51
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FTIR spectroscopic studies and DFT calculations on the binary solution of methyl acetate with m-xylene. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113491] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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52
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Zheng L, Migliore A, Beratan DN. Electrostatic Field-Induced Oscillator Strength Focusing in Molecules. J Phys Chem B 2020; 124:6376-6388. [PMID: 32600048 DOI: 10.1021/acs.jpcb.0c04783] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The development of light-harvesting devices based on molecular materials depends critically on the ability to focus the electronic oscillator strength of molecules into the UV-vis spectral window. Typical molecular chromophores have only about 1% of their total electronic oscillator strength in this spectral region and thus perform at a small fraction of their possible effectiveness. This theoretical study finds that the electronic oscillator strength of polyenes in the UV-vis region may be enhanced by 1 order of magnitude using electrostatic fields, motivating specific experimental studies of oscillator strength focusing. We find scaling relationships between the polyene length, the intensity of the applied field, and the field-induced increase in oscillator strength that are useful for the implementation of light-harvesting strategies based on polyenes.
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Affiliation(s)
- Lianjun Zheng
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Agostino Migliore
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States.,Department of Physics, Duke University, Durham, North Carolina 27708, United States.,Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States
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53
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Lewis NHC, Iscen A, Felts A, Dereka B, Schatz GC, Tokmakoff A. Vibrational Probe of Aqueous Electrolytes: The Field Is Not Enough. J Phys Chem B 2020; 124:7013-7026. [DOI: 10.1021/acs.jpcb.0c05510] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Nicholas H. C. Lewis
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Aysenur Iscen
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Alanna Felts
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Bogdan Dereka
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - George C. Schatz
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
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54
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Wu Y, Fried SD, Boxer SG. A Preorganized Electric Field Leads to Minimal Geometrical Reorientation in the Catalytic Reaction of Ketosteroid Isomerase. J Am Chem Soc 2020; 142:9993-9998. [PMID: 32378409 DOI: 10.1021/jacs.0c00383] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Electrostatic interactions play a pivotal role in enzymatic catalysis and are increasingly modeled explicitly in computational enzyme design; nevertheless, they are challenging to measure experimentally. Using vibrational Stark effect (VSE) spectroscopy, we have measured electric fields inside the active site of the enzyme ketosteroid isomerase (KSI). These studies have shown that these fields can be unusually large, but it has been unclear to what extent they specifically stabilize the transition state (TS) relative to a ground state (GS). In the following, we use crystallography and computational modeling to show that KSI's intrinsic electric field is nearly perfectly oriented to stabilize the geometry of its reaction's TS. Moreover, we find that this electric field adjusts the orientation of its substrate in the ground state so that the substrate needs to only undergo minimal structural changes upon activation to its TS. This work provides evidence that the active site electric field in KSI is preorganized to facilitate catalysis and provides a template for how electrostatic preorganization can be measured in enzymatic systems.
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Affiliation(s)
- Yufan Wu
- Department of Chemistry, Stanford University, Stanford, California 94305-5012, United States
| | - Stephen D Fried
- Department of Chemistry, Stanford University, Stanford, California 94305-5012, United States
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305-5012, United States
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55
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The Volumetric Source Function: Looking Inside van der Waals Interactions. Sci Rep 2020; 10:7816. [PMID: 32385337 PMCID: PMC7210285 DOI: 10.1038/s41598-020-64261-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/14/2020] [Indexed: 01/23/2023] Open
Abstract
The study of van der Waals interactions plays a central role in the understanding of bonding across a range of biological, chemical and physical phenomena. The presence of van der Waals interactions can be identified through analysis of the reduced density gradient, a fundamental parameter at the core of Density Functional Theory. An extension of Bader’s Quantum Theory of Atoms in Molecules is developed here through combination with the analysis of the reduced density gradient. Through this development, a new quantum chemical topological tool is presented: the volumetric source function. This technique allows insight into the atomic composition of van der Waals interactions, offering the first route towards applying the highly successful source function to these disperse interactions. A new algorithm has been implemented in the open-source code, CRITIC2, and tested on acetone, adipic and maleic acids molecular crystals, each stabilized by van der Waals interactions. This novel technique for studying van der Waals interactions at an atomic level offers unprecedented opportunities in the fundamental study of intermolecular interactions and molecular design for crystal engineering, drug design and bio-macromolecular processes.
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56
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Kempfer-Robertson EM, Thompson LM. Effect of Oriented External Electric Fields on the Photo and Thermal Isomerization of Azobenzene. J Phys Chem A 2020; 124:3520-3529. [PMID: 32286821 DOI: 10.1021/acs.jpca.0c00492] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Azobenzene is a prototype molecule with potential applications in molecular switches, solar thermal batteries, sensors, photoresponsive membranes, molecular electronics, data storage, and nonlinear optics. Photo and thermal isomerization pathways exhibit different charge-transfer character and dipole moments, implying that the use of electric fields can be used to modulate the reactivity of azobenzene. This article examines the differential effect of orientated electric fields on the rotation and inversion thermal and photoisomerization pathways of azobenzene to explore the feasibility of using electric fields in the design of azobenzene-based molecular devices. Our findings demonstrate that the application of orientated electric fields modifies the accessibility of the S0/S1 seam of electronic degeneracy, as well as changes the energetically favored relaxation pathway in the branching space to yield different photoproducts. In addition, we observed strong-field dipole-inversion effects that cause a topographical change in the response of the potential energy surface to the applied field and can result in geometric minima that do not exist under field-free conditions. On the S0 surface, transition barriers can be modified on the order of ±10 kcal mol-1, enabling control of thermal isomerization rates.
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Affiliation(s)
| | - Lee M Thompson
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40205, United States
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57
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Valentine ML, Cardenas AE, Elber R, Baiz CR. Calcium-Lipid Interactions Observed with Isotope-Edited Infrared Spectroscopy. Biophys J 2020; 118:2694-2702. [PMID: 32362342 DOI: 10.1016/j.bpj.2020.04.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 03/20/2020] [Accepted: 04/10/2020] [Indexed: 01/17/2023] Open
Abstract
Calcium ions bind to lipid membranes containing anionic lipids; however, characterizing the specific ion-lipid interactions in multicomponent membranes has remained challenging because it requires nonperturbative lipid-specific probes. Here, using a combination of isotope-edited infrared spectroscopy and molecular dynamics simulations, we characterize the effects of a physiologically relevant (2 mM) Ca2+ concentration on zwitterionic phosphatidylcholine and anionic phosphatidylserine lipids in mixed lipid membranes. We show that Ca2+ alters hydrogen bonding between water and lipid headgroups by forming a coordination complex involving the lipid headgroups and water. These interactions distort interfacial water orientations and prevent hydrogen bonding with lipid ester carbonyls. We demonstrate, experimentally, that these effects are more pronounced for the anionic phosphatidylserine lipids than for zwitterionic phosphatidylcholine lipids in the same membrane.
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Affiliation(s)
- Mason L Valentine
- Department of Chemistry, University of Texas at Austin, Austin, Texas
| | - Alfredo E Cardenas
- Department of Chemistry, University of Texas at Austin, Austin, Texas; Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas
| | - Ron Elber
- Department of Chemistry, University of Texas at Austin, Austin, Texas; Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas
| | - Carlos R Baiz
- Department of Chemistry, University of Texas at Austin, Austin, Texas.
