scholarly journals Molecular structure of calcium, magnesium, strontium and barium m-nitrobenzoates

2010 ◽  
Vol 24 (3-4) ◽  
pp. 433-437 ◽  
Author(s):  
Mariola Samsonowicz
Keyword(s):  
Molecular Structure ◽  
Electronic Structure ◽  
Ir Spectra ◽  
Dipole Moments ◽  
Atomic Charges ◽  
Barium Ions ◽  
Nitrobenzoic Acid ◽  
Calcium Magnesium ◽  
Ft Ir

The effect of calcium, magnesium, strontium and barium ions on the electronic structure of m-nitrobenzoates was studied. The FT-IR spectra of m-nitrobenzoic acid and its salts were registered, assigned and analyzed. Characteristic shifts and changes in intensities of bands along the metal series were observed. The structures of m-nitrobenzoic acid and its calcium, magnesium, strontium and barium salts were optimized at the B3LYP/LANL2DZ level. Geometric aromaticity indices, atomic charges, dipole moments and energies were also calculated.

Benchmarking Electronic Structure Methods for Accurate Fixed-Charge Electrostatic Models

2019 ◽  
Author(s):  
Alex Zhou ◽  
Michael Schauperl ◽  
Paul Nerenberg
Keyword(s):  
Electronic Structure ◽  
Gas Phase ◽  
Condensed Phase ◽  
Force Fields ◽  
Dipole Moments ◽  
Fixed Charge ◽  
Basis Set ◽  
Atomic Charges ◽  
Molecular Dipole ◽  
Partial Atomic Charges

<p>The accuracy of classical molecular mechanics (MM) force fields used for condensed phase molecular simulations depends strongly on the accuracy of modeling nonbonded interactions between atoms, such as electrostatic interactions. Some popular fixed-charge MM force fields use partial atomic charges derived from gas phase electronic structure calculations using the Hartree-Fock method with the relatively small 6-31G* basis set (HF/6-31G*). It is generally believed that HF/6-31G* generates fortuitously overpolarized electron distributions, as would be expected in the higher dielectric environment of the condensed phase. Using a benchmark set of 47 molecules we show that HF/6-31G* overpolarizes molecules by just under 10% on average with respect to experimental gas phase dipole moments. The overpolarization of this method/basis set combination varies significantly though and, in some cases, even leads to molecular dipole moments that are lower than experimental gas phase measurements. We further demonstrate that using computationally inexpensive density functional theory (DFT) methods, together with appropriate augmented basis sets and a continuum solvent model, can yield molecular dipole moments that are both more strongly and more uniformly overpolarized. These data suggest that these methods – or ones similar to them – should be adopted for the derivation of accurate partial atomic charges for next-generation MM force fields.<br></p>

Experimental Study on DNA Molecular Structure of Acute Myeloid Leukemia and Myelodysplastic Syndrome by FT-IR Spectra.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 4409-4409
Author(s):  
Shihong Wang ◽  
Zhijian Xiao ◽  
Ming-Zhe Han ◽  
Qiang Wu
Keyword(s):  
Molecular Structure ◽  
Acute Myeloid Leukemia ◽  
Ir Spectra ◽  
Myeloid Leukemia ◽  
Control Groups ◽  
Diagnosis And Prognosis ◽  
Significant Difference ◽  
Ft Ir ◽  
And Control ◽  
Acute Myeloid

Abstract So for, there were no definite molecular markers in most acute myeloid leukemia(AML) and myelodysplastic syndrome(MDS), and their molecular mechanisms have not been clarified. Their clinical diagnosis were mainly based on morphology of bone marrow and peripheral blood cells. The current study aimed to explore the mechanisms of abnormal DNA molecular structure in AML and MDS by Fourier Transform Infrared(FT-IR) spectra, and to explore the methods of early diagnosis and prognosis. At first, we segregated the mononuclear cells of AML-M2a, MDS and control groups samples, extracted the DNA of these cells, then we checked the completely dry DNA by FT-IR spectra and analysed the identity and difference among AML-M2a, MDS and Control groups. Comparing the mean DNA spectra of the AML-M2a, MDS and control groups revealed statistically significant difference(p&lt;0.001). Each group has an almost concordant FT-IR spectra rule. Compared with the control group, AML-M2a and MDS both were significant different(p&lt;0.001). Absorbance increasing of DNA in AML-M2a, MDS at the wavenumber 2880cm-1 and 2940cm-1 shown hypermethylation of nucleotide base(p&lt;0.001). Absorbance decreasing at wavenumber 1420cm-1 demonstrated deacetylation(p&lt;0.001). Absorbance decreasing at wavenumber 1150cm-1 indicated the abnormality of C—O,S=O,C—OH,C—C,C—O—C,C—N, and the absorbance increasing at wavenumber 1660–1590cm-1 reflected in-plane ring, C=N stretching vibrations and hypermethylation of cytosine. There were also other mild difference among AML-M2a, MDS and control groups. In summary, The principal chain, phosphonic backbone and nucleotide base of DNA in AML-M2a and MDS have significant difference with the control and could be the initial changes of DNA in AML and MDS occurrence and development. Based on the rules of change, FT-IR spectra is a potential method of early diagnosis and prognosis in AML and MDS.

