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Prognostic impact of permanent pacemaker implantation after transcatheter aortic valve replacement. ARCHIVES OF CARDIOVASCULAR DISEASES SUPPLEMENTS 2023. [DOI: 10.1016/j.acvdsp.2022.10.160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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2
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Ratio of Pulmonary Artery Diameter to Ascending Aortic Diameter as a Predictive Tool for Severe Primary Graft Dysfunction in Heart Transplants. J Heart Lung Transplant 2020. [DOI: 10.1016/j.healun.2020.01.659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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3
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Reduced order model for patient specific fluid transient simulation of blood flow in aortic cross. Comput Methods Biomech Biomed Engin 2019. [DOI: 10.1080/10255842.2020.1713477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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4
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Surgical management of an epithelioid hemangioendothelioma of the superior vena cava protruding into the right atrium. J Card Surg 2014; 29:779-81. [PMID: 24893561 DOI: 10.1111/jocs.12370] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Epithelioid hemangioendothelioma (EH) is a rare malignant tumor of vascular origin that often involves soft tissues and visceral organs, and less commonly, large veins. We report a case of EH of the superior vena cava protruding into the right atrium and its surgical management.
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Calculation and analysis of the harmonic vibrational frequencies in molecules at extreme pressure: Methodology and diborane as a test case. J Chem Phys 2012; 137:154112. [DOI: 10.1063/1.4757285] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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Modelling of molecular interactions and inclusion phenomena in substituted β-cyclodextrin: From simple probes to proteins. ACTA ACUST UNITED AC 2011. [DOI: 10.1002/masy.19991380106] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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8
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Quantum-mechanical studies of environmental effects on biomolecules. I. Hydration of formamide. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 2009; 5:251-9. [PMID: 4759568 DOI: 10.1111/j.1399-3011.1973.tb03459.x] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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9
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Electronic excitation energies of molecules in solution within continuum solvation models: Investigating the discrepancy between state-specific and linear-response methods. J Chem Phys 2005; 123:134512. [PMID: 16223319 DOI: 10.1063/1.2039077] [Citation(s) in RCA: 175] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In a recent article [R. Cammi, S. Corni, B. Mennucci, and J. Tomasi, J. Chem. Phys. 122, 104513 (2005)], we demonstrated that the state-specific (SS) and the linear-response (LR) approaches, two different ways to calculate solute excitation energies in the framework of quantum-mechanical continuum models of solvation, give different excitation energy expressions. In particular, they differ in the terms related to the electronic response of the solvent. In the present work, we further investigate this difference by comparing the excitation energy expressions of SS and LR with those obtained through a simple model for solute-solvent systems that bypasses one of the basic assumptions of continuum solvation models, i.e., the use of a single Hartree product of a solute and a solvent wave function to describe the total solute-solvent wave function. In particular, we consider the total solute-solvent wave function as a linear combination of the four products of two solute states and two solvent electronic states. To maximize the comparability with quantum-mechanical continuum model the resulting excitation energy expression is recast in terms of response functions of the solvent and quantities proper for the solvated molecule. The comparison of the presented expressions with the LR and SS ones enlightens the physical meaning of the terms included or neglected by these approaches and shows that SS agrees with the results of the four-level model, while LR includes a term classified as dispersion in previous treatments and neglects another related to electrostatic. A discussion on the possible origin of the LR flaw is finally given.
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Electronic excitation energies of molecules in solution: State specific and linear response methods for nonequilibrium continuum solvation models. J Chem Phys 2005; 122:104513. [PMID: 15836338 DOI: 10.1063/1.1867373] [Citation(s) in RCA: 219] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a formal comparison between the two different approaches to the calculation of electronic excitation energies of molecules in solution within the continuum solvation model framework, taking also into account nonequilibrium effects. These two approaches, one based on the explicit evaluation of the excited state wave function of the solute and the other based on the linear response theory, are here proven to give formally different expressions for the excitation energies even when exact eigenstates are considered. Calculations performed for some illustrative examples show that this formal difference has sensible effects on absolute solvatochromic shifts (i.e., with respect to gas phase) while it has small effects on relative (i.e., nonpolar to polar solvent) solvatochromic shifts.