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58
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Verma N, Tao Y, Zou W, Chen X, Chen X, Freindorf M, Kraka E. A Critical Evaluation of Vibrational Stark Effect (VSE) Probes with the Local Vibrational Mode Theory. SENSORS 2020; 20:s20082358. [PMID: 32326248 PMCID: PMC7219233 DOI: 10.3390/s20082358] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 02/06/2023]
Abstract
Over the past two decades, the vibrational Stark effect has become an important tool to measure and analyze the in situ electric field strength in various chemical environments with infrared spectroscopy. The underlying assumption of this effect is that the normal stretching mode of a target bond such as CO or CN of a reporter molecule (termed vibrational Stark effect probe) is localized and free from mass-coupling from other internal coordinates, so that its frequency shift directly reflects the influence of the vicinal electric field. However, the validity of this essential assumption has never been assessed. Given the fact that normal modes are generally delocalized because of mass-coupling, this analysis was overdue. Therefore, we carried out a comprehensive evaluation of 68 vibrational Stark effect probes and candidates to quantify the degree to which their target normal vibration of probe bond stretching is decoupled from local vibrations driven by other internal coordinates. The unique tool we used is the local mode analysis originally introduced by Konkoli and Cremer, in particular the decomposition of normal modes into local mode contributions. Based on our results, we recommend 31 polyatomic molecules with localized target bonds as ideal vibrational Stark effect probe candidates.
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Affiliation(s)
- Niraj Verma
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, TX 75275-0314, USA; (N.V.); (Y.T.); (M.F.)
| | - Yunwen Tao
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, TX 75275-0314, USA; (N.V.); (Y.T.); (M.F.)
| | - Wenli Zou
- Institute of Modern Physics, Northwest University, Xi’an 710127, China;
| | - Xia Chen
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China;
| | - Xin Chen
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China;
| | - Marek Freindorf
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, TX 75275-0314, USA; (N.V.); (Y.T.); (M.F.)
| | - Elfi Kraka
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, TX 75275-0314, USA; (N.V.); (Y.T.); (M.F.)
- Correspondence:
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59
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Ren HC, Yuan JN, Chen TN, Selvaraj G, Kaliamurthi S, Zhang XQ, Wei D, Ji GF, Zhang ZM. Computational insights of two‐dimensional infrared spectroscopy under electric fields in phosphorylcholine. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 2020. [DOI: 10.1002/qua.26169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Hai Chao Ren
- School of Physical SciencesUniversity of Science and Technology of China Hefei China
- National Key Laboratory for Shock Wave and Detonation Physics Research, Institute of Fluid PhysicsChinese Academy of Engineering Physics Mianyang China
| | - Jiao Nan Yuan
- College of ScienceHenan University of Technology Zhengzhou China
| | - Tu Nan Chen
- The First Affiliated HospitalArmy Medical University Chongqing China
| | - Gurudeeban Selvaraj
- College of Food Science and EngineeringHenan University of Technology Zhengzhou China
| | - Satyavani Kaliamurthi
- College of Food Science and EngineeringHenan University of Technology Zhengzhou China
| | - Xiu Qing Zhang
- National Key Laboratory for Shock Wave and Detonation Physics Research, Institute of Fluid PhysicsChinese Academy of Engineering Physics Mianyang China
- Institude of Atomic and Molecular Physics, College of Physical Science and TechnologySichuan University Chengdu China
| | - Dong‐Qing Wei
- College of Food Science and EngineeringHenan University of Technology Zhengzhou China
- College of Life Science and BiotechnologyShanghai Jiao Tong University Shanghai China
| | - Guang Fu Ji
- National Key Laboratory for Shock Wave and Detonation Physics Research, Institute of Fluid PhysicsChinese Academy of Engineering Physics Mianyang China
| | - Zeng Ming Zhang
- School of Physical SciencesUniversity of Science and Technology of China Hefei China
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60
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Chatterjee S, Haldar T, Ghosh D, Bagchi S. Electrostatic Manifestation of Micro-Heterogeneous Solvation Structures in Deep-Eutectic Solvents: A Spectroscopic Approach. J Phys Chem B 2020; 124:3709-3715. [DOI: 10.1021/acs.jpcb.9b11352] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Srijan Chatterjee
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Tapas Haldar
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Deborin Ghosh
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
| | - Sayan Bagchi
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
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61
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Baryiames CP, Baiz CR. Slow Oil, Slow Water: Long-Range Dynamic Coupling across a Liquid–Liquid Interface. J Am Chem Soc 2020; 142:8063-8067. [DOI: 10.1021/jacs.0c00817] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Christopher P. Baryiames
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Stop A5300, Austin, Texas 78712-1224, United States
| | - Carlos R. Baiz
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Stop A5300, Austin, Texas 78712-1224, United States
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62
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Abstract
Infrared difference spectroscopy probes vibrational changes of proteins upon their perturbation. Compared with other spectroscopic methods, it stands out by its sensitivity to the protonation state, H-bonding, and the conformation of different groups in proteins, including the peptide backbone, amino acid side chains, internal water molecules, or cofactors. In particular, the detection of protonation and H-bonding changes in a time-resolved manner, not easily obtained by other techniques, is one of the most successful applications of IR difference spectroscopy. The present review deals with the use of perturbations designed to specifically change the protein between two (or more) functionally relevant states, a strategy often referred to as reaction-induced IR difference spectroscopy. In the first half of this contribution, I review the technique of reaction-induced IR difference spectroscopy of proteins, with special emphasis given to the preparation of suitable samples and their characterization, strategies for the perturbation of proteins, and methodologies for time-resolved measurements (from nanoseconds to minutes). The second half of this contribution focuses on the spectral interpretation. It starts by reviewing how changes in H-bonding, medium polarity, and vibrational coupling affect vibrational frequencies, intensities, and bandwidths. It is followed by band assignments, a crucial aspect mostly performed with the help of isotopic labeling and site-directed mutagenesis, and complemented by integration and interpretation of the results in the context of the studied protein, an aspect increasingly supported by spectral calculations. Selected examples from the literature, predominately but not exclusively from retinal proteins, are used to illustrate the topics covered in this review.
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63
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Protein polarization effects in the thermodynamic computation of vibrational Stark shifts. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2522-2] [Citation(s) in RCA: 2] [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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64
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Lin CY, Romei MG, Oltrogge LM, Mathews II, Boxer SG. Unified Model for Photophysical and Electro-Optical Properties of Green Fluorescent Proteins. J Am Chem Soc 2019; 141:15250-15265. [PMID: 31450887 DOI: 10.1021/jacs.9b07152] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Green fluorescent proteins (GFPs) have become indispensable imaging and optogenetic tools. Their absorption and emission properties can be optimized for specific applications. Currently, no unified framework exists to comprehensively describe these photophysical properties, namely the absorption maxima, emission maxima, Stokes shifts, vibronic progressions, extinction coefficients, Stark tuning rates, and spontaneous emission rates, especially one that includes the effects of the protein environment. In this work, we study the correlations among these properties from systematically tuned GFP environmental mutants and chromophore variants. Correlation plots reveal monotonic trends, suggesting that all these properties are governed by one underlying factor dependent on the chromophore's environment. By treating the anionic GFP chromophore as a mixed-valence compound existing as a superposition of two resonance forms, we argue that this underlying factor is defined as the difference in energy between the two forms, or the driving force, which is tuned by the environment. We then introduce a Marcus-Hush model with the bond length alternation vibrational mode, treating the GFP absorption band as an intervalence charge transfer band. This model explains all of the observed strong correlations among photophysical properties; related subtopics are extensively discussed in the Supporting Information. Finally, we demonstrate the model's predictive power by utilizing the additivity of the driving force. The model described here elucidates the role of the protein environment in modulating the photophysical properties of the chromophore, providing insights and limitations for designing new GFPs with desired phenotypes. We argue that this model should also be generally applicable to both biological and nonbiological polymethine dyes.
