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1.
Nanoscale Adv ; 6(2): 428-442, 2024 Jan 16.
Artículo en Inglés | MEDLINE | ID: mdl-38235085

RESUMEN

The unique electrical properties of carbon nanotubes (CNTs) are highly desired in many technological applications. Unfortunately, in practice, the electrical conductivity of most CNTs and their assemblies has fallen short of expectations. One reason for this poor performance is that electrical resistance develops at the interface between carbon nanomaterials and metal surfaces when traditional metal-metal type contacts are employed. Here, a method for overcoming this resistance using covalent bond formation between open-ended CNTs and Cu surfaces is investigated experimentally and supported by theoretical calculations. The open-ended CNTs are vertically oriented compared to the substrate and have carboxylic functional groups that react with aminophenyl groups (linkers) grafted on metal surfaces. The covalent bond formation, crosslinking carboxylic and amine, via amide bond formation occurs at 120 °C. The covalent bonding nature of the aminophenyl linker is demonstrated theoretically using (100), (110), and (111) Cu surfaces, and bridge-like bond formation between carbon and two adjacent Cu atoms is revealed. The electrical conductivity calculated for a single intramolecular-type junction supports covalent bond formation between Cu and CNTs. Experimentally, the robustness of the covalent bonding between vertically oriented CNTs is tested by exposing CNTs on Cu to sonication, which reveals that CNTs remain fixed to the Cu supports. Since bonding CNTs to metals was performed at low temperatures, the reported method of covalent bond formation is expected to facilitate the application of CNTs in multiple fields, including electronics.

2.
Nat Chem ; 16(3): 456-465, 2024 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-38114816

RESUMEN

Through the actuation of vibronic modes in cell-membrane-associated aminocyanines, using near-infrared light, a distinct type of molecular mechanical action can be exploited to rapidly kill cells by necrosis. Vibronic-driven action (VDA) is distinct from both photodynamic therapy and photothermal therapy as its mechanical effect on the cell membrane is not abrogated by inhibitors of reactive oxygen species and it does not induce thermal killing. Subpicosecond concerted whole-molecule vibrations of VDA-induced mechanical disruption can be achieved using very low concentrations (500 nM) of aminocyanines or low doses of light (12 J cm-2, 80 mW cm-2 for 2.5 min), resulting in complete eradication of human melanoma cells in vitro. Also, 50% tumour-free efficacy in mouse models for melanoma was achieved. The molecules that destroy cell membranes through VDA have been termed molecular jackhammers because they undergo concerted whole-molecule vibrations. Given that a cell is unlikely to develop resistance to such molecular mechanical forces, molecular jackhammers present an alternative modality for inducing cancer cell death.


Asunto(s)
Melanoma , Fotoquimioterapia , Ratones , Animales , Humanos , Melanoma/tratamiento farmacológico , Fotoquimioterapia/métodos , Muerte Celular , Especies Reactivas de Oxígeno/metabolismo
3.
Nat Energy ; 8(12): 1345-1354, 2023 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-38249622

RESUMEN

The solid-electrolyte interphase (SEI) critically governs the performance of rechargeable batteries. An ideal SEI is expected to be electrically insulative to prevent persistently parasitic reactions between the electrode and the electrolyte and ionically conductive to facilitate Faradaic reactions of the electrode. However, the true nature of the electrical properties of the SEI remains hitherto unclear due to the lack of a direct characterization method. Here we use in situ bias transmission electron microscopy to directly measure the electrical properties of SEIs formed on copper and lithium substrates. We reveal that SEIs show a voltage-dependent differential conductance. A higher rate of differential conductance induces a thicker SEI with an intricate topographic feature, leading to an inferior Coulombic efficiency and cycling stability in Li∣∣Cu and Li∣∣LiNi0.8Mn0.1Co0.1O2 cells. Our work provides insight into the targeted design of the SEI with desired characteristics towards better battery performance.

