjugate is 1 (corresponding to one payload attached per biomolecule). It is noteworthy that DoC 1 is often difficult to achieve through site-specific conjugation techniques due to the symmetry of many protein substrates (e.g., antibodies). Site selection is a more intricate process, which usually relies on a systematic screening of conjugation sites for some specific criteria, such as stability or reactivity.¹⁷Herein, we introduce a method of accessing an entirely new class of protein conjugates with multiple conjugation sites but strictly homogenous DoCs (Fig. 1c). To achieve this, we combined (a) iterative low conversion chemical modification, (b) process automation, and (c) bioorthogonal trans-tagging in one workflow.The method has been exemplified for protein substrates, but it is applicable to virtually any native bio-macromolecule and payload. Importantly, this method allows for the first time the disentangling of the effects of homogeneous DoC and site-specificity on conjugate properties, which is especially intriguing in the light of recent publications revealing the complexity of the interplay between payload conjugation sites and DoC for in vivo efficacy of therapeutic bioconjugates.¹⁸ Finally, it is noteworthy that this method can be readily combined with an emerging class of site-selective bioconjugation reagents to produce site-specific DoC 1 conjugates, thus further expanding their potential for biotechnology applications.¹⁹     

Phenylated polyimides: Diels-Alder reaction of biscyclopentadienones with dimaleimides

A series of phenylated polydihydrophthalimides has been synthesized by the Diels-Alder reactions of 3,3′-(oxydi-p-phenylene)bis(2,4,5-triphenylcyclopentadienone) and 3,3′-(p-phenylene)bis(2,4,5-triphenylcyclopentadienone) with N,N′-o-, -m-, and -p-phenylenedimaleimide. The polydihydrophthalimides were soluble in dimethylformamide (DMF) and had intrinsic viscosities that ranged from 0.33 to 1.01, the polymers were dehydrogenated thermally and chemically to afford the corresponding phenylated polyphthalimides. The totally aromatic polyimides were also soluble in DMF but had intrinsic viscosities only as high as 0.41. The thermogravimetric analyses of the polyphthalimides showed breaks near 530°C in air and in nitrogen atmospheres.     

Drinfeld algebra deformations, homotopy comodules and the associahedra

The aim of this work is to construct a cohomology theory controlling the deformations of a general Drinfel'd algebra and thus finish the program which began in [13], [14]. The task is accomplished in three steps. The first step, which was taken in the aforementioned articles, is the construction of a modified cobar complex adapted to a non-coassociative comultiplication. The following two steps each involves a new, highly non-trivial, construction. The first construction, essentially combinatorial, defines a differential graded Lie algebra structure on the simplicial chain complex of the associahedra. The second construction, of a more algebraic nature, is the definition of a map of differential graded Lie algebras from the complex defined above to the algebra of derivations on the bar resolution. Using the existence of this map and the acyclicity of the associahedra we can define a so-called homotopy comodule structure (Definition 3.3 below) on the bar resolution of a general Drinfel'd algebra. This in turn allows us to define the desired cohomology theory in terms of a complex which consists, roughly speaking, of the bimodule and bicomodule maps from the bar resolution to the modified cobar resolution. The complex is bigraded but not a bicomplex as in the Gerstenhaber-Schack theory for bialgebra deformations. The new components of the coboundary operator are defined via the constructions mentioned above. The results of the paper were announced in [12].

     

A high performance liquid chromatography – inductively coupled plasma-mass spectrometry interface employing desolvation for speciation studies of platinum in chemotherapy drugs

A novel interface between high performance liquid chromatography (HPLC) and inductively coupled plasma-mass spectrometry (ICP-MS) is described. The eluent from the HPLC is nebulised into a heated cyclone spray-chamber and the solvent removed using a Nafion membrane drier, held at 75 degrees C, and a cryogenic condenser. The condenser consists of 6 Peltier heat pumps connected to liquid cooled aluminium blocks. At a nebuliser gas flow rate of 0.6 l min(-1), the membrane drier removes 58% of the vapour and the Peltier condenser 75% of the remaining vapour, i.e. a total desolvation efficiency of 89%. This enables the use of HPLC solvents which otherwise would destabilise the ICP, e.g. 100% acetonitrile or methanol, and permits the use of solvent gradients with minimal baseline drift. The system has been applied to the determination of platinum species in an organoplatinum drug used for chemotherapy in human plasma ultrafiltrate of patients treated with this new drug (JM-216). The limit of detection for platinum species has been 0.6 ng nl(-1) (i.e. 120 pg of Pt) and several species have been separated with good resolution.     

Project Management Duration/Resource Tradeoff Analysis: an Application of the Cut Search Approach

The paper presents an application oriented procedure for solving the project management duration/resource tradeoff problem. A procedure is presented for reducing a project from a normal to a crash duration state at a minimum amount of additional resource expenditure assuming a linear utilization functions. The procedure is network based using a graphical Cut Search Approach to locate the minimal resource level at each reduction in total project duration. Activity-on-arc networks and flow networks are utilized. The paper is presented for practical application and for conceptual development as compared to a theoretical treatment.