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Affiliation(s)
- Chi-Yun Lin
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Matthew G Romei
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Luke M Oltrogge
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Irimpan I Mathews
- Stanford Synchrotron Radiation Lightsource , 2575 Sand Hill Road , Menlo Park , California 94025 , United States
| | - Steven G Boxer
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
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65
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Baryiames CP, Teel M, Baiz CR. Interfacial H-Bond Dynamics in Reverse Micelles: The Role of Surfactant Heterogeneity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:11463-11470. [PMID: 31407910 DOI: 10.1021/acs.langmuir.9b01693] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Characterizing the hydrogen bond structure and dynamics at surfactant interfaces is essential for understanding how microscopic interactions translate to bulk microemulsion properties. Heterogeneous blends containing tens or hundreds of surfactants are common in the industry, but the most fundamental studies have been carried out on micelles composed of a single surfactant species. Therefore, the effect of surfactant heterogeneity on the interfacial structure and dynamics remains poorly understood. Here, we use ultrafast two-dimensional infrared spectroscopy and molecular dynamics simulations to characterize sub-picosecond solvation dynamics as a function of the surfactant composition in ∼120 nm water-in-oil reverse micelles. We probe the ester carbonyl vibrations of nonionic sorbitan surfactants, which are located precisely at the interface between the polar and nonpolar regions, and as such, report on the interfacial water dynamics. We show a 7% increase in hydrogen bond populations together with a 37% slowdown of interfacial hydrogen bond dynamics in heterogeneous mixtures containing hundreds of species, compared to more uniform compositions. Simulations, which are in semiquantitative agreement with experiments, indicate that structural diversity leads to decreased packing efficiency, which in turn drives water further into the otherwise hydrophobic region. Interestingly, this increase in hydration is accompanied by a slowdown of dynamics, indicating that water molecules solvating surfactants are conformationally constrained. These studies demonstrate that the composition and heterogeneity are key factors in determining interfacial properties.
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Affiliation(s)
| | - Morgan Teel
- University of Texas at Austin , Austin 78712 , Texas , United States
| | - Carlos R Baiz
- University of Texas at Austin , Austin 78712 , Texas , United States
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66
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Nifosì R, Mennucci B, Filippi C. The key to the yellow-to-cyan tuning in the green fluorescent protein family is polarisation. Phys Chem Chem Phys 2019; 21:18988-18998. [PMID: 31464320 DOI: 10.1039/c9cp03722e] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Computational approaches have to date failed to fully capture the large (about 0.4 eV) excitation energy tuning displayed by the nearly identical anionic chromophore in different green fluorescent protein (GFP) variants. Here, we present a thorough comparative study of a set of proteins in this sub-family, including the most red- (phiYFP) and blue-shifted (mTFP0.7) ones. We employ a classical polarisable embedding through induced dipoles and combine it with time-dependent density functional theory and multireference perturbation theory in order to capture both state-specific induction contributions and the coupling of the polarisation of the protein to the chromophore transition density. The obtained results show that only upon inclusion of both these two effects generated by the mutual polarisation between the chromophore and the protein can the full spectral tuning be replicated. We finally discuss how this mutual polarisation affects the correlation between excitation energies, dipole moment variation, and molecular electrostatic field.
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Affiliation(s)
- Riccardo Nifosì
- NEST, CNR - Istituto Nanoscienze and Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy.
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi 13, 56124 Pisa, Italy
| | - Claudia Filippi
- MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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67
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Attia S, Schmidt MC, Schröder C, Schauermann S. Formation and Stabilization Mechanisms of Enols on Pt through Multiple Hydrogen Bonding. ACS Catal 2019. [DOI: 10.1021/acscatal.9b01481] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Smadar Attia
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Max-Eyth-Strasse 2, 24118 Kiel, Germany
| | - Marvin C. Schmidt
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Max-Eyth-Strasse 2, 24118 Kiel, Germany
| | - Carsten Schröder
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Max-Eyth-Strasse 2, 24118 Kiel, Germany
| | - Swetlana Schauermann
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Max-Eyth-Strasse 2, 24118 Kiel, Germany
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68
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Abaskharon RM, Mukherjee D, Gai F. 4-Oxoproline as a Site-Specific Infrared Probe: Application To Assess Proline Isomerization and Dimer Formation. J Phys Chem B 2019; 123:5079-5085. [PMID: 31135160 DOI: 10.1021/acs.jpcb.9b03766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Due to its unique structure, proline plays important structural and functional roles in proteins. However, this special amino acid lacks an adequate vibrational mode that can be exploited to probe its local electrostatic and hydration status via infrared spectroscopy. Herein, we show that the C═O stretching vibration of a proline derivative, 4-oxoproline, is sensitive to local environment and hence can be used as a site-specific infrared probe. We further validate this notion by applying this unnatural amino acid to assess the thermodynamics of proline cis-trans isomerization in a peptide environment and examine the amino acid dimer formation in concentrated proline and glycine solutions.
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Affiliation(s)
- Rachel M Abaskharon
- Department of Chemistry , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Debopreeti Mukherjee
- Department of Chemistry , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Feng Gai
- Department of Chemistry , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
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69
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The electronic origin of the ground state spectral features and excited state deactivation in cycloalkanones: the role of intermolecular H-bonding in neat and binary mixtures of solvents. J Mol Model 2019; 25:133. [DOI: 10.1007/s00894-019-4015-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 03/29/2019] [Indexed: 10/26/2022]
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70
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Ramos S, Thielges MC. Site-Specific 1D and 2D IR Spectroscopy to Characterize the Conformations and Dynamics of Protein Molecular Recognition. J Phys Chem B 2019; 123:3551-3566. [PMID: 30848912 DOI: 10.1021/acs.jpcb.9b00969] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Proteins exist as ensembles of interconverting states on a complex energy landscape. A complete, molecular-level understanding of their function requires knowledge of the populated states and thus the experimental tools to characterize them. Infrared (IR) spectroscopy has an inherently fast time scale that can capture all states and their dynamics with, in principle, bond-specific spatial resolution, and 2D IR methods that provide richer information are becoming more routine. Although application of IR spectroscopy for investigation of proteins is challenged by spectral congestion, the issue can be overcome by site-specific introduction of amino acid side chains that have IR probe groups with frequency-resolved absorptions, which furthermore enables selective characterization of different locations in proteins. Here, we briefly introduce the biophysical methods and summarize the current progress toward the study of proteins. We then describe our efforts to apply site-specific 1D and 2D IR spectroscopy toward elucidation of protein conformations and dynamics to investigate their involvement in protein molecular recognition, in particular mediated by dynamic complexes: plastocyanin and its binding partner cytochrome f, cytochrome P450s and substrates or redox partners, and Src homology 3 domains and proline-rich peptide motifs. We highlight the advantages of frequency-resolved probes to characterize specific, local sites in proteins and uncover variation among different locations, as well as the advantage of the fast time scale of IR spectroscopy to detect rapidly interconverting states. In addition, we illustrate the greater insight provided by 2D methods and discuss potential routes for further advancement of the field of biomolecular 2D IR spectroscopy.
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Affiliation(s)
- Sashary Ramos
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Megan C Thielges
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
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71
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Shi MW, Thomas SP, Hathwar VR, Edwards AJ, Piltz RO, Jayatilaka D, Koutsantonis GA, Overgaard J, Nishibori E, Iversen BB, Spackman MA. Measurement of Electric Fields Experienced by Urea Guest Molecules in the 18-Crown-6/Urea (1:5) Host-Guest Complex: An Experimental Reference Point for Electric-Field-Assisted Catalysis. J Am Chem Soc 2019; 141:3965-3976. [PMID: 30761898 DOI: 10.1021/jacs.8b12927] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
High-resolution synchrotron and neutron single-crystal diffraction data of 18-crown-6/(pentakis)urea measured at 30 K are combined, with the aim of better appreciating the electrostatics associated with intermolecular interactions in condensed matter. With two 18-crown-6 molecules and five different urea molecules in the crystal, this represents the most ambitious combined X-ray/synchrotron and neutron experimental charge density analysis to date on a cocrystal or host-guest system incorporating such a large number of unique molecules. The dipole moments of the five urea guest molecules in the crystal are enhanced considerably compared to values determined for isolated molecules, and 2D maps of the electrostatic potential and electric field show clearly how the urea molecules are oriented with dipole moments aligned along the electric field exerted by their molecular neighbors. Experimental electric fields in the range of 10-19 GV m-1, obtained for the five different urea environments, corroborate independent measurements of electric fields in the active sites of enzymes and provide an important experimental reference point for recent discussions focused on electric-field-assisted catalysis.
