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The role of alkali metal cations in the stabilization of guanine quadruplexes: why K(+) is the best.

Physical chemistry chemical physics : PCCP

Zaccaria F, Paragi G, Fonseca Guerra C.
PMID: 27185388
Phys Chem Chem Phys. 2016 Aug 21;18(31):20895-904. doi: 10.1039/c6cp01030j. Epub 2016 May 17.

The alkali metal ion affinity of guanine quadruplexes has been studied using dispersion-corrected density functional theory (DFT-D). We have done computational investigations in aqueous solution that mimics artificial supramolecular conditions where guanine bases assemble into stacked quartets as well...

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Zaccaria F, Paragi G, Fonseca Guerra C. The role of alkali metal cations in the stabilization of guanine quadruplexes: why K(+) is the best. Phys Chem Chem Phys. 2016;18(31):20895-904doi: 10.1039/c6cp01030j.
Zaccaria, F., Paragi, G., & Fonseca Guerra, C. (2016). The role of alkali metal cations in the stabilization of guanine quadruplexes: why K(+) is the best. Physical chemistry chemical physics : PCCP, 18(31), 20895-904. https://doi.org/10.1039/c6cp01030j
Zaccaria, F, et al. "The role of alkali metal cations in the stabilization of guanine quadruplexes: why K(+) is the best." Physical chemistry chemical physics : PCCP vol. 18,31 (2016): 20895-904. doi: https://doi.org/10.1039/c6cp01030j
Zaccaria F, Paragi G, Fonseca Guerra C. The role of alkali metal cations in the stabilization of guanine quadruplexes: why K(+) is the best. Phys Chem Chem Phys. 2016 Aug 21;18(31):20895-904. doi: 10.1039/c6cp01030j. Epub 2016 May 17. PMID: 27185388.
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Bis[N,N'-diisopropylbenzamidinato(-)]silicon(II): Lewis acid/base reactions with triorganylboranes.

Chemistry (Weinheim an der Bergstrasse, Germany)

Junold K, Baus JA, Burschka C, Fonseca Guerra C, Bickelhaupt FM, Tacke R.
PMID: 25113173
Chemistry. 2014 Sep 22;20(39):12411-5. doi: 10.1002/chem.201403995. Epub 2014 Aug 11.

Reaction of the donor-stabilized silylene 1 (which is three-coordinate in the solid state and four-coordinate in solution) with BEt3 and BPh3 leads to the formation of the Lewis acid/base complexes 2 and 3, respectively, which are the first five-coordinate...

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Junold K, Baus JA, Burschka C, et al. Bis[N,N'-diisopropylbenzamidinato(-)]silicon(II): Lewis acid/base reactions with triorganylboranes. Chemistry. 2014;20(39):12411-5doi: 10.1002/chem.201403995.
Junold, K., Baus, J. A., Burschka, C., Fonseca Guerra, C., Bickelhaupt, F. M., & Tacke, R. (2014). Bis[N,N'-diisopropylbenzamidinato(-)]silicon(II): Lewis acid/base reactions with triorganylboranes. Chemistry (Weinheim an der Bergstrasse, Germany), 20(39), 12411-5. https://doi.org/10.1002/chem.201403995
Junold, Konstantin, et al. "Bis[N,N'-diisopropylbenzamidinato(-)]silicon(II): Lewis acid/base reactions with triorganylboranes." Chemistry (Weinheim an der Bergstrasse, Germany) vol. 20,39 (2014): 12411-5. doi: https://doi.org/10.1002/chem.201403995
Junold K, Baus JA, Burschka C, Fonseca Guerra C, Bickelhaupt FM, Tacke R. Bis[N,N'-diisopropylbenzamidinato(-)]silicon(II): Lewis acid/base reactions with triorganylboranes. Chemistry. 2014 Sep 22;20(39):12411-5. doi: 10.1002/chem.201403995. Epub 2014 Aug 11. PMID: 25113173.
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Alkali Metal Cation versus Proton and Methyl Cation Affinities: Structure and Bonding Mechanism.