4.
Spectrochim Acta A Mol Biomol Spectrosc ; 269: 120740, 2022 Mar 15.
Artículo en Inglés | MEDLINE | ID: mdl-34968837

RESUMEN

We evaluate the fullerene C60 binding effect; through the metal (Al) and through the ligand (Pc,TPP), on the photophysical and charge transport properties of M-porphyrin(TPP)/phthalocyanine(Pc) (M = Al(III), Zn(II)). We perform density functional theory (DFT) and time-dependent DFT calculations for the macrocycle-C60 dyads, showing that all systems studied are thermodynamically favorable. The C60 binding effect on the absorption spectrum is a red-shift of the Q and Soret (B) bands of TPPs and Pcs. The Pc-dyads show longer λ for Q bands (673 nm) than those with TPP (568 nm). AlTPP-C60 and ZnTPP-C60 show a more favorable electron injection to TiO2 than the analogs Pcs, and the regeneration of the dye is preferred in AlTPP-C60 and AlPc-C60. Zero-bias conductance is computed (10-4-10-7 G0) for the dyads using molecular junctions with Au(111)-based electrodes. When a bias voltage of around 0.6 V up to 1 V is applied, an increase in current is obtained for AlTPP-C60 (10-7 A), ZnTPP-C60 (10-7 A), and AlPc-C60 (10-8 A). Although there is not a unique trend in the behavior of the dyads, Pcs have better photophysical properties than TPPs and the latter are better in the charge transport. We conclude that AlTPP(ZnTPP)-C60 dyads are an excellent alternative for designing new materials for dye-sensitized solar cells or optoelectronic devices.

5.
Angew Chem Int Ed Engl ; 60(34): 18845-18851, 2021 Aug 16.
Artículo en Inglés | MEDLINE | ID: mdl-34196094

RESUMEN

Aqueous Zn batteries promise high energy density but suffer from Zn dendritic growth and poor low-temperature performance. Here, we overcome both challenges by using an eutectic 7.6 m ZnCl2 aqueous electrolyte with 0.05 m SnCl2 additive, which in situ forms a zincophilic/zincophobic Sn/Zn5 (OH)8 Cl2 ⋅H2 O bilayer interphase and enables low temperature operation. Zincophilic Sn decreases Zn plating/stripping overpotential and promotes uniform Zn plating, while zincophobic Zn5 (OH)8 Cl2 ⋅H2 O top-layer suppresses Zn dendrite growth. The eutectic electrolyte has a high ionic conductivity of ≈0.8 mS cm-1 even at -70 °C due to the distortion of hydrogen bond network by solvated Zn2+ and Cl- . The eutectic electrolyte enables Zn∥Ti half-cell a high Coulombic efficiency (CE) of >99.7 % for 200 cycles and Zn∥Zn cell steady charge/discharge for 500 h with a low overpotential of 8 mV at 3 mA cm-2 . Practically, Zn∥VOPO4 batteries maintain >95 % capacity with a CE of >99.9 % for 200 cycles at -50 °C, and retain ≈30 % capacity at -70 °C of that at 20 °C.

6.
Phys Chem Chem Phys ; 23(1): 597-606, 2021 Jan 06.
Artículo en Inglés | MEDLINE | ID: mdl-33331379

RESUMEN

Present Li-ion battery (LIB) technology requires strong improvements in performance, energy capacity, charging-time, and cost to expand their application to e-mobility and grid storage. Li-metal is one of the most promising materials to replace commercial anodes such as graphite because of its 10 times higher specific capacity. However, Li-metal has high reactivity with commercial liquid electrolytes; thus, new solid materials are proposed to replace liquid electrolytes when Li-metal anodes are used. We present a theoretical analysis of the charging process in a full nanobattery, containing a LiCoO2 cathode, a Li7P2S8I solid-state electrolyte (SSE), a Li-metal anode as well as Al and Cu collectors for the cathode and anode, respectively. In addition, we added a Li3P/Li2S film as a solid electrolyte interphase (SEI) layer between the Li-anode and SSE. Thus, we focus this study on the SEI and SSE. We simulated the charging of the nanobattery with an external voltage by applying an electric field. We estimated temperature profiles within the nanobattery and analyzed Li-ion transport through the SSE and SEI. We observed a slight temperature rise at the SEI due to reactions forming PS3- and P2S74- fragments at the interfaces; however, this temperature profile changes due to the charging current under the presence of the external electric field ε = 0.75 V Å-1. Without the external field, the calculated open-circuit voltage (OCV) was 3.86 V for the battery, which is within the range of values of commercial cobalt-based LIBs. This voltage implies a spontaneous fall of available Li-ions from the anode to the cathode (during discharge). The charge of this nanobattery requires overcoming the OCV plus an additional voltage that determines the charging current. Thus, we applied an external potential able to neutralize the OCV, plus an additional 1.6 V to induce the transport of Li+ from the cathode up to the anode. Several interesting details about Li+ transport paths through the SSE and SEI are discussed.

