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Showing 1 to 12 of 476 entries
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Zero-Cost Estimation of Zero-Point Energies.

The journal of physical chemistry. A

Császár AG, Furtenbacher T.
PMID: 26398318
J Phys Chem A. 2015 Oct 08;119(40):10229-40. doi: 10.1021/acs.jpca.5b07156. Epub 2015 Sep 23.

An additive, linear, atom-type-based (ATB) scheme is developed allowing no-cost estimation of zero-point vibrational energies (ZPVE) of neutral, closed-shell molecules in their ground electronic states. The atom types employed correspond to those defined within the MM2 molecular mechanics force...

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Császár AG, Furtenbacher T. Zero-Cost Estimation of Zero-Point Energies. J Phys Chem A. 2015;119(40):10229-40doi: 10.1021/acs.jpca.5b07156.
Császár, A. G., & Furtenbacher, T. (2015). Zero-Cost Estimation of Zero-Point Energies. The journal of physical chemistry. A, 119(40), 10229-40. https://doi.org/10.1021/acs.jpca.5b07156
Császár, Attila G, and Furtenbacher, Tibor. "Zero-Cost Estimation of Zero-Point Energies." The journal of physical chemistry. A vol. 119,40 (2015): 10229-40. doi: https://doi.org/10.1021/acs.jpca.5b07156
Császár AG, Furtenbacher T. Zero-Cost Estimation of Zero-Point Energies. J Phys Chem A. 2015 Oct 08;119(40):10229-40. doi: 10.1021/acs.jpca.5b07156. Epub 2015 Sep 23. PMID: 26398318.
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Establishing Effective Simulation Protocols for β- and α/β-Mixed Peptides. I. QM and QM/MM Models.

Journal of chemical theory and computation

Zhu X, Yethiraj A, Cui Q.
PMID: 26633224
J Chem Theory Comput. 2007 Jul;3(4):1538-49. doi: 10.1021/ct600352e.

A quantum mechanical (QM) model for non-natural β- and α/β-mixed peptides is investigated using an approximate density functional method (called SCC-DFTB). In the gas phase the predictions of the model for cyclic and acyclic dipeptides and several acyclic heptapeptides...

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Zhu X, Yethiraj A, Cui Q. Establishing Effective Simulation Protocols for β- and α/β-Mixed Peptides. I. QM and QM/MM Models. J Chem Theory Comput. 2007;3(4):1538-49doi: 10.1021/ct600352e.
Zhu, X., Yethiraj, A., & Cui, Q. (2007). Establishing Effective Simulation Protocols for β- and α/β-Mixed Peptides. I. QM and QM/MM Models. Journal of chemical theory and computation, 3(4), 1538-49. https://doi.org/10.1021/ct600352e
Zhu, Xiao, et al. "Establishing Effective Simulation Protocols for β- and α/β-Mixed Peptides. I. QM and QM/MM Models." Journal of chemical theory and computation vol. 3,4 (2007): 1538-49. doi: https://doi.org/10.1021/ct600352e
Zhu X, Yethiraj A, Cui Q. Establishing Effective Simulation Protocols for β- and α/β-Mixed Peptides. I. QM and QM/MM Models. J Chem Theory Comput. 2007 Jul;3(4):1538-49. doi: 10.1021/ct600352e. PMID: 26633224.
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Excited State Electron Distribution and Role of the Terminal Amine in Acidic and Basic Tryptophan Dipeptide Fluorescence.

Journal of molecular structure

Eisenberg AS, Nathan M, Juszczak LJ.
PMID: 27152052
J Mol Struct. 2016 Aug 15;1118:56-67. doi: 10.1016/j.molstruc.2016.03.098.

The results of quantum yield (QY) study of tryptophanyl glutamate (Trp-Glu), tryptophanyl lysine (Trp-Lys) and lysinyl tryptophan (Lys-Trp) dipeptides over the pH range, 1.5 - 13, show that the charge state of the N-terminal amine, and not the nominal...