ChemistryOpen

Boughlala Z, Fonseca Guerra C, Bickelhaupt FM.
PMID: 27551660
ChemistryOpen. 2016 Feb 22;5(3):247-53. doi: 10.1002/open.201500208. eCollection 2016 Jun.

We have analyzed the structure and bonding of gas-phase Cl-X and [HCl-X](+) complexes for X(+)= H(+), CH3 (+), Li(+), and Na(+), using relativistic density functional theory (DFT). We wish to establish a quantitative trend in affinities of the anionic...

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Boughlala Z, Fonseca Guerra C, Bickelhaupt FM. Alkali Metal Cation versus Proton and Methyl Cation Affinities: Structure and Bonding Mechanism. ChemistryOpen. 2016;5(3):247-53doi: 10.1002/open.201500208.
Boughlala, Z., Fonseca Guerra, C., & Bickelhaupt, F. M. (2016). Alkali Metal Cation versus Proton and Methyl Cation Affinities: Structure and Bonding Mechanism. ChemistryOpen, 5(3), 247-53. https://doi.org/10.1002/open.201500208
Boughlala, Zakaria, et al. "Alkali Metal Cation versus Proton and Methyl Cation Affinities: Structure and Bonding Mechanism." ChemistryOpen vol. 5,3 (2016): 247-53. doi: https://doi.org/10.1002/open.201500208
Boughlala Z, Fonseca Guerra C, Bickelhaupt FM. Alkali Metal Cation versus Proton and Methyl Cation Affinities: Structure and Bonding Mechanism. ChemistryOpen. 2016 Feb 22;5(3):247-53. doi: 10.1002/open.201500208. eCollection 2016 Jun. PMID: 27551660; PMCID: PMC4984409.
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The Role of Aromaticity, Hybridization, Electrostatics, and Covalency in Resonance-Assisted Hydrogen Bonds of Adenine-Thymine (AT) Base Pairs and Their Mimics.

ChemistryOpen

Guillaumes L, Simon S, Fonseca Guerra C, Bhagavatula P.
PMID: 26246994
ChemistryOpen. 2015 Jun;4(3):318-27. doi: 10.1002/open.201402132. Epub 2015 Mar 09.

Hydrogen bonds play a crucial role in many biochemical processes and in supramolecular chemistry. In this study, we show quantum chemically that neither aromaticity nor other forms of π assistance are responsible for the enhanced stability of the hydrogen...

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Guillaumes L, Simon S, Fonseca Guerra C, et al. The Role of Aromaticity, Hybridization, Electrostatics, and Covalency in Resonance-Assisted Hydrogen Bonds of Adenine-Thymine (AT) Base Pairs and Their Mimics. ChemistryOpen. 2015;4(3):318-27doi: 10.1002/open.201402132.
Guillaumes, L., Simon, S., Fonseca Guerra, C., & Bhagavatula, P. (2015). The Role of Aromaticity, Hybridization, Electrostatics, and Covalency in Resonance-Assisted Hydrogen Bonds of Adenine-Thymine (AT) Base Pairs and Their Mimics. ChemistryOpen, 4(3), 318-27. https://doi.org/10.1002/open.201402132
Guillaumes, L, et al. "The Role of Aromaticity, Hybridization, Electrostatics, and Covalency in Resonance-Assisted Hydrogen Bonds of Adenine-Thymine (AT) Base Pairs and Their Mimics." ChemistryOpen vol. 4,3 (2015): 318-27. doi: https://doi.org/10.1002/open.201402132
Guillaumes L, Simon S, Fonseca Guerra C, Bhagavatula P. The Role of Aromaticity, Hybridization, Electrostatics, and Covalency in Resonance-Assisted Hydrogen Bonds of Adenine-Thymine (AT) Base Pairs and Their Mimics. ChemistryOpen. 2015 Jun;4(3):318-27. doi: 10.1002/open.201402132. Epub 2015 Mar 09. PMID: 26246994; PMCID: PMC4522182.
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Voronoi deformation density (VDD) charges: Assessment of the Mulliken, Bader, Hirshfeld, Weinhold, and VDD methods for charge analysis.

