1
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Giribet CG. IPPP-CLOPPA Analysis of the Hydrogen Bonds of the Adenine-Thymine Base Pair. Is C-H···O the Third Hydrogen Bond? J Phys Chem A 2024; 128:7568-7580. [PMID: 39190865 DOI: 10.1021/acs.jpca.4c03817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
The IPPP-CLOPPA method is applied to investigate the feasibility of the C-H···O moiety as a third hydrogen bond in the adenine-thymine base pair, and the role of this intermolecular contact in its stability. For this purpose, an analysis of the interaction energy and the potential energy of the protons of the "conventional" intermolecular hydrogen bonds and the "unconventional" C-H···O contact is performed, in order to assess how much they contribute to the intermolecular stabilization energy of the base pair. On the same grounds, this study is complemented by the analysis of the molecular electric dipolar polarizability of the hydrogen bond moieties, in order to determine the information that this property can give about the electronic mechanisms that affect the stabilization of the hydrogen bonds, the influence of the π system on each one, and the cooperativity effects among them. The results obtained seem to confirm that the C-H···O moiety contributes to the stability of the adenine-thymine pair almost as much as the "conventional" hydrogen bonds do. Besides, this stabilization effect is strengthened by cooperativity between hydrogen bonds and, particularly and mostly, with the π system.
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Affiliation(s)
- Claudia G Giribet
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Física, Buenos Aires 1428, Argentina
- CONICET, Universidad de Buenos Aires, Instituto de Física de Buenos Aires (IFIBA), Buenos Aires 1428, Argentina
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2
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Cormanich RA, da Silva GD. Autobench V1.0: Benchmarking Automation for Electronic Structure Calculations. J Chem Inf Model 2024; 64:3322-3331. [PMID: 38536765 DOI: 10.1021/acs.jcim.4c00250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
This work reports on new software for automatic conformer energy benchmarking calculations for flexible molecules. The software workflow consists of four parts: conformational search, preoptimization, optimization, and frequency calculations at a higher level and last calculations using several theoretical levels. The software was written to be user-friendly and versatile to be used by nonexperts in computational chemistry. Any theoretical levels available in either Gaussian 16 or ORCA 5 may be applied in the benchmarking study. The workflow will automatically run conformational search calculations and deal with conformers that converge to the same minimum and those that show a negative frequency. At the end of the workflow, the user will have the mean absolute deviations and the most accurate method/DFT functional and basis set in comparison to the benchmark to be applied for the molecular system of interest. Case examples are given at the end of the paper that may help users to get insight into the software's main features.
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Affiliation(s)
- Rodrigo A Cormanich
- Instituto de Química, Departamento de Química Orgânica, Universidade Estadual de Campinas, PO Box 6154, Campinas 13083-970, São Paulo, Brazil
| | - Gabriel D da Silva
- Instituto de Química, Departamento de Química Orgânica, Universidade Estadual de Campinas, PO Box 6154, Campinas 13083-970, São Paulo, Brazil
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3
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Cuesta Calvo PV, Rodrigues Batista P, Rodrigues de Oliveira Silva R, Converti A, Al Arni S, Solisio C, Ducati LC, Alves Palma MS. Flow Synthesis of 2‐[Methyl(pyridin‐2‐yl)amino]ethanol: An Experimental and Computational Study. Chem Eng Technol 2020. [DOI: 10.1002/ceat.202000423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Paulo Victor Cuesta Calvo
- University of São Paulo School of Pharmaceutical Sciences Av. Prof. Lineu Prestes, 580 – Butantã 05508-000 São Paulo SP Brazil
| | - Patrick Rodrigues Batista
- University of São Paulo Institute of Chemistry Av. Prof. Lineu Prestes, 748 – Butantã 05508-000 São Paulo SP Brazil
| | | | - Attilio Converti
- University of Genoa, Pole of Chemical Engineering Department of Civil, Chemical and Environmental Engineering via Opera Pia 15 16145 Genoa Italy
| | - Saleh Al Arni
- University of Ha'il Department of Chemical Engineering College of Engineering P.O. Box 2440 81441 Ha'il Saudi Arabia
| | - Carlo Solisio
- University of Genoa, Pole of Chemical Engineering Department of Civil, Chemical and Environmental Engineering via Opera Pia 15 16145 Genoa Italy
| | - Lucas C. Ducati
- University of São Paulo Institute of Chemistry Av. Prof. Lineu Prestes, 748 – Butantã 05508-000 São Paulo SP Brazil
| | - Mauri Sergio Alves Palma
