scholarly journals MINDO/3 Study of the Protonation of Phenol and Methylphenols

1982 ◽  
Vol 37 (7) ◽  
pp. 688-696
Author(s):  
M. Eckert-Maksić
Keyword(s):  
Structural Changes ◽  
Molecular Structures ◽  
Good Agreement

Abstract The electronic and molecular structures of phenol and its ortho-meta-, and para-methyl derivates as well as their conjugate acids were studied by the semiempirical MINDO/3 method. The calculations predict substantial structural changes upon protonation. Theoretically predict-ed protonation sites are in very good agreement with experimentally observed modes of protonation under superacidic conditions.

Computational Investigations of the Transmembrane Italian-Mutant (E22K) 3A\(\beta_{11 - 40}\) in Aqueous Solution

2018 ◽  
Vol 28 (3) ◽  
pp. 265 ◽  
Author(s):  
Son Tung Ngo
Keyword(s):  
Structural Changes ◽  
Replica Exchange ◽  
Aβ Oligomers ◽  
Replica Exchange Molecular Dynamics ◽  
Charged Residue ◽  
Intermolecular Contacts ◽  
Structural Details ◽  
Positively Charged ◽  
Dynamic Fluctuation ◽  
Good Agreement

The Amyloid beta (Aβ) oligomers are characterized as critical cytotoxic materials in Alzheimer’s disease (AD) pathogenesis. Structural details of transmembrane oligomers are inevitably necessary to design/search potential inhibitor due to treat AD. However, the experimental detections for structural modify of low-order Aβ oligomers are precluded due to the extremely dynamic fluctuation of the oligomers. In this project, the transmembrane Italian-mutant (E22K) 3Aβ11-40 (tmE22K 3Aβ11-40) was extensively investigated upon the temperature replica exchange molecular dynamics (REMD) simulations. The structural changes of the trimer when replacing the negative charged residue E22 by a positively charged residue K were monitored over simulation intervals. The oligomer size was turned to be larger and the increase of β-content was recorded. The momentous gain of intermolecular contacts with DPPC molecules implies that tmE22K 3Aβ11-40 easier self-inserts into the membrane than the WT one. Furthermore, the tighter interaction between constituting monomers was indicated implying that the E22K mutation probably enhances the Aβ fibril formation. The results are in good agreement with experiments that E22K amyloid is self-aggregate faster than the WT form. Details information of tmE22K trimer structure and kinetics probably yield the understanding of AD mechanism.

SHELL DEFORMATION AND SPIN EFFECTS IN NUCLEON SEPARATION ENERGIES

1993 ◽  
Vol 02 (04) ◽  
pp. 789-807
Author(s):  
D. CALEB CHANTHI RAJ ◽  
M. RAJASEKARAN ◽  
R. PREMANAND
Keyword(s):  
Structural Changes ◽  
Shell Correction ◽  
Separation Energy ◽  
Systematic Analysis ◽  
Spin Effects ◽  
Wide Range ◽  
Type Calculation ◽  
Nucleon Separation Energy ◽  
New Formula ◽  
Good Agreement

A new formula to obtain shell correction to separation energy is derived from a Strutinsky type calculation. A systematic analysis of shell and deformation effects on nucleon separation energy is made. Spin induced structural changes are also evident in shape changes along the spin coordinate. Calculations are performed for a wide range of nuclei from Zr to Cm. The results are generally in very good agreement with experimental analysis.

ab initio MO Optimization of Molecular Structures of Fluoro- and Chloro-Substituted Dibenzo-p-dioxines and the Effect of Halogen Substitution at the 2,3,7,8-Positions on Metabolic Attack

1997 ◽  
Vol 52 (11) ◽  
pp. 1418-1431 ◽  
Author(s):  
Roland Weber ◽  
Till Kühn ◽  
Hanspaul Hagenmaier ◽  
Günter Häfelinger
Keyword(s):  
Ab Initio Calculations ◽  
Ab Initio ◽  
Energy Gap ◽  
Substituent Effects ◽  
Molecular Structures ◽  
X Ray ◽  
Degree Pattern ◽  
Chlorine Substituent ◽  
Homo Lumo ◽  
Good Agreement

