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...  Conjugate 
PyCPR – a python-based implementation of the Conjugate Peak Refinement (CPR) algorithm for finding transition state structures
PyCPR – a python-based implementation of the Conjugate Peak Refinement (CPR) algorithm for finding transition state structures
Gisdon, Florian J.; Culka, Martin; Ullmann, G. Matthias
peak refinement (CPR) is a powerful and ...
... 17 benzoic acids and their respective  conjugate 
Relationships between aqueous acidities and computed surface-electrostatic potentials and local ionization energies of substituted phenols and benzoic acids
Relationships between aqueous acidities and computed surface-electrostatic potentials and local ionization energies of substituted phenols and benzoic acids
Ma, Yuguang; Gross, Kevin C.; Hollingsworth, Chad A.; Seybold, Paul G.; Murray, Jane S.
bases were computed at the ...
... efficiency. While for TPA dyes, the longer  conjugate 
Comparative study on electronic structures and optical properties of indoline and triphenylamine dye sensitizers for solar cells
Comparative study on electronic structures and optical properties of indoline and triphenylamine dye sensitizers for solar cells
Zhang, Cai-Rong; Liu, Li; Zhe, Jian-Wu; Jin, Neng-Zhi; Yuan, Li-Hua; Chen, Yu-Hong; Wei, Zhi-Qiang; Wu, You-Zhi; Liu, Zi-Jiang; Chen, Hong-Shan
bridges generate the larger oscillator ...
... results of this study show that the novel  conjugate 
Spectroscopic and nonlinear optical properties of new chalcone fluorescent probes for bioimaging applications: a theoretical and experimental study
Spectroscopic and nonlinear optical properties of new chalcone fluorescent probes for bioimaging applications: a theoretical and experimental study
Krawczyk, Przemysław; Pietrzak, Marek; Janek, Tomasz; Jędrzejewska, Beata; Cysewski, Piotr
PKA-Concanavalin A could be a promising new ...
... Caffeic acid (C9H8O4) and its  conjugate 
Revisiting caffeate’s capabilities as a complexation agent to silver cation in mining processes by means of the dual descriptor—a conceptual DFT approach
Revisiting caffeate’s capabilities as a complexation agent to silver cation in mining processes by means of the dual descriptor—a conceptual DFT approach
Martínez-Araya, Jorge Ignacio
base C9H7O4 − (anionic form—known as ...
... this work. To that end, we made use of five  conjugate 
Evaluating frontier orbital energy and HOMO/LUMO gap with descriptors from density functional reactivity theory
Evaluating frontier orbital energy and HOMO/LUMO gap with descriptors from density functional reactivity theory
Huang, Ying; Rong, Chunying; Zhang, Ruiqin; Liu, Shubin
molecular chains, such as trans-ethylene, ...
... in Fig. 2 Grimme (kcal/mol) TS (kcal/mol)  Conjugate 
DFT study of the interaction between the conjugated fluorescein and dabcyl system, using fluorescene quenching method
DFT study of the interaction between the conjugated fluorescein and dabcyl system, using fluorescene quenching method
Alvarado-González, Mónica; Gallo, Marco; Lopez-Albarran, Pablo; Flores-Holguín, Norma; Glossman-Mitnik, Daniel
1 −40.33627852 −21.11090878 ...
... The first family goes under the name “  conjugate 
Modeling of hydrogen-assisted cracking in iron crystal using a quasi-Newton method
Modeling of hydrogen-assisted cracking in iron crystal using a quasi-Newton method
Telitchev, Igor Ye.; Vinogradov, Oleg
gradient methods” and the second, ...
... dimensional model is employed. The  conjugate 
Design of laser pulses for selective vibrational excitation of the N6-H bond of adenine and adenine-thymine base pair using optimal control theory
Design of laser pulses for selective vibrational excitation of the N6-H bond of adenine and adenine-thymine base pair using optimal control theory
Sharma, Sitansh; Sharma, Purshotam; Singh, Harjinder; Balint-Kurti, Gabriel G.
gradient method is used for the ...
... can successfully estimate the molecular  conjugate 
Theoretical characterization on photoelectric properties of benzothiadiazole- and fluorene-based small molecule acceptor materials for the organic photovoltaics
Theoretical characterization on photoelectric properties of benzothiadiazole- and fluorene-based small molecule acceptor materials for the organic photovoltaics
Sui, Mingyue; Li, Shuangbao; Pan, Qingqing; Sun, Guangyan; Geng, Yun
degree [44–47]. ...
... -derived), followed by optimization with  conjugate 
Multiple templates-based homology modeling enhances structure quality of AT1 receptor: validation by molecular dynamics and antagonist docking
Multiple templates-based homology modeling enhances structure quality of AT1 receptor: validation by molecular dynamics and antagonist docking
Sokkar, Pandian; Mohandass, Shylajanaciyar; Ramachandran, Murugesan
gradients and molecular dynamics to ...
... steepest descent, followed by 2500 steps of  conjugate 
Computational design of a full-length model of HIV-1 integrase: modeling of new inhibitors and comparison of their calculated binding energies with those previously studied
Computational design of a full-length model of HIV-1 integrase: modeling of new inhibitors and comparison of their calculated binding energies with those previously studied
Ercan, Selami; Pirinccioglu, Necmettin
gradient (igb = 0) with a cutoff of 999. ...