7.
RSC Adv ; 10(15): 9000-9015, 2020 Feb 27.
Artículo en Inglés | MEDLINE | ID: mdl-35496544

RESUMEN

An ab initio molecular dynamics study of an electrochemical interface between a solid-state-electrolyte Li0.29La0.57TiO3 and Li-metal is performed to analyze interphase formation and evolution when external electric fields of 0, 0.5, 1.0 and 2.0 V Å-1 are applied. From this electrochemical stability analysis, it was concluded that lithium-oxide (Li2O) and lanthanum-oxide (La2O3) phases were formed at the electrolyte/anode interphase. As the electric field increased, oxygen from the electrolyte diffused through the Li-metal anode, increasing the amount of O from deeper crystallographic planes of the electrolyte that reacted with Li and La. A strong reduction of Ti was expected from their Bader charge variation from +3.5 in the bulk to +2.5 at the interface. Due to the loss of Li atoms from the anode to form Li-oxide at the interphase, vacancies were created on the Li-metal, causing anode structure amorphization near the Li-oxide phase and keeping the rest of the anode structure as BCC. Therefore, the interface was unstable because of the continuous Li-oxide and La-oxide formation and growth, which were more pronounced when increasing the external electric field.

8.
J Mol Model ; 25(6): 160, 2019 May 14.
Artículo en Inglés | MEDLINE | ID: mdl-31089893

RESUMEN

Visualization of the halobenzene σ-hole region of molecules (PhX, X = Cl, Br, I) was conducted to investigate the nature of the σ-hole present between covalently bonded elements of groups IVB-VIIB (known as halogen bonding for group VIIB) and corresponding negative sites, such as Lewis base lone electron pairs, π-electrons, or anions. The σ-hole consists of a region of poor electron density and often relatively positive electrostatic potential surrounding the outermost portion of the halogen atom along the A-X bond axis. In this work, molecular electrostatic potential (MEP) isosurfaces for PhX obtained from ab initio calculations are examined to determine the σ-hole in 3D, showing the surfaces of corresponding positive and negative regions. Surfaces were mapped for isopotentials of PhX molecules as low as 0.003 V and scaled up by factors of 10 up to 3 V. The σ-hole is revealed as a positive region exposed underneath a predominantly negative MEP isosurface. As isopotential values move away from zero, this hole grows in radius; conversely, its presence completely fades as potential approaches zero with increasing distance from the molecule. This technique can also be used to compare behaviors of neutral molecules and their ionic counterparts like the case of neutral PF6 (not observed experimentally) and the hexafluorophosphate anion, PF6-, a typical counter-ion in commercial Li-ion batteries. The pnictogen halide PF5 features similar MEP trends as the neutral PF6, which features reactive sites, shown as negative potential caps, at specific points in the molecule, similar to those of PF5. The portrayal of MEP behavior in iso-surfaces at specific and practical values of chemical interest is crucial when defining lump parameter sets for Coulombic force fields for molecular dynamics simulations to be used in systems that go from biological macromolecules to crystal engineering to devices to final products. Active chemical sites can be described by the MEP function, V(r), more proficiently than just wavefunctions or electron densities that intrinsically contain the same information, and this is fully enhanced when color-coding electron densities on isopotential surfaces are shown. Graphical abstract The hidden features of orbital holes depicted by iso-potentials.