- University of São Paulo School of Pharmaceutical Sciences Av. Prof. Lineu Prestes, 580 – Butantã 05508-000 São Paulo SP Brazil
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4
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Silva DR, Silla JM, Santos LA, da Cunha EFF, Freitas MP. The Role of Intramolecular Interactions on the Bioactive Conformation of Epinephrine. Mol Inform 2019; 38:e1800167. [PMID: 30945816 DOI: 10.1002/minf.201800167] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 03/09/2019] [Indexed: 11/07/2022]
Abstract
The structure of bioactive compounds inside their biological target is mainly dictated by the intermolecular interactions present in the binding side, whereas intramolecular interactions are responsible for the structure of an isolated molecule. Accordingly, this work reports the relative significance of these interactions for the bioactive conformation of the N-protonated epinephrine. The crystallized structure of epinephrine has a gauche orientation of the O-C-C-N torsion angle. Conformational analysis in the gas phase and implicit water was performed to investigate the main intramolecular forces favoring this conformational preference, which was primarily attributed to the electrostatic interaction between hydroxyl and ammonium groups. However, when the conformers were docked into the active site, intramolecular interactions were surpassed by intermolecular hydrogen bonds with neighboring amino acid residues. Nonetheless, structural modifications aiming at strengthening intramolecular interactions could be used to modulate a bioactive conformation, thereby assisting in the structure-based design of new chemical entities.
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Affiliation(s)
- Daniela R Silva
- Department of Chemistry, Federal University of Lavras, 37200-000, Lavras, MG, Brazil
| | - Josué M Silla
- Department of Chemistry, Federal University of Lavras, 37200-000, Lavras, MG, Brazil
| | - Lucas A Santos
- Department of Chemistry, Federal University of Lavras, 37200-000, Lavras, MG, Brazil
| | - Elaine F F da Cunha
- Department of Chemistry, Federal University of Lavras, 37200-000, Lavras, MG, Brazil
| | - Matheus P Freitas
- Department of Chemistry, Federal University of Lavras, 37200-000, Lavras, MG, Brazil
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5
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Yatsyna V, Mallat R, Gorn T, Schmitt M, Feifel R, Rijs AM, Zhaunerchyk V. Conformational Preferences of Isolated Glycylglycine (Gly-Gly) Investigated with IRMPD-VUV Action Spectroscopy and Advanced Computational Approaches. J Phys Chem A 2019; 123:862-872. [DOI: 10.1021/acs.jpca.8b10881] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Vasyl Yatsyna
- Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
- Radboud University, Institute of Molecules and Materials, FELIX Laboratory, Toernoovield 7-c, 6525 ED Nijmegen, The Netherlands
| | - Ranim Mallat
- Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
| | - Tim Gorn
- Institut für Physikalische Chemie I, Heinrich-Heine-Universität, D-40225 Düsseldorf, Germany
| | - Michael Schmitt
- Institut für Physikalische Chemie I, Heinrich-Heine-Universität, D-40225 Düsseldorf, Germany
| | - Raimund Feifel
- Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
| | - Anouk M. Rijs
- Radboud University, Institute of Molecules and Materials, FELIX Laboratory, Toernoovield 7-c, 6525 ED Nijmegen, The Netherlands
| | - Vitali Zhaunerchyk
- Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
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6
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Abstract
Hydrogen bond complexation between glycine and THF and between glycine and water involving four lowest-energy glycine conformers have been studied. The complexes have been investigated in the gas phase at the ab initio molecular orbital theory (MP2) with aug-cc-pVDZ basis set and density functional theory (B3LYP) with aug-cc-pVTZ basis set. Bader’s theory of atoms in molecules (AIM), natural bond orbital (NBO), and symmetry adapted perturbation theory (SAPT) analyses are employed to elucidate the interaction characteristics in the complexes. The premise that the hydrogen bond donor ability of the O–H group of the carboxyl group dominates the interaction between glycine and THF and between glycine and water is confirmed. It is found that in comparison with water, THF binds more strongly to glycine. The quantum studies indicate that contribution of N–H···O and C–H···O hydrogen bonds in the complexes, although lower in magnitude to O–H···O interactions, play an important role in the stability of complexes. The blue and red shifts in the stretching frequencies of the hydrogen bond donors X–H (X = O, C, N) have also been related to stabilization energies. Decomposition of the stabilization energy based on the SAPT method clearly indicates the dominant role of the electrostatic interactions in all the complexes under study; however, induction and dispersion interaction terms are relatively higher in glycine–THF complexes.
