Molecular polarizabilities and induced dipole moments in molecular mechanics

Ma, Buyong; Lii, Jenn‐Huei; Allinger, Norman L.

doi:10.1002/1096-987x(20000730)21:10<813::aid-jcc1>3.0.co;2-t

Cited by 85 publications

(72 citation statements)

References 21 publications

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“…Actually, fourteen 〈R〉 values (25% of the values) have been obtained with quantum mechanical methods (denoted with an asterisk in Table 1). 18 Table 1. The agreement with the corresponding "quantum" values is noteworthy.…”

Section: Resultsmentioning

confidence: 99%

Encoding the Core Electrons with Graph Concepts

Pogliani¹

2004

J. Chem. Inf. Comput. Sci.

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The core electron problem of atoms in chemical graph studies has always been considered as a minor problem. Usually, chemical graphs had to encode just a small set of second row atoms, i.e., C, N, O, and F, thus, graph and, in some cases, pseudograph concepts were enough to "graph" encode the molecules at hand. Molecular connectivity theory, together with its side-branch the electrotopological state, introduced two "ad hoc" algorithms for the core electrons of higher-row atoms based, mainly, on quantum concepts alike. Recently, complete graphs, and, especially, odd complete graphs have been introduced to encode the core electrons of higher-row atoms. By the aid of these types of graphs a double-valued algorithm has been proposed for the valence delta, deltav, of any type of atoms of the periodic table with a principal quantum number n > or =2. The new algorithm is centered on an invariant suggested by the hand-shaking theorem, and the values it gives rise to parallel in some way the values derived by the aid of the two old "quantum" algorithms. A thorough comparative analysis of the newly proposed algorithms has been undertaken for atoms of the group 1A-7A of the periodic table. This comparative study includes the electronegativity, the size of the atoms, the first ionization energy, and the electron affinity. The given algorithm has also been tested with sequential complete graphs, while the even complete graphs give rise to conceptual difficulties. QSAR/QSPR studies do not show a clear-cut preference for any of the two values the algorithm gives rise to, even if recent results seem to prefer one of the two values.

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Section: Resultsmentioning

confidence: 99%

Encoding the Core Electrons with Graph Concepts

Pogliani¹

2004

J. Chem. Inf. Comput. Sci.

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“…for ethanol from 1.68 to 1.61 Debyes, ammonium from 1.472 to 1.334 Debyes, toluene from 0.375 to 0.421 Debyes, etc. [8]. Fig.…”

Section: Influence Of Dipole Moment Of Organic Vapors On Pl Decay Timementioning

confidence: 99%

“…We used the multi-component "polymix" buffer with following composition: 2.5 mM Tris, 2.5 mM citric acid, 2.5 mM sodium tetraborate, 2.5 mM potassium phosphate, pH was adjusted with 1 M HCl or 1 M NaOH solutions in order to obtain the expected pH value. Its buffer capacity is stable over a wide range of pH (5)(6)(7)(8)(9). This buffer is used for studying of pH influence on the ISFET responses, (especially enzyme-modified ISFETs) [5].…”

Section: Samples and Principles Of Pl Decay Time Measurementmentioning

confidence: 99%

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IMPACT OF GAS ADSORPTION AND pH OF SOLUTIONS ON RADIATIVE LIFETIME OF MODIFIED POROUS SILICON LAYERS

