Structure Of Molecules In Solution Research Articles

Reference interaction site model self-consistent field with constrained spatial electron density approach for nuclear magnetic shielding in solution.

We propose a new hybrid approach combining quantum chemistry and statistical mechanics of liquids for calculating the nuclear magnetic resonance (NMR) chemical shifts of solvated molecules. Based on the reference interaction site model self-consistent field with constrained spatial electron density distribution (RISM-SCF-cSED) method, the electronic structure of molecules in solution is obtained, and the expression for the nuclear magnetic shielding tensor is derived as the second-order derivative of the Helmholtz energy of the solution system. We implemented a method for calculating chemical shifts and applied it to an adenine molecule in water, where hydrogen bonding plays a crucial role in electronic and solvation structures. We also performed the calculations of 17O chemical shifts, which showed remarkable solvent dependence. While converged results could not be sometimes obtained using the conventional method, in the present framework with RISM-SCF-cSED, an adequate representation of electron density is guaranteed, making it possible to obtain an NMR shielding constant stably. This introduction of cSED is key to extending the method's applicability to obtain the chemical shift of various chemical species. The present demonstration illustrates our approach's superiority in terms of numerical robustness and accuracy.

Growth defects of organic crystals: A review

During the growth of organic crystals, crystal defects can be formed. Microscopic defects, which include point, line, and planar defects, appearing as vacancies, growth dislocations, striations, and others, play an important role in the mechanical properties, optical properties, and electrical conductivity of organic crystals. In addition, macroscopic defects, such as fluid inclusions and cavities, may cause toxicity during crystal dehydration and degradation while favorable cavity defects can satisfy certain functions. Herein, this paper summarizes the growth defects of organic crystals from four perspectives; formation mechanism, characterization methods, control methods, and applications. We conclude three kinds of formation mechanism which are related to diffusion of solute molecules, impurities participating in the crystal growth, and structure of solute molecules respectively. Next, the characterization methods are exhibited from the perspectives of microscopy, spectroscopy, and others for different research areas. Then, we offer some control methods of defects which include adjustment of crystallization operation parameters, assistant of ultrasound and additives, irradiation, and ion implantation. As for applications, organic crystal defects have application potential in the fields of pharmacy and materials, for example, nonlinear optical materials, energetic materials, and semiconductor materials. Finally, we put forward the future outlooks on the growth defects of organic crystals.

Three-state conical intersection optimization methods: development and implementation at QM/MM level

Two-state conical intersection optimization methods at both QM and QM/MM levels have been extensively implemented in many commercial and noncommercial packages in the past decade. In contrast, three-state conical intersection optimization methods are less concerned, in particular the QM/MM-based ones. In this work, we have developed a penalty function-based three-state conical intersection optimization approach in the framework of the QM/MM method. We first present the fundamental formulation of this approach, and its algorithm and implementation in our package; then, we have carried out several pilot applications on molecular systems in vacuo and aqueous solution to demonstrate the efficiency of our implemented method. Our current developments enable efficient determination of three-state conical intersection structures of molecules in solution and biological systems, which is at the heart of understanding the photophysical and photochemical mechanisms of large systems at the atomistic level.

Molecular dynamics simulation of diffusion and structure of n-alkane/n-alkanol mixtures at infinite dilution

Infinite dilute diffusion coefficients (D12) of normal alkanes (C1 to C14) in 1-octanol (C8-OH), as well as primary alkanols (C1-OH to C14-OH) in n-octane (C8) have been studied using molecular dynamics simulation in the temperature range from 298 to 374K and at atmosphere pressure. Simulated D12 values for short-chain solute molecules show a good agreement with the experimental ones taken from literature, while for the long-chain solute molecules the overestimation is large. Besides, the structures of solute molecules in above fluid mixtures are investigated by calculating radial distribution functions, radius of gyration, end-to-end distance, and root mean square fluctuation of atomic positions. These results confirm long-chain n-alkanes and n-alkanols molecules are curved and curled up, which we call it flexibility. Moreover, flexibilities for solute molecules (5≤n≤9) are symmetric but for much long-chain solute molecules like n-tetradecane (C14) and 1-tetradecanol (C14-OH) are asymmetric. We believe that strong chain-chain interactions are existed between different long-chain molecules, and it will result in the solute and solvent molecules are intertwisted. The serious overestimation of simulated D12 for long-chain solute molecules can be reasonably explained by the intertwist effect.

Partial Molar Volumes and Partial Molar Isentropic Compressions of Selected Branched Diols at Infinite Dilution in Water at Temperatures T = (278 to 318) K and Atmospheric Pressure

Speed of sound and density data for dilute aqueous solutions of four branched diols derived from propane-1,3-diol (2-methyl-2-propylpropane-1,3-diol, 2,2-diethylpropane-1,3-diol, and 2-ethyl-2-butylpropane-1,3-diol) and 3-methylpentane-1,5-diol were obtained using the Anton Paar DSA 5000 vibrating-tube densimeter and sound analyzer in the temperature range from (278.15 to 318.15) K and at atmospheric pressure. Standard molar isentropic compressions and standard molar volumes were evaluated from the measured data. Present data were combined with those obtained previously for related solutes, and relations to the structures of solute molecules are discussed. The predictions of standard molar volumes based on the group contribution approach were tested and analyzed.

