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Niemöller H, Blasius J, Hollóczki O, Kirchner B. How do alternative amino acids behave in water? A comparative ab initio molecular dynamics study of solvated α-amino acids and α-amino amidines. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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2
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A DFT study on the tautomerization of vitamin B3 (niacin). COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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3
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Koralewski M, Baranowski M, Ryzner A. Probing physical invariance between enantiomers: The magnetooptical and refractive properties of the simplest chiral amino acid – Alanine. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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4
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Manjula V, Prasad TV, Balakrishna K, Murthy VRK, Vishwam T. Relaxation dynamics of l-alanine in water medium investigated by dielectric relaxation spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 222:117274. [PMID: 31229918 DOI: 10.1016/j.saa.2019.117274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/09/2019] [Accepted: 06/13/2019] [Indexed: 06/09/2023]
Abstract
The complex dielectric permittivity of L-alanine in aqueous medium at different concentrations and different temperatures were measured in the microwave (0.02 < ν/GHz < 20) frequency region by using open-ended coaxial probe technique. From the reflection coefficient and impedance data, the real and imaginary part of the dielectric permittivity values is determined. It is observed that there is a decrease in the real part of the dielectric permittivity up to certain frequency and an increase in the imaginary part of the dielectric permittivity with increase in the molar concentration of L-alanine in water medium. Based on the experimental data the average relaxation time values are calculated and its behavior is analyzed in terms of bound water and free water molecules. The theoretical dipole moment of L-alanine is calculated at gaseous state as well as in aqueous medium by using PCM and IEFPCM model at HF, DFT/B3LYP and MP2 calculations using 6-311G* basis set. Analysis between experimentally determined parameters and computed dipole moments were discussed. The mean molecular polarizability is calculated from the Lippincott δ function potential model and compared with the Le Fèvre method of polarizability values.
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Affiliation(s)
- V Manjula
- Department of Physics, GITAM (Deemed to be University)-Hyderabad, Rudraram, Patancheru (M), TS 502329, India; Department of Physics, Geethanjali College of Engineering and Technology, Hyderabad, Telangana 501301, India
| | - T Vamshi Prasad
- Department of Physics, Jawaharlal Nehru Technological University-Hyderabad, Hyderabad 500085, India
| | - K Balakrishna
- Department of Physics, GITAM (Deemed to be University)-Hyderabad, Rudraram, Patancheru (M), TS 502329, India
| | - V R K Murthy
- Microwave Laboratory, Department of Physics, Indian Institute of Technology Madras, Chennai 600036, India
| | - T Vishwam
- Department of Physics, GITAM (Deemed to be University)-Hyderabad, Rudraram, Patancheru (M), TS 502329, India.
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5
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Aiswarya T, Prasad TV, Raju KJ, Vishwam T. Dielectric relaxation studies of aqueous l-glutamine-ethanol mixtures in the microwave frequency range. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111506] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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6
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Matus Rivas OM, Rey AD. Molecular Dynamics Study of the Effect of l-Alanine Chiral Dopants on Diluted Chromonic Solutions. J Phys Chem B 2019; 123:8995-9010. [PMID: 31525883 DOI: 10.1021/acs.jpcb.9b06111] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Atomistic molecular dynamics simulations have been performed for disodium cromoglycate (DSCG) chromonic solutions mixed with l-alanine chiral dopants. We study the fundamental molecular mechanisms induced by low concentrations of l-alanine on diluted DSCG solutions, including their effect on the chromonic aggregates, the solvent, and sodium counterions. Simulations reveal that l-alanine molecules primarily interact with DSCG stacks establishing salt bridges between their respective ammonium and carboxylate groups. Our results demonstrate that l-alanine and sodium counterions jointly establish an intricate network of noncovalent interactions around DSCG aggregates that decreases the global electrostatic repulsion of the chromonic system. Two possible structural effects in DSCG aggregates arise from this electronic stabilization: the increment of the total number of consecutively stacked aromatic planes per DSCG aggregate (intracolumnar effect) or the partial separation reduction between neighboring DSCG columnar sections due to the simultaneous bridging of intercolumnar DSCG carboxylate sites by sodium counterions, forming sodium bridges (intercolumnar effect). Sodium bridges may be responsible for the formation of stacking faults in DSCG aggregates in the form of lateral overlap junctions. This mechanism would explain the difference between lower X-ray correlation lengths with the expected persistence length in chromonics.
