Further Quantum Mechanical Evidence that Difluorotoluene does not Hydrogen Bond

Calculations were run on the methylated DNA base pairs adenine:thymine and adenine:difluorotoluene to further investigate the hydrogen-bonding properties of difluorotoluene (F). Geometries were optimized using hybrid density functional theory. Single-point calculations at the MP2(full) level were performed to obtain more rigorous energies. The functional counterpoise method was used to correct for the basis set superposition error (BSSE), and the interaction energies were also corrected for fragment relaxation. These corrections brought the B3LYP and MP2 interaction energies into excellent agreement. In the gas phase, the Gibbs free energies calculated at the B3LYP and MP2 levels of theory predict that A and T will spontaneously form an A:T pair while A:F spontaneously dissociates into A and F. Solvation effects on the pairing of the bases were explored using implicit solvent models for water and chloroform. In aqueous solution, both A:T and A:F are predicted to dissociate into their component monomers. Semiempirical calculations were performed on small sections of B-form DNA containing the two pairs, and the results provide support for the concept that base stacking is more important than hydrogen bonding for the stability of the A:F pair within a DNA helix.

Quantum Mechnical Investion of Cyclic 3',5'- Adenosine Monophosphate, the Second Hormonal Messenger

Full geometry optimizations using the PM3, AM1, 3-21G∗/HF and 6-31G∗/HF levels of theory were conducted on the syn and anti conformations of cyclic3′,5′-adenosine monophosphate (cAMP). Comparison of the anti crystal structures with the semiempirical and ab initio results revealed that the ab initio results agree well with the experimental results. The results of semiempirical calculations are in qualitative agreement with experimental and ab initio values, with the exception of the glycosyl torsion angle for the anti conformer. Sugar puckering, which is not handled properly by semiempirical methods for unconstrained sugars, nucleosides, nucleotides and nucleotide base pairs, is modeled reasonably well by the semiempirical methods for cAMP. This improvement results from the constraints introduced by the cyclization of AMP to form the phosphodiester.

Quantum Mechanical Study of Sulfuric Acid Hydration: Atmospheric Implications

The role of the binary nucleation of sulfuric acid in aerosol formation and its implications for global warming is one of the fundamental unsettled questions in atmospheric chemistry. We have investigated the thermodynamics of sulfuric acid hydration using ab initio quantum mechanical methods. For H2SO4(H2O)n where n = 1–6, we used a scheme combining molecular dynamics configurational sampling with high-level ab initio calculations to locate the global and many low lying local minima for each cluster size. For each isomer, we extrapolated the Møller–Plesset perturbation theory (MP2) energies to their complete basis set (CBS) limit and added finite temperature corrections within the rigid-rotor-harmonic-oscillator (RRHO) model using scaled harmonic vibrational frequencies. We found that ionic pair (HSO4–·H3O+)(H2O)n−1 clusters are competitive with the neutral (H2SO4)(H2O)n clusters for n ≥ 3 and are more stable than neutral clusters for n ≥ 4 depending on the temperature. The Boltzmann averaged Gibbs free energies for the formation of H2SO4(H2O)n clusters are favorable in colder regions of the troposphere (T = 216.65–273.15 K) for n = 1–6, but the formation of clusters with n ≥ 5 is not favorable at higher (T > 273.15 K) temperatures. Our results suggest the critical cluster of a binary H2SO4–H2O system must contain more than one H2SO4 and are in concert with recent findings(1) that the role of binary nucleation is small at ambient conditions, but significant at colder regions of the troposphere. Overall, the results support the idea that binary nucleation of sulfuric acid and water cannot account for nucleation of sulfuric acid in the lower troposphere.