Nuclear Magnetic Resonance Spectroscopyan Evolutionary Approach to Drug Design

Ever since Nuclear Magnetic Resonance (NMR) spectroscopy hit the analytical scene; its capabilities and applications continue to evolve. Originally designed as a way to verify the structure of relatively small compounds, the technology of NMR has exploded and become a valuable means for studying protein structure. NMR has proved to be a valuable tool in pharmaceutical research, as it has entered new arena of drug discovery and structural genomics. NMR can provide information on the three‐dimensional structures of small molecules in solution, high‐molecular‐weight complexes, and the details of enzyme mechanisms that can be used to aid in drug design. In the present scenario, the availability of high magnetic fields; improved software, high resolution probes, and electronics; more versatile pulse programmers; and most importantly the development of 2D, 3D and 4D NMR, have revolutionized the field of drug discovery and development.

Orientation of molecules by magnetic field as a new source of information on their structures

A complex procedure for quantitative allowance for small but significant effects of molecular orientation by strong static magnetic fields was elaborated. A series of high-resolution 1H NMR spectra of 1,2,3-trichloronaphthalene recorded at magnetic field strength varied over a wide range was analyzed in the framework of a unified approach with high accuracy. The spin-spin coupling constants and the dipole-dipole coupling constants for all pairs of 1H nuclei and the anisotropy and rhombicity parameters of the magnetic susceptibility tensor of the molecule were determined. Ab initio CSGT/RHF quantum chemical calculations of this property using a wide range of conventional diffuse and polarization basis set functions were carried out. Augmentation of the basis set with polarization functions affects the values of the calculated parameters to a lesser extent compared to augmentation with diffuse functions. The results of calculations using the 6-311G(df) and 6-311++G(df) basis sets are in good agreement with the experimental values of the magnetic susceptibility anisotropy for 1,2,3-trichloronaphthalene. The advantages of the method proposed and specific features of the effects of orientation by magnetic field as a new source of information on the structure of molecules in solution are discussed.

Calculation of the Weights of Resonance Structures of Molecules in Solution

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCalculation of the Weights of Resonance Structures of Molecules in SolutionRamon M. Parrondo, Padeleimon Karafiloglou, Rafael R. Pappalardo, and Enrique Sanchez MarcosCite this: J. Phys. Chem. 1995, 99, 17, 6461–6467Publication Date (Print):April 1, 1995Publication History Published online1 May 2002Published inissue 1 April 1995https://doi.org/10.1021/j100017a027RIGHTS & PERMISSIONSArticle Views150Altmetric-Citations32LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (841 KB) Get e-Alerts

Determination of the Relative Configuration by Distance Geometry Calculations with Proton–Proton Distances from NOESY Spectra

The determination of the structures of molecules in solution is a challenge. Now the relative configuration, and to a certain extent, the preferred conformation of a flexible chiral compound can be determined by calculations employing data obtained from NMR cross‐relaxation experiments. Force field parameters and conformational preferences need not be specified.

Multicavity reaction field method for the solvent effect description in flexible molecular systems

A multicavity reaction field method is proposed for the quantum-chemical calculation of medium dielectric effects on the electronic structure of molecules in solution. This method is based on the gauge-independent partitioning of the molecule total reaction field in the polarizable medium into the partial reaction fields which belong to the rotationally or inversionally flexible groups in the molecule. The results of the calculations of the solvation free energies in aqueous solution of molecules containing such groups are presented and compared with the results obtained using the single spherical cavity self-consistent reaction field (SCRF) method

Processing of two-dimensional nuclear magnetic resonance time domain signals

2-D NMR is the method of choice for determining the structure of molecules in solution. This technique yields a 2-D time domain signal comprising many decaying 2-D sinusoids. Accurate estimation of the parameters of these sinusoids is of paramount importance. Three alternative 2-D signal processing methods are considered, one of which is new.

Cover Picture (Angew. Chem. Int. Ed. Engl. 4/1988)

Angewandte Chemie International Edition in EnglishVolume 27, Issue 4 Cover PictureFree Access Cover Picture (Angew. Chem. Int. Ed. Engl. 4/1988) First published: April 1988 https://doi.org/10.1002/anie.198804471Citations: 1AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Abstract The cover shows part of a homonuclear two-dimensional NMR spectrum (E. COSY) of the cyclic hexapeptide cyclo(-Pro-Phe2-D-Pro-Phe2-), which exists in two slowly interconverting conformations in CDCl3. In order to show clearly the resolution now possible, a single cross peak is enlarged with a magnifying glass. These and similar spectra allow the spectroscopic parameters (e.g., coupling constants J and NOE effects) of even complex molecules to be determined with great accuracy and thus make it possible to elucidate the structures of molecules in solution. The article by H. Kessler, M. Gehrke, and C. Griesinger on page 490ff. describes how such spectra are recorded and discusses the various techniques available. The basic concepts required for their proper application and further development are dealt with in detail. Citing Literature Volume27, Issue4April 1988 RelatedInformation

Method of modeling protein structure by the two-dimensional nuclear magnetic resonance spectroscopy data; application to the proteinase inhibitor BUSI IIA from bull seminal plasma.