Benilov

Gavrilchenko

Benilova

et al. 2007

SEMST

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IMPACT OF GAS ADSORPTION AND pH OF SOLUTIONS ON RADIATIVE LIFETIME OF MODIFIED POROUS SILICON LAYERSA. I. Benilov, I. V. Gavrilchenko, I. V. Benilova, V. A. Skryshevsky, M. CabreraThe time-resolved photoluminescence and radiative decay time of modified layers of porous silicon (PS) were studied at the adsorption of saturated organic vapors and buffers solutions with different pH. As-prepared PS samples were compared with ones after oxidation and deposition of poly (3,4-ethylenedioxythiophene) film. New type transducer for pH meter based on radiative decay time measurement of modified PS layers is proposed. The 1.9 times reduction of radiative lifetime of Sband is observed at the increasing of pH value from 2 to 9.Key words: porous silicon, photoluminescence, adsorption, buffers solutions. Áóëî äîñë³äaeåíî ê³íåòèêó ôîòîëþì³íåñöåíö³¿ òà ÷àñ aeèòòÿ âèïðîì³íþâàëüíî¿ ðåêîìá³-íàö³¿ ìîäèô³êîâàíèõ øàð³â ïîðóâàòîãî êðåìí³þ â óìîâàõ àäñîðáö³¿ íàñè÷åíèõ îðãàí³÷íèõ ïàð³â òà áóôåðíèõ ðîç÷èí³â ç ð³çíèìè çíà÷åííÿìè pH. Ùîéíî âèãîòîâëåí³ çðàçêè ïîðóâà-òîãî êðåìí³þ áóëî ïîð³âíÿíî ³ç çðàçêàìè, ùî áóëî îêèñëåíî òà ïîêðèòî øàðîì ïîë³-3,4-åòèëäèîêñèòèîôåíó. Çàïðîïîíîâàíî íîâèé òèï òðàíñäþñåðà, ùî áàçóºòüñÿ íà âèì³ð³ âèïðî-ì³íþâàëüíîãî ÷àñó aeèòòÿ, ùî ÷óòëèâèé äî ð³âíÿ pH. Ñïîñòåð³ãàºòüñÿ çìåíøåííÿ ó 1.9 ðàç³â âèïðîì³íþâàëüíîãî ÷àñó aeèòòÿ S-ñìóãè ïðè çì³í³ pH ç 2 äî 9.Êëþ÷îâ³ ñëîâà: ïîðóâàòèé êðåìí³é, ôîòîëþì³íåñöåíö³ÿ, àäñîðáö³ÿ, áóôåðí³ ðîç÷èíè.A. I. Benilov, I. V. Gavrilchenko, I. V. Benilova, V. A. Skryshevsky, M. Cabrera

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“…8 Various strategies to dynamically incorporate electronic polarizability into MM calculations have been previously developed 9 including fluctuating charges, 10, 11 inducible dipoles, 10,12,13 and classical Drude oscillators. 14 While parameter fitting for biomolecular systems, with well defined residues, is a tractable problem, the exercise can become extremely labor intensive if not prohibitive for adequate coverage of small molecule chemical space.…”

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confidence: 99%

Communication: Quantum polarized fluctuating charge model: A practical method to include ligand polarizability in biomolecular simulations

Kimura

Rajamani

Langley

2011

The Journal of Chemical Physics

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We present a simple and practical method to include ligand electronic polarization in molecular dynamics (MD) simulation of biomolecular systems. The method involves periodically spawning quantum mechanical (QM) electrostatic potential (ESP) calculations on an extra set of computer processors using molecular coordinate snapshots from a running parallel MD simulation. The QM ESPs are evaluated for the small-molecule ligand in the presence of the electric field induced by the protein, solvent, and ion charges within the MD snapshot. Partial charges on ligand atom centers are fit through the multi-conformer restrained electrostatic potential (RESP) fit method on several successive ESPs. The RESP method was selected since it produces charges consistent with the AMBER/GAFF force-field used in the simulations. The updated charges are introduced back into the running simulation when the next snapshot is saved. The result is a simulation whose ligand partial charges continuously respond in real-time to the short-term mean electrostatic field of the evolving environment without incurring additional wall-clock time. We show that (1) by incorporating the cost of polarization back into the potential energy of the MD simulation, the algorithm conserves energy when run in the microcanonical ensemble and (2) the mean solvation free energies for 15 neutral amino acid side chains calculated with the quantum polarized fluctuating charge method and thermodynamic integration agree better with experiment relative to the Amber fixed charge force-field.

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Molecular polarizabilities and induced dipole moments in molecular mechanics

Cited by 85 publications

References 21 publications

Encoding the Core Electrons with Graph Concepts

Encoding the Core Electrons with Graph Concepts

IMPACT OF GAS ADSORPTION AND pH OF SOLUTIONS ON RADIATIVE LIFETIME OF MODIFIED POROUS SILICON LAYERS

Communication: Quantum polarized fluctuating charge model: A practical method to include ligand polarizability in biomolecular simulations

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