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Eisenberg AS, Nathan M, Juszczak LJ. Excited State Electron Distribution and Role of the Terminal Amine in Acidic and Basic Tryptophan Dipeptide Fluorescence. J Mol Struct. 2016;1118:56-67doi: 10.1016/j.molstruc.2016.03.098.
Eisenberg, A. S., Nathan, M., & Juszczak, L. J. (2016). Excited State Electron Distribution and Role of the Terminal Amine in Acidic and Basic Tryptophan Dipeptide Fluorescence. Journal of molecular structure, 111856-67. https://doi.org/10.1016/j.molstruc.2016.03.098
Eisenberg, Azaria S, et al. "Excited State Electron Distribution and Role of the Terminal Amine in Acidic and Basic Tryptophan Dipeptide Fluorescence." Journal of molecular structure vol. 1118 (2016): 56-67. doi: https://doi.org/10.1016/j.molstruc.2016.03.098
Eisenberg AS, Nathan M, Juszczak LJ. Excited State Electron Distribution and Role of the Terminal Amine in Acidic and Basic Tryptophan Dipeptide Fluorescence. J Mol Struct. 2016 Aug 15;1118:56-67. doi: 10.1016/j.molstruc.2016.03.098. PMID: 27152052; PMCID: PMC4852485.
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Dipeptide concave nanospheres based on interfacially controlled self-assembly: from crescent to solid.

Physical chemistry chemical physics : PCCP

Wang J, Shen G, Ma K, Jiao T, Liu K, Yan X.
PMID: 27722335
Phys Chem Chem Phys. 2016 Nov 16;18(45):30926-30930. doi: 10.1039/c6cp06150h.

Concave nanospheres based on the self-assembly of simple dipeptides not only provide alternatives for modeling the interactions between biomacromolecules, but also present a range of applications for purification and separation, and delivery of active species. The kinetic control of...

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Wang J, Shen G, Ma K, et al. Dipeptide concave nanospheres based on interfacially controlled self-assembly: from crescent to solid. Phys Chem Chem Phys. 2016;18(45):30926-30930doi: 10.1039/c6cp06150h.
Wang, J., Shen, G., Ma, K., Jiao, T., Liu, K., & Yan, X. (2016). Dipeptide concave nanospheres based on interfacially controlled self-assembly: from crescent to solid. Physical chemistry chemical physics : PCCP, 18(45), 30926-30930. https://doi.org/10.1039/c6cp06150h
Wang, Juan, et al. "Dipeptide concave nanospheres based on interfacially controlled self-assembly: from crescent to solid." Physical chemistry chemical physics : PCCP vol. 18,45 (2016): 30926-30930. doi: https://doi.org/10.1039/c6cp06150h
Wang J, Shen G, Ma K, Jiao T, Liu K, Yan X. Dipeptide concave nanospheres based on interfacially controlled self-assembly: from crescent to solid. Phys Chem Chem Phys. 2016 Nov 16;18(45):30926-30930. doi: 10.1039/c6cp06150h. PMID: 27722335.
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Improved Statistical Sampling and Accuracy with Accelerated Molecular Dynamics on Rotatable Torsions.

Journal of chemical theory and computation

Doshi U, Hamelberg D.
PMID: 26605567
J Chem Theory Comput. 2012 Nov 13;8(11):4004-12. doi: 10.1021/ct3004194. Epub 2012 Sep 11.

In enhanced sampling techniques, the precision of the reweighted ensemble properties is often decreased due to large variation in statistical weights and reduction in the effective sampling size. To abate this reweighting problem, here, we propose a general accelerated...

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Doshi U, Hamelberg D. Improved Statistical Sampling and Accuracy with Accelerated Molecular Dynamics on Rotatable Torsions. J Chem Theory Comput. 2012;8(11):4004-12doi: 10.1021/ct3004194.
Doshi, U., & Hamelberg, D. (2012). Improved Statistical Sampling and Accuracy with Accelerated Molecular Dynamics on Rotatable Torsions. Journal of chemical theory and computation, 8(11), 4004-12. https://doi.org/10.1021/ct3004194
Doshi, Urmi, and Hamelberg, Donald. "Improved Statistical Sampling and Accuracy with Accelerated Molecular Dynamics on Rotatable Torsions." Journal of chemical theory and computation vol. 8,11 (2012): 4004-12. doi: https://doi.org/10.1021/ct3004194
Doshi U, Hamelberg D. Improved Statistical Sampling and Accuracy with Accelerated Molecular Dynamics on Rotatable Torsions. J Chem Theory Comput. 2012 Nov 13;8(11):4004-12. doi: 10.1021/ct3004194. Epub 2012 Sep 11. PMID: 26605567.
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Bioactive Plant Metabolites in the Management of Non-Communicable Metabolic Diseases: Looking at Opportunities beyond the Horizon.

Metabolites

Prasad C, Imrhan V, Juma S, Maziarz M, Prasad A, Tiernan C, Vijayagopal P.
PMID: 26703752
Metabolites. 2015 Dec 12;5(4):733-65. doi: 10.3390/metabo5040733.