Journal of computational chemistry

Fonseca Guerra C, Handgraaf JW, Baerends EJ, Bickelhaupt FM.
PMID: 14648618
J Comput Chem. 2004 Jan 30;25(2):189-210. doi: 10.1002/jcc.10351.

We present the Voronoi Deformation Density (VDD) method for computing atomic charges. The VDD method does not explicitly use the basis functions but calculates the amount of electronic density that flows to or from a certain atom due to...

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Fonseca Guerra C, Handgraaf JW, Baerends EJ, et al. Voronoi deformation density (VDD) charges: Assessment of the Mulliken, Bader, Hirshfeld, Weinhold, and VDD methods for charge analysis. J Comput Chem. 2004;25(2):189-210doi: 10.1002/jcc.10351.
Fonseca Guerra, C., Handgraaf, J. W., Baerends, E. J., & Bickelhaupt, F. M. (2004). Voronoi deformation density (VDD) charges: Assessment of the Mulliken, Bader, Hirshfeld, Weinhold, and VDD methods for charge analysis. Journal of computational chemistry, 25(2), 189-210. https://doi.org/10.1002/jcc.10351
Fonseca Guerra, Célia, et al. "Voronoi deformation density (VDD) charges: Assessment of the Mulliken, Bader, Hirshfeld, Weinhold, and VDD methods for charge analysis." Journal of computational chemistry vol. 25,2 (2004): 189-210. doi: https://doi.org/10.1002/jcc.10351
Fonseca Guerra C, Handgraaf JW, Baerends EJ, Bickelhaupt FM. Voronoi deformation density (VDD) charges: Assessment of the Mulliken, Bader, Hirshfeld, Weinhold, and VDD methods for charge analysis. J Comput Chem. 2004 Jan 30;25(2):189-210. doi: 10.1002/jcc.10351. PMID: 14648618.
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Impact of Conformational Effects on the Ring-Chain Equilibrium of Hydrogen-Bonded Dinucleosides.

Chemistry (Weinheim an der Bergstrasse, Germany)

Montoro-García C, Bilbao N, Tsagri IM, Zaccaria F, Mayoral MJ, Fonseca Guerra C, González-Rodríguez D.
PMID: 29742299
Chemistry. 2018 Aug 14;24(46):11983-11991. doi: 10.1002/chem.201801704. Epub 2018 Jul 02.

Supramolecular ring-versus-chain equilibria are ubiquitous in biological and synthetic systems. Understanding the factors that decide whether a system will fall on one side or the other is crucial to the control of molecular self-assembly. This work reports results with...

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Montoro-García C, Bilbao N, Tsagri IM, et al. Impact of Conformational Effects on the Ring-Chain Equilibrium of Hydrogen-Bonded Dinucleosides. Chemistry. 2018;24(46):11983-11991doi: 10.1002/chem.201801704.
Montoro-García, C., Bilbao, N., Tsagri, I. M., Zaccaria, F., Mayoral, M. J., Fonseca Guerra, C., & González-Rodríguez, D. (2018). Impact of Conformational Effects on the Ring-Chain Equilibrium of Hydrogen-Bonded Dinucleosides. Chemistry (Weinheim an der Bergstrasse, Germany), 24(46), 11983-11991. https://doi.org/10.1002/chem.201801704
Montoro-García, Carlos, et al. "Impact of Conformational Effects on the Ring-Chain Equilibrium of Hydrogen-Bonded Dinucleosides." Chemistry (Weinheim an der Bergstrasse, Germany) vol. 24,46 (2018): 11983-11991. doi: https://doi.org/10.1002/chem.201801704
Montoro-García C, Bilbao N, Tsagri IM, Zaccaria F, Mayoral MJ, Fonseca Guerra C, González-Rodríguez D. Impact of Conformational Effects on the Ring-Chain Equilibrium of Hydrogen-Bonded Dinucleosides. Chemistry. 2018 Aug 14;24(46):11983-11991. doi: 10.1002/chem.201801704. Epub 2018 Jul 02. PMID: 29742299.
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Stable Four-Coordinate Guanidinatosilicon(IV) Complexes with SiN3El Skeletons (El = S, Se, Te) and Si=El Double Bonds.

