Silicon,germanium, tin and lead analogues of acetylenes

Recent experimental results which have described the characterization of the first, stable heavier group 14 element analogues of acetylenes are outlined. It is shown that the use of large terphenyl substituents allows the isolation of transition metal-heavier group 14 element complexes that can achieve essential triple bonding by a three-fold orbital interaction between the transition metal and group 14 moiety. On the other hand the alkyne analogues RMMR (R = Ge, Sn or Pb) display increasing distortions from linearity to trans-bent geometry due to the accumulation of non-bonding electron density at the group 14 element. The non-bonding electron density comes at the expense of electron density in the bonding region between the group 14 elements. Accordingly the bond orders are decreased to values that are near double for the germanium and tin derivatives and single for the lead compound.     

Why do the heavy-atom analogues of acetylene E2H2 (E = Si-Pb) exhibit unusual structures?

DFT calculations at BP86/QZ4P have been carried out for different structures of E(2)H(2) (E = C, Si, Ge, Sn, Pb) with the goal to explain the unusual equilibrium geometries of the heavier group 14 homologues where E = Si-Pb. The global energy minima of the latter molecules have a nonplanar doubly bridged structure A followed by the singly bridged planar form B, the vinylidene-type structure C, and the trans-bent isomer D1. The energetically high-lying trans-bent structure D2 possessing an electron sextet at E and the linear form HEEH, which are not minima on the PES, have also been studied. The unusual structures of E(2)H(2) (E = Si-Pb) are explained with the interactions between the EH moieties in the (X(2)Pi) electronic ground state which differ from C(2)H(2), which is bound through interactions between CH in the a(4)Sigma(-) excited state. Bonding between two (X(2)Pi) fragments of the heavier EH hydrides is favored over the bonding in the a(4)Sigma(-) excited state because the X(2)Pi --> a(4)Sigma(-) excitation energy of EH (E = Si-Pb) is significantly higher than for CH. The doubly bridged structure A of E(2)H(2) has three bonding orbital contributions: one sigma bond and two E-H donor-acceptor bonds. The singly bridged isomer B also has three bonding orbital contributions: one pi bond, one E-H donor-acceptor bond, and one lone-pair donor-acceptor bond. The trans-bent form D1 has one pi bond and two lone-pair donor-acceptor bonds, while D2 has only one sigma bond. The strength of the stabilizing orbital contributions has been estimated with an energy decomposition analysis, which also gives the bonding contributions of the quasi-classical electrostatic interactions.     

4-Methylpseudoproline derived from α-methylserine - synthesis and conformational studies

This paper presents the synthesis and solution conformational studies of the tripeptides Fmoc-Ala-(R)-(αMe)Ser(Ψ(H,H)Pro)-Ala-OBu(t) (6a) and Fmoc-Ala-(S)-(αMe)Ser(Ψ(H,H)Pro)-Ala-OBu(t) (6b). Additionally, the X-ray structure of 6a is given. NMR analysis corroborated by theoretical calculations (XPLOR) shows that in both peptides the amide bond between pseudoproline and the preceding amino acid is in the trans conformation. The same amide bond geometry was observed in the crystal state of 6a. The latter is additionally influenced by the presence of two symmetrically independent molecules in an asymmetric unit. Both molecules adopt a conformation which resembles β-turn type II, stabilized by hydrogen bonding. The conformational preferences and prolyl cis-trans isomerization of Ac-(αMe)Ser(Ψ(H,H)Pro)-NHMe (7) were explored at the IEFPCM/B3LYP/6-31+G(d) level of theory in vacuum, water and chloroform. It has been shown that the trans isomer predominates in water solutions and the cis isomer is preferred in chloroform. The conformation of 7 is down-puckered independently of the geometry of the amide bonds, with lower puckering in the transition state of the cis-trans isomerization.     

Single quintuple bond [PhCrCrPh] molecule as a possible molecular switch

The electronic transport properties of a single quintuple bond [PhCrCrPh] molecule sandwiched between two Au(111) surfaces with the trans-bent and linear configurations are studied by a fully self-consistent nonequilibrium Green's function method combined with density functional theory. The calculated transmission spectra of two chemical isomers are remarkably distinctive. Theoretical results suggest that the current through the trans-bent configuration is significantly larger than the corresponding linear one. The predicted on-off ratio of currents ranging from around 50 to 200 in the applied bias window [-1.5 V, 1.5 V] suggests that multiple bond compounds have attractive potential in molecular switch technology.     