Full ab initio optimizations were performed on the molecular structures of 24 fluorinated and chlorinated dibenzodioxines (PFDD/PCDD ) and dibenzofurans (PFDF/PCDF). Reasonable agreement was found by comparing the geometries of four calculated structures with known X-ray data from the literature. For the fluorine substituent, calculated electron densities (Mulliken total charges and π-electron charges) clearly demonstrate the opposite influence of the inductive (I) and mesomeric (M) effect. The changes in π-densities at carbons in ortho-, meta- and para-position are constant for each fluorine substituent (independent of degree, pattern, and position of substitution). It is thus possible to calculate the π-densities of the substituted dioxines by increments starting from dibenzodioxine. π-Charges from quantum mechanical calculations and the increment system show good agreement even for OctaFDD (O8FDD ), where eight substituent effects are acting additively. Compared with fluorine, the chlorine substituent exercises a smaller -I-effect and a clearly weaker +M-effect. The HOMO coefficients of the unsubstituted dibenzodioxine and dibenzofuran, extracted from ab initio calculations, yield a good explanation for the observed regioselective metabolic attack at the 2,3,7,8-positions. The squares of the HOMO-coefficients of the 2,3,7,8-positions in dibenzodioxine (DD ) are about ten times greater than those of the 1,4,6,9-positions. These HOMO coefficients are practically unaffected by halide substitution. But halogen substitution reduces strongly the electron density at the halogen-bound carbon, which, however, is a necessary prerequisite for the electrophilic oxygen transfer during metabolism. One would therefore expect halogen substitution of dibenzodioxine and dibenzofuran (DF) at the 2,3,7,8-position to hinder metabolism, as is indeed found. This provides a plausible explanation for the highly selective tissue retention of 2,3,7,8-substituted PCDDs and PCDFs. Our ab initio calculations of five tetra CDDs (T4CDDs) confirm the postulate of Kobayashi et al. [1 ] who, using semiempirical calculations, found a correlation between the toxicity of a dioxine congener and its absolute molecular hardness. The 2,3,7,8-T4CDD also exhibits the smallest absolute hardness (derived from the HOMO-LUMO energy gap) in our calculations.

Tests of second-generation and third-generation density functionals for electron affinities of the alkylthio radicals

2014 ◽  
Vol 13 (04) ◽  
pp. 1450030 ◽  
Author(s):  
Aifang Gao ◽  
Aiguo Li
Keyword(s):  
Dft Method ◽  
Absolute Error ◽  
Molecular Structures ◽  
Basis Set ◽  
Density Functionals ◽  
Electron Affinities ◽  
Generalized Gradient ◽  
Experimental Values ◽  
P Type ◽  
Good Agreement

The molecular structures and electron affinities of the R – S / R – S -( R = CH 3, C 2 H 5, n- C 3 H 7, n- C 4 H 9, n- C 5 H 11, i- C 3 H 7, i- C 4 H 9, t- C 4 H 9) species have been studied using 17 pure and hybrid density functionals (five generalized gradient approximation (GGA) methods, six hybrid GGAs, one meta GGA method and five hybrid meta GGAs). The basis set used in this work is of double-ζ plus polarization quality with additional diffuse s- and p-type functions, denoted by DZP++. The geometries are fully optimized with each DFT method and discussed. Harmonic vibrational frequencies are found to be within 3.5% of available experimental values for most functionals. Three different types of the neutral-anion energy separations have been presented. The theoretical electron affinities of alkylthio radicals are in good agreement with the experiment data. The M06 method is very good for the adiabatic electron affinity calculations, and the average absolute error is 0.0439 eV. The HCTH method performs better for EA prediction. The M06-HF, mPWPW91, VSXC and B98 are also reasonable. The most reliable adiabatic electron affinities are predicted to be 1.864 eV ( CH 3 S ), 1.946 eV ( C 2 H 5 S ), 1.959 eV (n- C 3 H 7 S ), 1.970 eV (n- C 4 H 9 S ), 1.982 eV (n- C 5 H 11 S ), 2.053 eV (i- C 3 H 7 S ), 1.991 eV (i- C 4 H 9 S ) and 2.100 eV (t- C 4 H 9 S ) at the M06/DZP++ level of theory, respectively.