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Affiliation(s)
- Ming W Shi
- School of Molecular Sciences , University of Western Australia , 35 Stirling Highway , Crawley , WA 6009 , Australia
| | - Sajesh P Thomas
- School of Molecular Sciences , University of Western Australia , 35 Stirling Highway , Crawley , WA 6009 , Australia.,Center for Materials Crystallography and Department of Chemistry , Aarhus University , Langelandsgade 140 , DK-8000 Aarhus C , Denmark
| | - Venkatesha R Hathwar
- Center for Materials Crystallography and Department of Chemistry , Aarhus University , Langelandsgade 140 , DK-8000 Aarhus C , Denmark.,Division of Physics, Faculty of Pure and Applied Sciences , University of Tsukuba , 1-1-1 Tennodai , Tsukuba , Ibaraki 305-8571 , Japan
| | - Alison J Edwards
- Australian Nuclear Science and Technology Organization , Australian Centre for Neutron Scattering , New Illawarra Road , Lucas Heights , New South Wales 2234 , Australia
| | - Ross O Piltz
- Australian Nuclear Science and Technology Organization , Australian Centre for Neutron Scattering , New Illawarra Road , Lucas Heights , New South Wales 2234 , Australia
| | - Dylan Jayatilaka
- School of Molecular Sciences , University of Western Australia , 35 Stirling Highway , Crawley , WA 6009 , Australia
| | - George A Koutsantonis
- School of Molecular Sciences , University of Western Australia , 35 Stirling Highway , Crawley , WA 6009 , Australia
| | - Jacob Overgaard
- Center for Materials Crystallography and Department of Chemistry , Aarhus University , Langelandsgade 140 , DK-8000 Aarhus C , Denmark
| | - Eiji Nishibori
- Division of Physics, Faculty of Pure and Applied Sciences , University of Tsukuba , 1-1-1 Tennodai , Tsukuba , Ibaraki 305-8571 , Japan
| | - Bo B Iversen
- Center for Materials Crystallography and Department of Chemistry , Aarhus University , Langelandsgade 140 , DK-8000 Aarhus C , Denmark
| | - Mark A Spackman
- School of Molecular Sciences , University of Western Australia , 35 Stirling Highway , Crawley , WA 6009 , Australia
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72
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Roberson MG, Smith DK, White SM, Wallace IS, Tucker MJ. Interspecies Bombolitins Exhibit Structural Diversity upon Membrane Binding, Leading to Cell Specificity. Biophys J 2019; 116:1064-1074. [PMID: 30824115 DOI: 10.1016/j.bpj.2019.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 02/07/2019] [Accepted: 02/08/2019] [Indexed: 02/05/2023] Open
Abstract
Bombolitins, a class of peptides produced by bees of the genus Bombus, target and disrupt cellular membranes, leading to lysis. Antimicrobial peptides exhibit various mechanisms of action resulting from the interplay between peptide structure, lipid composition, and cellular target membrane selectivity. Herein, two bombolitins displaying significant amino-acid-sequence similarity, BII and BL6, were assessed for antimicrobial activity as well as correlated dodecylphosphocholine (DPC) micelle binding and membrane-induced peptide conformational changes. Infrared and circular dichroism spectroscopies were used to assess the structure-function relationship of each bombolitin, and the results indicate that BII forms a rigid and helically ordered secondary structure upon binding to DPC micelles, whereas BL6 largely lacks secondary structural order. Moreover, the binding affinity of each peptide to DPC micelles was determined, revealing that BL6 displayed a difference in binding affinity by over two orders of magnitude. Further investigations into the growth-inhibitory activity of the two bombolitins were performed against Escherichia coli and Saccharomyces cerevisiae. Interestingly, BII specifically targeted S. cerevisiae, whereas BL6 more effectively inhibited E. coli growth. Overall, the antimicrobial selectivity and specificity of BII and BL6 are largely dependent on the primary as well as secondary structural content of the peptides and the membrane composition.
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Affiliation(s)
| | - Devin K Smith
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada
| | - Simon M White
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada
| | - Ian S Wallace
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada; Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada.
| | - Matthew J Tucker
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada.
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73
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Saggu M, Fried SD, Boxer SG. Local and Global Electric Field Asymmetry in Photosynthetic Reaction Centers. J Phys Chem B 2019; 123:1527-1536. [PMID: 30668130 DOI: 10.1021/acs.jpcb.8b11458] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The origin of unidirectional electron transfer in photosynthetic reaction centers (RCs) has been widely discussed. Despite the high level of structural similarity between the two branches of pigments that participate in the initial electron transfer steps of photosynthesis, electron transfer only occurs along one branch. One possible explanation for this functional asymmetry is the differences in the electrostatic environment between the active and the inactive branches arising from the charges and dipoles of the organized protein structure. We present an analysis of electric fields in the RC of the purple bacterium Rhodobacter sphaeroides using the intrinsic carbonyl groups of the pigments as vibrational reporters whose vibrational frequency shifts can be converted into electric fields based on the vibrational Stark effect and also provide Stark effect data for plant pigments that can be used in future studies. The carbonyl stretches of the isolated pigments show pronounced Stark effects. We use these data, solvatochromism, molecular dynamics simulations, and data in the literature from IR and Raman spectra to evaluate differences in fields at symmetry-related positions, in particular at the 9-keto and 2-acetyl positions of the pigments involved in primary charge separation.
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Affiliation(s)
- Miguel Saggu
- Department of Chemistry , Stanford University , Stanford , California 94305-5080 , United States
| | - Stephen D Fried
- Department of Chemistry , Stanford University , Stanford , California 94305-5080 , United States
| | - Steven G Boxer
- Department of Chemistry , Stanford University , Stanford , California 94305-5080 , United States
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74
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Shahriar I, Islam MKB, Iqfath M, Rahman A, Halim MA. Solvent effect on vibrational circular dichroism of chiral amino acids. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2419-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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75
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Attia S, Schmidt MC, Schröder C, Pessier P, Schauermann S. Surface-Driven Keto-Enol Tautomerization: Atomistic Insights into Enol Formation and Stabilization Mechanisms. Angew Chem Int Ed Engl 2018; 57:16659-16664. [PMID: 30311717 DOI: 10.1002/anie.201808453] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/07/2018] [Indexed: 11/06/2022]
Abstract
Tautomerisation of simple carbonyl compounds to their enol counterparts on metal surfaces is envisaged to enable an easier route for hydrogenation of the C=O bond in heterogeneously catalyzed reactions. To understand the mechanisms of enol formation and stabilization over catalytically active metal surfaces, we performed a mechanistic study on keto-enol tautomerization of a monocarbonyl compound acetophenon over Pt(111) surface. By employing infrared reflection adsorption spectroscopy in combination with scanning tunneling microscopy, we found that enol can be formed by building a ketone-enol dimer, in which one molecule in the enol form is stabilized through hydrogen bonding to the carbonyl group of the second ketone molecule. Based on the investigations of the co-adsorption behavior of acetophenone and hydrogen, we conclude that keto-enol tautomerization occurs in the intramolecular process and does not involve hydrogen transfer through the surface hypothesized previously.
