The effect of polymorphism on the structural, dynamic and dielectric properties of plastic crystal water: A molecular dynamics simulation perspective

We have employed molecular dynamics simulations based on the TIP4P/2005 water model to investigate the local structural, dynamical, and dielectric properties of the two recently reported body-centered-cubic and face-centered-cubic plastic crystal phases of water. Our results reveal significant differences in the local orientational structure and rotational dynamics of water molecules for the two polymorphs. The probability distributions of trigonal and tetrahedral order parameters exhibit a multi-modal structure, implying the existence of significant local orientational heterogeneities, particularly in the face-centered-cubic phase. The calculated hydrogen bond statistics and dynamics provide further indications of the existence of a strongly heterogeneous and rapidly interconverting local orientational structural network in both polymorphs. We have observed a hindered molecular rotation, much more pronounced in the body-centered-cubic phase, which is reflected by the decay of the fourth-order Legendre reorientational correlation functions and angular Van Hove functions. Molecular rotation, however, is additionally hindered in the high-pressure liquid compared to the plastic crystal phase. The results obtained also reveal significant differences in the dielectric properties of the polymorphs due to the different dipolar orientational correlation characterizing each phase

Structural and dipolar fluctuations in liquid water: a Car–Parrinello molecular dynamics study

A Car–Parrinello molecular dynamics simulation was performed to investigate the local tetrahedral order, molecular dipole fluctuations and their interrelation with hydrogen bonding in liquid water. Water molecules were classified in three types, exhibiting low, intermediate and high tetrahedral order. Transitions from low to high tetrahedrally ordered structures take place only through transitions to the intermediate state. The molecular dipole moments depend strongly on the tetrahedral order and hydrogen bonding. The average dipole moment of water molecules with a strong tetrahedral order around them comes in excellent agreement with previous estimations of the dipole moment of ice Ih molecules.Postprint (author's final draft

Li+ solvation in pure, binary and ternary mixtures of organic carbonate electrolytes

Classical molecular dynamics (MD) simulations and quantum chemical density functional theory (DFT) calculations have been employed in the present study to investigate the solvation of lithium cations in pure organic carbonate solvents (ethylene carbonate (EC), propylene carbonate (PC) and dimethyl carbonate (DMC)) and their binary (EC-DMC, 1:1 molar composition) and ternary (EC-DMC-PC, 1:1:3 molar composition) mixtures. The results obtained by both methods indicate that the formation of complexes with four solvent molecules around Li+, exhibiting a strong local tetrahedral order, is the most favorable. However, the molecular dynamics simulations have revealed the existence of significant structural heterogeneities, extending up to a length scale which is more than five times the size of the first coordination shell radius. Due to these significant structural fluctuations in the bulk liquid phases, the use of larger size clusters in DFT calculations has been suggested. Contrary to the findings of the DFT calculations on small isolated clusters, the MD simulations have predicted a preference of Li+ to interact with DMC molecules within its first solvation shell and not with the highly polar EC and PC ones, in the binary and ternary mixtures. This behavior has been attributed to the local tetrahedral packing of the solvent molecules in the first solvation shell of Li+, which causes a cancellation of the individual molecular dipole vectors, and this effect seems to be more important in the cases where molecules of the same type are present. Due to these cancellation effects, the total dipole in the first solvation shell of Li+ increases when the local mole fraction of DMC is high

Solvation structure and dynamics of the dimethylammonium cation diluted in liquid water: a molecular dynamics approach

Classical molecular dynamics simulation techniques were employed to investigate the local solvation structure and related dynamics of the dimethylammonium cation diluted in liquid water at ambient conditions. The translational and orientational order around the dimethylammonium cation was investigated in terms of the corresponding radial and angular distribution functions. The results obtained revealed that the first solvation shell of the dimethylammonium consists mainly of two and, less frequently, three water molecules. The two nearest water neighbors form hydrogen bonds with the ammonium hydrogen atoms of the cation, whereas the third neighbor interacts with the methyl hydrogen atoms as well. The distribution of the trigonal order parameter exhibits a bimodal behavior, signifying the existence of local orientational heterogeneities in the solvation shell of the dimethylammonium cation. The calculated continuous and intermittent residence and hydrogen bond lifetimes for the cation–water pairs have also been found to be longer in comparison with the water–water ones. The very similar self-diffusion coefficients of the dimethylammonium cation and the water molecules in the bulk dilute solution indicate that the translational motions of the cation are mainly controlled by the translational mobility of the surrounding water molecules.Postprint (published version

