A new approach to the geometry optimization of molecular structures: the sliding-range method

1991 ◽  
Vol 228 ◽  
pp. 323-328
Author(s):  
C. ünaleroǧlu ◽  
T. Firat ◽  
N. Balcioǧlu
Keyword(s):  
Geometry Optimization ◽  
Molecular Structures ◽  
New Approach

Factors Affecting Molecular Self-Assembly and Its Mechanism

2012 ◽  
Vol 9 (1) ◽  
pp. 43 ◽  
Author(s):  
Hueyling Tan
Keyword(s):  
Self Assembly ◽  
Building Blocks ◽  
Molecular Engineering ◽  
Molecular Structures ◽  
Polymer Science ◽  
New Approach ◽  
Factors Affecting ◽  
Dna Structures ◽  
Self Assembling ◽  
Wide Range

Molecular self-assembly is ubiquitous in nature and has emerged as a new approach to produce new materials in chemistry, engineering, nanotechnology, polymer science and materials. Molecular self-assembly has been attracting increasing interest from the scientific community in recent years due to its importance in understanding biology and a variety of diseases at the molecular level. In the last few years, considerable advances have been made in the use ofpeptides as building blocks to produce biological materials for wide range of applications, including fabricating novel supra-molecular structures and scaffolding for tissue repair. The study ofbiological self-assembly systems represents a significant advancement in molecular engineering and is a rapidly growing scientific and engineering field that crosses the boundaries ofexisting disciplines. Many self-assembling systems are rangefrom bi- andtri-block copolymers to DNA structures as well as simple and complex proteins andpeptides. The ultimate goal is to harness molecular self-assembly such that design andcontrol ofbottom-up processes is achieved thereby enabling exploitation of structures developed at the meso- and macro-scopic scale for the purposes oflife and non-life science applications. Such aspirations can be achievedthrough understanding thefundamental principles behind the selforganisation and self-synthesis processes exhibited by biological systems.

Ion solvation by dipolar aprotic solvents. An ab initio study

1987 ◽  
Vol 52 (1) ◽  
pp. 6-13 ◽  
Author(s):  
Petr Kyselka ◽  
Zdeněk Havlas ◽  
Ivo Sláma
Keyword(s):  
Ab Initio ◽  
Geometry Optimization ◽  
Molecular Structures ◽  
Dimethyl Sulphoxide ◽  
Ion Solvation ◽  
Interaction Energies ◽  
Ab Initio Study ◽  
Solvation Energies ◽  
Dipolar Aprotic Solvents ◽  
Complete Geometry Optimization

The paper deals with the solvation of Li+, Be2+, Na+, Mg2+, and Al3+ ions in dimethyl sulphoxide, dimethylformamide, acetonitrile, and water. The ab initio quantum chemical method was used to calculate the solvation energies, molecular structures, and charge distributions for the complexes water···ion, acetonitrile···ion, dimethyl sulphoxide···ion, and dimethylformamide···ion. The interaction energies were corrected for the superposition error. Complete geometry optimization was performed for the complex water···ion. Some generalizations are made on the basis of the results obtained.

scholarly journals Plutonium complexes in water: new approach to ab initio modeling

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Mikhail V. Ryzhkov ◽  
Andrei N. Enyashin ◽  
Bernard Delley
Keyword(s):  
Quantitative Estimation ◽  
Water Solution ◽  
Geometry Optimization ◽  
Model Potential ◽  
Water Dissociation ◽  
New Approach ◽  
Molecular Systems ◽  
Screening Model ◽  
Solvent Environment ◽  
Structure Calculations

Abstract Geometry optimization and the electronic structure calculations of Pu Z+ complexes (Z = 3–6) in water solution have been performed, within the framework of the DMol3 and Relativistic Discrete-Variational (RDV) methods. For the simulation of Pu Z+ molecular environment in aqueous solution we used 22 and 32 water molecules randomly distributed around cation. To model the effect of bulk solvent environment we used COSMO (Conductor-like Screening Model) potential for water (ε = 78.54). The obtained results showed that this approach allows the modeling of water dissociation and the formation of hydrolysis products. Our previously suggested scheme for the calculation of interaction energies between selected fragments of multi-molecular systems provides the quantitative estimation of the interaction strengths between plutonium in various oxidation states and each ligand in the first and second coordination shells in water solution.

