Toward Accurate Quantum Chemical Methods for Molecules of Increasing Dimension: The New Family of Pisa Composite Schemes.

The new versions of the Pisa composite scheme introduced in the present paper are based on the careful selection of different quantum chemical models for energies, geometries, and vibrational frequencies, with the aim of maximizing the accuracy of the overall description while retaining a reasonable cost for all the steps. In particular, the computation of accurate electronic energies has been further improved introducing more reliable complete basis set extrapolations and estimation of core-valence correlation, together with improved basis sets for third-row atoms. Furthermore, the reduced-cost frozen natural orbital (FNO) model has been introduced and validated for large molecules. Accurate molecular structures can be obtained avoiding complete basis set extrapolation and evaluating core-valence correlation at the MP2 level. Unfortunately, analytical gradients are not available for the FNO version of the model. Therefore, for large molecules, an accurate reduced-cost alternative is offered by evaluation of valence contributions with a double-hybrid functional in conjunction with the same MP2 contribution for core-valence correlation or by means of a one-parameter approximation. The same double-hybrid functional and basis set are employed to evaluate zero-point energies and partition functions. After the validation of the new models for small systems, a panel of molecular bricks of life has been used to analyze their performances for problems of current fundamental or technological interest. The fully black-box implementation of the computational workflow paves the way toward the accurate yet not prohibitively expensive study of medium- to large-sized molecules also by experimentally oriented researchers.

Accurate Structures and Rotational Constants of Steroid Hormones at DFT Cost: Androsterone, Testosterone, Estrone, ß-Estradiol, and Estriol.

A comprehensive analysis of the structural, conformational, and spectroscopic properties in the gas phase has been performed for five prototypical steroid hormones, namely, androsterone, testosterone, estrone, ß-estradiol, and estriol. The revDSD-PBEP86 double-hybrid functional in conjunction with the D3BJ empirical dispersion and a suitable triple-ζ basis set provides accurate conformational energies and equilibrium molecular structures, with the latter being further improved by proper account of core-valence correlation. Average deviations within 0.1% between computed and experimental ground state rotational constants are reached when adding to those equilibrium values vibrational corrections obtained at the cost of standard harmonic frequencies thanks to the use of a new computational tool. Together with the intrinsic interest of the studied hormones, the accuracy of the results obtained at DFT cost for molecules containing about 50 atoms paves the way toward the accurate investigations of other flexible bricks of life.

Toward an Accurate Black-Box Tool for the Kinetics of Gas-Phase Reactions Involving Barrier-less Elementary Steps.

An enhanced computational protocol has been devised for the accurate characterization of gas-phase barrier-less reactions in the framework of the reaction-path (RP) and variable reaction coordinate variational transition-state theory. In particular, the synergistic combination of density functional theory and Monte Carlo sampling to optimize reactive fluxes led to a reliable yet effective computational workflow. A black-box strategy has been developed for selecting the most suited density functional with reference to a high-level one-dimensional reference potential. At the same time, different descriptions of hindered rotations are automatically selected, depending on the corresponding harmonic frequencies along the RP. The performance of the new tool is investigated by means of two prototypical reactions involving different degrees of static and dynamic correlation, namely, H2S + Cl and CH3 + CH3. The remarkable agreement of the computed kinetic parameters with the available experimental data confirms the accuracy and robustness of the proposed approach. Together with their intrinsic interest, these results also pave the way toward systematic investigations of gas-phase reactions involving barrier-less elementary steps by a reliable, user-friendly tool, which can be confidently used also by nonspecialists.

Accurate Thermochemical and Kinetic Parameters at Affordable Cost by Means of the Pisa Composite Scheme (PCS).

A new strategy for the computation at an affordable cost of geometrical structures, thermochemical parameters, and rate constants for medium-sized molecules in the gas phase is proposed. The most distinctive features of the new model are the systematic use of cc-pVnZ-F12 basis sets, the addition of MP2 core-valence correlation in geometry optimizations by a double-hybrid functional, the separate extrapolation of MP2 and post-MP2 contributions, and the inclusion of anharmonic contributions in zero-point energies and thermodynamic functions. A thorough benchmark based on a wide range of prototypical systems shows that the new scheme outperforms the most well-known model chemistries without the need for any empirical parameter. Additional tests show that the computed zero-point energies and thermal contributions can be confidently used for obtaining accurate thermochemical and kinetic parameters. Since the whole computational workflow is translated in a black-box procedure, which can be followed with standard electronic structure codes, the way is paved for the accurate yet not prohibitively expensive study of medium- to large-sized molecules also by nonspecialists.