9.
RSC Adv ; 9(48): 27835-27848, 2019 Sep 03.
Artículo en Inglés | MEDLINE | ID: mdl-35530483

RESUMEN

Lithium-metal is a desired material for anodes of Li-ion and beyond Li-ion batteries because of its large theoretical specific capacity of 3860 mA h g-1 (the highest known so far), low density, and extremely low potential. Unfortunately, there are several problems that restrict the practical application of lithium-metal anodes, such as the formation of dendrites and reactivity with electrolytes. We present here a study of lithium dendrite formation on a Li-metal anode covered by a cracked solid electrolyte interface (SEI) of LiF in contact with a typical liquid electrolyte composed of 1 M LiPF6 salt solvated in ethylene carbonate. The study uses classical molecular dynamics on a model nanobattery. We tested three ways to charge the nanobattery: (1) constant current at a rate of one Li+ per 0.4 ps, (2) pulse train 10 Li+ per 4 ps, and (3) constant number ions in the electrolyte: one Li+ enters the electrolyte from the cathode as one Li+ exits the electrolyte to the anode. We found that although the SEI does not interfere with the lithiation, the mere presence of a crack in the SEI boosts and guides dendrite formation at temperatures between 325 K and 410.7 K at any C-rate, being more favorable at 325 K than at 410.7 K. On the other hand, we find that a higher C-rate (2.2C) favors the lithium dendrite formation compared to a lower C-rate (1.6C). Thus the battery could store more energy in a safe way at a lower C-rate.

10.
J Mol Model ; 24(10): 290, 2018 Sep 21.
Artículo en Inglés | MEDLINE | ID: mdl-30242746

RESUMEN

Due to recent advances in the field of microelectronics, the growth in microelectronics applications, and the exponentially increasing demand for microelectronic devices in the power sector, it is important to study the behavior of silicon at the nanoscale, given that nanoclusters of silicon could be used to design a new kind of lithium-ion batteries with strongly enhanced performance. Here, molecular dynamics was employed to calculate the self-diffusion coefficients of silicon clusters at room temperature and at a temperature approaching the melting point of silicon, complementing experimental efforts in this field. Silicon clusters of the same spherical geometry and size but with different vacancy fractions were studied using molecular dynamics using the Tersoff potential in order to estimate phase changes and self-diffusion coefficients. At 300 K, the self-diffusion coefficient was found to vary non-monotonically: the self-diffusion coefficient at a vacancy fraction of 7.5% is half than the vacancy at a fraction of 0%, while the self-diffusion coefficient at a vacancy fraction of 20% is two orders of magnitude larger than that at a vacancy fraction of 0%. However, there is only a marginal monotonic increase in the self-diffusion coefficient values with vacancy fraction at 2000 K. The results of this investigation of vacancy-mediated self-diffusion could aid attempts to improve diffusion control, which is crucial to nanocluster applications in various devices, and the results also provide insight into how the temperature, energy, pressure, and phase changes of the silicon clusters depend on vacancy fraction. This may ultimately allow the design and selection of materials for thermoelectric and optoelectronic devices and thermal transducers to be optimized. Our results also indicated that the findings we obtained for the clusters are independent of the particular random vacancy distribution considered and the heating rate applied to the clusters. Graphical Abstract Silicon nanoparticles (SNP) are among the best options to choose from for the design of devices for renewable energies; SNP based material performance can be effectively tailored by controling the vacancy, temperature and other properties of the SNP.

11.
J Mol Model ; 24(4): 103, 2018 Mar 23.
Artículo en Inglés | MEDLINE | ID: mdl-29572731

RESUMEN

To facilitate the development of new materials for use in batteries, it is necessary to develop ab initio full-electron computational techniques for modeling potential new battery materials. Here, we tested density functional theory procedures that are accurate enough to obtain the energetics of a zinc/copper voltaic cell. We found the magnitude of the zero-point energy correction to be 0.01-0.2 kcal/mol per atom or molecule and the magnitude of the dispersion correction to be 0.1-0.6 kcal/mol per atom or molecule for Zn n , (H2O) n , [Formula: see text], [Formula: see text], and Cu n . Counterpoise correction significantly affected the values of ∆[Formula: see text], ∆[Formula: see text], and ∆Esolv by 1.0-3.1 kcal/mol per atom or molecule at the B3PW91/6-31G(d) level of theory, but by only 0.04-0.4 kcal/mol per atom or molecule at the B3PW91/cc-pVTZ level of theory. The application of B3PW91/6-31G(d) yielded results that differed from macroscopic experimental values by 0.1-7.1 kcal/mol per atom or molecule, whereas applying B3PW91/cc-pVTZ produced results that differed from macroscopic experimental values by 0.1-4.8 kcal/mol per atom or molecule, with the smallest differences occurring for reactions with a small macroscopic experimental ∆E and the largest differences occurring for reactions with a large macroscopic experimental ∆E, implying size consistency.