Quantum Mechanical Study of Sulfuric Acid Hydration: Atmospheric Implications

The role of the binary nucleation of sulfuric acid in aerosol formation and its implications for global warming is one of the fundamental unsettled questions in atmospheric chemistry. We have investigated the thermodynamics of sulfuric acid hydration using ab initio quantum mechanical methods. For H2SO4(H2O)n where n = 1–6, we used a scheme combining molecular dynamics configurational sampling with high-level ab initio calculations to locate the global and many low lying local minima for each cluster size. For each isomer, we extrapolated the Møller–Plesset perturbation theory (MP2) energies to their complete basis set (CBS) limit and added finite temperature corrections within the rigid-rotor-harmonic-oscillator (RRHO) model using scaled harmonic vibrational frequencies. We found that ionic pair (HSO4–·H3O+)(H2O)n−1clusters are competitive with the neutral (H2SO4)(H2O)n clusters for n ≥ 3 and are more stable than neutral clusters for n ≥ 4 depending on the temperature. The Boltzmann averaged Gibbs free energies for the formation of H2SO4(H2O)n clusters are favorable in colder regions of the troposphere (T = 216.65–273.15 K) for n = 1–6, but the formation of clusters with n ≥ 5 is not favorable at higher (T > 273.15 K) temperatures. Our results suggest the critical cluster of a binary H2SO4–H2O system must contain more than one H2SO4 and are in concert with recent findings(1) that the role of binary nucleation is small at ambient conditions, but significant at colder regions of the troposphere. Overall, the results support the idea that binary nucleation of sulfuric acid and water cannot account for nucleation of sulfuric acid in the lower troposphere.

Effect of external electric field on hydrogen adsorption over activated carbon separated by dielectric materials

Energy crisis and worldwide environmental problem make hydrogen a prospective energy carrier. However, storage and transportation of hydrogen in large quantities at small volume is currently not practical. Lots of materials and devices have been developed for storage hydrogen, but to today none is able to meet the DOE targets. Activated carbon has been found to be a good hydrogen adsorbent due to its high surface area. However, the weak van der Waals force between hydrogen and the adsorbent has limited the adsorption capacity. Previous studies have found that enhanced adsorption can be obtained with applied electric field. Stronger interaction between the polarized hydrogen and the charged sorbents under high voltage is considered as the reason. This study was initiated to investigate if the adsorption can be further enhanced when the activated carbon particles are separated with a dielectric coating. Dielectric TiO2 nanoparticles were first utilized. Hydrogen adsorption measurements on the TiO2-coated carbon materials, with or without an external electric field, were made. The results showed that the adsorption capacity enhancement increased with the increasing amount of TiO2 nanoparticles with an applied electric field. Since the hydrogen adsorption capacity on TiO2 particles is very low and there is no hydrogen adsorption enhancement on TiO2 particles alone when electric field is applied, the effect of dielectric coating is demonstrated. Another set of experiments investigated the behavior of hydrogen adsorption over TiO2-coated activated carbon under various electric potentials. The results revealed that the hydrogen adsorption first increased and then decreased with the increase of electric field. The improved storage was due to a stronger interaction between charged carbon surface and polarized hydrogen molecule caused by field induced polarization of TiO2 coating. When the electric field was sufficient to cause considerable ionization of hydrogen, the decrease of hydrogen adsorption occurred. The current leak detected at 3000 V was a sign of ionization of hydrogen. Experiments were also carried out to examine the hydrogen adsorption performances over activated carbon separated by other dielectric materials, MgO, ZnO and BaTiO3, respectively. For the samples partitioned with MgO and ZnO, the measurements with and without an electric field indicated negligible differences. Electric field enhanced adsorption has been observed on the activated carbon separated with BaTiO3, a material with unusually high dielectric constant. Corresponding computational calculations using Density Functional Theory have been performed on hydrogen interaction with charged TiO2 molecule as well as TiO2 molecule, coronene and TiO2-doped coronene in the presence of an electric field. The simulated results were consistent with the observations from experiments, further confirming the proposed hypotheses.

