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Molecular modeling theory: Applications in the geosciences

Geoscience Opportunities for Leadership in Diversity AND Program Evaluation

Cygan RT, Kubicki JD.
GSID: cEuU29JW53kJ
RT Cygan, JD Kubicki - 2018 - books.google.com

Volume 42 of Reviews in Mineralogy and Geochemistry covers the Applications in the Geosciences via Molecular Modeling Theory. We hope the content of this review volume will help the interested reader to quickly develop an appreciation for the fundamental...

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Cygan, R. T., & Kubicki, J. D. (Eds.). (2018). Molecular modeling theory: Applications in the geosciences (Vol. 42). Walter de Gruyter GmbH & Co KG.
Cygan, Randall T., and James D. Kubicki, eds. Molecular modeling theory: Applications in the geosciences. Vol. 42. Walter de Gruyter GmbH & Co KG, 2018.
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Hydrothermal syntheses, crystal structures and physicochemical properties of 2-D and 3-D inorganic coordination cobalt(II)-sulfite polymers.

Dalton transactions (Cambridge, England : 2003)

Chilas GI, Lalioti N, Vaimakis T, Kubicki M, Kabanos T.
PMID: 20694241
Dalton Trans. 2010 Sep 21;39(35):8296-305. doi: 10.1039/b920710d. Epub 2010 Aug 09.

The hydrothermal reaction of [Co(III)(NH(3))(6)]Cl(3) with Na(2)SO(3) yields, depending on the concentration of Na(2)SO(3), compounds {Na[Co(II)(2)(SO(3))(2)(mu(3)-OH)(H(2)O)]}(infinity) (1) and {Na(4)[Co(II)(2)(SO(3))(4)]}(infinity) (2). When (NH(4))(2)SO(3) x H(2)O was substituted for Na(2)SO(3), the trinuclear mixed valence cobalt(II/III) complex (NH(4))(4){Co(II)[Co(III)(SO(3))(3)(NH(3))(3)](2)} x 2H(2)O (3 x...

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Chilas GI, Lalioti N, Vaimakis T, et al. Hydrothermal syntheses, crystal structures and physicochemical properties of 2-D and 3-D inorganic coordination cobalt(II)-sulfite polymers. Dalton Trans. 2010;39(35):8296-305doi: 10.1039/b920710d.
Chilas, G. I., Lalioti, N., Vaimakis, T., Kubicki, M., & Kabanos, T. (2010). Hydrothermal syntheses, crystal structures and physicochemical properties of 2-D and 3-D inorganic coordination cobalt(II)-sulfite polymers. Dalton transactions (Cambridge, England : 2003), 39(35), 8296-305. https://doi.org/10.1039/b920710d
Chilas, George I, et al. "Hydrothermal syntheses, crystal structures and physicochemical properties of 2-D and 3-D inorganic coordination cobalt(II)-sulfite polymers." Dalton transactions (Cambridge, England : 2003) vol. 39,35 (2010): 8296-305. doi: https://doi.org/10.1039/b920710d
Chilas GI, Lalioti N, Vaimakis T, Kubicki M, Kabanos T. Hydrothermal syntheses, crystal structures and physicochemical properties of 2-D and 3-D inorganic coordination cobalt(II)-sulfite polymers. Dalton Trans. 2010 Sep 21;39(35):8296-305. doi: 10.1039/b920710d. Epub 2010 Aug 09. PMID: 20694241.
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Phase Segregation in Cs-, Rb- and K-Doped Mixed-Cation (MA).

Journal of the American Chemical Society

Kubicki DJ, Prochowicz D, Hofstetter A, Zakeeruddin SM, Grätzel M, Emsley L.
PMID: 28892374
J Am Chem Soc. 2017 Oct 11;139(40):14173-14180. doi: 10.1021/jacs.7b07223. Epub 2017 Sep 27.

Hybrid (organic-inorganic) multication lead halide perovskites hold promise for a new generation of easily processable solar cells. Best performing compositions to date are multiple-cation solid alloys of formamidinium (FA), methylammonium (MA), cesium, and rubidium lead halides which provide power...