Fingerprints of the crossing of the Frenkel and melting line on the properties of high-pressure supercritical water

Using molecular dynamics simulations in combination with the two-phase thermodynamic model, we reveal novel characteristic fingerprints of the crossing of the Frenkel and melting line on the properties of high-pressure water at a near-critical temperature (1.03Tc). The crossing of the Frenkel line at about 1.17 GPa is characterized by a crossover in the rotational and translational entropy ratio Srot/Strans, indicating a change in the coupling between translational and rotational motions which is also reflected in the shape of the rotational density of states. The observed isosbestic points in the translational and rotational density of states are also blue-shifted at density and pressure conditions higher than the ones corresponding to the Frenkel line. The first-order phase transition from a rigid liquid to a face-centered cubic plastic crystal phase at about 8.5 GPa is reflected in the discontinuous changes in the translational and rotational entropy, particularly in the significant increase of the ratio Srot/Strans. A noticeable discontinuous increase of the dielectric constant has also been revealed when crossing this melting line, which is attributed to the different arrangement of the water molecules in the plastic crystal phase. The reorientational dynamics in the plastic crystal phase is faster in comparison with the “rigid” liquid-like phase, but it remains unchanged upon a further pressure increase in the range of 8.5–11 GPa.Postprint (author's final draft

On the different faces of the supercritical phase of water at a near-critical temperature: pressure-induced structural transitions ranging from a gaslike fluid to a plastic crystal polymorph

The present study reports a systematic analysis of a wide variety of structural, thermodynamic, and dynamic properties of supercritical water along the near-critical isotherm of T = 1.03Tc and up to extreme pressures, using molecular dynamics and Monte Carlo simulations. The methodology employed provides solid evidence about the existence of a structural transition from a liquidlike fluid to a compressed, tightly packed liquid, in the density and pressure region around 3.4¿c and 1.17 GPa, introducing an alternative approach to locate the crossing of the Frenkel line. Around 8.5 GPa another transition to a face-centered-cubic plastic crystal polymorph with density 5.178¿c is also observed, further confirmed by Gibbs free energy calculations using the two-phase thermodynamic model. The isobaric heat capacity maximum, closely related to the crossing of the Widom line, has also been observed around 0.8¿c, where the local density augmentation is also maximized. Another structural transition has been observed at 0.2¿c, related to the transformation of the fluid to a dilute gas at lower densities. These findings indicate that a near-critical isotherm can be divided into different domains where supercritical water exhibits distinct behavior, ranging from a gaslike one to a plastic crystal one.Postprint (author's final draft

Hydrogen bonding and related properties in liquid water: a Car-Parrinello molecular dynamics simulation study

The local hydrogen-bonding structure and dynamics of liquid water have been investigated using the Car-Parrinello molecular dynamics simulation technique. The radial distribution functions and coordination numbers around water molecules have been found to be strongly dependent on the number of hydrogen bonds formed by each molecule, revealing also the existence of local structural heterogeneities in the structure of the liquid. The results obtained have also revealed the strong effect of the local hydrogen-bonding network on the local tetrahedral structure and entropy. The investigation of the dynamics of the local hydrogen-bonding network in liquid water has shown that this network is very labile, and the hydrogen bonds break and reform very rapidly. Nevertheless, it has been found that the hydrogen-bonding states associated with the formation of four hydrogen bonds by a water molecule exhibit the largest survival probability and corresponding lifetime. The reorientational motions of water molecules have also been found to be strongly dependent on their initial hydrogen-bonding state. Finally, the dependence of the librational and vibrational modes of water molecules on the local hydrogen-bonding network has been carefully examined, revealing a significant effect upon the libration and bond-stretching peak frequencies. The calculated low frequency peaks come in agreement with previously reported interpretations of the experimental low-frequency Raman spectrum of liquid water.Peer ReviewedPostprint (author’s final draft

Local structural fluctuations, hydrogen bonding and structural transitions in supercritical water