ALTERNATING CURRENT DIELECTROPHORESIS OF CORE-SHELL NANOPARTICLES: EXPERIMENTS AND COMPARISON WITH THEORY

Nanoparticles are fascinating where physical and optical properties are related to size. Highly controllable synthesis methods and nanoparticle assembly are essential [6] for highly innovative technological applications. Among nanoparticles, nonhomogeneous core-shell nanoparticles (CSnp) have new properties that arise when varying the relative dimensions of the core and the shell. This CSnp structure enables various optical resonances, and engineered energy barriers, in addition to the high charge to surface ratio. Assembly of homogeneous nanoparticles into functional structures has become ubiquitous in biosensors (i.e. optical labeling) [7, 8], nanocoatings [9-13], and electrical circuits [14, 15]. Limited nonhomogenous nanoparticle assembly has only been explored. Many conventional nanoparticle assembly methods exist, but this work explores dielectrophoresis (DEP) as a new method. DEP is particle polarization via non-uniform electric fields while suspended in conductive fluids. Most prior DEP efforts involve microscale particles. Prior work on core-shell nanoparticle assemblies and separately, nanoparticle characterizations with dielectrophoresis and electrorotation [2-5], did not systematically explore particle size, dielectric properties (permittivity and electrical conductivity), shell thickness, particle concentration, medium conductivity, and frequency. This work is the first, to the best of our knowledge, to systematically examine these dielectrophoretic properties for core-shell nanoparticles. Further, we conduct a parametric fitting to traditional core-shell models. These biocompatible core-shell nanoparticles were studied to fill a knowledge gap in the DEP field. Experimental results (chapter 5) first examine medium conductivity, size and shell material dependencies of dielectrophoretic behaviors of spherical CSnp into 2D and 3D particle-assemblies. Chitosan (amino sugar) and poly-L-lysine (amino acid, PLL) CSnp shell materials were custom synthesized around a hollow (gas) core by utilizing a phospholipid micelle around a volatile fluid templating for the shell material; this approach proves to be novel and distinct from conventional core-shell models wherein a conductive core is coated with an insulative shell. Experiments were conducted within a 100 nl chamber housing 100 um wide Ti/Au quadrapole electrodes spaced 25 um apart. Frequencies from 100kHz to 80MHz at fixed local field of 5Vpp were tested with 10-5 and 10-3 S/m medium conductivities for 25 seconds. Dielectrophoretic responses of ~220 and 340(or ~400) nm chitosan or PLL CSnp were compiled as a function of medium conductivity, size and shell material.

Spin ladders and quantum simulators for Tomonaga–Luttinger liquids

Magnetic insulators have proven to be usable as quantum simulators for itinerant interacting quantum systems. In particular the compound (C5H12N)2CuBr4 (for short: (Hpip)2CuBr4) was shown to be a remarkable realization of a Tomonaga–Luttinger liquid (TLL) and allowed us to quantitatively test the TLL theory. Substitution weakly disorders this class of compounds and thus allows us to use them to tackle questions pertaining to the effect of disorder in TLL as well, such as that of the formation of the Bose glass. In this paper we present, as a first step in this direction, a study of the properties of the related (Hpip)2CuCl4 compound. We determine the exchange couplings and compute the temperature and magnetic field dependence of the specific heat, using a finite temperature density matrix renormalization group procedure. Comparison with the measured specific heat at zero magnetic field confirms the exchange parameters and Hamiltonian for the (Hpip)2CuCl4 compound, giving the basis needed to begin studying the disorder effects.

50th anniversary of the Judd–Ofelt theory: An experimentalist's view of the formalism and its application

The theory on the intensities of 4f-4f transitions introduced by B.R. Judd and G.S. Ofelt in 1962 has become a center piece in rare-earth optical spectroscopy over the past five decades. Many fundamental studies have since explored the physical origins of the Judd–Ofelt theory and have proposed numerous extensions to the original model. A great number of studies have applied the Judd–Ofelt theory to a wide range of rare-earth doped materials, many of them with important applications in solid-state lasers, optical amplifiers, phosphors for displays and solid state lighting, upconversion and quantum-cutting materials, and fluorescent markers. This paper takes the view of the experimentalist who is interested in appreciating the basic concepts, implications, assumptions, and limitations of the Judd–Ofelt theory in order to properly apply it to practical problems. We first present the formalism for calculating the wavefunctions of 4f electronic states in a concise form and then show their application to the calculation and fitting of 4f-4f transition intensities. The potential, limitations and pitfalls of the theory are discussed, and a detailed case study of LaCl3:Er3+ is presented.

The (2 + 1)-d U (1) quantum link model masquerading as deconfined criticality

The (2 + 1)-d U(1) quantum link model is a gauge theory, amenable to quantum simulation, with a spontaneously broken SO(2) symmetry emerging at a quantum phase transition. Its low-energy physics is described by a (2 + 1)-d RP(1) effective field theory, perturbed by an SO(2) breaking operator, which prevents the interpretation of the emergent pseudo-Goldstone boson as a dual photon. At the quantum phase transition, the model mimics some features of deconfined quantum criticality, but remains linearly confining. Deconfinement only sets in at high temperature.