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Affiliation(s)
- Oscar M Matus Rivas
- Department of Chemical Engineering , McGill University , Montreal , Quebec H3A 0C5 , Canada
| | - Alejandro D Rey
- Department of Chemical Engineering , McGill University , Montreal , Quebec H3A 0C5 , Canada
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7
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Anju K, Sumita A, Gayathri S, Vasanthi R, Rajendran K. Fluorescence Spectral Studies on the Interaction of Alanine and Valine with Resorcinol-Based Acridinedione Dyes in Aqueous Solution: A Comparative Study with Glycine. ACS OMEGA 2019; 4:12357-12365. [PMID: 31460353 PMCID: PMC6682030 DOI: 10.1021/acsomega.9b01011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 06/26/2019] [Indexed: 06/10/2023]
Abstract
Photophysical studies were carried out for simple amino acids like alanine and valine with resorcinol-based aqueous acridinedione (ADDR) dyes. ADDR dyes exhibit interesting excited-state characteristics on altering the substituents at the 9th and 10th sites (Scheme 1). The longest-wavelength absorption maxima remain the same on adding the amino acids to the fluorophore, whereas the excited-state behavior varies significantly mostly based on the nature of the substituent at the 9th position. The absence of fluorescence enhancement was observed with addition of β-alanine, l-alanine, and l-valine to ADDR1 dye (photoinduced electron transfer, PET), whereas addition of glycine exhibits enhancement accompanied with a shift toward a longer-wavelength region. Interestingly, the addition of amino acids to non-PET dyes results in a fluorescence quenching accompanied with a larger shift toward the shorter-wavelength region. The properties of fluorophore and nonfluorophore dyes in the presence of alanine or valine are found to be entirely different from those of glycine. The interaction of alanine with ADDR dyes is predominantly through H-bonding, but the structural aspects of H-bonding interactions of alanine and water are completely different from those of glycine and water. The time-correlated single-photon counting method portrays the existence of fluorophore in two distinguishable microenvironments in the presence of amino acids. The fluorescence spectral technique used as a tool in elucidating the mode of interaction of dye with neutral amino acids in aqueous solution is illustrated in the present study.
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Affiliation(s)
- Krishnan Anju
- Department
of Chemistry, Dwaraka Doss, Goverdhan Doss,
Vaishnav College (Autonomous), 833, Gokul Bagh, E.V.R. Periyar Road, Arumbakkam, Chennai 600106, Tamil Nadu, India
| | - Anupurath Sumita
- Department
of Chemistry, Anna Adarsh College for Women
College, Anna Nagar, Chennai 600040, Tamil Nadu, India
| | - Somasundaram Gayathri
- Department
of Chemistry, Dwaraka Doss, Goverdhan Doss,
Vaishnav College (Autonomous), 833, Gokul Bagh, E.V.R. Periyar Road, Arumbakkam, Chennai 600106, Tamil Nadu, India
| | - Rajaraman Vasanthi
- Department
of Chemistry, Dwaraka Doss, Goverdhan Doss,
Vaishnav College (Autonomous), 833, Gokul Bagh, E.V.R. Periyar Road, Arumbakkam, Chennai 600106, Tamil Nadu, India
| | - Kumaran Rajendran
- Department
of Chemistry, Dwaraka Doss, Goverdhan Doss,
Vaishnav College (Autonomous), 833, Gokul Bagh, E.V.R. Periyar Road, Arumbakkam, Chennai 600106, Tamil Nadu, India
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8
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Gupta PK, Esser A, Forbert H, Marx D. Toward theoretical terahertz spectroscopy of glassy aqueous solutions: partially frozen solute-solvent couplings of glycine in water. Phys Chem Chem Phys 2019; 21:4975-4987. [PMID: 30758388 DOI: 10.1039/c8cp07489e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The molecular-level understanding of THz spectra of aqueous solutions under ambient conditions has been greatly advanced in recent years. Here, we go beyond previous analyses by performing ab initio molecular dynamics simulations of glycine in water with artificially frozen solute or solvent molecules, respectively, while computing the total THz response as well as its decomposition into mode-specific resonances based on the "supermolecular solvation complex" technique. Clamping the water molecules and keeping glycine moving breaks the coupling of glycine to the structural dynamics of the solvent, however, the polarization and dielectric solvation effects in the static solvation cage are still at work since the full electronic structure of the quenched solvent is taken into account. The complementary approach of fixing glycine reveals both the dynamical and electronic response of the solvation cage at the level of its THz response. Moreover, to quantitatively account for the electronic contribution solely due to solvent embedding, the solute species is "vertically desolvated", thus preserving the fully coupled solute-solvent motion in terms of the solute's structural dynamics in solution, while its electronic structure is no longer subject to solute-solvent polarization and charge transfer effects. When referenced to the free simulation of Gly(aq), this three-fold approach allows us to decompose the THz spectral contributions due to the correlated solute-solvent dynamics into entirely structural and purely electronic effects. Beyond providing hitherto unknown insights, the observed systematic changes of THz spectra in terms of peak shifts and lineshape modulations due to conformational freezing and frozen solvation cages might be useful to investigate the solvation of molecules in highly viscous H-bonding solvents such as ionic liquids and even in cryogenic ices as relevant to polar stratospheric and dark interstellar clouds.
