Antibacterial activity of N-quaternary chitosan derivatives: Synthesis, characterization and structure activity relationship (SAR) investigations

Quaternary N-(2-(N,N,N-tri-alkyl ammoniumyl and 2-pyridiniumyl) acetyl) derivatives of chitosan polymer, chitooligomer, and glucosamine (monomer) were synthesized for the purpose of investigating the structure activity relationship (SAR) for the antibacterial effect. Novel methods were used in the synthesis. The final chitosan and chitooligomer derivatives could thus be obtained in two steps without prior protection of the hydroxyl groups. However, in order to obtain chitosan derivatives with the bulky N,N-dimethyl-N-dodecyl- and N,N-dimethyl-N-butyl side chains three steps were needed, starting from 3,6-O-di-tert-butyldimethylsilyl chitosan (3,6-O-di-TBDMS chitosan) as the key intermediate. The quaternary ammoniumyl acetyl derivatives of glucosamine were synthesized from glucosamine or tetra-O-acetylglucosamine. N,N,N-trimethyl chitosan (TMC) was used as reference compound for investigation of antibacterial activity. Clinical Laboratory Standard Institute (CLSI) protocols were used to determine MIC and MLC for activity against clinically important Gram-positive strains Staphylococcus aureus (ATCC 25923), and S. aureus (MRSA) (ATCC 43300), and Gram-negative strains of Escherichia coli (ATCC 25922), P. aeriginosa (ATCC 27853) and Enterococcus facialis (ATCC 29212). The MIC values for the compounds ranged from 8 to ?8192 mg/L. In general the N-(2-(N,N-dimethyl-N-dodecyl ammoniumyl) acetyl) derivatives of chitooligomer and glucosamine monomer were more active against bacteria than derivatives with shorter alkyl chains. In contrast the N-(2-(N,N-dimethyl-N-dodecyl ammoniumyl) acetyl) derivatives of chitosan were less active than derivatives with N-(2-N,N,N-trimetylammoniumyl) acetyl or N-(2-(N-pyridiniumyl) acetyl) quaternary moiety. N,N,N-trimethyl chitosan (TMC) was the most active compound in this study.     

A Bayesian method for construction of Markov models to describe dynamics on various time-scales

The dynamics of many biological processes of interest, such as the folding of a protein, are slow and complicated enough that a single molecular dynamics simulation trajectory of the entire process is difficult to obtain in any reasonable amount of time. Moreover, one such simulation may not be sufficient to develop an understanding of the mechanism of the process, and multiple simulations may be necessary. One approach to circumvent this computational barrier is the use of Markov state models. These models are useful because they can be constructed using data from a large number of shorter simulations instead of a single long simulation. This paper presents a new Bayesian method for the construction of Markov models from simulation data. A Markov model is specified by (τ,P,T), where τ is the mesoscopic time step, P is a partition of configuration space into mesostates, and T is an N(P)×N(P) transition rate matrix for transitions between the mesostates in one mesoscopic time step, where N(P) is the number of mesostates in P. The method presented here is different from previous Bayesian methods in several ways. (1) The method uses Bayesian analysis to determine the partition as well as the transition probabilities. (2) The method allows the construction of a Markov model for any chosen mesoscopic time-scale τ. (3) It constructs Markov models for which the diagonal elements of T are all equal to or greater than 0.5. Such a model will be called a "consistent mesoscopic Markov model" (CMMM). Such models have important advantages for providing an understanding of the dynamics on a mesoscopic time-scale. The Bayesian method uses simulation data to find a posterior probability distribution for (P,T) for any chosen τ. This distribution can be regarded as the Bayesian probability that the kinetics observed in the atomistic simulation data on the mesoscopic time-scale τ was generated by the CMMM specified by (P,T). An optimization algorithm is used to find the most probable CMMM for the chosen mesoscopic time step. We applied this method of Markov model construction to several toy systems (random walks in one and two dimensions) as well as the dynamics of alanine dipeptide in water. The resulting Markov state models were indeed successful in capturing the dynamics of our test systems on a variety of mesoscopic time-scales.     

Singlet and triplet potential surfaces for the O2+C2H4 reaction

Electronic structure calculations at the CASSCF and UB3LYP levels of theory with the aug-cc-pVDZ basis set were used to characterize structures, vibrational frequencies, and energies for stationary points on the ground state triplet and singlet O(2)+C(2)H(4) potential energy surfaces (PESs). Spin-orbit couplings between the PESs were calculated using state averaged CASSCF wave functions. More accurate energies were obtained for the CASSCF structures with the MRMP2/aug-cc-pVDZ method. An important and necessary aspect of the calculations was the need to use different CASSCF active spaces for the different reaction paths on the investigated PESs. The CASSCF calculations focused on O(2)+C(2)H(4) addition to form the C(2)H(4)O(2) biradical on the triplet and singlet surfaces, and isomerization reaction paths ensuing from this biradical. The triplet and singlet C(2)H(4)O(2) biradicals are very similar in structure, primarily differing in their C-C-O-O dihedral angles. The MRMP2 values for the O(2)+C(2)H(4)→C(2)H(4)O(2) barrier to form the biradical are 33.8 and 6.1 kcal/mol, respectively, for the triplet and singlet surfaces. On the singlet surface, C(2)H(4)O(2) isomerizes to dioxetane and ethane-peroxide with MRMP2 barriers of 7.8 and 21.3 kcal/mol. A more exhaustive search of reaction paths was made for the singlet surface using the UB3LYP/aug-cc-pVDZ theory. The triplet and singlet surfaces cross between the structures for the O(2)+C(2)H(4) addition transition states and the biradical intermediates. Trapping in the triplet biradical intermediate, following (3)O(2)+C(2)H(4) addition, is expected to enhance triplet→singlet intersystem crossing.     