Biphenyl: A stress tensor and vector‐based perspective explored within the quantum theory of atoms in molecules

We use quantum theory of atoms in molecules (QTAIM) and the stress tensor topological approaches to explain the effects of the torsion φ of the C‐C bond linking the two phenyl rings of the biphenyl molecule on a bond‐by‐bond basis using both a scalar and vector‐based analysis. Using the total local energy density H( r _b), we show the favorable conditions for the formation of the controversial H–H bonding interactions for a planar biphenyl geometry. This bond‐by‐bond QTAIM analysis is found to be agreement with an earlier alternative QTAIM atom‐by‐atom approach that indicated that the H–H bonding interaction provided a locally stabilizing effect that is overwhelmed by the destabilizing role of the C‐C bond. This leads to a global destabilization of the planar biphenyl conformation compared with the twisted global minimum. In addition, the H( r _b) analysis showed that only the central torsional C‐C bond indicated a minimum for a torsion φ value coinciding with that of the conventional global energy minimum. The H–H bonding interactions are found to be topologically unstable for any torsion of the central C‐C bond away from the planar biphenyl geometry. Conversely, we demonstrate that for 0.0° < φ < 39.95° there is a resultant increase in the topological stability of the C nuclei comprising the central torsional C‐C bond. Evidence is found of the effect of the H–H bonding interactions on the torsion φ of the central C‐C bond of the biphenyl molecule in the form of the QTAIM response β of the total electronic charge density ρ( r _b). Using a vector‐based treatment of QTAIM we confirm the presence of the sharing of chemical character between adjacent bonds. In addition, we present a QTAIM interpretation of hyperconjugation and conjugation effects, the former was quantified as larger in agreement with molecular orbital (MO) theory. The stress tensor and the QTAIM H atomic basin path set areas are independently found to be new tools relevant for the incommensurate gas to solid phase transition occurring in biphenyl for a value of the torsion reaction coordinate φ ≈ 5°. © 2015 Wiley Periodicals, Inc.     

The molecular and crystal structure of tert-butyl Nalpha-tert-butoxycarbonyl-L-(S-trityl)cysteinate and the conformation-stabilizing function of weak intermolecular bonding

The title compound, C31H37NO4S [systematic name: (R)-tert-butyl-2-[(tert-butoxycarbonyl)amino]-3-(tritylsulfanyl)propanoate] is an L-cysteine derivative with three functions: NH2, COOH and SH, blocked by protecting groups tert-butoxycarbonyl, tert-butyl and trityl, respectively. The main chain of the molecule adopts the extended, nearly all-trans C5 conformation with the intramolecular N-H...O=C hydrogen bond. The urethane group is not involved in any intermolecular hydrogen bonding. Only weak intermolecular hydrogen bonds and hydrophobic contacts are observed in the crystal structure. These are C-H...O hydrogen bonds and CH/pi interactions with donor...acceptor distances, C...O ca. 3.5 A and C...C ca. 3.7 A, respectively. The first type of interaction links phenyl H-atoms and carbonyl groups. The second type of interaction is formed between a methyl group of the tert-butyl fragment and a trityl phenyl ring. The resulting molecular conformation in the crystal is very close to an ab initio minimum energy conformer of the isolated molecule. The extended C5 conformation of the main peptide chain is the same and there is slight discrepancy in the disposition of trityl phenyl rings. Their small dislocation creates the possibility of forming the entire network above of extensive, specific, weak intermolecular interactions; these constrain the molecule and permit it to retain the minimum energy C5 conformation of its main chain in the solid state. In contrast, in n-hexane solution, where such specific interactions cannot occur, only a small population of the molecules adopts the extended C5 conformation.     