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Affiliation(s)
- Smadar Attia
- Institute of Physical Chemistry, Christian-Albrechts-University Kiel, Max-Eyth-Str. 2, 24118, Kiel, Germany.,Department of Chemical Physics, Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Marvin-Christopher Schmidt
- Institute of Physical Chemistry, Christian-Albrechts-University Kiel, Max-Eyth-Str. 2, 24118, Kiel, Germany
| | - Carsten Schröder
- Institute of Physical Chemistry, Christian-Albrechts-University Kiel, Max-Eyth-Str. 2, 24118, Kiel, Germany
| | - Pascal Pessier
- Institute of Physical Chemistry, Christian-Albrechts-University Kiel, Max-Eyth-Str. 2, 24118, Kiel, Germany
| | - Swetlana Schauermann
- Institute of Physical Chemistry, Christian-Albrechts-University Kiel, Max-Eyth-Str. 2, 24118, Kiel, Germany
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76
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Attia S, Schmidt M, Schröder C, Pessier P, Schauermann S. Surface‐Driven Keto–Enol Tautomerization: Atomistic Insights into Enol Formation and Stabilization Mechanisms. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201808453] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Smadar Attia
- Institute of Physical ChemistryChristian-Albrechts-University Kiel Max-Eyth-Str. 2 24118 Kiel Germany
- Department of Chemical PhysicsFritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Germany
| | | | - Carsten Schröder
- Institute of Physical ChemistryChristian-Albrechts-University Kiel Max-Eyth-Str. 2 24118 Kiel Germany
| | - Pascal Pessier
- Institute of Physical ChemistryChristian-Albrechts-University Kiel Max-Eyth-Str. 2 24118 Kiel Germany
| | - Swetlana Schauermann
- Institute of Physical ChemistryChristian-Albrechts-University Kiel Max-Eyth-Str. 2 24118 Kiel Germany
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77
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Zhou Y, Wang Z, Gong S, Yu Z, Xu X. Comparative study of hydrogen bonding interactions between N-methylacetamide and Methyl Acetate/Ethyl Formate. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.07.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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78
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Ghosh A, Cohn B, Prasad AK, Chuntonov L. Quantifying conformations of ester vibrational probes with hydrogen-bond-induced Fermi resonances. J Chem Phys 2018; 149:184501. [PMID: 30441918 DOI: 10.1063/1.5055041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Solvatochromic shifts of local vibrational probes report on the strength of the surrounding electric fields and the probe's hydrogen bonding status. Stretching vibrational mode of the ester carbonyl group is a popular solvatochromic reporter used in the studies of peptides and proteins. Small molecules, used to calibrate the response of the vibrational probes, sometimes involve Fermi resonances (FRs) induced by inter-molecular interactions. In the present work, we focus on the scenario where FR does not appear in the infrared spectrum of the ester carbonyl stretching mode in aprotic solvents; however, it is intensified when a hydrogen bond with the reporter is established. When two molecules form hydrogen bonds to the same carbonyl oxygen atom, FR leads to strong hybridization of the involved modes and splitting of the absorption peak. Spectral overlap between the Fermi doublets associated with singly and doubly hydrogen-bonded carbonyl groups significantly complicates quantifying different hydrogen-bonded conformations. We employed a combination of linear and third-order (2DIR) infrared spectroscopy with chemometrics analysis to reveal the individual line shapes and to estimate the occupations of the hydrogen-bonded conformations in methyl acetate, a model small molecule. We identified a hydrogen-bond-induced FR in complexes of methyl acetate with alcohols and water and found that FR is lifted in larger molecules used for control experiments-cholesteryl stearate and methyl cyanoacetate. Applying this methodology to analyze acetonitrile-water solutions revealed that when dissolved in neat water, methyl acetate occupies a single hydrogen-bonding conformation, which is in contrast to the conclusions of previous studies. Our approach can be generally used when FRs prevent direct quantification of the hydrogen bonding status of the vibrational probe.
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Affiliation(s)
- Anup Ghosh
- Schulich Faculty of Chemistry and Solid State Institute, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Bar Cohn
- Schulich Faculty of Chemistry and Solid State Institute, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Amit K Prasad
- Schulich Faculty of Chemistry and Solid State Institute, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Lev Chuntonov
- Schulich Faculty of Chemistry and Solid State Institute, Technion-Israel Institute of Technology, Haifa 3200003, Israel
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79
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Punihaole D, Workman RJ, Upadhyay S, Bruggen CV, Schmitz AJ, Reineke TM, Frontiera RR. New Insights into Quinine-DNA Binding Using Raman Spectroscopy and Molecular Dynamics Simulations. J Phys Chem B 2018; 122:9840-9851. [PMID: 30336027 PMCID: PMC6425490 DOI: 10.1021/acs.jpcb.8b05795] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Quinine's ability to bind DNA and potentially inhibit transcription and translation has been examined as a mode of action for its antimalarial activity. UV absorption and fluorescence-based studies have lacked the chemical specificity to develop an unambiguous molecular-level picture of the binding interaction. To address this, we use Raman spectroscopy and molecular dynamics (MD) to investigate quinine-DNA interactions. We demonstrate that quinine's strongest Raman band in the fingerprint region, which derives from a symmetric stretching mode of the quinoline ring, is highly sensitive to the local chemical environment and pH. The frequency shifts observed for this mode in solvents of varying polarity can be explained in terms of the Stark effect using a simple Onsager solvation model, indicating that the vibration reports on the local electrostatic environment. However, specific chemical interactions between the quinoline ring and its environment, such as hydrogen bonding and π-stacking, perturb the frequency of this mode in a more complicated but predictable manner. We use this vibration as a spectroscopic probe to investigate the binding interaction between quinine and DNA. We find that, when the quinoline ring is protonated, quinine weakly intercalates into DNA by forming π-stacking interactions with the base pairs. The Raman spectra indicate that quinine can intercalate into DNA with a ratio reaching up to roughly one molecule per 25 base pairs. Our results are confirmed by MD simulations, which also show that the quinoline ring adopts a t-shaped π-stacking geometry with the DNA base pairs, whereas the quinuclidine head group weakly interacts with the phosphate backbone in the minor groove. We expect that the spectral correlations determined here will enable future studies to probe quinine's antimalarial activities, such as disrupting hemozoin biocrystallization, which is hypothesized to be, among other things, one of its primary modes of action against Plasmodium parasites.
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Affiliation(s)
- David Punihaole
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Riley J. Workman
- Department of Chemistry and Biochemistry, Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Shiv Upadhyay
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Craig Van Bruggen
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Andrew J. Schmitz
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Theresa M. Reineke
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Renee R. Frontiera
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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80
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Affiliation(s)
- Valerie Vaissier Welborn
- Kenneth S. Pitzer Center for Theoretical Chemistry and Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Teresa Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry and Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, California 94720, United States
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81
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An Ab Initio QM/MM Study of the Electrostatic Contribution to Catalysis in the Active Site of Ketosteroid Isomerase. Molecules 2018; 23:molecules23102410. [PMID: 30241317 PMCID: PMC6222312 DOI: 10.3390/molecules23102410] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/16/2018] [Accepted: 09/17/2018] [Indexed: 01/28/2023] Open
Abstract
The electric field in the hydrogen-bond network of the active site of ketosteroid isomerase (KSI) has been experimentally measured using vibrational Stark effect (VSE) spectroscopy, and utilized to study the electrostatic contribution to catalysis. A large gap was found in the electric field between the computational simulation based on the Amber force field and the experimental measurement. In this work, quantum mechanical (QM) calculations of the electric field were performed using an ab initio QM/MM molecular dynamics (MD) simulation and electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method. Our results demonstrate that the QM-derived electric field based on the snapshots from QM/MM MD simulation could give quantitative agreement with the experiment. The accurate calculation of the electric field inside the protein requires both the rigorous sampling of configurations, and a QM description of the electrostatic field. Based on the direct QM calculation of the electric field, we theoretically confirmed that there is a linear correlation relationship between the activation free energy and the electric field in the active site of wild-type KSI and its mutants (namely, D103N, Y16S, and D103L). Our study presents a computational protocol for the accurate simulation of the electric field in the active site of the protein, and provides a theoretical foundation that supports the link between electric fields and enzyme catalysis.
