scholarly journals Monitoring of the Pre-Equilibrium Step in the Alkyne Hydration Reaction Catalyzed by Au(III) Complexes: A Computational Study Based on Experimental Evidences

Molecules ◽  
2021 ◽  
Vol 26 (9) ◽  
pp. 2445
Author(s):  
Flavio Sabatelli ◽  
Jacopo Segato ◽  
Leonardo Belpassi ◽  
Alessandro Del Zotto ◽  
Daniele Zuccaccia ◽  
...  
Keyword(s):  
Computational Study ◽  
Computational Modelling ◽  
Ligand Substitution ◽  
Hydration Reaction ◽  
Experimental Conditions ◽  
Net Charge ◽  
Coordination Ability ◽  
Nmr Sensitivity ◽  
Equilibrium Step ◽  
Shed Light

The coordination ability of the [(ppy)Au(IPr)]2+ fragment [ppy = 2-phenylpyridine, IPr = 1,3-bis(2,6-di-isopropylphenyl)-imidazol-2-ylidene] towards different anionic and neutral X ligands (X = Cl−, BF4−, OTf−, H2O, 2-butyne, 3-hexyne) commonly involved in the crucial pre-equilibrium step of the alkyne hydration reaction is computationally investigated to shed light on unexpected experimental observations on its catalytic activity. Experiment reveals that BF4− and OTf− have very similar coordination ability towards [(ppy)Au(IPr)]2+ and slightly less than water, whereas the alkyne complex could not be observed in solution at least at the NMR sensitivity. Due to the steric hindrance/dispersion interaction balance between X and IPr, the [(ppy)Au(IPr)]2+ fragment is computationally found to be much less selective than a model [(ppy)Au(NHC)]2+ (NHC = 1,3-dimethylimidazol-2-ylidene) fragment towards the different ligands, in particular OTf− and BF4−, in agreement with experiment. Effect of the ancillary ligand substitution demonstrates that the coordination ability of Au(III) is quantitatively strongly affected by the nature of the ligands (even more than the net charge of the complex) and that all the investigated gold fragments coordinate to alkynes more strongly than H2O. Remarkably, a stabilization of the water-coordinating species with respect to the alkyne-coordinating one can only be achieved within a microsolvation model, which reconciles theory with experiment. All the results reported here suggest that both the Au(III) fragment coordination ability and its proper computational modelling in the experimental conditions are fundamental issues for the design of efficient catalysts.

Theoretical–computational modelling of the temperature dependence of the folding–unfolding thermodynamics and kinetics: the case of a Trp-cage

2019 ◽  
Vol 21 (41) ◽  
pp. 23162-23168
Author(s):  
Marco D'Abramo ◽  
Sara Del Galdo ◽  
Andrea Amadei
Keyword(s):  
Temperature Dependence ◽  
Computational Study ◽  
Computational Modelling ◽  
Thermodynamics And Kinetics ◽  
Kinetics Of ◽  
Unfolding Thermodynamics

Here we present a theoretical–computational study of the thermodynamics and kinetics of an aqueous Trp-cage, a 20-residue long miniprotein.

Computational Modelling of High Temperature Steady State Crack Growth Using a Damage-Based Approach

2003 ◽  
Author(s):  
Masataka Yatomi ◽  
Noel P. O’Dowd ◽  
Kamran M. Nikbin
Keyword(s):  
Crack Growth ◽  
Plane Strain ◽  
Plane Stress ◽  
Computational Study ◽  
Creep Crack Growth ◽  
Computational Modelling ◽  
Crack Tip ◽  
Creep Damage ◽  
Creep Model ◽  
Manganese Steel

In this work a computational study of creep crack growth in a carbon manganese steel is presented. The constitutive behaviour of the steel is described by a power law creep model and the accumulation of creep damage is accounted for through the use of a well-established model for void growth in creeping materials. Two dimensional finite element analyses have been performed for a compact tension specimen and it has been found that the predicted crack growth rate under plane strain conditions approaches that under plane stress conditions at high C* levels. Furthermore it has been shown, both experimentally and numerically, that an increase in test temperature causes the convergence of the cracking rate to occur at higher values of C*. This trend may be explained by the influence of crack-tip plasticity, which reduces the relative difference in constraint between plane stress and plane strain conditions. The constraint effect has been quantified through the use of a two-parameter characterisation of the crack tip fields under creep conditions.