Structures and electron affinities of the di-arsenic fluorides As2Fn/As2Fn- (n=1-8)

Developments in the preparation of new materials for microelectronics are focusing new attention on molecular systems incorporating several arsenic atoms. A systematic investigation of the As2Fn/As2Fn- systems was carried out using Density Functional Theory methods and a DZP++ quality basis set. Global and low-lying local geometric minima and relative energies are discussed and compared. The three types of neutral-anion separations reported in this work are: the adiabatic electron affinity (EAad), the vertical electron affinity (EAvert), and the vertical detachment energy (VDE). Harmonic vibrational frequencies pertaining to the global minimum for each compound are reported. From the first four studied species (As2Fn, n=1-4), all neutral molecules and their anions are shown to be stable with respect to As-As bond breaking. The neutral As2F molecule and its anion are predicted to have Cs symmetry. We find the trans F-As-As-F isomer of C2h symmetry and a pyramidalized vinylidene-like As-As-F2- isomer of Cs symmetry to be the global minima for the As2F2 and As2F2- species, respectively. The lowest lying minima of As2F3 and As2F3- are vinyl radical-like structures F-As-As-F2 of Cs symmetry. The neutral As2F4 global minimum is a trans-bent (like Si2H4) F2-As-As-F2 isomer of C2 symmetry, while its anion is predicted to have an unusual fluorine-bridged (C(1)) structure. The global minima of the neutral As2Fn species, n=5-8, are weakly bound complexes, held together by dipole-dipole interactions. All such structures have the AsFm-AsFn form, where (m,n) is (2,3) for As2F5, (3,3) for As2F6, (4,3) for As2F7), and (5,3) for As2F8. For As2F8 the beautiful pentavalent F4As-AsF4 structure (analogous to the stable AsF5 molecule) lies about 30 kcal/mol above the AsF3 . . . AsF5 complex. The stability of AsF(5) depends crucially on the strong As-F bonds, and replacing one of these with an As-As bond (in F4As-AsF4) has a very negative impact on the molecule's stability. The anions As2Fn-, n=5-8, are shown to be stable with respect to the As-As bond breaking, and we predict that all of them have fluorine-bridged or fluorine-linked structures. The zero-point vibrational energy corrected adiabatic electron affinities are predicted to be 2.28 eV (As2F), 1.95 eV (As2F2), 2.39 eV (As2F3), 1.71 eV (As2F4), 2.72 eV (As2F5), 1.79 eV (As2F6), 5.26 eV (As2F7), and 3.40 eV (As2F8) from the BHLYP method. Vertical detachment energies are rather large, especially for species with fluorine-bridged global minima, having values up to 6.45 eV (As2F7, BHLYP).     

Binuclear and polynuclear transition metal complexes with macrocyclic ligands. 2. New macrocyclic Schiff"s base in the reaction of 4-tert-butyl-2,6-diformylphenol with 1,2-diaminobenzene. Synthesis and structural,spectroscopic, and theoretical study

Condensation of 4-tert-butyl-2,6-diformylphenol with 1,2-diaminobenzene in ethanol is accompanied by partial reduction of the azomethine double bonds to form symmetrical macrocyclic Schiff"s base containing the alternating >C=N and >CH—NH fragments. In solution, this compound exists as the only isomer in which two endocyclic hydrogen atoms are bound to the oxygen atoms of the phenol groups and two other endocyclic H atoms are attached to the nitrogen atoms of the CH₂—NH fragments. All endocyclic protons are involved in hydrogen bonding and undergo rapid exchange with each other at room temperature. In the crystal, the planar macrocyclic molecules are arranged in closely packed stacks. The steric hindrances resulting from overlapping of the bulky tert-butyl groups are eliminated through rotation of the molecules with respect to each other in the adjacent layers. Study of the potential energy surface for the Schiff"s base under consideration by the DFT method demonstrated that the structure corresponding to the global minimum is similar to that found in solution. However, the isolated molecule is nonplanar, its macrocycle adopting a ladder conformation. The local minimum on the potential energy surface whose energy is 2.6 kcal mol^–1 higher than that of the global minimum corresponds to the zwitterionic structure in which all four endocyclic hydrogen atoms are attached to the nitrogen atoms and the macrocycle adopts a tub conformation. Flattening of the ring is considered as a consequence of stacking interactions between the molecules in the crystal.     