DFT Meets Wave-Function Methods for Accurate Structures and Rotational Constants of Histidine, Tryptophan, and Proline.

A new computational strategy has been applied to the conformational and spectroscopic properties in the gas phase of amino acids with very distinctive features, ranging from different tautomeric forms (histidine) to ring puckering (proline), and heteroaromatic structures with non-equivalent rings (tryptophan). The integration of modern double-hybrid functionals and wave-function composite methods has allowed us to obtain accurate results for a large panel of conformers with reasonable computer times. The remarkable agreement between computations and microwave experiments allows an unbiased interpretation of the latter in terms of stereoelectronic effects.

Accurate Structures and Spectroscopic Parameters of Guanine Tautomers in the Gas Phase by the Pisa Conventional and Explicitly Correlated Composite Schemes (PCS and PCS-F12).

A general strategy for the accurate computation of structural and spectroscopic properties of biomolecule building blocks in the gas phase is proposed and validated for tautomeric equilibria. The main features of the new model are the inclusion of core-valence correlation in geometry optimizations by a double hybrid functional and the systematic use of wave-function composite methods in conjunction with cc-pVnZ-F12 basis sets with separate extrapolation of MP2 and post-MP2 contributions. The resulting Pisa composite scheme employing conventional (PCS) or explicitly correlated (PCS-F12) approaches is applied to the challenging problem of guanine tautomers in the gas phase. The results are in remarkable agreement with the experimental structures, relative stabilities, and spectroscopic signatures of different tautomers. The accuracy of the results obtained at reasonable cost by means of black-box parameter-free approaches paves the way toward systematic investigations of other molecular bricks of life also by non-specialists.

Toward Accurate yet Effective Computations of Rotational Spectroscopy Parameters for Biomolecule Building Blocks.

The interplay of high-resolution rotational spectroscopy and quantum-chemical computations plays an invaluable role in the investigation of biomolecule building blocks in the gas phase. However, quantum-chemical methods suffer from unfavorable scaling with the dimension of the system under consideration. While a complete characterization of flexible systems requires an elaborate multi-step strategy, in this work, we demonstrate that the accuracy obtained by quantum-chemical composite approaches in the prediction of rotational spectroscopy parameters can be approached by a model based on density functional theory. Glycine and serine are employed to demonstrate that, despite its limited cost, such a model is able to predict rotational constants with an accuracy of 0.3% or better, thus paving the way toward the accurate characterization of larger flexible building blocks of biomolecules.

Absorption Spectra of Flexible Fluorescent Probes by a Combined Computational Approach: Molecular Dynamics Simulations and Time-Dependent Density Functional Theory.

A detailed understanding and interpretation of absorption spectra of molecular systems, especially in condensed phases, requires computational models that allow their structural and electronic features to be connected to the observed macroscopic spectra. This work is focused on modeling the electronic absorption spectrum of a fluorescent probe, namely, the 9-(4-((bis(2-((2-(ethylthio)ethyl)thio)ethyl)amino)methyl)phenyl)-6-(pyrrolidin-1-yl)-3H-xanthen-3-one molecule, depicted by a combined classical-quantum chemical approach. Particularly, first classical molecular dynamics (MD) has been used to explore the configurational space, and next, the absorption spectrum has been reconstructed by averaging the results of time-dependent density functional theory (TD-DFT) calculations performed on equispaced molecular conformations extracted from MD to properly sample the configurational space explored at finite temperature. To verify the effect of molecular conformation on the spectral profile, the generated electronic absorption spectra were compared with those obtained considering a single structure corresponding to the optimized one, an approach also referred to as static. This comparison allows one to highlight a sizable though small shift between the maxima of the corresponding reconstructed absorption spectra, highlighting the importance of conformational sampling in the case of this rather flexible molecule. Four different exchange and correlation functionals (PBE, BLYP, PBE0, B3LYP) were considered to compute vertical transition via TD-DFT calculations. From the results obtained in gas and in condensed, here solution, phases, it appears that the magnitude of the shift is actually more affected by the phase in which the system is found than by the functional used. This fact underlines the central importance of conformational mobility, that is flexibility, of this molecule. From a more quantitative point of view, a comparison with available experimental data shows that hybrid functionals, such as PBE0 and B3LYP, enable one to faithfully reproduce the observed absorption maxima.

