Potentials of mean force for single, nonpolarizable monovalent halide anions and alkali cations are computed for transversing the water-air interface (modeling using polarizable TIP4P-FQ and TIP4P-QDP). Iodide and bromide in TIP4P-FQ show interfacial stability, whereas chloride, bromide, and iodide show interfacial stability in TIP4P-QDP. A monotonic decrease in coordination number and an increasingly anisotropic distribution of solvating water molecules is shown to accompany movement of the ions towards vapor conditions; these effects are most noticeable with increases in ion size/decreases in magnitude of hydration free energy.
Ions; Polarizable Force Fields; Molecular Dynamics; TIP4P-FQ; TIP4P-QDP; Potential of Mean Force; Solvation Structure
Becke’s B05 method for nondynamic correlation is simplified for self-consistent implementation. An alternative form is proposed for the nondynamic correlation factors that do not require solving a complicated nonlinear algebraic equation. The four linear parameters of B05 are re-optimized together with one extra parameter entering a modified expression for the second-order same-spin energy contribution. The latter is co-linear with the exact-exchange energy density and does not require higher moments of the relaxed exchange hole. Preliminary tests of this method show that it leads to a slight improvement over the resolution-of-identity B05 results reported previously for atomization energies, and to a definite improvement for reaction barriers of Hydrogen abstraction.
The rotation around the amide bond in N,N-diethyl-m-toluamide (m-DEET) has been studied extensively and often used in laboratory instructions to demonstrate the phenomenon of chemical exchange. Herein, we show that a simple modification to N,N-diethyl-o-toluamide (o-DEET) significantly alters the dynamics of the restricted rotation around the amide bond due to steric interactions between the ring methyl group and the two N-ethyl groups. This alters the classic two-site exchange due to restricted rotation around the amide bond, to a three-site exchange, with the third conformation trapped at a higher-energy state compared to the other two. This often overlooked phenomenon is elucidated using variable-temperature NMR, two-dimensional exchange spectroscopy and molecular modeling studies.
Dynamic NMR; chemical exchange; restricted rotation
We present a comparative study of xanthorhodopsin, a proton pump with the carotenoid salinixanthin serving as an antenna, and the closely related bacteriorhodopsin. Upon excitation of retinal, xanthorhodopsin exhibits a wavy transient absorption pattern in the region between 470 and 540 nm. We interpret this signal as due to electrochromic effect of the transient electric field of excited retinal on salinixanthin. The spectral shift decreases during the retinal dynamics through the ultrafast part of the photocycle. Differences in dynamics of bacteriorhodopsin and xanthorhodopsin are discussed.
Continuum modeling of electrostatic interactions based upon the numerical solutions of the Poisson-Boltzmann equation has been widely adopted in biomolecular applications. To extend their applications to molecular dynamics and energy minimization, robust and efficient methodologies to compute solvation forces must be developed. In this study, we have first reviewed the theory for the computation of dielectric boundary forces based on the definition of the Maxwell stress tensor. This is followed by a new formulation of the dielectric boundary force suitable for the finite-difference Poisson-Boltzmann methods. We have validated the new formulation with idealized analytical systems and realistic molecular systems.
The conformations of gambogic acid were studied using force fields, MM3*, AMBER*, MMFFs and OPLS2005, and B3LYP methods. In a model molecule, only the MM3* and AMBER* methods produced the same number of conformers as B3LYP, generating two conformations for rings 1 and 2, and a single conformation for rings 3 and 4. The preferred conformations of these rings are maintained in a conformer of the actual gambogic acid generated using the AMBER* and B3LYP methods. Although this calculated conformer matches well with the crystal structure, it shows that H43, C25=C26 and C30=C31 bonds may be misassigned in the crystal structure.
Force field; conformation; gambogic acid; ring system
The thermal stability of funtionalized carbon nanotubes (CNTs) has been studied experimentally by direct in-situ observations using a heating stage in a transmission electron microscope, from room temperature (RT) to about 1000 °C. It was found that the thermal stability of the functionalized CNTs was significantly reduced during the in-situ heating process. Their average diameter dramatically expanded from RT to about 500 °C, and then tended to be stable until about 1000 °C. The X-ray energy dispersive spectroscopy analysis suggested that the diameter expansion was associated with coalescence of the carbon structure instead of deposition with additional foreign elements during the heating process.
Carbon nanotubes; functionalization; in-situ; thermal stability; transmission electron microscopy
The side-chains of the residues of glutamine (Q) and asparagine (N) contain amide groups. These can H-bond to each other in patterns similar to those of the backbone amides in α-helices. We show that mutating multiple Q's for alanines (A's) in a polyalanine helix stabilizes the helical structure, while similar mutations with multiple N's do not. We suggest that modification of peptides by incorporating Q's in such positions can make more robust helices that can be used to test the effects of secondary structures in biochemical experiments linked to proteins with variable structures such as tau and α-synuclein.