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Affiliation(s)
- Prashant Kumar Gupta
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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9
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10
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Roggatz CC, Lorch M, Benoit DM. Influence of Solvent Representation on Nuclear Shielding Calculations of Protonation States of Small Biological Molecules. J Chem Theory Comput 2018; 14:2684-2695. [PMID: 29566332 DOI: 10.1021/acs.jctc.7b01020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In this study, we assess the influence of solvation on the accuracy and reliability of isotropic nuclear magnetic shielding calculations for amino acids in comparison to experimental data. We focus particularly on the performance of solvation methods for different protonation states, as biological molecules occur almost exclusively in aqueous solution and are subject to protonation with pH. We identify significant shortcomings of current implicit solvent models and present a hybrid solvation approach that improves agreement with experimental data by taking into account the presence of direct interactions between amino acid protonation state and water molecules.
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11
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Kairaliyeva T, Aksenenko EV, Mucic N, Makievski AV, Fainerman VB, Miller R. Surface Tension and Adsorption Studies by Drop Profile Analysis Tensiometry. J SURFACTANTS DETERG 2017; 20:1225-1241. [PMID: 29200810 PMCID: PMC5686271 DOI: 10.1007/s11743-017-2016-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 08/23/2017] [Indexed: 10/25/2022]
Abstract
Surface tension and dilational viscoelasticity of solutions of various surfactants measured with bubble and drop profile analysis tensiometry are discussed. The study also includes experiments on the co-adsorption of surfactant molecules from a solution drop and alkane molecules from saturated alkane vapor phase. Using experimental data for 12 surfactants with different surface activities, it is shown that depletion due to adsorption of surfactant from the drop bulk can be significant. An algorithm is proposed quantitatively to take into consideration the depletion effect which is required for a correct description of the co-adsorption of alkanes on the solution drop surface and the correct analysis of experimental dynamic surface tension data to determine the adsorption mechanism. Bubble and drop profile analysis tensiometry is also the method of choice for measuring the dilational viscoelasticity of the adsorbed interfacial layer. The same elasticity moduli are obtained with the bubble and drop method only when the equilibrium surface pressures are sufficiently small (Π < 15 mN m-1). When the surface pressure for a surfactant solution is larger than this value, the viscoelasticity moduli determined from drop profile experiments become significantly larger than those obtained from bubble profile measurements.
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Affiliation(s)
- T. Kairaliyeva
- Max-Planck-Institut für Kolloid-und Grenzflächenforschung, Potsdam, Germany
| | - E. V. Aksenenko
- Institute of Colloid Chemistry and Chemistry of Water, Kyiv (Kiev), Ukraine
| | - N. Mucic
- Faculty of Technology, University of Novi Sad, Novi Sad, Serbia
| | | | | | - Reinhard Miller
- Max-Planck-Institut für Kolloid-und Grenzflächenforschung, Potsdam, Germany
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12
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Miller R, Aksenenko EV, Fainerman VB. Dynamic interfacial tension of surfactant solutions. Adv Colloid Interface Sci 2017; 247:115-129. [PMID: 28063521 DOI: 10.1016/j.cis.2016.12.007] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/14/2016] [Accepted: 12/21/2016] [Indexed: 11/19/2022]
Abstract
The dynamics of surfactant interfacial layers was first discussed more than a century ago. In 1946 the most important work by Ward and Tordai was published which is still the theoretical basis of all new models to describe the time dependence of interfacial properties. In addition to the diffusion controlled adsorption mechanism, many other models have been postulated in literature, however, well performed experiments with well defined surfactant systems have shown that the diffusional transport is the main process governing the entire formation of surfactant adsorption layers. The main prerequisite, in addition to the diffusional transport, is the consideration of the right boundary condition at the interface, given by a respective equation of state. In addition to the classical models of Langmuir and Frumkin, also the so-called reorientation or interfacial aggregation models are to be assumed to reach a quantitative description of respective experimental data. Moreover, the adsorption of surfactants at the interface between water and a gas phase different from air can be strongly influenced by the type of molecules within the gas phase, such as alkane vapours. These oil molecules co-adsorb from the gas phase and change the adsorption kinetics strongly. Besides the discussion of how to apply theoretical adsorption kinetics models correctly, a large number of experimental data are presented and the way of a quantitative analysis of the adsorption mechanism and the main characteristic parameters is presented. This includes micellar solutions as well as mixtures of surfactants of ionic and non-ionic nature.