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Affiliation(s)
- Damanjit Kaur
- Department of Chemistry, Guru Nanak Dev University, Amritsar 143005, India
- Department of Chemistry, Guru Nanak Dev University, Amritsar 143005, India
| | - Geetanjali Chopra
- Department of Chemistry, Guru Nanak Dev University, Amritsar 143005, India
- Department of Chemistry, Guru Nanak Dev University, Amritsar 143005, India
| | - Rajinder Kaur
- Department of Chemistry, Guru Nanak Dev University, Amritsar 143005, India
- Department of Chemistry, Guru Nanak Dev University, Amritsar 143005, India
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7
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Lazreg A, Taleb-Mokhtari IN, Yousfi N, Sekkal-Rahal M. Density Functional Theory Investigations on Vibrational Spectra, Molecular Structure, and Properties of the L-Serine, L-Cysteine, and L-Aspartic Acid Molecules. J CHIN CHEM SOC-TAIP 2017. [DOI: 10.1002/jccs.201600810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Abbassia Lazreg
- Laboratoire de Microscopie, Microanalyse de la matière et Spectroscopie Moléculaire (L2MSM), Département de Chimie, Faculté des Sciences; Université Djillali Liabes de Sidi Bel Abbés; Sidi Bel Abbés 22000 Algérie
| | - Ilham Naoual Taleb-Mokhtari
- Laboratoire de Microscopie, Microanalyse de la matière et Spectroscopie Moléculaire (L2MSM), Département de Chimie, Faculté des Sciences; Université Djillali Liabes de Sidi Bel Abbés; Sidi Bel Abbés 22000 Algérie
| | - Noureddine Yousfi
- Laboratoire de Microscopie, Microanalyse de la matière et Spectroscopie Moléculaire (L2MSM), Département de Chimie, Faculté des Sciences; Université Djillali Liabes de Sidi Bel Abbés; Sidi Bel Abbés 22000 Algérie
| | - Majda Sekkal-Rahal
- Laboratoire de Microscopie, Microanalyse de la matière et Spectroscopie Moléculaire (L2MSM), Département de Chimie, Faculté des Sciences; Université Djillali Liabes de Sidi Bel Abbés; Sidi Bel Abbés 22000 Algérie
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8
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Chang X, Chen Z, Su P, Wu W. The C O rotation in the gaseous glycine. An energy decomposition analysis study. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.10.043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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9
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Cormanich RA, Bühl M, Rittner R. Understanding the conformational behaviour of Ac-Ala-NHMe in different media. A joint NMR and DFT study. Org Biomol Chem 2015. [PMID: 26219244 DOI: 10.1039/c5ob01296a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The conformational behaviour of Ac-Ala-NHMe was studied in the gas-phase and in solution by theoretical calculations (B3LYP-D3/aug-cc-pVDZ level) and experimental (1)H NMR. The conformational preferences of this compound were shown to result from a complex interplay between the strengths of possible intramolecular hydrogen bonds, steric interactions, hyperconjugation, entropy effects and the overall dipole moments. The Ac-Ala-N(Me)2 derivative was studied in addition, to design a system akin to Ac-Ala-NHMe, but with disrupted intramolecular hydrogen bonds involving the -NHMe group, mimicking the effect of polar protic solvents.