Chemistry (Weinheim an der Bergstrasse, Germany)

Mück FM, Kloß D, Baus JA, Burschka C, Bertermann R, Poater J, Fonseca Guerra C, Bickelhaupt FM, Tacke R.
PMID: 26284318
Chemistry. 2015 Sep 28;21(40):14011-21. doi: 10.1002/chem.201501789. Epub 2015 Aug 18.

To get information about the reactivity profile of the donor-stabilized guanidinatosilicon(II) complexes 2 and 3, a series of oxidative addition reactions was studied. Treatment of 2 and 3 with S8, Se, or Te afforded the respective four-coordinate silicon(IV) complexes...

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Mück FM, Kloß D, Baus JA, et al. Stable Four-Coordinate Guanidinatosilicon(IV) Complexes with SiN3El Skeletons (El = S, Se, Te) and Si=El Double Bonds. Chemistry. 2015;21(40):14011-21doi: 10.1002/chem.201501789.
Mück, F. M., Kloß, D., Baus, J. A., Burschka, C., Bertermann, R., Poater, J., Fonseca Guerra, C., Bickelhaupt, F. M., & Tacke, R. (2015). Stable Four-Coordinate Guanidinatosilicon(IV) Complexes with SiN3El Skeletons (El = S, Se, Te) and Si=El Double Bonds. Chemistry (Weinheim an der Bergstrasse, Germany), 21(40), 14011-21. https://doi.org/10.1002/chem.201501789
Mück, Felix M, et al. "Stable Four-Coordinate Guanidinatosilicon(IV) Complexes with SiN3El Skeletons (El = S, Se, Te) and Si=El Double Bonds." Chemistry (Weinheim an der Bergstrasse, Germany) vol. 21,40 (2015): 14011-21. doi: https://doi.org/10.1002/chem.201501789
Mück FM, Kloß D, Baus JA, Burschka C, Bertermann R, Poater J, Fonseca Guerra C, Bickelhaupt FM, Tacke R. Stable Four-Coordinate Guanidinatosilicon(IV) Complexes with SiN3El Skeletons (El = S, Se, Te) and Si=El Double Bonds. Chemistry. 2015 Sep 28;21(40):14011-21. doi: 10.1002/chem.201501789. Epub 2015 Aug 18. PMID: 26284318.
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Rational design of near-infrared absorbing organic dyes: Controlling the HOMO-LUMO gap using quantitative molecular orbital theory.

Journal of computational chemistry

Narsaria AK, Poater J, Fonseca Guerra C, Ehlers AW, Lammertsma K, Bickelhaupt FM.
PMID: 30515900
J Comput Chem. 2018 Dec 15;39(32):2690-2696. doi: 10.1002/jcc.25731.

Principles are presented for the design of functional near-infrared (NIR) organic dye molecules composed of simple donor (D), spacer (π), and acceptor (A) building blocks in a D-π-A fashion. Quantitative Kohn-Sham molecular orbital analysis enables accurate fine-tuning of the...

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Narsaria AK, Poater J, Fonseca Guerra C, et al. Rational design of near-infrared absorbing organic dyes: Controlling the HOMO-LUMO gap using quantitative molecular orbital theory. J Comput Chem. 2018;39(32):2690-2696doi: 10.1002/jcc.25731.
Narsaria, A. K., Poater, J., Fonseca Guerra, C., Ehlers, A. W., Lammertsma, K., & Bickelhaupt, F. M. (2018). Rational design of near-infrared absorbing organic dyes: Controlling the HOMO-LUMO gap using quantitative molecular orbital theory. Journal of computational chemistry, 39(32), 2690-2696. https://doi.org/10.1002/jcc.25731
Narsaria, Ayush K, et al. "Rational design of near-infrared absorbing organic dyes: Controlling the HOMO-LUMO gap using quantitative molecular orbital theory." Journal of computational chemistry vol. 39,32 (2018): 2690-2696. doi: https://doi.org/10.1002/jcc.25731
Narsaria AK, Poater J, Fonseca Guerra C, Ehlers AW, Lammertsma K, Bickelhaupt FM. Rational design of near-infrared absorbing organic dyes: Controlling the HOMO-LUMO gap using quantitative molecular orbital theory. J Comput Chem. 2018 Dec 15;39(32):2690-2696. doi: 10.1002/jcc.25731. PMID: 30515900; PMCID: PMC6587560.
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New light on an old debate: does the RCN-PtCl.