Fabrication and Plasma Modification of Nanofibrous Tissue Engineering Scaffolds.

This paper provides a comprehensive overview of nanofibrous structures for tissue engineering purposes and the role of non-thermal plasma technology (NTP) within this field. Special attention is first given to nanofiber fabrication strategies, including thermally-induced phase separation, molecular self-assembly, and electrospinning, highlighting their strengths, weaknesses, and potentials. The review then continues to discuss the biodegradable polyesters typically employed for nanofiber fabrication, while the primary focus lies on their applicability and limitations. From thereon, the reader is introduced to the concept of NTP and its application in plasma-assisted surface modification of nanofibrous scaffolds. The final part of the review discusses the available literature on NTP-modified nanofibers looking at the impact of plasma activation and polymerization treatments on nanofiber wettability, surface chemistry, cell adhesion/proliferation and protein grafting. As such, this review provides a complete introduction into NTP-modified nanofibers, while aiming to address the current unexplored potentials left within the field.

Radicals and Ions Formed in Plasma-Treated Organic Solvents: A Mechanistic Investigation to Rationalize the Enhancement of Electrospinnability of Polycaprolactone.

This paper reports and discusses the beneficial effects on the quality of electrospun polycaprolactone nanofibers brought about by pretreatment of the solvent with non-thermal plasma. Chloroform/dimethylformamide 9:1 (CHCl3:DMF 9:1) and pure chloroform were pretreated by a few minute exposure to the plasma generated by an atmospheric pressure plasma jet (APPJ). Interestingly, when pure chloroform was used, the advantages of plasma pretreatment of the solvent were way less pronounced than found with the CHCl3:DMF 9:1 mixture. The chemical modifications induced by the plasma in the solvents were investigated by means of complementary analytical techniques. GC-MS revealed the formation of solvent-derived volatile products, notably tetrachloroethylene (C2Cl4), 1,1,2,2-tetrachloroethane (C2H2Cl4), pentachloroethane (C2HCl5), hexachloroethane (C2Cl6) and, in the case of the mixed solvent, also N-methylformamide (C2H5NO). The chlorinated volatile products are attributed to reactions of ·Cl and Cl-containing methyl radicals and carbenes formed in the plasma-treated solvents. ·Cl and ·CCl3 radicals were detected and identified by EPR spectroscopy analyses. Ion chromatography revealed the presence of Cl-, NO 3 - , and HCOO- (the latter only in the presence of DMF) in the plasma-treated solvents, thus accounting for the observed increased conductivity and acidification of the solvent after plasma treatment. Mechanisms for the formation of these solvent derived products induced by plasma are proposed and discussed. The major role of radicals and ions in the plasma chemistry of chloroform and of the chloroform/dimethylformamide mixture is highlighted. The results provide insight into the interaction of plasma with organic solvents, a field so far little explored but holding promise for interesting applications.

Fabrication of PEOT/PBT Nanofibers by Atmospheric Pressure Plasma Jet Treatment of Electrospinning Solutions for Tissue Engineering.

