Molecular mechanics force fields from ab initio calculations

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/87595/2/224_1.pd

Optical nonlinearity and charge transfer analysis of 4-[(E)-2-(2,4,6-Trinitrophenyl) ethylidene] benzonitrile adsorbed on silver nanoparticles : Computational and experimental investigations

The search for a potential nonlinear optical (NLO) material has led to the investigation of an organic compound 4-[(E)-2-(2,4,6-Trinitrophenyl)ethylidene]benzonitrile (TEB), which has a possibility of enhancing the NLO properties by the charge transfer mechanism if metal atoms are adsorbed on it. The experimental characterization of TEB is done using Fourier Transform Infrared (FT-IR), Fr-Raman, Ultraviolet-visible (UV-Visible), Photoluminescence (PL), Thermogravimetric/Differential Thermal Analysis (TG/DTA) and Z-scan techniques. The third order NLO properties evaluated using Z-scan technique proves that the material can be used as a good optical limiter. TEB is attached with silver atoms and the theoretical studies including geometry optimization, NBO analysis and hyperpolarizability calculations are carried out. The TEB molecule with silver atoms adsorbed is found to have increased hyperpolarizability values. The charge transfer from the metal atom to the nitrile group of the molecule is evident from the Surface Enhanced Raman Scattering (SERS) spectra using the silver nanoparticles. (C) 2018 Elsevier Ltd. All rights reserved.Peer reviewe

A combined study on structures and vibrational spectra of the antiviral rimantadine using SQMFF and DFT calculations

In this research, a combined study on structures and vibrational spectra of antiviral rimantadine have been performed using hybrid B3LYP/6-311 thorn thorn G** calculations and the scaled quantum force field (SQMFF) proced-ure. Harmonic force fields and scaled force constants of Free Base (FB), Cationic (CA) and Hydrochloride (HCl) species derived from the antiviral rimantadine have been calculated in gas phase and in aqueous solution using normal internal coordinates and scaling factors. Good correlations were acquired comparing the theoretical IR, Raman, 1H- 13C-NMR and UV spectra of three species with the analogous experimental ones, suggesting probably, the presence of all them in both phases. The main force constants of three species have evidenced lower values than the corresponding to antiviral amantadine. The ionic character of N1-H33 center dot center dot center dot Cl36 bond of HCl species in aqueous solution evidence positive Mulliken charge on N1 atom indicating that this species is as CA one. Rimantadine presents higher solvation energies in water than other antiviral species, such as chloroquin, niclo-samide, cidofovir and brincidofovir. The FB and HCl species of rimantadine are slightly less reactive than the corresponding to amantadine while the opposite is observed for the CA species. The predicted ECD spectra for the FB and CA species show positive Cotton effect different from the negative observed for the HCl one. These different behaviours of three species of rimantadine could probably explain the differences observed in the in-tensities of bands predicted in the electronic spectra of these species.Peer reviewe

Qualitative and quantitative approach towards the molecular understanding of structural, vibrational and optical features of urea ninhydrin monohydrate

In this study, single crystals of urea ninhydrin monohydrate (UNMH) have been grown by slow evaporation method. The grown crystals were characterized by FT-IR, FT-Raman and UV-Vis-NIR spectroscopies. The Kurtz and Perry powder method was employed to confirm the near-zero SHG efficiency of the as-grown centrosymmetric UNMH crystal. The third order nonlinearity of the crystal has been studied by the open aperture Z-scan method. The nonlinear absorption coefficient is calculated and the potentiality of UNMH in optical limiting applications is identified. The molecular geometry and the origin of optical non-linearity at the molecular level have been investigated by the density functional theory. The normal coordinate analysis was carried out to assign the molecular vibrational modes. Vibrational spectral studies confirms the presence of weak O-H ... O and moderate O-H ... O type hydrogen bonds in the molecule as well as O-H ... O, N-H ... O and blue-shifted C-H ... O type H-bonds in the crystal. The intramolecular charge transfer interactions and the electronic absorption mechanisms have been discussed. The static and the dynamic values of hyperpolarizabilities for UNMH were estimated theoretically by DFT methods. (C) 2017 Elsevier B.V. All rights reserved.Peer reviewe

Vibrational analysis of crystalline triglycine

We have refined vibrational force fields for polypeptides that permit excellent reproduction of the normal mode frequencies of such molecules. This is demonstrated in the present study, in which 80 IR and Raman bands of crystalline triglycine between 1800 and 200 cm-1 are reproduced with an average error of 6 cm-1. A deuterated sample is shown by normal mode analysis to have remained protonated at the C-terminal peptide group. Such results show that normal mode analysis can now provide a rigorous base for spectral studies of conformation in peptides and proteins.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/27648/1/0000029.pd