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Kubicki DJ, Prochowicz D, Hofstetter A, et al. Phase Segregation in Cs-, Rb- and K-Doped Mixed-Cation (MA). J Am Chem Soc. 2017;139(40):14173-14180doi: 10.1021/jacs.7b07223.
Kubicki, D. J., Prochowicz, D., Hofstetter, A., Zakeeruddin, S. M., Grätzel, M., & Emsley, L. (2017). Phase Segregation in Cs-, Rb- and K-Doped Mixed-Cation (MA). Journal of the American Chemical Society, 139(40), 14173-14180. https://doi.org/10.1021/jacs.7b07223
Kubicki, Dominik J, et al. "Phase Segregation in Cs-, Rb- and K-Doped Mixed-Cation (MA)." Journal of the American Chemical Society vol. 139,40 (2017): 14173-14180. doi: https://doi.org/10.1021/jacs.7b07223
Kubicki DJ, Prochowicz D, Hofstetter A, Zakeeruddin SM, Grätzel M, Emsley L. Phase Segregation in Cs-, Rb- and K-Doped Mixed-Cation (MA). J Am Chem Soc. 2017 Oct 11;139(40):14173-14180. doi: 10.1021/jacs.7b07223. Epub 2017 Sep 27. PMID: 28892374; PMCID: PMC5719467.
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Expression of genes encoding the calcium signalosome in cellular and transgenic models of Huntington's disease.

Frontiers in molecular neuroscience

Czeredys M, Gruszczynska-Biegala J, Schacht T, Methner A, Kuznicki J.
PMID: 24324398
Front Mol Neurosci. 2013 Nov 25;6:42. doi: 10.3389/fnmol.2013.00042. eCollection 2013.

Huntington's disease (HD) is a hereditary neurodegenerative disease caused by the expansion of a polyglutamine stretch in the huntingtin (HTT) protein and characterized by dysregulated calcium homeostasis. We investigated whether these disturbances are correlated with changes in the mRNA...

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Czeredys M, Gruszczynska-Biegala J, Schacht T, et al. Expression of genes encoding the calcium signalosome in cellular and transgenic models of Huntington's disease. Front Mol Neurosci. 2013;6:42doi: 10.3389/fnmol.2013.00042.
Czeredys, M., Gruszczynska-Biegala, J., Schacht, T., Methner, A., & Kuznicki, J. (2013). Expression of genes encoding the calcium signalosome in cellular and transgenic models of Huntington's disease. Frontiers in molecular neuroscience, 642. https://doi.org/10.3389/fnmol.2013.00042
Czeredys, Magdalena, et al. "Expression of genes encoding the calcium signalosome in cellular and transgenic models of Huntington's disease." Frontiers in molecular neuroscience vol. 6 (2013): 42. doi: https://doi.org/10.3389/fnmol.2013.00042
Czeredys M, Gruszczynska-Biegala J, Schacht T, Methner A, Kuznicki J. Expression of genes encoding the calcium signalosome in cellular and transgenic models of Huntington's disease. Front Mol Neurosci. 2013 Nov 25;6:42. doi: 10.3389/fnmol.2013.00042. eCollection 2013. PMID: 24324398; PMCID: PMC3838962.
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A new class of silica-supported chromo-fluorogenic chemosensors for anion recognition based on a selenourea scaffold.

Chemical communications (Cambridge, England)

Casula A, Llopis-Lorente A, Garau A, Isaia F, Kubicki M, Lippolis V, Sancenón F, Martínez-Máñez R, Owczarzak A, Santi C, Andrea Scorciapino M, Caltagirone C.
PMID: 28300250
Chem Commun (Camb). 2017 Mar 28;53(26):3729-3732. doi: 10.1039/c7cc01214d.

The first example of a chemosensor (L) containing a selenourea moiety is described here. L is able to colorimetrically sense the presence of CN

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Casula A, Llopis-Lorente A, Garau A, et al. A new class of silica-supported chromo-fluorogenic chemosensors for anion recognition based on a selenourea scaffold. Chem Commun (Camb). 2017;53(26):3729-3732doi: 10.1039/c7cc01214d.
Casula, A., Llopis-Lorente, A., Garau, A., Isaia, F., Kubicki, M., Lippolis, V., Sancenón, F., Martínez-Máñez, R., Owczarzak, A., Santi, C., Andrea Scorciapino, M., & Caltagirone, C. (2017). A new class of silica-supported chromo-fluorogenic chemosensors for anion recognition based on a selenourea scaffold. Chemical communications (Cambridge, England), 53(26), 3729-3732. https://doi.org/10.1039/c7cc01214d
Casula, Arianna, et al. "A new class of silica-supported chromo-fluorogenic chemosensors for anion recognition based on a selenourea scaffold." Chemical communications (Cambridge, England) vol. 53,26 (2017): 3729-3732. doi: https://doi.org/10.1039/c7cc01214d
Casula A, Llopis-Lorente A, Garau A, Isaia F, Kubicki M, Lippolis V, Sancenón F, Martínez-Máñez R, Owczarzak A, Santi C, Andrea Scorciapino M, Caltagirone C. A new class of silica-supported chromo-fluorogenic chemosensors for anion recognition based on a selenourea scaffold. Chem Commun (Camb). 2017 Mar 28;53(26):3729-3732. doi: 10.1039/c7cc01214d. PMID: 28300250.
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Ultrafast carbene-carbene isomerization.