Benchmarking Electronic Structure Methods for Accurate Fixed-Charge Electrostatic Models

2019 ◽  
Author(s):  
Alex Zhou ◽  
Michael Schauperl ◽  
Paul Nerenberg
Keyword(s):  
Electronic Structure ◽  
Gas Phase ◽  
Condensed Phase ◽  
Force Fields ◽  
Dipole Moments ◽  
Fixed Charge ◽  
Basis Set ◽  
Atomic Charges ◽  
Molecular Dipole ◽  
Partial Atomic Charges

<p>The accuracy of classical molecular mechanics (MM) force fields used for condensed phase molecular simulations depends strongly on the accuracy of modeling nonbonded interactions between atoms, such as electrostatic interactions. Some popular fixed-charge MM force fields use partial atomic charges derived from gas phase electronic structure calculations using the Hartree-Fock method with the relatively small 6-31G* basis set (HF/6-31G*). It is generally believed that HF/6-31G* generates fortuitously overpolarized electron distributions, as would be expected in the higher dielectric environment of the condensed phase. Using a benchmark set of 47 molecules we show that HF/6-31G* overpolarizes molecules by just under 10% on average with respect to experimental gas phase dipole moments. The overpolarization of this method/basis set combination varies significantly though and, in some cases, even leads to molecular dipole moments that are lower than experimental gas phase measurements. We further demonstrate that using computationally inexpensive density functional theory (DFT) methods, together with appropriate augmented basis sets and a continuum solvent model, can yield molecular dipole moments that are both more strongly and more uniformly overpolarized. These data suggest that these methods – or ones similar to them – should be adopted for the derivation of accurate partial atomic charges for next-generation MM force fields.<br></p>

scholarly journals The FT-IR, FT-Raman,1H and13C NMR study on molecular structure of sodium(I), calcium(II), lanthanum(III) and thorium(IV) cinnamates

2010 ◽  
Vol 24 (3-4) ◽  
pp. 277-281 ◽  
Author(s):  
M. Kalinowska ◽  
W. Lewandowski ◽  
R. Swislocka ◽  
E. Regulska
Keyword(s):  
Molecular Structure ◽  
Nuclear Magnetic Resonance ◽  
Electronic Structure ◽  
Magnetic Resonance ◽  
Chemical Shifts ◽  
1H And13c Nmr ◽  
Nmr Study ◽  
Ft Ir ◽  
C Nmr ◽  
Ft Raman

In this work the effect of sodium(I), calcium(II), lanthanum(III) and thorium(IV) ions on the electronic structure of cinnamic acid (phenylacrylic acid) was studied. In this research: infrared (FT-IR), Raman (FT-Raman), nuclear magnetic resonance (1H,13C NMR) were used. In the series of Na(I)→ Ca(II)→ La(III)→ Th(IV) cinnamates: (1) systematic shifts of several bands in the FT-IR and FT-Raman spectra, and (2) regular chemical shifts of protons1H and13C nuclei were observed.

Benchmarking Electronic Structure Methods for Accurate Fixed-Charge Electrostatic Models

2019 ◽  
Author(s):  
Alex Zhou ◽  
Michael Schauperl ◽  
Paul Nerenberg
Keyword(s):  
Electronic Structure ◽  
Gas Phase ◽  
Condensed Phase ◽  
Force Fields ◽  
Dipole Moments ◽  
Fixed Charge ◽  
Basis Set ◽  
Atomic Charges ◽  
Molecular Dipole ◽  
Partial Atomic Charges