A robust force field based method for calculating conformational energies of charged drug-like molecules

The binding affinity of a drug-like molecule depends among other things on the availability of the bioactive conformation. If the bioactive conformation has a significantly higher energy than the global minimum energy conformation, then the molecule is unlikely to bind to its target. Determination of the global minimum energy conformation and calculation of conformational penalties of binding is a prerequisite for prediction of reliable binding affinities. Here, we present a simple and computationally efficient procedure to estimate the global energy minimum for a wide variety of structurally diverse molecules, including polar and charged compounds. Identifying global energy minimum conformations of such compounds with force field methods is problematic due to the exaggeration of intramolecular electrostatic interactions. We demonstrate that the global energy minimum conformations of zwitterionic compounds generated by conformational analysis with modified electrostatics are good approximations of the conformational distributions predicted by experimental data and with molecular dynamics performed in explicit solvent. Finally the method is used to calculate conformational penalties for zwitterionic GluA2 agonists and to filter false positives from a docking study.     

Conformational study of the structure of free 18-crown-6

A conformational search was performed for 18-crown-6 using the CONLEX method at the MM3 level. To have a more accurate energy order of the predicted conformations, the predicted conformations were geometry optimized at the HF/STO-3G level and the 198 lowest energy conformations, according to the HF/STO-3G energy order, were geometry optimized at the HF/6-31+G level. In addition, the 47 nonredundant lowest energy conformations, according to the MP2/6-31+G energy order at the HF/6-31+G optimized geometry, hereafter the MP2/6-31+G//HF/6-31+G energy order, were geometry optimized at the B3LYP/6-31+G level. According to the MP2/6-31+G//B3LYP/6-31+G energy order, three conformations had energies lower than the experimentally known Ci conformation of 18c6. At the MP2/6-31+G//B3LYP/6-31+G level, the S6 lowest energy conformation is more stable by 1.96 kcal/mol than this Ci conformation. This was confirmed by results at the MP2/6-31+G level with an energy difference of 1.84 kcal/mol. Comparison between the structure of the S6 conformation of 18c6 and the S4 lowest energy conformation of 12-crown-4, as well as other important conformations of both molecules, is made. It is concluded that the correlation energy is necessary to have an accurate energy order of the predicted conformations. A rationalization of the conformational energy order in terms of the hydrogen bonding and conformational dihedral angles is given. It is also suggested that to have a better energy order of the predicted conformations at the MM3 level, better empirical force fields corresponding to the hydrogen bond interactions are needed.     

Origin of trans-bent geometries in maximally bonded transition metal and main group molecules

Recent crystallographic data unambiguously demonstrate that neither Ar'GeGeAr' nor Ar'CrCrAr' molecules adopt the expected linear (VSEPR-like) geometries. Does the adoption of trans-bent geometries indicate that Ar'MMAr' molecules are not "maximally bonded" (i.e., bond order of three for M = Ge and five for M = Cr)? We employ theoretical hybrid density functional (B3LYP/6-311++G) computations and natural bond orbital-based analysis to quantify molecular bond orders and to elucidate the electronic origin of such unintuitive structures. Resonance structures based on quintuple M-M bonding dominate for the transition metal compounds, especially for molybdenum and tungsten. For the main group, M-M bonding consists of three shared electron pairs, except for M = Pb. For both d- and p-block compounds, the M-M bond orders are reflected in torsional barriers, bond-antibond splittings, and heats of hydrogenation in a qualitatively intuitive way. Trans-bent structures arise primarily from hybridization tendencies that yield the strongest sigma-bonds. For transition metals, the strong tendency toward sd-hybridization in making covalent bonds naturally results in bent ligand arrangements about the metal. In the p-block, hybridization tendencies favor high p-character, with increasing avidity as one moves down the Group 14 column, and nonlinear structures result. In both the p-block and the d-block, bonding schemes have easily identifiable Lewis-like character but adopt somewhat unconventional orbital interactions. For more common metal-metal multiply bonded compounds such as [Re2Cl8]2-, the core Lewis-like fragment [Re2Cl4]2+ is modified by four hypervalent three-center/four-electron additions.     

Hydrogen Bond Cooperativity and the Three‐Dimensional Structures of Water Nonamers and Decamers

Broadband rotational spectroscopy of water clusters produced in a pulsed molecular jet expansion has been used to determine the oxygen atom geometry in three isomers of the nonamer and two isomers of the decamer. The isomers for each cluster size have the same nominal geometry but differ in the arrangement of their hydrogen bond networks. The nearest neighbor O? O distances show a characteristic pattern for each hydrogen bond network isomer that is caused by three‐body effects that produce cooperative hydrogen bonding. The observed structures are the lowest energy cluster geometries identified by quantum chemistry and the experimental and theoretical O? O distances are in good agreement. The cooperativity effects revealed by the hydrogen bond O? O distance variations are shown to be consistent with a simple model for hydrogen bonding in water that takes into account the cooperative and anticooperative bonding effects of nearby water molecules.     