Modern charge density studies: the entanglement of experiment and theory

This tutorial review article is intended to provide a general guidance to a reader interested to learn about the methodologies to obtain accurate electron density mapping in molecules and crystalline solids, from theory or from experiment, and to carry out a sensible interpretation of the results, for chemical, biochemical or materials science applications. The review mainly focuses on X-ray diffraction techniques and refinement of experimental models, in particular multipolar models. Neutron diffraction, which was widely used in the past to fix accurate positions of atoms, is now used for more specific purposes. The review illustrates three principal analyses of the experimental or theoretical electron density, based on quantum chemical, semi-empirical or empirical interpretation schemes, such as the quantum theory of atoms in molecules, the semi-classical evaluation of interaction energies and the Hirshfeld analysis. In particular, it is shown that a simple topological analysis based on a partition of the electron density cannot alone reveal the whole nature of chemical bonding. More information based on the pair density is necessary. A connection between quantum mechanics and observable quantities is given in order to provide the physical grounds to explain the observations and to justify the interpretations.

Interfaces, strings, and a soft mode in the square lattice quantum dimer model

The quantum dimer model on the square lattice is a U(1) gauge theory that addresses aspects of the physics of high-Tc superconductors. Using a quantum Monte Carlo method, we show that the theory exists in a confining columnar valence bond solid phase. The interfaces separating distinct columnar phases display plaquette order, which, however, is not realized as a bulk phase. Static “electric” charges are confined by flux tubes that consist of multiple strands, each carrying a fractionalized flux ¼. A soft pseudo-Goldstone mode (which becomes exactly massless at the Rokhsar-Kivelson point) extends deep into the columnar phase, with potential implications for high-Tc physics.

Loop formulation of supersymmetric Yang-Mills quantum mechanics

We derive the fermion loop formulation of N=4 supersymmetric SU(N) Yang-Mills quantum mechanics on the lattice. The loop formulation naturally separates the contributions to the partition function into its bosonic and fermionic parts with fixed fermion number and provides a way to control potential fermion sign problems arising in numerical simulations of the theory. Furthermore, we present a reduced fermion matrix determinant which allows the projection into the canonical sectors of the theory and hence constitutes an alternative approach to simulate the theory on the lattice.

Quarks and a Unified Theory of Nature Fundamental Forces

Quarks were introduced 50 years ago opening the road towards our understanding of the elementary constituents of matter and their fundamental interactions. Since then, a spectacular progress has been made with important discoveries that led to the establishment of the Standard Theory that describes accurately the basic constituents of the observable matter, namely quarks and leptons, interacting with the exchange of three fundamental forces, the weak, electromagnetic and strong force. Particle physics is now entering a new era driven by the quest of understanding of the composition of our Universe such as the unobservable (dark) matter, the hierarchy of masses and forces, the unification of all fundamental interactions with gravity in a consistent quantum framework, and several other important questions. A candidate theory providing answers to many of these questions is string theory that replaces the notion of point particles by extended objects, such as closed and open strings. In this short note, I will give a brief overview of string unification, describe in particular how quarks and leptons can emerge and discuss what are possible predictions for particle physics and cosmology that could test these ideas.

Quarks and a unified theory of Nature fundamental forces

Quarks were introduced 50 years ago opening the road towards our understanding of the elementary constituents of matter and their fundamental interactions. Since then, a spectacular progress has been made with important discoveries that led to the establishment of the Standard Theory that describes accurately the basic constituents of the observable matter, namely quarks and leptons, interacting with the exchange of three fundamental forces, the weak, electromagnetic and strong force. Particle physics is now entering a new era driven by the quest of understanding of the composition of our Universe such as the unobservable (dark) matter, the hierarchy of masses and forces, the unification of all fundamental interactions with gravity in a consistent quantum framework, and several other important questions. A candidate theory providing answers to many of these questions is string theory that replaces the notion of point particles by extended objects, such as closed and open strings. In this short note, I will give a brief overview of string unification, describe in particular how quarks and leptons can emerge and discuss what are possible predictions for particle physics and cosmology that could test these ideas.