There has been an unprecedented worldwide rise in non-communicable metabolic diseases (NCDs), particularly cardiovascular diseases (CVD) and diabetes. While modern pharmacotherapy has decreased the mortality in the existing population, it has failed to stem the rise. Furthermore, a large...

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Prasad C, Imrhan V, Juma S, et al. Bioactive Plant Metabolites in the Management of Non-Communicable Metabolic Diseases: Looking at Opportunities beyond the Horizon. Metabolites. 2015;5(4):733-65doi: 10.3390/metabo5040733.
Prasad, C., Imrhan, V., Juma, S., Maziarz, M., Prasad, A., Tiernan, C., & Vijayagopal, P. (2015). Bioactive Plant Metabolites in the Management of Non-Communicable Metabolic Diseases: Looking at Opportunities beyond the Horizon. Metabolites, 5(4), 733-65. https://doi.org/10.3390/metabo5040733
Prasad, Chandan, et al. "Bioactive Plant Metabolites in the Management of Non-Communicable Metabolic Diseases: Looking at Opportunities beyond the Horizon." Metabolites vol. 5,4 (2015): 733-65. doi: https://doi.org/10.3390/metabo5040733
Prasad C, Imrhan V, Juma S, Maziarz M, Prasad A, Tiernan C, Vijayagopal P. Bioactive Plant Metabolites in the Management of Non-Communicable Metabolic Diseases: Looking at Opportunities beyond the Horizon. Metabolites. 2015 Dec 12;5(4):733-65. doi: 10.3390/metabo5040733. PMID: 26703752; PMCID: PMC4693193.
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Dietary supplemental vitamin B6 increases carnosine and anserine concentrations in the heart of rats.

SpringerPlus

Suidasari S, Hasegawa T, Yanaka N, Kato N.
PMID: 26101732
Springerplus. 2015 Jun 19;4:280. doi: 10.1186/s40064-015-1074-8. eCollection 2015.

This study was performed to examine the effect of dietary level of vitamin B6 on the concentrations of carnosine and anserine, antioxidants, in the heart of rats. Analysis using UPLC-MS/MS showed that the concentrations of these dipeptides in the...

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Suidasari S, Hasegawa T, Yanaka N, et al. Dietary supplemental vitamin B6 increases carnosine and anserine concentrations in the heart of rats. Springerplus. 2015;4:280doi: 10.1186/s40064-015-1074-8.
Suidasari, S., Hasegawa, T., Yanaka, N., & Kato, N. (2015). Dietary supplemental vitamin B6 increases carnosine and anserine concentrations in the heart of rats. SpringerPlus, 4280. https://doi.org/10.1186/s40064-015-1074-8
Suidasari, Sofya, et al. "Dietary supplemental vitamin B6 increases carnosine and anserine concentrations in the heart of rats." SpringerPlus vol. 4 (2015): 280. doi: https://doi.org/10.1186/s40064-015-1074-8
Suidasari S, Hasegawa T, Yanaka N, Kato N. Dietary supplemental vitamin B6 increases carnosine and anserine concentrations in the heart of rats. Springerplus. 2015 Jun 19;4:280. doi: 10.1186/s40064-015-1074-8. eCollection 2015. PMID: 26101732; PMCID: PMC4472654.
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Opening a Can of Worm(-like Micelle)s: The Effect of Temperature of Solutions of Functionalized Dipeptides.

Angewandte Chemie (International ed. in English)

Draper ER, Su H, Brasnett C, Poole RJ, Rogers S, Cui H, Seddon A, Adams DJ.
PMID: 28653804
Angew Chem Int Ed Engl. 2017 Aug 21;56(35):10467-10470. doi: 10.1002/anie.201705604. Epub 2017 Jul 28.

A simple heat/cool cycle can be used to significantly affect the properties of a solution of a low-molecular-weight gelator at high pH. The viscosity and extensional viscosity are increased markedly, leading to materials with very different properties than when...