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Affiliation(s)
- R Miller
- Max-Planck-Institut für Kolloid- und Grenzflächenforschung, Am Mühlenberg 1, 14424 Potsdam, Germany.
| | - E V Aksenenko
- Institute of Colloid Chemistry and Chemistry of Water, 42 Vernadsky Avenue, 03680 Kyiv (Kiev), Ukraine
| | - V B Fainerman
- Donetsk Medical University, 16 Ilych Avenue, 83003 Donetsk, Ukraine
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13
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Conformational analysis of short polar side-chain amino-acids through umbrella sampling and DFT calculations. J Mol Model 2016; 22:273. [PMID: 27783230 DOI: 10.1007/s00894-016-3139-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 10/09/2016] [Indexed: 10/20/2022]
Abstract
Molecular and quantum mechanics calculations were carried out in a series of tripeptides (GXG, where X = D, N and C) as models of the unfolded states of proteins. The selected central amino acids, especially aspartic acid (D) and asparagine (N) are known to present significant average conformations in partially allowed areas of the Ramachandran plot, which have been suggested to be important in unfolded protein regions. In this report, we present the calculation of the propensity values through an umbrella sampling procedure in combination with the calculation of the NMR J-coupling constants obtained by a DFT model. The experimental NMR observations can be reasonably explained in terms of a conformational distribution where PPII and β basins sum up propensities above 0.9. The conformational analysis of the side chain dihedral angle (χ1), along with the computation of 3J(HαHβ), revealed a preference for the g - and g + rotamers. These may be connected with the presence of intermolecular H-bonding and carbonyl-carbonyl interactions sampled in the PPII and β basins. Taking into account all those results, it can be established that these residues show a similar behavior to other amino acids in short peptides regarding backbone φ,ψ dihedral angle distribution, in agreement with some experimental analysis of capped dipeptides.
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14
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Meng L, Wu W, Lin Z. Electronic structures of intermolecular hydrogen bond contacts with solute in aqueous solution: glycine as a working prototype. Phys Chem Chem Phys 2016; 18:15894-8. [PMID: 27243041 DOI: 10.1039/c5cp07968c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The intermolecular hydrogen bond (H-bond) interactions play vital roles in many biological systems. Despite continued interest, the nature of their electronic structures has remained elusive. Based on the unique features of aqueous solution, a simple model depicting the H-bond electronic states by orbital hybridizations is developed. The model is demonstrated by reproducing the experimental IR data and yielding favorable solute-solvent interactions for the prototype glycine. The H-bond state for solute H, O and N atoms is found to be characterized by sp(1), sp(2), and sp(3) hybridizations, respectively. The model provides a new way for probing the intricate solute-solvent contacts.
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Affiliation(s)
- Lingbiao Meng
- Research Center of Laser Fusion, China Academy of Engineering Physics, Mianyang 621900, China.
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15
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Herrmann N, Heinz N, Dolg M, Cao X. Quantum chemical study of the autoxidation of ascorbate. J Comput Chem 2016; 37:1914-23. [DOI: 10.1002/jcc.24408] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 04/25/2016] [Accepted: 04/26/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Nils Herrmann
- Department of Chemistry; Institute for Theoretical Chemistry, University of Cologne; Greinstr. 4 Cologne 50939 Germany
| | - Norah Heinz
- Department of Chemistry; Institute for Theoretical Chemistry, University of Cologne; Greinstr. 4 Cologne 50939 Germany
| | - Michael Dolg
- Department of Chemistry; Institute for Theoretical Chemistry, University of Cologne; Greinstr. 4 Cologne 50939 Germany
| | - Xiaoyan Cao
- Department of Chemistry; Institute for Theoretical Chemistry, University of Cologne; Greinstr. 4 Cologne 50939 Germany
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16
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Trunaeva ES, Khokhlova ON, Khokhlov VY. Quantum chemical simulation of hydration and association of phenylalanine in solution. J STRUCT CHEM+ 2015. [DOI: 10.1134/s0022476615060050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Ion-selective interactions of biologically relevant inorganic ions with alanine zwitterion: a 3D-RISM study. Amino Acids 2015; 47:1015-23. [DOI: 10.1007/s00726-015-1930-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 01/25/2015] [Indexed: 11/27/2022]
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18
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Structural parameters of alanine zwitterion hydration from the data of the integral equation method in the RISM approximation. Russ Chem Bull 2014. [DOI: 10.1007/s11172-013-0286-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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19
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Ojha AK, Bhunia S. Different proton transfer channels for the transformation of zwitterionic alanine-(H₂O)(n=2-4) to nonzwitterionic alanine-(H₂O)(n=2-4): a density functional theory study. J Mol Model 2014; 20:2124. [PMID: 24573496 DOI: 10.1007/s00894-014-2124-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 12/20/2013] [Indexed: 11/24/2022]
Abstract
We report here the various possibilities of proton transfer between the zwitterionic and the non-zwetterionic form of alanine (Ala) via (H₂O)(n=2-4) clusters by calculating the transition state structures of zwitterionic alanine (ZAla)-(H₂O)(n=2-4) and non-zwitterionic alanine (Ala)-(H₂O)(n=2-4) complexes at B3LYP/6-311++G(d,p) and CAM-B3LYP/6-311++G(d,p) level of theory. In order to determine the most feasible channel for proton transfer, the barrier energy corresponding to each channel was calculated. For the transformation of ZAla-(H₂O)(n=2) to Ala-(H₂O)(n=2), we identified eight channels for proton transfer. The lowest barrier energy (2.57 kcal mol⁻¹) channel, where ZAla-(H₂O)(n=2) transforms to Ala-(H₂O)(n=2) via triple proton transfer, is said to be the energetically most feasible channel. The values of barrier energy corresponding to the least energy pathway for proton transfer were calculated to be 1.14 and 9.82 kcal mol⁻¹ for n = 3 and n = 4 complexes, respectively, at B3LYP/6-311++G(d,p) level of theory. For complex n = 3, the structure where proton transfer takes place directly from -NH₃⁺ to -COO⁻ has the lowest energy pathway. However, the complexes for n = 2 and 3--the channels where proton transferred from -NH₃⁺ to -COO⁻ via two water molecules have the lowest barrier energy. For each n, the values of barrier energy calculated at CAM-B3LYP/6-311++G(d,p) level of theory were always less compared those calculated at B3LYP/6-311++G(d,p) level of theory. The value of rate constants corresponding to each proton transfer channel was also calculated.