The contribution of hydrogen bonding interactions to the formation of local density inhomogeneities in supercritical water at near-critical conditions has been extensively studied by means of molecular dynamics simulations. The results obtained have revealed the strong effect of water molecules forming one and two hydrogen bonds on the determination of the local density augmentation in the fluid. The local structural order has also been studied in terms of the trigonal and tetrahedral order parameters, revealing the correlation between local orientational order and hydrogen bonding. The dynamics of the structural order parameters exhibit similarities with local density ones. The local structural analysis performed in terms of nearest neighbors around the individual molecules provides additional significant evidence about the existence of a liquid-like to gas-like structural transition in supercritical water at the density range close to 0.2 ¿c, further supporting previous suggestions based on the interpretation of experimental thermodynamic data.Postprint (author's final draft

Hyaluronic acid and hyaluronidase as possible novel urine biomarkers for the diagnosis of prostate cancer

PCa is the second most commonly diagnosed cancer and the sixth cause of cancer death in men. In addition, PCa in Europe is the second most common cause of death in men The biological behavior of prostate cancer is complex. The mechanisms that control the prostate cell and the characteristics that determine its course have not yet been fully understood. It is of utmost importance to understand the biology of prostate cancer, with the ultimate goal of discovering new diagnostic methods and therapeutic strategies for treating the disease. Particularly in prostate cancer, both the slow progression of the disease and the improvement of our therapeutic options contribute to the successful treatment of at least the localized disease. Most of this increase can be attributed to the widespread use of PSA in Western countries, which can detect both invasive cancers and non-lethal latent patients who, without the use of PSA, would remain asymptomatic and undiagnosed over the course of their lives of the patient. However, PSA, although the best biomarker available for PCA, is a marker specific to the prostate but not for a disease, often creating diagnostic dilemmas. The search for new biomarkers for prostate cancer is imperative. Based on a previous proteomic study of the U. U. Uro group performed on prostate tissue and based on bibliographic data, a protein was selected to be studied in the urine of the participants. 118 urine specimens of high-risk individuals were collected for Pca based on either the dascal or elevated PSA or the abnormal change in PSA time. RACE analysis for HAase, HAase / Cr, HA and HA / Cr showed that all markers had a significant prostate cancer predictive capacity with an AUC of 0.69 , 0.65 and 0.67 respectively. The optimal cleavage point for HAase was 183.71 with 70% sensitivity and 55.2% specificity. Also, the optimal cut-off for HA was 50.13 with 65% sensitivity and 53.9% specificity. In addition, an optimal cleavage point of 155.94 for HAase / Cr was found and equal to 42.48 for HA / Cr. The predictive capacity of HAase did not differ significantly from the predictive capacity of HA (p = 0.507).Ο PCa αποτελεί τον δεφτερο πιο ςυχνά διαγνωςμζνο καρκίνο και τθν ζκτθ αιτίακανάτου από καρκίνο ςτουσ άντρεσ.Επιπλζον ο PCa ςτθν Ευρϊπθ αποτελεί τθν δεφτερθ πιο κοινι αιτία κανάτουςτουσ άντρεσΘ βιολογικι ςυμπεριωορά του καρκίνου του προςτάτθ είναι πολφπλοκθ. Οιμθχανιςμοί που ελζγχουν το προςτατικό κφτταρο και τα χαρακτθριςτικά πουκακορίηουν τθν πορεία του δεν ζχουν γίνει ακόμα πλιρωσ κατανοθτά.Λδαίτερθ ςθμαςία ζχει να κατανοιςουμε τθ βιολογία του καρκίνου τουπροςτάτθ, με τελικό ςτόχο τθν ανακάλυψθ νζων διαγνωςτικϊν μεκόδων καικεραπευτικϊν ςτρατθγικϊν για τθν αντιμετϊπιςθ τθσ νόςου. Λδιαίτερα ςτον καρκίνοτου προςτάτθ που τόςο θ αργι εξζλιξθ τθσ νόςου, όςο και θ βελτίωςθ τωνκεραπευτικϊν μασ επιλογϊν,ςυμβάλουν ςτθν επιτυχι αντιμετϊπιςθ τουλάχιςτοντθσ εντοπιςμζνθσ νόςου.Το μεγαλφτερο ποςοςτό αυτισ τθσ αφξθςθσ μπορεί να αποδοκεί ςτθνεκτεταμζνθ χριςθ του PSA ςτισ δυτικζσ χϊρεσ, το οποίο μπορεί να εντοπίςει τόςοτουσ διθκθτικοφσ καρκίνουσ, όςο και τουσ λανκάνοντεσ μθ κανατθωόρουσ πουχωρίσ τθν χριςθ του PSA κα ζμεναν αςυμπτωματικοί και αδιάγνωςτοι κατά τθνδιάρκεια τθσ ηωισ του αςκενοφσ.Ραρόλα αυτά το PSA αν και ο καλφτεροσ βιοδείκτθσ που υπάρχει για τον Pca,αποτελεί ζναν δείκτθ ειδικό για τον προςτάτθ αλλά όχι για κάποια νόςοτου,δθμιουργϊντασ πολλζσ ωορζσ διαγνωςτικά διλιμματα. Θ αναηιτθςθ νζωνβιοδεικτϊν για τον καρκίνο του προςτάτθ αποτελεί επιτακτικι ανάγκθ. Στθριηόμενοιςε προθγοφμενθ πρωτεομικι μελζτθ τθσ Ά Ρανεπιςτθμιακισ Ουρολογικισ ομάδασπου ζγινε ςε προςτατικό ιςτό και με βάςθ τα βιβλιογραωικά δεδομζνα επιλζχκθκεμια πρωτεϊνθ για να μελετθκεί ςτα οφρα των ςυμμετζχοντων. Συλλζχκθκαν 118δείγματα οφρων ατόμων υψθλοφ κινδφνου για Pca με βάςθ είτε τθν δακτυλικι, είτετο αυξθμζνο PSA είτε τθν μθ ωυςιολογικι μεταβολι ςτο χρόνο του PSA.Θ ανάλυςθ ROC για τθν Haase, HAase / Cr, HA και HA / Cr ζδειξε ότι όλοι οιδείκτεσ είχαν ςθμαντικι προγνωςτικι ικανότθτα για καρκίνο του προςτάτθ με AUC ίςο με 0.69, 0,65 και 0,67 αντίςτοιχα. Το βζλτιςτο ςθμείο αποκοπισ για ΘΑάςθ ιταν183,71 με 70% ευαιςκθςία και 55,2% εξειδίκευςθ. Επίςθσ, το βζλτιςτο ςθμείοαποκοπισ για ΘΑ ιταν 50,13 με 65% ευαιςκθςία και 53,9% εξειδίκευςθ. Επιπλζον,βρζκθκε ζνα βζλτιςτο ςθμείο αποκοπισ ίςο με 155,94 για τθν HAase / Cr και ίςο με42,48 για το HA / Cr. Θ προβλεπτικι ικανότθτα τθσ ΘΑάςθσ δεν διζωερε ςθμαντικάαπό τθν προβλεπτικι ικανότθτα του ΘΑ (ρ = 0,507)