Optical response of small closed-shell sodium clusters

Absorption spectra of closed-shell Na(2), Na(3) (+), Na(4), Na(5) (+), Na(6), Na(7) (+), and Na(8) clusters are calculated using a complex Bethe-Salpeter equation derived using a conserving linear response method. In the framework of a quasiparticle approach, we determine electron-hole correlations in the presence of an external field. The calculated results are in excellent agreement with experimental spectra, and some possible cluster geometries that occur in experiments are analyzed. The position and the broadening of the resonances in the spectra arise from a consistent treatment of the scattering and dephasing contributions in the linear response calculation. Comparison between the experimental and the theoretical results yields information about the cluster geometry, which is not accessible experimentally.     

Electronic effects on atom tunneling: conformational isomerization of monomeric para-substituted benzoic acid derivatives

We present the first generation and spectroscopic identification of the higher-lying E conformer of the simplest aromatic carboxylic acid, benzoic acid (1a), as its O-deuterated isotopologue (E)-d(1)-1a using matrix-isolation techniques; the parent (E)-1a could not be observed because of fast H-tunneling to the more stable conformer (Z)-1a. Even deuterated (E)-d(1)-1a converts quickly back to (Z)-d(1)-1a through D-tunneling with a half-life (τ) of ～12 min in Ar at 11 K. Tunneling computations using an Eckart barrier in conjunction with a CCSD(T)/cc-pVTZ//MP2/cc-pVDZ + ZPVE intrinsic reaction path revealed that τ of (E)-1a is only ～10(-5) min, in marked contrast to those of simple aliphatic acids, which are in the range of minutes. The electronic substituent effects on D-tunneling in para-substituted benzoic acid derivatives (p-X-PhCOOD, d(1)-1) were systematically studied in Ar matrices at 11 K to derive the first Hammett relationships for atom tunneling. σ-Electron donors (X = alkyl) increase the half-life of d(1)-1, while σ-acceptor/π-donor groups (X = OD, NH(2), halogen) and to an even greater extent a σ-/π-acceptor group (X = NO(2)) decrease τ. The latter finding is in line with the smaller E-to-Z reaction barriers and narrower reaction widths for the isomerization. Tunneling substituent constants (σ(t)) for this conformational isomerization were derived experimentally and computationally.     

Synthesis and Molecular Structures of Tetrasilyl Ethers of Calix[4]arenes

The tetrasilyl ethers calix[4]areneOSiMe₂R (R = Me, H, vinyl, allyl) were prepared by salt elimination; the calix[4]arene was deprotonated with sodium hydride and subsequently reacted with chlorosilanes ClSiMe₂R. In general, DMF was chosen as solvent in order to steer the reactions in terms of a preference for the cone‐conformation of the products. In the case of calix[4]areneOSiMe₃ both, partial‐cone‐ and cone‐conformers, were synthesised. All products were characterised by NMR (¹H, ¹³C, ²⁹Si) spectroscopy, mass spectrometry and single‐crystal X‐ray diffraction.     

Syntheses, structures and intermolecular interactions of tetraorganoammonium, -phosphonium and -stibonium dimethyl- and diphenyltetrahaloantimonates

The syntheses and spectroscopic (NMR, MS) investigations of the antimonates [Ph₄P]⁺[Me₂SbCl₄]⁻ (1), [Me₄Sb]⁺[Me₂SbCl₄]⁻ (2), [Et₄N]⁺[Ph₂SbCl₄]⁻ (3), [Bu₄N]⁺[Ph₂SbCl₄]⁻ (4), [Me₄Sb]⁺[Ph₂SbCl₄]⁻ (5), [Et₃MeSb]⁺[Ph₂SbCl₄]⁻ (6), [Et₄N]⁺[Ph₂SbF₄]⁻ (7) and [Et₄N]⁺[Ph₂SbBr₄]⁻ (8) are reported. Halogen scrambling reactions of Et₄NBr or Ph₄EBr (E = P, Sb) with R₂SbCl₃ (R = Me, Ph) produce mixtures of compounds from which crystals of [Et₄N]⁺[Ph₂SbBr_1.24Cl_2.76]⁻ (9), [Et₄N]⁺[Ph₂SbBr_2.92Cl_1.08]⁻ (10) or [Ph₄Sb]⁺[Me₂SbCl₄]⁻ (11) were isolated. The crystal and molecular structures of 1 and 3-11 are reported.     

Non-adiabatic dynamics of pyrrole: Dependence of deactivation mechanisms on the excitation energy

Non-adiabatic dynamics simulations were performed for pyrrole at time-dependent density functional theory level using the trajectory surface hopping approach. Initial conditions were prepared based on the UV-absorption spectrum so as to simulate monochromatic absorption in three distinct spectral regions. The results showed predominance of the NH-stretch mechanism for excited-state relaxation. With increasing initial energy, however, other mechanisms are activated as well, even though they still occurred for a minor fraction of the trajectories. Dynamics starting at the origin of the absorption spectrum exhibited internal conversion to the ground state with a time constant of 20 fs. In contrast, dynamics starting at higher energies gave rise to much longer time constants for internal conversion near 200 fs.