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Affiliation(s)
- Animesh K Ojha
- Department of Physics, Motilal Nehru National Institute of Technology, Allahabad, 211004, India,
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20
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Wei Z, Chen D, Zhao H, Li Y, Zhu J, Liu B. Ab initio investigation of the first hydration shell of protonated glycine. J Chem Phys 2014; 140:085103. [DOI: 10.1063/1.4862985] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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21
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Quesada-Moreno MM, Márquez-García AÁ, Avilés-Moreno JR, López-González JJ. Conformational landscape of l-threonine in neutral, acid and basic solutions from vibrational circular dichroism spectroscopy and quantum chemical calculations. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.tetasy.2013.09.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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22
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Campaña AG, Buñuel E, Cuerva JM, Cárdenas DJ. The role of water-based hydrogen atom wires in long-range electron-transfer reactions in aqueous media for the FeII-FeIII self-exchange and related systems. Chemistry 2013; 19:16187-91. [PMID: 24249687 DOI: 10.1002/chem.201301971] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Indexed: 12/17/2022]
Abstract
Extended reach: A calculated mechanism for long-range proton-coupled electron transfer (PCET, see picture) through an array of structured water molecules between Fe(III)-Fe(III) complexes accounts for the reaction enthalpy and kinetic isotope effect previously measured for this reaction. This mechanism may be general and occur for other hydroxo-metal complexes.
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Affiliation(s)
- Araceli G Campaña
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva, 18071 Granada (Spain)
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23
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l-Serine in aqueous solutions at different pH: Conformational preferences and vibrational spectra of cationic, anionic and zwitterionic species. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.04.038] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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24
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Mineva T, Tsoneva Y, Kevorkyants R, Goursot A. 13C NMR chemical shift calculations of charged surfactants in water — A combined density functional theory (DFT) and molecular dynamics (MD) methodological study. CAN J CHEM 2013. [DOI: 10.1139/cjc-2012-0505] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Structural and magnetic properties of one anionic and one cationic amphiphile molecule (sodium octanoate and hexadecyltrimethylammonium chloride, respectively) in water are studied comparing different methods to account for the presence of the solvent. Calculated 13C NMR chemical shifts are used as the probe for accuracy of the theoretical electronic structures obtained with different descriptions of the surfactants in water solution. The best agreement with the experimental data are obtained by averaging 13C NMR isotropic chemical shifts over a large number of conformational structures of sodium octanoate while considering the electronic structure of the solvent molecules. The 13C chemical shift values of the hexadecyltrimethylammonium alkane chain are systematically overestimated by 10–15 ppm even if an extensive conformational sampling and water as the polarized continuum medium have been taken into consideration. The role of the basis set quality has been studied and discussed as well.
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Affiliation(s)
- T. Mineva
- Institut Charles Gerhardt, UMR 5253 CNRS, École de Chimie de Montpellier, 8 rue de l'École Normale, 23296 Montpellier, Cédex 5, France
| | - Y. Tsoneva
- Institut Charles Gerhardt, UMR 5253 CNRS, École de Chimie de Montpellier, 8 rue de l'École Normale, 23296 Montpellier, Cédex 5, France
| | - R. Kevorkyants
- Institut Charles Gerhardt, UMR 5253 CNRS, École de Chimie de Montpellier, 8 rue de l'École Normale, 23296 Montpellier, Cédex 5, France
- Department of Chemistry, Olson Hall, Rutgers University, Newark, NJ 07102, USA
| | - A. Goursot
- Institut Charles Gerhardt, UMR 5253 CNRS, École de Chimie de Montpellier, 8 rue de l'École Normale, 23296 Montpellier, Cédex 5, France
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Abstract
Molecular dynamics simulations of biomolecules have matured into powerful tools of structural biology. In addition to the commonly used empirical force field potentials, quantum mechanical descriptions are gaining popularity for structure optimization and dynamic simulations of peptides and proteins. In this chapter, we introduce methodological developments such as the QM/MM framework and linear-scaling QM that make efficient calculations on large biomolecules possible. We identify the most common scenarios in which quantum descriptions of peptides and proteins are employed, such as structural refinement, force field development, treatment of unusual residues, and predicting spectroscopic and exited state properties. The benefits and shortcomings of QM potentials, in comparison to classical force fields, are discussed, with special emphasis on the sampling problems of protein conformational space. Finally, recent examples of QM/MM calculations in light-sensitive membrane proteins illustrate typical applications of the reviewed methods.