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82
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Valentine ML, Cardenas AE, Elber R, Baiz CR. Physiological Calcium Concentrations Slow Dynamics at the Lipid-Water Interface. Biophys J 2018; 115:1541-1551. [PMID: 30269885 DOI: 10.1016/j.bpj.2018.08.044] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 08/20/2018] [Accepted: 08/27/2018] [Indexed: 02/07/2023] Open
Abstract
Phospholipids can interact strongly with ions at physiological concentrations, and these interactions can alter membrane properties. Here, we describe the effects of calcium ions on the dynamics in phospholipid membranes. We used a combination of time-resolved ultrafast two-dimensional infrared spectroscopy and molecular dynamics simulations. We found that millimolar Ca2+ concentrations lead to slower fluctuations in the local environment at the lipid-water interface of membranes with phosphatidylserine. The effect was only observed in bilayers containing anionic phosphatidylserine; membranes composed of only zwitterionic phosphatidylcholine did not experience a slowdown. Local water dynamics were measured using the ester groups as label-free probes and were found to be up to 50% slower with 2.5 mM Ca2+. Molecular dynamics simulations show that Ca2+ primarily binds to the carboxylate group of phosphatidylserines. These findings have implications for apoptotic and diseased cells in which phosphatidylserine is exposed to extracellular calcium and for the biophysical effects of divalent cations on lipid bilayers.
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Affiliation(s)
- Mason L Valentine
- Department of Chemistry, University of Texas at Austin, Austin, Texas
| | - Alfredo E Cardenas
- Department of Chemistry, University of Texas at Austin, Austin, Texas; Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas
| | - Ron Elber
- Department of Chemistry, University of Texas at Austin, Austin, Texas; Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas
| | - Carlos R Baiz
- Department of Chemistry, University of Texas at Austin, Austin, Texas.
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83
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Ihalainen JA, Gustavsson E, Schroeder L, Donnini S, Lehtivuori H, Isaksson L, Thöing C, Modi V, Berntsson O, Stucki-Buchli B, Liukkonen A, Häkkänen H, Kalenius E, Westenhoff S, Kottke T. Chromophore–Protein Interplay during the Phytochrome Photocycle Revealed by Step-Scan FTIR Spectroscopy. J Am Chem Soc 2018; 140:12396-12404. [DOI: 10.1021/jacs.8b04659] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Janne A. Ihalainen
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Emil Gustavsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden
| | - Lea Schroeder
- Physical and Biophysical Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Serena Donnini
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Heli Lehtivuori
- Nanoscience Center, Department of Physics, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Linnéa Isaksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden
| | - Christian Thöing
- Physical and Biophysical Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Vaibhav Modi
- Nanoscience Center, Department of Chemistry, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Oskar Berntsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden
| | - Brigitte Stucki-Buchli
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Alli Liukkonen
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Heikki Häkkänen
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Elina Kalenius
- Nanoscience Center, Department of Chemistry, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden
| | - Tilman Kottke
- Physical and Biophysical Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
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84
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Biava H, Schreiber T, Katz S, Völler JS, Stolarski M, Schulz C, Michael N, Budisa N, Kozuch J, Utesch T, Hildebrandt P. Long-Range Modulations of Electric Fields in Proteins. J Phys Chem B 2018; 122:8330-8342. [PMID: 30109934 DOI: 10.1021/acs.jpcb.8b03870] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Electrostatic interactions are essential for controlling the protein structure and function. Whereas so far experimental and theoretical efforts focused on the effect of local electrostatics, this work aims at elucidating the long-range modulation of electric fields in proteins upon binding to charged surfaces. The study is based on cytochrome c (Cytc) variants carrying nitrile reporters for the vibrational Stark effect that are incorporated into the protein via genetic engineering and chemical modification. The Cytc variants were thoroughly characterized with respect to possible structural perturbations due to labeling. For the proteins in solution, the relative hydrogen bond occupancy and the calculated electric fields, both obtained from molecular dynamics (MD) simulations, and the experimental nitrile stretching frequencies were used to develop a relationship for separating hydrogen-bonding and non-hydrogen-bonding electric field effects. This relationship provides an excellent description for the stable Cytc variants in solution. For the proteins bound to Au electrodes coated with charged self-assembled monolayers (SAMs), the underlying MD simulations can only account for the electric field changes Δ Eads due to the formation of the electrostatic SAM-Cytc complexes but not for the additional contribution, Δ Eint, representing the consequences of the potential drops over the electrode/SAM/protein interfaces. Both Δ Eads and Δ Eint, determined at distances between 20 and 30 Å with respect to the SAM surface, are comparable in magnitude to the non-hydrogen-bonding electric field in the unbound protein. This long-range modulation of the internal electric field may be of functional relevance for proteins in complexes with partner proteins (Δ Eads) and attached to membranes (Δ Eads + Δ Eint).
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Affiliation(s)
- Hernan Biava
- Institut für Chemie , Technische Universität Berlin , Sekr. L1, Müller-Breslau-Straße 10 , D-10623 Berlin , Germany
| | - Toni Schreiber
- Institut für Chemie , Technische Universität Berlin , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Sagie Katz
- Institut für Chemie , Technische Universität Berlin , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Jan-Stefan Völler
- Institut für Chemie , Technische Universität Berlin , Sekr. L1, Müller-Breslau-Straße 10 , D-10623 Berlin , Germany
| | - Michael Stolarski
- Institut für Chemie , Technische Universität Berlin , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Claudia Schulz
- Institut für Chemie , Technische Universität Berlin , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Norbert Michael
- Institut für Chemie , Technische Universität Berlin , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Nediljko Budisa
- Institut für Chemie , Technische Universität Berlin , Sekr. L1, Müller-Breslau-Straße 10 , D-10623 Berlin , Germany
| | - Jacek Kozuch
- Institut für Chemie , Technische Universität Berlin , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Tillmann Utesch
- Institut für Chemie , Technische Universität Berlin , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Peter Hildebrandt
- Institut für Chemie , Technische Universität Berlin , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
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85
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Grafton AB, Cheatum CM. Two-dimensional infrared study of the C D and C O stretching vibrations in strongly hydrogen-bonded complexes. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.05.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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86
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Slocum JD, Webb LJ. Measuring Electric Fields in Biological Matter Using the Vibrational Stark Effect of Nitrile Probes. Annu Rev Phys Chem 2018; 69:253-271. [DOI: 10.1146/annurev-physchem-052516-045011] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Joshua D. Slocum
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712-1224, USA
| | - Lauren J. Webb
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712-1224, USA
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87
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Kearney C, Olenginski LT, Hirn TD, Fowler GD, Tariq D, Brewer SH, Phillips-Piro CM. Exploring local solvation environments of a heme protein using the spectroscopic reporter 4-cyano-l-phenylalanine. RSC Adv 2018; 8:13503-13512. [PMID: 29780583 PMCID: PMC5944249 DOI: 10.1039/c8ra02000k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 03/20/2018] [Indexed: 11/21/2022] Open
Abstract
The vibrational reporter unnatural amino acid (UAA) 4-cyano-l-phenylalanine (pCNF) was genetically incorporated individually at three sites (5, 36, and 78) in the heme protein Caldanaerobacter subterraneus H-NOX to probe local hydration environments. The UAA pCNF was incorporated site-specifically using an engineered, orthogonal tRNA synthetase in E. coli. The ability of all of the pCNF-containing H-NOX proteins to form the ferrous CO, NO, or O2 ligated and unligated states was confirmed with UV-Vis spectroscopy. The solvation state at each site of the three sites of pCNF incorporation was assessed using temperature-dependent infrared spectroscopy. Specifically, the frequency-temperature line slope (FTLS) method was utilized to show that the nitrile group at site 36 was fully solvated and the nitrile group at site 78 was de-solvated (buried) in the heme pocket. The nitrile group at site 5 was found to be partially solvated suggesting that the nitrile group was involved in moderate strength hydrogen bonds. These results were confirmed by the determination of the X-ray crystal structure of the H-NOX protein construct containing pCNF at site 5.