scholarly journals A New Approach to Design Light Emitting Devices Using Electroactive Dyes

2002 ◽  
Vol 734 ◽  
Author(s):  
Michael Pan ◽  
Amitava Patra ◽  
Christopher S. Friend ◽  
Tzu-Chau. Lin ◽  
Alexander N. Cartwright ◽  
...  
Keyword(s):  
Light Emission ◽  
Organic Dyes ◽  
Single Layer ◽  
Molecular Structures ◽  
Structural Motif ◽  
New Approach ◽  
Light Emitting ◽  
Light Emitting Devices ◽  
Two Photon ◽  
A Value

ABSTRACTOrganic electroluminescence (EL) single layer devices using electroactive dyes incorporated in poly-vinylcarbazole (PVK) were fabricated. The molecular structures of the two-photon dyes are the generic D-π-A;, D-π-D, and A-π-A;, structural motif, composed of a diphenylamine donor (D), a distyrylfluorene π-bridge, and an oxadiazole acceptor (A). A single layer type of EL device of ITO/PVK:DYE/Ca/Al was fabricated. The light emission peak and the threshold of the electroluminescence emission depend on the structure and concentration of the dye. The EL intensity increases with the dye concentration and it was found that as the voltage is increased the brightness increases and reaches a value 498 cd/m2 at an applied voltage of 25 V for the D-π-A; dye. We present a physical explanation of this observed behavior and show that this has significant impact on the design of light emitting devices using these organic dyes.

Markov chain models, time series analysis and extreme value theory

1996 ◽  
Vol 28 (02) ◽  
pp. 405-425 ◽  
Author(s):  
D. S. Poskitt ◽  
Shin-Ho Chung
Keyword(s):  
Markov Chain ◽  
Moving Average ◽  
Value Theory ◽  
The State ◽  
Molecular Structures ◽  
Process Conditions ◽  
Autoregressive Moving Average ◽  
New Approach ◽  
Markov Chain Models ◽  
Outstanding Question

Markov chain processes are becoming increasingly popular as a means of modelling various phenomena in different disciplines. For example, a new approach to the investigation of the electrical activity of molecular structures known as ion channels is to analyse raw digitized current recordings using Markov chain models. An outstanding question which arises with the application of such models is how to determine the number of states required for the Markov chain to characterize the observed process. In this paper we derive a realization theorem showing that observations on a finite state Markov chain embedded in continuous noise can be synthesized as values obtained from an autoregressive moving-average data generating mechanism. We then use this realization result to motivate the construction of a procedure for identifying the state dimension of the hidden Markov chain. The identification technique is based on a new approach to the estimation of the order of an autoregressive moving-average process. Conditions for the method to produce strongly consistent estimates of the state dimension are given. The asymptotic distribution of the statistic underlying the identification process is also presented and shown to yield critical values commensurate with the requirements for strong consistency.

Self-Assembly of Peptide Amphiphiles: Molecularly Engineered Bionanomaterials

2015 ◽  
Vol 1113 ◽  
pp. 586-593 ◽  
Author(s):  
Hamizah Shamsudeen ◽  
Huey Ling Tan
Keyword(s):  
Self Assembly ◽  
Building Blocks ◽  
Molecular Engineering ◽  
Molecular Structures ◽  
Significant Advance ◽  
Polymer Science ◽  
New Approach ◽  
Dna Structures ◽  
Self Assembling ◽  
Wide Range