Dalton transactions (Cambridge, England : 2003)

Casella G, Fonseca Guerra C, Carlotto S, Sgarbossa P, Bertani R, Casarin M.
PMID: 31397469
Dalton Trans. 2019 Sep 14;48(34):12974-12985. doi: 10.1039/c9dt02440a. Epub 2019 Aug 09.

For a series of organonitrile [RCN (R = Me, CF

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Casella G, Fonseca Guerra C, Carlotto S, et al. New light on an old debate: does the RCN-PtCl. Dalton Trans. 2019;48(34):12974-12985doi: 10.1039/c9dt02440a.
Casella, G., Fonseca Guerra, C., Carlotto, S., Sgarbossa, P., Bertani, R., & Casarin, M. (2019). New light on an old debate: does the RCN-PtCl. Dalton transactions (Cambridge, England : 2003), 48(34), 12974-12985. https://doi.org/10.1039/c9dt02440a
Casella, Girolamo, et al. "New light on an old debate: does the RCN-PtCl." Dalton transactions (Cambridge, England : 2003) vol. 48,34 (2019): 12974-12985. doi: https://doi.org/10.1039/c9dt02440a
Casella G, Fonseca Guerra C, Carlotto S, Sgarbossa P, Bertani R, Casarin M. New light on an old debate: does the RCN-PtCl. Dalton Trans. 2019 Sep 14;48(34):12974-12985. doi: 10.1039/c9dt02440a. Epub 2019 Aug 09. PMID: 31397469.
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Nature of Alkali- and Coinage-Metal Bonds versus Hydrogen Bonds.

Chemistry, an Asian journal

Larrañaga O, Arrieta A, Fonseca Guerra C, Bickelhaupt FM, de Cózar A.
PMID: 33372401
Chem Asian J. 2021 Feb 15;16(4):315-321. doi: 10.1002/asia.202001201. Epub 2021 Jan 14.

We have quantum chemically studied the structure and nature of alkali- and coinage-metal bonds (M-bonds) versus that of hydrogen bonds between A-M and B

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Larrañaga O, Arrieta A, Fonseca Guerra C, et al. Nature of Alkali- and Coinage-Metal Bonds versus Hydrogen Bonds. Chem Asian J. 2021;16(4):315-321doi: 10.1002/asia.202001201.
Larrañaga, O., Arrieta, A., Fonseca Guerra, C., Bickelhaupt, F. M., & de Cózar, A. (2021). Nature of Alkali- and Coinage-Metal Bonds versus Hydrogen Bonds. Chemistry, an Asian journal, 16(4), 315-321. https://doi.org/10.1002/asia.202001201
Larrañaga, Olatz, et al. "Nature of Alkali- and Coinage-Metal Bonds versus Hydrogen Bonds." Chemistry, an Asian journal vol. 16,4 (2021): 315-321. doi: https://doi.org/10.1002/asia.202001201
Larrañaga O, Arrieta A, Fonseca Guerra C, Bickelhaupt FM, de Cózar A. Nature of Alkali- and Coinage-Metal Bonds versus Hydrogen Bonds. Chem Asian J. 2021 Feb 15;16(4):315-321. doi: 10.1002/asia.202001201. Epub 2021 Jan 14. PMID: 33372401; PMCID: PMC7898866.
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Not Carbon s-p Hybridization, but Coordination Number Determines C-H and C-C Bond Length.