Vibrational and electronic properties of 4 '-halomethyl-2-biphenylcarbonitrile compounds

In this paper we studied the structural, vibrational and electronic properties of the 4'-bromomethyl-2-biphenylcarbonitrile (BMBP) 4'-chloromethyl-2-biphenylcarbonitrile (CMBP) and 4'-fluoromethyl-2-biphenylcarbonitrile (FMBP) compounds using experimental and theoretical methods. The FT-IR and FT-Raman spectra of BMBP in solid phase were recorded in the region 4000-400 cm(-1) and 4000 -50 cm(-1), respectively. The UV absorption spectrum of BMBP was recorded in dichloromethane and methanol solvents in the range 180-400 nm. The theoretical spectral properties of title compounds were simulated using density functional theory (DFT) and time dependent DFT methods. Scaling of the vibrational frequencies was carried out with the MOLVIB program using multiple scaling factors and assignment to each vibrational frequency was consigned on the basis of potential energy distribution (PED). The electronic spectrum of BMBP in two different solvents (methanol and dichloromethane), calculated at the CAM-B3LYP/6-31G(d,p) level compares well with the experimental data and validates the current method for predicting the absorption spectrum of CMBP and FMBP. Furthermore, the electronic, nonlinear optical and thermodynamics properties of the three compounds were discussed in detailed. (C) 2017 Elsevier B.V. All rights reserved.Peer reviewe

Crystal structure, Hirshfeld surfaces and DFT computation of NLO active (2E)-2-(ethoxycarbonyl)-3-[(1-methoxy-1-oxo-3-phenylpropan-2-yl)amino] prop-2-enoic acid

Nonlinear optical (NLO) activity of the compound (2E)-2-(ethoxycarbonyl)-3-[(1-methoxy-l-oxo-3phenylpropan-2-yl)amino] prop-2-enoic add is investigated experimentally and theoretically using X-ray crystallography and quantum chemical calculations. The NLO activity is confirmed by both powder Second Harmonic Generation (SHG) experiment and first hyper polarizability calculation. The title compound displays 8 fold excess of SHG activity when compared with the standard compound KDP. The gas phase geometry optimization and vibrational frequencies calculations are performed using density functional theory (DFT) incorporated in B3LYP with 6-311G++ (d,p) basis set. The title compound crystallizes in non-centrosymmetric space group P21. Moreover, the crystal structure is primarily stabilized through intramolecular N-H center dot center dot center dot O and O-H center dot center dot center dot O hydrogen bonds and intermolecular C-H center dot center dot center dot O and C-H center dot center dot center dot pi interactions. These intermolecular interactions are analyzed and quantified using Hirshfeld surface analysis and PIXEL method. The detailed vibrational assignments are performed on the basis of the potential energy distributions (PED) of the vibrational modes. (C) 2015 Elsevier B.V. All rights reserved.Peer reviewe

IL-22 affects smooth muscle cell phenotype and plaque formation in apolipoprotein E knockout mice.

IL-22 is a recently discovered cytokine that belongs to the family of IL-10 related cytokines. It is produced by activated T-cells and innate lymphoid cells and has been suggested to be involved in tissue repair. As both inflammation and repair play important roles in atherosclerosis we investigated if IL-22 deficiency influences the disease process in Apoe(-/-) mice

The geology of Tianshui‐Qin'an area of the western Loess Plateau and the chemical characteristics of its Neolithic pottery

The difference in the chemical compositions between Neolithic pottery from the eastern and western ends of the northern Chinese Loess Plateau has been known for some time and a number of possible explanations have been proposed. However, a full understanding of the difference is yet to be achieved. Based on recent geological studies of the Tianshui-Qin’an area on the western Loess Plateau, the present study establishes a logical connection between the chemical characteristics of Neolithic pottery from the western Loess Plateau and the primary sediments available in the area. Moreover, this study reveals that the chemical compositions of clay used for fine wares and coarse wares at Dadiwan also bear some clear differences. Based on these findings, the paper discusses possible clay selection methods by potters in the Neolithic western Loess Plateau to make their different wares based on the locales where suitable raw materials are available. The paper demonstrates that the raw materials available for pottery making on the eastern and western Loess Plateau differ significantly and this explains the marked difference in ceramic composition between the two locations