We investigate permeation energetics of water entering a model dimyristoylphosphatidylcholine (DMPC) bilayer via molecular dynamics simulations using polarizable Charge Equilibration (CHEQ) models. Potentials of mean force show 4.5–5.5 kcal/mol barriers for water permeation into bilayers. Barriers are highest when water coordination within the bilayer is prevented, and also when using force fields that accurately reproduce experimental alkane hydration free energies. The magnitude of the average water dipole moment decreases from 2.6 Debye (in bulk) to 1.88 Debye (in membrane interior). This variation correlates with the change in a water molecule’s coordination number.
LIPID BILAYER; DMPC; WATER; TIP4P-FQ; CHARGE EQUILIBRATION; POLARIZABILITY; FORCEFIELDS
In systems where the dipolar couplings are partially averaged by molecular motion, cross-polarization is modulated by sample spinning. The cross-polariation efficiency in Variable Angle Spinning (VAS) and Switched Angle Spinning (SAS) experiments on mobile samples is therefore strongly dependent on the spinning angle. We describe simulations and experimental measurements of these effects over a range of spinning angles from 0° to 90°.
solid-state NMR; cross polarization; variable angle spinning; switched angle spinning; adamantane
Catechol O-methyltransferase (COMT) metabolizes catechol moieties by methylating a single hydroxyl group at the meta- or para- hydroxyl position. Hydrophobic amino acids near the active site of COMT influence the regioselectivity of this reaction. Our sequence analysis highlights their importance by showing that these residues are highly conserved throughout evolution. Reaction barriers calculated in the gas phase reveal a lower barrier during methylation at the meta- position, suggesting that the observed meta-regioselectivity of COMT can be attributed to the substrate itself, and that COMT has evolved residues to orient the substrate in a manner that increases the rate of catalysis.
► The size of amorphous SiO2
nanoparticles coincides for different test methods. ► Different
measurement methods deliver different values for crystalline
ZrO2 nanoparticles. ► The use of complementary
methods is favourable.
The aim of this work is a systematic comparison of size
characterisation methods for two completely different model systems of oxide
nanoparticles, i.e. amorphous spherical silica and anisotropic facet-shaped
crystalline zirconia. Size and/or size distribution were determined in a wide
range from 5 to 70 nm using small-angle X-ray scattering
(SAXS), dynamic light scattering (DLS), nitrogen sorption (BET), X-ray
diffraction (XRD) and transmission electron microscopy (TEM). A nearly perfect
coincidence was observed only for SAXS and TEM for both types of particles. For
zirconia nanoparticles considerable differences between different measurement
methods were observed.
This Letter concerns two-photon excitation of 2,5-Diphenyloxazole (PPO) upon illumination from a pulsed 532 nm solid state laser, with an average power of 30 mW, and a repetition rate of 20 MHz. A very agreeable emission spectrum position and shape has been achieved for PPO receiving one- and two-photon excitation, which suggests that the same excited state is involved for both excitation modes. Also, a perfect quadratic dependence of laser power in the emission intensity function has been recorded. We tested the application of a small solid state green laser to two-photon induced time-resolved fluorescence, revealing the emission anisotropy of PPO to be considerably higher for two-photon than for one-photon excitation.
The effects of water multipole moments on the aqueous solvation of ions were determined in Monte Carlo simulations using soft-sticky dipole-quadrupole-octupole (SSDQO) water. Water molecules formed linear hydrogen bonds to Cl− using the new SSDQO1 parameters, similar to multi-site models. However, the dipole vector was tilted rather than parallel to the oxygen-Na+ internuclear vector as in most multi-site model, while experiment and ab initio molecular dynamics simulations generally indicate a range of values between tilted and parallel. By varying the multipoles in SSDQO, the octupole was found to determine the orientation around Na+. Moreover, analysis of the multipoles of more conventional models is predictive of their performance as solvents.
Ultrasmall nanocrystals are a growing sub-class of traditional nanocrystals that exhibit new properties at diameters typically below 2 nm. In this review, we define what constitutes an ultrasmall nanoparticle while distinguishing between ultrasmall and magic-size nanoparticles. After a brief overview of ultrasmall nanoparticles, including ultrasmall gold clusters, our recent work is presented covering the optical properties, structure, and application of ultrasmall CdSe nanocrystals. This unique material has potential application in solid state lighting due to its balanced white emission. This section is followed by a discussion on the blurring boundary between what can be considered a nanoparticle and a molecule.
►Concise treatment of highly charged ions with very different properties. ► Performed by ab initio simulations with the recent QMCF-MD methodology. ► Treating hydrates with extreme stability, labile hydrates and instable systems with (sub-)picosecond proton transfer reactions.
Based on a series of ab initio quantum mechanical charge field molecular dynamics (QMCF MD) simulations, the broad spectrum of structural and dynamical properties of hydrates of trivalent and tetravalent ions is presented, ranging from extreme inertness to immediate hydrolysis. Main group and transition metal ions representative for different parts of the periodic system are treated, as are 2 threefold negatively charged anions. The results show that simple predictions of the properties of the hydrates appear impossible and that an accurate quantum mechanical simulation in cooperation with sophisticated experimental investigations seems the only way to obtain conclusive results.
