Molecular Force Field Calculations Research Articles

Regularized ab initio molecular force fields for key biological molecules: melatonin and pyridoxal-5′-phosphate methylamine Shiff base (Vitamin B6)

The main mathematical results on the data processing in vibrational spectroscopy are presented. The approaches and algorithms proposed for molecular force field calculations have been constructed on a base of regularizing methods for solving nonlinear ill-posed problems and have been implemented in the software package SPECTRUM. These algorithms were used for constructing the regularized ab initio force fields of important biological molecules including the melatonin and Vitamin B6 derivatives.

Geometry and Stability of Small Gold Cluster Ions by Graph Theory and Hückel model

Structure and stability of the gold cluster ions of which skeleton are synthesized as a complex were analyzed using the Hückel method based on graph theory. Hückel Energy (HE) and Topological Resonance Energy (TRE) were determined for neutral, positive ion, and negative ion clusters, where all the isomers of the gold cluster up to octamer were considered. Since some graphically designed isomers include bonds that cannot be realized in three- dimensional space, the screening was carried out by a molecular force field calculation with LAMMPS (lammps.sandia.gov/.). Among the isomers thus obtained, both HE and TRE were most stable when the tetramer was Au4 2 + with a tetrahedral structure, and with the hexamer, Au6 2+ with two tetrahedrons sharing one side. The complexes with these structures have actually been synthesized. On the other hand, the synthesis example of the most stable cluster for octamer Au8 has not been reported.

Nc-AFM Imaging and Manipulation of a Triphenylene Derivative on KBr(001)

The adsorption of single hexamethoxyltriphenylene molecules on KBr(001) at low temperature (T < 10 K) was studied by low-temperature (T = 5 K) noncontact atomic force microscopy in ultrahigh vacuum. Images of the frequency shift, measured at constant height, show intramolecular features that are interpreted on the basis of molecular force-field calculations. The main conclusion is that the experimental contrast originates from the electrostatic interaction between a negatively terminated ionic tip and the atomic charges of the molecule. The main trends of the experimental observations of lateral manipulations could also be reproduced by the same method, giving some insight into the manipulation mechanisms. In particular, it is shown that the strong interaction of the oxygen atoms of the molecule with positive ions of the tip plays a major role by facilitating the partial lifting of the molecule from the substrate during the intermediate stages of these manipulation processes.

X-ray structure and conformational study of tris(2-(dimethylamino)phenyl)methanol salt derivatives: Roles of anions and hydrogen bond

The tris(2-(dimethylamino)phenyl)methanol, a tertiary alcohol, can form stable salts with acids in water. X-ray crystallographic analysis reveals that the organic cation of the tetrachlorocobaltate salt, [(2-(Me)2N+H–C6H4)3C–O−]2+, was constructed by three zwitterionic hydrogen bonds which share a trifurcated oxygen anion center. The influences of the anions on the hydrogen-bond structure of the organic cation were studied by using 1H NMR spectroscopy, as well as Merck Molecular Force Field (MMFF94) calculation and analysis.

Atomistic modelling of CVD synthesis of carbon nanotubes and graphene

We discuss the synthesis of carbon nanotubes (CNTs) and graphene by catalytic chemical vapour deposition (CCVD) and plasma-enhanced CVD (PECVD), summarising the state-of-the-art understanding of mechanisms controlling their growth rate, chiral angle, number of layers (walls), diameter, length and quality (defects), before presenting a new model for 2D nucleation of a graphene sheet from amorphous carbon on a nickel surface. Although many groups have modelled this process using a variety of techniques, we ask whether there are any complementary ideas emerging from the different proposed growth mechanisms, and whether different modelling techniques can give the same answers for a given mechanism. Subsequently, by comparing the results of tight-binding, semi-empirical molecular orbital theory and reactive bond order force field calculations, we demonstrate that graphene on crystalline Ni(111) is thermodynamically stable with respect to the corresponding amorphous metal and carbon structures. Finally, we show in principle how a complementary heterogeneous nucleation step may play a key role in the transformation from amorphous carbon to graphene on the metal surface. We conclude that achieving the conditions under which this complementary crystallisation process can occur may be a promising method to gain better control over the growth processes of both graphene from flat metal surfaces and CNTs from catalyst nanoparticles.