scholarly journals Assessing tACS-induced phosphene perception using closed-loop Bayesian optimization

2017 ◽  
Author(s):  
Romy Lorenz ◽  
Laura E. Simmons ◽  
Ricardo P. Monti ◽  
Joy L. Arthur ◽  
Severin Limal ◽  
...  
Keyword(s):  
Relative Phase ◽  
Rating Scale ◽  
Computational Modelling ◽  
Human Perception ◽  
Past Research ◽  
Bayesian Optimization ◽  
Optimization Approach ◽  
Experimental Conditions ◽  
Combinatorial Explosion ◽  
Transcranial Alternating Current Stimulation

AbstractTranscranial alternating current stimulation (tACS) can evoke illusory flash-like visual percepts known as phosphenes. The perception of phosphenes represents a major experimental challenge when studying tACS-induced effects on cognitive performance. Besides growing concerns that retinal phosphenes themselves could potentially have neuromodulatory effects, the perception of phosphenes may also modify the alertness of participants. Past research has shown that stimulation intensity, frequency and electrode montage affect phosphene perception. However, to date, the effect of an additional tACS parameter on phosphene perception has been completely overlooked: the relative phase difference between stimulation electrodes. This is a crucial and timely topic given the confounding nature of phosphene perception and the increasing number of studies reporting changes in cognitive function following tACS phase manipulations. However, studying phosphene perception for different frequencies and phases simultaneously is not tractable using standard approaches, as the physiologically plausible range of parameters results in a combinatorial explosion of experimental conditions, yielding impracticable experiment durations. To overcome this limitation, here we applied a Bayesian optimization approach to efficiently sample an exhaustive tACS parameter space. Moreover, unlike conventional methodology, which involves subjects judging the perceived phosphene intensity on a rating scale, our study leveraged the strength of human perception by having the optimization driven based on a subject’s relative judgement. Applying Bayesian optimization for two different montages, we found that phosphene perception was affected by differences in the relative phase between cortical electrodes. The results were replicated in a second study involving new participants and validated using computational modelling. In summary, our results have important implications for the experimental design and conclusions drawn from future tACS studies investigating the effects of phase on cognition.

scholarly journals Viscoelasticity in simple indentation-cycle experiments: a computational study

2020 ◽  
Author(s):  
Yu.M. Efremov ◽  
S.L. Kotova ◽  
P.S. Timashev
Keyword(s):  
Young’S Modulus ◽  
Relaxation Function ◽  
Young's Modulus ◽  
Computational Study ◽  
Viscoelastic Behavior ◽  
Elastic Model ◽  
Experimental Conditions ◽  
Relaxation Functions ◽  
Force Curves ◽  
Linear Viscoelastic Theory

Instrumented indentation has become an indispensable tool for quantitative analysis of the mechanical properties of soft polymers and biological samples at different length scales. These types of samples are known for their prominent viscoelastic behavior, and attempts to calculate such properties from the indentation data are constantly made. The simplest indentation experiment presents a cycle of approach (deepening into the sample) and retraction of the indenter, with the output of the force and indentation depth as functions of time and a force versus indentation dependency (force curve). The linear viscoelastic theory based on the elastic-viscoelastic correspondence principle might predict the shape of force curves based on the experimental conditions and underlying relaxation function of the sample. Here, we conducted a computational analysis based on this theory and studied how the force curves were affected by the indenter geometry, type of indentation (triangular or sinusoidal ramp), and the relaxation functions. The relaxation functions of both traditional and fractional viscoelastic models were considered. The curves obtained from the analytical solutions, numerical algorithm and finite element simulations matched each other well. Common trends for the curve-related parameters (apparent Young’s modulus, normalized hysteresis area, and curve exponent) were revealed. Importantly, the apparent Young’s modulus, obtained by fitting the approach curve to the elastic model, demonstrated a direct relation to the relaxation function for all the tested cases. The study will help researchers to verify which model is more appropriate for the sample description without extensive calculations from the basic curve parameters and their dependency on the indentation rate.

scholarly journals 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase in rat brain