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Affiliation(s)
- Rodrigo A Cormanich
- Chemistry Institute, University of Campinas, Campinas, SP 13083-970, Brazil.
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10
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Braga CB, Ducati LC, Rittner R. Experimental and theoretical evaluation on the conformational behavior of l-aspartic acid dimethyl ester and its N-acetylated derivative. RSC Adv 2015. [DOI: 10.1039/c4ra14480e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The AspOMe and AcAspOMe conformational preferences and their corresponding intramolecular interactions were studied through spectroscopic and theoretical methodologies.
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Affiliation(s)
- Carolyne B. Braga
- Physical Organic Chemistry Laboratory
- Chemistry Institute
- University of Campinas
- Campinas
- Brazil
| | | | - Roberto Rittner
- Physical Organic Chemistry Laboratory
- Chemistry Institute
- University of Campinas
- Campinas
- Brazil
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11
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Abstract
The conformational behaviour of Ac-Gly-NHMe and its fluorinated [CF3-C(O)-Gly-NHMe] and N-methyl[Ac-Gly-N(Me)2] derivatives is investigated in nonpolar, polar and polar protic solutions by NMR and IR spectroscopies and theoretical calculations.
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Affiliation(s)
- R. A. Cormanich
- EastChem School of Chemistry
- University of St Andrews
- St Andrews
- UK
- Chemistry Institute
| | - R. Rittner
- Chemistry Institute
- State University of Campinas
- Campinas
- Brazil
| | - M. Bühl
- EastChem School of Chemistry
- University of St Andrews
- St Andrews
- UK
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12
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Andrade LA, Silla JM, Freitas MP. The gauche effect is governed by internal hydrogen bond in 2-amino-2-methyl-propanol. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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13
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Cormanich RA, Santiago RT, La Porta FA, Freitas MP, Rittner R, da Cunha EF, Andres J, Longo E, Ramalho TC. Quantum chemical topological analysis of hydrogen bonding in HX…HX and CH3X…HX dimers (X = Br, Cl, F). MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.904514] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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14
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Cormanich RA, Ducati LC, Tormena CF, Rittner R. Phenylalanine and tyrosine methyl ester intramolecular interactions and conformational analysis by (1)H NMR and infrared spectroscopies and theoretical calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 123:482-489. [PMID: 24434201 DOI: 10.1016/j.saa.2013.12.088] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 11/29/2013] [Accepted: 12/21/2013] [Indexed: 06/03/2023]
Abstract
Amino acid conformational analysis in solution are scarce, since these compounds present a bipolar zwitterionic structure ((+)H3NCHRCOO(-)) in these media. Also, intramolecular hydrogen bonds have been classified as the sole interactions governing amino acid conformational behavior in the literature. In the present work we propose phenylalanine and tyrosine methyl ester conformational studies in different solvents by (1)H NMR and infrared spectroscopies and theoretical calculations. Both experimental and theoretical results are in agreement and suggest that the conformational behavior of the phenylalanine and tyrosine methyl esters are similar and are dictated by the interplay between steric and hyperconjugative interactions.
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Affiliation(s)
- Rodrigo A Cormanich
- Chemistry Institute, University of Campinas, P.O. Box 6154, 13083-970 Campinas, Brazil
| | - Lucas C Ducati
- Chemistry Institute, University of São Paulo, P.O. Box 26077, 05508-900 São Paulo, Brazil
| | - Cláudio F Tormena
- Chemistry Institute, University of Campinas, P.O. Box 6154, 13083-970 Campinas, Brazil
| | - Roberto Rittner
- Chemistry Institute, University of Campinas, P.O. Box 6154, 13083-970 Campinas, Brazil.