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Affiliation(s)
- Thomas Steinbrecher
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
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26
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Yamabe S, Guan W, Sakaki S. Presence or absence of a novel charge-transfer complex in the base-catalyzed hydrolysis of N-ethylbenzamide or ethyl benzoate. Beilstein J Org Chem 2013; 9:185-96. [PMID: 23400273 PMCID: PMC3566851 DOI: 10.3762/bjoc.9.22] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 01/04/2013] [Indexed: 12/03/2022] Open
Abstract
Reaction paths of base-catalyzed hydrolyses of isoelectronic substrates, Ph–C(=O)–X–Et [X = O (ethyl benzoate) and X = NH (N-ethylbenzamide)], were traced by DFT calculations. To simulate bond interchanges accompanied by proton transfers, a cluster model of Ph–C(=O)–X–Et + OH−(H2O)16 was employed. For X = O, three elementary processes and for X = NH four ones were obtained. The rate-determining step of X = O is the first TS (TS1, the OH− addition step), while that of X = NH is TS2. TS2 of X = NH leads to a novel Mulliken charge-transfer complex, Ph–(OH)(O=)C∙∙∙N(H2)–Et. The superiority or inferiority between the direct nucleophilic process or the general base-catalyzed process for TS1 was examined with the model Ph–C(=O)–X–Et + OH−(H2O)n, n = 3, 5, 8, 12, 16, 24 and 32. The latter process was calculated to be more favorable regardless of the number (n, except n = 3) of water molecules. The counter ion Na+ works unfavorably on the ester hydrolysis, particularly on TS1. A minimal model of TS1 was proposed and was found to be insensitive to n.
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Affiliation(s)
- Shinichi Yamabe
- Fukui Institute for Fundamental Chemistry, Kyoto University, Takano-Nishihiraki-cho 34-4, Sakyo-ku, Kyoto 606-8103, Japan, phone: +81-075-711-7907
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Ojha AK, Vyas N, Dubey SP. Gas phase structural stability of neutral and zwitterionic forms of alanine in presence of (H2O)n=1–7 clusters: A density functional theory study. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.09.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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28
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A new and consistent model for dynamic adsorption of CTAB at air/water interface. Colloids Surf A Physicochem Eng Asp 2012. [DOI: 10.1016/j.colsurfa.2012.04.044] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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29
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Bouchoux G. Gas phase basicities of polyfunctional molecules. Part 3: Amino acids. MASS SPECTROMETRY REVIEWS 2012; 31:391-435. [PMID: 22611554 DOI: 10.1002/mas.20349] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The present article is the third part of a general overview of the gas-phase protonation thermochemistry of polyfunctional molecules (first part: Mass Spectrom. Rev., 2007, 26:775-835, second part: Mass Spectrom. Rev., 2011, in press). This review is devoted to the 20 proteinogenic amino acids and is divided in two parts. In the first one, the experimental data obtained during the last 30 years using the equilibrium, thermokinetic and kinetic methods are presented. A general re-assignment of the values originating from these various experiments has been done on the basis of the commonly accepted Hunter & Lias 1998 gas-phase basicity scale in order to provide an homogeneous set of data. In the second part, theoretical investigations on gaseous neutral and protonated amino acids are reviewed. Conformational landscapes of both types of species were examined in order to provide theoretical protonation thermochemistry based on the truly identified most stable conformers. Proton affinities computed at the presently highest levels of theory (i.e. composite methods such as Gn procedures) are presented. Estimates of thermochemical parameters calculated using a Boltzmann distribution of conformers at 298K are also included. Finally, comparison between experiment and theory is discussed and a set of evaluated proton affinities, gas-phase basicities and protonation entropies is proposed.
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Affiliation(s)
- Guy Bouchoux
- Département de Chimie, Laboratoire des Mécanismes Réactionnels, Ecole Polytechnique, 91120 Palaiseau, France.
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30
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Takis PG, Melissas VS, Troganis AN. A “hidden” role of amino and imino groups is unveiled during the micro-solvation study of three biomolecule groups in water. NEW J CHEM 2012. [DOI: 10.1039/c2nj40390k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Cruz VL, Ramos J, Martinez-Salazar J. Assessment of the intrinsic conformational preferences of dipeptide amino acids in aqueous solution by combined umbrella sampling/MBAR statistics. A comparison with experimental results. J Phys Chem B 2011; 116:469-75. [PMID: 22136632 DOI: 10.1021/jp206757j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The propensities of 19 amino acid dipeptides have been calculated by a distributed umbrella sampling molecular dynamics simulation procedure using the OPLS-AA force field. The potential of mean force maps was estimated with the multiple Bennett acceptance ratio statistics. The resulting propensities compare satisfactorily well with very recently published experimental data on equivalent systems. In particular, α conformation-probabilities for all of the dipeptides remain much lower than either β or P(II) propensities. This result is in agreement with most experimental data for dipeptides. However, it is also in contrast with most simulation studies performed so far with other force fields, where α conformations result even more probable than P(II) or β ones. We discuss the behavior of the OPLS-AA force field, which can be useful for the improvement of this model in reproducing the recent experimental observations on amino acid dipeptides.
