The Coordinate Reaction Model: An Obstacle to Interpreting the Emergence of Chemical Complexity

The way chemical transformations are described by models based on microscopic reversibility does not take into account the irreversibility of natural processes, and therefore, in complex chemical networks working in open systems, misunderstandings may arise about the origin and causes of the stability of non-equilibrium stationary states, and general constraints on evolution in systems that are far from equilibrium. In order to be correctly simulated and understood, the chemical behavior of complex systems requires time-dependent models, otherwise the irreversibility of natural phenomena is overlooked. Micro reversible models based on the reaction-coordinate model are time invariant and are therefore unable to explain the evolution of open dissipative systems. The important points necessary for improving the modeling and simulations of complex chemical systems are: a) understanding the physical potential related to the entropy production rate, which is in general an inexact differential of a state function, and b) the interpretation and application of the so-called general evolution criterion (GEC), which is the general thermodynamic constraint for the evolution of dissipative chemical systems.     

A reduced-restricted-quasi-Newton–Raphson method for locating and optimizing energy crossing points between two potential energy surfaces

We present a method for the location and optimization of an intersection energy point between two potential energy surfaces. The procedure directly optimizes the excited state energy using a quasi-Newton–Raphson method coupled with a restricted step algorithm. A linear transformation is also used for the solution of the quasi-Newton–Raphson equations. The efficiency of the algorithm is analyzed and demonstrated in some examples. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 :992–1003, 1997     

Protein secondary structure and stability determined by combining exoproteolysis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

In the post-genomic era, several projects focused on the massive experimental resolution of the three-dimensional structures of all the proteins of different organisms have been initiated. Simultaneously, significant progress has been made in the ab initio prediction of protein three-dimensional structure. One of the keys to the success of such a prediction is the use of local information (i.e. secondary structure). Here we describe a new limited proteolysis methodology, based on the use of unspecific exoproteases coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), to map quickly secondary structure elements of a protein from both ends, the N- and C-termini. We show that the proteolytic patterns (mass spectra series) obtained can be interpreted in the light of the conformation and local stability of the analyzed proteins, a direct correlation being observed between the predicted and the experimentally derived protein secondary structure. Further, this methodology can be easily applied to check rapidly the folding state of a protein and characterize mutational effects on protein conformation and stability. Moreover, given global stability information, this methodology allows one to locate the protein regions of increased or decreased conformational stability. All of this can be done with a small fraction of the amount of protein required by most of the other methods for conformational analysis. Thus limited exoproteolysis, together with MALDI-TOF MS, can be a useful tool to achieve quickly the elucidation of protein structure and stability.     

Synthesis of microcin SF608

The first total synthesis of aquatic peptide microcin SF608 is described. Coupling of L-Hpla with the dipeptide L-Phe-L-Choi followed by coupling with agmatine and a deprotection step gave microcin SF608. In addition, the levorotatory character of L-Hpla (5) was thoroughly established, and the conformational analysis of L-Choi containing peptides 1 and 8-10 was performed using NMR spectroscopy to examine the cis-trans isomer equilibrium of the L-Phe-L-Choi amide bond.     

Synthetic Haptens and Monoclonal Antibodies to the Cyanotoxin Anatoxin‐a

Early warning systems for monitoring toxic events may benefit from the availability of monoclonal antibodies enabling the sensitive and specific detection of anatoxin‐a, a cyanotoxin involved in numerous cases of animal poisoning resulting from toxic algal blooms in freshwaters. Through the synthesis of three functionalized derivatives of anatoxin‐a, we have succeeded in generating the first‐ever reported immunoreagents (bioconjugates and antibodies) suitable for the development of immunoanalytical approaches aimed at rapid and onsite detection of this harmful cyanotoxin.     

Synthesis of Azabicyclic Building Blocks for Daphniphyllum Alkaloid Intermediates Featuring N‐Trichloroacetyl Enamide 5‐endo‐trig Radical Cyclizations

A general procedure is reported for the synthesis of cis ring fused azapolycyclic compounds bearing an all‐carbon quaternary stereocenter at the ring fusion and an adequate functionalization for the assembly of new rings leading to advanced synthetic intermediates for Daphniphyllum alkaloid synthesis. The key carbon?carbon bond‐forming step in this approach is a radical cyclization of an N‐cycloalkenyl trichloroacetamide derivative involving a tetrasubstituted enamide to achieve polyfunctionalized lactams.     

Long‐Term Photostability in Terephthalate Metal–Organic Frameworks

Prolonged (weeks) UV/Vis irradiation under Ar of UiO‐66(Zr), UiO66 Zr‐NO₂, MIL101 Fe, MIL125 Ti‐NH₂, MIL101 Cr and MIL101 Cr(Pt) shows that these MOFs undergo photodecarboxylation of benzenedicarboxylate (BDC) linker in a significant percentage depending on the structure and composition of the material. Routine characterization techniques such as XRD, UV/Vis spectroscopy and TGA fail to detect changes in the material, although porosity and surface area change upon irradiation of powders. In contrast to BCD‐containing MOFs, zeolitic imidazolate ZIF‐8 does not evolve CO₂ or any other gas upon irradiation.     

Algebraic approach to the asymmetric rigid rotor

A pure algebraic treatment of the eigenvalue equation corresponding to the asymmetric top is presented. The algebraic method employs the Holstein–Primakoff bosonic realization of the angular momentum algebra. Explicit determination of the linear boson transformation coefficients of the eigenstates is carried out by means of the coherent states formalism. No reference to special functions is needed and a completely algebraic approach is achieved. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 77: 704–709, 2000     

Exploring the accuracy level of new potential energy surfaces for the F + HD reactions: from exact quantum rate constants to the state-to-state reaction dynamics

Exact quantum reactive scattering calculations in the collision energy range 1-250 meV have been carried out for both the isotopic product channels of the title system. The dynamical studies compares an ab initio potential energy surface (PES) recently appeared in the literature (J. Chem. Phys., 2008, 129, 011103) with other phenomenological PESs. Vibrational branching ratios, cross sections and rate constants are presented and compared with molecular beam scattering experiments as well as with chemical kinetics data. In particular, the agreement of the vibrational branching ratios with experimental measurements is improved with respect to previous studies on other PESs, mainly because of the presence of a broad peak in the HF(v' = 3) integral cross section completely absent in the previous simulations. This feature, observed by molecular beam experiments, is the fingerprint of a new reaction mechanism operative in the dynamics described by the new PES. A conjecture for its origin, able to explain many of its characteristic aspects, is analyzed and discussed.