12.
RSC Adv ; 8(10): 5255-5267, 2018 Jan 29.
Artículo en Inglés | MEDLINE | ID: mdl-35542415

RESUMEN

Rechargeable lithium-ion batteries require a vigorous improvement if we want to use them massively for high energy applications. Silicon and metal lithium anodes are excellent alternatives because of their large theoretical capacity when compared to graphite used in practically all rechargeable Li-ion batteries. However, several problems need to be addressed satisfactorily before a major fabrication effort can be launched; for instance, the growth of lithium dendrites is one of the most important to take care due to safety issues. In this work we attempt to predict the mechanism of dendrite growth by simulating possible behaviors of charge distributions in the anode of an already cracked solid electrolyte interphase of a nanobattery, which is under the application of an external field representing the charging of the battery; thus, elucidating the conditions for dendrite growth. The extremely slow drift velocity of the Li-ions of ∼1 mm per hour in a typical commercial Li-ion battery, makes the growth of a dendrite take a few hours; however, once a Li-ion arrives at an active site of the anode, it takes an extremely short time of ∼1 ps to react. This large difference in time-scales allows us to perform the molecular dynamics simulation of the ions at much larger drift velocities, so we can have valuable results in reasonable computational times. The conditions before the growth are assumed and conditions that do not lead to the growth are ignored. We performed molecular dynamics simulations of a pre-lithiated silicon anode with a Li : Si ratio of 21 : 5, corresponding to a fully charged battery. We simulate the dendrite growth by testing a few charge distributions in a nanosized square representing a crack of the solid electrolyte interphase, which is where the electrolyte solution comes into direct contact with the LiSi alloy anode. Depending on the selected charge distributions for such an anode surface, the dendrites grow during the simulation when an external field is applied. We found that dendrites grow when strong deviations of charge distributions take place on the surface of the crack. Results from this work are important in finding ways to constrain lithium dendrite growth using tailored coatings or pre-coatings covering the LiSi alloy anode.

13.
Chem Rev ; 117(14): 9674-9754, 2017 Jul 26.
Artículo en Inglés | MEDLINE | ID: mdl-28394578

RESUMEN

This Review focuses on research oriented toward elucidation of the various aspects that determine adsorption of CO2 in metal-organic frameworks and its separation from gas mixtures found in industrial processes. It includes theoretical, experimental, and combined approaches able to characterize the materials, investigate the adsorption/desorption/reaction properties of the adsorbates inside such environments, screen and design new materials, and analyze additional factors such as material regenerability, stability, effects of impurities, and cost among several factors that influence the effectiveness of the separations. CO2 adsorption, separations, and membranes are reviewed followed by an analysis of the effects of stability, impurities, and process operation conditions on practical applications.

14.
J Mol Model ; 23(4): 120, 2017 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-28303437

RESUMEN

Rechargeable lithium-ion batteries are the most popular devices for energy storage but still a lot of research needs to be done to improve their cycling and storage capacity. Silicon has been proposed as an anode material because of its large theoretical capacity of ∼3600 mAh/g. Therefore, focus is needed on the lithiation process of silicon anodes where it is known that the anode increases its volume more than 300%, producing cracking and other damages. We performed molecular dynamics atomistic simulations to study the swelling, alloying, and amorphization of a silicon nanocrystal anode in a full nanobattery model during the first charging cycle. A dissolved salt of lithium hexafluorophosphate in ethylene carbonate was chosen as the electrolyte solution and lithium cobalt oxide as cathode. External electric fields are applied to emulate the charging, causing the migration of the Li-ions from the cathode to the anode, by drifting through the electrolyte solution, thus converting pristine Si gradually into Li14Si5 when fully lithiated. When the electric field is applied to the nanobattery, the temperature never exceeds 360 K due to a temperature control imposed resembling a cooling mechanism. The volume of the anode increases with the amorphization of the silicon as the external field is applied by creating a layer of LiSi alloy between the electrolyte and the silicon nanocrystal and then, at the arrival of more Li-ions changing to an alloy, where the drift velocity of Li-ions is greater than the velocity in the initial nanocrystal structure. Charge neutrality is maintained by concerted complementary reduction-oxidation reactions at the anode and cathode, respectively. In addition, the nanobattery model developed here can be used to study charge mobility, current density, conductance and resistivity, among several other properties of several candidate materials for rechargeable batteries and constitutes the initial point for further studies on the formation of the solid electrolyte interphase in the anode. Graphical Abstract Nanobattery: LiCoO2 cathode, electrolyte solution of 1M Li+PF6- in ethylene carbonate, and Si crystal anode, which changes its volume due to lithiation during the first charge.