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Erratum to: Theoretical evaluation of Raman spectra and enhancement factors for a molecule adsorbed on a complex-shaped metal particle [Chem. Phys. Lett. 342 (2001) 135–140]. Chem Phys Lett 2002. [DOI: 10.1016/s0009-2614(02)01506-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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15
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Polarizable Continuum Model (PCM) Calculations of Solvent Effects on Optical Rotations of Chiral Molecules. J Phys Chem A 2002. [DOI: 10.1021/jp020124t] [Citation(s) in RCA: 512] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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17
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Conformational energy of glycine in aqueous solutions and relative stability of the zwitterionic and neutral forms. An ab initio study. J Am Chem Soc 2002. [DOI: 10.1021/ja00319a008] [Citation(s) in RCA: 198] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Nonempirical investigations on the azomethine group. 1. The effect of the conjugation with a phenyl ring. A comparison of the electronic structure of the ground and lowest excited states in benzaldimine and N-phenylformaldimine. J Am Chem Soc 2002. [DOI: 10.1021/ja00446a027] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Theoretical treatment of electrophilic reactivity in nitroxides and ketyl radicals through ab-initio molecular electrostatic potentials. ACTA ACUST UNITED AC 2002. [DOI: 10.1021/j100589a020] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Preferential solvation of Ca2+ in aqueous solutions containing ammonia: A molecular dynamics study. J Chem Phys 2002. [DOI: 10.1063/1.1453957] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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21
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Extending the polarizable continuum model to effective ab initio pair potentials in multicomponent solutions: A test on calcium–water and calcium–ammonia potentials. J Chem Phys 2002. [DOI: 10.1063/1.1453956] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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22
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Surface enhanced Raman scattering from a single molecule adsorbed on a metal particle aggregate: A theoretical study. J Chem Phys 2002. [DOI: 10.1063/1.1428349] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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23
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Health policy in action. J Nurs Scholarsh 2001; 33:206. [PMID: 11552542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
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24
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Expression level-dependent contribution of glucocorticoid receptor domains for functional interaction with STAT5. Mol Cell Biol 2001; 21:3266-79. [PMID: 11287629 PMCID: PMC86973 DOI: 10.1128/mcb.21.9.3266-3279.2001] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The action of the glucocorticoid receptor (GR) on beta-casein gene transcription serves as a well-studied example of a case where the action of the GR is dependent on the activity of another transcription factor, STAT5. We have investigated the domain-requirement of the GR for this synergistic response in transfection experiments employing GR mutants and CV-1 or COS-7 cells. The results were influenced by the expression levels of the GR constructs. At low expression, STAT5-dependent transactivation by mutants of the GR DNA binding domain or N-terminal transactivation domain was impaired and the antiglucocorticoid RU486 exhibited a weak agonistic activity. When the N-terminal region of the GR was exchanged with the respective domain of the progesterone receptor, STAT5-dependent transactivation was reduced at low and high expression levels. Only at high expression levels did the GR exhibit the properties of a coactivator and enhanced STAT5 activity in the absence of a functional DNA binding domain and of GR binding sites in the proximal region of the beta-casein gene promoter. Furthermore, at high GR expression levels RU486 was nearly as efficient as dexamethasone in activating transcription via the STAT5 dependent beta-casein gene promoter. The results reconcile the controversial issue regarding the DNA binding-independent action of the GR together with STAT5 and provide evidence that the mode of action of the GR depends not only on the type of the particular promoter at which it acts but also on the concentration of the GR. GR DNA binding function appears to be mandatory for beta-casein gene expression in mammary epithelial cells, since the promoter function is completely dependent on the integrity of GR binding sites in the promoter.
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Glycine and alanine: a theoretical study of solvent effects upon energetics and molecular response properties. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s0166-1280(00)00390-0] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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27
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The IEF version of the PCM solvation method: an overview of a new method addressed to study molecular solutes at the QM ab initio level. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s0166-1280(98)00553-3] [Citation(s) in RCA: 1582] [Impact Index Per Article: 63.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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28
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Analytical free energy second derivatives with respect to nuclear coordinates: Complete formulation for electrostatic continuum solvation models. J Chem Phys 1999. [DOI: 10.1063/1.478591] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Miertus S, Nair AC, Frecer V, Chiellini E, Chiellini F, Solaro R, Tomasi J. J INCL PHENOM MACRO 1999; 34:69-84. [DOI: 10.1023/a:1008098708797] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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30
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Analytical derivatives for geometry optimization in solvation continuum models. II. Numerical applications. J Chem Phys 1998. [DOI: 10.1063/1.476559] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Evaluation of Solvent Effects in Isotropic and Anisotropic Dielectrics and in Ionic Solutions with a Unified Integral Equation Method: Theoretical Bases, Computational Implementation, and Numerical Applications. J Phys Chem B 1997. [DOI: 10.1021/jp971959k] [Citation(s) in RCA: 1672] [Impact Index Per Article: 61.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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33