A new approach is suggested to model the spatial structure of protein molecules in solution based on combined use of the methods of theoretical conformational analysis and NMR spectroscopy data. At the first stage, special means are used to convert d connectivity information into the most probable values of dihedral angles. This allows search for possible spatial structures in the limited regions of the conformational space at further stages using the methods of the theoretical conformational analysis. The suggested approach was verified in reconstructing the spatial backbone structure of the fragment 17-57 of the proteinase inhibitor BUSI IIA from the bull seminal plasma. The structural model parameters are compared with the corresponding characteristics obtained from the X-ray analysis data for the homologic proteinase inhibitor from the Japanese quail ovomucoid. The suggested approach is shown to correctly reproduce both the general molecule topology and the conformations of individual amino acid residues.

Laser-Based Instrument for Electric Dichroism Spectroscopy of Small Molecules

While the chemical information provided by electric dichroism spectroscopy can be useful for studying the conformation and electronic structures of molecules in solution, the dichroism signals produced at fields approaching the dielectric strength of organic solvents are extremely small and difficult to detect. A double-beam, laser-based instrument for electric dichroism measurements is described which allows detection of dichroism signals corresponding to changes in absorbance of less than 10−6 with only a 1.2-kV high-voltage source.

ChemInform Abstract: SOLID‐STATE NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY OF MINERALS

Nuclear magnetic resonance (NMR) spectroscopy has been a useful tool for examining the structure of molecules in solution since the 1950s. It has only been since the late 1970s and early 1980s, though, that developments in very high field superconducting magnets and magic-angle sample-spinning (MASS) have made NMR routinely useful for examining the structure of solids. In this paper, we briefly review the theory of MASS NMR spectroscopy and some of the recent experimental results for minerals. N MR spectroscopy examines the local structural environment of atoms, to at most the third and fourth nearest neighbors. For crystalline silicates, silicon-29 and aluminum-27 MASS NMR have already proven useful in examining the validity of the aluminum avoidance principle and the extent of Al(4)/Si order/disorder, in determining the extent of polymerization, in determining the number of crystallographically distinct silicon sites present, in estimating bond strength sums and Si-O-(Si, AI) bond angles, and in detecting the presence of Al(4) and Al(6) and estimating Al(4)/Si and Al(6)/Al(4) ratios. As the NMR behavior of more nuclides (certainly including boron-H, nitrogen-IS, oxygen-17, fluorine-19, sodium-23, magnesium-25, and phosphorus-31) becomes better understood, we feel that this method will become a powerful tool for examining the local structural environment of a wide variety of species in a broad range of

SOLID-STATE NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY OF MINERALS

Nuclear magnetic resonance (NMR) spectroscopy has been a useful tool for examining the structure of molecules in solution since the 1950s. It has only been since the late 1970s and early 1980s, though, that developments in very high field superconducting magnets and magic-angle sample-spinning (MASS) have made NMR routinely useful for examining the structure of solids. In this paper, we briefly review the theory of MASS NMR spectroscopy and some of the recent experimental results for minerals. N MR spectroscopy examines the local structural environment of atoms, to at most the third and fourth nearest neighbors. For crystalline silicates, silicon-29 and aluminum-27 MASS NMR have already proven useful in examining the validity of the aluminum avoidance principle and the extent of Al(4)/Si order/disorder, in determining the extent of polymerization, in determining the number of crystallographically distinct silicon sites present, in estimating bond strength sums and Si-O-(Si, AI) bond angles, and in detecting the presence of Al(4) and Al(6) and estimating Al(4)/Si and Al(6)/Al(4) ratios. As the NMR behavior of more nuclides (certainly including boron-H, nitrogen-IS, oxygen-17, fluorine-19, sodium-23, magnesium-25, and phosphorus-31) becomes better understood, we feel that this method will become a powerful tool for examining the local structural environment of a wide variety of species in a broad range of

Comparison of linear and branched non-polar chemically bonded stationary phases in high-performance liquid chromatography

Non-polar chemically bonded stationary phases having branched or unbranched structure were synthesized, and their specific surface areas, pore size distributions and carbon contents were estimated. Based on these data the number of silane molecules bonded to unit surface area of the original silica was calculated for each phase. Retentions of selected solute groups were measured in four mobile phases of various elution strength, prepared from methanol-water mixtures at various ratios. Dependences of k′ on the length of the “bristle”, on the size and structure of solute molecule and the elution strength of mobile phase were plotted. Results are compared for pairs of phases having different structures but either the same total number of carbon atoms in the bonded molecule or the same length of the “bristle”.

Structure of molecules in solution

Structure of molecules in solution