15.
ACS Appl Mater Interfaces ; 7(22): 11948-55, 2015 Jun 10.
Artículo en Inglés | MEDLINE | ID: mdl-25985821

RESUMEN

Coating silicon particles with a suitable thin film has appeared as a possible solution to accommodate the swelling of silicon upon lithiation and its posterior cracking and pulverization during cycling of Li-ion batteries. In particular, aluminum alkoxide (alucone) films have been recently deposited over Si anodes, and the lithiation and electrochemical behavior of the system have been characterized. However, some questions remain regarding the lithium molecular migration mechanisms through the film and the electronic properties of the alucone film. Here we use density functional theory, ab initio molecular dynamics simulations, and Green's function theory to examine the film formation, lithiation, and reactivity in contact with an electrolyte solution. It is found that the film is composed of Al-O complexes with 3-O or 4-O coordination. During lithiation, Li atoms bind very strongly to the O atoms in the most energetically favorable sites. After the film is irreversibly saturated with Li atoms, it becomes electronically conductive. The ethylene carbonate molecules in liquid phase are found to be reduced at the surface of the Li-saturated alucone film following similar electron transfer mechanisms as found previously for lithiated silicon anodes. The theoretical results are in agreement with those from morphology and electrochemical analyses.

16.
J Phys Chem A ; 119(4): 689-703, 2015 Jan 29.
Artículo en Inglés | MEDLINE | ID: mdl-25563344

RESUMEN

In order to determine how actinide atoms are dressed when solvated in water, density functional theory calculations have been carried out to study the equilibrium structure of uranium plutonium and thorium salts (UO2(2+), PuO2(2+), Pu(4+), and Th(4+)) both in vacuum as well as in solution represented by a conductor-like polarizable continuum model. This information is of paramount importance for the development of sensitive nanosensors. Both UO2(2+) and PuO2(2+) ions show coordination number of 4-5 with counterions replacing one or two water molecules from the first coordination shell. On the other hand, Pu(4+), has a coordination number of 8 both when completely solvated and also in the presence of chloride and nitrate ions with counterions replacing water molecules in the first shell. Nitrates were found to bind more strongly to Pu(IV) than chloride anions. In the case of the Th(IV) ion, the coordination number was found to be 9 or 10 in the presence of chlorides. Moreover, the Pu(IV) ion shows greater affinity for chlorides than the Th(IV) ion. Adding dispersion and ZPE corrections to the binding energy does not alter the trends in relative stability of several conformers because of error cancelations. All structures and energetics of these complexes are reported.

17.
J Phys Chem B ; 118(34): 10065-75, 2014 Aug 28.
Artículo en Inglés | MEDLINE | ID: mdl-25055049

RESUMEN

Mycobacterium tuberculosis pyrazinamidase (PZAse) is a key enzyme to activate the pro-drug pyrazinamide (PZA). PZAse is a metalloenzyme that coordinates in vitro different divalent metal cofactors in the metal coordination site (MCS). Several metals including Co(2+), Mn(2+), and Zn(2+) are able to reactivate the metal-depleted PZAse in vitro. We use quantum mechanical calculations to investigate the Zn(2+), Fe(2+), and Mn(2+) metal cofactor effects on the local MCS structure, metal-ligand or metal-residue binding energy, and charge distribution. Results suggest that the major metal-dependent changes occur in the metal-ligand binding energy and charge distribution. Zn(2+) shows the highest binding energy to the ligands (residues). In addition, Zn(2+) and Mn(2+) within the PZAse MCS highly polarize the O-H bond of coordinated water molecules in comparison with Fe(2+). This suggests that the coordination of Zn(2+) or Mn(2+) to the PZAse protein facilitates the deprotonation of coordinated water to generate a nucleophile for catalysis as in carboxypeptidase A. Because metal ion binding is relevant to enzymatic reaction, identification of the metal binding event is important. The infrared vibrational mode shift of the C═Nε (His) bond from the M. tuberculosis MCS is the best IR probe to metal complexation.