This study focuses on the enhanced electrospinning of 300-Polyethylene oxide-polyethylene oxide terephthalate/polybutylene terephthalate (PEOT/PBT). An atmospheric pressure plasma jet for liquid treatment is applied to a solution with 9 w/v% PEOT/PBT dissolved in either chloroform (CHCl3 ), CHCl3  + N,N-dimethylformamide (DMF), CHCl3  + methanol (MeOH), or CHCl3  + hexafluoroisopropanol (HFIP). For all conditions, the plasma-treated samples present better-quality fibers: less or no-beads and uniform fiber diameter distribution. Except for CHCl3  + DMF, no significant changes to the material bulk are detected, as shown with size exclusion chromatography (SEC). X-ray photoelectron spectroscopy (XPS) spectra performed on nanofibers record an increase in C-C bonds for the CHCl3  + DMF combination upon plasma modification, while a shift and slight increase in oxygen-containing bonds is found for the CHCl3  + HFIP and CHCl3  + MeOH mixtures. MTT assay shows no-cytotoxic effects for CHCl3  + DMF, while a better cellular adhesion is found on nanofibers from CHCl3  + MeOH and CHCl3  + HFIP. Among the examined additives, MeOH is preferable as it produces beadless electrospun nanofibers with an average diameter of 290 ± 100 nm without causing significant changes to the final nanofiber surface properties.

Atmospheric Pressure Plasma Jet Treatment of Poly-ε-caprolactone Polymer Solutions To Improve Electrospinning.

An atmospheric pressure plasma jet (APPJ) specifically designed for liquid treatment has been used in this work to improve the electrospinnability of a 5 w/v % solution of poly-ε-caprolactone (PCL) in a mixture of chloroform and N,N-dimethylformamide. Untreated PCL solutions were found to result in nonuniform fibers containing a large number of beads, whereas plasma-treated solutions (exposure time of 2-5 min) enabled the generation of beadless, uniform nanofibers with an average diameter of 450 nm. This enhanced electrospinnability was found to be mainly due to the highly increased conductivity of the plasma-modified PCL solutions. Consequently, more stretching of the polymer jet occurred during electrospinning, leading to the generation of bead-free fibers. Plasma treatment also results in an increased viscosity and decreased pH values. To explain these observed changes, optical emission spectroscopy (OES) has been used to examine the excited species present in the APPJ in contact with the PCL solution. This study revealed that the peaks attributed to H, CH, CH2, and C2 species could be responsible for the degradation of solvent molecules and/or PCL structures during the plasma treatment. Size exclusion chromatography and X-ray photoelectron spectroscopy results showed that the molecular weight and the chemical composition of PCL were not significantly affected by the APPJ treatment. Plasma exposure mainly results in the degradation of the solvent molecules instead of modifying the PCL macromolecules, preserving the original polymer as much as possible. A hypothesis for the observed macroscopic changes in viscosity and pH values could be the generation of new chemical species such as HCl and/or HNO3. These species are characterized by their high conductivity, low pH values, and strong polarity and could enhance the solvent quality for PCL, leading to the expansion of the polymer coil, which could in turn explain the observed enhanced viscosity after plasma modification.

Obesity is an independent risk factor for pre-transplant portal vein thrombosis in liver recipients.

BACKGROUND: Portal vein thrombosis is a frequent complication in end-stage cirrhosis with a considerable peri-operative risk for liver transplant candidates. We aimed to characterize the pre-transplant portal vein thrombosis in a cohort of liver transplant recipients, and to identify independent risk factors for this complication. METHODS: 380 consecutive primary orthotopic liver transplants were performed in the Digestive Surgery Department of "12 de Octubre" Hospital (Madrid, Spain), between January 2001 and December 2006. The main risk factors considered were smoking, obesity, metabolic disorders, previous immobility, surgery or trauma, nephrotic syndrome, associated tumor, inflammatory disease, neoplasm myeloprolipherative. Furthermore we have reported genetic thrombophilia results for 271 recipients. RESULTS: Sixty-two (16.3%) patients developed pre-transplant portal vein thrombosis and its presence had no impact in the overall survival of liver recipients. Obesity was the only independent risk factor for pre-transplant portal vein thrombosis. CONCLUSION: We recommend close control of cardiovascular factors in patients with liver cirrhosis in order to avoid associated thrombosis.

Long-term follow-up of donor chimerism and tolerance after human liver transplantation.