Acid and Alkali Effects on the Decomposition of HMX Molecule: A Computational Study

The stored and wasted explosives are usually in an acid or alkali environment, leading to the importance of exploring the acid and alkali effects on the decomposition mechanism of explosives. The acid and alkali effects on the decomposition of HMX molecule in gaseous state and in aqueous solution at 298 K are studied using quantum chemistry and molecular force field calculations. The results show that both H(+) and OH(-) make the decomposition in gaseous state energetically favorable. However, the effect of H(+) is much different from that of OH(-) in aqueous solution: OH(-) can accelerate the decomposition but H(+) cannot. The difference is mainly caused by the large aqueous solvation energy difference between H(+) and OH(-). The results confirm that the dissociation of HMX is energetically favored only in the base solutions, in good agreement with previous HMX base hydrolysis experimental observations. The different acid and alkali effects on the HMX decomposition are dominated by the large aqueous solvation energy difference between H(+) and OH(-).

Conformation and Dynamics of 18-Membered Hexathiametacyclophanes: A Two Step Racemization as Studied by Deuterium NMR in Chiral Lyotropic Liquid Crystals

The conformation and interconversion dynamics of two derivatives of the 18-membered hexathia metacyclophane 1 and 2 were studied by (1)H NMR spectroscopy in isotropic solvents and by (2)H NMR in chiral liquid crystalline (CLC) solutions, as well as by molecular structure computations. For the analysis of the dynamic effects, we made use of the concepts of "average symmetry" and "isodynamic groups", introduced by Altmann (Altmann, Proc. R. Soc.1967, 184, A298). Compound 1, which is unsubstituted in the inner aromatic site, has, according to the NMR and molecular force field calculations, a boat shaped ground conformation with C(2) symmetry. It is highly flexible and in the NMR spectrum exhibits two successive dynamic processes. There is a low temperature (170-210 K, E(a) = 10.5 kcal/mol) alternate "wing flipping", which corresponds to interchange between pairs of enantiomers and results, in the fast exchange limit, in an average prochiral molecule with C(2v) symmetry. This process is followed, at higher temperatures (290-320 K, E(a) = 28.5 kcal/mol), by an umbrella flipping type inversion with an average structure of D(2h) symmetry. This second process involves averaging of effective enantiotopic into homotopic sites and can only be studied in chiral solvents. The origin of the chiral discrimination and of their stepwise averaging is discussed. Compound 2, which is substituted with methoxy groups at the inner sites of the benzene rings, is much less flexible and exhibits dynamic effects in the NMR spectrum only at temperatures above 370 K. We were able to study the kinetic parameters of this process in isotropic solvents (E(a) = 21.4 kcal/mol). As for 1, the detailed mechanism of this process can in principle be established using dynamic NMR in CLC; however, experimental limitation precluded us from doing so. Possible alternatives and their effect on the 1D and 2D exchange spectra in CLC are discussed in a concluding section.

Interlayer modification of a layered H-octosilicate (H-RUB-18) with methanol: formation of a highly ordered organosilicate nanohybrid

Highly ordered silicate–organic nanohybrids were prepared by the modification of interlayer silanol groups of a layered polysilicic acid (H-octosilicate, H-RUB-18) with methanol. The grafting reaction was performed in a Teflon-lined stainless steel autoclave at 120 °C for various reaction periods. The grafting of methoxy groups onto the interlayer surface was evidenced by the downfield chemical shifts of the methyl groups in the solid state 13C NMR spectra and the exothermic DTA peaks with substantial weight losses due to combustion of methyl groups. The degree of modification with the methoxy groups was variable in the range between 0.42 and 0.95, depending on the reaction time. The retention of the layered silicate structure was proved by XRD and 29Si HD/MAS NMR. The structure was also analyzed by molecular mechanics force field calculation and Rietveld analysis, indicating the expansion of the silicate plane composed of the 54 cage with six-membered rings in the structure. This small structural distortion, caused by repulsion between the grafted methoxy groups, resulted in transformation of the crystal system from tetragonal to monoclinic. Hydrogen molecules were sorbed into the grafted products.