1991 ◽  
Vol 276 (2) ◽  
pp. 455-460 ◽  
Author(s):  
F Ventura ◽  
J L Rosa ◽  
S Ambrosio ◽  
J Gil ◽  
R Bartrons
Keyword(s):  
Protein Kinase ◽  
Cdna Probe ◽  
Dependent Protein Kinase ◽  
Experimental Conditions ◽  
Net Charge ◽  
Major Band ◽  
Kinase C ◽  
Dependent Protein ◽  
A Minor ◽  
The Brain

The concentration of fructose 2,6-bisphosphate in the brain remained stable during starvation and early stages of ischaemia, but decreased in diabetes or after lengthened ischaemia. 6-Phosphofructo-1-kinase activity was also decreased in diabetic and ischaemic animals, whereas 6-phosphofructo-2-kinase was not modified. The concentration of the bisphosphorylated metabolite seems to be remarkably constant under a wide variety of experimental conditions, suggesting that it plays an essential role in the basal activation of 6-phosphofructo-1-kinase. Purified 6-phosphofructo-2-kinase also showed fructose-2,6-bisphosphatase activity with an activity ratio similar to that of the purified heart isoenzyme. The brain enzyme also has a net charge similar to that of the heart isoenzyme. Its activity is not modified by sn-glycerol 3-phosphate, and it is more sensitive to citrate than the liver or muscle isoenzyme. Moreover, the enzyme from brain, similarly to that from heart and muscle, is not modified by the cyclic AMP-dependent protein kinase or protein kinase C. A near-full-length cDNA probe from liver hybridized with RNA from brain and heart. In both cases, a major band of 6.8 kb of RNA and a minor one of 4 kb of RNA were detected. All these properties support the hypothesis that brain contains a different isoenzymic form from that of liver and muscle, and it is probably related to the heart isoform.

Using lithium to probe sequential cation interactions with GAT1

2012 ◽  
Vol 302 (11) ◽  
pp. C1661-C1675 ◽  
Author(s):  
Anne-Kristine Meinild ◽  
Ian C. Forster
Keyword(s):  
Steady State ◽  
Binding Site ◽  
Voltage Dependence ◽  
Cation Binding ◽  
Experimental Conditions ◽  
Net Charge ◽  
Cation Binding Site ◽  
Voltage Dependent ◽  
Experimental Findings ◽  
Kinetics Of

Li+ interacts with the Na+/Cl−-dependent GABA transporter, GAT1, under two conditions: in the absence of Na+ it induces a voltage-dependent leak current; in the presence of Na+ and GABA, Li+ stimulates GABA-induced steady-state currents. The amino acids directly involved in the interaction with the Na+ and Li+ ions at the so-called “ Na2” binding site have been identified, but how Li+ affects the kinetics of GABA cotransport has not been fully explored. We expressed GAT1 in Xenopus oocytes and applied the two-electrode voltage clamp and 22Na uptake assays to determine coupling ratios and steady-state and presteady-state kinetics under experimental conditions in which extracellular Na+ was partially substituted by Li+. Three novel findings are: 1) Li+ reduced the coupling ratio between Na+ and net charge translocated during GABA cotransport; 2) Li+ increased the apparent Na+ affinity without changing its voltage dependence; 3) Li+ altered the voltage dependence of presteady-state relaxations in the absence of GABA. We propose an ordered binding scheme for cotransport in which either a Na+ or Li+ ion can bind at the putative first cation binding site ( Na2). This is followed by the cooperative binding of the second Na+ ion at the second cation binding site ( Na1) and then binding of GABA. With Li+ bound to Na2, the second Na+ ion binds more readily GAT1, and despite a lower apparent GABA affinity, the translocation rate of the fully loaded carrier is not reduced. Numerical simulations using a nonrapid equilibrium model fully recapitulated our experimental findings.