<div><div><div><p>The accuracy of classical molecular mechanics (MM) force fields used for condensed phase molecular simulations depends strongly on the accuracy of modeling nonbonded interactions between atoms, such as electrostatic interactions. Some popular fixed-charge MM force fields use partial atomic charges derived from gas phase electronic structure calculations using the Hartree-Fock method with the relatively small 6-31G* basis set (HF/6-31G*). It is generally believed that HF/6-31G* generates fortuitously overpolarized electron distributions, as would be expected in the higher dielectric environment of the condensed phase. Using a benchmark set of 47 molecules, we show that HF/6-31G* does not uniformly overpolarize molecules and in some cases even leads to molecular dipole moments that are lower than experimental gas phase measurements. We further demonstrate that using computationally inexpensive density functional theory (DFT) methods, together with appropriate augmented basis sets and a continuum solvent model, can yield molecular dipole moments that are both more strongly and more uniformly overpolarized. These data suggest that these methods – or ones similar to them – should be adopted for the derivation of accurate partial atomic charges for next-generation MM force fields.</p></div></div></div>

scholarly journals Application of FT-IR technique to bituminous materials

2014 ◽  
Vol 13 (4) ◽  
pp. 317-324
Author(s):  
Adam Zofka ◽  
Dominika Maliszewska ◽  
Maciej Maliszewski
Keyword(s):  
Molecular Structure ◽  
Quality Assurance ◽  
Ir Spectra ◽  
Material Science ◽  
Functional Group ◽  
Construction Materials ◽  
Practical Applications ◽  
Bituminous Materials ◽  
Ft Ir ◽  
Detection And Quantification

Spectroscopy is a fundamental method used in the material science that relies on the interaction of the electromagnetic radiation with a matter. Infrared spectroscopy allows for material fingerprinting as well as detection and quantification of compounds in a sample. In principle, IR spectrometers record the absorption of electromagnetic energy by chemical bounds in a sample as a function of wavelength. Chemical bounds have unique spectra bands at specific wavelengths regardless of the composition of the remaining molecular structure. The absorbance at these specific wavelengths can be used to quantify a particular functional group in the analyzed material. Absorbance peaks are easily identified on the IR spectra and can be used to fingerprint a compound in a mixture, especially when compared to the original unmodified IR spectra. In the recent years, the FT-IR method has become a popular tool for the quality assurance in the practical applications as well as it became a very useful tool in studying various construction materials, e.g. portland cement, bitumen, etc.

Facile Synthesis of Pyrene/Pyrrole Copolymer with Strong Green Fluorescence

2012 ◽  
Vol 482-484 ◽  
pp. 835-838
Author(s):  
Zhen Zhong Hou ◽  
Qing Hao Yang ◽  
Ying Li
Keyword(s):  
Molecular Structure ◽  
Ir Spectra ◽  
Stokes Shift ◽  
Linear Structure ◽  
Green Fluorescence ◽  
Facile Synthesis ◽  
Copolymer Solution ◽  
Ft Ir ◽  
Fluorescence Spectrometer ◽  
Oxidative Copolymerization

The pyrene/pyrrole copolymer (Pn/Py copolymer) has been sucessfully synthesized by the facile chemically oxidative copolymerization. UV-vis and FT-IR spectra are used to investigate the molecular structure of the copolymer. The results show that pyrene and pyrrole units in the copolymer chain are interconnected via α, α-coupling to form a linear structure. At the same concentration, the copolymer solution exhibits the strongest green fluorescence with a maximum emission at 503 nm and a large stokes shift of about 113 nm by fluorescence spectrometer. The excellent fluorescence of Pn/Py copolymer may be due to its better planar molecular structure and higher large π-conjugation, that is confirmed by UV-vis spectra and molecular simulation.

Light- or Dark-Colored, L-DOPA-Based Melanins

2018 ◽  
Author(s):  
Koen Vercruysse ◽  
Margaret M. Whalen
Keyword(s):  
Human Physiology ◽  
Ir Spectra ◽  
Immune Cells ◽  
Chemical Properties ◽  
Chemical Signature ◽  
Ft Ir

<p>This report is a continuation of previous research on the H<sub>2</sub>O<sub>2</sub>-mediated synthesis of melanin-like pigments. We synthesized and characterized L-DOPA-based pigments using air- or H<sub>2</sub>O<sub>2</sub>-mediated<sub> </sub>oxidation. We compared their physic-chemical properties and evaluated their capacity to affect the interleukin release from immune cells. The use of higher concentrations of H<sub>2</sub>O<sub>2</sub> resulted in melanin-like materials with a distinct chemical signature in their FT-IR spectra and a lighter color. All pigments enhanced the interleukin release from immune cells. The possibility that lighter-colored melanins can be generated is discussed in the context of the importance of melanin-based pigmentation in human physiology.</p>

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