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Affiliation(s)
- Caroline Kearney
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA. ;
| | - Lukasz T Olenginski
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA. ;
| | - Trexler D Hirn
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA. ;
| | - Gwendolyn D Fowler
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA. ;
| | - Daniyal Tariq
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA. ;
| | - Scott H Brewer
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA. ;
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88
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A quantum mechanical computational method for modeling electrostatic and solvation effects of protein. Sci Rep 2018; 8:5475. [PMID: 29615707 PMCID: PMC5882933 DOI: 10.1038/s41598-018-23783-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 03/19/2018] [Indexed: 12/28/2022] Open
Abstract
An efficient computational approach for modeling protein electrostatic is developed according to static point-charge model distributions based on the linear-scaling EE-GMFCC (electrostatically embedded generalized molecular fractionation with conjugate caps) quantum mechanical (QM) method. In this approach, the Electrostatic-Potential atomic charges are obtained from ab initio calculation of protein, both polarization and charge transfer effect are taken into consideration. This approach shows a significant improvement in the description of electrostatic potential and solvation energy of proteins comparing with current popular molecular mechanics (MM) force fields. Therefore, it has gorgeous prospect in many applications, including accurate calculations of electric field or vibrational Stark spectroscopy in proteins and predicting protein-ligand binding affinity. It can also be applied in QM/MM calculations or electronic embedding method of ONIOM to provide a better electrostatic environment.
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89
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Zhang L, Laborda E, Darwish N, Noble BB, Tyrell JH, Pluczyk S, Le Brun AP, Wallace GG, Gonzalez J, Coote ML, Ciampi S. Electrochemical and Electrostatic Cleavage of Alkoxyamines. J Am Chem Soc 2018; 140:766-774. [PMID: 29258306 DOI: 10.1021/jacs.7b11628] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Alkoxyamines are heat-labile molecules, widely used as an in situ source of nitroxides in polymer and materials sciences. Here we show that the one-electron oxidation of an alkoxyamine leads to a cation radical intermediate that even at room temperature rapidly fragments, releasing a nitroxide and carbocation. Digital simulations of experimental voltammetry and current-time transients suggest that the unimolecular decomposition which yields the "unmasked" nitroxide (TEMPO) is exceedingly rapid and irreversible. High-level quantum computations indicate that the collapse of the alkoxyamine cation radical is likely to yield a neutral nitroxide radical and a secondary phenylethyl cation. However, this fragmentation is predicted to be slow and energetically very unfavorable. To attain qualitative agreement between the experimental kinetics and computational modeling for this fragmentation step, the explicit electrostatic environment within the double layer must be accounted for. Single-molecule break-junction experiments in a scanning tunneling microscope using solvent of low dielectric (STM-BJ technique) corroborate the role played by electrostatic forces on the lysis of the alkoxyamine C-ON bond. This work highlights the electrostatic aspects played by charged species in a chemical step that follows an electrochemical reaction, defines the magnitude of this catalytic effect by looking at an independent electrical technique in non-electrolyte systems (STM-BJ), and suggests a redox on/off switch to guide the cleavage of alkoxyamines at an electrified interface.
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Affiliation(s)
- Long Zhang
- Department of Chemistry, Curtin University , Bentley, Western Australia 6102, Australia.,ARC Centre of Excellence for Electromaterials Science, Intelligent Polymer Research Institute, University of Wollongong , Wollongong, New South Wales 2500, Australia
| | - Eduardo Laborda
- Departamento de Quimica Fisica, Universidad De Murcia , Murcia 30003, Spain
| | - Nadim Darwish
- Department of Chemistry, Curtin University , Bentley, Western Australia 6102, Australia
| | - Benjamin B Noble
- ARC Centre of Excellence for Electromaterials Science, Research School of Chemistry, Australian National University , Canberra, Australian Capital Territory 2601, Australia
| | - Jason H Tyrell
- ARC Centre of Excellence for Electromaterials Science, Research School of Chemistry, Australian National University , Canberra, Australian Capital Territory 2601, Australia
| | - Sandra Pluczyk
- Faculty of Chemistry, Silesian University of Technology , Gliwice 44-100, Poland
| | - Anton P Le Brun
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organization (ANSTO), Lucas Heights, New South Wales 2234, Australia
| | - Gordon G Wallace
- ARC Centre of Excellence for Electromaterials Science, Intelligent Polymer Research Institute, University of Wollongong , Wollongong, New South Wales 2500, Australia
| | - Joaquin Gonzalez
- Departamento de Quimica Fisica, Universidad De Murcia , Murcia 30003, Spain
| | - Michelle L Coote
- ARC Centre of Excellence for Electromaterials Science, Research School of Chemistry, Australian National University , Canberra, Australian Capital Territory 2601, Australia
| | - Simone Ciampi
- Department of Chemistry, Curtin University , Bentley, Western Australia 6102, Australia
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90
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Wang XW, Zhang JZH, He X. Ab initio Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulation of CO in the Heme Distal Pocket of Myoglobin. CHINESE J CHEM PHYS 2017. [DOI: 10.1063/1674-0068/30/cjcp1709169] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Xian-wei Wang
- College of Science, Zhejiang University of Technology, Hangzhou 310023, China
- College of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- Zhejiang Provincial Collaborative Innovation Center of High-end Laser Manufacturing Equipment, Hangzhou 310014, China
| | - John Z. H. Zhang
- College of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Department of Chemistry, New York University, New York 10003, USA
| | - Xiao He
- College of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
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91
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A novel lignin-based nanofibrous dressing containing arginine for wound-healing applications. Drug Deliv Transl Res 2017; 8:111-122. [DOI: 10.1007/s13346-017-0441-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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92
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Hamm P, Meuwly M, Johnson SL, Beaud P, Staub U. Perspective: THz-driven nuclear dynamics from solids to molecules. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:061601. [PMID: 29308420 PMCID: PMC5741436 DOI: 10.1063/1.4992050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 11/14/2017] [Indexed: 06/07/2023]
Abstract
Recent years have seen dramatic developments in the technology of intense pulsed light sources in the THz frequency range. Since many dipole-active excitations in solids and molecules also lie in this range, there is now a tremendous potential to use these light sources to study linear and nonlinear dynamics in such systems. While several experimental investigations of THz-driven dynamics in solid-state systems have demonstrated a variety of interesting linear and nonlinear phenomena, comparatively few efforts have been made to drive analogous dynamics in molecular systems. In the present Perspective article, we discuss the similarities and differences between THz-driven dynamics in solid-state and molecular systems on both conceptual and practical levels. We also discuss the experimental parameters needed for these types of experiments and thereby provide design criteria for a further development of this new research branch. Finally, we present a few recent examples to illustrate the rich physics that may be learned from nonlinear THz excitations of phonons in solids as well as inter-molecular vibrations in liquid and gas-phase systems.