Asunto(s)
Amidohidrolasas/metabolismo , Complejos de Coordinación/metabolismo , Metales/farmacología , Mycobacterium tuberculosis/enzimología , Pirazinamida/metabolismo , Teoría Cuántica , Espectrofotometría Infrarroja/métodos , Agua/metabolismo , Amidohidrolasas/química , Complejos de Coordinación/química , Modelos Moleculares , Conformación Proteica , Pirazinamida/química , Vibración , Agua/química
18.
J Mol Model ; 20(3): 2150, 2014 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-24573498

RESUMEN

The detection of uranium is very important, especially in water and, more importantly, in the form of uranyl ion (UO2)²âº, which is one of its most abundant moieties. Here, we report analyses and simulations of uranyl in water using ab initio modified force fields for water with improved parameters and charges of uranyl. We use a TIP4P model, which allows us to obtain accurate water properties such as the boiling point and the second and third shells of water molecules in the radial distribution function thanks to a fictitious charge that corrects the 3-point models by reproducing the exact dipole moment of the water molecule. We also introduced non-bonded interaction parameters for the water-uranyl intermolecular force field. Special care was taken in testing the effect of a range of uranyl charges on the structure of uranyl-water complexes. Atomic charges of the solvated ion in water were obtained using density functional theory (DFT) calculations taking into account the presence of nitrate ions in the solution, forming a neutral ensemble. DFT-based force fields were calculated in such a way that water properties, such as the boiling point or the pair distribution function stand. Finally, molecular dynamics simulations of a water box containing uranyl cations and nitrate anions are performed at room temperature. The three peaks in the oxygen-oxygen radial distribution function for water were found to be kept in the presence of uranyl thanks to the improvement of interaction parameters and charges. Also, we found three shells of water molecules surrounding the uranyl ion instead of two as was previously thought.


Asunto(s)
Algoritmos , Modelos Químicos , Simulación de Dinámica Molecular , Compuestos de Uranio/química , Iones/química , Nitratos/química , Oxígeno/química , Teoría Cuántica , Soluciones/química , Termodinámica , Agua/química
19.
J Mol Model ; 19(12): 5237-44, 2013 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-24126827

RESUMEN

Because of the potential importance of carbon nanotubes (CNT) in renewable energy and other fields, molecular orbital ab initio calculations are used to study the relation between mechanical and electronic properties of such structures. We estimate a modulus of elasticity of 1.3 TPa and find out that the mechanism of CNT structure deformation is dependent on their chirality. Armchair and chiral nanotubes have ductile deformation fracture while zigzag have both ductile and brittle; on the other hand armchair nanotubes fracture and form two caps while chiral nanotubes adopt a helical-structure conformation. In addition, the energy gap between occupied and unoccupied molecular orbitals increases when nanotubes are under plastic deformation. This strong coupling between mechanical and electrical properties can be used to tune CNT mechanically to specific electronic bandgaps, affecting directly their electromagnetic absorption properties.


Asunto(s)
Nanotecnología , Nanotubos de Carbono/química , Energía Renovable , Absorción , Simulación por Computador , Radiación Electromagnética
20.
J Mol Model ; 19(10): 4419-32, 2013 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-23918223

RESUMEN

We calculate the interactions of two atomic layer deposition (ALD) reactants, trimethylaluminium (TMA) and tetrakis(ethylmethylamino) hafnium (TEMAH) with the hydroxylated Ga-face of GaN clusters when aluminum oxide and hafnium oxide, respectively, are being deposited. The GaN clusters are suitable as testbeds for the actual Ga-face on practical GaN nanocrystals of importance not only in electronics but for several other applications in nanotechnology. We find that TMA spontaneously interacts with hydroxylated GaN; however it does not follow the atomic layer deposition reaction path unless there is an excess in potential energy introduced in the clusters at the beginning of the optimization, for instance, using larger bond lengths of various bonds in the initial structures. TEMAH also does not interact with hydroxylated GaN, unless there is an excess in potential energy. The formation of a Ga-N(CH3)(CH2CH3) bond during the ALD of HfO2 using TEMAH as the reactant without breaking the Hf-N bond could be the key part of the mechanism behind the formation of an interface layer at the HfO2/GaN interface.

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