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Free energy and entropy for inserting cavities in water: Comparison of Monte Carlo simulation and scaled particle theory results. J Chem Phys 1997. [DOI: 10.1063/1.474296] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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34
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A new integral equation formalism for the polarizable continuum model: Theoretical background and applications to isotropic and anisotropic dielectrics. J Chem Phys 1997. [DOI: 10.1063/1.474659] [Citation(s) in RCA: 5262] [Impact Index Per Article: 194.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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35
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Modelling of the 3-D structure of IFN-alpha-k and characterization of its surface molecular properties. Int J Biol Macromol 1997; 20:85-95. [PMID: 9184940 DOI: 10.1016/s0141-8130(96)01143-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The 3-D structure of IFN-alpha-k (one of the alpha-interferon family) was constructed and optimized by molecular modelling starting from the X-ray structure of IFN-beta. The molecular surface of the optimized 3-D structure of IFN-alpha-k was then evaluated and characterized for its hydrophobicity/hydrophilicity. The structure of IFN-alpha-k was completed with its first segment (23 amino acid residues) called signal peptide. The 3-D structure of this segment was predicted to be in helical form bonded to the core by one loop. It was found that the complete structure of IFN-alpha-k can exist in at least two main conformations as far as the orientation of the signal peptide is concerned, i.e. in the open form (in which the signal peptide is directed outward of the 'body' of the molecule) and the closed form (where the signal peptide is aligned with the body). The relative stability of these forms strongly depends on the stabilization by the environment (e.g. by solvation) due to the prevailing hydrophilicity of the body and hydrophobic character of the signal peptide.
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36
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MEP: a tool for interpretation and prediction. From molecular structure to solvation effects. THEORETICAL AND COMPUTATIONAL CHEMISTRY 1996. [DOI: 10.1016/s1380-7323(96)80041-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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38
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Remarks on the use of the apparent surface charges (ASC) methods in solvation problems: Iterative versus matrix-inversion procedures and the renormalization of the apparent charges. J Comput Chem 1995. [DOI: 10.1002/jcc.540161202] [Citation(s) in RCA: 1063] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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39
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Application of Continuum Solvation Models Based on a Quantum Mechanical Hamiltonian. STRUCTURE AND REACTIVITY IN AQUEOUS SOLUTION 1994. [DOI: 10.1021/bk-1994-0568.ch002] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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40
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Analytical derivatives for molecular solutes. II. Hartree–Fock energy first and second derivatives with respect to nuclear coordinates. J Chem Phys 1994. [DOI: 10.1063/1.467506] [Citation(s) in RCA: 86] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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41
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Analytical derivatives for molecular solutes. I. Hartree–Fock energy first derivatives with respect to external parameters in the polarizable continuum model. J Chem Phys 1994. [DOI: 10.1063/1.466842] [Citation(s) in RCA: 119] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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42
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Nonequilibrium solvation: An ab initio quantum‐mechanical method in the continuum cavity model approximation. J Chem Phys 1993. [DOI: 10.1063/1.464728] [Citation(s) in RCA: 168] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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43
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Molecular reactivity in solution. Modelling of the effects of the solvent and of its stochastic fluctuation on an SN2 reaction. Chem Phys 1992. [DOI: 10.1016/0301-0104(92)87162-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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44
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Dispersion and repulsion contributions to the solvation energy: Refinements to a simple computational model in the continuum approximation. J Comput Chem 1991. [DOI: 10.1002/jcc.540120703] [Citation(s) in RCA: 273] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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45
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Electron correlation and solvation effects. I. Basic formulation and preliminary attempt to include the electron correlation in the quantum mechanical polarizable continuum model so as to study solvation phenomena. Chem Phys 1991. [DOI: 10.1016/0301-0104(91)80124-z] [Citation(s) in RCA: 108] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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46
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Evaluation of the dispersion contribution to the solvation energy. A simple computational model in the continuum approximation. J Comput Chem 1989. [DOI: 10.1002/jcc.540100504] [Citation(s) in RCA: 304] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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48
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Decomposition of the interaction energy with counterpoise corrections to the basis set superposition error for dimers in solution. Method and application to the hydrogen fluoride dimer. Chem Phys 1988. [DOI: 10.1016/0301-0104(88)87260-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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49
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Electrostatic interaction of a solute with a continuum. Improved description of the cavity and of the surface cavity bound charge distribution. J Comput Chem 1987. [DOI: 10.1002/jcc.540080605] [Citation(s) in RCA: 326] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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50
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A conformational basis for the description of the thermal E/Z isomerization of aromatic azo and azomethine compounds. ACTA ACUST UNITED AC 1987. [DOI: 10.1016/0166-1280(87)87003-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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