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Affiliation(s)
- Victor L Cruz
- BIOPHYM, Department of Macromolecular Physics, Instituto de Estructura de la Materia, CSIC Serrano 113-bis, Madrid, Spain.
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32
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Burakowski A, Gliński J. Hydration numbers of nonelectrolytes from acoustic methods. Chem Rev 2011; 112:2059-81. [PMID: 22148760 DOI: 10.1021/cr2000948] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrzej Burakowski
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland.
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33
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Dailidonis VV, Danilov VI, Früchtl HA, van Mourik T. The nature of base stacking: a Monte Carlo study. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-1046-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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34
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Pomogaev V, Pomogaeva A, Avramov P, Jalkanen KJ, Kachin S. Thermo-dynamical contours of electronic-vibrational spectra simulated using the statistical quantum–mechanical methods. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-0936-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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35
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Yamabe S, Kawagishi N. A computational study on the relationship between formation and electrolytic dissociation of carbonic acid. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-0929-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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36
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Yao Y, Chen D, Zhang S, Li Y, Tu P, Liu B, Dong M. Building the First Hydration Shell of Deprotonated Glycine by the MCMM and ab Initio Methods. J Phys Chem B 2011; 115:6213-21. [DOI: 10.1021/jp1117097] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yuheng Yao
- Institute of Photo-Biophysics, Physics and Electronics Department, Henan University, 475004, Kaifeng, China
| | - Dong Chen
- Institute of Photo-Biophysics, Physics and Electronics Department, Henan University, 475004, Kaifeng, China
| | - Shuai Zhang
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000 Aarhus C, Denmark
| | - Yinli Li
- Institute of Photo-Biophysics, Physics and Electronics Department, Henan University, 475004, Kaifeng, China
| | - Pinghui Tu
- Institute of Photo-Biophysics, Physics and Electronics Department, Henan University, 475004, Kaifeng, China
| | - Bo Liu
- Institute of Photo-Biophysics, Physics and Electronics Department, Henan University, 475004, Kaifeng, China
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000 Aarhus C, Denmark
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37
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Cruz V, Ramos J, Martínez-Salazar J. Water-Mediated Conformations of the Alanine Dipeptide as Revealed by Distributed Umbrella Sampling Simulations, Quantum Mechanics Based Calculations, and Experimental Data. J Phys Chem B 2011; 115:4880-6. [DOI: 10.1021/jp2022727] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Víctor Cruz
- BIOPHYM, Instituto de Estructura de la Materia, CSIC, Serrano 113bis, 28006, Madrid, Spain
| | - Javier Ramos
- BIOPHYM, Instituto de Estructura de la Materia, CSIC, Serrano 113bis, 28006, Madrid, Spain
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Effect of regular hydration on gas phase structural stability of [zwitterionic alanine+M+] (M+=Li+, Na+, K+) complexes: A quantum chemical study. Chem Phys 2011. [DOI: 10.1016/j.chemphys.2010.11.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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40
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Sun J, Bousquet D, Forbert H, Marx D. Glycine in aqueous solution: solvation shells, interfacial water, and vibrational spectroscopy from ab initio molecular dynamics. J Chem Phys 2010; 133:114508. [DOI: 10.1063/1.3481576] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [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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The gas phase conformers and vibrational spectra of valine, leucine and isoleucine: An ab initio study. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2010.04.033] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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42
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Kamiya K, Boero M, Shiraishi K, Oshiyama A, Shigeta Y. Energy Compensation Mechanism for Charge-Separated Protonation States in Aspartate−Histidine Amino Acid Residue Pairs. J Phys Chem B 2010; 114:6567-78. [DOI: 10.1021/jp906148m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Katsumasa Kamiya
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo, 678-1297, Japan, CREST, Japan Science and Technology Agency, Sanban-cho, Tokyo 102-0075, Japan, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS and University of Strasbourg, 23, rue du Loess, F-67034 Strasbourg 2, France, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan, Center for Computational
| | - Mauro Boero
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo, 678-1297, Japan, CREST, Japan Science and Technology Agency, Sanban-cho, Tokyo 102-0075, Japan, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS and University of Strasbourg, 23, rue du Loess, F-67034 Strasbourg 2, France, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan, Center for Computational
| | - Kenji Shiraishi
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo, 678-1297, Japan, CREST, Japan Science and Technology Agency, Sanban-cho, Tokyo 102-0075, Japan, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS and University of Strasbourg, 23, rue du Loess, F-67034 Strasbourg 2, France, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan, Center for Computational
| | - Atsushi Oshiyama