Computational modelling of convective heat transfer in a simulated engine cooling gallery

2007 ◽  
Vol 221 (9) ◽  
pp. 1147-1157 ◽  
Author(s):  
K Robinson ◽  
M Wilson ◽  
M J Leathard ◽  
J G Hawley
Keyword(s):  
Heat Transfer ◽  
Convective Heat Transfer ◽  
Convective Heat ◽  
Computational Study ◽  
Convective Heat Transfer Coefficient ◽  
Computational Modelling ◽  
Operating Conditions ◽  
Ic Engine ◽  
Engine Cooling ◽  
Cfd Models

Experimental data from internal combustion (IC) engines suggests that the use of proprietary computational fluid dynamics (CFD) codes for the prediction of coolant-side heat transfer within IC engine coolant jackets often results in underprediction of the convective heat transfer coefficient. An experimental and computational study, based on a coolant gallery simulator rig designed specifically to reproduce realistic IC engine operating conditions, has been conducted to explore this issue. It is shown that the standard ‘wall function’ approach normally used in CFD models to model near-wall conditions does not adequately represent some features of the flow that are relevant in convective heat transfer. Alternative modelling approaches are explored to account for these shortcomings and an empirical approach is shown to be successful; however, the methodology is not easily transferable to other situations.

scholarly journals NOTE ON HAWKING–UNRUH EFFECTS IN GRAPHENE

2012 ◽  
Vol 27 (37) ◽  
pp. 1250218 ◽  
Author(s):  
PISIN CHEN ◽  
HARET ROSU
Keyword(s):  
Radiative Heat ◽  
Large Strain ◽  
Condensed Matter ◽  
Near Field ◽  
Scanning Tunneling ◽  
Graphene Sheets ◽  
Experimental Conditions ◽  
Surface Polariton ◽  
Shed Light ◽  
Plasmon Modes

Beltrami-shaped graphene sheets have been recently proposed as analogs of curved spacetimes with Hawking–Unruh effects detected through typical condensed matter measurements involving scanning tunneling microscopes and spectroscopy. However, such deformed sheets, if ever fabricated, will contain large strain-induced pseudo-magnetic fields with important guiding effects on the motion of the electrons in the conduction band. Besides, possible surface polariton and plasmon modes are known to be important players in the radiative heat transfer which takes place in the natural near-field nanoscale experimental conditions. Therefore, we suggest that the latter class of experiments could shed light on phenomena related to the black hole membrane paradigm instead.

In Silico Functional and Structural Insight of Prenylated Pyrazolocurcumin Derivative Associated with the PGE2 Inhibition through mPGES-1 Blocking

2021 ◽  
Vol 1025 ◽  
pp. 219-223
Author(s):  
Mohd Fadhlizil Fasihi Mohd Aluwi ◽  
Fatimah Salim ◽  
A.K.M. Moyeenul Huq ◽  
Kamal Rullah ◽  
Lam Kok Wai
Keyword(s):  
In Silico ◽  
Density Functional ◽  
Molecular Conformation ◽  
Computational Modelling ◽  
3D Qsar ◽  
Functional Theory ◽  
Modelling Studies ◽  
Structural Insight ◽  
Lead Inhibitors ◽  
Shed Light

The search of novel mPGES-1 lead inhibitors has recently become subject of interest to medicinal chemists due to the safety in comparison to existing NSAIDs such as coxibs drugs. The recent published work revealed that prenylated pyrazolocurcumin derivative as mPGES-1 has been sucessfully designed and synthesized through computational guided 3D-QSAR approach. To improve our understanding, the present paper aimed to develop in silico functional and structural insight of the compound including pharmacophore mapping, molecular electrostatic potential (MEP) simulation using Density Functional Theory (DFT) and druglikeness prediction associated with PGE2 suppression through mPGES-1 blocking. The data collected from computational modelling studies provide important insight on the molecular conformation and further shed light towards structural modification of the future novel mPGES-1 inhibitors.

Ligand substitution and electron transfer reactions of trans-(diaqua)(salen)manganese(iii) with oxalate: an experimental and computational study

RSC Advances ◽  
2014 ◽  
Vol 4 (102) ◽  
pp. 58867-58879 ◽  
Author(s):  
Akshaya K. Kar ◽  
Achyut N. Acharya ◽  
V. Rao Mundlapati ◽  
Guru C. Pradhan ◽  
Himansu S. Biswal ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Computational Study ◽  
Ligand Substitution ◽  
Transfer Reactions ◽  
Electron Transfer Reactions

MnIII(salen)(OH2)2+ undergoes reversible anation by HOX−via Ia mechanism followed by proton controlled electron transfer involving MnIII(salen)(HOX) and H2OX.

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