Local density augmentation and dynamic properties of hydrogen-and non-hydrogen-bonded supercritical fluids: A molecular dynamics study

The local density inhomogeneities in neat supercritical fluids were investigated via canonical molecular dynamics simulations. The selected systems under investigation were the polar and hydrogen-bonded fluid methanol as well as the quadrupolar non-hydrogen-bonded carbon dioxide one. Effective local densities, local density augmentation, and enhancement factors were calculated at state points along an isotherm close to the critical temperature of each system (T-r=1.03). The results obtained reveal strong influence of the polarity and hydrogen bonding upon the intensity of the local density augmentation. It is found that this effect is sufficiently larger in the case of the polar and associated methanol in comparison to those predicted for carbon dioxide. For both fluids the local density augmentation values are maximized in the bulk density region near 0.7 rho(c), a result that is in agreement with experiment. In addition, the local density dynamics of each fluid were investigated in terms of the appropriate time correlation functions. The behavior of these functions reveals that the bulk density dependence of the local density reorganization times is very sensitive to the specific intermolecular interactions and to the size of the local region. Also, the estimated local density reorganization time as a function of bulk density of each fluid was further analyzed and successfully related to two different time-scale relaxation mechanisms. Finally, the results obtained indicate a possible relationship between the single-molecule reorientational dynamics and the local density reorganization ones. (c) 2007 American Institute of Physics