Journal of the American Chemical Society

Wang J, Burdzinski G, Kubicki J, Gustafson TL, Platz MS.
PMID: 18366167
J Am Chem Soc. 2008 Apr 23;130(16):5418-9. doi: 10.1021/ja8002827. Epub 2008 Mar 26.

The photochemistry of two isomeric aryl diazo ketones was investigated by fs time-resolved UV-vis and IR spectroscopies. Both diazo ketone excited states decompose in less than 300 fs by multiple pathways. One pathway involves concerted Wolff rearrangement and nitrogen...

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Wang J, Burdzinski G, Kubicki J, et al. Ultrafast carbene-carbene isomerization. J Am Chem Soc. 2008;130(16):5418-9doi: 10.1021/ja8002827.
Wang, J., Burdzinski, G., Kubicki, J., Gustafson, T. L., & Platz, M. S. (2008). Ultrafast carbene-carbene isomerization. Journal of the American Chemical Society, 130(16), 5418-9. https://doi.org/10.1021/ja8002827
Wang, Jin, et al. "Ultrafast carbene-carbene isomerization." Journal of the American Chemical Society vol. 130,16 (2008): 5418-9. doi: https://doi.org/10.1021/ja8002827
Wang J, Burdzinski G, Kubicki J, Gustafson TL, Platz MS. Ultrafast carbene-carbene isomerization. J Am Chem Soc. 2008 Apr 23;130(16):5418-9. doi: 10.1021/ja8002827. Epub 2008 Mar 26. PMID: 18366167.
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The presence of a kinase of amylase in trypsin preparation.

The Biochemical journal

Chrzaszcz T, Janicki J.
PMID: 16745594
Biochem J. 1934;28(6):1949-54. doi: 10.1042/bj0281949.

No abstract available.

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Chrzaszcz T, Janicki J. The presence of a kinase of amylase in trypsin preparation. Biochem J. 1934;28(6):1949-54doi: 10.1042/bj0281949.
Chrzaszcz, T., & Janicki, J. (1934). The presence of a kinase of amylase in trypsin preparation. The Biochemical journal, 28(6), 1949-54. https://doi.org/10.1042/bj0281949
Chrzaszcz, T, and Janicki, J. "The presence of a kinase of amylase in trypsin preparation." The Biochemical journal vol. 28,6 (1934): 1949-54. doi: https://doi.org/10.1042/bj0281949
Chrzaszcz T, Janicki J. The presence of a kinase of amylase in trypsin preparation. Biochem J. 1934;28(6):1949-54. doi: 10.1042/bj0281949. PMID: 16745594; PMCID: PMC1253423.
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Anatomical preconditions for the postero-lateral approach to the spine.

Ortopedia, traumatologia, rehabilitacja

Ciszek B, Glinkowski W, Kunicki J.
PMID: 18034128
Ortop Traumatol Rehabil. 2000 Jun 30;2(2):85-8.

No abstract available.

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Ciszek B, Glinkowski W, Kunicki J. Anatomical preconditions for the postero-lateral approach to the spine. Ortop Traumatol Rehabil. 2000;2(2):85-8
Ciszek, B., Glinkowski, W., & Kunicki, J. (2000). Anatomical preconditions for the postero-lateral approach to the spine. Ortopedia, traumatologia, rehabilitacja, 2(2), 85-8.
Ciszek, B, et al. "Anatomical preconditions for the postero-lateral approach to the spine." Ortopedia, traumatologia, rehabilitacja vol. 2,2 (2000): 85-8.
Ciszek B, Glinkowski W, Kunicki J. Anatomical preconditions for the postero-lateral approach to the spine. Ortop Traumatol Rehabil. 2000 Jun 30;2(2):85-8. PMID: 18034128.
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Ion adsorption at the rutile-water interface: linking molecular and macroscopic properties.