Molecular self-assembly is ubiquitous in nature and has now emerged as a new approach in chemical synthesis, engineering, nanotechnology, polymer science, and materials. Molecular self-assembly has been attracting increasing interest from the scientific community in the recent years due to its importance in understanding biology and a variety of diseases at the molecular level. In the last few years, considerable advances have been made in the use of peptides as building blocks to produce biological materials for wide range of applications, including fabricating novel supra-molecular structures and scaffolding for tissue repair. Today, the study of biological self-assembly systems represent a significant advance in the molecular engineering and is a rapidly growing scientific and engineering field that crosses the boundaries of existing disciplines. Many self-assembling systems are range from bi-and tri-block copolymers to complex DNA structures as well as simple and complex proteins and peptides. The attractiveness of such bottom-up processes lies in their capability to build uniform, functional units or arrays and the possibility to exploit such structures at meso-and macroscopic scale for life and non-life science applications.

scholarly journals First Principles Study on the Stability and Electronic Structures of 7,8-Dichloro-4-Oxo-4H-Chromene-3-Carbaldehyde

2016 ◽  
Vol 855 ◽  
pp. 31-36
Author(s):  
Pek Lan Toh ◽  
Montha Meepripruk ◽  
Lee Sin Ang ◽  
Shukri Sulaiman ◽  
Mohamed Ismail Mohamed-Ibrahim
Keyword(s):  
Electronic Structures ◽  
Density Functional ◽  
Molecular System ◽  
Population Analysis ◽  
Measurement Data ◽  
Geometry Optimization ◽  
Molecular Structures ◽  
Basis Sets ◽  
Mulliken Population ◽  
Homo Lumo

The molecular structures and electronic properties of 7,8-Dichloro-4-Oxo-4H-Chromene-3-Carbaldehyde, C10H4Cl2O3 have been studied using Density Functional Theory (DFT) method. The calculation of geometry optimization was conducted to find the local energy minimum of C10H4Cl2O3 molecular system. The equilibrium geometries were used to determine the HOMO-LUMO gaps, Mulliken atomic charges, and other electronic structures of C10H4Cl2O3. The significant findings from DFT/B3LYP functional within the basis sets of 6-31G**, 6-31++G**, 6-311G**, and 6-311++G** show that the optimized geometries of C10H4Cl2O3 are in good agreement with that of measurement data. To further investigate this, using a variety of basis sets (3-21G, 6-31G, 6-31++G, 6-31G**, 6-31++G**, 6-311G, 6-311++G, 6-311G**, and 6-311++G**), it is found that the calculated total energy values of C10H4Cl2O3 are close to each other. Similarly, the computed HOMO-LUMO energy gaps obtained are also close to each other. Using the scheme of Mulliken Population Analysis (MPA), the trend of findings are the same for both cases of B3LYP/6-31G and B3LYP/6-31G** level of calculations. For the method of B3LYP/6-31G, it is clearly found that C4 and C6 have the highest positively charge, with the corresponding values about +0.284 and +0.238, respectively. On the other hand, the charge values of +0.157 and +0.206 are found on Cl1 and Cl2 atoms. The atoms of O1, O2, and O3 have the negatively charges, with the values of about 0.398, -0.512, and -0.424, respectively. Similarly, in the case of DFT/B3LYP/6-31G** level of theory, the computed charge values of C2 and C4 are about +0.311 and +0.393, respectively. Furthermore, the Cl1 and Cl2 atoms have the positively charge values of about +0.043 and +0.070, whereas for the O1, O2, and O3 atoms, the charges values obtained are about -0.421, -0.467, and -0.498, respectively.

Markov chain models, time series analysis and extreme value theory

1996 ◽  
Vol 28 (2) ◽  
pp. 405-425 ◽  
Author(s):  
D. S. Poskitt ◽  
Shin-Ho Chung
Keyword(s):  
Markov Chain ◽  
Moving Average ◽  
Value Theory ◽  
The State ◽  
Molecular Structures ◽  
Process Conditions ◽  
Autoregressive Moving Average ◽  
New Approach ◽  
Markov Chain Models ◽  
Outstanding Question