Ion-Molecular Memory Model. Memorizing

2015 ◽  
Vol 22 (2) ◽  
pp. 103-108 ◽  
Author(s):  
Герасимов ◽  
I. Gerasimov ◽  
Яшин ◽  
A. Yashin
Keyword(s):  
Structural Changes ◽  
Molecular Structures ◽  
Memory Model ◽  
Actual Process ◽  
Structural Elements ◽  
Molecular Models ◽  
Internal Environment ◽  
Molecular Memory ◽  
Multiple Copies ◽  
Specific Implementation

This article is from the series on the creation of ion-molecular models of memory, dedicated memorizing, i.e., the process of storing information in memory. The authors believe that the process of memorizing is carried out by images, and for the physical model, the question is the theory of soliton-holographic system. The process of memorizing is implemented in the structural changes of molecules and sub-molecular structures, and the way memory is formed during a finite time. The quality memorization requires multiple copies, for example, fractal, soliton-holographic and other images. The authors reviewed more "thin" issues, the specific implementation of the memory. The authors present one of the possible variants of memorizing in the framework of ion-molecular memory model. The concept of memorizing is discussed below in the duality of memory: memorizing and its retrieving as system duality of the mechanism of memory. Regarding the actual images memorizing, we are talking about a set of specific characters, which allow an adequate degree of accuracy to recover memory when retrieving from memory the stored image. The actual process of memorizing is realized in the process of structural transformations of molecular and sub-molecular structures, as a result of certain physic and chemical interactions. Such changes are to be under any influences from the external environment through the senses and evolution in the internal environment. Here the authors emphasize the electromagnetic basis of processes of memorizing and memory, i.e., electrical signals from neurons to structural elements of the library memory. It is important to emphasize that the (real) memorizing not all the information, but only volume that allows to restoring it completely, saves space and time needed to remember.

Understanding membrane-active antimicrobial peptides

2017 ◽  
Vol 50 ◽  
Author(s):  
Huey W. Huang ◽  
Nicholas E. Charron
Keyword(s):  
Antimicrobial Peptides ◽  
Soft Matter ◽  
Structural Changes ◽  
Molecular Mechanisms ◽  
Bacterial Resistance ◽  
Antimicrobial Agents ◽  
Molecular Structures ◽  
Membrane Domain ◽  
Defense Proteins ◽  
Bacterial Membranes

AbstractBacterial membranes represent an attractive target for the design of new antibiotics to combat widespread bacterial resistance to traditional inhibitor-based antibiotics. Understanding how antimicrobial peptides (AMPs) and other membrane-active agents attack membranes could facilitate the design of new, effective antimicrobials. AMPs, which are small, gene-encoded host defense proteins, offer a promising basis for the study of membrane-active antimicrobial agents. These peptides are cationic and amphipathic, spontaneously binding to bacterial membranes and inducing transmembrane permeability to small molecules. Yet there are often confusions surrounding the details of the molecular mechanisms of AMPs. Following the doctrine of structure–function relationship, AMPs are often viewed as the molecular scaffolding of pores in membranes. Instead we believe that the full mechanism of AMPs is understandable if we consider the interactions of AMPs with the whole membrane domain, where interactions induce structural transformations of the entire membrane, rather than forming localized molecular structures. We believe that it is necessary to consider the entire soft matter peptide-membrane system as it evolves through several distinct states. Accordingly, we have developed experimental techniques to investigate the state and structure of the membrane as a function of the bound peptide to lipid ratio, exactly as AMPs in solution progressively bind to the membrane and induce structural changes to the entire system. The results from these studies suggest that global interactions of AMPs with the membrane domain are of fundamental importance to understanding the antimicrobial mechanisms of AMPs.