A procedure for computing accurate ab initio quartic force fields: Application to HO2+ and H2O

A procedure for the calculation of molecular quartic force fields (QFFs) is proposed and investigated. The goal is to generate highly accurate ab initio QFFs that include many of the so-called "small" effects that are necessary to achieve high accuracy. The small effects investigated in the present study include correlation of the core electrons (core correlation), extrapolation to the one-particle basis set limit, correction for scalar relativistic contributions, correction for higher-order correlation effects, and inclusion of diffuse functions in the one-particle basis set. The procedure is flexible enough to allow for some effects to be computed directly, while others may be added as corrections. A single grid of points is used and is centered about an initial reference geometry that is designed to be as close as possible to the final ab initio equilibrium structure (with all effects included). It is shown that the least-squares fit of the QFF is not compromised by the added corrections, and the balance between elimination of contamination from higher-order force constants while retaining energy differences large enough to yield meaningful quartic force constants is essentially unchanged from the standard procedures we have used for many years. The initial QFF determined from the least-squares fit is transformed to the exact minimum in order to eliminate gradient terms and allow for the use of second-order perturbation theory for evaluation of spectroscopic constants. It is shown that this step has essentially no effect on the quality of the QFF largely because the initial reference structure is, by design, very close to the final ab initio equilibrium structure. The procedure is used to compute an accurate, purely ab initio QFF for the H(2)O molecule, which is used as a benchmark test case. The procedure is then applied to the ground and first excited electronic states of the HO(2) (+) molecular cation. Fundamental vibrational frequencies and spectroscopic constants from these highly accurate QFFs are compared and contrasted with previous experiment and theory. It is concluded that the spectroscopic constants determined for the X(3)A(") and A(1)A(') states of HO(2) (+) are the most accurately available.

Hindered rotation of a copper phthalocyanine molecule onC60: Experiments and molecular mechanics calculations

If copper phthalocyanine (CuPc) molecules are deposited on a Au(111) surface covered with a monolayer of ${\mathrm{C}}_{60}$, the molecules are found to adsorb individually onto the close-packed layer of ${\mathrm{C}}_{60}$. As the adsorption site of the CuPc is not symmetric with respect to the underlying ${\mathrm{C}}_{60}$ layer, the CuPc molecule has six equivalent orientations according to the hexagonal packing of the ${\mathrm{C}}_{60}$. Scanning tunneling microscopy (STM) measurements reveal that at room temperature, the molecules may hop between these adsorption sites due to thermal activation and therefore appear as a ring with six maxima. This paper reviews the STM measurements carried out by St\"ohr et al. in the light of molecular force field calculations. The potential energy for an individual CuPc molecule has been calculated as a function of the lateral position on the ${\mathrm{C}}_{60}$ layer based on the van der Waals interactions between molecules. For each position, the minimal energy has been evaluated, taking the vertical and the rotational degrees of freedom into account. A map of the potential energy not only reveals the preferred adsorption sites, it also indicates several favorable paths between these minima. The calculations consistently explain the experimental observations at low and ambient temperature.

An Information Theoretic Approach to Macromolecular Modeling: II. Force Fields

In this article, we explore the information content of molecular force-field calculations. We make use of exhaustive lattice models of molecular conformations and reduced alphabet sequences to determine the relative resolving power of pairwise interaction-based force fields. We find that sequence-specific interactions that operate over longer distances offer greater amounts of information than nearest-neighbor or non-sequence-specific interactions. In a companion article in this issue, we explored the information content of sequence alignment procedures and the calculation of gap penalties. Both articles have implications for protein and nucleic-acid computations.

Aspirin blocks binding of photosensitizer SnET2 into human serum albumin: Implications for photodynamic therapy

Tin etiopurpurin dichloride (SnET2) is one of the photosensitizers under investigation to be used in photodynamic therapy of prostate cancer. The drug is delivered intravenously, transported in vivo by liposomes and plasma proteins and localized within the prostate. SnET2 exists in two tautomeric forms (I - closed ring, II - open ring) with I converting spontaneously into the more energetically stable form II at physiological pH. Up to approximately 50% of the drug can be carried by serum albumin, although this association can increase photo-bleaching and diminish the drug efficiency. Molecular modeling and force field calculations indicate that Sudlow Site I in human serum albumin (HSA) is the most probable binding site for both forms of SnET2, with the porphyrin moiety nestling between domains IIA and IB, and the esterolytic side group oriented toward domain IIIA of HSA. Other drugs, including aspirin, bind to the same part of HSA. SnET2 does not bind to HSA when pre-incubated with aspirin, which confirms that its place of binding to this protein must be located near Lys199. This observation could be exploited to improve photo-efficiency of SnET2 by finding drugs that could compete with the photosensitizer for binding into Sudlow Site I of HSA.