Langmuir : the ACS journal of surfaces and colloids

Zhang Z, Fenter P, Cheng L, Sturchio NC, Bedzyk MJ, Predota M, Bandura A, Kubicki JD, Lvov SN, Cummings PT, Chialvo AA, Ridley MK, Bénézeth P, Anovitz L, Palmer DA, Machesky ML, Wesolowski DJ.
PMID: 15984256
Langmuir. 2004 Jun 08;20(12):4954-69. doi: 10.1021/la0353834.

A comprehensive picture of the interface between aqueous solutions and the (110) surface of rutile (alpha-TiO2) is being developed by combining molecular-scale and macroscopic approaches, including experimental measurements, quantum calculations, molecular simulations, and Gouy-Chapman-Stern models. In situ X-ray reflectivity...

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Zhang Z, Fenter P, Cheng L, et al. Ion adsorption at the rutile-water interface: linking molecular and macroscopic properties. Langmuir. 2004;20(12):4954-69doi: 10.1021/la0353834.
Zhang, Z., Fenter, P., Cheng, L., Sturchio, N. C., Bedzyk, M. J., Predota, M., Bandura, A., Kubicki, J. D., Lvov, S. N., Cummings, P. T., Chialvo, A. A., Ridley, M. K., Bénézeth, P., Anovitz, L., Palmer, D. A., Machesky, M. L., & Wesolowski, D. J. (2004). Ion adsorption at the rutile-water interface: linking molecular and macroscopic properties. Langmuir : the ACS journal of surfaces and colloids, 20(12), 4954-69. https://doi.org/10.1021/la0353834
Zhang, Z, et al. "Ion adsorption at the rutile-water interface: linking molecular and macroscopic properties." Langmuir : the ACS journal of surfaces and colloids vol. 20,12 (2004): 4954-69. doi: https://doi.org/10.1021/la0353834
Zhang Z, Fenter P, Cheng L, Sturchio NC, Bedzyk MJ, Predota M, Bandura A, Kubicki JD, Lvov SN, Cummings PT, Chialvo AA, Ridley MK, Bénézeth P, Anovitz L, Palmer DA, Machesky ML, Wesolowski DJ. Ion adsorption at the rutile-water interface: linking molecular and macroscopic properties. Langmuir. 2004 Jun 08;20(12):4954-69. doi: 10.1021/la0353834. PMID: 15984256.
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Cyano-cyano and chloro-cyano interactions in two imidazole derivatives.

Acta crystallographica. Section C, Crystal structure communications

Kubicki M.
PMID: 15071227
Acta Crystallogr C. 2004 Apr;60:o255-7. doi: 10.1107/S0108270104003294. Epub 2004 Mar 11.

In two closely related 1-aryl-2-methyl-4-nitro-5-cyanoimidazoles, namely 2-methyl-4-nitro-1-phenyl-1H-imidazole-5-carbonitrile, C(11)H(8)N(4)O(2), and 1-(4-chlorophenyl)-2-methyl-4-nitro-1H-imidazole-5-carbonitrile, C(11)H(7)ClN(4)O(2), different weak intermolecular interactions determine the crystal packing. In the 1-phenyl derivative, dipole-dipole interactions between antiparallel cyano groups connect molecules into centrosymmetric dimers, while in the 1-(4-chlorophenyl) derivative,...

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Kubicki M. Cyano-cyano and chloro-cyano interactions in two imidazole derivatives. Acta Crystallogr C. 2004;60:o255-7doi: 10.1107/S0108270104003294.
Kubicki, M. (2004). Cyano-cyano and chloro-cyano interactions in two imidazole derivatives. Acta crystallographica. Section C, Crystal structure communications, 60o255-7. https://doi.org/10.1107/S0108270104003294
Kubicki, Maciej. "Cyano-cyano and chloro-cyano interactions in two imidazole derivatives." Acta crystallographica. Section C, Crystal structure communications vol. 60 (2004): o255-7. doi: https://doi.org/10.1107/S0108270104003294
Kubicki M. Cyano-cyano and chloro-cyano interactions in two imidazole derivatives. Acta Crystallogr C. 2004 Apr;60:o255-7. doi: 10.1107/S0108270104003294. Epub 2004 Mar 11. PMID: 15071227.
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Pentaaza macrocyclic ytterbium(III) complex and solvent controlled supramolecular self-assembly of its dimeric mu-eta 2:eta 2 peroxo-bridged derivatives.