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15
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Pereira DH, Ducati LC, Rittner R, Custodio R. A study of the rotational barriers for some organic compounds using the G3 and G3CEP theories. J Mol Model 2014; 20:2199. [DOI: 10.1007/s00894-014-2199-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 03/02/2014] [Indexed: 10/25/2022]
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16
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Braga CB, Ducati LC, Tormena CF, Rittner R. Conformational analysis and intramolecular interactions of L-proline methyl ester and its N-acetylated derivative through spectroscopic and theoretical studies. J Phys Chem A 2014; 118:1748-58. [PMID: 24533966 DOI: 10.1021/jp5007632] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This work reports a detailed study regarding the conformational preferences of L-proline methyl ester (ProOMe) and its N-acetylated derivative (AcProOMe) to elucidate the effects that rule their behaviors, through nuclear magnetic resonance (NMR) and infrared (IR) spectroscopies combined with theoretical calculations. These compounds do not present a zwitterionic form in solution, simulating properly amino acid residues in biological media, in a way closer than amino acids in the gas phase. Experimental (3)JHH coupling constants and infrared data showed excellent agreement with theoretical calculations, indicating no variations in conformer populations on changing solvents. Natural bond orbital (NBO) results showed that hyperconjugative interactions are responsible for the higher stability of the most populated conformer of ProOMe, whereas for AcProOMe both hyperconjugative and steric effects rule its conformational equilibrium.
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Affiliation(s)
- Carolyne B Braga
- Physical Organic Chemistry Laboratory, Chemistry Institute, University of Campinas , 13083-970 Campinas, SP, Brazil
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17
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Cormanich RA, Ducati LC, Tormena CF, Rittner R. A theoretical and experimental 1
H NMR spectroscopy study of the stereoelectronic interactions that rule the conformational energies of alanine and valine methyl ester. J PHYS ORG CHEM 2013. [DOI: 10.1002/poc.3180] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rodrigo A. Cormanich
- Chemistry Institute; University of Campinas; P.O. Box 6154 13083-970 Campinas Brazil
| | - Lucas C. Ducati
- Chemistry Institute; University of São Paulo; P. O. Box 26077 05508-900 São Paulo Brazil
| | - Cláudio F. Tormena
- Chemistry Institute; University of Campinas; P.O. Box 6154 13083-970 Campinas Brazil
| | - Roberto Rittner
- Chemistry Institute; University of Campinas; P.O. Box 6154 13083-970 Campinas Brazil
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18
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Cormanich RA, Ducati LC, Tormena CF, Rittner R. A theoretical investigation of the dictating forces in small amino acid conformational preferences: The case of glycine, sarcosine and N,N-dimethylglycine. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.05.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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19
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Bazsó G, Magyarfalvi G, Tarczay G. Tunneling Lifetime of the ttc/VIp Conformer of Glycine in Low-Temperature Matrices. J Phys Chem A 2012; 116:10539-47. [DOI: 10.1021/jp3076436] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gábor Bazsó
- Laboratory of Molecular
Spectroscopy, Institute of
Chemistry, Eötvös University, P.O. Box 32, H-1518, Budapest 112, Hungary
| | - Gábor Magyarfalvi
- Laboratory of Molecular
Spectroscopy, Institute of
Chemistry, Eötvös University, P.O. Box 32, H-1518, Budapest 112, Hungary
| | - György Tarczay
- Laboratory of Molecular
Spectroscopy, Institute of
Chemistry, Eötvös University, P.O. Box 32, H-1518, Budapest 112, Hungary
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20
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Bazsó G, Magyarfalvi G, Tarczay G. Near-infrared laser induced conformational change and UV laser photolysis of glycine in low-temperature matrices: Observation of a short-lived conformer. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2012.04.066] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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21
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22
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Cormanich RA, Freitas MP, Tormena CF, Rittner R. The F⋯HO intramolecular hydrogen bond forming five-membered rings hardly appear in monocyclic organofluorine compounds. RSC Adv 2012. [DOI: 10.1039/c2ra00039c] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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