Assessment of various density functionals and basis sets for the calculation of molecular anharmonic force fields

AbstractIn a previous contribution, we established the suitability of density functional theory (DFT) for the calculation of molecular anharmonic force fields. In the present work, we have assessed a wide variety of basis sets and exchange‐correlation functionals for harmonic and fundamental frequencies, equilibrium, and ground‐state rotational constants, and thermodynamic functions beyond the rigid rotor‐harmonic oscillator (RRHO) approximation. The fairly good performance of double‐zeta plus polarization basis sets for frequencies results from an error compensation between basis set incompleteness and the intrinsic error of exchange‐correlation functionals. Triple‐zeta plus polarization basis sets are recommended, with an additional high‐exponent d function on second‐row atoms. All conventional hybrid generalized gradient approximation (GGA) functionals perform about equally well: high‐exchange hybrid GGA and meta‐GGA functionals designed for kinetics yield poor results, with the exception of of the very recently developed BMK functional, which takes a middle position along with the HCTH/407 (second‐generation GGA) and TPSS (meta‐GGA) functionals. Second‐order Møller–Plesset perturbation theory (MP2) performs similarly to these functionals but is inferior to hybrid GGAs such as B3LYP and B97‐1. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005

Adsorption of (S)-Histidine on Cu(110) and Oxygen-Covered Cu(110), a Combined Fourier Transform Reflection Absorption Infrared Spectroscopy and Force Field Calculation Study

Adsorption of (S)-histidine on Cu(110), and Cu(110) modified by adsorbed oxygen, has been studied by reflection absorption infrared spectroscopy (RAIRS). The molecular form and the orientation of the histidine molecule were deduced from experimental RAIRS data; moreover, vibrational spectra were simulated with a molecular mechanics force field (MMFF) calculation to address vibrational modes and the geometry of the adsorbate. The molecule preferentially binds to the surface in its HHis- molecular form. On the metallic Cu(110) surface, the adsorption occurs via the carboxylate group (COO-), with the two oxygen atoms equidistant from the surface, and via the dehydrogenated nitrogen of the imidazole group; the latter adopts an upright position with respect to the copper surface. The amino group (NH2) is likely to be maintained close to the surface, thus facilitating the interaction with the metal. Preadsorption of oxygen (θ ≈ 0.3) on the copper surface induces minor changes in the molecular orientation: the ring tends to be less upright than in the absence of oxygen; the ring now interacts via its NH group as deduced from RAIRS and MMFF calculations. The molecule does not reorient with increasing oxygen coverage (θ ≈ 0.6), and no surface blocking was observed upon oxygen adsorption; both the orientation and the amount of histidine only slightly vary when the oxygen coverage is increased.

Dipolar Couplings in Multiple Alignments Suggest α Helical Motion in Ubiquitin

Recently, residual dipolar couplings (RDCs) of backbone N-HN vectors measured in 11 different alignment media were analyzed with respect to structure and dynamics in a model-free way in terms of generalized order parameters and motional anisotropies. The anisotropies in the central alpha-helix were found to be strikingly uniformly distributed. In this communication, these parameters are further interpreted in terms of physically feasible cooperative reorientational motion of the helix with respect to the core of the protein. The RDCs are compatible with a model in which all N-HN vectors of the alpha-helix of ubiquitin exhibit correlated anisotropic excursions with amplitudes of 21 degrees and 12 degrees along two orthogonal directions x' ' and y' ' of a coordinate system C' ', if z' ' represents the helix axis. Such motion contradicts neither NOE data nor molecular force-field calculations.