Why isn't the N20 dodecahedron ideal for three-coordinate nitrogen?

Nitrogen molecules are the focus of much attention for their potential as high-energy density materials. The usefulness of such molecules as energy sources depends on the stability of the molecules with respect to dissociation. Many such molecules dissociate too easily to be a stable fuel, and the reasons for such instability are related to the details of structure and bonding of the molecule. Such details will be examined for isomers of the molecule N20. N20 has a highly symmetric isomer in which the 20 atoms occupy the vertexes of a dodecahedron. This isomer is a cage molecule in which all of the faces are regular pentagons that have interior angles of 108 degrees . These angles are very close to the known bond angles in very stable nitrogen compounds such as ammonia. Such a structure with only pentagons should provide an ideal bonding environment for three-coordinate nitrogen. However, by use of theoretical calculations including density-functional theory and fourth-order perturbation theory, along with the Dunning correlation-consistent basis sets, it will be shown that dodecahedral N20 is not the most stable cage for N20. The reasons why will be discussed in terms of the structure and bonding of the molecules.     

Silaacetylene: A possible target for experimental studies

The equilibrium geometries and transition states for interconversion of the CSiH₂ isomers in the singlet electronic ground state are optimized at the MP2 and CCSD(T) levels of theory using a TZ2P basis set. The heats of formation, vibrational frequencies, infrared intensities, and rotational constants are also predicted. There are three energy minima on the CSiH₂ potential energy surface. Energy calculations at CCSD(T)/TZ2P(fd) + ZPE predict that the global energy minimum is silavinylidene (1), which is 34.1 kcal mol⁻¹ lower in energy than trans-bent silaacetylene (2) and 84.1 kcal mol⁻¹ more stable than the vinylidene isomer (3). The barrier for rearrangement 2→1 is calculated at the same level of theory to be 5.1 kcal mol⁻¹, while for the rearrangement 3→2 a barrier of 2.7 kcal mol⁻¹ is predicted. The natural bond orbital (NBO) population scheme indicates a clear polarization of the C(SINGLE BOND)Si bonds toward the carbon end. A significant ionic contribution to the C(SINGLE BOND)Si bonds of 1 and 2 is suggested by the NBO analysis. The C(SINGLE BOND)Si bond length of trans-bent silaacetylene (2) is longer than previously calculated [1.665 Å at CCSD(T)/TZ2P)]. The calculated carbon-silicon bond length of 2 is in the middle between the C(SINGLE BOND)Si double bond length of 1 (1.721 Å) and the C(SINGLE BOND)Si triple bond of the linear form HCSiH (4), which is 1.604 Å. Structure 4 is a higher-order saddle point on the potential energy surface. © 1996 by John Wiley & Sons, Inc.     

Coordination to metal centers: a tool to fix high energy conformations in organic molecules. Application to 2,4,4-trimethyl-1,5,9-triazacyclododec-1-ene and related macrocycles

The solid state conformational preferences of ligand 2,4,4-trimethyl-1,5,9-triazacyclododec-1-ene (L1) and its 9-methyl derivative (L2) in transition metal complexes have been determined by a probabilistic method using data retrieved from the Cambridge Structural Database. These macrocyclic compounds, as ligands, tend to adopt a preferential conformation (85% of cases). The ring containing the C=N bond adopts a distorted half-chair conformation, the ring defined by both the N-sp(3) shows a distorted envelope conformation, and the remaining ring exhibits a chair conformation. This conformation corresponds to the enantiomer pair R(N5)S(N9)S(P)/S(N5)R(N9)R(P). Molecular mechanics calculations demonstrate that this is a high energy conformation for the organic molecule, far from the energy minimum. Two other enantiomer pairs are observed in experimental structures. The influence of the coordination on the conformation of the organic ligands has been studied by DFT calculations, and a clear correlation with the geometry of the coordination sphere has been found.     