We aimed to quantify peripheral donor chimerism (DC) and to analyze its association with graft and recipient outcome. Forty-two liver transplant recipients and their respective donors were studied, providing a total of 148 posttransplantation serum samples. DC was assessed with real-time quantitative polymerase chain reaction (qPCR) to detect polymorphic markers. DC did not decrease with time post-transplantation and was higher in child recipients versus adults and in recipients of deceased donor liver transplants versus recipients of live donor liver transplants. Higher levels of DC were detected in Rh-positive blood group donors, in O blood group recipients versus A blood group recipients, and in recipients with hepatitis C virus versus recipients with alcoholic cirrhosis. High DC was associated with patients with organ damage due to recurrent disease and rejection. Stable, high levels of DC, in the absence of other major clinical events, may thus be a marker of transplantation tolerance, and this knowledge may help to tailor immunosuppressive treatment. In conclusion, qPCR is a useful technique for DC follow-up in liver transplantation, although the evolution of DC levels should be analyzed in accordance with the clinical outcome of the patient.

High resolution melting analysis for JAK2 Exon 14 and Exon 12 mutations: a diagnostic tool for myeloproliferative neoplasms.

JAK2 mutations are important criteria for the diagnosis of Philadelphia chromosome-negative myeloproliferative neoplasms. We aimed to assess JAK2 exon 14 and exon 12 mutations by high-resolution melting (HRM) analysis, which allows variation screening. The exon 14 analysis included 163 patients with polycythemia vera, secondary erythrocytoses, essential thrombocythemia, or secondary thrombocytoses, and 126 healthy subjects. The study of exon 12 included 40 JAK2 V617F-negative patients (nine of which had polycythemia vera, and 31 with splanchnic vein thrombosis) and 30 healthy subjects. HRM analyses of JAK2 exons 14 and 12 gave analytical sensitivities near 1% and both intra- and interday coefficients of variation of less than 1%. For HRM analysis of JAK2 exon 14 in polycythemia vera and essential thrombocythemia, clinical sensitivities were 93.5% and 67.9%, clinical specificities were 98.8% and 97.0%, positive predictive values were 93.5% and 79.2%, and negative predictive values were 98.8% and 94.6, respectively. Correlations were observed between the results from HRM and three commonly used analytical methods. The JAK2 exon 12 HRM results agreed completely with those from sequencing analysis, and the three mutations in exon 12 were detected by both methods. Hence, HRM analysis of exons 14 and 12 in JAK2 shows better diagnostic values than three other routinely used methods against which it was compared. In addition, HRM analysis has the advantage of detecting unknown mutations.

Validity test study of JAK2 V617F and allele burden quantification in the diagnosis of myeloproliferative diseases.

Several sensitive methods for the detection of JAK2 V617F mutation have been published recently, most of them based on Real Time polymerase chain reaction (PCR). However, only some of them have performed studies of diagnostic validity. This study compares three methods based on Real Time PCR to detect JAK2 V617F mutation: two based on hybridization probes (HP) and peptide nucleic acid probe (PNA) and a third employing allele specific oligonucleotide primers for JAK2 V617F quantification. One hundred forty-nine healthy subjects, 61 essential thrombocythemia (ET), 32 polycythemia vera (PV), 38 secondary thrombocytoses, and 35 secondary erythrocytoses were included. Validity test study for JAK2 617 HP PCR in PV Sensitivity (Se) was 88% and in Specificity (Sp), 100%. In ET, Se was 57% and Sp, 100%. For JAK2 617 PNA PCR in PV, Se was 94% and Sp, 97.8%. In ET, Se was 70% and Sp, 95.7%. In JAK2 V671F allelo-specific-oligonucleotide (ASO) quantitative PCR (qPCR), cutoff point of 1% was established by receiving operating characteristic (ROC) curves. In PV, Se was 93.8% and Sp, 98.5%. In ET, Se was 80% and Sp, 95.9%. Two percent of the healthy subjects were positive by JAK2 617 PNA PCR and 2% by JAK2 617 ASO qPCR. JAK2 V617F mutation was detected in healthy subjects by cloning and sequencing. JAK2 617 HP is an adequate test in differential diagnosis for both erythrocytosis and thrombocytosis. When JAK2 V617F allele burden is low, JAK2 617 ASO qPCR should be performed. Simultaneous determination of JAK2 V617F and PRV-1 overexpression does not improve the diagnostic value of JAK2 V617F tests in MPD.