Structure of Alkanethiolate Monolayers on Cu(100): Self-Assembly on the Four-Fold-Symmetry Surface

We have studied the structure and growth process of hexanethiolate self-assembled monolayers (SAMs) on Cu(100) by means of scanning tunneling microscopy (STM) and X-ray absorption fine structure (XAFS) spectroscopy. At saturated coverage, the thiolates are assembled into a c(2 × 6) structure with zigzag chains along the close-packed Cu rows. The sulfur atom of the thiolate occupies the 4-fold hollow site of the unreconstructed Cu(100) surface with a nearest-neighbor S−S distance of 3.6 Å. Such sulfur adsorption results in a large lattice mismatch between the S/Cu layer and the alkyl chain layer, since the interchain distance of the alkyl group is ca. 4.5 Å. However, it is reconciled by the internal degree of freedom for the S−C bond which bridges the two layers, as is confirmed by the geometrical optimization based on molecular force-field calculations. The SAM film formation is well-described by a two-step process; in the first step, a full-coverage monolayer is rapidly formed, which is characterized by a highly oriented but two-dimensionally disordered structure, followed by a much slower evolution to the c(2 × 6) structure with surface diffusion of the thiolate.

A first comparison of solid state and solution structure of a complex between lanthanum nitrate and 1,9-diaza-18-crown-6.

[figure: see text] The structure of the complex between lanthanum(III)nitrate and 1,9-diaza-18-crown-6 is analyzed with three independent methods. The conformation observed by analysis of vicinal NMR coupling constants in solution agrees with both the one found by a single crystal X-ray study and with simulations by molecular orbital and force field calculations. In the acetonitrile solution, the NMR data show a bent crown conformation with nearly C2v symmetry, which is stable on the NMR time scale.

Photochemistry of valerophenone in solid solutions

Photoreactivity of valerophenone was investigated in frozen solid solvents: benzene, cyclohexane, t-butanol, hexadecane, and water. Different product and mass distributions were followed during the course of the photoreaction. It was evidenced that a portion of ketone molecules is almost unreactive in the solid state due to physical restraints of the solid solvent cavity. Free rotation along the C–C bonds becomes difficult inside the cavity and it is probable that larger conformational changes are totally restricted. It was shown that a fraction of molecules having the favorable conformation for hydrogen abstraction reacts with the same photochemical efficiency no matter what solvent was used. The elimination/cyclization ratio of the Norrish Type II reaction was studied as a function of temperature. Variation of the ratios, characteristic for each solvent, diminished with decreasing temperature what has been rationalized in terms of the effective reaction cavity. The semi-empirical PM3 method and molecular mechanics MM3 force field calculations were performed to evaluate stabilities of the ground state valerophenone conformations.

Synthesis of Lysine-Core Dendrimer Containing Long Pyrrole-Terminated Alkylene Derivative.

A new functional pyrrole-terminated lysine core-dendrimer (G3-R) in which the core part and the surface part were hydrophilic and lipophilic, respectively, was synthesized by condensing an amine-terminated third-generation lysine dendrimer with N-{{10-{4-[4-(12-carboxyl)dodecylenecarbonyloxy]biphenyleneoxy}decyl}}pyrrole (C12B10P). Structure analysis by 1H and 13C one- and two-dimensional NMR spectroscopy and MALDI-TOF mass spectrometry demonstrated that the condensation gave a fully substituted G3-R with molecular weight of 5926. Phase transitions were determined by DSC and optical polarizing microscope measurements. However, no mesomorphic textures were observed. Molecular force field calculation by use of a Cache3.9 program showed that each C12B10P terminal group points outward three-dimensionally. Pyrrole moiety on the surface of the G3-R might be useful for surface conducting applications.

Conformational analysis of crown ether analogs in solution: cis‐cyclohexano‐8‐crown‐3 as studied via low‐temperature 13C and 1H NMR spectroscopy and molecular mechanics calculations

Two conformations of the cis-cyclohexano-8-crown-3 molecule were detected at 185 K. From relative 13C NMR peak area measurements, the conformation with the O— CH2— O unit equatorial was found to be favoured by 4.4 ± 0.4 kJ mol−1. In the spectrum of the minor conformer at low temperature, a 9.6 ppm 13C chemical shift difference is present between the two methine carbons. Transannular 1,4 H–H interactions are deemed to be partly responsible for this effect. Merck Molecular Force Field (MMFF) calculations indicate a preference of ca 1.8 kJ mol−1 for the most populated conformation. A boat–chair conformation is present in the 1,3,6-trioxocane ring of the major conformer whereas a twist boat–chair is preferred in the minor form. Two other conformations with populations of ≥ 1% were identified. Copyright © 1999 John Wiley & Sons, Ltd.