The atomic structure of small molecules and polypeptides can be attained from anisotropic NMR parameters such as dipolar couplings (DC) and chemical shifts (CS). Separated local field experiments resolve DC and CS correlations into two dimensions. However, crowded NMR spectra represent a significant obstacle for the complete resolution of these anisotropic parameters. Using the PISEMA (Polarization Inversion Spin Exchange at the Magic Angle) experiment as a foundation, we designed new pulse schemes that use a constant time evolution in the dipolar (indirect) dimension to measure DC and CS correlations at high resolution. We demonstrated this approach on a 4-pentyl-4′-cyanobiphenyl (5CB) liquid crystal sample, achieving a resolution enhancement ranging from 30 to 60 % for the resonances in the dipolar dimension. These new experiments open the possibility of obtaining significant resolution enhancement for multidimensional NMR experiments carried out on oriented liquid crystalline samples as well as oriented membrane proteins.
PISEMA; SE-PISEMA; Solid-state NMR; Sensitivity Enhancement; Resolution Enhancement; Separated Local Field Experiments; Constant Time Evolution
Becke’s B05 method of describing nondynamic electron correlation in Density Functional Theory is implemented self-consistently with computational efficiency. Important modifications of the method are proposed in order to make the self-consistency feasible. Resolution-of-identity technique is used to reduce dramatically the cost of the required exact-exchange energy density. The method is briefly validated on a variety of properties. It describes accurately for the first time the subtle energetics of the NO dimer, an exemplary system of strong nondynamic correlation. The efficient algorithm for the exact-exchange energy density can be applied to other functionals that use this quantity.
Water structure around sugars modeled by partial charges is compared for soft-sticky dipole-quadrupole-octupole (SSDQO), a fast single-site multipole model, and commonly used multi-site models in Monte Carlo simulations. Radial distribution functions and coordination numbers of all the models indicate similar hydration by hydrogen-bond donor and acceptor waters. However, the new optimized SSDQO1 parameters as well as TIP4P-Ew and TIP5P predict a “lone-pair” orientation for the water accepting the sugar hydroxyl hydrogen bond that is more consistent with the limited experimental data than the “dipole” orientation in SPC/E, which has important implications for studies of the cryoprotectant properties of sugars.
For three indolylfulgides the quantum efficiency of the ring-opening reaction upon pre-excitation is investigated in a multipulse experiment. The quantum efficiency grows by factor of up to 3.4, when the pre-excitation pulse immediately precedes the excitation process. The change in quantum efficiency after pre-excitation is discussed as a function of reaction time, steady-state quantum efficiency and energetic barriers in the excited electronic state. The observed differences can be explained by the molecular properties of the investigated indolylfulgides.
indolylfulgide; ultrafast spectroscopy; pump-repump spectroscopy; photochromism
The non-natural amino acid p-cyanophenylalanine (PheCN) has recently emerged as a useful fluorescent probe of proteins; however, its photophysical properties have not been systematically examined. Herein, we measure the fluorescence quantum yield and the fluorescence lifetime of PheCN in a series of solvents. It is found that the fluorescence lifetime of PheCN shows a linear dependence on the Kamlet-Taft parameter α of the protic solvents used, indicating that the solute-solvent hydrogen bonding interactions mediate the non-radiative decay rate. Thus, results of this study provide a basis for quantitative application of PheCN fluorescence in protein conformational studies.
Nanostructures fabricated by a novel technique, termed On-Wire-Lithography (OWL), can be combined with organic and biological molecules to create systems with emergent and highly functional properties. OWL is a template-based, electrochemical process for forming gapped cylindrical structures on a solid support, with feature sizes (both gap and segment length) that can be controlled on the sub-100 nm length scale. Structures prepared by this method have provided valuable insight into the plasmonic properties of noble metal nanomaterials and have formed the basis for novel molecular electronic, encoding, and biological detection devices.
The soft sticky dipole-quadrupole-octupole (SSDQO) potential energy function represents a water molecule by a single site with a van der Waals sphere and point multipoles. Previously, SSDQO was shown to give good properties for liquid water and solvation of simple ions and is faster than three point models. Here, SSDQO is assessed for solvating biologically relevant molecules having a multi-site, partial charge description. Monte Carlo simulations of ethanol, benzene, and N-methylacetamide in SSDQO with SPC/E moments showed the water structure was as good as in SPC/E. Thus, SSDQO is potentially useful for simulations of biological macromolecules in aqueous solution.
Carbon nanotubes (CNTs) have emerged as some of the most promising materials for the technologies of the future. One of the most significant limitations to furthering the understanding and application of these fascinating systems is the lack of atomic-level structural control in their syntheses. Current synthetic methods produce mixtures of structures with varying physical properties. In this article, we describe the potential advantages, recent advances, and challenges that lie ahead for the bottom-up organic synthesis of homogeneous carbon nanotubes with well-defined structures.