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Draper ER, Su H, Brasnett C, et al. Opening a Can of Worm(-like Micelle)s: The Effect of Temperature of Solutions of Functionalized Dipeptides. Angew Chem Int Ed Engl. 2017;56(35):10467-10470doi: 10.1002/anie.201705604.
Draper, E. R., Su, H., Brasnett, C., Poole, R. J., Rogers, S., Cui, H., Seddon, A., & Adams, D. J. (2017). Opening a Can of Worm(-like Micelle)s: The Effect of Temperature of Solutions of Functionalized Dipeptides. Angewandte Chemie (International ed. in English), 56(35), 10467-10470. https://doi.org/10.1002/anie.201705604
Draper, Emily R, et al. "Opening a Can of Worm(-like Micelle)s: The Effect of Temperature of Solutions of Functionalized Dipeptides." Angewandte Chemie (International ed. in English) vol. 56,35 (2017): 10467-10470. doi: https://doi.org/10.1002/anie.201705604
Draper ER, Su H, Brasnett C, Poole RJ, Rogers S, Cui H, Seddon A, Adams DJ. Opening a Can of Worm(-like Micelle)s: The Effect of Temperature of Solutions of Functionalized Dipeptides. Angew Chem Int Ed Engl. 2017 Aug 21;56(35):10467-10470. doi: 10.1002/anie.201705604. Epub 2017 Jul 28. PMID: 28653804; PMCID: PMC5577516.
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Isomer-Specific IR-IR Double Resonance Spectroscopy of D2-Tagged Protonated Dipeptides Prepared in a Cryogenic Ion Trap.

The journal of physical chemistry letters

Leavitt CM, Wolk AB, Fournier JA, Kamrath MZ, Garand E, Van Stipdonk MJ, Johnson MA.
PMID: 26288043
J Phys Chem Lett. 2012 May 03;3(9):1099-105. doi: 10.1021/jz3003074. Epub 2012 Apr 12.

Isomer-specific vibrational predissociation spectra are reported for the gas-phase GlySarH(+) and SarSarH(+) [Gly = glycine; Sar = sarcosine] ions prepared by electrospray ionization and tagged with weakly bound D2 adducts using a cryogenic ion trap. The contributions of individual...

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Leavitt CM, Wolk AB, Fournier JA, et al. Isomer-Specific IR-IR Double Resonance Spectroscopy of D2-Tagged Protonated Dipeptides Prepared in a Cryogenic Ion Trap. J Phys Chem Lett. 2012;3(9):1099-105doi: 10.1021/jz3003074.
Leavitt, C. M., Wolk, A. B., Fournier, J. A., Kamrath, M. Z., Garand, E., Van Stipdonk, M. J., & Johnson, M. A. (2012). Isomer-Specific IR-IR Double Resonance Spectroscopy of D2-Tagged Protonated Dipeptides Prepared in a Cryogenic Ion Trap. The journal of physical chemistry letters, 3(9), 1099-105. https://doi.org/10.1021/jz3003074
Leavitt, Christopher M, et al. "Isomer-Specific IR-IR Double Resonance Spectroscopy of D2-Tagged Protonated Dipeptides Prepared in a Cryogenic Ion Trap." The journal of physical chemistry letters vol. 3,9 (2012): 1099-105. doi: https://doi.org/10.1021/jz3003074
Leavitt CM, Wolk AB, Fournier JA, Kamrath MZ, Garand E, Van Stipdonk MJ, Johnson MA. Isomer-Specific IR-IR Double Resonance Spectroscopy of D2-Tagged Protonated Dipeptides Prepared in a Cryogenic Ion Trap. J Phys Chem Lett. 2012 May 03;3(9):1099-105. doi: 10.1021/jz3003074. Epub 2012 Apr 12. PMID: 26288043.
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More Is Different: Experimental Results on the Effect of Biomolecules on the Dynamics of Hydration Water.

The journal of physical chemistry letters

Comez L, Lupi L, Morresi A, Paolantoni M, Sassi P, Fioretto D.
PMID: 26282040
J Phys Chem Lett. 2013 Apr 04;4(7):1188-92. doi: 10.1021/jz400360v. Epub 2013 Mar 25.

Biological interfaces characterized by a complex mixture of hydrophobic, hydrophilic, or charged moieties interfere with the cooperative rearrangement of the hydrogen-bond network of water. In the present study, this solute-induced dynamical perturbation is investigated by extended frequency range depolarized...