Dalton transactions (Cambridge, England : 2003)

Patroniak V, Kubicki M, Mondry A, Lisowski J, Radecka-Paryzek W.
PMID: 15483714
Dalton Trans. 2004 Oct 21;(20):3295-304. doi: 10.1039/B408157A. Epub 2004 Sep 01.

The unprecedented template action of ytterbium ion in the synthesis of pentaaza macrocyclic Schiff bases is exemplified by isolation and definitive identification of the seven-coordinate pentagonal bipyramidal complex with the formula of [YbLCl(2)]ClO(4) (1), where L is 2,14-dimethyl-3,6,10,13,19-pentaazabicyclo[13.3.1]nonadeca-1(19),2,13,15,17-pentaene, providing...

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Patroniak V, Kubicki M, Mondry A, et al. Pentaaza macrocyclic ytterbium(III) complex and solvent controlled supramolecular self-assembly of its dimeric mu-eta 2:eta 2 peroxo-bridged derivatives. Dalton Trans. 2004;(20):3295-304doi: 10.1039/B408157A.
Patroniak, V., Kubicki, M., Mondry, A., Lisowski, J., & Radecka-Paryzek, W. (2004). Pentaaza macrocyclic ytterbium(III) complex and solvent controlled supramolecular self-assembly of its dimeric mu-eta 2:eta 2 peroxo-bridged derivatives. Dalton transactions (Cambridge, England : 2003), (20), 3295-304. https://doi.org/10.1039/B408157A
Patroniak, Violetta, et al. "Pentaaza macrocyclic ytterbium(III) complex and solvent controlled supramolecular self-assembly of its dimeric mu-eta 2:eta 2 peroxo-bridged derivatives." Dalton transactions (Cambridge, England : 2003) vol. ,20 (2004): 3295-304. doi: https://doi.org/10.1039/B408157A
Patroniak V, Kubicki M, Mondry A, Lisowski J, Radecka-Paryzek W. Pentaaza macrocyclic ytterbium(III) complex and solvent controlled supramolecular self-assembly of its dimeric mu-eta 2:eta 2 peroxo-bridged derivatives. Dalton Trans. 2004 Oct 21;(20):3295-304. doi: 10.1039/B408157A. Epub 2004 Sep 01. PMID: 15483714.
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Effect of dehydration on sulfate coordination and speciation at the Fe-(hydr)oxide-water interface: a molecular orbital/density functional theory and Fourier transform infrared spectroscopic investigation.

Langmuir : the ACS journal of surfaces and colloids

Paul KW, Borda MJ, Kubicki JD, Sparks DL.
PMID: 16285773
Langmuir. 2005 Nov 22;21(24):11071-8. doi: 10.1021/la050648v.

The effect of dehydration on the coordination and speciation of sulfate at the Fe-(hydr)oxide-H2O interface was investigated using molecular orbital/density functional theory (MO/DFT) and Fourier transform infrared (FTIR) spectroscopy. IR frequency calculations were performed at the UB3LYP/6-31+G(d) level of...

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Paul KW, Borda MJ, Kubicki JD, et al. Effect of dehydration on sulfate coordination and speciation at the Fe-(hydr)oxide-water interface: a molecular orbital/density functional theory and Fourier transform infrared spectroscopic investigation. Langmuir. 2005;21(24):11071-8doi: 10.1021/la050648v.
Paul, K. W., Borda, M. J., Kubicki, J. D., & Sparks, D. L. (2005). Effect of dehydration on sulfate coordination and speciation at the Fe-(hydr)oxide-water interface: a molecular orbital/density functional theory and Fourier transform infrared spectroscopic investigation. Langmuir : the ACS journal of surfaces and colloids, 21(24), 11071-8. https://doi.org/10.1021/la050648v
Paul, Kristian W, et al. "Effect of dehydration on sulfate coordination and speciation at the Fe-(hydr)oxide-water interface: a molecular orbital/density functional theory and Fourier transform infrared spectroscopic investigation." Langmuir : the ACS journal of surfaces and colloids vol. 21,24 (2005): 11071-8. doi: https://doi.org/10.1021/la050648v
Paul KW, Borda MJ, Kubicki JD, Sparks DL. Effect of dehydration on sulfate coordination and speciation at the Fe-(hydr)oxide-water interface: a molecular orbital/density functional theory and Fourier transform infrared spectroscopic investigation. Langmuir. 2005 Nov 22;21(24):11071-8. doi: 10.1021/la050648v. PMID: 16285773.
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Showing 1 to 12 of 386 entries