Chemistry (Weinheim an der Bergstrasse, Germany)

Vermeeren P, van Zeist WJ, Hamlin TA, Fonseca Guerra C, Bickelhaupt FM.
PMID: 33513281
Chemistry. 2021 Apr 26;27(24):7074-7079. doi: 10.1002/chem.202004653. Epub 2021 Mar 03.

A fundamental and ubiquitous phenomenon in chemistry is the contraction of both C-H and C-C bonds as the carbon atoms involved vary, in s-p hybridization, along sp

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Vermeeren P, van Zeist WJ, Hamlin TA, et al. Not Carbon s-p Hybridization, but Coordination Number Determines C-H and C-C Bond Length. Chemistry. 2021;27(24):7074-7079doi: 10.1002/chem.202004653.
Vermeeren, P., van Zeist, W. J., Hamlin, T. A., Fonseca Guerra, C., & Bickelhaupt, F. M. (2021). Not Carbon s-p Hybridization, but Coordination Number Determines C-H and C-C Bond Length. Chemistry (Weinheim an der Bergstrasse, Germany), 27(24), 7074-7079. https://doi.org/10.1002/chem.202004653
Vermeeren, Pascal, et al. "Not Carbon s-p Hybridization, but Coordination Number Determines C-H and C-C Bond Length." Chemistry (Weinheim an der Bergstrasse, Germany) vol. 27,24 (2021): 7074-7079. doi: https://doi.org/10.1002/chem.202004653
Vermeeren P, van Zeist WJ, Hamlin TA, Fonseca Guerra C, Bickelhaupt FM. Not Carbon s-p Hybridization, but Coordination Number Determines C-H and C-C Bond Length. Chemistry. 2021 Apr 26;27(24):7074-7079. doi: 10.1002/chem.202004653. Epub 2021 Mar 03. PMID: 33513281; PMCID: PMC8248318.
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The donor-stabilized silylene bis[N,N'-diisopropylbenzamidinato(-)]silicon(II): synthesis, electronic structure, and reactivity.

Chemistry (Weinheim an der Bergstrasse, Germany)

Junold K, Nutz M, Baus JA, Burschka C, Fonseca Guerra C, Bickelhaupt FM, Tacke R.
PMID: 24903711
Chemistry. 2014 Jul 21;20(30):9319-29. doi: 10.1002/chem.201402483. Epub 2014 Jun 05.

A convenient and robust synthesis of bis[N,N'-diisopropylbenzamidinato(-)]silicon(II) (1), a donor-stabilized silylene, has been developed (35 g scale). To get further information about the reactivity profile of 1, a series of oxidative addition reactions were studied. Treatment of 1 with...

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Junold K, Nutz M, Baus JA, et al. The donor-stabilized silylene bis[N,N'-diisopropylbenzamidinato(-)]silicon(II): synthesis, electronic structure, and reactivity. Chemistry. 2014;20(30):9319-29doi: 10.1002/chem.201402483.
Junold, K., Nutz, M., Baus, J. A., Burschka, C., Fonseca Guerra, C., Bickelhaupt, F. M., & Tacke, R. (2014). The donor-stabilized silylene bis[N,N'-diisopropylbenzamidinato(-)]silicon(II): synthesis, electronic structure, and reactivity. Chemistry (Weinheim an der Bergstrasse, Germany), 20(30), 9319-29. https://doi.org/10.1002/chem.201402483
Junold, Konstantin, et al. "The donor-stabilized silylene bis[N,N'-diisopropylbenzamidinato(-)]silicon(II): synthesis, electronic structure, and reactivity." Chemistry (Weinheim an der Bergstrasse, Germany) vol. 20,30 (2014): 9319-29. doi: https://doi.org/10.1002/chem.201402483
Junold K, Nutz M, Baus JA, Burschka C, Fonseca Guerra C, Bickelhaupt FM, Tacke R. The donor-stabilized silylene bis[N,N'-diisopropylbenzamidinato(-)]silicon(II): synthesis, electronic structure, and reactivity. Chemistry. 2014 Jul 21;20(30):9319-29. doi: 10.1002/chem.201402483. Epub 2014 Jun 05. PMID: 24903711.
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