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Affiliation(s)
- Peter Hamm
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Steve L Johnson
- Institute for Quantum Electronics, ETH Zurich, Zurich, Switzerland
| | - Paul Beaud
- Paul Scherrer Institute, Villigen, Switzerland
| | - Urs Staub
- Paul Scherrer Institute, Villigen, Switzerland
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93
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Chalyavi F, Hogle DG, Tucker MJ. Tyrosine as a Non-perturbing Site-Specific Vibrational Reporter for Protein Dynamics. J Phys Chem B 2017; 121:6380-6389. [DOI: 10.1021/acs.jpcb.7b04999] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Farzaneh Chalyavi
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557, United States
| | - David G. Hogle
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557, United States
| | - Matthew J. Tucker
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557, United States
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94
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Abstract
What happens inside an enzyme's active site to allow slow and difficult chemical reactions to occur so rapidly? This question has occupied biochemists' attention for a long time. Computer models of increasing sophistication have predicted an important role for electrostatic interactions in enzymatic reactions, yet this hypothesis has proved vexingly difficult to test experimentally. Recent experiments utilizing the vibrational Stark effect make it possible to measure the electric field a substrate molecule experiences when bound inside its enzyme's active site. These experiments have provided compelling evidence supporting a major electrostatic contribution to enzymatic catalysis. Here, we review these results and develop a simple model for electrostatic catalysis that enables us to incorporate disparate concepts introduced by many investigators to describe how enzymes work into a more unified framework stressing the importance of electric fields at the active site.
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Affiliation(s)
- Stephen D Fried
- Proteins and Nucleic Acid Chemistry Division, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305;
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95
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Kashid SM, Jin GY, Chakrabarty S, Kim YS, Bagchi S. Two-Dimensional Infrared Spectroscopy Reveals Cosolvent-Composition-Dependent Crossover in Intermolecular Hydrogen-Bond Dynamics. J Phys Chem Lett 2017; 8:1604-1609. [PMID: 28326785 DOI: 10.1021/acs.jpclett.7b00270] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Cosolvents have versatile composition-dependent applications in chemistry and biology. The simultaneous presence of hydrophobic and hydrophilic groups in dimethyl sulfoxide (DMSO), an industrially important amphiphilic cosolvent, when combined with the unique properties of water, plays key roles in the diverse fields of pharmacology, cryoprotection, and cell biology. Moreover, molecules dissolved in aqueous DMSO exhibit an anomalous concentration-dependent nonmonotonic behavior in stability and activity near a critical DMSO mole fraction of 0.15. An experimental identification of the origin of this anomaly can lead to newer chemical and biological applications. We report a direct spectroscopic observation of the anomalous behavior using ultrafast two-dimensional infrared spectroscopy experiments. Our results demonstrate the cosolvent-concentration-dependent nonmonotonicity arises from nonidentical mechanisms in ultrafast hydrogen-bond-exchange dynamics of water above and below the critical cosolvent concentration. Comparison of experimental and theoretical results provides a molecular-level mechanistic understanding: a distinct difference in the stabilization of the solute through dynamic solute-solvent interactions is the key to the anomalous behavior.
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Affiliation(s)
- Somnath M Kashid
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, India
| | - Geun Young Jin
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST) , 50 UNIST-gil, Ulsan 44919, Korea
| | - Suman Chakrabarty
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, India
| | - Yung Sam Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST) , 50 UNIST-gil, Ulsan 44919, Korea
| | - Sayan Bagchi
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, India
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96
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Stevenson P, Tokmakoff A. Ultrafast Fluctuations of High Amplitude Electric Fields in Lipid Membranes. J Am Chem Soc 2017; 139:4743-4752. [DOI: 10.1021/jacs.6b12412] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Paul Stevenson
- Department
of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts
Ave., Cambridge, Massachusetts 02139, United States
- Department
of Chemistry, James Frank Institute, and The Institute
for Biophysical Dynamics, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, United States
| | - Andrei Tokmakoff
- Department
of Chemistry, James Frank Institute, and The Institute
for Biophysical Dynamics, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, United States
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97
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Schneider SH, Kratochvil HT, Zanni MT, Boxer SG. Solvent-Independent Anharmonicity for Carbonyl Oscillators. J Phys Chem B 2017; 121:2331-2338. [PMID: 28225620 DOI: 10.1021/acs.jpcb.7b00537] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The physical origins of vibrational frequency shifts have been extensively studied in order to understand noncovalent intermolecular interactions in the condensed phase. In the case of carbonyls, vibrational solvatochromism, MD simulations, and vibrational Stark spectroscopy suggest that the frequency shifts observed in simple solvents arise predominately from the environment's electric field due to the vibrational Stark effect. This is contrary to many previously invoked descriptions of vibrational frequency shifts, such as bond polarization, whereby the bond's force constant and/or partial nuclear charges are altered due to the environment, often illustrated in terms of favored resonance structures. Here we test these hypotheses using vibrational solvatochromism as measured using 2D IR to assess the solvent dependence of the bond anharmonicity. These results indicate that the carbonyl bond's anharmonicity is independent of solvent as tested using hexanes, DMSO, and D2O and is supported by simulated 2D spectra. In support of the linear vibrational Stark effect, these 2D IR measurements are consistent with the assertion that the Stark tuning rate is unperturbed by the electric field generated by both hydrogen and non-hydrogen bonding environments and further extends the general applicability of carbonyl probes for studying intermolecular interactions.
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Affiliation(s)
- Samuel H Schneider
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
| | - Huong T Kratochvil
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Steven G Boxer
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
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98
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Sorenson SA, Patrow JG, Dawlaty JM. Solvation Reaction Field at the Interface Measured by Vibrational Sum Frequency Generation Spectroscopy. J Am Chem Soc 2017; 139:2369-2378. [DOI: 10.1021/jacs.6b11940] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shayne A. Sorenson
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Joel G. Patrow
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Jahan M. Dawlaty
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
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99
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Adhikary R, Zimmermann J, Romesberg FE. Transparent Window Vibrational Probes for the Characterization of Proteins With High Structural and Temporal Resolution. Chem Rev 2017; 117:1927-1969. [DOI: 10.1021/acs.chemrev.6b00625] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ramkrishna Adhikary
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jörg Zimmermann
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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100
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van Wilderen LJGW, Kern-Michler D, Müller-Werkmeister HM, Bredenbeck J. Correction: Vibrational dynamics and solvatochromism of the label SCN in various solvents and hemoglobin by time dependent IR and 2D-IR spectroscopy. Phys Chem Chem Phys 2017; 19:9676-9678. [PMID: 28349151 DOI: 10.1039/c7cp90063e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Correction for 'Vibrational dynamics and solvatochromism of the label SCN in various solvents and hemoglobin by time dependent IR and 2D-IR spectroscopy' by Luuk J. G. W. van Wilderen et al., Phys. Chem. Chem. Phys., 2014, 16, 19643-19653.
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Affiliation(s)
- Luuk J G W van Wilderen
- Johann Wolfgang Goethe-University, Institute of Biophysics, Max-von-Laue-Str. 1, 60438, Frankfurt am Main, Germany.
| | - Daniela Kern-Michler
- Johann Wolfgang Goethe-University, Institute of Biophysics, Max-von-Laue-Str. 1, 60438, Frankfurt am Main, Germany.
| | - Henrike M Müller-Werkmeister
- Johann Wolfgang Goethe-University, Institute of Biophysics, Max-von-Laue-Str. 1, 60438, Frankfurt am Main, Germany.
| | - Jens Bredenbeck
- Johann Wolfgang Goethe-University, Institute of Biophysics, Max-von-Laue-Str. 1, 60438, Frankfurt am Main, Germany.
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