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Comez L, Lupi L, Morresi A, et al. More Is Different: Experimental Results on the Effect of Biomolecules on the Dynamics of Hydration Water. J Phys Chem Lett. 2013;4(7):1188-92doi: 10.1021/jz400360v.
Comez, L., Lupi, L., Morresi, A., Paolantoni, M., Sassi, P., & Fioretto, D. (2013). More Is Different: Experimental Results on the Effect of Biomolecules on the Dynamics of Hydration Water. The journal of physical chemistry letters, 4(7), 1188-92. https://doi.org/10.1021/jz400360v
Comez, Lucia, et al. "More Is Different: Experimental Results on the Effect of Biomolecules on the Dynamics of Hydration Water." The journal of physical chemistry letters vol. 4,7 (2013): 1188-92. doi: https://doi.org/10.1021/jz400360v
Comez L, Lupi L, Morresi A, Paolantoni M, Sassi P, Fioretto D. More Is Different: Experimental Results on the Effect of Biomolecules on the Dynamics of Hydration Water. J Phys Chem Lett. 2013 Apr 04;4(7):1188-92. doi: 10.1021/jz400360v. Epub 2013 Mar 25. PMID: 26282040.
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The role of amino acid side chains in stabilizing dipeptides: the laser ablation Fourier transform microwave spectrum of Ac-Val-NH.

Physical chemistry chemical physics : PCCP

León I, Alonso ER, Mata S, Cabezas C, Rodríguez MA, Grabow JU, Alonso JL.
PMID: 28875198
Phys Chem Chem Phys. 2017 Sep 20;19(36):24985-24990. doi: 10.1039/c7cp03924g.

The steric effects imposed by the isopropyl group of valine in the conformational stabilization of the capped dipeptide N-acetyl-l-valinamide (Ac-Val-NH

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León I, Alonso ER, Mata S, et al. The role of amino acid side chains in stabilizing dipeptides: the laser ablation Fourier transform microwave spectrum of Ac-Val-NH. Phys Chem Chem Phys. 2017;19(36):24985-24990doi: 10.1039/c7cp03924g.
León, I., Alonso, E. R., Mata, S., Cabezas, C., Rodríguez, M. A., Grabow, J. U., & Alonso, J. L. (2017). The role of amino acid side chains in stabilizing dipeptides: the laser ablation Fourier transform microwave spectrum of Ac-Val-NH. Physical chemistry chemical physics : PCCP, 19(36), 24985-24990. https://doi.org/10.1039/c7cp03924g
León, I, et al. "The role of amino acid side chains in stabilizing dipeptides: the laser ablation Fourier transform microwave spectrum of Ac-Val-NH." Physical chemistry chemical physics : PCCP vol. 19,36 (2017): 24985-24990. doi: https://doi.org/10.1039/c7cp03924g
León I, Alonso ER, Mata S, Cabezas C, Rodríguez MA, Grabow JU, Alonso JL. The role of amino acid side chains in stabilizing dipeptides: the laser ablation Fourier transform microwave spectrum of Ac-Val-NH. Phys Chem Chem Phys. 2017 Sep 20;19(36):24985-24990. doi: 10.1039/c7cp03924g. PMID: 28875198.
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Cysteine containing dipeptides show a metal specificity that matches the composition of seawater.

Physical chemistry chemical physics : PCCP

Belmonte L, Rossetto D, Forlin M, Scintilla S, Bonfio C, Mansy SS.
PMID: 27182665
Phys Chem Chem Phys. 2016 Jul 27;18(30):20104-8. doi: 10.1039/c6cp00608f.

Model prebiotic dipeptide sequences were identified by bioinformatics and DFT and molecular dynamics calculations. The peptides were then synthesized and evaluated for metal affinity and specificity. Cysteine containing dipeptides were not associated with metal affinities that followed the Irving-Williams...

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Belmonte L, Rossetto D, Forlin M, et al. Cysteine containing dipeptides show a metal specificity that matches the composition of seawater. Phys Chem Chem Phys. 2016;18(30):20104-8doi: 10.1039/c6cp00608f.
Belmonte, L., Rossetto, D., Forlin, M., Scintilla, S., Bonfio, C., & Mansy, S. S. (2016). Cysteine containing dipeptides show a metal specificity that matches the composition of seawater. Physical chemistry chemical physics : PCCP, 18(30), 20104-8. https://doi.org/10.1039/c6cp00608f
Belmonte, Luca, et al. "Cysteine containing dipeptides show a metal specificity that matches the composition of seawater." Physical chemistry chemical physics : PCCP vol. 18,30 (2016): 20104-8. doi: https://doi.org/10.1039/c6cp00608f
Belmonte L, Rossetto D, Forlin M, Scintilla S, Bonfio C, Mansy SS. Cysteine containing dipeptides show a metal specificity that matches the composition of seawater. Phys Chem Chem Phys. 2016 Jul 27;18(30):20104-8. doi: 10.1039/c6cp00608f. PMID: 27182665.
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Showing 1 to 12 of 476 entries