Nitrile- and thiocyanate-derivatized amino acids have been found to be useful IR probes for investigating their local electrostatic environments in proteins. To shed light on the CN stretch frequency shift and spectral lineshape change induced by interactions with hydrogen-bonding solvent molecules, we carried out both classical and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations for MeCN and MeSCN in water. These QM/MM and conventional force field MD simulation results were found to be inconsistent with the experimental results as well as with the high-level ab initio calculation results of MeCN-water and MeSCN-water potential energies. Thus, a new set of atomic partial charges of MeCN and MeSCN is obtained. By using the MD simulation trajectories and the electrostatic potential model recently developed, the CN and SCN stretching mode frequency trajectories were obtained and used to simulate the IR spectra. The C[Triple Bond]N frequency blueshifts of MeCN and MeSCN in water are estimated to be 9.0 and 1.9 cm(-1), respectively, in comparison with those of gas phase values. These values are found to be in reasonable agreement with the experimentally measured IR spectra of MeCN, MeSCN, beta-cyano-L-alanine, and cyanylated cysteine in water and other polar solvents.

The explicit polarization (X-Pol) method has been examined using ab initio molecular orbital theory and density functional theory. The X-Pol potential was designed to provide a novel theoretical framework for developing next-generation force fields for biomolecular simulations. Importantly, the X-Pol potential is a general method, which can be employed with any level of electronic structure theory. The present study illustrates the implementation of the X-Pol method using ab initio Hartree -Fock theory and hybrid density functional theory. The computational results are illustrated by considering a set of bimolecular complexes of small organic molecules and ions with water. The computed interaction energies and hydrogen bond geometries are in good accord with CCSD(T) calculations and B3LYP/aug-cc-pVDZ optimizations.

Carbon nanotubes (CNTs) were grown vertically aligned on silicon oxide substrates by pyrolyzing iron phthalocyanine (FePc), cobalt phthalocyanine (CoPc), and nickel phthalocyanine (NiPc) in the temperature range 700−1000 °C. As the temperature increases from 700 to 1000 °C, the growth rate of CNTs increases by a factor of approximately 45 and the average diameter increases from 30 to 80 nm. The CNTs grown using FePc exhibit about 2 times higher growth rate than those using CoPc and NiPc. The CNTs usually have a cylindrical structure, and a bamboo-like structure with a larger diameter at the higher temperature. The CNTs are doped with 2−6 at. % nitrogen atoms. The nitrogen content tends to decrease with the temperature increase. The CNTs grown using NiPc contain a higher nitrogen concentration compared to those grown using FePc and CoPc. The degree of crystalline perfection of the graphitic sheets increases with the temperature, but depends on the catalyst and the nitrogen content. The Arrhenius plot provides the activation energy 30 ± 3 kcal/mol for all three sources, which is similar to the diffusion energy of carbon in bulk metal. This suggests that the bulk diffusion of carbon plays a decisive role in the growth of CNTs. The strain for the joint between the compartment layer and the wall determines the structure of the CNTs.

Molecular dynamics (MD) simulations and quantum mechanical electronic structure calculations are used to investigate the nature and dynamics of the phenol-benzene complex in the mixed solvent, benzene/CCl4. Under thermal equilibrium conditions, the complexes are continuously dissociating and forming. The MD simulations are used to calculate the experimental observables related to the phenol hydroxyl stretching mode, i.e., the two dimensional infrared vibrational echo spectrum as a function of time, which directly displays the formation and dissociation of the complex through the growth of off-diagonal peaks, and the linear absorption spectrum, which displays two hydroxyl stretch peaks, one for the complex and one for the free phenol. The results of the simulations are compared to previously reported experimental data and are found to be in quite reasonable agreement. The electronic structure calculations show that the complex is T shaped. The classical potential used for the phenol-benzene interaction in the MD simulations is in good accord with the highest level of the electronic structure calculations. A variety of other features is extracted from the simulations including the relationship between the structure and the projection of the electric field on the hydroxyl group. The fluctuating electric field is used to determine the hydroxyl stretch frequency-frequency correlation function (FFCF). The simulations are also used to examine the number distribution of benzene and CCl4 molecules in the first solvent shell around the phenol. It is found that the distribution is not that of the solvent mole fraction of benzene. There are substantial probabilities of finding a phenol in either a pure benzene environment or a pure CCl4 environment. A conjecture is made that relates the FFCF to the local number of benzene molecules in phenol's first solvent shell.

Intimate partner violence (IPV) survivors often do not seek critically needed help. A good understanding of the relationship between the pattern of violence and help-seeking is critical to developing adequate services for the survivors, as well as for reaching out to those who do not seek help. This study used the National Intimate Partner and Sexual Violence Survey to examine how IPV survivor's help-seeking varies, depending on the characteristics of the survivors and the pattern of victimization. Logistic regression analyses were conducted, with the survivors' help-seeking and use of formal or informal help as the dependent variables. The study results show that women are the primary victims of IPV, that the pattern of victimization is associated with both whether survivors seek help or not, and which help sources they utilize, if any. IPV consequences are also associated with survivors' help-seeking, as are demographic factors such as age, gender, race, and immigration status.