... for the total energy minimization using the  conjugate 
Graphene-based pressure nano-sensors
Graphene-based pressure nano-sensors
Sorkin, Viacheslav; Zhang, Yong Wei
gradient method. ...
... charges) were first minimized using the  conjugate 
Studying the mechanism that enables paullones to selectively inhibit glycogen synthase kinase 3 rather than cyclin-dependent kinase 5 by molecular dynamics simulations and free-energy calculations
Studying the mechanism that enables paullones to selectively inhibit glycogen synthase kinase 3 rather than cyclin-dependent kinase 5 by molecular dynamics simulations and free-energy calculations
Chen, Quan; Cui, Wei; Cheng, Yuanhua; Zhang, Fushi; Ji, Mingjuan
gradient method to a gradient of ...
... steepest descent followed by 250 cycles of  conjugate 
Explaining the inhibition of cyclin-dependent kinase 5 by peptides derived from p25 with molecular dynamics simulations and MM-PBSA
Explaining the inhibition of cyclin-dependent kinase 5 by peptides derived from p25 with molecular dynamics simulations and MM-PBSA
Tan, Vincent B. C.; Zhang, Bing; Lim, Kian Meng; Tay, Tong Earn
gradient minimization. ...
... than the nicotinoid compounds. The  conjugate 
A novel halogen bond and a better-known hydrogen bond cooperation of neonicotinoid and insect nicotinic acetylcholine receptor recognition
A novel halogen bond and a better-known hydrogen bond cooperation of neonicotinoid and insect nicotinic acetylcholine receptor recognition
Duan, Hongxia; Zhang, Weiwei; Zhao, Jin; Liang, Desheng; Yang, Xinling; Jin, Shuhui
guanidine or amidine plane formed a Π–Π ...
... The above data indicate that the donor-  conjugate 
Molecular modeling of 4-methylphthalonitrile for dye sensitized solar cells using quantum chemical calculations
Molecular modeling of 4-methylphthalonitrile for dye sensitized solar cells using quantum chemical calculations
Senthilkumar, Palanivel; Anbarasan, Ponnusamy Munusamy
pi bridge-acceptor (D-pi-A) chain-like dyes ...
... including the formation of iminium ion, the  conjugate 
Theoretical study of the mechanism of highly diastereoselective formation of a strained 3-azabicyclo[3.2.0]heptane derivative
Theoretical study of the mechanism of highly diastereoselective formation of a strained 3-azabicyclo[3.2.0]heptane derivative
Nemati, Maryam; Arshadi, Nematollah
addition of 3 to the iminium ion, and the ...
... of steepest-descent and 200 iterations of  conjugate 
Ab initio construction of all-atom loop conformations
Ab initio construction of all-atom loop conformations
Jiang, Haiyan; Blouin, Christian
-gradient minimization. ...
... energy minimization for 1,000 steps of the  conjugate 
Homology model of human corticosteroid binding globulin: a study of its steroid binding ability and a plausible mechanism of steroid hormone release at the site of inflammation
Homology model of human corticosteroid binding globulin: a study of its steroid binding ability and a plausible mechanism of steroid hormone release at the site of inflammation
Dey, Raja; Roychowdhury, Priyobroto
technique that led to a refined structure ...
... [26] and Kollman all-atom charges [17]; and  conjugate 
Study of a ligand complexed with Cdk2/Cdk4 by computer simulation
Study of a ligand complexed with Cdk2/Cdk4 by computer simulation
Jiang, Yongjun; Zou, Jianwei; Gui, Chunshan
gradient minimized until the energy ...
... by Ψ(R)* (the star * is for the complex  conjugate 
Dissociation quenching using exceptional points
Dissociation quenching using exceptional points
Lefebvre, R.; Atabek, O.
) and subtracting from this expression the ...
... PAMAM dendrimer and dendrimer glucosamine  conjugate 
Structural studies of biologically active glycosylated polyamidoamine (PAMAM) dendrimers
Structural studies of biologically active glycosylated polyamidoamine (PAMAM) dendrimers
Barata, Teresa Silva; Shaunak, Sunil; Teo, Ian; Zloh, Mire; Brocchini, Steve
as generated by molecular dynamics ...
... was carried out employing the Polak–Ribiere  conjugate 
A molecular mechanics and semiempirical molecular orbital study on the conformation of polynorbornene chains
A molecular mechanics and semiempirical molecular orbital study on the conformation of polynorbornene chains
Yılmaz, Sevil Savaşkan; Abbasoğlu, Rza; Hazer, Baki
-gradient method until an RMS gradient of ...
... Bio+ force field (charmm22) [11] and the  conjugate 
Three-dimensional model of zeaxanthin binding PsbS protein associated with nonphotochemical quenching of excess quanta of light energy absorbed by the photosynthetic apparatus
Three-dimensional model of zeaxanthin binding PsbS protein associated with nonphotochemical quenching of excess quanta of light energy absorbed by the photosynthetic apparatus
Haripal, Prafulla K.; Raval, Hemant K.; Raval, Mukesh K.; Rawal, Rakesh M.; Biswal, Basanti; Biswal, Udaya C.
-gradient method followed by thorough ...

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