Markov chain processes are becoming increasingly popular as a means of modelling various phenomena in different disciplines. For example, a new approach to the investigation of the electrical activity of molecular structures known as ion channels is to analyse raw digitized current recordings using Markov chain models. An outstanding question which arises with the application of such models is how to determine the number of states required for the Markov chain to characterize the observed process. In this paper we derive a realization theorem showing that observations on a finite state Markov chain embedded in continuous noise can be synthesized as values obtained from an autoregressive moving-average data generating mechanism. We then use this realization result to motivate the construction of a procedure for identifying the state dimension of the hidden Markov chain. The identification technique is based on a new approach to the estimation of the order of an autoregressive moving-average process. Conditions for the method to produce strongly consistent estimates of the state dimension are given. The asymptotic distribution of the statistic underlying the identification process is also presented and shown to yield critical values commensurate with the requirements for strong consistency.

scholarly journals Studi Teoritis Senyawa Turunan Kalkon Hidroksi Sebagai Sensor Kimia Berbagai Anion

2019 ◽  
Vol 3 (2) ◽  
pp. 95
Author(s):  
Fitra Perdana ◽  
Karna Wijaya ◽  
Ria Armunanto
Keyword(s):  
Hydrogen Bond ◽  
Geometry Optimization ◽  
Dft Method ◽  
Molecular Structures ◽  
Energy Change ◽  
Lumo Energy ◽  
Interaction Models ◽  
Chalcone Derivatives ◽  
The Difference ◽  
Homo Lumo

AbstrakStudi secara teoritis telah dilakukan untuk mempelajari interaksi senyawa turunan kalkon hidroksi (CH) sebagai sensor kimia dengan anion F-, Cl-, Br-, CN-, CH3COO-, dan NO3-. Penelitian ini bertujuan untuk memodelkan struktur molekul senyawa turunan kalkon hidroksi (CH) dan sifat sensornya serta model interaksinya dengan anion dengan metode DFT. Hasil optimasi geometri menunjukkan terjadinya pemanjangan ikatan O-H sebesar 0,63-0,85 Å dengan adanya anion F-, CN-, and CH3COO-. Hal ini mengindikasikan terjadinya deprotonasi sensor kalkon hidroksi (CH) oleh anion. Sedangkan interaksi sensor kalkon hidroksi (CH) dengan anion Cl-, Br-, dan NO3- hanya berupa ikatan hidrogen dengan pemanjangan ikatan O-H sebesar 0,08-0,46 Å. Sensor kalkon hidroksi (CH) yang mengalami deprotonasi memiliki energi interaksi yang lebih besar yaitu -209,37 – -424,06 kJ/mol dibandingkan sensor yang hanya membentuk ikatan hidrogen yaitu -98,60 – -125,59 kJ/mol. Sensor yang mengalami deprotonasi mengakibatkan turunnya selisih energi HOMO-LUMO dari -3,94 – -4,06 eV menjadi -2,62 – -2,75 eV.Kata kunci: sensor kimia, kalkon hidroksi, anion, DFT  AbstractTheoretical study had been carried out to investigate interaction between hydroxy chalcone derivatives (CH) as chemosensors with F-, Cl-, Br-, CN-, CH3COO-, and NO3- anions. This study was aimed to design molecular structures of chemosensor hydroxy chalcone (CH) properties for the anions and their interaction models with DFT method. The result of geometry optimization showed 0,63-0,85 Å O-H bond elongation of the hydroxy chalcone was occured by F-, CN-, and CH3COO-. It was indicated deprotonation of sensor hydroxy chalcone (CH) by anions. Where as the interaction of the hydroxy chalcone (CH) with Cl-, Br-, and NO3- just formed an hydrogen bond with 0,08-0,46 Å O-H bond elongation. Deprotonized sensor hydroxy chalcone (CH) had more energy change of interaction -209,37– -424,06 kJ/mol than sensor which just formed the hydrogen bond -98,60 – -125,59 kJ/mol. Deprotonized sensor caused reduction of the difference of HOMO-LUMO energy from - 3,94 – -4,06 eV to -2,62 – -2,75 eV.Keywords: chemosensor, hydroxy chalcone, anion, DFT

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