Accurate assessment of the strain energy in a protein-bound drug using QM/MM X-ray refinement and converged quantum chemistry

An ongoing question regarding the energetics of protein‐ligand binding has been; what is the strain energy that a ligand pays (if any) when binding to its protein target? The traditional method to estimate strain energy uses force fields to calculate the energy difference between the ligand bound conformation and its nearest local minimum/global minimum on the gas‐phase or aqueous phase potential energy surface. This makes the implicit assumption that the underlying force field as well as the reference crystal structure is accurate. Herein, we use ibuprofen as a test case and compare MMFF and ab initio QM methods to identify the local and global minimum conformations. Nine low energy conformations were identified with HF/6‐31G* geometry optimization in vacuo. We also obtained highly accurate relative energies for ibuprofen's conformational energy surface based on M06/aug‐cc‐pVXZ (X = D and T), MP2/aug‐cc‐pVXZ (X = D and T) and the MP2/CBS method (with and without solvent corrections). Moreover, we curate and re‐refine the ibuprofen‐protein complex (PDB 2BXG) using QM/MM X‐ray refinement approaches (HF/6‐31G* was the QM method and the MM model was the AMBER force field ff99sb), which were compared with the low energy conformers to calculate the strain energy. The result indicates that there was an 88% reduction in ibuprofen conformation strain using the QM/MM refined structure versus the original PDB ibuprofen conformations. Furthermore, our results indicate that, due to its inherent limitations in estimating electrostatic interactions, force fields are not suitable to gauge strain energy for charged drug molecules like ibuprofen. The present work offers a carefully validated conformational potential energy surface for a drug molecule as well as a reliable QM/MM re‐refined X‐ray structure that can be used to test current structure‐based drug design approaches. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

SiCNN--a new stable isomer with Si(triple bond)C triple bonding

To predict potentially stable molecules with Si(triple bond)C triple bonding, theoretical calculations at the B3LYP/ 6-311G(d) and CCSD(T)/6-311G(2df) (single-point) levels were employed to study the structures, energetics, and isomerization of various SiCN2 isomers. A schematic potential energy surface (PES) of SiCN2 was established to discuss the kinetic stability of the isomers. A new isomer SiCNN was found to possess a typical Si(triple bond)C triple bond, as confirmed by comparative calculations at the B3LYP, QCISD, QCISD(T), CCSD, and CCSD(T) levels on the bond lengths of SiCNN and other experimentally or theoretically known species of RSiCH (R = H, F, Cl, OH). Moreover, SiCNN resides in a very deep potential, the stabilization barrier is at least 53.2 kcal mol(-1). Thus, SiCNN may be considered as the most kinetically stable isomer with Si(triple bond)C triple bonding known to date, and it may represent a very promising molecule for future experimental characterization. In addition, the stability of the other isomers, such as the four linear species SiNCN, SiNNC, NSiCN and NSiNC, a three-membered NNC ring isomer with exocyclic C-Si bonding, and a four-membered SiCNN ring isomer is discussed and compared with SiCNN.     

Self-recognition and hydrogen bonding by polycyclic bridgehead monoalcohols

Our interest in the relationship between the hydrogen bonding motifs displayed by monoalcohols and the properties of the solids which contain these motifs has led us to determine the crystal structures of three polycyclic bridgehead monoalcohols. One C10H16O isomer crystallises in the space group P2(1)2(1)2(1) but the three molecules which comprise the asymmetric unit are related approximately by the operations of a 3(1) screw axis. They are linked by hydrogen bonds to form an infinite helix. A second C10H16O isomer forms rings containing four molecules joined by cooperative hydrogen bonds. The chiral space group P4(1)2(1)2 accommodates molecules of the S,S and R,R enantiomers in the molar ratio 92:8 (ee 84%) owing to disorder. A related C9H14O2 keto-alcohol forms infinite chains by C-OH...O = C hydrogen bonding. These hydrogen bond motifs are shown to be typical for 45 tertiary monoalcohols, CmHnOH, present in the Cambridge Structural Database. Tertiary monoalcohols display in a more pronounced form the strong preferences for trigonal and tetragonal space groups and for asymmetric units containing several molecules which are established features of the crystallochemistry of monoalcohols.     

Interaction between benzenedithiolate and gold: classical force field for chemical bonding

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as approximately 100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.