scholarly journals The quasi-unchanged gas-phase molecular structures of the atmospheric aerosol precursor β-pinene and its oxidation product nopinone

2017 ◽  
Vol 19 (21) ◽  
pp. 13819-13827 ◽  
Author(s):  
E. M. Neeman ◽  
J.-R. Avilés-Moreno ◽  
T. R. Huet
Keyword(s):  
Gas Phase ◽  
Oxidation Product ◽  
Atmospheric Aerosol ◽  
Structural Changes ◽  
Microwave Spectroscopy ◽  
Molecular Structures

Gas-phase structural changes associated with the oxidation of β-pinene into nopinone have been experimentally unveiled, using impulse microwave spectroscopy.

Predicting Impact Sensitivity of Heterocyclic Nitroarenes from Molecular Structures Selected by Genetic Algorithm

2012 ◽  
Vol 535-537 ◽  
pp. 2550-2553
Author(s):  
Rui Wang ◽  
Yong Gu Wang ◽  
Hui Liu
Keyword(s):  
Genetic Algorithm ◽  
Cross Validation ◽  
Correlation Coefficients ◽  
Molecular Structures ◽  
Impact Sensitivity ◽  
Optimal Subset ◽  
Leave One Out ◽  
The Impact ◽  
Prediction Capability ◽  
Good Agreement

A novel theoretical model was constructed to predict the impact sensitivity of 44 heterocyclic nitroarenes. The optimal subset of the molecular structures descriptors were selected by genetic algorithm (GA). The multiple linear regression (MLR) was then applied to build a prediction model of impact sensitivity for the 44 compounds. The correlation coefficients (R2) together with correlation coefficient of the leave-one-out cross validation (Q2CV) of the model is 0.928 and 0.865, respectively. The new model is highly statistically significant, and the robustness as well as internal prediction capability of which is satisfactory. The predicted impact sensitivity values are in good agreement with the experimental data.

Textural and structural changes of dehydrofreeze-thawed strawberry slices: Effects of different dehydration pretreatments / Cambios texturales y estructurales de rodajas de fresa deshidratadas y descongeladas: Efectos de diferentes pretratamientos de deshidratación

1999 ◽  
Vol 5 (6) ◽  
pp. 479-485 ◽  
Author(s):  
A. Sormani ◽  
D. Maffi ◽  
G. Bertolo ◽  
D. Torreggiani
Keyword(s):  
Structural Damage ◽  
Structural Changes ◽  
Microscopic Analysis ◽  
Structural Level ◽  
Concentrated Solutions ◽  
Partial Removal ◽  
Tissue Organization ◽  
Air Dehydration ◽  
Textural Changes ◽  
Good Agreement

Partial removal of water through air dehydration, dewatering-impregnation-soaking in concentrated solutions (DIS) or their combination, has been applied to strawberry slices before freezing in order to reduce structural cullapse after thawing. The changes produced at the structural level have been studied through both texture and microscopic analysis, so defining the structure-texture relation ships in the freeze-thawed fruit. Tissues subjected to DIS in a 60% (w/w) glucose solution for 4 hours at room temperature showed structural damage to the cell walls and cell ruptures, which are in agree ment with the observed decrease of texture. After thawing, the pre-dehydrated strawberry slices showed a much better tissue organization than the strawberry frozen without pretreatment. Air dry ing and the combination DIS-air drying gave the highest texture improvement of the fruit after thaw ing. A good agreement was obtained between structural and textural changes observed after both pre-dehydration and freeze-thawing of strawberry slices.

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