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo, 678-1297, Japan, CREST, Japan Science and Technology Agency, Sanban-cho, Tokyo 102-0075, Japan, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS and University of Strasbourg, 23, rue du Loess, F-67034 Strasbourg 2, France, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan, Center for Computational
| | - Yasuteru Shigeta
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo, 678-1297, Japan, CREST, Japan Science and Technology Agency, Sanban-cho, Tokyo 102-0075, Japan, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS and University of Strasbourg, 23, rue du Loess, F-67034 Strasbourg 2, France, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan, Center for Computational
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43
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Trivella A, Gaillard T, Stote RH, Hellwig P. Far infrared spectra of solid state aliphatic amino acids in different protonation states. J Chem Phys 2010; 132:115105. [DOI: 10.1063/1.3356027] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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44
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Zhang RB, Eriksson LA. Theoretical study on conformational preferences of ribose in 2-thiouridine--the role of the 2'OH group. Phys Chem Chem Phys 2010; 12:3690-7. [PMID: 20358065 DOI: 10.1039/b921646d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Conformational changes in ribose are well-known to play a significant role in biomolecular identification. The mechanism of selectivity towards C3'-endo conformation (conformer b) in ribose of 2-thiouridine has been studied using DFT (B3LYP) and MP2 methodology, together with 6-31+G(d,p) basis set. The polarity of the C2S2 bond is enhanced due to the orientation of H2' towards the S2 atoms, which leads to a difference in the corresponding bond lengths, the atomic charges and the vO2'H2' stretch vibrations in all the conformers. NBO analysis shows that charge transfer mainly occurs in the C2N3 and C2S2 orbitals. The higher stability of conformer b is attributed to its larger orbital interaction energies within the 2-thiouracil base, and total orbital interaction energies of conformer b. Our conclusion is that the distant electrostatic rather than hydrogen bonding effects between 2'OH and the S2 atoms play the dominant role in the orbital interaction, and enhance the selectivity towards the C3'-endo conformation of ribose.
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Affiliation(s)
- Ru bo Zhang
- Institute for Chemical Physics, School of Science, Beijing Institute of Technology, Beijing 100081, China
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45
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Barneto JL, Avalos M, Babiano R, Cintas P, Jiménez JL, Palacios JC. A new model for mapping the peptide backbone: predicting proton chemical shifts in proteins. Org Biomol Chem 2010; 8:857-63. [PMID: 20135044 DOI: 10.1039/b921121g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper describes a methodology that correlates experimental chemical shifts (at the alpha proton) of proteins with their geometrical data (both dihedral angles and distances) obtained from 13 representative proteins, which are taken from the Protein Data Bank (PDB) and the BioMagRes Data Bank (BMRB). To this end, the experimentally measured proton chemical shifts of simple amides have been correlated with DFT-based calculated structures, at the B3PW91/6-31G* level. This results in a series of mathematical relationships, which are extrapolated to the above-mentioned proteins giving rise to a modified equation for such skeleta. It is relevant to note that the equation is also supported by a clear comparison with NMR data of a protein beyond the chosen set, such as insulin, even with lower errors. The model also relates the dependence of chemical shifts on hydrophobic and anisotropic effects at the amino acid residues.
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Affiliation(s)
- José Luis Barneto
- Departamento de Química Orgánica e Inorgánica, QUOREX Research Group, Facultad de Ciencias, Universidad de Extremadura, E-06071, Badajoz, Spain.
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46
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Density functional theory study of 1:1 glycine-water complexes in the gas phase and in solution. Sci China Chem 2010. [DOI: 10.1007/s11426-010-0065-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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47
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Min CG, Ren AM, Guo JF, Li ZW, Zou LY, Goddard JD, Feng JK. A Time-Dependent Density Functional Theory Investigation on the Origin of Red Chemiluminescence. Chemphyschem 2010; 11:251-9. [DOI: 10.1002/cphc.200900607] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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48
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Pagnotta SE, Cerveny S, Alegría A, Colmenero J. The dynamical behavior of hydrated glutathione: a model for protein–water interactions. Phys Chem Chem Phys 2010; 12:10512-7. [DOI: 10.1039/c003493b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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49
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Zimmermann T, Burda JV. Reactions of cisplatin with cysteine and methionine at constant pH; a computational study. Dalton Trans 2010; 39:1295-301. [DOI: 10.1039/b913803j] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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50
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Yoshikawa T, Motegi H, Kakizaki A, Takayanagi T, Shiga M, Tachikawa M. Path-integral molecular dynamics simulations of glycine·(H2O)n (n=1–7) clusters on semi-empirical PM6 potential energy surfaces. Chem Phys 2009. [DOI: 10.1016/j.chemphys.2009.09.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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